bluuebunny/crossref_metadata_2025_split huggingface dataset:
Delineating the heterogeneity of senescence-induced-functional alterations in hepatocytes
Authors: Kumar Pavitra , Hassan Mohsin , Tacke Frank , Engelmann Cornelius 
Published: April 2024

Abstract
Background and aim
Cellular senescence of hepatocytes involves permanent cell cycle arrest, disrupted cellular bioenergetics, resistance to cell death, and the release of pro-inflammatory cytokines. This ‘zombie-like’ state perpetuates harmful effects on tissues and holds potential implications for liver disease progression. Remarkably, senescence exhibits heterogeneity, stemming from two crucial factors: the inducing stressor and the cell type. As such, our present study endeavors to characterize stressor-specific changes in senescence phenotype, its related molecular patterns, and cellular bioenergetics in primary mouse hepatocytes (PMH) and hepatocyte-derived liver organoids (HepOrgs).

Methods
PMH, isolated by collagenase-perfused mouse liver (C57B6/J; 18–23 weeks), were cultured overnight in William’s E-medium supplemented with 2% FBS, l-glutamine, and hepatocyte growth supplements. HepOrgs were developed by culturing cells in a 3D matrix for two weeks. The senescence was induced by DNA damage (doxorubicin, cisplatin, and etoposide), oxidative stress (H2O2, and ethanol), and telomere inhibition (BIBR-1532), p53 activation (nutlin-3a), DNA methyl transferase inhibition (5-azacitidine), and metabolism inhibitors (galactosamine and hydroxyurea). SA-β galactosidase activity, immunofluorescence, immunoblotting, and senescence-associated secretory phenotype (SASP), and cellular bioenergetics were used to assess the senescence phenotype.

Results
Each senescence inducer triggers a unique combination of senescence markers in hepatocytes. All senescence inducers, except hydroxyurea and ethanol, increased SA-β galactosidase activity, the most commonly used marker for cellular senescence. Among the SASP factors, CCL2 and IL-10 were consistently upregulated, while Plasminogen activator inhibitor-1 exhibited global downregulation across all modes of senescence. Notably, DNA damage response was activated by DNA damage inducers. Cell cycle markers were most significantly reduced by doxorubicin, cisplatin, and galactosamine. Additionally, DNA damage-induced senescence shifted cellular bioenergetics capacity from glycolysis to oxidative phosphorylation. In HepOrgs exposed to senescence inducers, there was a notable increase in γH2A.X, p53, and p21 levels. Interestingly, while showing a similar trend, SASP gene expression in HepOrgs was significantly higher compared to PMH, demonstrating a several-fold increase.

Conclusion
In our study, we demonstrated that each senescence inducer activates a unique combination of senescence markers in PMH. Doxorubicin demonstrated the highest efficacy in inducing senescence, followed by cisplatin and H2O2, with no impact on apoptosis. Each inducer prompted DNA damage response and mitochondrial dysfunction, independent of MAPK/AKT.

Graphical Abstract
Microplastic in Dredged Sediments: From Databases to Strategic Responses
Authors: Wilkens J. L. , Calomeni-Eck A. J. , Boyda J. , Kennedy A. , McQueen A. D. 
Published: April 2024

AbstractMicroplastics (MPs) accumulate in sediments, yet guidelines for evaluating MP risks in dredged sediments are lacking. The objective of this study was to review existing literature on MPs in sediments to improve fundamental knowledge of MP exposures and develop a publicly available database of MPs in sediments. Twelve percent of the reviewed papers (nine studies) included sediment core samples with MP concentrations generally decreasing with depth, peaking in the top 15 cm. The remaining papers evaluated surficial grab samples (0 to 15 cm depth) from various water bodies with MPs detected in almost every sample. Median MP concentrations (items/kg dry sediment) increased in this order: lakes and reservoirs (184), estuarine (263), Great Lakes nearshore areas and tributaries (290), riverine (410), nearshore marine areas (487), dredge activities (817), and harbors (948). Dredging of recurrent shoaling sediments could be expected to contain MPs at various depths with concentrations influenced by the time elapsed since the last dredging event. These results offer key insights into the presence and variability of MPs in dredged sediments, informing environmental monitoring and risk assessment strategies.
Asymmetric Myocardial Involvement as an Early Indicator of Cardiac Dysfunction in Pediatric Dystrophinopathies: A Study on Cardiac Magnetic Resonance (CMR) Parametric Mappings
Authors: Esmel-Vilomara Roger , Riaza Lucía , Costa-Comellas Laura , Sabaté-Rotés Anna , Gran Ferran 
Published: April 2024

