bluuebunny/crossref_metadata_2025 huggingface dataset:
Mehmet Şemseddin Bey’in (1855-1917) İran’daki Siyasi ve Toplumsal Olaylara Etkisi
Authors: KARACAN Osman
Published: May 2022

Kafkasyalı Çerkes bir aileye mensup olan Mehmet Şemseddin Bey, ailesi ile birlikte İstanbul’a yerleşmiş ve eğitimini burada tamamlamıştır. Başarılı bir eğitim hayatından sonra Osmanlı Devleti’nde çeşitli görevler icra eden Mehmet Şemseddin Bey’in yaptığı görevlerden biri de Tahran Büyükelçiliği’dir. İran’ın buhranlı yıllarında on yılı aşkın süre Tahran Büyükelçiliği görevini sürdüren Mehmet Şemseddin Bey, gerek iktidar ve gerekse muhalefet ile kurduğu dostluk sayesinde İran’ın siyasi ve toplumsal olaylarında belirleyici bir rol üstlenmiştir. Başta Rusya ve İngiltere gibi yabancı güçlerin siyasi müdahalelerine ve Osmanlı-İran istibdat yönetimlerinin meclis ve meşrutiyet karşıtı politikalarına rağmen ahrar lehine arabulucu olan Mehmet Şemseddin Bey, İran’daki siyasi krizlerin sulh yoluyla çözülmesine önemli katkılar sunmuştur. Uyguladığı barış diplomasisi ile başta meşrutiyet olayları olmak üzere İran’daki sorunların çözümünde kolaylaştırıcı bir rol oynayan Mehmet Şemseddin Bey, aynı zamanda hem Şah hem de meşrutiyet taraftarlarıyla zaman zaman müzakerelerde bulunarak meselelerin doğru bir zeminde çözülmesine çalışmıştır. Fakat Mehmet Şemseddin Bey, uyguladığı etkin ve başarılı diplomatik faaliyetleriyle İran’daki siyasi ve toplumsal olaylarda önemli bir rol üstlenmesine rağmen bu başarısı temsil ettiği iktidar tarafından takdir edilmek yerine adeta cezalandırılmıştır. Biz de bu çalışmamızda Mehmet Şemseddin Bey’in Tahran Büyükelçiliği görevini sürdürdüğü yıllarda İran’da meydana gelen siyasi ve toplumsal olaylara değinip onun bu gelişmelerdeki rolünü irdeledik.
Fiscal expansions and debt sustainability problems during a pandemic
Authors:   NGO “Growford Institute”, BOHDAN Tetiana
Published: May 2022

Unprecedented epidemic and economic world-wide crises in 2020-2021 and large-scaled actions of state support for economies and humanitarian areas attracted attention to the problems of developments and effects of the active fiscal policy, as well as the methods of securing a long-term debt sustainability for public finances. The purpose of this article is revealing the common global and country-specific forms of expression of the fiscal and debt expansions in the course of pandemic and economic uncertainty, identification of their potential effects as well as defining paths for making public debt manageable over the long run. To achieve this purpose, the author reviews theoretical sources, research and advisory papers of the international organizations, elaborates on international databases of economic and financial indicators, applies a generalization method, historical and logical methods, methods of comparisons, analysis and synthesis. As a result, the author identifies the major achievements and problems of active implementation of the anti-crisis fiscal policy in the global context, analyses the dynamics of debt expansions in the different country groups and emphasizes the problem of accumulation of the debt-related risks. The common and distinguished features of the fiscal policy stance and debt position in Ukraine are revealed as compared to situations in other countries. The author suggests a set of debt burden indicators and calculates their values for Ukraine, that enables to establish a debt risk profile for Ukraine’s public finances. Taking into account the global problems of fiscal rules modifications, enhancing their role for debt sustainability, as well as particularities of the fiscal policy and debt position of Ukraine’s government, the author develops the proposals, aimed at strengthening the fiscal sustainability of Ukraine with simultaneous application of the anti-crisis potential of fiscal policy.
Methods and models of real estate mass appraisal
Authors:   SHEE “Kyiv National Economic University named after Vadym Hetman”, BONDAR Mykola , KULYK Andriy ,   SHEE “Kyiv National Economic University named after Vadym Hetman”
Published: May 2022

This article examines the approaches, methods and models of mass appraisal. The article also considers features of application of valuation approaches and methods when conducting mass appraisal taking into account the type of real estate, the impact of price-forming factors of demand and supply and etc. Based on the analysis of scientific works of foreign and domestic scientists, the classification of mass appraisal models is given, which includes parametric multiple regression models, spatial and nonparametric models, as well as more modern methods, in particular, artificial neural networks, genetic algorithms, rough set theory and etc. Hedonistic models as the most common type of parametric multiple regression have been studied. In particular, the mathematical interpretation of this model is given, the key pricing factors that are used as explanatory variables in the construction of the model are analyzed, as well as different types of hedonistic models, their advantages and disadvantages are considered. As complementation of the traditional hedonistic model, spatial models are investigated , while nonparametric models are studied as an alternative. In particular, foreign scientists’ works are analyzed, which consider the comparative analysis of the effectiveness of use of the above-mentioned models. The article also considers modern methods, in particular artificial neural networks, genetic algorithms, rough set theory and expert models, the use of which in the context of mass appraisal is the subject of discussion among scientists. Based on the results of the analysis, criteria are formulated which impact the choice of application of specific mass appraisal methods and models. Further research will be directed towards a more detailed study of the hedonistic model in order to develop the latter as a basic model of mass appraisal on the example of the residential real estate market of one of the districts in Kyiv.
Accounting in information sustainability of business processes of the enterprise
Authors:   National University of Life and Environmental Sciences of Ukraine, HUTSALENKO Liubov , MARCHUK Uliana ,   SHEE “Kyiv National Economic University named after Vadym Hetman”, CHABANYUK Olha ,   SHEE “Kyiv National Economic University named after Vadym Hetman”
Published: May 2022

