bluuebunny/crossref_metadata_2025 huggingface dataset:
A Review of Antifungal Susceptibility Testing for Dermatophyte Fungi and It’s Correlation with Previous Exposure and Clinical Responses
Authors: Khan Sidra Saleem , Hay Roderick James , Saunte Ditte Marie Lindhardt
Published: December 2022

Background: An increase in the number of recurrent and recalcitrant dermatophytoses calls for a tool to guide the clinician to correlate in vitro minimum inhibitory concentration (MIC) data, antifungal treatment with clinical outcomes. This systematic review aims to explore a possible correlation between one aspect of this, previous antifungal exposure, and clinical outcomes. Methods: A systematic literature search for articles on previous antifungal treatment, treatment outcome, susceptibility methods used, organism (genus/species), and MIC values was conducted. Results: A total of 720 records were identified of which 19 articles met the inclusion criteria. Forty percent of the cases had contact with or travel to India, 28% originated from or had traveled to other countries where treatment unresponsive tinea infections had been reported. Tinea corporis was the most common clinical presentation and the species involved were Trichophyton (T.) indotineae and T. rubrum, followed by T. mentagrophyte/interdigitale complex and T. tonsurans. Nearly all patients had previously been exposed to one or more antifungals. The studies were too heterogeneous to perform a statistical analysis to test if previous antifungal exposure was related to resistance. Conclusions: Only a few studies were identified, which had both sufficient and robust data on in vitro susceptibility testing and clinical treatment failure. Further research on the value of susceptibility testing to improve clinical practice in the management of dermatophyte infections is needed.
Fungal Taxonomy, Phylogeny, and Ecology: A Themed Issue Dedicated to Academician Wen-Ying Zhuang
Authors: Gao Cheng , Cai Lei
Published: December 2022

We are honored and privileged to edit this Special Issue, “Fungal Taxonomy, Phylogeny, and Ecology: A Themed Issue Dedicated to Academician Wen-Ying Zhuang” [...]
Factors Likely to Affect the Uptake of Genomic Approaches to Cancer Screening in Primary Care: A Scoping Review
Authors: Davis Kaitlyn V. , Hallman Mie H. , DiCarlo Melissa , Wambua Sophie M. , Jaffe Rachel L. , Welsh Allison W. , Kerber Cameron , Yang Hushan , Chambers Christopher V. , Myers Ronald E.
Published: December 2022

Genomic tests are being developed for use in cancer screening. As most screening is offered in primary care settings, primary care provider and patient perceptions of such tests are likely to affect uptake. We conducted a scoping review to synthesize information on factors likely to affect patient and provider use of biospecimen collection and analysis for cancer screening, methods referred to as liquid biopsy or multi-cancer early detection (MCED) testing when used to detect multiple cancers. We ultimately identified 7 articles for review and analyzed them for major themes. None reported on primary care provider perspectives. Six articles focused on patient perceptions about testing for a single cancer (colorectal), and 1 reported on patient views related to testing for multiple cancers. Factors favoring this type of testing included its non-invasiveness, and the perceived safety, convenience, and effectiveness of testing. There is a dearth of information in the literature on primary care provider perceptions about liquid biopsy and MCED testing. The limited information on patient perceptions suggests that they are receptive to such tests. Research on primary care provider and patient test-related knowledge, attitudes, and behavior is needed to guide future implementation in primary care settings.
Vitiligo—Thyroid Disease Association: When, in Whom, and Why Should It Be Suspected? A Systematic Review
Authors: Chivu Ana , Bălășescu Elena , Pandia Larisa , Nedelcu Roxana , Brînzea Alice , Turcu Gabriela , Antohe Mihaela , Ion Daniela
Published: December 2022

In most dermatological pathologies, the phenomena observed on the skin are a reflection of internal disorders. In patients with associated acral involvement on the dorsal sides of the hands, this “vitiligo phenotype” may lead to the investigation of certain associated pathologies that sometimes have no obvious clinical impact. To assess the link between skin depigmentation and autoimmune pathologies, we conducted a systematic review involving article selection from the PubMed database. Patients with coexisting thyroid pathologies were found to have a predisposition for developing acral vitiligo and depigmentation of the wrists, and autoimmune thyroid pathologies appeared to be the only coexisting autoimmune or inflammatory diseases in vitiligo patients to show a pattern of distribution. The association of concomitant thyroid dysfunction with depigmentation of the hands was found to be so strong that the absence of depigmented macules on the hands may exclude the coexistence of an autoimmune thyroid pathology. Although the frequency of acral involvement in patients with vitiligo and autoimmune pathologies is higher, the mechanism by which thyroid dysfunction influences this distribution pattern remains incompletely elucidated and requires future studies.
Distribution of Soil Microbes in Urban Parks: An Effect of Under-Tree Crown and Hillside Position on Testate Amoeba Assemblages in Subtropics (Shenzhen, China)
Authors: Zhong Yuantan , Ivanovskii Aleksandr , Ndayishimiye Jean Claude , Tsyganov Andrey N. , Babeshko Kirill , Saldaev Damir , Mazei Yuri
Published: December 2022

