bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global Co-regulatory Cross Talk Between m6A and m5C RNA Methylation Systems Coordinate Cellular Responses and Brain Disease Pathways
Authors: Orji Oliver Chukwuma , Stones Joseph , Rajani Seema , Markus Robert , öz Merve Demirbugen , Knight Helen Miranda 
Published: November 2024

AbstractN6 adenosine and C5 cytosine modification of mRNAs, tRNAs and rRNAs are regulated by the behaviour of distinct sets of writer, reader and eraser effector proteins which are conventionally considered to function independently. Here, we provide evidence of global cross-regulatory and functional interaction between the m6A and m5C RNA methylation systems. We first show that m6A and m5C effector protein transcripts are subject to reciprocal base modification supporting the existence of co-regulatory post-transcriptional feedback loops. Using global mass spectrometry proteomic data generated after biological perturbation to identify proteins which change in abundance with effector proteins, we found novel co-regulatory cellular response relationships between m6A and m5C proteins such as between the m6A eraser, ALKBH5, and the m5C writer, NSUN4. Gene ontology analysis of co-regulated proteins indicated that m6A and m5C RNA cross-system control varies across cellular processes, e.g. proteasome and mitochondrial mechanisms, and post-translational modification processes such as SUMOylation and phosphorylation. We also uncovered novel relationships between effector protein networks including contributing to intellectual disability pathways. Finally, we provided in vitro confirmation of colocalisation between m6A-RNAs and the m5C reader protein, ALYREF, after synaptic NMDA activation. These findings have important implications for understanding control of RNA metabolism, cellular proteomic responses, and brain disease mechanisms.
Mapping of Spatial Variance of Family Policy that Could Increase Fertility: Indices for 23 OECD Countries across 21 Year Period
Authors: Šmeringaiová Monika 
Published: November 2024

AbstractIn a period of falling fertility rates and increasing number of various family policies (FPs) that are designed to address this trend, our study explores spatial and temporal variance of such FP measures which could be associated with increased fertility. They have been implemented in a range of countries, but their variance has not yet been systematically mapped. We employ a novel approach, examining gender and economic dimensions of FP measures to develop FP indices scoring 23 European OECD countries throughout the 2000–2021 period and uncover spatial similarities and discrepancies therein. Our findings indicate that degenderizing FP measures are increasingly being adopted across countries, with both genderizing and generous financial measures also enduring. Interestingly, despite an overall decline in fertility rates, FP has become more robust across countries according to the indices. We agree with recent studies that degenderizing FPs are most common in Nordic countries and least so in Central and Eastern Europe. We provide evidence that Hungary and Estonia are exceptions, with different types and more extensive FP. We also found that countries categorised in different contextual clusters sometimes score similarly strongly on genderizing FP (Czechia, Luxembourg, Spain) or weakly on financial FP measures (Slovakia, the UK, Greece). In countries where index scores increased only recently (e.g., Switzerland, Spain), we expect potential increases in fertility rates in the future.
A scientific research training programme for teaching biomedical students to identify the horizontal transfer of antibiotic resistance genes
Authors: Fu Jiafang , Zhang Peipei , Yin Xunzhe , Zhu Lingjia , Zong Gongli , Zhong Chuanqing , Cao Guangxiang 
Published: November 2024

AbstractWorldwide prevalence of multi-antibiotic resistant bacteria is rapidly increasing, and the education of undergraduates and graduates about antibiotic resistance and its associated horizontal gene transfer is critical in the general effort to confront the spread of antibiotic resistance. In this study, a deeper understanding of antibiotic resistance and horizontal gene transfer was achieved by biomedical undergraduate students through a scientific research programme. The enthusiasm of students to participate in the training programme was very high, and results revealed that each student could identify the antibiotic resistance integrative and conjugative element from the Stenotrophomonas maltophilia MER1 genome. Each student could also draw the phylogenetic relationship of the antibiotic resistance integrative and conjugative element. In addition, students proved the horizontal transfer of antibiotic resistance genes from S. maltophilia MER1 to Escherichia coli strain 25DN through conjugation and PCR assays. Each group of students was able to obtain the expected results, indicating that the outcome of the scientific research programme was highly reproducible. This programme improved the theoretical knowledge about antibiotic resistance and horizontal gene transfer and the research skills of biomedical sciences students. Through this programme, students learned that antibiotic resistance genes can be horizontally transferred among different bacteria, laying a solid foundation for students to value the importance of the appropriate use of antibiotics in their future work and life.
Seven Years of Monitoring the Development of an Oyster Reef Living Shoreline
Authors: Shinn Jenny P. , Bredes Amy , Bushek David , Kerr Laura , Kreeger Danielle , McCulloch Danielle , Miller Jon , Moody Joshua , Rothermel Ella , Zito-Livingston Adrianna 
Published: November 2024

