bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ballast Water Treatment with Heat Exchanger Modeling Simulation
Authors: Iswantoro A , Semin  , Pitana T , Zaman M B , Ahsan F I 
Published: July 2023

Abstract
Pollution of the marine environment has become a global issue, including marine pollution from ballast water. The impact is it can damage ecosystems and even affect humans. Therefore, pollution from ballast water is something that must be prevented by ballast water treatment. In this research, the author carried out a modeling simulation on a heat exchanger with a mechanical-type ballast water treatment method by utilizing the heat generated by the ship’s engine. Heat is used to kill microorganisms. So that the ballast water becomes cleaner than without treatment. In this research, the calculation of the need for heat exchangers on certain types of ships with certain sizes is carried out. In this calculation, the ship used is a container type with 3 categories based on cargo capacity and ballast tank capacity. Then the heat from the exhaust gases is used to heat the ballast water of the ship. The simulation results show that the maximum ballast water temperature of each ship category is in the range of 68-75 C. With this temperature, it is sufficient to kill and reduce microorganisms in the ballast water.
Optimization design of remotely operated vehicle (ROV) for Madura Strait Area
Authors: Afifudin I N , Nasirudin A , Aryawan W D , Kurniawati H A , Hasanudin  , Utama D , Putra E I 
Published: July 2023

Abstract
Nowadays, the development of unmanned vehicles is significantly increased. Since the remotely operated vehicle (ROV) has more advantages than Diver. Then, ROV has an important role in underwater inspection and research in various sectors, such as offshore infrastructure development. ROV will give some critical information to the operator about an underwater inspection like bathymetry, pipeline inspection, and the other crucial subsea structure that the divers can’t reach. The optimization design has been carried out to determine ROV operational requirements in Madura Strait by Total-Based Method. ROV will be divided into 3 leading function groups, they are Features, Survive and Operate. Every group will be divided into Function Breakdown Structure (FBS). FBS will be divided again into Work Breakdown Structure (WBS). The optimum design will be determined by linking every breakdown function. The results are the ROV has 2MP 1080P resolution for camera, 2000 lumens for lighting, 50 m detection area for sonar and echosounder, 100 N grip force for Gripper, equipped with stainless steel frame, 2 hours long for operational duration, 5kg.f for thruster, operated with cable 300 m long and equipped with 6-unit thruster.
Study of Wave Parameters in the West side of Java Sea using Wave Spectral Analysis and Zero Up-Crossing Methods
Authors: Panalaran S. , Suntoyo  
Published: July 2023

Abstract
Waves in the sea have a random shape, where the height, length, and direction of the waves change during the observation time. Due to the unpredictable nature of the waves with certain patterns, a statistical and probability approach is needed in analyzing waves. Before carrying out statistical and probability analysis, it is necessary to extract the wave parameters from the random wave data. There are two methods commonly used to extract wave parameters: the first is the individual wave analysis method, using a zero up/down-crossing technique. The second method is the wave spectral analysis method. In this study, both methods will be applied to observation data from the Pabelokan station [1] in the West Java Sea for a six-day. From this study, it was found that the significant wave height parameter generated by the spectral analysis technique and the zero up-crossing technique showed a positive correlation, which the correlation coefficient is 0.9891. In the study of the wave period investigation, both of method have a positive correlation, but the value of the wave period is very likely to be different. The correlation coefficient values for the average wave period are 0.5848 for Tm01
and 0.5757 for Tm02
.
Comparative Analysis of Welding Mechanical Properties FCAW Welding Joint of A36 and A53
Authors: Dhanistha W L , Pratikno H , Maharani S D P , Suntoyo  , Silvianita  , Satrio D 
Published: July 2023