The article focuses on the importance of information in the business management process. The changes in the economy of states and enterprises related to the COVID-19 pandemic and appropriate quarantine measures are indicated. The dynamics of changes in the financial results of large and medium enterprises of Ukraine is shown. The assessment of small business and its vulnerability to the impact external factors and unstable economic situations are carried out. The problem of unemployment growth in Ukraine in 2019-2020 and the impact of COVID-19 on employment are highlighted. It is proved that information support of sustainability of enterprise’s business processes is important in the context of obtaining information that is key to business decisions. The algorithm of interaction of external business environment (suppliers, buyers, competitors, agents of interaction) and internal business environment (goals, resource potential, infrastructure, key influences, risks and opportunities of economic entity) for objective assessment of enterprise and role of information in the strategy of its performance has been created. The special place and role of strategic accounting in the enterprise management system is highlighted. It is stated that the increase in problems and premature closure of small businesses are confirmed by the lack of adequate anticrisis management strategies. Ukraine's tasks in restoring public confidence (stability of macroeconomic environment, integration strengthening, strengthening of financial stability, creating a favorable environment for business, stopping further loss of investment potential, improving living standards and well-being) are pointed out. It is stated that the accounting system is designed, along with the formation of information for external users, to provide management with the necessary and timely information in order to make strategic decisions. The system of strategic accounting plays a special role in providing information to the effective operation of the enterprise and its structural units.
Был ли российский этнограф в Средней Азии колонизатором?
Authors: Абашин Сергей
Published: May 2022

В эссе я задаюсь следующим вопросом: почему российская этнография, в отличие от европейской или американской антропологии, совершенно не готова проблематизировать свои истоки и свой статус как колониального и постколониального знания? Рассматривая примеры В.П. Наливкина и Хорезмской экспедиции, я аргументирую, что неактуальность (пост)колониальной самокритики в российской этнографии оказывается результатом радикального деколонизационного жеста отстра-нения от «запада», в том числе его травм, и последующих попыток построить свой собственный самодостаточный и изолированный универсализирующий этнографический язык. В этой концепту-альной логике симпатия и сочувствие этнографов к «объектам» своего исследования не требовала осуждения своих колониальных корней и своей (пост)колониальной роли, и в какой-то момент стала даже цензурировать такой взгляд.

In the essay, I ask myself the following question: why is Russian ethnography, unlike European or American anthropology, completely unprepared to problematize its origins and its status as colonial and postcolonial knowledge? Considering the examples of V.P. Nalivkin and the Khorezm expedition, I argue that the irrelevance of (post) colonial self-criticism in Russian ethnography is the result of its radical de-colonizing detachment from the “West”, including its traumas, and subsequent attempts to build its own self-sufficient and isolationist universalizing ethnographic language. In this conceptual logic, ethnographers’ sympathy and empathy for the «objects» of their research did not require condemnation of their colonial roots and their (post)colonial role, and at some point even began to censor such a view.
Wave Effects of the Fractional Shallow Water Equation and the Fractional Optical Fiber Equation
Authors: Phoosree Sirasrete , Thadee Weerachai
Published: May 2022

The non-linear space-time fractional Estevez-Mansfield-Clarkson (EMC) equation and the non-linear space-time fractional Ablowitz-Kaup-Newell-Segur (AKNS) equation showed the motion of waves in the shallow water equation and the optical fiber equation, respectively. The process used to solve these equations is to transform the non-linear fractional partial differential equations (PDEs) into the non-linear ordinary differential equations by using the Jumarie's Riemann-Liouville derivative and setting the solution in the finite series combined with the simple equation (SE) method with the Bernoulli equation. The new traveling wave solutions were the exponential functions resulting in the physical wave effects are produced in the form of kink waves and represented by the two-dimensional graph, three-dimensional graph, and contour graph. In addition, the comparison of the solutions revealed that the new solutions have a more convenient and easier format.
Pan-Cancer Single-Cell Analysis Reveals the Core Factors and Pathway in Specific Cancer Stem Cells of Upper Gastrointestinal Cancer
Authors: Li Leijie , Zhang Yujia , Ren Yongyong , Cheng Zhiwei , Zhang Yuening , Wang Xinbo , Zhao Hongyu , Lu Hui
Published: May 2022

Upper gastrointestinal cancer (UGIC) is an aggressive carcinoma with increasing incidence and poor outcomes worldwide. Here, we collected 39,057 cells, and they were annotated into nine cell types. By clustering cancer stem cells (CSCs), we discovered the ubiquitous existence of sub-cluster CSCs in all UGICs, which is named upper gastrointestinal cancer stem cells (UGCSCs). The identification of UGCSC function is coincident with the carcinogen of UGICs. We compared the UGCSC expression profile with 215,291 single cells from six other cancers and discovered that UGCSCs are specific tumor stem cells in UGIC. Exploration of the expression network indicated that inflammatory genes (CXCL8, CXCL3, PIGR, and RNASE1) and Wnt pathway genes (GAST, REG1A, TFF3, and ZG16B) are upregulated in tumor stem cells of UGICs. These results suggest a new mechanism for carcinogenesis in UGIC: mucosa damage and repair caused by poor eating habits lead to chronic inflammation, and the persistent chronic inflammation triggers the Wnt pathway; ultimately, this process induces UGICs. These findings establish the core signal pathway that connects poor eating habits and UGIC. Our system provides deeper insights into UGIC carcinogens and a platform to promote gastrointestinal cancer diagnosis and therapy.
Space Flight-Promoted Insulin Resistance as a Possible Disruptor of Wound Healing
Authors: Strollo F. , Gentile S. , Pipicelli A. M. V. , Mambro A. , Monici M. , Magni P.
Published: May 2022

