bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic Model of Segara Anakan Mangrove Crab’s Habitat Management, Indonesia
Authors: Ismail Ismail , Sulistiono Sulistiono , Hariyadi Sigid , Suruaki A , Katili V
Published: March 2023

The mangrove area in Segara Anakan lagoon (Cilacap, Central Java) is a good habitat for mangrove crabs and other mangrove biota life and growth. However, in recent years, the condition of the mangroves in the area has been degraded due to land conversion. This condition also occurs in the production of mangrove crabs in the Cilacap Regency which has decreased (2012-2017 production data). Good management efforts of the mangrove forests will also have a good impact on the growth and production of these biota in nature. This study aims to create a dynamic model of mangrove crab habitat management at Segara Anakan Lagoon in order to increase the optimization of mangrove crab production in that regency. The study method used was a dynamic systems approach that considers the relationship between crab production and the conversion of mangrove land. The results of the study showed a model of the relationship between mangrove crab production and changes in mangrove area in the Segara Anakan area with the equation: Y = 14951X − 88357 (R2 = 0.5382), with structural validation as follows: land conversion increases (rice field area) (+) and then increase the income from rice fields (+). Meanwhile, land conversion reduces mangrove area (-), reduces crab habitat function (-), reduces crab catch (-), further reduces mud crab production, and finally reduces income from mud crab production (-). The validation of the model output is the average mean error (AME) of crabs at 4.93%, while the AME of mangroves is 7.38%. This model can be concluded as a valid (acceptable) model and can be continued to the simulation stage.
The Aquatic Environment of Bengawan Solo Estuary, Gresik, East Java As The Basis for Fisheries Development
Authors: Dewi N N , Mubarak A S , Triastuti J , Tjahjaningsih W , Asriansyah A , Aiswantari  , Wildan D M , Lukman
Published: March 2023

The waters of the Bengawan Solo River estuary have an important role in enriching the waters of north Gresik and its surroundings areas, and become one of the fishing grounds for coastal fish in that region. This study aims to reveal the aquatic environment condition at the area as the basis for fisheries development. The study was carried out bimonthly through water sampling and analysis both in situ and ex situ at 5-8 stations from January to July 2022. Observations were made on water physical parameters (temperature, transparency, and turbidity) and water chemical parameters (pH, salinity, dissolved oxygen-DO, nitrite, nitrate, ammonia and phosphate). Based on analysis on the physical and chemical parameters, it was known that the range (and standard deviation) of waters quality varied, i.e. temperature 28.20-29.80°C (28.91±0.32oC), transparency 5.00-70.00 cm (21.61±16.19 cm), turbidity 5.84-947.00 NTU (324.40±325.80 NTU), pH 5.00-7.30 (6.66±0.45), salinity 0.00-28.00 psu (4.69±8.34 psu), DO 3.65-7.80 mg/l (5.48±1.09 mg/l). The concentration of nitrite, nitrate, ammonia and phosphate were 0.000-0.100 mg/l (0.007±0.021 mg/l), 1.000-5.000 mg/l (2.483±1.430 mg/l), 0.100.-0.600 mg/l (0.193±0.112 mg/l) and 0.100-6.000 mg/l (0.366±0.114 mg/l), respectively. From the analysis of the aquatic environment condition, it can be seen that the waters of the Bengawan Solo estuary are quite good, and suitable for fisheries development. However, based on the pollution index value, it can be stated that the estuary waters of the Bengawan Solo River are in good category
Adaptation performance of immature broodstock Oryzias woworae post-transportation of closed system
Authors: Mulyatama R , Mustahal  , Syamsunarno MB , Herjayanto M
Published: March 2023

Oryzias woworae, one of the endemic ricefish species from Sulawesi, is threatened with extinction in their habitat. Domestication of aquaculture is one way to preserve the conservation of these fish. The success factor for cultivation is the adaptation of the immature broodstock in a controlled environment for gonadal maturation. Adaptation performance of immature broodstock after closed system transport is the first study of O. woworae at the start of an adjustment in a controlled rearing. This study aimed to examine the survival during transportation and adaptation performance of immature broodstock O. woworae post-transportation. O. woworae has been transported for 5 hours. The transport system used a closed system in 2 plastic bags (separated male and female) measuring 1 kg with a density of 35 fish/2 L. Fish were adapted in the aquarium for 20 days. The result showed that O. woworae could adapt well after being transported in a closed system after 20 days of rearing post-transportation. Survival of immature broodstock O. woworae during transport was 100% for females and 91.42% for males. Rearing post-transportation showed that survival rate was 94.28% for females and 100% for males, with swimming activity had been active since day 2, and good response for feed. After rearing, the average final weight and total length of O. woworae were 0.48 g and 2.2 cm for females and 0.47 g and 2 cm for males, respectively. The partially fertilized eggs during rearing indicated that O. woworae have been ready as broodstock.
Biodiversity and Community Structure of Zooplankton in The Domas Coastal waters of Banten Bay, West Java, Indonesia
Authors: Fitriya N , Thoha H , Sulistiono  , Asriansyah A , Wulandari D Y , Wildan D M , Rohim N , Srimariana E , Hestirianoto T , Rastina  , Subhan B.
Published: March 2023

