bluuebunny/crossref_metadata_2025 huggingface dataset:
A Study on Sputtering of Copper Seed Layer for Interconnect Metallization via Molecular Dynamics Simulation
Authors: Ho Cheng-Hsuan , Chen Cha’o-Kuang , Chen Chieh-Li
Published: October 2021

Interconnects are significant elements in integrated circuits (ICs), as they connect individual components of the circuit into a functioning whole. To form a void-free interconnect, a thin and uniform copper seed layer must be deposited as a basis for electroplating. In this paper, process parameters of sputtering including incident energy, incident angle, substrate temperature, and deposition rate were studied to form a uniform copper seed layer. Different liner/barrier materials and properties including crystal planes were also studied to enhance the quality of the copper seed layer. The study was carried out by molecular dynamics simulation. It revealed that increasing the incident energy and substrate temperature during the sputtering process increases their diffusivity but results in poorer uniformity and larger alloy percentage. By decreasing the deposition rate, the Ostwald ripening effect becomes dominant and increases the uniformity. An adequate incident angle could increase necking and uniformity. Among the sputtering process parameters and material properties discussed in this study, surface diffusion barrier energy of different crystal planes is the most decisive factor, which leads to good uniformity.
On the Omnipresence and Potential of Plasma Technology
Authors: Gerhard Christoph
Published: October 2021

Even though plasma is the most common state of aggregation in the known universe, its complex chemistry and physics, as well as its specifics and particular characteristics, are not yet fully understood [...]
Ontology-Based Regression Testing: A Systematic Literature Review
Authors: Hasnain Muhammad , Ghani Imran , Pasha Muhammad Fermi , Jeong Seung-Ryul
Published: October 2021

Web systems evolve by adding new functionalities or modifying them to meet users’ requirements. Web systems require retesting to ensure that existing functionalities are according to users’ expectations. Retesting a web system is challenging due to high cost and time consumption. Existing ‘systematic literature review’ (SLR) studies do not comprehensively present the ontology-based regression testing approaches. Therefore, this study focuses on ontology-based regression testing approaches because ontologies have been a growing research solution in regression testing. Following this, a systematic search of studies was performed using the “Preferred Reporting Items for Systematic Reviews and Meta-Analyses” (PRISMA) guidelines. A total of 24 peer-reviewed studies covering ontologies (semantic and inference rules) and regression testing, published between 2007 and 2019, were selected. The results showed that mainly ontology-based regression testing approaches were published in 2011–2012 and 2019 because ontology got momentum in research in other fields of study during these years. Furthermore, seven challenges to ontology-driven regression testing approaches are reported in the selected studies. Cost and validation are the main challenges examined in the research studies. The scalability of regression testing approaches has been identified as a common problem for ontology-based and other benchmark regression testing approaches. This SLR presents that the safety of critical systems is a possible future research direction to prevent human life risks.
Optimal Reserve and Energy Scheduling for a Virtual Power Plant Considering Reserve Activation Probability
Authors: Nguyen Duc Huy , Nguyen Hong Nhung
Published: October 2021

With the increasing share of variable and limitedly predictable renewable energy in power systems worldwide, ensuring reserve capacity to maintain the balance of supply and demand becomes more important. On the other hand, the development of the virtual power plant model (VPP) allows renewable sources and energy storage to participate in reserve service. This paper addresses the optimal reserve bidding strategy problem of a VPP comprising of renewable energy resources (RESs), energy storage systems (ESSs), and several customers. The VPP participates in balance capacity (BC), day-ahead (DA), and intra-day (ID) markets. The scheduling problem is formulated as a two-stage chance-constrained optimization model taking the uncertainty of RESs production, load consumption, and probability of reserve activation into account. The response of VPP after its reserve capacity is called and generated is also considered to increase the operational flexibility of VPP. The proposed model is implemented on a test VPP system, and the effects of RESs sizing, ESSs sizing, and the probability of reserve activation are analyzed. Results indicate that the proposed model can perform well under real-world conditions.
Theoretical Study of the Acoustic Installation Effects in Closed-Vein Wind Tunnels for the Experimental Characterization of Trailing Edge Noise
Authors: Redonnet Stéphane
Published: October 2021

