bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fixed and Distributed Gene Expression Time Delays in Reaction–Diffusion Systems
Authors: Sargood Alec , Gaffney Eamonn A. , Krause Andrew L. 
Published: August 2022

AbstractTime delays, modelling the process of intracellular gene expression, have been shown to have important impacts on the dynamics of pattern formation in reaction–diffusion systems. In particular, past work has shown that such time delays can shrink the Turing space, thereby inhibiting patterns from forming across large ranges of parameters. Such delays can also increase the time taken for pattern formation even when Turing instabilities occur. Here, we consider reaction–diffusion models incorporating fixed or distributed time delays, modelling the underlying stochastic nature of gene expression dynamics, and analyse these through a systematic linear instability analysis and numerical simulations for several sets of different reaction kinetics. We find that even complicated distribution kernels (skewed Gaussian probability density functions) have little impact on the reaction–diffusion dynamics compared to fixed delays with the same mean delay. We show that the location of the delay terms in the model can lead to changes in the size of the Turing space (increasing or decreasing) as the mean time delay, $$\tau $$
τ
, is increased. We show that the time to pattern formation from a perturbation of the homogeneous steady state scales linearly with $$\tau $$
τ
, and conjecture that this is a general impact of time delay on reaction–diffusion dynamics, independent of the form of the kinetics or location of the delayed terms. Finally, we show that while initial and boundary conditions can influence these dynamics, particularly the time-to-pattern, the effects of delay appear robust under variations of initial and boundary data. Overall, our results help clarify the role of gene expression time delays in reaction–diffusion patterning, and suggest clear directions for further work in studying more realistic models of pattern formation.
Value-assessment of computer-assisted navigation strategies during percutaneous needle placement
Authors: Boekestijn Imke , Azargoshasb Samaneh , van Oosterom Matthias N. , Slof Leon J. , Dibbets-Schneider Petra , Dankelman Jenny , van Erkel Arian R. , Rietbergen Daphne D. D. , van Leeuwen Fijs W. B. 
Published: August 2022

Abstract
Purpose
Navigational strategies create a scenario whereby percutaneous needle-based interventions of the liver can be guided using both pre-interventional 3D imaging datasets and dynamic interventional ultrasound (US). To score how such technologies impact the needle placement process, we performed kinematic analysis on different user groups.

Methods
Using a custom biopsy phantom, three consecutive exercises were performed by both novices and experts (n = 26). The exercise came in three options: (1) US-guidance, (2) US-guidance with pre-interventional image-registration (US + Reg) and (3) US-guidance with pre-interventional image-registration and needle-navigation (US + Reg + Nav). The traveled paths of the needle were digitized in 3D. Using custom software algorithms, kinematic metrics were extracted and related to dexterity, decision making indices to obtain overall performance scores (PS).

Results
Kinematic analysis helped quantifying the visual assessment of the needle trajectories. Compared to US-guidance, novices yielded most improvements using Reg (PSavg(US) = 0.43 vs. PSavg(US+Reg) = 0.57 vs. PSavg(US+Reg+Nav) = 0.51). Interestingly, the expert group yielded a reversed trend (PSavg(US) = 0.71 vs PSavg(US+Reg) = 0.58 vs PSavg(US+Reg+Nav) = 0.59).

Conclusion
Digitizing the movement trajectory allowed us to objectively assess the impact of needle-navigation strategies on percutaneous procedures. In particular, our findings suggest that these advanced technologies have a positive impact on the kinematics derived performance of novices.
Graph theory and combinatorial calculus: an early approach to enhance robust understanding
Authors: Ferrarello Daniela , Gionfriddo Mario , Grasso Federico , Mammana Maria Flavia 
Published: August 2022