Domas coastal waters, located east of Banten Bay, have an enormous potential for fisheries resources closely related to the presence of plankton in the area. This study was carried out for 6 months, from August 2021 to January 2022, to examine the biodiversity and community structure of zooplankton in the Domas coastal waters. Sampling was carried out monthly at six stations distributed from coastal areas to the sea. Data on the zooplankton were examined for abundance, diversity, evenness, and dominance indices. Based on the observations, zooplankton in these waters consisted of 19 classes, namely Actinopteri, Appendicularia, Bivalvia, Branchiopoda, Cirripedia, Cnidaria, Copepoda, Ctenophora, Enteropneusta, Gastropoda, Gymnolaemata, Hydrozoa, Malacostraca, Ostracoda, Ophiuroidea, Phoronida, Polychaeta, Sagittoidea, and Thaliacea. The zooplankton found in abundance were Calanoida, Cyclopoida, and Nauplius. The number of taxa and abundance varied according to sampling time and location, 7-34 inds/m3 and 627-41386 inds/m3, respectively. The diversity, evenness, and dominance indices varied, 0.885-2.108, 0.327-0.797, and 0.172-0.601, respectively. Based on the results of these calculations, it can be stated that the diversity, evenness, and dominance of the zooplankton in these waters are classified as moderate.
Domestication of Bileh Fish Rasbora sp. Origin of Aceh Waters Through Different Feed Therapy
Authors: Zulfadhli  , fadhillah Radhi , Jusadi Dedi , Fujaya Yushinta
Published: March 2023

Domestication is the process of taming fish from the wild to the aquaculture environment. There are 3 stages of the domestication process, namely: taming/adapting to the aquaculture environment, seeking fish to grow, and seeking fish to reproduce. Bileh fish can already be adapted to aquaculture containers, which is the first stage of the domestication process. However, information on suitable feed for fish growth is still limited. The aim of this study was to determine the effect of different feeding on the growth of bileh fish reared in controlled containers. The research method was experimental and used a completely randomized design (CRD), which consisted of 4 treatments (P) with 3 replications. The treatments given were artificial feed (P1), artemia (P2), rotifer (P3) and daphnia (P4). The research phase included preparation of containers, collection of bileh fish, experimental feed, maintenance, and data collection. Parameters taken and evaluated included: specific growth rate (SGR), absolute length growth (ALG), and survival rate (SR). The data were processed and analyzed with statistics (Anova). The results of statistical analysis showed that feed treatment had a significant effect on SGR (P<0.05), but had no significant effect on ALG and SR (P>0.05). The best treatment was P1 (artificial feeding) with an SGR value of 0.91%/day, ALG of 1.03 cm and SR of 100%.
Calculation of Waste Generation and Composition in Tegal City as an Effort to Increase Waste Reduction
Authors: Widiyanto Bayu , Aji Fathurakhaman M. , Munadi
Published: March 2023

The generation of waste will increase along with the increase in population. Meanwhile, the composition of waste will change every year due to changes in the lifestyle and economic level of the community. Tegal is a densely populated city, and the accumulation of garbage in the city of Tegal in the last two years has increased by 38.9%. The existing waste management paradigm is still conventional so the amount of generation that enters the Final Disposal Site is still quite large. The purpose of this study is 1) to determine the generation and composition of waste in the Educational Area, offices, markets, and other public facilities. 2) find out the percentage of managed waste. The study began with surveys and interviews regarding the sources of waste and the existing conditions of waste management in the city of Tegal. The survey was conducted by reviewing the facilities of garbage bins, temporary shelters, and sources of waste. This research is quantitative in nature and becomes the basis for the proposed solid waste management design. Waste generation and composition were calculated using the SNI 19-3964-1995 method. The results showed that the waste generated was around 261.93 kg/day. Meanwhile, the composition of waste in Tegal City is dominated by organic waste by 66%. The rest is in the form of waste such as; plastic (15%), paper (13%), cloth & leather (4%) the rest is glass and metal, and others. The percentage of Tegal city waste that is managed is 88.8%, which is divided into two, namely: the first is waste handling with a percentage of 77.61% and the second is a waste reduction with a percentage of 11.19%. While the remaining 11.2% is still unmanaged waste.
Competency Evaluation Of Non-Convention Fishing Vessel Crew (Case Study: 30-100 Gt Purseiner In Pati Regency And Pekalongan City)
Authors: Setianto T , Wisudo S H , Imron M , Wiyono E S , Novita Y
Published: March 2023

Indonesia has ratified the international regulations concerning the competence of fishing vessel crews in the form of Standard of Training, Certification and Watchkeeping for Fishing Vessel Personnel (STCW-F) 1995. Many Indonesian fishermen’s competences are not up to standard. The study was conducted on non-conventional fishing vessels because in Indonesia the numbers are dominated.The purpose of this research is to identify and map the competency quality of non-conventional Fishing Vessel Crew in Pati Regency and Pekalongan City with regard to the marine certificates owned by ship crews according to the STCW-F standard. The analysis uses content analysis of regulations and Gap analysis of expertise competence for the Skipper, Chief Engineer, Chief Officer and First Engineer for Purseiner 30-100 GT in Pati and Pekalongan against Minister of Maritime Affairs and Fisheries Regulation Number 33 of 2021. The results show in Pati district and Pekalongan City: the competence of masters is 66.9% and 81.4%, Head of Engine Room 23.1% and 30%, Chief officer 66.9% and 9.1%, and First Engineers are 4.1% and 0%. Recommendations for the fulfillment of the provisions of the Expertise Competency Certification according to the ministerial regulation are by: increasing Awareness, increasing extension of the importance of certification,and strict enforcement of certification rules.
Green finance, energy consumption, and carbon dioxide emissions: A GMM panel data analysis from China
Authors: Tan Jingrong , Chen Lin
Published: March 2023

