bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss of MTA2‐mediated downregulation of PTK7 inhibits hepatocellular carcinoma metastasis progression by modulating the FAK‐MMP7 axis
Authors: Hu Huang‐Ming , Lee Hsiang‐Lin , Liu Chung‐Jung , Hsieh Yi‐Hsien , Chen Yong‐Syuan , Hsueh Kuan‐Chun 
Published: December 2023

AbstractThe expression of metastasis tumor‐associated protein 2 (MTA2) and protein tyrosine kinase 7 (PTK7) is associated with hepatocellular carcinoma (HCC) progression. However, the functional effect and mechanism through which MTA2 regulates PTK7‐mediated HCC progression remains unclear. Here, we found that MTA2 knockdown significantly down‐regulated PTK7 expression in HCC cells (SK‐Hep‐1 and PLC/PRF/5). Data from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases show that the PTK7 expression level was higher in HCC tissues than in normal liver tissues. In HCC patients, the PTK7 expression level clearly correlated with tumor stage and grade, lower overall survival (OS) correlated positively with MTA2 level, and PTK7 expression acted as a downstream factor for MTA2 expression. In addition, matrix metalloproteinase 7 (MMP7) expression was closely regulated by PTK7, and the mRNA and protein expression levels of MTA2 and PTK7 correlated positively with lower OS. MMP7 downregulation by PTK7 knockdown clearly decreased the migration and invasion abilities of HCC cells. In HCC cells, recombinant human MMP7 reversed the PTK7 knockdown‐induced suppression of migration and invasion. Furthermore, deactivation of FAK using siFAK or FAK inhibitor (PF‐573228, PF) synergistically contributed to PTK7 knockdown‐inhibited FAK activity, MMP7 expression, and the migration and invasion abilities of HCC cells. Collectively, our findings show that PTK7 mediates HCC progression by regulating the MTA2‐FAK‐MMP7 axis and may be a diagnostic value for HCC patients.
An Estimate of the Effect of 3D Heterogeneous Density Distribution on Coseismic Deformation Using a Spectral Finite-Element Approach
Authors: Tanaka Yoshiyuki , Klemann Volker , Martinec Zdeněk 
Published: December 2023

AbstractThe advancement of the Global Geodetic Observing System (GGOS) has enabled monitoring of mass transport and solid-Earth deformation processes with unprecedented accuracy. Coseismic deformation is modelled as an elastic response of the solid Earth to an internal dislocation. Self-gravitating spherical Earth models can be employed in modelling regional to global scale deformations. Recent seismic tomography and high-pressure/high-temperature experiments have revealed finer-scale lateral heterogeneities in the elasticity and density structures within the Earth, which motivates us to quantify the effects of such finer structures on coseismic deformation. To achieve this, fully numerical approaches including the Finite Element Method (FEM) have often been used. In our previous study, we presented a spectral FEM, combined with an iterative perturbation method, to consider lateral heterogeneities in the bulk and shear moduli for surface loading. The distinct feature of this approach is that the deformation of the entire sphere is modelled in the spectral domain with finite elements dependent only on the radial coordinate. By this, self-gravitation can be treated without special treatments employed when using an ordinary FEM. In this study, we extend the formulation so that it can deal with lateral heterogeneities in density in the case of coseismic deformation. We apply this approach to a longer-wavelength vertical deformation due to a large earthquake. The result shows that the deformation for a laterally heterogeneous density distribution is suppressed mainly where the density is larger, which is consistent with the fact that self-gravitation reduces longer-wavelength deformations for 1-D models. The effect on the vertical displacement is relatively small, but the effect on the gravity change could amount to the same order of magnitude of a given heterogeneity if the horizontal scale of the heterogeneity is large enough.
A Dynamic-Based Methodology for Optimising Insulation Retrofit to Reduce Total Carbon
Authors: Rakshit D. M. , Robinson Anthony , Byrne Aimee 
Published: December 2023