AbstractThe objective of this work is to show an educational path for combinatorics and graph theory that has the aim, on one hand, of helping students understand some discrete mathematics properties, and on the other, of developing modelling skills through a robust understanding. In particular, for the path proposed to middle-school students, we used a connection betweenk-permutations and colourings of graphs: we indicated a way to solve problems related to counting all the possible arrangements of given objects in ak-tuple under given constraints. We solve this kind of problem by associating a graph with the constraints related to thek-tuple and by using graphs’ colourings, in which every colour is associated with one of the objects. The number of arrangements is given by finding the number of colourings through an algorithm called the Connection-Contraction Algorithm. The educational path is set within the Teaching for Robust Understanding framework and the goal, from the mathematical skills perspective, is to enhance modelling, passing from real situations (the fish problem in our experiment) to mathematical problems (the graph’s colouring in our experiment) and vice versa through the use of technology (the Connection-Contraction Algorithm with yEd editor, in our experiment), by using an extended modelling cycle. The meetings with students were videotaped and some results of the experimentation are given.
The role of insulin and incretin-based drugs in biliary tract cancer: epidemiological and experimental evidence
Authors: Sun Hua , Qi Xiaohui 
Published: August 2022

AbstractInsulin and incretin-based drugs are important antidiabetic agents with complex effects on cell growth and metabolism. Emerging evidence shows that insulin and incretin-based drugs are associated with altered risk of biliary tract cancer (BTC). Observational study reveals that insulin is associated with an increased risk of extrahepatic cholangiocarcinoma (ECC), but not intrahepatic cholangiocarcinoma (ICC) or gallbladder cancer (GBC). This type-specific effect can be partly explained by the cell of origin and heterogeneous genome landscape of the three subtypes of BTC. Similar to insulin, incretin-based drugs also exhibit very interesting contradictions and inconsistencies in response to different cancer phenotypes, including BTC. Both epidemiological and experimental evidence suggests that incretin-based drugs can be a promoter of some cancers and an inhibitor of others. It is now more apparent that this type of drugs has a broader range of physiological effects on the body, including regulation of endoplasmic reticulum stress, autophagy, metabolic reprogramming, and gene expression. In particular, dipeptidyl peptidase-4 inhibitors (DPP-4i) have a more complex effect on cancer due to the multi-functional nature of DPP-4. DPP-4 exerts both catalytic and non-enzymatic functions to regulate metabolic homeostasis, immune reaction, cell migration, and proliferation. In this review, we collate the epidemiological and experimental evidence regarding the effect of these two classes of drugs on BTC to provide valuable information.
Closed linear spaces consisting of strongly norm attaining Lipschitz functionals
Authors: Kadets Vladimir , Roldán Óscar 
Published: August 2022

AbstractGiven a pointed metric space M, we study when there exist n-dimensional linear subspaces of $$\mathrm {Lip}_0(M)$$

Lip
0

(
M
)

consisting of strongly norm-attaining Lipschitz functionals, for $$n\in {\mathbb {N}}$$

n
∈
N

. We show that this is always the case for infinite metric spaces, providing a definitive answer to the question. We also study the possible sizes of such infinite-dimensional closed linear subspaces Y, as well as the inverse question, that is, the possible sizes for a metric space M in order to such a subspace Y exist. We also show that if the metric space M is $$\sigma $$
σ
-precompact, then the aforementioned subspaces Y need to be always separable and isomorphically polyhedral, and we show that for spaces containing [0, 1] isometrically, they can be infinite-dimensional.
Reasonable location of stopping line in close-distance underlying coal seam and partition support of large cross-section roadway
Authors: Chen Dongdong , Wu Yiyi , Xie Shengrong , Guo Fangfang , He Fulian , Liu Ruipeng 
Published: August 2022