Environmental and energy issues have become a stumbling block to China’s sustainable development, so opening up a green development path has become the focus of much attention. To investigate the impact of green finance on carbon dioxide (CO2) emissions, this paper uses the difference and systematic generalized method of moment (GMM) estimators. The research sample includes panel data for Chinese 30 provinces from 2000 to 2020. The empirical results indicate that the objective of green finance is to reduce CO2 emissions. Meanwhile, the analysis of the mediation effect leads to the conclusion that green finance reduces CO2 emissions by regulating energy consumption. Finally, this study provides policymakers with new ideas for green finance development and energy conservation.
Study on fracture conductivity under dynamic sand laying mode
Authors: Pan Zhikun , Chen Tunhao , Hu Longqiao , Lv Wenjing , Wang Ming , Li Ben
Published: March 2023

The existing API static sand laying fracture conductivity evaluation experiment ideally believes that the proppant is evenly and statically laid in the fracture, without considering the actual fracturing conditions, the proppant migrates along the fracture and leaks into the formation. In order to more truly simulate the actual fracturing conditions, the experimental study of fracture conductivity is carried out by using the dynamic conductivity testing device, which is closer to the field reality than static sand laying. The parameters of the indoor dynamic sand laying diversion experiment are determined by the similarity criterion and the indoor fracturing fluid rheology experiment. The orthogonal experiment and the shear support fracture dynamic diversion experiment are designed to study the effects of pumping displacement, fracturing fluid viscosity and construction sand ratio on the dynamic sand laying diversion ability, and optimize the on-site construction parameters. The experimental results show that increasing the construction displacement, sand ratio and selecting the appropriate fracturing fluid viscosity have a positive impact on the fracture conductivity of dynamic sand laying support, among which the sand ratio has the greatest impact. Under the condition of effective closure stress of the reservoir, the natural non sanding shear fracture and the dynamic paving shear fracture with 12% sand ratio have no conductivity, which is difficult to meet the requirements of field production. When the 1-3 mm shear joint is dynamically paved with 18% sand ratio and the closing pressure is 30-70 MPa, the conductivity is positively correlated with the sand concentration, but it is nonlinear with the shear dislocation. The shear joint pump injects 18% proppant with sand ratio, which can support the fracture under high closing pressure and provide conductivity. It is necessary to appropriately increase the pump injection ratio of more than 18% sand ratio according to the proportion of on-site shear cracks to effectively support shear cracks.
Research on the development potential of fuel-cell medium-and-heavy trucks in China
Authors: Fang Haifeng , Ding Zhensen , Yao Zhanhui , Wang Jia
Published: March 2023

The development of fuel-cell vehicles is an important opportunity and inevitable choice for China to cope with the challenges of energy security and industrial upgrading and then achieve the “Carbon Peaking and Carbon Neutrality” goal. Taking fuel-cell medium-and-heavy trucks as the research object, this paper builds a multi-dimensional analysis framework of policy, market and technology, further discuss and analyze the development potential of fuel-cell medium-and-heavy trucks in China by sorting out the current situation and studying the development trend of the industry. The analysis results show that China’s fuel-cell medium-and-heavy trucks not only have policy support, market demand and technical support, but also are an important path for the development of fuel-cell vehicles. The research results can be used as a reference for the formulation of industrial policies related to fuel-cell vehicles and have a high reference value for the strategic selection of enterprises’ products in the industry.
Study of the impact of DC distribution network under large-scale electric-powered vehicle access
Authors: Zhang Guangru , Zhang Jiawu , Ma Zhenqi , Chen Jie , Zhang Jialin , Kang Yongqiang
Published: March 2023

As a high-standard verdant method of transportation, electric-powered-vehicles have become the development hotspot of the automotive business in recent years. Large scale access to electric-powered vehicles can form a distributed energy storage system, which can improve the operational performance of power grid peak shaving and frequency modulation, and improve the comprehensive utilization efficiency of system energy. But at the same time, large-scale electric-powered vehicles connected to the DC distribution network will have a certain impact on its topology. Therefore, this paper studies the impact of the access location and number of electric-powered vehicles on the network topology and establishes a multi-dimensional evaluation system of the DC distribution network topology. The application of this result can play an evaluation and guidance role in the operation stability of the DC distribution network in the case of large-scale access to electric-powered vehicles.
Preparation of hydrophobic nano calcium carbonate and its application in EOR
Authors: Kaiping Tian , Wanfen Pu , Siying Li , Hongzhou Wang , Wei He , Minghong Xia
Published: March 2023

W/O emulsification flooding is a new type of oil displacement method, which can effectively improve oil recovery, but there are few materials used for W/O emulsification at present. Therefore, we prepared a hydrophobic nano calcium carbonate (WS-Ca) and compounded it with Span80 to form a nano oil displacement system. The contact angle experiment demonstrates that WS-Ca is lipophilic material. After testing the emulsification performance, viscosity, interfacial tension and oil displacement performance of the oil displacement system, it is found that the nano oil displacement system with the best performance is WS-Ca (800ppm) +Span80 (1%), and the displacement system and oil are emulsified into W/O emulsion, and the viscosity of emulsion is 25 times that of crude oil. Furthermore, the oil displacement system can successfully lower the oil-water interfacial tension and increase the oil recovery of injection water to 62.63%.
Power distribution system for Xiangshan Internet of Underwater Things
Authors: Duan Zhiyong , Xing Zilin , He Bohao , Hu Jiaqi , Yang Canjun
Published: March 2023