During space flight, especially when prolonged, exposure to microgravity results in a number of pathophysiological changes such as bone loss, muscle atrophy, cardiovascular and metabolic changes and impaired wound healing, among others. Interestingly, chronic low-grade inflammation and insulin resistance appear to be pivotal events linking many of them. Interestingly, real and experimental microgravity is also associated to altered wound repair, a process that is becoming increasingly important in view of prolonged space flights. The association of insulin resistance and wound healing impairment may be hypothesized from some dysmetabolic conditions, like the metabolic syndrome, type 2 diabetes mellitus and abdominal/visceral obesity, where derangement of glucose and lipid metabolism, greater low-grade inflammation, altered adipokine secretion and adipocyte dysfunction converge to produce systemic effects that also negatively involve wound healing. Indeed, wound healing impairment after traumatic events and surgery in space remains a relevant concern for space agencies. Further studies are required to clarify the molecular connection between insulin resistance and wound healing during space flight, addressing the ability of physical, endocrine/metabolic, and pharmacological countermeasures, as well as nutritional strategies to prevent long-term detrimental effects on tissue repair linked to insulin resistance. Based on these considerations, this paper discusses the pathophysiological links between microgravity-associated insulin resistance and impaired wound healing.
A Computational Pitting Corrosion Model of Magnesium Alloys
Authors: Chang Chia-Jung , Chang Chih-Han , Hung Tin-Kan
Published: May 2022

Controlling the corrosion rate of implants to maintain mechanical properties during tissue healing is significant in developing magnesium alloy implants. In addition to surface treatment and material properties, the study of geometric alteration and mechanical strength are also vital for implant development. In this study, we developed a three-dimensional model for semi-autonomous computational pitting corrosion. It is based on the Monte Carlo method, modeling magnesium alloy implants toward clinical application. The corrosion probability is based on the number of exposed surfaces to saline and the oxidation characteristics of the elements. The computational results are well compared with the experimental measurement using micro-computed tomography (micro-CT) in 500 h. Subsequently, the computational analysis is extended to 3,000 h of corrosion analysis. The 3D model appears promising to assist the development of biodegradable implants.
Recent Progress on Systems and Synthetic Biology of Diatoms for Improving Algal Productivity
Authors: Chen Jiwei , Huang Yifan , Shu Yuexuan , Hu Xiaoyue , Wu Di , Jiang Hangjin , Wang Kui , Liu Weihua , Fu Weiqi
Published: May 2022

Microalgae have drawn much attention for their potential applications as a sustainable source for developing bioactive compounds, functional foods, feeds, and biofuels. Diatoms, as one major group of microalgae with high yields and strong adaptability to the environment, have shown advantages in developing photosynthetic cell factories to produce value-added compounds, including heterologous bioactive products. However, the commercialization of diatoms has encountered several obstacles that limit the potential mass production, such as the limitation of algal productivity and low photosynthetic efficiency. In recent years, systems and synthetic biology have dramatically improved the efficiency of diatom cell factories. In this review, we discussed first the genome sequencing and genome-scale metabolic models (GEMs) of diatoms. Then, approaches to optimizing photosynthetic efficiency are introduced with a focus on the enhancement of biomass productivity in diatoms. We also reviewed genome engineering technologies, including CRISPR (clustered regularly interspaced short palindromic repeats) gene-editing to produce bioactive compounds in diatoms. Finally, we summarized the recent progress on the diatom cell factory for producing heterologous compounds through genome engineering to introduce foreign genes into host diatoms. This review also pinpointed the bottlenecks in algal engineering development and provided critical insights into the future direction of algal production.
Characterization of a Novel LUCAT1/miR-4316/VEGF-A Axis in Metastasis and Glycolysis of Lung Adenocarcinoma
Authors: Wang Lishui , Xie Yan , Wang Jing , Zhang Ying , Liu Shibiao , Zhan Yao , Zhao Yinghui , Li Juan , Li Peilong , Wang Chuanxin
Published: May 2022

Objective: Accumulating literatures suggested that long non-coding RNAs (lncRNAs) were involved in tumorigenesis and cancer progression in lung adenocarcinoma (LUAD). However, the precise regulatory mechanism of lncRNA Lung cancer-associated transcript 1 (LUCAT1) in LUAD is not well defined. In this study, we aimed to investigate the biological function and mechanism of lncRNA LUCAT1 in regulating tumor migration and glycolysis of LUAD.

Methods: High throughput sequencing was performed to identify differentially expressed lncRNAs between LUAD patients and healthy controls. The expression levels of LUCAT1 in LUAD clinical specimens or cell lines were evaluated by In situ hybridization (ISH) and quantitative Real-Time Polymerase Chain Reaction (qRT-PCR). Functional experiments, including wound-healing, transwell invasion assays, glucose absorption, lactate metabolism and tumor xenograft experiments were conducted to identify the biological functions of LUCAT1 in LUAD. Silencing of LUCAT1, over-expression of LUCAT1 and miR-4316 were generated in LUAD cell lines to verify the regulatory mode of LUCAT1-mir-4316-VEGFA axis.