Abstract
A36 and A53 steels are low carbon steel with relatively similar carbon percentage, respectively 0,25-0,30% and 0,25-0,29%. Both steels are often used within the marine industry. The objective of this research is to figure out the effect of the variation of the groove angle and the heat input to the process of welding two different steel plates towards a metallography, tensile, and bending test with E71T electrode, as well as figuring out the groove angle and heat input to weld 18 mm thick steel plates. The variation of the groove angle used are 55°, 60°, and 70° with heat input variation of 140 and 180 A. Results of this experimental study shows that specimen with groove angle 70° and heat input 180 A with the largest sum of HAZ length, which is 8,4 mm, as well as the largest perlite phase, which are respectively, 67% within A36 base metal, 65% on A36 HAZ, 62% on weld metal,63% on A53 HAZ, and 66% on A53 base metal. The largest open defect value in bending tests is 1.87 mm owned by specimens with groove angle of 55° and heat input of 140 A.
Bed shear stress and sediment transport equations for predicting morphological and shoreline changes: a review
Authors: Hidayati N , Suntoyo  , Pratikto W A 
Published: July 2023

Abstract
Coastal sediments can be transported as bedload and suspended-load transport by waves and currents. The waves stir up the sediments, then currents transport sediments. Waves on the bottom can generate bed-shear stress. Meanwhile, the combination of bedload and suspended-load transport is known as total sediment transport. Prediction of total sediment transport has become important related to coastal morphological change and also shoreline change. Most of the sediment transport equations and approaches are developed from the physical principles. There are so many researchers proposed some formulas and methods with some considerations and difficulties. Due to the complexity of coastal conditions, the existing sediment transport rate prediction formulas are still not finished yet. Several well-known equations of bed-shear stress, bedload-suspended transport, and cross shore-longshore sediment transport; are discussed and reviewed in the present study. Thus, an overview of approaches and formulations that are reliable and nearly accurate for calculating the total sediment transport rate based on the characteristics of each coastal waters will be obtained. Accurate estimation of sediment transport rates will provide good results for predicting and monitoring changes in coastal morphology and shoreline changes. Moreover, coastal monitoring can be used for actions related to coastal protection system and coastal management.
Sedimentation of particles with various shapes and orientations in a closed channel using smoothed particle hydrodynamics
Authors: Huang Lizhong , Shao Chun , Wang Ruijin , Du Jiayou , Zhu Zefei 
Published: July 2023

Abstract
The sedimentation of particles with various shapes and orientations in a closed channel using smoothed particle hydrodynamics is investigated in this paper. The continuity and momentum equations of both fluid and solid are discretized using kernel approximation in the Lagrangian frame. The sedimentation behavior of different general shapes, including circle, pentagon, square, ellipse, rectangle, and triangle, at various initial orientations in the suspending fluid is simulated. The stable equilibrium orientation (SEO) of these shapes is examined, excluding the circle which serves as a validation case. Specifically, the major axis of the ellipse and rectangle tends to align horizontally, whereas the orientations of the pentagon and square seem to be random due to the lack of a major axis and the finite channel height. The settling behavior of the three types of triangles is also discussed, and the von Mises stress of these shapes during their settling is presented. This study offers valuable insights into fluid-particle interactions, specifically regarding the SEO and internal stress of settling particles with varying shapes and orientations.
Alternative dental impression fillers made of nanorod glutinous rice flour particles through precipitation
Authors: Takarini Veni , Asri Lia A T W , Djustiana Nina , Hadi Bambang Kismono 
Published: July 2023

Abstract
In this work, nanorod particles were synthesized from a locally available source, glutinous rice flour, using sodium hydroxide (NaOH) through a simple precipitation process. The synthesized nanofillers were then presented as an alternative organic filler for dental impression application to support the making of a diagnostic and working model. Dynamic Light Scattering, Scanning Electron Microscope, Fourier Transform Infrared Spectroscopy, x-ray Diffraction, Energy Dispersive Spectroscopy, Thermogravimetric Analysis, and Differential Scanning Colorimeter were used to characterize the fillers. The particle size measurement, morphology interaction, and composition of glutinous rice flour nanorod particles were also investigated. The cell viability using 3T3L1 cells was assessed to determine the safety of nanorod particles using the MTT assay and trypan blue solution. All treated samples exhibit a change in particle morphology from polyhedral to rod. Additionally, a decrease in crystallinity, dehydration, and gelatinization temperature was observed. The functional group interacting with sodium hydroxide also changes slightly after size reduction. The samples treated with 3000 centrifugation speed without surfactant addition showed changes from the control sample’s 3931.71 nm to the smallest average width particle size of 73.26 nm with an average length of 865.15 nm. All of the treated samples with NaOH and NaOH-surfactant additions met the non-cytotoxicity acceptance criteria in the range of 73.54%–99.58%, according to the cell viability results. The incorporation of 15 wt% of the synthesized nanorod fillers resulted in a 20 μm continuous line as the impression materials specimen, yielding a satisfactory detail reproduction test result. In conclusion, nanorod particles with biocompatible properties have been successfully manufactured and can potentially be used in the future as an alternative dental impression filler materials.
BERTwalk for integrating gene networks to predict gene- to pathway-level properties
Authors: Nasser Rami , Sharan Roded 
Published: July 2023