This study focuses on the acoustic installation effects that may occur during typical aeroacoustic experiments when the latter are conducted in a closed-vein wind tunnel. More precisely, in regard to the specific problem of airfoil trailing edge noise, an analytical model is derived, which allows predicting the wall-induced reverberation effects that such a noise shall be subjected to, when radiating within a closed-vein, hard-wall, wind tunnel. These effects are then assessed through a parametric investigation so as to characterize their impact on in situ acoustic measurements that would be performed using flush-mounted microphones located on the vein’s walls. From a phenomenological perspective, the study highlights how important the reverberation effects by the vein can be. In particular, results reveal how their impact on the noise measurements may greatly vary, depending on the trailing edge noise source location (i.e., the airfoil incidence) and, to a lesser extent, its frequency. The outcomes allow identifying these locations where the installation effects are least, i.e., where to better position a flush-mounted microphone, should in situ noise measurements be conducted. From a methodological viewpoint, the study showcases how the proposed formalism could constitute a simple albeit useful diagnosis tool for mitigating the experimental biases weighing on airfoil trailing edge noise tests to be conducted within closed-vein facilities, whether this would be done a priori by flush-mounting the microphone(s) where these biases are minimal or a posteriori by de-biasing the noise measurements accordingly.
Kinetic Study on Acrylic Acid Polymerisations in Isopropanol
Authors: Betz Kai C. , Westhues Anna , Pauer Werner
Published: October 2021

The radical polymerisation of acrylic acid is largely concentration dependent and affected by the type of the surrounding solvent. This work investigates reaction rate constants, the activation energy, heat flux and the molecular weight in the industrially relevant synthesis of low molecular mass acrylic acid polymers in 2-propanol. The polymerisations were carried out isothermally in an RC1e calorimeter with inline Raman spectroscopy for monomer concentration monitoring. For a non-neutralised acrylic acid in isopropanol (150 g/L), a monomer reaction order of 1.73 ± 0.15, an activation energy of 58.6 ± 0.8 kJ/mol (0.5 mol% AIBN) and 88.5 ± 1.5 kJ/mol (1.0 mol% AIBN), and a reaction enthalpy of 66.4 ± 4.8 kJ/mol could be shown. This data is in accordance with the literature values for acrylic acid polymerisation in water. In addition, linear correlations between the respective reaction parameters and the molecular weight for customised polymer synthesis in the range from 1.2 to 1.7 × 104 g/mol could be established. In comparison with aqueous acrylic acid polymerisation, it was found that the reaction rate constants in isopropanol were slower by a factor of approximately 10 under similar reaction conditions.
Emerging and Persistent Pollutants in the Aquatic Ecosystems of the Lower Danube Basin and North West Black Sea Region—A Review
Authors: Chiţescu Carmen Lidia , Ene Antoaneta , Geana Elisabeta-Irina , Vasile Aida Mihaela , Ciucure Corina Teodora
Published: October 2021

The tremendous impact of natural and anthropogenic organic and inorganic substances continuously released into the environment requires a better understanding of the chemical status of aquatic ecosystems. Water contamination monitoring studies were performed for different classes of substances in different regions of the world. Reliable analytical methods and exposure assessment are the basis of a better management of water resources. Our research comprised publications from 2010 regarding the Lower Danube and North West Black Sea region, considering regulated and unregulated persistent and emerging pollutants. The frequently reported ones were: pharmaceuticals (carbamazepine, diclofenac, sulfamethoxazole, and trimethoprim), pesticides (atrazine, carbendazim, and metolachlor), endocrine disruptors—bisphenol A and estrone, polycyclic aromatic hydrocarbons, organochlorinated pesticides, and heavy metals (Cd, Zn, Pb, Hg, Cu, Cr). Seasonal variations were reported for both organic and inorganic contaminants. Microbial pollution was also a subject of the present review.
New Sintered Porous Scaffolds of Mg,Sr Co-Substituted Hydroxyapatite Support Growth and Differentiation of Primary Human Osteoblasts In Vitro
Authors: Galli Carlo , Landi Elena , Belletti Silvana , Colangelo Maria Teresa , Guizzardi Stefano
Published: October 2021