Results: Our findings revealed that lncRNA LUCAT1 was significantly up-regulated in LUAD serum exosomes, tumor tissues, and LUAD cells in comparison with corresponding controls. Receiver operating characteristic curve (ROC) analysis indicated that the area under the curve (AUC) value of serum exosomal LUCAT1 reached 0.852 in distinguishing LUAD patients from healthy individuals. High expression of LUCAT1 in LUAD patient tissues was associated with enhanced Lymph Node Metastasis (LNM), advanced Tumor Node Metastasis (TNM) stage and poorer clinical outcome in LUAD patients. Knockdown of LUCAT1 inhibited LUAD cell metastasis and glycolysis in vitro as well as tumor metastasis in vivo, while overexpression of LUCAT1 induced a promoted LUAD metastasis and glycolysis. Furthermore, mechanistic investigations revealed that LUCAT1 elevated LUAD cell metastasis and glycolysis by sponging miR-4316, which further led to the upregulation of VEGFA. Finally, the regulatory axis LUCAT1-miR-4316-VEGFA was verified in LUAD.

Conclusion: Our present research suggested that LUCAT1 facilitate LUAD cell metastasis and glycolysis via serving as a competing endogenous RNA to regulate miR-4316/VEGFA axis, which provided a novel diagnostic marker and therapeutic target for LUAD patients.
Mycoplasmas as Host Pantropic and Specific Pathogens: Clinical Implications, Gene Transfer, Virulence Factors, and Future Perspectives
Authors: Dawood Ali , Algharib Samah Attia , Zhao Gang , Zhu Tingting , Qi Mingpu , Delai Kong , Hao Zhiyu , Marawan Marawan A. , Shirani Ihsanullah , Guo Aizhen
Published: May 2022

Mycoplasmas as economically important and pantropic pathogens can cause similar clinical diseases in different hosts by eluding host defense and establishing their niches despite their limited metabolic capacities. Besides, enormous undiscovered virulence has a fundamental role in the pathogenesis of pathogenic mycoplasmas. On the other hand, they are host-specific pathogens with some highly pathogenic members that can colonize a vast number of habitats. Reshuffling mycoplasmas genetic information and evolving rapidly is a way to avoid their host’s immune system. However, currently, only a few control measures exist against some mycoplasmosis which are far from satisfaction. This review aimed to provide an updated insight into the state of mycoplasmas as pathogens by summarizing and analyzing the comprehensive progress, current challenge, and future perspectives of mycoplasmas. It covers clinical implications of mycoplasmas in humans and domestic and wild animals, virulence-related factors, the process of gene transfer and its crucial prospects, the current application and future perspectives of nanotechnology for diagnosing and curing mycoplasmosis, Mycoplasma vaccination, and protective immunity. Several questions remain unanswered and are recommended to pay close attention to. The findings would be helpful to develop new strategies for basic and applied research on mycoplasmas and facilitate the control of mycoplasmosis for humans and various species of animals.
Reservoir Parameter Prediction Based on the Neural Random Forest Model
Authors: Wang Mingchuan , Feng Dongjun , Li Donghui , Wang Jiwei
Published: May 2022

Porosity and saturation are the basis for describing reservoir properties and formation characteristics. The traditional, empirical, and formulaic methods are unable to accurately capture the nonlinear mapping relationship between log data and reservoir physical parameters. To solve this problem, in this study, a novel hybrid model (NRF) combining neural network (NN) and random forest (RF) was proposed based on well logging data to predict the porosity and saturation of shale gas reservoirs. The database includes six horizontal wells, and the input logs include borehole diameter, neutron, density, gamma-ray, and acoustic and deep investigate double lateral resistivity log. The porosity and saturation were chosen as outputs. The NRF model with independent and joint training was designed to extract key features from well log data and physical parameters. It provides a promising method for forecasting the porosity and saturation with R2above 0.94 and 0.82 separately. Compared with baseline models (NN and RF), the NRF model with joint training obtains the unsurpassed performance to predict porosity with R2above 0.95, which is 1.1% higher than that of the NRF model with independent training, 3.9% higher than RF, and superiorly greater than NN. For the prediction of saturation, the NRF model with joint training is still superior to other algorithms, with R2above 0.84, which is 2.1% higher than that of the NRF model with independent training and 7.0% higher than RF. Furthermore, the NRF model has a similar data distribution with measured porosity and saturation, which demonstrates the NRF model can achieve greater stability. It was proven that the proposed NRF model can capture the complex relationship between the logging data and physical parameters more accurately, and can serve as an economical and reliable alternative tool to give a reliable prediction.
Co-creation of Research and Design During a Coding Club With Autistic Students Using Multimodal Participatory Methods and Analysis
Authors: Ward Verity , Parsons Sarah , Kovshoff Hanna , Crump Ben
Published: May 2022

