bluuebunny/crossref_metadata_2025_split huggingface dataset:
Building Treatments in Numerical Modeling of Dam Break Induced Flow in Urban Area
Authors: Sandi C , Adityawan M B , Nurendyastuti A K , Farid M , Harlan D , Kuntoro A A , Widyaningtias  
Published: October 2023

Abstract
Dam break is one of the most dangerous disasters, which cause a large mass of water from the reservoir is suddenly released to the downstream. Although dam break events are still rare, the occurrences can cause severe damage to the downstream area, especially if the downstream is an urban area. Urban flood due to dam break has a different characteristic compared to the flood in nature. Modeling the flood is good way to learn the urban flood characteristic. Therefore, further studies are needed to develop an urban dam break model. Numerical modeling is one of the most effective methods to simulate the flood. In numerical modeling, buildings can be modeled with 3 approaches, as a wall boundary, as an area with high manning value, and as a contour. This paper discusses about two-dimensional flow of a dam break which flows through a sloping channel and single building, particularly comparing 3 approaches to modeled the building. The case is based on laboratory experiment of previous study. The model was developed with 2D Shallow Water Equations (SWE) which are based on the conservation of mass and momentum derived from Navier Stokes equation. The equations then discretized using Mac-Cormack numerical scheme. Numerical filter is used to reduce the numerical instability or oscillation in the model. The numerical model results are then compared to the experimental result from previous study. The accuracy of the numerical model was checked using Root Mean Square Error (RMSE) to determine the best methods to modeled the building. The results indicate that modeling the building as a wall boundary have the best results with lowest RMSE value and also shown the closest comparison of water level compared to the experimental results. By conducting this study, it is hoped to assist the urban dam break modeling in the future.
Issues and Problems Affecting Post-Disaster Reconstruction Activities in Indonesia
Authors: Prawenti H , Susilowati F , Jannah R M , Susanto S H 
Published: October 2023

Abstract
Efforts to mitigate the danger of disasters continue. Both long-term and short-term Disaster Risk Reduction (DRR) activities have been undertaken by governments and International Organizations. One type of long-term post-disaster activity is rehabilitation and reconstruction, which are an important part of the catastrophe recovery phase Long-term reconstruction activities are activities that have uncertainty. The reconstruction necessitates the integration of long-term development plans that account for various catastrophic risks and the possibility of mitigating future dangers. Based on past research, uncertainty variables show a problem with the activity of reconstruction activities. Numerous countries, including Malaysia, Nepal, America, and Estonia, have conducted research on the challenges and issues associated with construction activity. This research variable was developed from several studies conducted in several countries to obtain more comprehensive variables for study in the disaster-prone. Assessment instruments were developed using questionnaires distributed to a sample of respondents who met the initial criteria. Relative importance index (RII) is used in data processing procedures, and this paper examines the concerns and difficulties experienced during the reconstruction process. The data analysis found that the most dominant aspect that influences the construction period is the delay in project completion. With the value of the Relative Importance Index (RII) at the High-Medium (H–M) level (0.6 RI 0.8) with a value of 0.769 and all research variables are included in the High-Medium (H–M), namely (0.6 ≤ RI ≤ 0.8).
Design of Vertical Evacuation Building at Painan City Using Results From Tsunami Propagation Modeling
Authors: Rahmasari P , Kusumastuti D , Adityawan M B 
Published: October 2023

Abstract
Fault under the Mentawai Islands has high potential to cause a large earthquake and triggering tsunami. Painan City, is located near the fault. With geographical condition on a bay surrounded by hills in the upstream area, a tsunami may cause a flow channeling effect and increase the inundation distance. An alternative of mitigation effort is to build a Vertical Evacuation Building (VEB) to help the community to reach a safe elevation within the evacuation time. Therefore, VEB should be designed to withstand tsunami impacts and to resist large earthquakes. This study conducts the design and analysis of the performance of multi-functional VEB structures at Painan City. The tsunami propagation simulation was carried out, and parameters obtained were used for structural design. Three VEB models were developed, i.e., (i) model with walls under tsunami and earthquake loads, (ii) model without walls under tsunami and earthquake loads, and (iii) model without walls under earthquake load only as the lateral load. Non-linear static pushover analyses were later conducted to evaluate the structural performances. The study revealed that debris force affects the most compared to other tsunami force components. Structural openings also affect the tsunami load received by the structure. Column moment force for models designed with tsunami load is greater than that of earthquake, while the difference is less significant for beam. The internal force differences occur along the tsunami inundated depth, thus influence the component design. From the pushover analysis, all models were found to meet the performance targets for earthquake.
Implementation of a quick assessment application called InaRISK for damaged houses after the West Pasaman Earthquake (2022)
Authors: Fauzan  , Carol N D , Ismail F A , Narny Y 
Published: October 2023