AbstractOptimisation is frequently mentioned in frameworks and assessments of design for a circular economy. Adopting circular economy principles in building retrofit can reduce the use of materials and minimise emissions embedded in building materials alongside reduced operational emissions. This paper presents the optimisation of retrofitted insulation thickness, using Ireland as a case study. Detailed and robust dynamic finite element models were developed based on in-situ boundary conditions and combined with economic and environmental considerations. It was determined that optimising insulation based on cost was considerably different to optimising based on carbon. Cost-optimised insulation can reduce overall cost which could expand the reach of retrofit, allowing for more existing homes to be used more efficiently. However, this approach can lead to significant increases in operational carbon and therefore a balanced decision must be made. The methodology presented can be adopted for different regions by inputting local data, which will facilitate the adoption of circular economy principals in European retrofit plans. The approach can benefit developing circular insulation materials of low embodied carbon by building a case for their use.
Stability constraints for geometrically nonlinear topology optimization
Authors: Dunning Peter D. 
Published: December 2023

AbstractThis paper compares four methods for formulating stability constraints in topology optimization with geometric nonlinearity. The methods are: a direct approach to compute the critical load factor, an approximation using an eigenvalue analysis at a load factor of 1, a new method based on an eigenvalue analysis at the constraint limit load factor, and an implicit method based on stiffness reduction, which has not previously been investigated for stability constraint formulation. These four methods are described in detail and then compared qualitatively and quantitatively (including optimization examples) in terms of accuracy, robustness, and computational efficiency. The results show that formulating the constraint using an eigenvalue analysis at a load factor of 1 is the most robust approach, as it is least likely to experience mode switching or mode skipping during optimization, which leads to poor convergence for the other three methods. It is also the most efficient, as it only requires a single eigenvalue solve, whereas other methods require additional linear solves to compute the constraint value. However, an eigenvalue analysis at a load factor of 1 only approximates the critical load factor, which may be over, or under-estimated. Therefore, none of the methods fully satisfy the criteria of accuracy, robustness, and efficiency, highlighting the need for further research, e.g., by improving the accuracy of the method based on an eigenvalue analysis at a load factor of 1, or by improving the robustness and efficiency of the direct approach.
Cosmic ray feedback in galaxies and galaxy clusters
Authors: Ruszkowski Mateusz , Pfrommer Christoph 
Published: December 2023

AbstractUnderstanding the physical mechanisms that control galaxy formation is a fundamental challenge in contemporary astrophysics. Recent advances in the field of astrophysical feedback strongly suggest that cosmic rays (CRs) may be crucially important for our understanding of cosmological galaxy formation and evolution. The appealing features of CRs are their relatively long cooling times and relatively strong dynamical coupling to the gas. In galaxies, CRs can be close to equipartition with the thermal, magnetic, and turbulent energy density in the interstellar medium, and can be dynamically very important in driving large-scale galactic winds. Similarly, CRs may provide a significant contribution to the pressure in the circumgalactic medium. In galaxy clusters, CRs may play a key role in addressing the classic cooling flow problem by facilitating efficient heating of the intracluster medium and preventing excessive star formation. Overall, the underlying physics of CR interactions with plasmas exhibit broad parallels across the entire range of scales characteristic of the interstellar, circumgalactic, and intracluster media. Here we present a review of the state-of-the-art of this field and provide a pedagogical introduction to cosmic ray plasma physics, including the physics of wave–particle interactions, acceleration processes, CR spatial and spectral transport, and important cooling processes. The field is ripe for discovery and will remain the subject of intense theoretical, computational, and observational research over the next decade with profound implications for the interpretation of the observations of stellar and supermassive black hole feedback spanning the entire width of the electromagnetic spectrum and multi-messenger data.
Anthropometric measurements of the foot cannot predict the screw diameter for fifth metatarsal fractures intramedullary fixation
Authors: Symeonidis Panagiotis D. , Totlis Trifon , Dermitzakis Iasonas , Papachristodoulou Athanasia , Giatas Ioannis , Beris Alexandros 
Published: December 2023

Abstract
Purpose
The present study aimed to evaluate the accuracy of anthropometric foot measurements in predicting the diameter of the intramedullary screw for fifth metatarsal fracture fixation. Secondary aim was to identify whether the fifth metatarsal intramedullary canal diameter is correlated to the fifth metatarsal length and the foot dimensions.