Participatory design aims to work with those who are often excluded from design processes so that their interests are better represented in design solutions. Autistic children are often marginalised and excluded from design processes due to concerns about how their social and communication differences may act as barriers to participation, leading to calls for design processes to be more inclusive and examined more closely to understand the value of participation for (autistic) children and young people. This research describes a participatory design project to develop a computer game during a weekly coding club at a special school. Fourteen autistic (neurodivergent) young people, eight staff members, four technology industry representatives and a Doctoral researcher worked together to design, develop, test, and evaluate the game. This article focuses specifically on the views and experiences of two of the students, which are captured primarily through a Digital Story. Digital Stories are short student-centred videos which show educational experiences. We use a social semiotic multimodal approach to analysis which does not prioritise linguistically encoded meaning, instead recognising the importance and validity of the many and varied ways in which students contributed to the project. The findings highlight the valuable opportunities that participatory design processes can provide for students as both learners and as expert knowers. It emphasises the need to allow room for students’ agency in the design process, so that they really canhave a sayin the outcomes of design and feel ownership over the process and outcomes of their research participation.
Day-Ahead Economic Dispatch Strategy for Distribution Network Considering Total Cost Price-Based Demand Response
Authors: Xu Lin , Wei Wei , Cai Xiaoting , Liu Chang , Jiang Xiaofeng , Yang Jianwei
Published: May 2022

The guidance of EV via a price-based demand response is of great significance to the security and economy of the distribution network. However, the current price-based demand response mechanisms fail to consider the spatial-temporal distribution of large-scale EVs connected to the distribution network. For tackling this challenge, this paper proposes a day-ahead economic dispatch strategy for distribution networks considering total cost price-based demand response. A two-layer model of the day-ahead economic dispatch for the distribution network is utilized to obtain the interactive calculation framework for the total cost price. The total cost price iterates between the economic dispatch model of the distribution network and the total cost price-based demand response model until no significant changes in total cost price are observed. Among them, the price-responsive load considers spatial-temporal shift of the EV charging load. Finally, simulation study case based on a modified IEEE 33-bus system is employed to demonstrate the effectiveness of this strategy for the economic operation of the distribution network.
Energy Management Without Iteration—A Regional Dispatch Event-Triggered Algorithm for Energy Internet
Authors: Tan Jiaming
Published: May 2022

Centralized algorithms and distributed algorithms have gained great attention on the energy Internet nowadays. The centralized algorithm presses too much communication and numeration load to its control center in large-scale and neterogeny EI. The distributed algorithm requests too many times of iteration, and the performance and convergence speed is quite slow. The current literature presents a regional dispatch event-triggered algorithm (RDETA). Energy management in RDETA can transform between a centralized model and distributed model. With the effort, the energy management does notrequire iteration times in quantity. And due to event-triggered asynchronous communication, energy management not only relieson a global synchronous clock but also decreasecommunication frequency in most cases and increasecommunication frequency in exigency. In addition, RDETA adopts regional communication and regional energy dispatch, which can automatically modulate the scale of dispatch area by the degree of the energy problem. Finally, simulation results and theoretical demonstration show the aforementioned contributions of the proposed algorithm.
Do Oil Price Shocks Matter for Environmental Degradation? Evidence of the Environmental Kuznets Curve in GCC Countries
Authors: Ebaid Ali , Lean Hooi Hooi , Al-Mulali Usama
Published: May 2022

This paper aims to examine the asymmetric impact of oil price shocks on environmental degradation for a panel of six Gulf Cooperation Council (GCC) countries from 1996 to 2016. We use the dynamic seemingly unrelated regressions (DSUR) approach that considers cross-sectional dependency to reveal the interrelations between oil price shocks and carbon dioxide (CO2) emissions. The finding shows that the positive shocks of oil prices have a statistically significant negative effect on CO2 emissions, while negative shocks of oil prices did not affect CO2 emissions. More specifically, the positive oil price shocks have negatively influenced the CO2 emissions in Oman, Bahrain, Saudi Arabia, Qatar, and United Emirates Arab. In turn, the most negative effect is found in Qatar and Saudi Arabia. Meanwhile, the negative shocks of oil prices have statistically significant effects on the CO2 emission of Oman and Saudi Arabia. While for other countries, it does not have a significant impact. Also, the results support an environmental Kuznets curve in Kuwait, Oman, Qatar, Saudi Arabia, and the United Arab Emirates; in contrast, the hypothesis was rejected in Bahrain and Oman. This study could help policymakers adopt renewable energy policies and use energy-saving technologies to sustain economic development and improve environmental quality.
The Role of Secondary Metabolites and Bark Chemistry in Shaping Diversity and Abundance of Epiphytic Lichens
Authors: Paukov Alexander , Teptina Anzhelika , Ermoshin Alexander , Kruglova Ekaterina , Shabardina Lada
Published: May 2022

Diversity of secondary lichen metabolites was studied in epiphytic lichens on six phorophytes—spruce, pine, birch, alder, aspen and poplar in the Middle Urals of Russia. Atranorin, usnic, fumarprotocetraric acid, zeorin, and gyrophoric acid were found in 31, 24, 23, 18, and 14 species, respectively, of 237 taxa collected. Seventy-seven species (i.e., 32% of total species documented) contained no secondary metabolites. Spectra of secondary metabolites of fruticose and foliose lichens varied on different phorophytes, while in crustose species the strong dependence on the tree species was not detected. This is different to the pH dependence of saxicolous lichens where crustose lichens were more susceptible to the rock chemistry. The results of Canonical Correspondence Analysis reveal the affinity of species containing depsides, depsidones or usnic acid to acidic substrata and those lacking secondary metabolites or containing terpenes and antraquinones to the pH-neutral bark. We suppose that phenolic compounds and flavonoids, as chemical constituents of bark, may interact with lichen symbioses and elements in phellem, and similarly to the lichen acids shape the affinity of species to the substrata.
Tyrosine Phosphorylation Profiling Revealed the Signaling Network Characteristics of CAMKK2 in Gastric Adenocarcinoma
Authors: Najar Mohd. Altaf , Arefian Mohammad , Sidransky David , Gowda Harsha , Prasad T. S. Keshava , Modi Prashant Kumar , Chatterjee Aditi
Published: May 2022

Calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2) is a serine/threonine protein kinase which functions via the calcium-triggered signaling cascade with CAMK1, CAMK4, and AMPKα as the immediate downstream substrates. CAMKK2 is reported to be overexpressed in gastric cancer; however, its signaling mechanism is poorly understood. We carried out label-free quantitative tyrosine phosphoproteomics to investigate tyrosine-mediated molecular signaling associated with CAMKK2 in gastric cancer cells. Using a high-resolution Orbitrap Fusion Tribrid Fourier-transform mass spectrometer, we identified 350 phosphotyrosine sites mapping to 157 proteins. We observed significant alterations in 81 phosphopeptides corresponding to 63 proteins upon inhibition of CAMKK2, among which 16 peptides were hyperphosphorylated corresponding to 13 proteins and 65 peptides were hypophosphorylated corresponding to 51 proteins. We report here that the inhibition of CAMKK2 leads to changes in the phosphorylation of several tyrosine kinases such as PKP2, PTK2, EPHA1, EPHA2, PRKCD, MAPK12, among others. Pathway analyses revealed that proteins are differentially phosphorylated in response to CAMKK2 inhibition involved in focal adhesions, actin cytoskeleton, axon guidance, and signaling by VEGF. The western blot analysis upon inhibition and/or silencing of CAMKK2 revealed a decrease in phosphorylation of PTK2 at Y925, c-JUN at S73, and STAT3 at Y705, which was in concordance with the mass spectrometry data. The study indicates that inhibition of CAMKK2 has an anti-oncogenic effect in gastric cells regulating phosphorylation of STAT3 through PTK2/c-JUN in gastric cancer.
A Novel Homozygous Missense Mutation of PIEZO1 Leading to Lymphatic Malformation-6 Identified in a Family With Three Adverse Pregnancy Outcomes due to Nonimmune Fetal Hydrops
Authors: Han Shuai , Guo Xin , Wang Xiaogang , Lin Huijun , Yu Yiqi , Shu Jing , Dong Minyue , Yang Liwei
Published: May 2022

Lymphatic malformation-6 (LMPHM6) is a rarer form of nonimmune hydrops that often manifests as widespread lymphedema involving all segments of the body, namely, subcutaneous edema, intestinal/pulmonary lymphangiectasia, chylothoraces, and pleural/pericardial effusions. Here, we detected one rare and previously unobserved homozygous missense variant in PIEZO1 (c.5162C>G, p.Ser1721Trp) as a novel genetic cause of autosomal recessive LMPHM6, in a family with three adverse pregnancy outcomes due to nonimmune fetal hydrops. Although, the loss-of-function mutations such as those usually including nonsense, frameshift, splice site, and also fewer missense variants in PIEZO1 have been proved to lead to LMPHM6, among these, the biallelic homozygous mutations resulting in the loss of function of PIEZO1 have not been reported before. Here, we first strongly implicated impaired PIEZO1 function–associated LMPHM6 with a homozygous missense mutation in PIEZO1.
Placental Gene Transcript Proportions are Altered in the Presence of In Utero Arsenic and Cadmium Exposures, Genetic Variants, and Birth Weight Differences
Authors: Deyssenroth Maya A. , Peng Shouneng , Hao Ke , Marsit Carmen J. , Chen Jia
Published: May 2022

Background:In utero arsenic and cadmium exposures are linked with reduced birth weight as well as alterations in placental molecular features. However, studies thus far have focused on summarizing transcriptional activity at the gene level and do not capture transcript specification, an important resource during fetal development to enable adaptive responses to the rapidly changing in utero physiological conditions. In this study, we conducted a genome-wide analysis of the placental transcriptome to evaluate the role of differential transcript usage (DTU) as a potential marker of in utero arsenic and cadmium exposure and fetal growth restriction.

Methods: Transcriptome-wide RNA sequencing was performed in placenta samples from the Rhode Island Child Health Study (RICHS, n = 199). Arsenic and cadmium levels were measured in maternal toenails using ICP-MS. Differential transcript usage (DTU) contrasting small (SGA) and appropriate (AGA) for gestational age infants as well as above vs. below median exposure to arsenic and cadmium were assessed using the DRIMSeq R package. Genetic variants that influence transcript usage were determined using the sQTLseeker R package.

Results: We identified 82 genes demonstrating DTU in association with SGA status at an FDR <0.05. Among these, one gene, ORMDL1, also demonstrated DTU in association with arsenic exposure, and fifteen genes (CSNK1E, GBA, LAMTOR4, MORF4L1, PIGO, PSG1, PSG3, PTMA, RBMS1, SLC38A2, SMAD4, SPCS2, TUBA1B, UBE2A, YIPF5) demonstrated DTU in association with cadmium exposure. In addition to cadmium exposure and SGA status, proportions of the LAMTOR4 transcript ENST00000474141.5 also differed by genetic variants (rs10231604, rs12878, and rs3736591), suggesting a pathway by which an in utero exposure and genetic variants converge to impact fetal growth through perturbations of placental processes.