Testate amoebae (TA) are important components of soil ecosystems, where they play an essential role in belowground food webs. In this study, we examined species composition, diversity, and structure of TA assemblages in soils beneath tree crowns (microscale) at three slope positions (mesoscale) in subtropical urban parks in Shenzhen, China. Forty-two species of TA belonging to 18 genera were identified in 81 samples. TA assemblages were the most diverse and abundant in the center of the tree crown comparing with other under-tree habitats. Foot of the hills harbored higher TA abundance and diversity comparing with upper locations along the hillslopes. The distribution of TA was mostly driven by under-crown and hillside positions but not by elementary environmental conditions such as pH, moisture content and thickness of leaf litter layer. None of later factors were sufficient in shaping TA assemblage composition. The findings of our study suggest that in regional studies of soil microbial eukaryotes both micro- (i.e., under-crown) and mesoscale (i.e., the slope position) heterogeneity should be considered.
Concatenating Daily Exercise Routes with Public Sports Facilities, Bicycle Lanes, and Green Spaces: A Feasibility Analysis in Nanjing, China
Authors: Chen Yan , Zhang Bing , Li Mingke , Zhou Ryan Zhenqi , Xu Zhen
Published: December 2022

Public sports facilities have the potential to improve their functions as active living infrastructures (ALIs) in combination with bicycle lanes and green spaces. A favorable sequence of exercise intensities in different scenes is important for individuals to take physical activity scientifically. Our research aimed to explore the feasibility of promoting and consolidating this sequence using reasonable daily exercise routes concatenated by public sports facilities, green spaces, and bicycle lanes. Taking 25 major public sports facilities in Nanjing as an example, we obtained the cycling routes from open-source data and delineated the facilities’ cycling catchment areas to assess the coordination of bicycle lanes and facilities. Further, we evaluated the potential interactions between facilities and green spaces by checking the spatial intersections between park entrances and the above routes. The results revealed that with the integration of bicycle lanes, public sports facilities could provide services to most residential areas, and potential interactions between the facilities and parks existed already. Therefore, it was feasible to design reasonable daily exercise routes coupled with the existing facility layout. Moreover, the service gaps and potential interactions were affected by the layout of the facilities, the density of the bicycle lanes, the configuration of green spaces, and the official planning proposals. This research advances the understanding of how public sports facilities can be pivotal to the cooperation of ALIs with other infrastructures.
Carbon Sequestration Potentials of Different Land Uses in Wondo Genet Sub-Catchment, Southern Ethiopia
Authors: Taddese Habitamu , Negash Mesele , Geda Tariku , Ayele Gebiaw T.
Published: December 2022

Forests play an important role in combating the challenges posed by changing climate through sequestering carbon in their living biomasses and the soil. Tropical forests, which harbour a large number of species, are anticipated to play a great role in this regard due to the favourable growing environments. However, there is limited knowledge of the variability in carbon stock among land use types and its relationship with biodiversity. Therefore, this study assessed the variability in storing the different carbon pools among natural forest, woodland and khat plantation land use types. It also explored the relationship between biodiversity and carbon storage in the different carbon pools. Plant inventory and sample collection were undertaken following standard methods. In addition, soil samples were taken at three depth profile classes of 0–30 cm (top layer), 30–60 cm (middle layer) and 60–100 cm (bottom layer). Results of the study revealed that there was no statistically significant relationship between biodiversity and total biomass carbon, soil organic carbon or total carbon stock at a 95% level of confidence. The results indicated that the natural forest had the highest plant biomass (456.93 Mg ha−1) followed by woodland (19.78 Mg ha−1) and khat plantation (2.46 Mg ha−1). Consequently, the total carbon stock estimate of the natural forest (366.47 Mg ha−1) was significantly larger than that of the woodland (141.85 Mg ha−1) and khat plantation (125.86 Mg ha−1). The variation in total carbon stock among land use types arises from the variation in the total biomass carbon stock. The study results also revealed that soil organic carbon stock decreased with soil depth in all the land-use types. The findings of this study have implication of improving topsoil management in monoculture crops such as khat plantation and conserving natural forests for enhancing carbon sequestration potentials.
Uncovering Stakeholders’ Participation to Better Understand Land Use Change Using Multi-Agent Modeling Approach: An Example of the Coal Mining Area of Shanxi, China
Authors: Guo Mengyuan , Zhang Hong , Cui Yan , Zhang Xiaoyu , Liu Yong
Published: December 2022