The Xiangshan Internet of Underwater Things was successfully deployed in Xiangshan in September 2022, which is the first multi-node constant current cabled observatory network in China. Instead of being a real scientific IOT, the main motivation of this network is to verify the main energy conversion technologies applied in the Internet of Underwater Things, including multi-module-stack architecture electrical energy conversion system, digital branch unit, and fast deployable in-cable submarine observation node. The experiments verified that the system can guarantee the reliability and high efficiency of the Internet of Underwater Things.
RETRACTED: A design of wet-mateable connector aiming for contactless power transfer and optical communication
Authors: Hu Jiaqi , Duan Zhiyong , Yi Anzhe , Zhang Yurui , Yang Canjun
Published: March 2023

At present, contact watertight connectors are commonly utilized for the connection between underwater electromechanical equipment and the seabed observation network. Such conventional watertight connectors are inevitably likely to be irreversibly worn when plugging and unplugging, besides complicated sealing structures and limited service life. This paper designs a Wet-Mateable connector aiming for Contactless Power Transfer and Optical Communication (PTOC-WMC), which is based on technology of Contactless Power Transmission (CLPT) and optical communication. Docking structure of the sockets and plugs are designed, facilitating Remotely Operated Vehicle (ROV) to operate. A prototype of the PTOC-WMC was established. The experimental results show that the connector designed can achieve 200W power transmission, with a maximum power transmission efficiency of 94%. The communication bandwidth reaches 18MHz. The PTOC-WMC can assist the rapid and safe deployment and operation of seabed observation network.
Study on the mechanical variation law of the integrated water plugging operation string in horizontal wells
Authors: Dajian Li , Wei Lin , Lijing Chang , Zubo Su , Hongzheng Zhu , Bai Wang
Published: March 2023

In order to study the force change law of the water plugging operation string in the complex wellbore, and to reduce the failure risk of the process string during the water plugging operation, this paper establishes the water plugging operation string based on the Euler-Bernoulli beam theory- The 3D full-well finite element model of the borehole wall was verified by field test data to verify the credibility of the numerical simulation model; according to the established finite element model, the force study of different types of tubing in complex horizontal wellbore was carried out, mainly for axial The force and the change law of the contact force between the pipe string and the well wall are analyzed, and finally, the force change law of the pipe string in different well sections is analyzed. The results show that the finite element model established in this paper has high simulation accuracy, and there is a large lateral contact force between the tubing and the inlet of the pitching section during the lifting process, and the contact between the pipe string and the borehole wall during the lowering process Mainly occurs at the entrance of the horizontal section. The research results provide theoretical guidance for the selection of tubing types and water plugging operations.
Experimental study of density gradient-driven micro-instabilities and the confinement degradation during H-mode in EAST
Authors: CHEN Fei , LI Yadong , WANG Xiaojie , WU Guojiang , LI Pan , GENG Jingsen , WANG Yuhao , SUN Pengjun , LI Erzhong , ZHOU Tianfu , ZHAO Hailin , ZANG Qing , WANG Shouxin , LIU Haiqing , JIN Yifei , LYU Bo , BAE Cheonho , LI Jiangang
Published: March 2023

A broadband (BB) mode is observed by collective Thomson scattering diagnostics in repeatable shots of EAST and analyzed for the first time. This BB mode usually grows during L–H transitions, featuring a BB quasi-coherent mode with increasing frequency. During H-mode operations, it is characterized by steady-state BB in the high-frequency range (f ∼ 200–2000 kHz), at the electron scale (k

θ

ρ
s = 1‒2), mainly driven by the density gradient, and is sensitive to the value of η
e in the region of interest (ρ = 0.4‒0.8), where

η

e

=

R
/

L

T

e

/

R
/

L

n

e

is the ratio of the normalized electron temperature gradient and density gradient, and the region ρ = 0.4‒0.8 usually has a relatively low collisionality (v
eff < 5). The frequency of BB is found to be dependent on the electron temperature and density gradient, which is a typical feature of electron-driven turbulence. A negative correlation between the energy confinement and the intensity of the BB turbulence during H-mode has been found, which indicates a strong electron thermal transport induced by the BB turbulence. The BB significantly decreases the electron temperature and causes flatter electron temperature profiles in the region of interest (ρ = 0.4‒0.8), thus making η
e decrease and the BB destabilize further. These characteristics of BB are related to the theoretical density gradient-driven trapped electron mode. It should be noted that this mode is not observed by other diagnostics in EAST, and shows very different features to the coherent modes in the edge.
A linear second-order maximum bound principle-preserving BDF scheme for the Allen-Cahn equation with a general mobility
Authors: Hou Dianming , Ju Lili , Qiao Zhonghua
Published: March 2023