Discussion: We report the first genome-wide characterization of placental transcript usage and associations with intrauterine metal exposure and fetal growth restriction. These results highlight the utility of interrogating the transcriptome at finer-scale transcript-level resolution to identify novel placental biomarkers of exposure-induced outcomes.
Enhancing Long-Read-Based Strain-Aware Metagenome Assembly
Authors: Luo Xiao , Kang Xiongbin , Schönhuth Alexander
Published: May 2022

Microbial communities are usually highly diverse and often involve multiple strains from the participating species due to the rapid evolution of microorganisms. In such a complex microecosystem, different strains may show different biological functions. While reconstruction of individual genomes at the strain level is vital for accurately deciphering the composition of microbial communities, the problem has largely remained unresolved so far. Next-generation sequencing has been routinely used in metagenome assembly but there have been struggles to generate strain-specific genome sequences due to the short-read length. This explains why long-read sequencing technologies have recently provided unprecedented opportunities to carry out haplotype- or strain-resolved genome assembly. Here, we propose MetaBooster and MetaBooster-HiFi, as two pipelines for strain-aware metagenome assembly from PacBio CLR and Oxford Nanopore long-read sequencing data. Benchmarking experiments on both simulated and real sequencing data demonstrate that either the MetaBooster or the MetaBooster-HiFi pipeline drastically outperforms the state-of-the-art de novo metagenome assemblers, in terms of all relevant metagenome assembly criteria, involving genome fraction, contig length, and error rates.
Structural Features of the Nucleosomal DNA Modulate the Functional Binding of a Transcription Factor and Productive Transcription
Authors: Vinayachandran Vinesh , Bhargava Purnima
Published: May 2022

A small non-histone protein of budding yeast, Nhp6 has been reported to specifically influence the transcription of a yeast gene, SNR6. The gene is essential, transcribed by the enzyme RNA polymerase III, and codes for the U6snRNA required for mRNA splicing. A translationally positioned nucleosome on the gene body enables the assembly factor TFIIIC binding by juxtaposing its otherwise widely separated binding sites, boxes A and B. We found histone depletion results in the loss of U6 snRNA production. Changing the rotational phase of the boxes and the linear distance between them with deletions in 5 bp steps displayed a helical periodicity in transcription, which gradually reduced with incremental deletions up to 40 bp but increased on further deletions enclosing the pseudoA boxes. Nhp6 influences the transcription in a dose-dependent manner, which is modulated by its previously reported co-operator, an upstream stretch of seven T residues centered between the TATA box and transcription start site. Nhp6 occupancy on the gene in vivo goes up at least 2-fold under the repression conditions. Nhp6 absence, T7 disruption, or shorter A–B box distance all cause the downstream initiation of transcription. The right +1 site is selected with the correct placement of TFIIIC before the transcription initiation factor TFIIIB. Thus, the T7 sequence and Nhp6 help the assembly and placement of the transcription complex at the right position. Apart from the chromatin remodelers, the relative rotational orientation of the promoter elements in nucleosomal DNA, and Nhp6 regulate the transcription of the SNR6 gene with precision.
Population Structure of Curraleiro Pé-Duro Cattle and its Relationship With the Serological Profile Against Pathogens of Economic and Zoonotic Interest
Authors: Freitas Thais Miranda Silva , Dias Juliana Moraes , Veríssimo Ana Carolina Ferreira , Lobo Joyce Rodrigues , Costa Gustavo Lage , Moura Maria Ivete de , Landi Vincenzo , Martínez Amparo Martínez , Carmo Adriana Santana do , Fioravanti Maria Clorinda Soares
Published: May 2022

Curraleiro Pé-Duro (CPD) cattle, a Brazilian local breed, are animals that are highly resistant to infectious and parasitic diseases. Strategies for the conservation of the breed and the genetic resistance to diseases should also consider the characteristics of the breed. The objective of this study was to analyze the diversity and population structure of the CPD breed using microsatellite markers and to correlate the serological profiles for causative agents of brucellosis, leptospirosis, neosporosis, leukosis, infectious bovine rhinotracheitis, and bovine viral diarrhea. DNA samples of 608 bovines were amplified and genotyped using 28 microsatellite markers for breed characterization. The genotypes were assigned to three clusters, indicating a substructure population related to the geographic distance. The observed heterozygosity was lower than that expected in most loci, and fixation index (Fst) in the subpopulation values ranged from 0.03073 (ETH3) to 0.402 (INRA63) on cluster 1, from 0.00 (INRA32) to 0.39359 (INRA63) on cluster 2, and from 0.00 (INRA32) to 0.28483 (TGLA53) on cluster 3. TheBrucella spp.,Neospora caninum, and Bovine Leukemia Virus frequencies were significantly different (p< 0.05) between clusters. The differences between the occurrences of diseases were not sufficient to indicate a genetic subpopulation with increased resistance to infections.
Comparative Transcriptome Analyses Characterize Expression Signatures Among Males, Females, Neo-Males, and Gynogenetic Females in the Yellow Drum (Nibea albiflora)
Authors: Zhu Qihui , Qin Zeqian , Chen Ruiyi , Wang Ligai , Tan Peng , Xu Dongdong
Published: May 2022