Abstract

Motivation
Graph representation learning is a fundamental problem in the field of data science with applications to integrative analysis of biological networks. Previous work in this domain was mostly limited to shallow representation techniques. A recent deep representation technique, BIONIC, has achieved state-of-the-art results in a variety of tasks but used arbitrarily defined components.

Results
Here, we present BERTwalk, an unsupervised learning scheme that combines the BERT masked language model with a network propagation regularization for graph representation learning. The transformation from networks to texts allows our method to naturally integrate different networks and provide features that inform not only nodes or edges but also pathway-level properties. We show that our BERTwalk model outperforms BIONIC, as well as four other recent methods, on two comprehensive benchmarks in yeast and human. We further show that our model can be utilized to infer functional pathways and their effects.

Availability and implementation
Code and data are available at https://github.com/raminass/BERTwalk.

Contact
roded@tauex.tau.ac.il
PyWGCNA: a Python package for weighted gene co-expression network analysis
Authors: Rezaie Narges , Reese Farilie , Mortazavi Ali 
Published: July 2023

Abstract

Motivation
Weighted gene co-expression network analysis (WGCNA) is frequently used to identify modules of genes that are co-expressed across many RNA-seq samples. However, the current R implementation is slow, is not designed to compare modules between multiple WGCNA networks, and its results can be hard to interpret as well as to visualize. We introduce the PyWGCNA Python package, which is designed to identify co-expression modules from large RNA-seq datasets. PyWGCNA has a faster implementation than the R version of WGCNA and several additional downstream analysis modules for functional enrichment analysis using GO, KEGG, and REACTOME, inter-module analysis of protein–protein interactions, as well as comparison of multiple co-expression modules to each other and/or external lists of genes such as marker genes from single cell.

Results
We apply PyWGCNA to two distinct datasets of brain bulk RNA-seq from MODEL-AD to identify modules associated with the genotypes. We compare the resulting modules to each other to find shared co-expression signatures in the form of modules with significant overlap across the datasets.

Availability and implementation
The PyWGCNA library for Python 3 is available on PyPi at pypi.org/project/PyWGCNA and on GitHub at github.com/mortazavilab/PyWGCNA. The data underlying this article are available in GitHub at github.com/mortazavilab/PyWGCNA/tutorials/5xFAD_paper.
RNAenrich: a web server for non-coding RNA enrichment
Authors: Zhang Song , Amahong Kuerbannisha , Zhang Yintao , Hu Xiaoping , Huang Shijie , Lu Mingkun , Zeng Zhenyu , Li Zhaorong , Zhang Bing , Qiu Yunqing , Dai Haibin , Gao Jianqing , Zhu Feng 
Published: July 2023

Abstract

Motivation
With the rapid advances of RNA sequencing and microarray technologies in non-coding RNA (ncRNA) research, functional tools that perform enrichment analysis for ncRNAs are needed. On the one hand, because of the rapidly growing interest in circRNAs, snoRNAs, and piRNAs, it is essential to develop tools for enrichment analysis for these newly emerged ncRNAs. On the other hand, due to the key role of ncRNAs’ interacting target in the determination of their function, the interactions between ncRNA and its corresponding target should be fully considered in functional enrichment. Based on the ncRNA–mRNA/protein-function strategy, some tools have been developed to functionally analyze a single type of ncRNA (the majority focuses on miRNA); in addition, some tools adopt predicted target data and lead to only low-confidence results.