Strontium (Sr) and Magnesium (Mg) are bioactive ions that have been proven to exert a beneficial effect on bone; therefore, their incorporation into bone substitutes has long been viewed as a possible approach to improve tissue integration. However, the thermal instability of Mg-substituted hydroxyapatites has hitherto limited development. We previously described the creation of thermally consolidated porous constructs of Mg,Sr co-substituted apatites with adequate mechanical properties for their clinical use. The present paper describes the biocompatibility of Mg,Sr co-substituted granules using an alveolar-bone-derived primary model of human osteoblasts. Cells were cultured in the presence of different amounts of hydroxyapatite (HA), Sr-substituted HA, or MgSrHA porous macrogranules (with a size of 400–600 microns, obtained by grinding and sieving the sintered scaffolds) for three and seven days, and their viability was measured by a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Protein content was measured using the Lowry assay at the same time points. Cell viability was not impaired by any of the tested compounds. Indirect and direct biocompatibility of these macrogranules was assessed by culturing cells in a previously conditioned medium with HA, SrHA, or MgSrHA, or in the presence of material granules. Osteoblasts formed larger and more numerous nodules around SrHA or MgSrHA granules. Furthermore, cell differentiation was evaluated by alkaline phosphatase staining of primary cells cultured in the presence of HA, SrHA, or MgSrHA granules, confirming the increased osteoconductivity of the doped materials.
A Mathematical Model for COVID-19 with Variable Transmissibility and Hospitalizations: A Case Study in Paraguay
Authors: Shin Hyun Ho , Sauer Ayala Carlos , Pérez-Estigarribia Pastor , Grillo Sebastián , Segovia-Cabrera Leticia , García-Torres Miguel , Gaona Carlos , Irala Sandra , Pedrozo María Esther , Sequera Guillermo , Vázquez Noguera José Luis , De Los Santos Eduardo
Published: October 2021

Forecasting the dynamics of the number of cases with coronavirus disease 2019 (COVID-19) in a given population is a challenging task due to behavioural changes which occur over short periods. Planning of hospital resources and containment measures in the near term require a scenario analysis and the use of predictive models to gain insight into possible outcomes for each scenario. In this paper, we present the SEIR-H epidemiological model for the spread dynamics in a given population and the impact of COVID-19 in the local health system. It was developed as an extension of the classic SEIR model to account for required hospital resources and behavioural changes of the population in response to containment measures. Time-varying parameters such as transmissibility are estimated using Bayesian methods, based on the database of reported cases with a moving time-window strategy. The assessment of the model offers reasonable results with estimated parameters and simulations, reflecting the observed dynamics in Paraguay. The proposed model can be used to simulate future scenarios and possible effects of containment strategies, to guide the public institution response based on the available resources in the local health system.
AEMB: An Automated Exploit Mitigation Bypassing Solution
Authors: Wang Ruipeng , Pan Zulie , Shi Fan , Zhang Min
Published: October 2021

Modern operating systems set exploit mitigations to thwart the exploit, which has also become a barrier to automated exploit generation (AEG). Many current AEG solutions do not fully account for exploit mitigations, and as a result, they are unable to accurately assess the exploitability of vulnerabilities in such settings.This paper proposes AEMB, an automated solution for bypassing exploit mitigations and generating useable exploits (EXPs). Initially, AEMB identifies exploit mitigations in the system based on characteristics of the program execution environment. Then, AEMB implements exploit mitigations bypassing the payload generation by modeling expert experience and constructs the corresponding constraints. Next, during the program’s execution, AEMB uses symbol execution to collect symbol information and create exploit constraints. Finally, AEMB utilizes a solver to solve the constraints, including payload constraints and exploit constraints, to generate the EXP. In this paper, we evaluated a prototype of AEMB on six test programs and seven real-world applications. Furthermore, we conducted 54 sets of experiments on six different combinations of exploit mitigations. Experiment results indicate that AEMB can automatically overcome exploit mitigations and produce successful exploits for 11 out of 13 applications.
Study on Establish a Brittle Fracture Prediction Considering Different Crack Opening Modes Using Mixed-Mode Ratio
Authors: Akahoshi Takuya , Azuma Koji , Iwashita Tsutomu , Itatani Toshiomi
Published: October 2021