Methods
In 29 cadaveric feet, the maximum length of the plantar surface of the foot (PL) and the perimeter of the foot at the level of the fifth metatarsal base (PBFM) were measured using a measuring tape. Subsequently, the fifth metatarsal was excised. Using Computed Tomography scan, the metatarsal length (FML), and the horizontal (HDI) and vertical diameter (VDI) at the isthmus level were measured. The HDI values were grouped in 5 mm increments to correspond to the recommended screw diameter (RSD) for intramedullary fixation. A univariate linear regression analysis considered RSD and HDI as the dependent variables and FML, PL, PBFM as the independent variables. A multivariate regression analysis was performed to examine the predictive value of the two anthropometric measurements. A p-value < 0.05 was considered statistically significant.

Results
All six univariate analyses revealed that the dependent variable was significantly correlated with the independent variable. However, the multivariate regression models showed that the anthropometric measurements were not significantly correlated with the RSD and HDI.

Conclusion
The current study found an association between the fifth metatarsal intramedullary canal diameter and the fifth metatarsal length and foot anthropometric dimensions. However, the anthropometric measurements of the foot presented a low predictive value for the decision of an intramedullary screw diameter in the treatment of fractures of the base of the fifth metatarsal.
The effects of flexible short protocol with gonadotropin-releasing hormone antagonist on preventing premature ovulation in poor responders
Authors: Zhang Yan , Wang Hongyou , Zhang Xinyue , Hao Yingying , Yang Jihong , Li Yangbai , Feng Ting , Chen Yandong , Qian Yun 
Published: December 2023

Abstract
Purpose
The proportion of patients with poor ovarian response (POR) is increasing, but effective treatment remains a challenge. To control the hidden peaks of luteinizing hormone (LH) and premature ovulation for poor responders, this study investigated the efficacy of flexible short protocol (FSP) with gonadotropin-releasing hormone antagonist (GnRH-ant) on trigger day.

Methods
The 662 cycles of POR patients were retrospectively analyzed. The cohort was divided into control and intervention groups. The intervention group (group A) with 169 cycles received a GnRH-ant given on trigger day. The control (group B) with 493 cycles received only FSP. The clinical outcomes of the two groups were compared.

Results
Compared with group B, with gonadotropin-releasing hormone antagonist (GnRH-ant) on trigger day in group A the incidences of spontaneous premature ovulation decreased significantly (2.37% vs. 8.72%, P < 0.05). The number of fresh embryo-transfer cycles was 45 in group A and 117 in group B. There were no significant differences in clinical outcomes, including implantation rate, clinical pregnancy rate, live birth rate and the cumulative live birth rate (12.0% vs. 9.34%; 22.22% vs. 21.93%; 17.78% vs. 14.91%; 20.51% vs. 20%, respectively; P > 0.05) between the two group.

Conclusion
FSP with GnRH-ant addition on trigger day had no effect on clinical outcomes, but could effectively inhibit the hidden peaks of luteinizing hormone (LH) and spontaneous premature ovulation in POR. Therefore, it is an advantageous option for POR women.
The dominant findings of a recessive man: from Mendel’s kid pea to kidney
Authors: Tory Kálmán 
Published: December 2023

AbstractThe research of Mendel, born two centuries ago, still has many direct implications for our everyday clinical work. He introduced the terms “dominant” and “recessive” characters and determined their 3:1 ratio in the offspring of heterozygous “hybrid” plants. This distribution allowed calculation of the number of the phenotype-determining “elements,” i.e., the alleles, and has been used ever since to prove the monogenic origin of a disorder. The Mendelian inheritance of monogenic kidney disorders is still of great help in distinguishing them from those with multifactorial origin in clinical practice. Inheritance of most monogenic kidney disorders fits to Mendel’s observations: the equal contribution of the two parents and the complete penetrance or the direct correlation between the frequency of the recessive character and the degree of inbreeding. Nevertheless, beyond the truth of these basic concepts, several observations have expanded their genetic characteristics. The extreme genetic heterogeneity, the pleiotropy of the causal genes and the role of modifiers in ciliopathies, the digenic inheritance and parental imprinting in some tubulopathies, and the incomplete penetrance and eventual interallelic interactions in podocytopathies, reflect this expansion. For all these reasons, the transmission pattern in a natural setting may depend not only on the “character” but also on the causal gene and the variant. Mendel’s passion for research combined with his modest personality and meticulous approach can still serve as an example in the work required to understand the non-Mendelian universe of genetics.
Strontium isotope compositions of Late Permian evaporites from the northernmost Thuringian Basin (Germany) indicate continental influence on the marine Zechstein Sea
Authors: Käßner A. , Tichomirowa M. , Tandler R. , Ziebell J. 
Published: December 2023