AbstractThe implementation of nature-based solutions (NbS), including living shorelines, to mitigate estuarine habitat loss is increasing at a pace exceeding the evaluation of their long-term success. Constructed oyster reefs (CORs) made of shell, concrete, stone, and other materials are one living shoreline tactic that is widely utilized, yet few studies have been conducted to understand the development of CORs within the context of both physical and ecological parameters over longer time scales (4 + years). A COR-based living shoreline project at the Gandy’s Beach Preserve (GBP) in Delaware Bay, NJ, USA, had dual goals of coastal protection and habitat provisioning, which prompted the development of a goal-driven monitoring framework to track project objectives. Methods were developed to quantify the following multi-disciplinary metrics over 7 years: elevations of CORs, waves (height, period, and direction), shoreline elevations, change in extent of vegetation patches, oyster density and size, nekton richness and community composition, and horseshoe crab impingement. The CORs met most of their habitat provisioning objectives as they were colonized by a multi-generational population of shellfish and created habitat for nekton, while posing negligible hazards to horseshoe crabs. However, none of the coastal protection objectives was fully achieved including material stability, wave attenuation, and sediment elevation increase. Results highlight the value of longer-term monitoring to understand performance and the need to match the scale and type of NbS tactic(s) with both the scale of the landscape and the site-specific hydrodynamic conditions to meet project goals.
Multiphase flow and reactive transport benchmark for radioactive waste disposal
Authors: Samper Javier , Mon Alba , Ahusborde Etienne , Yu Han , Narkuniene Asta , Hokr Milan , Montenegro Luis , Amaziane Brahim , El Ossmani Mustapha , Xu Tianfu , Yuan Yilong , Šembera Jan , Poskas Gintautas 
Published: November 2024

AbstractCompacted bentonite is part of the multi-barrier system of radioactive waste repositories. The assessment of the long-term performance of the barrier requires using reactive transport models. Here we present a multiphase flow and reactive transport benchmark for radioactive waste disposal. The numerical model deals with a 1D column of unsaturated bentonite through which water, dry air and $${\hbox {CO}_{2{(g)}}}$$

CO

2

(
g
)

may flow and with the following reactions; aqueous complexation, calcite and gypsum dissolution/precipitation, cation exchange and gas dissolution. INVERSE-FADES-CORE V2, $$\hbox {DuMu}^X$$

DuMu
X

, TOUGHREACT and iCP were benchmarked with 6 test cases of increasing complexity, starting with conservative tracer transport under variably unsaturated conditions and ending with water flow, gas diffusion, minerals and cation exchange. The solutions of all codes exhibit similar trends. Small discrepancies are found in conservative tracer transport due to differences in hydrodynamic dispersion. Computed $${\hbox {CO}_{2{(g)}}}$$

CO

2

(
g
)

pressures agree when a sufficiently refined grid is used. Small discrepancies in $${\hbox {CO}_{2{(g)}}}$$

CO

2

(
g
)

and pH are found near the no-flow boundary at early times which vanish later. Discrepancies are due differences in the formulations used for gas flow at nearly water-saturated conditions. Computed $${\hbox {CO}_{2{(g)}}}$$

CO

2

(
g
)

pressures show a fluctuation between $$10^{-4}$$

10

-
4

and $$10^{-3}$$

10

-
3

years which slows down the in-diffusion of $${\hbox {CO}_{2{(g)}}}$$

CO

2

(
g
)

. This fluctuation is associated with chemical reactions involving $${\hbox {CO}_{2}}$$