Abstract
Dystrophinopathies, such as Duchenne and Becker muscular dystrophy, frequently lead to cardiomyopathy, being its primary cause of mortality. Detecting cardiac dysfunction early is crucial, but current imaging methods lack insight into microstructural remodeling. This study aims to assess the potential of cardiac magnetic resonance (CMR) parametric mappings for early detection of myocardial involvement in dystrophinopathies and explores whether distinct involvement patterns may indicate impending dysfunction. In this prospective study, 23 dystrophinopathy patients underwent CMR with tissue mappings. To establish a basis for comparison, a control group of 173 subjects was analyzed. CMR protocols included SSFP, T2-weighted and T1-weighted sequences pre and post gadolinium, and tissue mappings for native T1 (nT1), extracellular volume (ECV), and T2 relaxation times. The difference between the left ventricular posterior wall and the interventricular septum was calculated to reveal asymmetric myocardial involvement. Significant differences in LV ejection fraction (LVEF), myocardial mass, and late gadolinium enhancement confirmed abnormalities in patients. Tissue mappings: nT1 (p < 0.001) and ECV (p = 0.002), but not T2, displayed substantial variations, suggesting sensitivity to myocardial involvement. Asymmetric myocardial involvement in nT1 (p = 0.01) and ECV (p = 0.012) between septal and LV posterior wall regions was significant. While higher mapping values didn’t correlate with dysfunction, asymmetric involvement in nT1 (ρ=-0.472, p = 0.023) and ECV (ρ=-0.460, p = 0.049) exhibited a significant negative correlation with LVEF. CMR mappings show promise in early myocardial damage detection in dystrophinopathies. Although mapping values may not directly correspond to dysfunction, the negative correlation between asymmetric involvement in nT1 and ECV with LVEF suggests their potential as early biomarkers. Larger, longitudinal studies are needed for a comprehensive understanding and improved risk stratification in dystrophinopathies.
Dynamic change in the peritoneal cancer index based on CT after chemotherapy in the overall survival prediction of gastric cancer patients with peritoneal metastasis
Authors: Wei Yi-Yuan , Cai Jie-Yuan , Wang Lin-Lin , Yang Jie , Li Yan-Ling , Li Xiao-Ting , Zhang Xiao-Tian , Shi Yan-Jie , Tang Lei 
Published: April 2024

Abstract
Purpose
The purpose of this research was to investigate the efficacy of the CT-based peritoneal cancer index (PCI) to predict the overall survival of patients with peritoneal metastasis in gastric cancer (GCPM) after two cycles of chemotherapy.

Methods
This retrospective study registered 112 individuals with peritoneal metastasis in gastric cancer in our hospital. Abdominal and pelvic enhanced CT before and after chemotherapy was independently analyzed by two radiologists. The PCI of peritoneal metastasis in gastric cancer was evaluated according to the Sugarbaker classification, considering the size and distribution of the lesions using CT. Then we evaluated the prognostic performance of PCI based on CT, clinical characteristics, and imaging findings for survival analysis using multivariate Cox proportional hazard regression.

Results
The PCI change ratio based on CT after treatment (ΔPCI), therapy lines, and change in grade of ascites were independent factors that were associated with overall survival (OS). The area under the curve (AUC) value of ΔPCI for predicting OS with 0.773 was higher than that of RECIST 1.1 with 0.661 (P < 0.05). Patients with ΔPCI less than −15% had significantly longer OS.