Recent decades have witnessed increasing human disruption and the acceleration of fragile natural habitats, especially in coal mining areas in developing countries or regions, which will inevitably lead to sharp land use and cover change (LUCC). Most LUCC models focus more on the research of “land” than “human” in human-land coupled systems, while the simulation and prediction of LUCC involving stakeholders are still deficient. Aiming to reveal the shaping process of LUCC through the stakeholders’ participation, we conducted an in-depth interview in a typical coal mining area of Shanxi, China, and developed an agent-based model by quantifying the stakeholders’ land-use decision-making rules to simulate and predict land use change in different scenarios. The analysis illustrated that the stakeholders’ participation in different periods had shaped the land use pattern in the coal mine area. The area of cultivated land has decreased from 272.34 hm2 to 118.89 hm2, while industrial and mining land increased dramatically by 78.66 hm2 from 2012 to 2019. The attitude and willingness of farmers towards land use varied greatly and were affected by livelihood capital. Part-time farmers whose agricultural income only accounted for 20–80% of the total income were in favor of farmland requisition by coal mining enterprises compared to full-time farmers. We quantified the rules between the attributes of the stakeholders at the micro level and land use changes at the macro level and proposed the multi-agent simulation model, which was effective and verified by a fitting test where the overall accuracy of the Kappa coefficient was 0.83 and could be used to predict future LUCC in research areas by setting the decision parameters in specific scenarios. These outcomes provided a scientific reference for landscape simulation and the prediction of a human-land coupling system while promoting the effectiveness of spatial planning policies.
Land-Use Changes on Ob River Floodplain (Western Siberia, Russia) in Context of Natural and Social Changes over Past 200 Years
Authors: Ivanov Vladimir , Milyaev Ivan , Konstantinov Alexander , Loiko Sergey
Published: December 2022

Over the past century, substantial changes in land use have taken place in the boreal zone of northern Eurasia. The consequences of these large-scale changes for the ecosystems of Europe have been well studied; however, they have not been addressed for the large expanses of Russia. We conducted a retrospective analysis of the landscape dynamics of the middle reaches of the Ob floodplain (Western Siberia) using multitemporal maps of the vegetation cover and land use for five time points (1830, 1910, 1950, 1976, and 2019). By the 1830s, all the land that was suitable for haymaking and plowing (rarely flooded and not swamped) had been put to agricultural use. The meadows of the Ob floodplain are human-controlled and were mainly formed before the 1830s. From the 1830s to the 1990s, the meadows were used in agriculture and their areas increased. The maximum development of the floodplain occurred in the 1970s and 1980s, when previous wetlands were put into operation through the construction of drainage systems. A massive abandonment of pastures and reclaimed land occurred in the late 20th century. According to the data over the last 30 years, abandoned meadows are resistant to overgrowth with trees and shrubs. The spatial configurations of the floodplain landscapes have also been quite stable. The main spatial changes are confined to the near-channel floodplain, with the formation of new near-channel shallows. The floodplain landscapes of the Ob River demonstrate substantial spatial and temporal stabilities, and long-standing agricultural development.
Unraveling the Differences in Landcover Patterns in High Mountains and Low Mountain Environments within the Valdivian Temperate Rainforest Biome in Chile
Authors: Hora Benedikt , Almonacid Fabian , González-Reyes Alvaro
Published: December 2022

The Valdivian temperate rainforest (VTR) is a biome on the South American continent with high endemism that has experienced an intensive land-cover change in recent decades due to the expansion of agriculture, plantations of introduced forests, and urban growth. Today, the biome hosts key parts of the country’s agricultural and forestry industries. Previous studies focused on quantifying native forest and plantation cover area and exotic forest plantation area, among others. However, the importance of mountain areas as refuge of native forest in Chile remains unexplored. The aim of this research is to highlight the role of latitude and slope on land cover in the VTR. A new methodological approach was used combining global classified datasets. Our results indicate that high mountain areas are the core location of the remaining primary forests and endemism whereas low mountain areas are dominated by exotic forest plantations. Between 40–48° S (The Los Ríos, Los Lagos, and Aysén Regions and high-mountain areas), in general, serve as a natural reservoir where human-induced land-cover change has not occurred on a large scale. Most public and private conservation areas are in high mountain areas, whereas low mountain areas and plain areas lack conservation schemes and are more prone to land cover change towards forestry. Considering geomorphological features in land cover change analysis can reveal interesting new perspectives in this research area.
Rice Husk and Its Biochar Have Contrasting Effects on Water-Soluble Organic Matter and the Microbial Community in a Bamboo Forest Soil
Authors: El-Naggar Ali , Zhou Rong , Tang Ronggui , Hur Jin , Cai Yanjiang , Chang Scott X.
Published: December 2022

Converting rice husk to biochar is one of the solutions to manage crop residues by transforming waste into a value-added material that has broad benefits to the environment when biochar is applied to the soil. This study investigated the impact of the application of rice husk and its biochar at different doses (i.e., 0, 10, and 30 t ha−1) on soil carbon stability, the property of water-soluble soil organic matter, and the abundance and diversity of microbial communities in a Lei bamboo (Phyllostachys praecox) forest soil 262 days after their application. The application of rice husk, especially at 30 t ha−1, increased dissolved organic carbon due to the high labile carbon (C) (e.g., cellulose, hemicellulose, polysaccharides) content in the rice husk. The biochar treatments stimulated the release of humic-like substances (e.g., (poly) phenols) into the soil solution, increased the aromatic C content by 412–557%, and increased the relative abundance of Chloroflexi, Planctomycetota, and Proteobacteria compared to the control. This study shows that biochar application, particularly at 30 t ha−1, enhanced the C stability by turning organic C into recalcitrant forms in the soil, demonstrating the merit of converting rice husk into biochar before its application to the soil.
An Axiology of Weak Areas: The Estimation of an Index of Abandonment for the Definition of a Cognitive Tool to Support the Enhancement of Inland Areas in Sicily
Authors: Trovato Maria Rosa , Nasca Ludovica
Published: December 2022