AbstractIn the Late Permian Zechstein Sea of Central Europe, up to 2000 m of evaporitic rocks were deposited in at least four consecutive cycles. The age of these evaporitic rocks could not yet be precisely determined, because they are virtually fossil-free and do not contain radiometrically datable volcanic layers. A chemostratigraphic age of the succession can be determined by comparing 87Sr/86Sr ratios of marine gypsum and anhydrite to the worldwide marine strontium evolution curve. Unfortunately, published 87Sr/86Sr data of the Zechstein succession are characterized by frequent outliers towards higher ratios, making an age assignment challenging. The scatter in 87Sr/86Sr ratios might be induced by different processes like the contribution of meteoric water to the brine, in-situ Rb decay, or post-depositional hydrothermal or diagenetic overprint. Here, we present a dataset of 26 new gypsum and anhydrite 87Sr/86Sr ratios from drill cores situated at “Alter Stolberg” in the northernmost Thuringian Basin. Evaporites of the Werra-, Staßfurt-, and Leine cycles were sampled. The close proximity of the drillings allows a very accurate assignment of the stratigraphic position of each sample, so that trends and outliers in 87Sr/86Sr ratios can easily be recognized. While the entire Werra Formation obviously revealed non-marine 87Sr/86Sr ratios, the lowermost 87Sr/86Sr ratios in the Staßfurt and Leine Formations can be assumed to represent marine ratios and allow estimating a chemostratigraphic age of 257‒254 Ma. The combination of the 87Sr/86Sr data with the mineral composition of the samples suggests a contribution of meteoric water, probably river water, to the Zechstein Sea as the main reason for the observed increase in 87Sr/86Sr ratios. Additional in-situ Rb decay, related to the riverine input of clay minerals, cannot be excluded. Modelling the amounts of sea water and meteoric water in the brine indicates that 83‒99% of meteoric water would be necessary to explain the highest 87Sr/86Sr ratios observed in the Werra Formation.
Graphical abstract
Inter-software and inter-threshold reliability of quantitative paraspinal muscle segmentation
Authors: Liu Sihai , Schmidt Hendrik , Ziegeler Katharina , Zhang Tianwei , Yang Daishui , Taheri Nima , Pumberger Matthias , Becker Luis 
Published: December 2023

Abstract
Purpose
Changes in the cross-sectional area (CSA) and functional cross-sectional area (FCSA) of the lumbar multifidus (MF) and erector spinae muscles (ES) are factors that can contribute to low back pain. For the assessment of muscle CSA and composition there are various software and threshold methods used for tissue segmentation in quantitative analysis. However, there is currently no gold standard for software as well as muscle segmentation. This study aims to analyze the measurement error between different image processing software and different threshold methods for muscle segmentation.

Methods
Magnetic resonance images (MRI) of 60 patients were evaluated. Muscle CSA and FCSA measurements were acquired from axial T2-weighted MRI of the MF and ES at L4/L5 and L5/S1. CSA, FCSA, and FCSA/CSA ratio were measured independently by two observers. The MRI images were measured using two different software programs (ImageJ and Amira) and with two threshold methods (Circle/Overlap method) for each software to evaluate FCSA and FCSA/CSA ratio.