Conclusion
CT analysis after chemotherapy could predict OS in patients with GCPM. The CT-PCI change ratio could contribute to the determination of an appropriate strategy for gastric cancer patients with peritoneal metastasis.
Influence of malocclusion on OHRQoL in adolescents in initial orthodontic treatment phase
Authors: Schwarz Linda , Ossmann Victor , Ritschl Valentin , Stamm Tanja , Jonke Erwin , Bekes Katrin 
Published: April 2024

Abstract
Objectives
Besides correcting malocclusions, another main objective of orthodontic treatment is to improve patients’ oral health-related quality of life (OHRQoL). This study aimed to assess changes in OHRQoL of children within the first six months of orthodontic therapy with fixed orthodontic appliances.

Methods
85 patients aged 11 to 14 years requiring fixed orthodontic appliance therapy were included. The children completed the German version of the Child Perceptions Questionnaire (CPQ-G-11-14) before (T0), 1 month (T1) and 6 months (T2) after the start of orthodontic treatment. The type of malocclusion was categorized according to the Index of Orthodontic Treatment Need (IOTN).

Results
The initial type of malocclusion affected the children’s OHRQoL, whereas gender and age did not. The IOTN dental health component (DHC) had a significant impact on the CPQ score (median CPQ of 15.00 for the group DHC 4 vs. 22.50 for DHC 5, p = 0.032). The onset of orthodontic treatment initially affected the CPQ domains “Oral symptoms” and “Functional limitations, with a change versus baseline of 2.00 (p = 0.001), but improved again after 6 months. Regression analysis demonstrated that children with an IOTN DHC 5 malocclusion experienced a greater impact on their ORHQoL, as indicated by a CPQ score 7.35 points higher than that of children with an IOTN DHC 4 malocclusion (p = 0.015).

Conclusions
At the beginning of orthodontic treatment, the OHRQoL slightly worsens, probably due to the discomfort and appearance of the appliances. However, 6 months after the start of orthodontic treatment, OHRQoL improved again in patients with severe malocclusion (IOTN 4 and 5), and approached baseline values.

Clinical relevance
The results help the clinician to better understand specific aspects of oral health that may be affected by different malocclusions, thereby improving the child’s satisfaction and overall quality of life.
A Systematic Investigation of the Applicability of Taylor’s Hypothesis in an Idealized Surface Layer
Authors: Hilland Rainer , Christen Andreas 
Published: April 2024

AbstractTaylor’s Frozen Turbulence Hypothesis (TH) is a critical assumption in turbulent theory and practice which allows time series of point measurements of turbulent variables to be translated to the spatial domain via the mean wind. Using a 3D array of fibre-optic distributed temperature sensing in the atmospheric surface layer over an idealized desert site we present a systematic investigation of the applicability of Taylor’s Hypothesis to atmospheric surface layer flows over a variety of conditions: unstable, near-neutral, and stable atmospheric stabilities; and multiple measurement heights between the surface and 3 m above ground level. Both spatially integrated and spatially scale-dependent eddy velocities are investigated by means of time-lagged streamwise two-point correlations and compared to the mean Eulerian wind. We find that eddies travel slower than predicted by TH at small spatial separations, as predicted by TH at separations typically between 5 and 16 m, and faster than predicted by TH at larger spatial separations. In unstable atmospheric conditions the spatial separation at which eddy velocity is larger than Eulerian velocity decreases with height.
On metaphors of mathematics: Between Blumenberg’s nonconceptuality and Grothendieck’s waves
Authors: Friedman Michael 
Published: April 2024

AbstractHow can metaphors account for the formation of mathematical concepts, for changes in mathematical practices, or for the handling of mathematical problems? Following Hans Blumenberg’s thought, this paper aims to unfold a possible answer to these questions by viewing the metaphorical frameworks accompanying these changes as essential for an understanding of how changes in mathematical practices have been accounted for. I will focus especially on cases in which these changes were caused by encounters with a mathematical object which did not yet have a well-defined concept, but also show that such indeterminacy remains with the mathematical concept even after it is considered ‘well-defined’. As the paper will show, this ‘forefield’ [Vorfeld] of the concept is addressed by Blumenberg’s account of metaphorology on the one hand, and accompanied by his later account of nonconceptuality [Unbegrifflichkeit] on the other hand. While Blumenberg himself did not develop a full-fledged philosophy of mathematics or of mathematical practices, I aim to show that one can nevertheless extract from his writings a unique position concerning the role metaphors play in mathematics. To this end, Blumenberg’s account of nautical and oceanic metaphors and Alexandre Grothendieck’s philosophy of mathematical practice provide fruitful starting points.
Expertise, moral subversion, and climate deregulation
Authors: Elabbar Ahmad 
Published: April 2024