The marginalization of areas due to a progressive increase in social, material, economic, and infrastructural vulnerability is a phenomenon that afflicts many countries today, and it is growing rapidly. Agenda 2030, in highlighting the need to identify measures to counter this phenomenon, has promoted the development of a growing awareness of addressing this issue that cannot be postponed. With this in mind, in Italy, a map of inland areas was produced by the Interministerial Committee for Economic Planning and Sustainable Development (ICEPSD), a publication aimed at measuring the extent of the phenomenon and support the development of specific strategies that collectively define the National Strategy for Inland Areas (NSIA). In this study, starting from a critical analysis of the classification of areas in the National Strategy for Inner Areas, we propose a new cognitive tool of the phenomenon of abandonment developed from the perspective of an axiological approach of marginal areas. This tool is based on the mapping of an abandonment index Ia on QGIS with reference to the clusters of municipalities identified based on the quartiles of its values. This index was estimated as an aggregate weighted sum of the components identified because of the Principal Component Analysis (PCA) used to analyze the indicators of different forms of territorial capital of weak areas.
Analysis of the Spatial and Temporal Distribution and Reuse of Urban Industrial Heritage: The Case of Tianjin, China
Authors: Zhang Jiahao , Sun Hao , Xu Subin , Aoki Nobuo
Published: December 2022

Urban industrial heritage is both a physical component of the city and an important carrier of urban memory, but there is still a lack of comprehensive analysis of industrial heritage in Tianjin and a need for a conservation system. This study took the industrial heritage of Tianjin built between 1860 and 1978 as the research object and used GIS technology to analyse the spatial and temporal distribution of industrial heritage and the current state of its reuse. The results show that in the temporal dimension, the distribution of industrial heritage in Tianjin shows a pattern of change of “gathering first, then scattering”, with the 1960s as the time point; in the spatial dimension, the existing industrial heritage shows a pattern of distribution along important transport routes—the Haihe River, the Jingfeng Railway and the Jinpu Railway, and there are three industrial heritage clusters. The conservation and reuse status of industrial heritage varies by resource type, but the overall state is poor. Based on the results of the above analysis, a holistic conservation concept of the “Tianjin Industrial Heritage Route” and a reuse strategy for different resource types of industrial heritage are proposed. This will help to integrate the reuse of Tianjin’s industrial heritage into the sustainable development of the city and provide a reference for the conservation of industrial heritage in other cities in China and even in the world.
Functioning of the Masticatory System in Patients with an Alloplastic Total Temporomandibular Joint Prostheses Compared with Healthy Individuals: A Pilot Study
Authors: Speksnijder Caroline M. , Mutsaers Nadiya E. A. , Walji Sajjad
Published: December 2022

Background: Most patients with temporomandibular joint (TMJ) issues are successfully treated with nonsurgical methods. However, when end-stage TMJ pathologies occur, invasive management can be required, such as a total TMJ replacement. This cross-sectional pilot study aimed to provide insight into the functioning of the masticatory system, pain, and patient satisfaction in patients treated with a total joint replacement (TJR). Methods: A cross-sectional pilot study was conducted to determine the postoperative clinical results of an alloplastic TJR TMJ. Masticatory performance and also insight into maximum voluntary bite force (MVBF), active and passive maximum mouth opening (aMMO/pMMO), pain, and patient satisfaction were measured. Masticatory performance, MVBF, and aMMO of patients with a TJR TMJ were compared with healthy individuals. Results: Masticatory performance is equal between patients with a TJR TMJ and healthy individuals, but both MVBF and aMMO were significantly smaller in patients with a TJR TMJ. However, patients had almost no pain and were very satisfied with the TJR TMJ treatment. Conclusion: This study revealed that most patients with an alloplastic TJR TMJ were able to function without pain, showed good masticatory performance, and were highly satisfied with their alloplastic TJR TMJ. However, MVBF and aMMO were lower than in healthy individuals.
COVID-19 and Semen Fluid Parameters, a Retrospective Study from Infertility Clinics
Authors: Al-Alami Zina M. , Albeitawi Soha , ALNatsheh Maha S. , Albakri Khaled , Qublan Hussein , Muhaidat Nadia , Abuhalaweh Mariam Ahmad , AlRawashdeh Maen Monketh , Alqam Hiba
Published: December 2022