AbstractClose-distance coal seams are widely distributed over China, and the coal pillars left by the overlying coal seams affect the retracement channel of the underlying coal seam in the stopping stage. Based on the engineering background of close-distance seam mining in a coal mine, the reasonable position of the underlying coal seam's stopping line and the support method of the large section roadway during stopping are investigated using field measurements, similar simulation experiments, and numerical simulations. There are three types of location relationships between the stopping line of the underlying coal seam and the stopping line of the overlying coal seam: "externally staggered with the upper stopping line" (ESUL, stops mining under the overlying goaf), "overlapped with upper stopping line" (OUL), and "internally staggered with the upper stopping line" (ISUL, ISUL-SD for shorter internal staggered distances, ISUL-LD for longer ones). There are different stress arch structures in the overlying strata of the above three positions, and the stress arch evolution process exists in the process of ESUL → OUL → ISUL-SD → ISUL-LD: a front and rear double stress arch structure → the front arch gradually decreases → the front arch dies out, and the double arch synthesizes the single arch → the single-arch range expands → the nested double arch. The relationship between the stress arch structure and the position of the stopping line is evaluated as follows: (1) ESUL: the stress concentration in the roof plate of the retracement channel of the underlying coal seam is the highest, because the overburden block of the extensive collapse zone acts directly on the roof plate of the retracement channel, resulting in relative difficulties in roof support. (2) OUL: although the retracement channel roof pressure is minimal, the overlying rock structure has the potential for rotation or slippage instability. (3) ISUL-SD: the pressure on the roof of the retracement channel is small and the overburden structure is stable, which is conducive to the safe retraction of the support and not limited by the width of the end-mining coal pillar. (4) ISUL-LD: it is basically the same as the condition of stopping under the non-goaf; however, it has a limitation on the width of the end-mining coal pillar. The location of the stopping line is selected as ISUL-SD, and the retraction process of the self-excavating retraction channel was adopted. A partition asymmetric support scheme which is proven by field practice is proposed, through a comprehensive analysis of the pre-stress field simulation of the support scheme, based on the different control requirements of the roof above the support and the roof of the retracement channel in the stopping area. This method realizes safe and smooth withdrawal of the support.
Predicting Lumbar Vertebral Osteopenia Using LvOPI Scores and Logistic Regression Models in an Exploratory Study of Premenopausal Taiwanese Women
Authors: Chen Chun-Wen , Liu Yi-Jui , Lin Shao-Chieh , Wang Chien-Yuan , Shen Wu-Chung , Cho Der-Yang , Lee Tung-Yang , Juan Cheng-Hsuan , Juan Cheng-En , Cheng Kai-Yuan , Juan Chun-Jung 
Published: August 2022

Abstract
Purpose
To propose hybrid predicting models integrating clinical and magnetic resonance imaging (MRI) features to diagnose lumbar vertebral osteopenia (LvOPI) in premenopausal women.

Methods
This prospective study enrolled 101 Taiwanese women, including 53 before and 48 women after menopause. Clinical information, including age, body height, body weight and body mass index (BMI), were recorded. Bone mineral density (BMD) was measured by the dual-energy X-ray absorptiometry. Lumbar vertebral fat fraction (LvFF) was measured by MRI. LvOPI scores (LvOPISs) comprising different clinical features and LvFF were constructed to diagnose LvOPI. Statistical analyses included normality tests, linear regression analyses, logistic regression analyses, group comparisons, and diagnostic performance. A P value less than 0.05 was considered as statistically significant.

Results
The post-menopausal women had higher age, body weight, BMI, LvFF and lower BMD than the pre-menopausal women (all P < 0.05). The lumbar vertebral osteoporosis group had significantly higher age, longer MMI, and higher LvFF than the LvOPI group (all P < 0.05) and normal group (all P < 0.005). LvOPISs (AUC, 0.843 to 0.864) outperformed body weight (0.747; P = 0.0566), BMI (0.737; P < 0.05), age (0.649; P < 0.05), and body height (0.5; P < 0.05) in diagnosing LvOPI in the premenopausal women. Hybrid predicting models using logistic regression analysis (0.894 to 0.9) further outperformed all single predictors in diagnosing LvOPI in the premenopausal women (P < 0.05).