Abstract
West Sumatra, located at the boundary of two of Earth’s shifting tectonic plates, is prone to natural disasters, especially earthquake. On 25th February 2022, an earthquake centered 18 km northeast of Simpang Empat, the capital city of West Pasaman, with a magnitude of 5.2 M, struck off at 08.35 WIB. This earthquake claimed lives and damaged buildings. After the earthquake, the need for rehabilitation and reconstruction is indispensable. Various methods are used in assessing the damaged houses, however, the assessment still use the manual method but is assessed as having many shortcomings. In the case of West Pasaman earthquake, the start of application-based to collect data is improvement to the manual method with its practicality and time-saving capability. This application, developed by National Agency for Disaster Countermeasure (BNPB) is called InaRisk. Although this application has made a breakthrough, improvement for this application is required as there are still drawbacks especially it cannot be be used without internet connection. This paper discusses the usage of a quick assessment application called InaRISK for damaged houses after the West Pasaman earthquake. A new assessment method developed by Andalas University Team called Earthquake Rapid Assessment (E-RA) is also discussed in this paper.
What governs the atomic structure of the interface between 2D transition metal dichalcogenides in lateral heterostructures?
Authors: Davies Francis H , Mehlich Kai , Busse Carsten , Krasheninnikov Arkady V 
Published: October 2023

Abstract
The development of lateral heterostructures (LHs) based on two-dimensional (2D) materials with similar atomic structure but distinct electronic properties, such as transition metal dichalcogenides (TMDCs), opened a new route towards realisation of optoelectronic devices with unique characteristics. In contrast to van der Waals vertical heterostructures, the covalent bonding at the interface between subsystems in LHs is strong, such that the morphology of the interface, which can be coherent or contain dislocations, strongly affects the properties of the LH. We predict the atomic structure of the interface with account for the mismatch between the primitive cell sizes of the components, and more important, the widths of the joined materials using parameters derived from first-principles calculations. We apply this approach to a variety of TMDCs and set a theoretical limit on when the transition of the interface from coherent to dislocation-type should occur. We validate our theoretical results by comparison with the initial stage of two-dimensional heteropitaxial growth of junctions between MoS2 and TaS2 on Au(111).
Effect of microstructure heterogeneity on the cryogenic fracture toughness of the dissimilar joint between SA645 and 304L made by laser welding
Authors: Zhou Fei , Wu Bingxin , Ji Junhao , Tu Jiaqing , Huang Yaoyao , Wu Chengzhe , Li Chao 
Published: October 2023

Abstract
The cryogenic fracture toughness of the SA645/304L dissimilar weld, produced using continuous wave IPG fiber laser welding with a 0.3 mm beam offset towards the 304L side, and the microstructural effects on the fracture behavior were systematically investigated. The weld metal consists of ∼89% columnar dendritic martensite and ∼11% retained austenite (RA), where the ununiform distribution of constituent phases as well as the distinctions between martensite and RA in terms of morphology and mechanical properties lead to the microstructure heterogeneity of weld metal. Pop-in phenomenon appears on the Force-Displacement (F-V) curve during the crack tip opening displacement (CTOD) test for the weld. The CTOD value for the weld is ∼0.057 mm, about 8 times less than that when pop-in effect is ignored (∼0.563 mm). Rapid propagation of the pre-fatigue crack tip along the center of the weld leads to the pop-in phenomenon. Fracture surface in pre-fatigue crack tip (PCT) region shows quasi-cleavage features, while fracture surface in stable crack propagation (SCP) region presents a ductile-fractured surface with dimples. The crack propagation path in SCP region is frequently deflected. Inhibition effect of grain boundaries on crack propagation and TRIP effect of retained austenite (RA) result in the improvement in fracture toughness of the SCP region.
The effective enhancement of information in 3D small-world networks of biological neuronal cells
Authors: Gentile F 
Published: October 2023

Abstract
The cardiovascular system, the kidney, or the brain, are examples of complex systems - where the properties of the systems arise because of the layout of cells in those systems. One way to characterize systems is using networks, where elements and interactions of the systems are represented as nodes and links of a graph. Network’s topology can be, in turn, measured by the small-world coefficient. Small world networks feature increased clustering and shorter paths compared to random or periodic networks of the same size. This suggests that systems with small world attributes can also efficiently transport signals, nutrients, or information within their body. While several reports in literature have illustrated that real biological systems are small-world, yet little is known about how information varies as a function of the small-world-ness (

sw

) of three dimensional graphs. Here, we used a model of the brain to estimate quantitatively the information processed in 3D networks. In the model, nodes of the graph are neuronal units capable to receive, integrate and transmit signals to other neurons of the system in parallel. The information encoded in the signals was then extracted using the techniques of information theory. In simulations where the topology of networks of