CO
2

. There are discrepancies in solute concentrations due to differences in the Debye–Hückel (DH) formulation. They are overcome when all codes use the same DH formulation. The results of this benchmark will contribute to increase the confidence on multiphase reactive transport models for radioactive waste disposal.
Unleash the power of values: how to conduct better science and cultivate thriving research groups
Authors: Schoenle Laura A. , O’Brien Caleb , Brousseau Jennifer , Wendler Amber 
Published: November 2024

AbstractIt is undesirable — and perhaps impossible — for scientific research to be value-free. In fact, scientists can enhance their research and build more engaged, motivated, and well-functioning research groups by reflecting on their values and intentionally embedding values into all aspects of their research (e.g., choice of research question, funding sources, methodology). Here, we posit that values shape the scientific process and interpersonal dynamics within research groups. We then provide concrete steps to embed values into research by using tools such as values statements, mentoring expectations agreements, and lab handbooks. Finally, we provide a framework for culture-building activities that can encourage productive and fulfilling interactions among all research group members.
Effects of Late-Passage Small Umbilical Cord–Derived Fast Proliferating Cells on Tenocytes from Degenerative Rotator Cuff Tears under an Interleukin 1β-Induced Tendinopathic Environment
Authors: Lee Ah-Young , Park Ju-Young , Hwang Sam Joongwon , Jang Kwi-Hoon , Jo Chris Hyunchul 
Published: November 2024

Abstract

Background
Tendinopathy is a chronic tendon disease. Mesenchymal stem cells (MSCs), known for their anti-inflammatory properties, may lose effectiveness with extensive culturing. Previous research introduced “small umbilical cord–derived fast proliferating cells” (smumf cells), isolated using a novel minimal cube explant method. These cells maintained their MSC characteristics through long-term culture. Thus, the purpose of the present study was to assess the anti-inflammatory effects of late-passage smumf cells at P10 on tenocytes derived from degenerative rotator cuff tears in a tendinopathic environment.

Methods
The mRNA expression with respect to aging of MSCs and secretion of growth factors (GFs) by smumf cells at P10 were measured. mRNA and protein synthesis in tenocytes with respect to the tenocyte phenotype, inflammatory cytokines, and matrix- degradation enzymes were measured. The inflammatory signal pathways involving nuclear factor kappa B (NF-κB) and mitogen-activated protein kinase (MAPK) in tenocytes were also investigated. The proliferative response of degenerative tenocytes to co-culture with smumf cells over 7 days in varying IL-1β induced tendinopathic environments was investigated.

Results
smumf cells at P10 showed no signs of aging compared to those at P3. smumf cells at P10, secreting 2,043 pg/ml of hepatocyte growth factor (HGF), showed a 1.88-fold (p = .002) increase in HGF secretion in a tendinopathic environment. Degenerative tenocytes co-cultured with smumf cells showed significantly increased protein expression levels of collagen type I (Col I) and the Col I/III ratio by 1.46-fold (p < .001) and 1.66-fold (p < .001), respectively. The smumf cells at P10 reduced both mRNA and protein expression levels of matrix metalloproteinases-1, -2, -3, -8, -9, and -13 in tenocytes and attenuated NF-κB (phosphorylated IκBα/IκBα and phosphorylated p65/p65) and MAPK (phosphorylated p38/p38 and phosphorylated JNK/JNK) pathways activated by IL-1β. Removal of IL-1β from the co-culture accelerated the growth of tenocytes by 1.42-fold (p < .001). Removal of IL-1β accelerated tenocyte growth in co-cultures.

Conculsion
Late-passage smumf cells exert anti-inflammatory effects on tenocytes derived from degenerative rotator cuff tears under a tendinopathic environment, primarily through the secretion of growth factors (GFs).
Tribocorrosion Performance and Cytotoxicity of Additive Manufactured CoCrMo: A Benchmark Against Wrought CoCrMo
Authors: Nothnagel Rosa Maria , Vukonic Leonarda , Bauer Christoph , Váradi Tímea , Linhardt Paul , Franek Friedrich , Nehrer Stefan , Rodríguez Ripoll Manel 
Published: November 2024