The study of the effects of SARS-CoV-2 infection and/or vaccination on semen fluid analysis (SFA) parameters is still incomplete. The aim of this study is to assess the effect of COVID-19 infection and vaccination on sperm parameters for a sample of individuals visiting multi-infertility clinics in Jordan. SFA records were collected retrospectively between September and November 2021 and analyzed using Jamovi software (version 2.2.5 for Windows); p-values < 0.05 were considered statistically significant. Sperm concentration, progressive motility, normal morphology, and semen liquefaction time, volume, and viscosity were compared among two data categories. In the first category of data, SFA records from 354 participants were separated into four groups: only vaccinated, infected and vaccinated, neither infected nor vaccinated, and only infected. In the other category, SFA from 49 subjects before their infection and/or vaccination and after were classified into the same mentioned groups and analyzed. There were no statistically significant differences between the studied parameters in the SFA records in the first data category and the second. Nevertheless, the sperm concentration was higher among vaccinated subjects compared to unvaccinated ones (p = 0.04). It is concluded that SARS-CoV-2 infection and vaccines have no negative effects on SFA parameters.
Caucasian Blueberry: Comparative Study of Phenolic Compounds and Neuroprotective and Antioxidant Potential of Vaccinium myrtillus and Vaccinium arctostaphylos Leaves
Authors: Shamilov Arnold A. , Olennikov Daniil N. , Pozdnyakov Dmitryi I. , Bubenchikova Valentina N. , Garsiya Ekaterina R. , Larskii Mikhail V.
Published: December 2022

(1) Background: Two Caucasian blueberries Vaccinium myrtillus L. and Vaccinium arctostaphylos L. are famous berry bushes growing in the Caucasus region and used to treat neurological diseases, but the chemistry and bioactivity of leaf extracts are still poorly studied. (2) Methods: Phenolic compounds of V. myrtillus and V. arctostaphylos leaf extracts were profiled and quantified by HPLC–PDA–ESI–tQ–MS. The neurotropic potential of Vaccinium extracts was studied using the model of middle cerebral artery permanent occlusion to determine cerebral blood flow, the area of the brain tissue necrosis, and antioxidant enzyme activity (including superoxide dismutase, succinate dehydrogenase, and cytochrome C oxidase), as well as the concentration of TBARS. (3) Results: Hydroxycinnamates and flavonoids were identified in the leaves of V. myrtillus and V. arctostaphylos, and the dominant metabolite of both extracts was 5-O-caffeoylquinic acid in the amount of 105–226 mg/g. The studied extracts enhanced the cerebral hemodynamics and decreased the frequency of necrotic and lipooxidative processes in the brain tissue, accompanied by an increase in the activity of antioxidant enzymes. The positive effect of V. arctostaphylos was stronger and exceeded the effectiveness of Ginkgo biloba standardized extract. (4) Conclusion: The leaf extracts of Caucasian blueberries V. myrtillus and V. arctostaphylos as a new source of hydroxycinnamates demonstrated a protective effect of the brain ischemia pathology and can be used as therapeutic agents to treat neurological diseases.
Ultrasound-Guided Interpectoral and Pectoserratus Plane Blocks in Breast Surgery: An Alternative Option to General Anaesthesia in an Elderly Woman with a Complex Medical History
Authors: Pirri Carmelo , Torre Debora Emanuela , Behr Astrid Ursula , De Caro Raffaele , Stecco Carla
Published: December 2022

With an incidence of over 1.5 million worldwide per annum, breast cancer continues to be the most common cancer affecting the female population. The main and most effective treatment in over 40% of these patients is a primary neoplasm resection. General anaesthesia, at times in association with loco-regional anaesthetics, is the most commonly used anaesthesia technique for radical mastectomies. Nausea, vomiting, and considerable postoperative pain, which are commonly experienced side effects and complications of general anaesthesia, tend, however, to augment most patients’ post-surgical morbidity. A growing body of research has shown that loco-regional anaesthesia often used together with and, in some cases, in the substitution of general anaesthesia can be a safe, effective alternative. This work is a case report regarding a 94-year-old elderly patient who was anaesthetised during a left radical mastectomy using exclusively combined interpectoral and pectoserratus plane blocks.
Effects of Different Types of Human Disturbance on Total and Nitrogen-Transforming Bacteria in Haihe River
Authors: Li Peiyang , Chen Tingyu , An Miao , Zhang Ying , Li Yanying , Li Yang , Wang Jing
Published: December 2022

Haihe River is the largest water system in North China and is injected into the Bohai Sea in Tianjin City. In this study, different types of human disturbance (urban sewage, industrial pollution, ship disturbance) were selected from the upper reaches of Haihe river Tianjin section down to the estuary that connected with Bohai Sea for evaluation. By metagenomic sequencing, the effects of different types of disturbances on bacteria communities in Haihe sediments were studied, with a special focus on the function of nitrogen-cycling bacteria that were further analyzed through KEGG comparison. By analyzing the physical and chemical characteristics of sediments, results showed that human disturbance caused a large amount of nitrogen input into Haihe River, and different types of human disturbance led to distinct spatial heterogeneity in different sections of Haihe River. The bacteria community was dominated by Proteobacteria, followed by Chloroflexi, Bacteroidetes, Actinobacteria and Acidobacteria. The relative abundance of each phylum varied at different sites as a response to different types of human disturbances. In nitrogen cycling, microorganisms including nitrogen fixation and removal were detected at each site, which indicated the active potential for nitrogen transformation in Haihe River. In addition, a large number of metabolic pathways relating to human diseases were also revealed in urban and pollution sites by function potential, which provided an important basis for the indicative role of urban river ecosystem for public health security. In summary, by evaluating both the ecological role and function potential of bacteria in Haihe River under different types of human disturbance, the knowledge of microorganisms for healthy and disturbed river ecosystems has been broadened, which is also informative for further river management and bioremediation.
MSALigMap—A Tool for Mapping Active-Site Amino Acids in PDB Structures onto Known and Novel Unannotated Homologous Sequences with Similar Function
Authors: Hassan Sameer , Haleemath Sameer Sameena , Töpel Mats , Aronsson Henrik
Published: December 2022