In this paper, we propose and analyze a linear second-order numerical method for solving the Allen-Cahn equation with a general mobility. The proposed fully-discrete scheme is carefully constructed based on the combination of first and second-order backward differentiation formulas with nonuniform time steps for temporal approximation and the central finite difference for spatial discretization. The discrete maximum bound principle is proved of the proposed scheme by using the kernel recombination technique under certain mild constraints on the time steps and the ratios of adjacent time step sizes. Furthermore, we rigorously derive the discrete

H

1

H^{1}

error estimate and energy stability for the classic constant mobility case and the

L

∞

L^{\infty }

error estimate for the general mobility case. Various numerical experiments are also presented to validate the theoretical results and demonstrate the performance of the proposed method with a time adaptive strategy.
Quantitative decompositions of Lipschitz mappings into metric spaces
Authors: David Guy , Schul Raanan
Published: March 2023

We study the quantitative properties of Lipschitz mappings from Euclidean spaces into metric spaces. We prove that it is always possible to decompose the domain of such a mapping into pieces on which the mapping “behaves like a projection mapping” along with a “garbage set” that is arbitrarily small in an appropriate sense. Moreover, our control is quantitative, i.e., independent of both the particular mapping and the metric space it maps into. This improves a theorem of Azzam-Schul from the paper “Hard Sard”, and answers a question left open in that paper. The proof uses ideas of quantitative differentiation, as well as a detailed study of how to supplement Lipschitz mappings by additional coordinates to form bi-Lipschitz mappings.
Projections of orbital measures and quantum marginal problems
Authors: Collins Benoît , McSwiggen Colin
Published: March 2023

This paper studies projections of uniform random elements of (co)adjoint orbits of compact Lie groups. Such projections generalize several widely studied ensembles in random matrix theory, including the randomized Horn’s problem, the randomized Schur’s problem, and the orbital corners process. In this general setting, we prove integral formulae for the probability densities, establish some properties of the densities, and discuss connections to multiplicity problems in representation theory as well as to known results in the symplectic geometry literature. As applications, we show a number of results on marginal problems in quantum information theory and also prove an integral formula for restriction multiplicities.
Limit cycle enumeration in random vector fields
Authors: Lundberg Erik
Published: March 2023

We study the number and distribution of the limit cycles of a planar vector field whose component functions are random polynomials. We prove a lower bound on the average number of limit cycles when the random polynomials are sampled from the Kostlan-Shub-Smale ensemble. Investigating a problem introduced by Brudnyi [Ann. of Math. (2) 154 (2001), pp. 227–243] we also consider a special local setting of counting limit cycles near a randomly perturbed center focus, and when the perturbation has i.i.d. coefficients, we prove a limit law showing that the number of limit cycles situated within a disk of radius less than unity converges almost surely to the number of real zeros of a logarithmically-correlated random univariate power series. We also consider infinitesimal perturbations where we obtain precise asymptotics on the global average count of limit cycles for a family of models. The proofs of these results use novel combinations of techniques from dynamical systems and random analytic functions.
F-actin–rich territories coordinate apoptosome assembly and caspase activation during DNA damage–induced intrinsic apoptosis
Authors: King Virginia L. , Campellone Kenneth G.
Published: March 2023

DNA damage–induced apoptosis relies on signaling platforms called apoptosomes and the activation of caspase proteases, but how their activities are coordinated in cells is not well understood. The cytoskeleton assembles into an F-actin–rich territory that couples the apoptosome biogenesis process to the initiation of caspase activation.
Centromere proteins are asymmetrically distributed between newly divided germline stem and daughter cells and maintain a balanced niche in Drosophila males
Authors: Kochendoerfer Antje M. , Keegan Rachel S. , Dunleavy Elaine M.
Published: March 2023

Centromere function in Drosophila germline stem cells is important for maintaining stem and daughter cell balance in the testes stem cell niche.
Space conservation: a plea for urgency
Authors: Wheeler Joanne , Burgman Mark , Maroothynaden Jason , Ramirez Rafael , Kello Lucas , Ali Taskeen
Published: March 2023

Joanne Wheeler and colleagues review the history of space sustainability challenges and discuss urgent contemporary issues in the effective environmental management of space
Astronomers ahoy!
Authors: Barclay Charles
Published: March 2023

Do you have what it takes to enthuse about the subject you love on a complimentary voyage? Charles Barclay is looking for Fellows to share their sciences on the high seas.
Evaluation of graphical models for multi-group metabolomics data
Authors: Zhao Hang , Dai Pin-yuan , Yu Xiao-jin , He Jie-yu , Zhao Chao , Yin Li-hong
Published: March 2023

Gaussian graphical model is a strong tool for identifying interactions from metabolomics data based on conditional correlation. However, data may be collected from different stages or subgroups of subjects with heterogeneity or hierarchical structure. There are different integrating strategies of graphical models for multi-group data proposed by data scientists. It is challenging to select the methods for metabolism data analysis.

This study aimed to evaluate the performance of several different integrating graphical models for multi-group data and provide support for the choice of strategy for similar characteristic data.

We compared the performance of seven methods in estimating graph structures through simulation study. We also applied all the methods in breast cancer metabolomics data grouped by stages to illustrate the real data application.