Results
Herein, an online tool named RNAenrich was developed to enable the comprehensive and accurate enrichment analysis of ncRNAs. It is unique in (i) realizing the enrichment analysis for various RNA types in humans and mice, such as miRNA, lncRNA, circRNA, snoRNA, piRNA, and mRNA; (ii) extending the analysis by introducing millions of experimentally validated data of RNA–target interactions as a built-in database; and (iii) providing a comprehensive interacting network among various ncRNAs and targets to facilitate the mechanistic study of ncRNA function. Importantly, RNAenrich led to a more comprehensive and accurate enrichment analysis in a COVID-19-related miRNA case, which was largely attributed to its coverage of comprehensive ncRNA–target interactions.

Availability and implementation
RNAenrich is now freely accessible at https://idrblab.org/rnaenr/.
Blocking an epitope of misfolded SOD1 ameliorates disease phenotype in a model of amyotrophic lateral sclerosis
Authors: Bakavayev Shamchal , Stavsky Alexandra , Argueti-Ostrovsky Shirel , Yehezkel Galit , Fridmann-Sirkis Yael , Barak Zeev , Gitler Daniel , Israelson Adrian , Engel Stanislav 
Published: July 2023

Abstract
The current strategies to mitigate the toxicity of misfolded superoxide dismutase 1 (SOD1) in familial amyotrophic lateral sclerosis via blocking SOD1 expression in the CNS are indiscriminative for misfolded and intact proteins, and as such, entail a risk of depriving CNS cells of their essential antioxidant potential. As an alternative approach to neutralize misfolded and spare unaffected SOD1 species, we developed scFv-SE21 antibody that blocks the β6/β7 loop epitope exposed exclusively in misfolded SOD1.
The β6/β7 loop epitope has previously been proposed to initiate amyloid-like aggregation of misfolded SOD1 and mediate its prion-like activity. The adeno-associated virus-mediated expression of scFv-SE21 in the CNS of hSOD1G37R mice rescued spinal motor neurons, reduced the accumulation of misfolded SOD1, decreased gliosis and thus delayed disease onset and extended survival by 90 days.
The results provide evidence for the role of the exposed β6/β7 loop epitope in the mechanism of neurotoxic gain-of-function of misfolded SOD1 and open avenues for the development of mechanism-based anti-SOD1 therapeutics, whose selective targeting of misfolded SOD1 species may entail a reduced risk of collateral oxidative damage to the CNS.
Integrin beta-like 1 mediates fibroblast–cardiomyocyte crosstalk to promote cardiac fibrosis and hypertrophy
Authors: Chen XiaoQiang , Li XinTao , Wu XiaoYu , Ding Yu , Li Ya , Zhou GenQing , Wei Yong , Chen SongWen , Lu XiaoFeng , Xu Juan , Liu ShaoWen , Li Jun , Cai LiDong 
Published: July 2023

Abstract

Aims
Crosstalk between fibroblasts and cardiomyocytes (CMs) plays a critical role in cardiac remodelling during heart failure (HF); however, the underlying molecular mechanisms remain obscure. Recently, a secretory protein, Integrin beta-like 1 (ITGBL1) was revealed to have detrimental effects on several diseases, such as tumours, pulmonary fibrosis, and hepatic fibrosis; whereas the effect of ITGBL1 on HF is unclear. The purpose of this study was to evaluate its contribution to volume overload-induced remodelling.

Methods and results
In this study, we identified ITGBL1 was highly expressed in varied heart diseases and validated in our TAC mice model, especially in fibroblasts. To investigate the role of ITGBL1 in in vitro cell experiments, neonatal rat fibroblasts (NRCFs) and cardiomyocytes (NRCMs) were performed for further study. We found that in comparison to NRCMs, NRCFs expressed high levels of ITGBL1. Meanwhile, ITGBL1 was upregulated in NRCFs, but not in NRCMs following angiotensin-II (AngII) or phenylephrine stimulation. Furthermore, ITGBL1 overexpression promoted NRCFs activation, whereas knockdown of ITGBL1 alleviated NRCFs activation under AngII treatment. Moreover, NRCFs-secreted ITGBL1 could induce NRCMs hypertrophy. Mechanically, ITGBL1-NME/NM23 nucleoside diphosphate kinase 1 (NME1)-TGF-β-Smad2/3 and Wnt signalling pathways were identified to mediate NRCFs activation and NRCMs hypertrophy, respectively. Finally, the knockdown of ITGBL1 in mice subjected to transverse aortic constriction (TAC) surgery recapitulated the in vitro findings, demonstrating blunted cardiac fibrosis, hypertrophy, and improved cardiac function.