Results
Inter-software comparisons revealed high inter-rater reliability. However, poor inter-rater reliability were obtained with different threshold methods. CSA, FCSA, and FCSA/CSA showed excellent inter-software agreement of 0.75–0.99 regardless of the threshold segmentation method. The inter-rater reliability between the two observers ranged between 0.75 and 0.99. Comparison of the two segmentation methods revealed agreement between 0.19 and 0.84. FCSA and FCSA/CSA measured via the Overlap method were significantly higher than those measured via the Circle method (P < 0.01).

Conclusion
The present study showed a high degree of reliability with very good agreement between the two software programs. However, study results based on different threshold methods should not be directly compared.
Multinomial Thompson sampling for rating scales and prior considerations for calibrating uncertainty
Authors: Deliu Nina 
Published: December 2023

AbstractBandit algorithms such as Thompson sampling (TS) have been put forth for decades as useful tools for conducting adaptively-randomised experiments. By skewing the allocation toward superior arms, they can substantially improve particular outcomes of interest for both participants and investigators. For example, they may use participants’ ratings for continuously optimising their experience with a program. However, most of the bandit and TS variants are based on either binary or continuous outcome models, leading to suboptimal performances in rating scale data. Guided by behavioural experiments we conducted online, we address this problem by introducing Multinomial-TS for rating scales. After assessing its improved empirical performance in unique optimal arm scenarios, we explore potential considerations (including prior’s role) for calibrating uncertainty and balancing arm allocation in scenarios with no unique optimal arms.
Are there hybrid zones in Fagus sylvatica L. sensu lato?
Authors: Hrivnák Matúš , Krajmerová Diana , Paule Ladislav , Zhelev Petar , Sevik Hakan , Ivanković Mladen , Goginashvili Nana , Paule Juraj , Gömöry Dušan 
Published: December 2023

AbstractThe complex of beech taxa in western Eurasia (Fagus sylvatica L. s.l.) represents one of the most widespread broad-leaved trees in the temperate forests of the northern hemisphere. Two subspecies are generally recognized, F. sylvatica ssp. sylvatica in Europe and F. sylvatica ssp. orientalis in southwestern Asia, but several strongly differentiated regional populations were identified within this complex. To reveal geographical and genomic patterns of hybridization and introgression, genetic variation at 6789 single-nucleotide polymorphisms (SNP) resulting from ddRAD sequencing was studied in 288 specimens representing 207 populations distributed across the whole range. Two clusters resulting from a Bayesian analysis of population Structure well coincided with the subspecies, while increasing the number of clusters allowed to distinguish divergent lineages within subspecies. Two zones of potential hybridization between such lineages were analyzed: western Balkans at the contact of both subspecies and the Alpine area at the contact of populations coming from different glacial refugia. Geographical distribution of hybrid indices in the Balkan hybrid zone indicates asymmetric gene flow preferentially directed from F. orientalis to F. sylvatica. Eight SNPs showed a significant shift of genomic cline centers, seven of them toward excess F. orientalis ancestry, suggesting that introgression irregularly affects different regions of the beech genome. On the other hand, no genomic cline outliers were found in the Alpine hybrid zone. Implications for assisted gene flow are shortly discussed.
Mind the gap: gender, micro-inequities and barriers in software development
Authors: Guzmán Emitzá , Fischer Ricarda Anna-Lena , Kok Janey 
Published: December 2023

AbstractGender diversity and equity are known problems in the software industry. However, relatively few studies has examined the everyday work experiences and barriers that software professionals in technical roles encounter through a gender perspective. In this work, we investigate micro-inequities (e.g., interruptions, lack of eye contact, being assigned menial tasks in a project) and barriers experienced by software professionals working in technical roles with a gender perspective. We also analyzed age as a confounding factor. In our study, we surveyed 359 software professionals (50:50, women:men ratio) from globally distributed locations. Our results show that women and respondents in certain age groups encounter micro-inequities significantly more than men and other age groups. Further, women experience and witness sexism and harassment in the workplace in significantly higher numbers. We also found that women report having significantly less support and authority to make necessary decisions in their work, are less satisfied with their pay, and feel less valued and recognized in their teams. Finally, we found that the main barriers reported by women are related to team dynamics and gender biases, while men report most on technical and project related issues. Our results can serve to create awareness in the community about the large disparity and help practitioners revise their training programs and internal policies.