The method of Shaddox et al. achieved the highest average area under the receiver operating characteristic curve and area under the precision-recall curve across most scenarios, and it was the only approach with all indicators ranked at the top. Nevertheless, it also cost the most time in all settings. Stochastic search structure learning tends to result in estimates that focus on the precision of identified edges, while BEAM, hierarchical Bayesian approach and birth–death Markov chain Monte Carlo may identify more potential edges. In the real metabolomics data analysis from three stages of breast cancer patients, results were in line with that in simulation study.
iEssLnc: quantitative estimation of lncRNA gene essentialities with meta-path-guided random walks on the lncRNA-protein interaction network
Authors: Zhang Ying-Ying , Liang De-Min , Du Pu-Feng
Published: March 2023

Gene essentiality is defined as the extent to which a gene is required for the survival and reproductive success of a living system. It can vary between genetic backgrounds and environments. Essential protein coding genes have been well studied. However, the essentiality of non-coding regions is rarely reported. Most regions of human genome do not encode proteins. Determining essentialities of non-coding genes is demanded. We developed iEssLnc models, which can assign essentiality scores to lncRNA genes. As far as we know, this is the first direct quantitative estimation to the essentiality of lncRNA genes. By taking the advantage of graph neural network with meta-path-guided random walks on the lncRNA-protein interaction network, iEssLnc models can perform genome-wide screenings for essential lncRNA genes in a quantitative manner. We carried out validations and whole genome screening in the context of human cancer cell-lines and mouse genome. In comparisons to other methods, which are transferred from protein-coding genes, iEssLnc achieved better performances. Enrichment analysis indicated that iEssLnc essentiality scores clustered essential lncRNA genes with high ranks. With the screening results of iEssLnc models, we estimated the number of essential lncRNA genes in human and mouse. We performed functional analysis to find that essential lncRNA genes interact with microRNAs and cytoskeletal proteins significantly, which may be of interest in experimental life sciences. All datasets and codes of iEssLnc models have been deposited in GitHub (https://github.com/yyZhang14/iEssLnc).
Inter-domain distance prediction based on deep learning for domain assembly
Authors: Ge Fengqi , Peng Chunxiang , Cui Xinyue , Xia Yuhao , Zhang Guijun
Published: March 2023

AlphaFold2 achieved a breakthrough in protein structure prediction through the end-to-end deep learning method, which can predict nearly all single-domain proteins at experimental resolution. However, the prediction accuracy of full-chain proteins is generally lower than that of single-domain proteins because of the incorrect interactions between domains. In this work, we develop an inter-domain distance prediction method, named DeepIDDP. In DeepIDDP, we design a neural network with attention mechanisms, where two new inter-domain features are used to enhance the ability to capture the interactions between domains. Furthermore, we propose a data enhancement strategy termed DPMSA, which is employed to deal with the absence of co-evolutionary information on targets. We integrate DeepIDDP into our previously developed domain assembly method SADA, termed SADA-DeepIDDP. Tested on a given multi-domain benchmark dataset, the accuracy of SADA-DeepIDDP inter-domain distance prediction is 11.3% and 21.6% higher than trRosettaX and trRosetta, respectively. The accuracy of the domain assembly model is 2.5% higher than that of SADA. Meanwhile, we reassemble 68 human multi-domain protein models with TM-score ≤ 0.80 from the AlphaFold protein structure database, where the average TM-score is improved by 11.8% after the reassembly by our method. The online server is at http://zhanglab-bioinf.com/DeepIDDP/.
Multivariable prediction model for both 90-day mortality and long-term survival for individual patients with perihilar cholangiocarcinoma: does the predicted survival justify the surgical risk?
Authors: van Keulen Anne-Marleen , Buettner Stefan , Erdmann Joris I , Pratschke Johann , Ratti Francesca , Jarnagin William R , Schnitzbauer Andreas A , Lang Hauke , Ruzzenente Andrea , Nadalin Silvio , Cescon Matteo , Topal Baki , Olthof Pim B , Groot Koerkamp Bas
Published: March 2023

Background

The risk of death after surgery for perihilar cholangiocarcinoma is high; nearly one in every five patients dies within 90 days after surgery. When the oncological benefit is limited, a high-risk resection may not be justified. This retrospective cohort study aimed to create two preoperative prognostic models to predict 90-day mortality and overall survival (OS) after major liver resection for perihilar cholangiocarcinoma.

Methods

Separate models were built with factors known before surgery using multivariable regression analysis for 90-day mortality and OS. Patients were categorized in three groups: favourable profile for surgical resection (90-day mortality rate below 10 per cent and predicted OS more than 3 years), unfavourable profile (90-day mortality rate above 25 per cent and/or predicted OS below 1.5 years), and an intermediate group.

Results

A total of 1673 patients were included. Independent risk factors for both 90-day mortality and OS included ASA grade III–IV, large tumour diameter, and right-sided hepatectomy. Additional risk factors for 90-day mortality were advanced age and preoperative cholangitis; those for long-term OS were high BMI, preoperative jaundice, Bismuth IV, and hepatic artery involvement. In total, 294 patients (17.6 per cent) had a favourable risk profile for surgery (90-day mortality rate 5.8 per cent and median OS 42 months), 271 patients (16.2 per cent) an unfavourable risk profile (90-day mortality rate 26.8 per cent and median OS 16 months), and 1108 patients (66.2 per cent) an intermediate risk profile (90-day mortality rate 12.5 per cent and median OS 27 months).