400

nodes was varied over large intervals, we found that in the

0

−

9

sw

range information scales linearly with the small world coefficient, with a five-fold increase. Results of the paper and review of the existing literature on model organisms suggest that a small-world architecture may offer an evolutionary advantage to biological systems.
Nonlinear position control of electro-hydraulic servo system based on lyapunov robust integral backstepping controller
Authors: Enyan Michael , Bing Zhang , Junsen Rao , Amu-Darko Jesse Nii Okai , Issaka Eliasu , Páez Luis Miguel Ruiz 
Published: October 2023

Abstract
In electro-hydraulic servo systems (EHSS), high nonlinearity and time-varying features limit the hydraulic actuator performance. In feedback-based systems, linearization reduces nonlinearities. Their cancellation may produce instability when modeling uncertainty exists. This work uses a robust nonlinear controller based on Lyapunov theory to control the nonlinear position of the electro-hydraulic servo system (EHSS). The dynamics of the system were modeled as extensively as possible, and then a simplified mathematical model based on the EHSS dynamics was created for the controller design. Integral backstepping was used to design the nonlinear robust controller utilizing the Lyapunov theory of nonlinear systems. Lyapunov functions theoretically ensured closed-loop stability. Comparative simulation analysis and experimental investigation in real-time with the proportional integral derivative (PID) controller optimized offline for position tracking control were carried out. Besides tracking performance and steady-state error, the mean square error (MSE), the root mean square error (RMSE), the maximum absolute value of tracking errors

(
M

e

)
,

and the standard deviation of tracking errors (σ) was utilized to evaluate the controllers’ performance. The simulation analysis and experimental verification were accomplished under various sinusoidal trajectories using different testing conditions (amplitudes, frequencies, and external disturbance), in all testing conditions the effectiveness of the robust nonlinear integral backstepping controller was demonstrated.
Comment on ‘Physics-based representations for machine learning properties of chemical reactions’
Authors: Spiekermann Kevin A , Stuyver Thijs , Pattanaik Lagnajit , Green William H 
Published: October 2023

Abstract
In a recent article in this journal, van Gerwen et al (2022 Mach. Learn.: Sci. Technol.
3 045005) presented a kernel ridge regression model to predict reaction barrier heights. Here, we comment on the utility of that model and present references and results that contradict several statements made in that article. Our primary interest is to offer a broader perspective by presenting three aspects that are essential for researchers to consider when creating models for chemical kinetics: (1) are the model’s prediction targets and associated errors sufficient for practical applications? (2) Does the model prioritize user-friendly inputs so it is practical for others to integrate into prediction workflows? (3) Does the analysis report performance on both interpolative and more challenging extrapolative data splits so users have a realistic idea of the likely errors in the model’s predictions?
Reply to Comment on ‘Physics-based representations for machine learning properties of chemical reactions’
Authors: van Gerwen Puck , Wodrich Matthew D , Laplaza Ruben , Corminboeuf Clemence 
Published: October 2023

Abstract
Recently, we published an article in this journal that explored physics-based representations in combination with kernel models for predicting reaction properties (i.e. TS barrier heights). In an anonymous comment on our contribution, the authors argue, amongst other points, that deep learning models relying on atom-mapped reaction SMILES are more appropriate for the same task. This raises the question: are deep learning models sounding the death knell for kernel based models? By studying several datasets that vary in the type of chemical (i.e. high-quality atom-mapping) and structural information (i.e. Cartesian coordinates of reactants and products) contained within, we illustrate that physics-based representations combined with kernel models are competitive with deep learning models. Indeed, in some cases, such as when reaction barriers are sensitive to the geometry, physics-based models represent the only viable candidate. Furthermore, we illustrate that the good performance of deep learning models relies on high-quality atom-mapping, which comes with significant human time-cost and, in some cases, is impossible. As such, both physics-based and graph models offer their own relative benefits to predict reaction barriers of differing datasets.
STAT3-dependent long non-coding RNA Lncenc1 contributes to mouse ES cells pluripotency via stabilizing Klf4 mRNA
Authors: Monteleone Emanuele , Corrieri Paola , Provero Paolo , Viavattene Daniele , Pulvirenti Lorenzo , Raggi Laura , Carbognin Elena , Bianchi Marco E , Martello Graziano , Oliviero Salvatore , Pandolfi Pier Paolo , Poli Valeria 
Published: October 2023