Conclusion
The diagnostic accuracy of the LvOPI can be improved by using our proposed hybrid predicting models in Taiwanese premenopausal women.
Comparison of Lower Stratosphere Wind Observations From the USTC's Rayleigh Doppler Lidar and the ESA's Satellite Mission Aeolus
Authors: Chen Chong , Xue Xianghui , Sun Dongsong , Zhao Ruocan , Han Yuli , Chen Tingdi , Liu Hengjia , Zhao Yiming 
Published: August 2022

AbstractSince the first spaceborne Doppler wind lidar, Aeolus, was launched, global wind field observations from space have been possible. Several ground‐ and air‐based validations followed, although most of these comparisons remained below 10 km in the troposphere, with rare validation work for the stratosphere. The Rayleigh Doppler lidar developed by the University of Science and Technology of China (USTC) was deployed in Xinjiang, China, in 2017. It can observe wind speed and temperature in the stratosphere and mesosphere. By setting two geographical ranges centered on the USTC lidar, the Aeolus Rayleigh winds within these ranges can be compared with ground‐based lidar wind data. Furthermore, after eliminating the effect of particulate backscatter on the USTC lidar, the lower limit of the detection range was extended to 10 km to obtain more samples. The mean biases between the Aeolus winds and the USTC lidar winds were 1.05 ± 5.98 (−0.35 ± 4.78) m/s, 1.80 ± 6.30 (−1.88 ± 4.97) m/s, and 0.17 ± 5.45 (0.51 ± 4.44) m/s for all data, ascending orbits, and descending orbits, respectively, in a large (small) geographical range. The geographical distance between the USTC lidar and the Aeolus observation swaths has a significant effect on the wind bias, the farther the distance between Aeolus observation swaths and the USTC lidar, the greater the bias. Whereas, the wind biases have no significant dependency on the time difference of the USTC lidar observation to Aeolus overflight time. Overall, the Aeolus winds are consistent with the USTC lidar winds in the stratosphere.
A Method for Clear‐Sky Identification and Long‐Term Trends Assessment Using Daily Surface Solar Radiation Records
Authors: Correa Lucas Ferreira , Folini Doris , Chtirkova Boriana , Wild Martin 
Published: August 2022

AbstractTime series of clear‐sky irradiance are fundamental for the understanding of changes in the Earth Radiation budget, since they allow to examine radiative processes in the cloud‐free atmosphere. Clear‐sky data is usually derived from all‐sky irradiances using one of several clear‐sky methods proposed in the literature. However, most of the available clear‐sky methods require additional in situ measurements and/or high temporal resolution (sub‐daily), which restricts the derivation of clear‐sky time series to a few well equipped stations. Here we propose a new clear‐sky identification method that aims to overcome this problem, with the ultimate goal of deriving multidecadal clear‐sky trends for many sites globally. The method uses site specific monthly transmittance thresholds to derive long term clear‐sky time series for any station worldwide that has daily mean irradiance data. We exemplify the method for 24 stations. Transmittance thresholds are derived by combining 29 years (1990–2018) of satellite cloud cover data with in situ irradiance measurements. The thresholds are then applied to the whole time series (independent of satellite data availability) to screen out cloudy days. Comparison of our results with reference data derived using Long and Ackerman's (2000, https://doi.org/10.1029/2000jd900077) method shows good agreement after bias correction, especially for decadal trends. While limitations of the method, such as anomalies representation, are highlighted and discussed, validation results encourage its use to derive long term clear‐sky time series and associated decadal‐scale trends around the globe.
Characterization of Viscous Dissipative Heating in the Earth's Mantle Caused by Surface Forces
Authors: Devin E. , Zhong S. 
Published: August 2022