Conclusion

Preoperative risk models for 90-day mortality and OS can help identify patients with resectable perihilar cholangiocarcinoma who are unlikely to benefit from surgical resection. Tailored shared decision-making is particularly essential for the large intermediate group.
Physical activity as an exogenous risk factor for amyotrophic lateral sclerosis: a review of the evidence
Authors: Chapman Laura , Cooper-Knock Johnathan , Shaw Pamela J
Published: March 2023

Amyotrophic lateral sclerosis (ALS) is a rapidly progressive and fatal neurodegenerative disorder. The only established epidemiological risk factors for ALS are male sex and increasing age. The role of physical activity has been debated as an environmental risk factor. Over the last decade multiple studies have attempted to delineate the architecture of ALS. These have not yet established definite risk factors, often due to low-powered studies, lack of focus on at-risk genotypes and sub-optimal methodology.

We have conducted a review of all the studies published between 2009 and December 2021. The free text search terms were [(motor neuron disease) OR (MND) OR (Amyotrophic Lateral Sclerosis) OR (ALS)] AND [(Exercise) or (Physical Activity) or (PA) or (sport)]. We identified common themes, for example soccer, head injury and the physiological mechanisms that differ in ALS patients. We have analysed the relevant, available studies (n = 93), highlighting the underlying reasons for any reported discrepancies.

Overall, we have found that the more highly powered studies using validated exposure methodologies, linked strenuous, anaerobic physical activity as a risk factor for ALS. Future large-scale studies focusing on specific at-risk genotypes and physical activity should be conducted to confirm this finding. This will strengthen the evidence already surrounding strenuous physical activity as an environmental risk factor for ALS and allow advice to be given to at-risk family members. Increasing our understanding of the genetic–environmental interactions in the pathophysiology of ALS will allow for the possibility of developing preventative therapeutic approaches.
Establishing Pragmatic Analytical Performance Specifications for Blood Beta-Hydroxybutyrate Testing
Authors: Kilpatrick Eric S , Butler Alexandra E , Atkin Stephen L , Sacks David B
Published: March 2023

Background

Currently, no authoritative guidelines exist recommending the analytical performance specification (APS) of blood beta-hydroxybutyrate (BOHB) testing in order to meet the clinical needs of patients. This study has applied existing diabetic ketoacidosis (DKA) BOHB diagnostic thresholds and the recommended rates of fall in BOHB concentrations during DKA treatment to establish pragmatic APSs for BOHB testing.

Methods

Required analytical performance was based on 2 clinical requirements: (a) to reliably distinguish between non-adjacent DKA BOHB diagnostic categories of <0.6, 0.6 to 1.5, 1.6 to 2.9, and ≥3 mmol/L, and (b) to be assured that a measured 0.5 mmol/L reduction in BOHB indicates the true concentration is at least falling (meaning >0 mmol/L decline).

Results

An analytical coefficient of variation (CV) of <21.5% could reliably distinguish all non-adjacent diagnostic categories with >99% certainty, assuming zero bias. In contrast, within-day CVs of 4.9%, 7.0%, and 9.1% at 3 mmol/L BOHB were required to assure truly falling ketone concentrations with 99% (optimal), 95% (desirable), and 90% (minimal) probability, respectively. These CVs are larger at lower BOHB concentrations and smaller at higher concentrations.

Conclusions

Reliable tracking of changes in BOHB during DKA treatment largely drives the requirement for analytical performance. These data can be used to guide minimal, desirable, and optimal performance targets for BOHB meters and laboratory assays.
Role of Machine Learning on Key Extraction for Data Privacy Preservation of Health Care Sectors in IoT Environment
Authors: Kathavate Pravin Narayan
Published: March 2023

Privacy and security in the medical field are major aspects to consider in the current era. This is due to the huge necessity for data among providers, payers and patients, respectively. Recently, more researchers are making their contributions in this field under different aspects. But, there need more enhancements concerning security. In this circumstance, this paper intends to propose a new IoT-dependent health care privacy preservation model with the impact of the machine learning algorithm. Here, the information or data from IoT devices is subjected to the proposed sanitization process via generating the optimal key. In this work, the utility of the machine learning model is the greatest gateway to generating optimal keys as it is already trained with the neural network. Moreover, identifying the optimal key is the greatest crisis, which is done by a new Improved Dragonfly Algorithm algorithm. Thereby, the sanitization process works, and finally, the sanitized data are uploaded to IoT. The data restoration is the inverse process of sanitization, which gives the original data. Finally, the performance of the proposed work is validated over state-of-the-art models in terms of sanitization and restoration analysis.
Accuracy of Transperineal Ultrasonography for Assessing Rectal Lesions in Paediatric Ulcerative Colitis: A Prospective Study
Authors: Jimbo Keisuke , Hosoi Kenji , Suzuki Mitsuyoshi , Kyodo Reiko , Maruyama Kimiko , Arai Nobuyasu , Sato Masamichi , Miyata Eri , Hoshino Eri , Kudo Takahiro , Shimizu Toshiaki
Published: March 2023

Background and Aims

Transabdominal ultrasonography [TAUS] appears comparable to colonoscopy for evaluating ulcerative colitis [UC] activity, but it has low accuracy in rectal evaluation. In this study, the accuracy of transperineal ultrasonography [TPUS] for evaluating rectal activity was compared to that of colonoscopy in paediatric UC cases.

Methods

Faecal calprotectin [FCP] values and TPUS and colonoscopic findings were compared prospectively in paediatric UC cases. Rectal wall thickening [RWT] and rectal wall flow [RWF] on power Doppler evaluated by TPUS were compared with the colonoscopy findings and were also measured on TAUS and assessed for the concordance rate of each finding.