Abstract
Additive Manufacturing (AM) has increasingly gained attention as a tool for the fabrication of complex biomedical components, due to the flexibility of the technique for accounting to the patient individuality. Additive manufacturing techniques, like laser beam melting, often result in highly anisotropic microstructures that greatly differ from those obtained in conventionally manufactured alloys. This study evaluates the potential of AM manufactured CoCrMo for body implants as an alternative to the wrought CoCrMo, especially considering tribocorrosion performance in buffered fluid. Its biocompatibility is also assessed via in-vitro cytotoxicity assays. The results show that both materials have a comparable tribocorrosion performance, independently of the manufacturing process, despite their radically different initial microstructure. This results from the microstructural convergence arising from the plastic deformation imparted by sliding motion. While the initially elongated grains of the AM CoCrMo tend to grain refinement, the microstructure of the wrought CoCrMo undergoes grain coarsening, resulting in a similar final grain size detected after the tribocorrosion experiments. The addition of albumin to the phosphate buffer testing fluid, simulating body fluid applications, reduces the grain refinement, particularly under constant 0.21 V, due to lower shear stresses caused by the lower coefficient of friction. Therefore, the initial dissimilarity found in the untested microstructure between the materials does not affect the wear rate nor lead to an increased metal release. As the cytotoxicity is neither impaired by the manufacturing process, the use of AM CoCrMo could be recommended on those biomedical applications requiring wear resistance in body fluid environment.
Variety of General Position Problems in Graphs
Authors: Tian Jing , Klavžar Sandi 
Published: November 2024

AbstractLet X be a vertex subset of a graph G. Then $$u, v\in V(G)$$

u
,
v
∈
V
(
G
)

are X-positionable if $$V(P)\cap X \subseteq \{u,v\}$$

V
(
P
)
∩
X
⊆
{
u
,
v
}

holds for any shortest u, v-path P. If each two vertices from X are X-positionable, then X is a general position set. The general position number of G is the cardinality of a largest general position set of G and has been already well investigated. In this paper a variety of general position problems is introduced based on which natural pairs of vertices are required to be X-positionable. This yields the total (resp. dual, outer) general position number. It is proved that the total general position sets coincide with sets of simplicial vertices, and that the outer general position sets coincide with sets of mutually maximally distant vertices. It is shown that a general position set is a dual general position set if and only if its complement is convex. Several sufficient conditions are presented that guarantee that a given graph has no dual general position set. The total general position number, the outer general position number, and the dual general position number of arbitrary Cartesian products are determined.
Für eine grundlegende Reform des öffentlich-rechtlichen Rundfunks
Authors: Feld Lars , Fuest Clemens , Haucap Justus , Schweitzer Heike , Wieland Volker , Wigger Berthold 
Published: November 2024

ZusammenfassungDer öffentlich-rechtliche Rundfunk (ÖRR) steht zu Recht in der Kritik. Mit dem technologischen Fortschritt und einem vielfältigen Medienangebot aus öffentlich-rechtlichen und privaten Sendern, dem Internet, diversen Streaming-Diensten und sozialen Medien haben die Rezipienten ihr Nutzungsverhalten stark verändert. Zudem schwindet die normative Rechtfertigung und gesellschaftliche Akzeptanz des ÖRR, der für kostenintensive Ausgaben sowie eine zu unausgewogene und zuweilen verzerrte Berichterstattung kritisiert wird. Auf Basis einer Analyse des 3. und 4. Medienänderungsstaatsvertrags entwickelt der Kronberger Kreis acht konkrete Reformschritte zur Stärkung der Governance des ÖRR. Eine Umsetzung dieser Reformempfehlungen würde dazu beitragen, einen möglichst hohen gesellschaftlichen Mehrwert durch den ÖRR und das zur Verfügung stehende Beitragsaufkommen zu generieren. Dadurch ließen sich nicht nur die Kosten des ÖRR senken, sondern auch seine Akzeptanz in der Bevölkerung stärken – und damit die Integrationsfunktion, die der ÖRR erfüllen soll.
Wie groß ist die Gefahr eines Fachkräftemangels in Zukunftsberufen?
Authors: Bachmann Ronald , Storm Eduard 
Published: November 2024