AbstractViscous dissipative heating has long been discussed as a heat source in solid celestial bodies experiencing exogenic forces such as tidal forcing or surface loading. We examine the characteristics of viscous dissipative heating in a Newtonian, Maxwell viscoelastic solid in a 2D Cartesian box subjected to a surface load. The solutions are analyzed to understand the general controls on the energetics of planetary mantle that are associated with exogenic forcing. We find that work done at the surface is partitioned between dissipative and elastic terms depending on mantle viscosity, loading period, and loading wavelength. For viscosity structures with a weak upper mantle layer, dissipation is spatially concentrated in the upper mantle for short loading periods, implying that exogenic forces may play a role in the generation of weak upper mantle layers. The results are also scaled to estimate how much energy is dissipated in Earth's mantle, both present and past, during surface mass movement processes and tidal forcing. We find that the dissipation from glacial loading cycles since Mid‐Pleistocene at a period of 100,000 years might contribute ∼3 mW/m2 heat flux in the formerly glaciated regions, but for glacial cycles with a period of 40,000 years during the Early Pleistocene, the heat flux may have been 3 times larger at ∼9 mW/m2. We find that tidal forcing for the early Earth at 4 Ga may have contributed ∼30 TW of heat to the upper mantle, suggesting that exogenic forces have the capacity to contribute significantly to early Earth's energy budget.
Spontaneously Exsolved Free Gas During Major Storms as an Ephemeral Gas Source for Pockmark Formation
Authors: Gupta S. , Schmidt C. , Böttner C. , Rüpke L. , Hartz E. H. 
Published: August 2022

AbstractAbrupt fluid emissions from shallow marine sediments pose a threat to seafloor installations like wind farms and offshore cables. Quantifying such fluid emissions and linking pockmarks, the seafloor manifestations of fluid escape, to flow in the sub‐seafloor remains notoriously difficult due to an incomplete understanding of the underlying physical processes. Here, using a compositional multi‐phase flow model, we test plausible gas sources for pockmarks in the south‐eastern North Sea, which recent observations suggest have formed in response to major storms. We find that the mobilization of pre‐existing gas pockets is unlikely because free gas, due to its high compressibility, damps the propagation of storm‐induced pressure changes deeper into the subsurface. Rather, our results point to spontaneous appearance of a free gas phase via storm‐induced gas exsolution from pore fluids. This mechanism is primarily driven by the pressure‐sensitivity of gas solubility, and the appearance of free gas is largely confined to sediments in the vicinity of the seafloor. We show that in highly permeable sediments containing gas‐rich pore fluids, wave‐induced pressure changes result in the appearance of a persistent gas phase. This suggests that seafloor fluid escape structures are not always proxies for overpressured shallow gas and that periodic seafloor pressure changes can induce persistent free gas phase to spontaneously appear.
Numerical Modeling of Structurally Controlled Ore Formation in Magmatic‐Hydrothermal Systems
Authors: Codeço Marta S. , Weis Philipp , Andersen Christine 
Published: August 2022

AbstractFaults and fractures can be permeable pathways for focused fluid flow in structurally controlled ore‐forming hydrothermal systems. However, quantifying their role in fluid flow on the scale of several kilometers with numerical models typically requires high‐resolution meshes. This study introduces a modified numerical representation of m‐scale fault zones using lower‐dimensional elements (here, one‐dimensional [1D] elements in a 2D domain) to resolve structurally controlled fluid flow with coarser mesh resolutions and apply the method to magmatic‐hydrothermal ore‐forming systems. We modeled horizontal and vertical structure‐controlled magmatic‐hydrothermal deposits to understand the role of permeability and structure connectivity on ore deposition. The simulation results of vertically extended porphyry copper systems show that ore deposition can occur along permeable vertical structures where ascending, overpressured magmatic fluids are cooled by downflowing ambient fluids. Structure permeability and fault location control the distribution of ore grades. In highly permeable structures, the mineralization can span up to 3 km vertically, resulting in heat‐pipe mechanisms that promote the ascent of a magmatic vapor phase to an overlying structurally controlled epithermal system. Simulations for the formation of subhorizontal vein‐type deposits suggest that the major control on fluid flow and metal deposition along horizontal structures is the absence of vertical structures above the injection location but their presence at greater distances. Using a dynamic permeability model mimicking crack‐seal mechanisms within the structures leads to a pulsating behavior of fracture‐controlled hydrothermal systems and prevents the inflow of ambient fluids under overpressured conditions.