Results

Thirty Mayo endoscopic sub-score [MES] 0–1 UC cases and 57 MES 2–3 UC cases were enrolled. FCP, RWT and RWF showed significant differences between the two groups [p < 0.05]. RWT and RWF were independent predictors of UC endoscopic activity, showing sensitivity of 95.8% and specificity of 100% with RWT ≥ 4.5 mm and positive RWF. The concordance rates between TPUS and TAUS findings in MES 2–3 were moderate to fair, whereas those in MES 0–1 were fair to poor. The concordance rates between ultrasonic examiners were good for both TAUS and TPUS.

Conclusions

TPUS may evaluate rectal activity of UC with accuracy comparable to endoscopy. If accurate ultrasonic screening for the total colon can be performed by TPUS and TAUS, repeated evaluation of short-term treatment response may be possible.
Inflammatory process of the COVID-19 fulminant myocarditis in the multimodality imaging: a case report
Authors: Hara Satoshi , Miwa Naoyuki , Hachiya Hitoshi , Sasano Tetsuo
Published: March 2023

Background

Cardiac manifest of COVID-19 infection was widely reported. The pathophysiology is thought the combination of direct damage caused by viruses and myocardial inflammation caused by immune responses. We tracked the inflammatory process of fulminant myocarditis associated with COVID-19 infection using multi-modality imaging.

Case Summary

A 49-year-old male with COVID-19 went into cardiac arrest from severe left ventricular dysfunction and cardiac tamponade. He was treated with steroids, remdesivir, and tocilizumab but failed to maintain circulation. He recovered with pericardiocentesis and veno-arterial extracorporeal membrane oxygenation in addition to the immune suppression treatment. In this case, a series of chest computed tomography (CT) was performed on Days 4, 7, and 18 and cardiac magnetic resonance (MR) on Days 21, 53, and 145.

Discussion

Analysis of the inflammatory findings on CT in this case showed that intense inflammation around the pericardial space was observed at an early stage of the disease. Although inflammatory findings in the pericardial space and chemical markers had improved according to non-magnetic resonance imaging (MRI) tests, the MRI revealed a notable long inflammatory period more than 50 days.
Sex-based differences in risk of ischaemic stroke or systemic embolism after BNT162b2 or CoronaVac COVID-19 vaccination in patients with atrial fibrillation: a self-controlled case series and nested case-control study
Authors: Ye Xuxiao , Huang Caige , Yan Vincent Ka Chun , Kang Wei , Fan Min , Tsang Gigi Kwan Chi , Ho Clarissa Mung Yee , Lip Gregory Y H , Yiu Kai-Hang , Tse Hung-Fat , Ma Tiantian , Qin Xiwen , Chui Celine Sze Ling , Lai Francisco Tsz Tsun , Wong Carlos King Ho , Wan Eric Yuk Fai , Li Xue , Lee Cheuk Kwong , Hung Ivan Fan Ngai , Wong Ian Chi Kei , Chan Esther Wai Yin
Published: March 2023

Aims

Patients with atrial fibrillation (AF) have a higher risk of ischaemic stroke or systemic embolism, with a greater risk for female patients. This study aims to evaluate the risk of ischaemic stroke or systemic embolism and bleeding following COVID-19 vaccination in patients with AF and the sex differences.

Methods and results

Self-controlled case series (SCCS) analysis was conducted to evaluate the risk of ischaemic stroke or systemic embolism and bleeding following BNT162b2 or CoronaVac in patients with AF, using the territory-wide electronic medical records from the Hospital Authority and vaccination records from the Department of Health in Hong Kong. Patients with a primary diagnosis of ischaemic stroke, systemic embolism, or bleeding in the inpatient setting between 23 February 2021 and 31 March 2022 were included. A nested case-control analysis was also conducted with each case randomly matched with 10 controls according to sex, age, Charlson comorbidity index, and date of hospital admission. Conditional Poisson regression was used in the SCCS analysis, and conditional logistic regression was used in the nested case-control analysis to assess the risks, and all analyses were stratified by sex and type of vaccines. Among 51 158 patients with AF, we identified an increased risk of ischaemic stroke or systemic embolism after the first dose of BNT162b2 in SCCS analysis during 0–13 days [incidence rate ratio 6.60, 95% confidence interval (CI) 1.51–28.77] and 14–27 days (6.53, 95% CI 1.31–32.51), and nested case-control analysis during 0–13 days (adjusted odds ratio 6.21, 95% CI 1.14–33.91) and 14–27 days (5.52, 95% CI 1.12–27.26) only in female patients. The increased risk in female patients following the first dose of CoronaVac was only detected during 0–13 days (3.88, 95% CI 1.67–9.03) in the nested case-control analysis. No increased risk of ischaemic stroke or systemic embolism was identified in male patients, and no increased risk of bleeding was detected in all patients with AF for both vaccines. An increased risk of ischaemic stroke or systemic embolism after COVID-19 was also observed in both females (17.42, 95% CI 5.08–59.73) and males (6.63, 95% CI 2.02–21.79).

Conclusions

The risk of ischaemic stroke or systemic embolism after COVID-19 vaccination was only increased in female patients with AF. However, as the risk after COVID-19 was even higher, proactive uptake of COVID-19 vaccines is recommended to prevent the potential severe outcomes after infection.