The yellow drum (Nibea albiflora) is one of the most important marine economic fish in China, and its sexually dimorphic growth makes it preferable for mono-sex culture. Although gynogenesis and neo-male induction techniques have been established, the molecular pathways and regulatory mechanisms of sex determination and maintenance in gynogenetic females and neo-males remains far from fully understood. In this study, the gene expression profiles were investigated in the gonads and brains of wild-type male, wild-type female, neo-male, and gynogenetic female yellow drum using comparative transcriptome analyses. Generally, a total of 52,999 novel transcripts were obtained in RNA-seq, of which 45,651 were isoforms of known protein-coding genes, 1,358 novel protein-coding genes, and 5,990 long non-coding RNAs. We found that the differences between wild-type males and neo-males and between wild-type females and gynogenetic females were relatively small at both the histological and transcriptomic levels, indicating that artificial gynogenesis or hormonal sex reversal may have minimal effects on normal female or male life function, respectively. In the brain, pathways such as “Oocyte meiosis”, “Cell cycle”, and “Riboflavin metabolism” were found to be significantly enriched. In the gonads, pathways such as “Prolactin signaling pathway”, “PPAR signaling pathway”, “Cholesterol metabolism”, and “Jak-STAT signaling pathway” were found to play important roles in maintaining the regular proliferation and differentiation of females and males in yellow drum. In particular, we found that zp4 might be an effective molecular marker to differentiate between gynogenetic and normal females owing to its unique expression pattern. The results of this study may help to elucidate the molecular mechanisms involved in sex maintenance in the gonads and brain and provide basic data for genetic breeding of the yellow drum.
Identification of Novel Imatinib-Resistant Genes in Gastrointestinal Stromal Tumors
Authors: Cao Lei , Zheng Kunming , Liu Yanhong , Song Peng , Wang Chuntao , Wang Hongzhi , Wang Nan , Zhang Shiwu , Zhao Yongjie
Published: May 2022

Gastrointestinal stromal tumors (GISTs) are common ICC precursor sarcomas, which are considered to be a potential malignant mesenchymal tumor driven by specific KIT or PDGFRA signals in the gastrointestinal tract. The standard treatment for GIST without metastasis is surgical resection. GIST with metastasis is usually treated with tyrosine kinase inhibitors (TKIs) only but cannot be cured. The TKI imatinib is the main drug of GIST drug therapy. In adjuvant therapy, the duration of imatinib adjuvant therapy is 3 years. It has been proved that imatinib can improve the overall survival time (OS). However, many GIST patients develop drug resistance due to the long-term use of imatinib. We were forced to look for new strategies to treat GIST. The purpose of the current academic work is to study the drug-resistant genes of imatinib and their potential mechanisms. A total of 897 differentially expressed genes (DEGs) were found between imatinib-sensitive cell line GIST882 and imatinib-resistant cell line GIST430 by RNA sequencing (RNA-seq). After analyzing the DEGs, 10 top genes were selected (NDN, FABP4, COL4A1, COLEC11, MEG3, EPHA3, EDN3, LMO3, RGS4, and CRISP2). These genes were analyzed by RT-PCR, and it was confirmed that the expression trend of FABP4, COL4A1, and RGS4 in different imatinib-resistant cell lines was in accord with the GEO database. It is suggested that these genes may play a potential role in the clinical diagnosis and treatment of imatinib resistance in GIST.
Amino Acid Metabolism-Related lncRNA Signature Predicts the Prognosis of Breast Cancer
Authors: Dai Yin-wei , Wen Zhi-kai , Wu Zhi-xuan , Wu Hao-dong , Lv Lin-xi , Yan Cong-zhi , Liu Cong-hui , Wang Zi-qiong , Zheng Chen
Published: May 2022

Background and Purpose: Breast cancer (BRCA) is the most frequent female malignancy and is potentially life threatening. The amino acid metabolism (AAM) has been shown to be strongly associated with the development and progression of human malignancies. In turn, long noncoding RNAs (lncRNAs) exert an important influence on the regulation of metabolism. Therefore, we attempted to build an AAM-related lncRNA prognostic model for BRCA and illustrate its immune characteristics and molecular mechanism.

Experimental Design: The RNA-seq data for BRCA from the TCGA-BRCA datasets were stochastically split into training and validation cohorts at a 3:1 ratio, to construct and validate the model, respectively. The amino acid metabolism-related genes were obtained from the Molecular Signature Database. A univariate Cox analysis, least absolute shrinkage and selection operator (LASSO) regression, and a multivariate Cox analysis were applied to create a predictive risk signature. Subsequently, the immune and molecular characteristics and the benefits of chemotherapeutic drugs in the high-risk and low-risk subgroups were examined.

Results: The prognostic model was developed based on the lncRNA group including LIPE-AS1, AC124067.4, LINC01655, AP005131.3, AC015802.3, USP30-AS1, SNHG26, and AL589765.4. Low-risk patients had a more favorable overall survival than did high-risk patients, in accordance with the results obtained for the validation cohort and the complete TCGA cohort. The elaborate results illustrated that a low-risk index was correlated with DNA-repair–associated pathways; a low TP53 and PIK3CA mutation rate; high infiltration of CD4+ T cells, CD8+ T cells, and M1 macrophages; active immunity; and less-aggressive phenotypes. In contrast, a high-risk index was correlated with cancer and metastasis-related pathways; a high PIK3CA and TP53 mutation rate; high infiltration of M0 macrophages, fibroblasts, and M2 macrophages; inhibition of the immune response; and more invasive phenotypes.

Conclusion: In conclusion, we attempted to shed light on the importance of AAM-associated lncRNAs in BRCA. The prognostic model built here might be acknowledged as an indispensable reference for predicting the outcome of patients with BRCA and help identify immune and molecular characteristics.