MSALigMap (Multiple Sequence Alignment Ligand Mapping) is a tool for mapping active-site amino-acid residues that bind selected ligands on to target protein sequences of interest. Users can also provide novel sequences (unavailable in public databases) for analysis. MSALigMap is written in Python. There are several tools and servers available for comparing and mapping active-site amino-acid residues among protein structures. However, there has not previously been a tool for mapping ligand binding amino-acid residues onto protein sequences of interest. Using MSALigMap, users can compare multiple protein sequences, such as those from different organisms or clinical strains, with sequences of proteins with crystal structures in PDB that are bound with the ligand/drug and DNA of interest. This allows users to easily map the binding residues and to predict the consequences of different mutations observed in the binding site. The MSALigMap server can be accessed at https://albiorix.bioenv.gu.se/MSALigMap/HomePage.py.
Mathematical Exchange Rates Modeling: Equilibrium and Nonequilibrium Dynamics
Authors: Kuzmin Anton
Published: December 2022

The development of the author’s concept of the International Flows Equilibrium Exchange Rate (IFEER) is the basis for the mathematical exchange rate modeling of two interconnected equal economies. IFEER-concept allows modeling the exchange rate dynamics of relatively medium-term equilibrium and short- and long-term disequilibrium. Discrete and integral versions of the concept are the basis for further modeling. New structural models of medium-, short- and long-term dynamics and new final structural dependencies of the exchange rate on the system of fundamental factors are the main results. The models include mathematically formalized export-import and capital flows and international competitive advantages indicators. The modeling allowed the revealing of the structural pricing mechanism of the exchange rate dynamics from new positions. We verify the US dollar to the Russian ruble exchange rate modeling during periods of financial and economic crises in recent Russian history, based on a systematic analysis of the exchange rate policy. Because of the analysis, the fall in export prices of oil and other energy carriers in international markets, the rise in consumer prices within the country, and the fall in aggregate output are the main reasons for the fall of the Russian ruble. The conducted modeling allows for the evaluation of the short-term contribution to the crisis depreciation dynamics. The mathematical tools allow for the development of the decision-making process on the exchange rate regulation.
Mathematical Modeling of a Non-Isothermal Flow in a Porous Medium Considering Gas Hydrate Decomposition: A Review
Authors: Borodin Stanislav L. , Musakaev Nail G. , Belskikh Denis S.
Published: December 2022

Deposits of natural gas hydrates are some of the most promising sources of hydrocarbons. According to studies, at the current level of natural gas consumption, the traditional reserves will last for about 50 years, and the gas hydrate deposits will last for at least 250 years. Therefore, interest in the study of gas hydrates is associated first of all with gas production from gas hydrate deposits. Additionally, gas hydrates are widely studied for solving practical problems, such as transportation and storage of natural gas, utilization of industrial gases and environmental and technological disasters associated with gas hydrates. When solving practical problems related to gas hydrates, in addition to laboratory and field studies, mathematical modeling is also widely used. This article presents the mathematical models of non-isothermal flow in a porous medium considering the decomposition of gas hydrate. The general forms of the mass conservation equations, Darcy’s law and the energy conservation equation are given. The article also presents derivations of the equations for taking into account the latent heat of phase transitions and non-isothermal filtration parameters for the energy conservation equation. This may be useful for researchers to better understand the construction of the model. For the parameters included in the basic equations, various dependencies are used in different works. In all the articles found, most often there was an emphasis on one or two of the parameters. The main feature of this article is summarizing various dependencies for a large number of parameters. Additionally, graphs of these dependencies are presented so that the reader can independently evaluate the differences between them. The most preferred dependencies for calculations are noted and explained.
Intelligent Generation of Cross Sections Using a Conditional Generative Adversarial Network and Application to Regional 3D Geological Modeling
Authors: Ran Xiangjin , Xue Linfu , Sang Xuejia , Pei Yao , Zhang Yanyan
Published: December 2022