AbstractThe weaponizing of scientific expertise to oppose regulation has been extensively studied. However, the relevant studies, belonging to the emerging discipline of agnotology, remain focused on the analysis of empirical corruption: of misinformation, doubt mongering, and other practices that cynically deploy expertise to render audiences ignorant of empirical facts. This paper explores the wrongful deployment of expertise beyond empirical corruption. To do so, I develop a broader framework of morally subversive expertise, building on recent work in political philosophy (Howard, 2016). Expertise is subversive if it sets up its audience to fail morally, either intentionally or negligently. I distinguish three modes of subversive expertise: empirical subversion (the focus of agnotology), normative subversion and motivational subversion. Drawing on these distinctions, I offer a revisionary account of the Trump Administration’s regulatory science as a case study. I show that the Trump Administration’s use of expertise to dismantle climate regulation, contra the standard charge, cannot be explained using the resources of agnotology alone: the Administration produced highly reliable climate assessments, detailing the risks of climate change, candidly admitting the harms of its proposed policies, and still successfully deployed these findings to justify massive climate deregulation. The lesson of the analysis is that dismissing the expertise that underpins climate deregulation as empirically corrupt ‘anti-science’ both obscures its actual role in the politics of climate change and understates its wrongfulness: it misses the breadth of the assault on moral agency that sustains climate injustice.
An introduction to causal mediation analysis
Authors: Qin Xu 
Published: April 2024

AbstractCausal mediation analysis has gained increasing attention in recent years. This article guides empirical researchers through the concepts and challenges of causal mediation analysis. I first clarify the difference between traditional and causal mediation analysis and highlight the importance of adjusting for the treatment-by-mediator interaction and confounders of the treatment–mediator, treatment–outcome, and mediator–outcome relationships. I then introduce the definition of causal mediation effects under the potential outcomes framework and different methods for the identification and estimation of the effects. After that, I highlight the importance of conducting a sensitivity analysis to assess the sensitivity of analysis results to potential unmeasured confounding. I also list various statistical software that can conduct causal mediation analysis and sensitivity analysis and provide suggestions for writing a causal mediation analysis paper. Finally, I briefly introduce some extensions that I made with my colleagues, including power analysis, multisite causal mediation analysis, causal moderated mediation analysis, and relaxing the assumption of no post-treatment confounding.
On Freedom from Remorse (Avipratisāra/Avippaṭisāra): Its Place on the Well-Trodden Path from Moral Discipline to Samādhi Meditation
Authors: Sun Hao 
Published: April 2024

AbstractThe primary objective of this study is to shed light on the role and significance of freedom from remorse (avipratisāra/avippaṭisāra) in the cultivation of Buddhist concentration (samādhi) meditation. The study delves into the progression from avipratisāra/avippaṭisāra to samādhi, examining how moral discipline influences an individual’s conscience and, consequently, meditation. We commence by examining the well-established path of cultivation leading toward samādhi. A comprehensive study was undertaken to understand the term avipratisāra/avippaṭisāra, its significance for Buddhist meditation, the context in which it originated, and the various English translations that have been provided for it. Furthermore, a comparison is made between avipratisāra/avippaṭisāra and a seemingly synonymous term, kaukṛtya/kukkucca, with areas being sought where one or the other tends to be (or is exclusively) used within the discourse about Buddhist ethics and meditation. From various Buddhist scriptures, it is suggested that a morally disciplined individual typically progresses through a series of states, starting with freedom from remorse and potentially leading to concentration (samādhi). Avipratisāra/avippaṭisāra is pivotal in fostering positive meditative states, serving as a catalyst that propels individuals from negative emotions to wholesome ones on the Buddhist path. By contrast, both vipratisāra/vippaṭisāra and kaukṛtya/kukkucca are identified as basically synonymous words for disturbing emotions with somewhat different contexts of use, the elimination of such emotions being necessary if individuals are to progress on their spiritual journey. Avipratisāra/avippaṭisāra plays a crucial intermediary role bridging Buddhist ethics and meditation. Moral discipline and the subsequent understanding and confession of any personal misconduct are integral to fostering freedom from remorse. Such freedom not only paves the way to deeper meditation but also fortifies one’s confidence in Buddhist teachings, and so provides a foundation for true spiritual progress.
Dietary analysis of wolf (Canis lupus) – a comparison of markers and methods
Authors: Eusemann Pascal , Rees Jana , Kuhlenkamp Vivian , Lippitsch Paul , Schumann Heiner 
Published: April 2024