Abstract
Embryonic stem cells (ESCs) preserve the unique ability to differentiate into any somatic cell lineage while maintaining their self-renewal potential, relying on a complex interplay of extracellular signals regulating the expression/activity of pluripotency transcription factors and their targets. Leukemia inhibitory factor (LIF)-activated STAT3 drives ESCs’ stemness by a number of mechanisms, including the transcriptional induction of pluripotency factors such as Klf4 and the maintenance of a stem-like epigenetic landscape. However, it is unknown if STAT3 directly controls stem-cell specific non-coding RNAs, crucial to balance pluripotency and differentiation. Applying a bioinformatic pipeline, here we identify Lncenc1 in mouse ESCs as an STAT3-dependent long non-coding RNA that supports pluripotency. Lncenc1 acts in the cytoplasm as a positive feedback regulator of the LIF–STAT3 axis by competing for the binding of microRNA-128 to the 3’UTR of the Klf4 core pluripotency factor mRNA, enhancing its expression. Our results unveil a novel non-coding RNA-based mechanism for LIF–STAT3-mediated pluripotency.
Homozygous MFN2 variants causing severe antenatal encephalopathy with clumped mitochondria
Authors: Chevrollier Arnaud , Bonnard Adeline Alice , Ruaud Lyse , Gueguen Naïg , Perrin Laurence , Desquiret-Dumas Valérie , Guimiot Fabien , Becker Pierre-Hadrien , Levy Jonathan , Reynier Pascal , Gaignard Pauline 
Published: October 2023

Abstract
Pathogenic variants in the MFN2 gene are commonly associated with autosomal dominant (CMT2A2A) or recessive (CMT2A2B) Charcot-Marie-Tooth disease, with possible involvement of the CNS. Here, we present a case of severe antenatal encephalopathy with lissencephaly, polymicrogyria and cerebellar atrophy.
Whole genome analysis revealed a homozygous deletion c.1717-274_1734 del (NM_014874.4) in the MFN2 gene, leading to exon 16 skipping and in-frame loss of 50 amino acids (p.Gln574_Val624del), removing the proline-rich domain and the transmembrane domain 1 (TM1). MFN2 is a transmembrane GTPase located on the mitochondrial outer membrane that contributes to mitochondrial fusion, shaping large mitochondrial networks within cells. In silico modelling showed that the loss of the TM1 domain resulted in a drastically altered topological insertion of the protein in the mitochondrial outer membrane. Fetus fibroblasts, investigated by fluorescent cell imaging, electron microscopy and time-lapse recording, showed a sharp alteration of the mitochondrial network, with clumped mitochondria and clusters of tethered mitochondria unable to fuse. Multiple deficiencies of respiratory chain complexes with severe impairment of complex I were also evidenced in patient fibroblasts, without involvement of mitochondrial DNA instability.
This is the first reported case of a severe developmental defect due to MFN2 deficiency with clumped mitochondria.
AgingReG: a curated database of aging regulatory relationships in humans
Authors: Piao Minghui , Feng Ke , Liu Xinyu , Bai Xuefeng , Zheng Yuqi , Sun Meiling , Zhao Peng , Wang Yani , Ban Xiaofang , Xiong Jie , Shi Chengyu , Meng Li , Liu Yuxin , Yu Li , Li Jing , Zhong Shan , Jiang Xinjian , Chen Yu , Sun Xin , Zheng Yan , Tian Jinwei 
Published: October 2023

Abstract
Aging and cellular senescence are characterized by a progressive loss of physiological integrity, which could be triggered by aging factors such as physiological, pathological and external factors. Numerous studies have shown that gene regulatory events play crucial roles in aging, increasing the need for a comprehensive repository of regulatory relationships during aging. Here, we established a manually curated database of aging factors (AgingReG, https://bio.liclab.net/Aging-ReG/), focusing on the regulatory relationships during aging with experimental evidence in humans. By curating thousands of published literature, 2157 aging factor entries (1345 aging gene entries, 804 external factor entries and eight aging-related pathway entries) and related regulatory information were manually curated. The regulatory relationships were classified into four types according to their functions: (i) upregulation, which indicates that aging factors upregulate the expression of target genes during aging; (ii) downregulation, which indicates that aging factors downregulate the expression of target genes during aging; (iii) activation, which indicates that aging factors influence the activity of target genes during aging and (iv) inhibition, which indicates that aging factors inhibit the activation of target molecule activity, leading to declined or lost target activity. AgingReG involves 651 upregulating pairs, 632 downregulating pairs, 330 activation-regulating pairs and 34 inhibition-regulating pairs, covering 195 disease types and more than 800 kinds of cells and tissues from 1784 published literature studies. AgingReG provides a user-friendly interface to query, browse and visualize detailed information about the regulatory relationships during aging. We believe that AgingReG will serve as a valuable resource database in the field of aging research.
Database URL: https://bio.liclab.net/Aging-ReG/