Conclusions
ITGBL1 is an important functional mediator between fibroblast–cardiomyocyte crosstalk and could be an effective target for cardiac remodelling in HF patients.
Deaf Identity, Social Relationships, and Social Support: Toward a Microsociological Perspective
Authors: Chapman Madeleine , Dammeyer Jesper , Jepsen Kim Sune Karrasch , Liebst Lasse Suonperä 
Published: July 2023

Abstract
This study is the first to analyze data from a national survey to investigate the significance for deaf identity of the different forms of social and technological support that deaf people rely upon. Data were derived from a survey among 839 deaf people and were analyzed with regard to social identification as deaf, hearing, bicultural, and marginal. Findings showed connections between technology and identity, including the use of a range of technology to support being culturally deaf. Findings also showed that the deaf and hearing groups had strong homophilous social networks, while the bicultural group tended toward more mixed but equally strong social connectivity. The marginal group had a much thinner social connectivity and relied more upon institutional social support, findings that are in line with previous research revealing a sub-group struggling with social participation and well-being. Theoretically, the paper builds bridges between the fields of social identity and microsociology and shows how a microsociological perspective brings attention to the significance of reiterated social relations and practice for constructing social identity.
The world Delhi wants: official Indian conceptions of international order, c. 1998–2023
Authors: Mishra Atul 
Published: July 2023

Abstract
Examining India's official thinking on international order over the past quarter-century, this article maps the shift in the country's preference from liberal internationalism to the rules-based international order (RIO). It argues that despite Delhi's current narrative of a ‘New India’, the country's order conception shows continuity in being essentially reformist and mostly consistent with the pillars of the 1945 order. While its marked unease with liberalism is a consequence of the changes afoot in India's domestic politics, this development is consistent with, and contributes to, the decline of liberalism as a global force. The current Indian preference for economic protectionism also reflects the larger trend of economic deglobalization. The description of India as a resurgent civilizational state rather than a liberal democracy, while discursively arresting, does not indicate a divergence with the West on the grand strategic question of order-building. Upon reconstructing the Indian iteration of the RIO, the article finds it to be geographical—focused on Asia and the Indo-Pacific—rather than universal. Finally, it posits that India's persisting problem of inadequate power and its risk-averse responses to great power revisionism are likely to undermine its efforts to effectively partner with democracies to shape the emergent RIO.
Singapore's conception of the liberal international order as a small state
Authors: Loh Dylan M H 
Published: July 2023

Abstract
The liberal international order (LIO) is undergoing significant challenges, and this has given rise to debates about its purported decline. In this context, most studies of the LIO focus on major powers with little attention paid to small states’ conceptualizations of the LIO despite its ubiquity in international life. Focusing on the Singaporean case as a small state, it asks the question: how does Singapore conceptualize the LIO and what are the effects of this conceptualization? Through a mixed-method thematic analysis of 192 parliamentary replies, media interviews and United Nations speeches by Singaporean officials between 2000 to 2022, I find Singapore accepting and defending the existing international order in two main ways: demonstrating respect for international law and the UN Charter, and supporting economic liberalism. Meanwhile, Singapore is contesting the universality of liberal democracy as it sees such discourse as a rebuke to its single-party dominant governance model. This perception of the LIO, in turn, informs Singapore's order-maintaining, order-modifying and order-contesting practices: it seeks to not only protect, but also to modify the LIO—through institutional and legal initiatives—to make it more equitable and open, giving us a glimpse into an instance of a small state's agency in relation to the LIO.