AbstractMetabarcoding is emerging as an alternative to morphological methods in noninvasive carnivore diet analysis based on scats. A number of metabarcoding markers have been developed but their comparative performance to recover DNA from scats remains mostly untested. We tested three markers covering a wide taxonomic range of prey items and compared them with the results of a morphological analysis. Morphological and genetic methods performed comparably regarding the identity of detected prey species, but the number of identified species varied strongly between markers. Only one, 12S-V5, amplified successfully in all samples and proved to be robust and reliable when working with the highly degraded DNA obtained from scats.
Development and Implementation of a Peer-Teaching Curriculum for Student Assistants
Authors: Dirmeier Meike , Schick Kristina , Lindemann Kathleen , Bethenod Larissa , Wijnen-Meijer Marjo 
Published: April 2024

AbstractWe have developed a peer-teaching program for student assistants involved in medical education. The offer comprises (1) an inventory of potentially relevant courses offered by other institutions at our university and (2) our own peer-teaching curriculum on pedagogy and teaching methodology. We describe a pilot scheme to implement the curriculum.
Enhanced network inference from sparse incomplete time series through automatically adapted $$L_1$$ regularization
Authors: Cai Zhongqi , Gerding Enrico , Brede Markus 
Published: April 2024

AbstractReconstructing dynamics of complex systems from sparse, incomplete time series data is a challenging problem with applications in various domains. Here, we develop an iterative heuristic method to infer the underlying network structure and parameters governed by Ising dynamics from incomplete spin configurations based on sparse and small-sized samples. Our method iterates between imputing missing spin states given current coupling strengths and re-estimating couplings from completed spin state data. Central to our approach is the novel application of adaptive $$l_1$$

l
1

regularization on updating coupling strengths, which features an automatic adjustment of the regularization strength throughout the iterative inference process. By doing so, we aim at preventing over-fitting and enforcing the sparsity of couplings without access to ground truth parameters. We demonstrate that this approach accurately recovers parameters and imputes missing spins even with substantial missing data and short time series, providing improvements in the inference of Ising model parameters even for relatively small sample sizes.
Einsam oder gemeinsam?
Authors: Müller Marcus 
Published: April 2024

ZusammenfassungDer Beitrag untersucht die Bedeutung der Unterscheidung zwischen Verstehen und Erklären für die digitale Linguistik. Es wird gezeigt, dass Verstehen und Erklären nicht als isolierte Praktiken betrachtet werden sollten, sondern eng miteinander verknüpft sind und sich gegenseitig ergänzen. Er setzt dazu bei der bekannten Begriffsdichotomie aus der romantischen Hermeneutik an und bezieht neuere Beträge zu einem einheitswissenschaftlichen Begriff des Erklärens wie auch zu einer pragmatischen Verstehenstheorie ein. Das Verstehen wird in der digitalen Linguistik als eine unreflektierte Nebenbei-Praxis behandelt, während das Erklären in seinen verschiedenen Typen gut methodologisiert ist. Der in verschiedenen Bereichen der Linguistik eingeführte Kontextualisierungsbegriff scheint geeignet, um korpuslinguistisches Verstehen methodologisch zu fassen. Auch wenn die Bedeutung statistischer Erklärungen bei wachsenden Beständen an quantifizierbaren Daten wächst, darf das Verstehen im Kontext nicht unreflektiert bleiben und bedarf einer methodischen Basis. Auf der Ebene des praktischen Zugriffs hebt der Beitrag Annotation als Methode hervor, die Verstehen und Erklären integriert. Dabei spielt insbesondere das kollaborative Verstehen in Annotationsprozessen eine Schlüsselrolle. Der Beitrag endet mit zwei Anwendungsbeispielen.