ZusammenfassungDie digitale und ökologische Transformation verändert die Arbeitsnachfrage sowie die geforderten Kompetenzen auf dem Arbeitsmarkt. Dieses Papier untersucht die resultierende Gefahr eines Fachkräftemangels in zehn Zukunftsberufen und fünf deutschen Metropolregionen. Erstens wird die Entwicklung der Beschäftigung mittels administrativer Daten untersucht. Dabei zeigt sich ein überdurchschnittliches Beschäftigungswachstum in Zukunftsberufen, besonders in digitalen Berufen wie der Softwareentwicklung oder grünen Berufen wie der Ver- und Entsorgung. Zweitens werden mit Hilfe von Online-Stellenanzeigen die Höhe der Arbeitsnachfrage nach Beschäftigten sowie die Nachfrage nach digitalen und grünen Kompetenzen innerhalb der Zukunftsberufe untersucht. Diese Analysen weisen auf unterschiedliche regionale Bewältigungsstrategien hin: Während digitale Berufe eine gleichmäßig hohe Nachfrage aufweisen, bestehen in grünen Berufen erhebliche regionale Unterschiede. Drittens zeigt eine Untersuchung des Arbeitsangebots aus dem tertiären und dualen Bildungssystem, dass das Arbeitsangebot, insbesondere in MINT-Fächern und dualen Ausbildungsberufen, hinter der wachsenden Nachfrage zurückbleibt. Abschließend wird erörtert, in welchen Berufen und Regionen zukünftig ein starker Fachkräftemangel zu erwarten ist und welche Maßnahmen zur Bewältigung dieser Herausforderung geeignet erscheinen.
Value adding bioconversion of residues and byproducts—a logistics challenge
Authors: Rudi Andreas , Schönrock Sonja , Laudensack Wolfgang , Schultmann Frank , Ulber Roland , Holtmann Dirk 
Published: November 2024

AbstractGlobal developments such as climate change, a growing world population and the depletion of fossil resources make the sustainable use of biogenic resources in chemical production inevitable. This would also provide a final product with a higher added value than just utilizing the raw materials for applications in energy generation. In recent years, many researchers have shown that e.g., grass clippings, carrots and potato peels can be biotechnologically converted into high-value chemicals thereby increasing resource efficiency. A particular challenge, however, is the decentralized production of such biogenic raw materials as well as degradation affecting the composition and quality within short periods of time. Therefore, appropriate logistics concepts must be developed and evaluated to economically valorize biogenic raw materials. Such concepts differ significantly in terms of material utilization for the production of chemicals, composting or energetic valorization. This overview presents relevant examples of the conversion of biogenic residues into chemicals investigating basic logistic concepts and highlighting major challenges along bio-based value chains.
EU digital law and the digital platform economy—an inquiry into the co-evolution of law and technology
Authors: Eckardt Martina 
Published: November 2024

AbstractEU digital policy is currently one of the most ambitious and far-reaching endeavors to regulate the digital economy. Online platforms in multisided markets with digital ecosystems lie at the heart of digital technologies and business models. Among others, they pose new challenges with regard to the abuse of a dominant market position, thus ultimately reducing competition and innovation. This paper outlines an evolutionary approach to the co-evolution of law and technology with collective cognitive constructs and wealth effects as essential drivers (Eckardt (2001, 2008). It is then applied to the evolution of EU law in this field. After an overview of the evolution from telecommunication monopolies to the current digital platform economy, a case study presents firstly the Google Search (Shopping) case (2010–2024). Based on traditional EU competition law, it resulted in gradual judge-made legal innovation. It also generated new knowledge about the shortcomings of the ex post approach of EU competition law when applying it to the digital platform economy. As a consequence, secondly, the introduction of the Digital Markets Act (DMA) (2020 onwards) as a radical statutory innovation is discussed. The DMA introduced a novel ex ante regulation for large online platforms to overcome the problems of traditional EU competition law. Finally, the paper reflects on the impact of wealth effects and the (co-evolving) cognitive constructs of the relevant players as drivers in this current example of the co-evolution of law and technology. The paper concludes with an outlook on further areas of empirical and conceptual research that can provide a better understanding of the co-evolution of law and technology and allow for better policies in regard to disruptive technological innovation.