The cross section is the basic data for building 3D geological models. It is inefficient to draw a large number of cross sections to build an accurate model. This paper reports the use of multi-source and heterogeneous geological data, such as geological maps, gravity and aeromagnetic data, by a conditional generative adversarial network (CGAN) and implements an intelligent generation method of cross sections to overcome the problem of inefficient modeling data based on CGAN. Intelligent generation of cross sections and 3D geological modeling are carried out in three different areas in Liaoning Province. The results show that: (a) the accuracy of the proposed method is higher than the GAN and Variational AutoEncoder (VAE) models, achieving 87%, 45% and 68%, respectively; (b) the 3D geological model constructed by the generated cross sections in our study is consistent with manual creation in terms of stratum continuity and thickness. This study suggests that the proposed method is significant for surmounting the difficulty in data processing involved in regional 3D geological modeling.
Analytical Modeling of Multistage Hydraulically Fractured Horizontal Wells Producing in Multilayered Reservoirs with Inter-Layer Pure-Planar Crossflow Using Source/Sink Function Method
Authors: Su Chang , Yuan Wanju , Zhao Gang
Published: December 2022

This study presents a comprehensive analytical modeling technology to model transient behaviors of multilayered reservoirs with inter-layer pure-planar crossflow induced by multi-stage hydraulically fractured horizontal well (MHFHW). The objective of this study is to develop an analytical model for multilayered reservoirs in conjunction with complex MHFHW and to achieve not only accurate and efficient computation, but also well-organized solutions expressed in a systematically integrated manner. The consideration of inter-layer crossflow across adjacent layers sets up the foundation for successful modeling of multilayered reservoirs. Source/sink function method (SSFM) is applied to describe fluid flow. Unsteady-state pressure or production rate solutions of MHFHW with the advantages of fast computation, accurate, and stable solutions are achieved. Comparative and consistent outcomes generated by this work and widely applied industry software have largely enhanced our technical confidence. More importantly, innovatively defined modified dimensionless terms that integrate systematic well-reservoir geometry information, as well as rock/fluid properties of each layer, have been newly applied to regulate the new modified dimensionless rate decline curve. This new technique sheds light on the reservoir characterization practice for complicated reservoir systems. Theoretical results in terms of transient pressure and rate were generated by the proposed multilayered model (SSFM-ML) for five scenarios of general concern, under various reservoir and well parameters, which were examined and discussed to demonstrate technical robustness. Not only does this study give solutions to the targeted multiple layered reservoirs, but it also provides insights into modeling three-dimensional fluid flow in heterogeneous reservoir with complex well configurations. It is recommended that future research should be conducted for more complicated two- and three-dimensional reservoirs, using the similar strategy of developing new type curves through adopting other new forms of modified dimensionless rate and time terms.
An Inventory Model in a Three-Echelon Supply Chain for Growing Items with Imperfect Quality, Mortality, and Shortages under Carbon Emissions When the Demand Is Price Sensitive
Authors: De-la-Cruz-Márquez Cynthia Griselle , Cárdenas-Barrón Leopoldo Eduardo , Mandal Buddhadev , Smith Neale R. , Bourguet-Díaz Rafael Ernesto , Loera-Hernández Imelda de Jesús , Céspedes-Mota Armando , Treviño-Garza Gerardo
Published: December 2022

This research develops an optimization model for growing items in a supply chain with three stages: farmer, processor, and retailer while considering imperfect quality, mortality, shortages with full backordering, and carbon emissions. In the farmer stage, during the growing period, not all articles survive until the end of the period, so a density function of the probability of survival and death of the growing articles is taken into account. Moreover, it is considered imperfect quality in the retailer’s stage because as the supply chain goes down, there exists a greater probability of product defects. Here, the end customer (consumer) can detect poor-quality aspects such as poorly cut, poorly packed, expired products, etc. An inventory model that maximizes the expected total profit is formulated for a single type of growing items with price-dependent polynomial demand. An algorithm is developed to solve the optimization problem generating the optimal solution for order quantity, backordering quantity, selling price, and the number of shipments that maximizes the expected total profit per unit of time, and a numerical example is used to describe the applicability of the proposed inventory model. Finally, a sensitivity analysis has been carried out for all the input parameters of the inventory model, where the effect of each of the parameters on the decision variables is shown to extract some management knowledge. It was found that holding costs in the three stages of the supply chain have a substantial impact on the total profit per unit of time. In addition, as the demand scale parameter increases, the company must raise the selling price, which directly impacts the expected total profit per unit of time. This inventory model has the advantage that it can be applied to any growing item, including animals or plants, so it helps the owners of farms or crops to generate the most significant possible profit with their existing resources.
Componentwise Perturbation Analysis of the QR Decomposition of a Matrix
Authors: Petkov Petko H.
Published: December 2022

The paper presents a rigorous perturbation analysis of the QR decomposition A=QR of an n×m matrix A using the method of splitting operators. New asymptotic componentwise perturbation bounds are derived for the elements of Q and R and the subspaces spanned by the first p≤m columns of A. The new bounds are less conservative than the known bounds and are significantly better than the normwise bounds. An iterative scheme is proposed to determine global componentwise bounds in the case of perturbations for which such bounds are valid. Several numerical results are given that illustrate the analysis and the quality of the bounds obtained.
A Novel Space-Time Marching Method for Solving Linear and Nonlinear Transient Problems
Authors: Hong Li-Dan , Ku Cheng-Yu , Liu Chih-Yu
Published: December 2022

In this study, a novel space-time (ST) marching method is presented to solve linear and nonlinear transient flow problems in porous media. The method divides the ST domain into subdomains along the time axis. The solutions are approximated using ST polyharmonic radial polynomial basis functions (RPBFs) in the ST computational domain. In order to proceed along the time axis, we use the numerical solution at the current timespan of the two ST subdomains in the computational domain as the initial conditions of the next stage. The fictitious time integration method (FTIM) is subsequently employed to solve the nonlinear equations. The novelty of the proposed method is attributed to the division of the ST domain along the time axis into subdomains such that the dense and ill-conditioned matrices caused by the excessive number of boundary and interior points and the large ST radial distances can be avoided. The results demonstrate that the proposed method achieves a high accuracy in solving linear and nonlinear transient problems. Compared to the conventional time marching and ST methods, the proposed meshless approach provides more accurate solutions and reduces error accumulation.
Critical Percolation on Temporal High-Speed Railway Networks
Authors: Liu Yi , Yu Senbin , Zhang Chaoyang , Zhang Peiran , Wang Yang , Gao Liang
Published: December 2022

Deeply understanding the dynamic operating characteristics of high-speed railway (HSR) systems is of essential significance in theory and practice for the planning, construction, and operational management of HSR systems. In this paper, the HSR system is described as a temporal network, and the evolution of connected clusters in the system is considered as a percolation process. The critical integration time Tc of the percolation process can determine the formation of a globally connected cluster and measure the transport performance of the HSR system. The appearance time of critical edges identified at Tc can significantly affect the reliability of the transport performance of an HSR system. Compared to random percolation in the static HSR network, it can be found that the critical fraction pc of the percolation process in a temporal HSR network is almost always larger. This indicates that the global connectivity and the transport performance of HSR systems is overestimated by the static network abstraction. This paper provides a promising way of understanding the dynamic characteristics of HSR systems, evaluating their transport performance, and improving their reliability.
The Natural Boundary Element Method of the Uniform Transmission Line Equation in 2D Unbounded Region
Authors: Teng Fei , Zhu Taiying , Jiang Zhixiong
Published: December 2022

Herein, we are mainly concerned with the natural boundary element (NBE) method of the uniform transmission line (UTL) equation defined in the two-dimensional (2D) boundless region, which has a real physical background. We first create the time semi-discretized scheme of the UTL equation, as well as analyze the convergence and stability for the series of time semi-discretized solutions. Then, we create a fully discretized NBE format by means of a natural boundary reduction and analyze the stability and errors between the fully discretized NBE solutions and the analytical solution. Lastly, we employ two numerical examples to verify the effectiveness of the NBE method.
Linear and Energy-Stable Method with Enhanced Consistency for the Incompressible Cahn–Hilliard–Navier–Stokes Two-Phase Flow Model
Authors: Huang Qiming , Yang Junxiang
Published: December 2022

The Cahn–Hilliard–Navier–Stokes model is extensively used for simulating two-phase incompressible fluid flows. With the absence of exterior force, this model satisfies the energy dissipation law. The present work focuses on developing a linear, decoupled, and energy dissipation-preserving time-marching scheme for the hydrodynamics coupled Cahn–Hilliard model. An efficient time-dependent auxiliary variable approach is first introduced to design equivalent equations. Based on equivalent forms, a BDF2-type linear scheme is constructed. In each time step, the unique solvability and the energy dissipation law can be analytically estimated. To enhance the energy stability and the consistency, we correct the modified energy by a practical relaxation technique. Using the finite difference method in space, the fully discrete scheme is described, and the numerical solutions can be separately implemented. Numerical results indicate that the proposed scheme has desired accuracy, consistency, and energy stability. Moreover, the flow-coupled phase separation, the falling droplet, and the dripping droplet are well simulated.
Research on Multi-Objective Multi-Robot Task Allocation by Lin–Kernighan–Helsgaun Guided Evolutionary Algorithms
Authors: Zhang Zhenqiang , Ma Sile , Jiang Xiangyuan
Published: December 2022

Multi-robot task allocation (MRTA) and route planning are crucial for a large-scale multi-robot system. In this paper, the problem is formulated to minimize the total energy consumption and overall task completion time simultaneously, with some constraints taken into consideration. To represent a solution, a novel one-chromosome representation technique is proposed, which eases the consequent genetic operations and the construction of the cost matrix. Lin–Kernighan–Helsgaun (LKH), a highly efficient sub-tour planner, is employed to generate prophet generation beforehand as well as guide the evolutionary direction during the proceeding of multi-objective evolutionary algorithms, aiming to promote convergence of the Pareto front. Numerical experiments on the benchmark show the LKH guidance mechanism is effective for two famous multi-objective evolutionary algorithms, namely multi-objective evolutionary algorithm based on decomposition (MOEA/D) and non-dominated sorting genetic algorithm (NSGA), of which LKH-guided NSGA exhibits the best performance on three predefined indicators, namely C-metric, HV, and Spacing, respectively. The generalization experiment on a multiple depots MRTA problem with constraints further demonstrates the effectiveness of the proposed approach for practical decision making.