In this study, we propose a method for predicting the occurrence of brittle fractures in the beam-to-column joints of steel structures, considering different crack opening modes. We conducted experiments on beam-to-diaphragm joint specimens with varying plastically constrained cracks to reproduce brittle fractures. The experiments’ results demonstrated the effectiveness of the toughness scale model and the Weibull stress approach. In addition, we propose the mixed-mode ratio, which is a quantitative index of the mode difference, and we applied it to the finite element models of the specimens. In this study, we evaluate the validity of the mixed-mode ratio and explore the differences in crack opening modes, as they pertain to the occurrence of brittle fractures.
Determine the Land-Use Land-Cover Changes, Urban Expansion and Their Driving Factors for Sustainable Development in Gazipur Bangladesh
Authors: Arifeen Hossain Mohammad , Phoungthong Khamphe , Mostafaeipour Ali , Yuangyai Nuttaya , Yuangyai Chumpol , Techato Kuaanan , Jutidamrongphan Warangkana
Published: October 2021

At present, urbanization is a very common phenomenon around the world, especially in developing countries, and has a significant impact on the land-use/land-cover of specific areas, producing some unwanted effects. Bangladesh is a tightly inhabited country whose urban population is increasing every day due to the expansion of infrastructure and industry. This study explores the land-use/land-cover change detection and urban dynamics of Gazipur district, Bangladesh, a newly developed industrial hub and city corporation, by using satellite imagery covering every 10-year interval over the period from 1990 to 2020. Supervised classification with a maximum likelihood classifier was used to gather spatial and temporal information from Landsat 5 (TM), 7 (ETM+) and 8 (OLI/TIRS) images. The Geographical Information System (GIS) methodology was also employed to detect changes over time. The kappa coefficient ranged between 0.75 and 0.90. The agricultural land was observed to be shrinking very rapidly, with an area of 716 km2 in 2020. Urbanization increased rapidly in this area, and the urban area grew by more than 500% during the study period. The urbanized area expanded along major roads such as the Dhaka–Mymensingh Highway and Dhaka bypass road. The urbanized area was, moreover, concentrated near the boundary line of Dhaka, the capital city of Bangladesh. Urban expansion was found to be influenced by demographic-, economic-, location- and accessibility-related factors. Therefore, similarly to many countries, concrete urban and development policies should be formulated to preserve the environment and, thereby, achieve sustainable development goal (SDG) 11 (sustainable cities and communities).
Research Progress for Dynamic Effects of Cities on Precipitation: A Review
Authors: Yue Caijun , Han Zhihui , Gu Wen , Tang Yuqi , Ao Xiangyu
Published: October 2021

Citization significantly changes original surface properties. City areas can cause surface winds to decrease; furthermore, ground friction can be transferred layer by layer through the momentum exchange of air movement, which affects the air layers above. Precipitation modification by city environments has been an active research area. Under the conditions of high wind speed, the dynamic effects of cities on precipitation are relatively obvious. Generally, the dynamic effects fall into two main categories: (1) for weather systems under weak forcing synoptic backgrounds, such as local convective systems, shorter-lived extreme precipitation events and fronts and city barrier effects can delay the movement of weather systems, directly change the horizontal distribution characteristics and occurrence time for precipitation, change the flow field and structure, cause the bifurcation of weather systems, and change the horizontal distribution characteristics of precipitation; (2) for weather systems under strong forcing synoptic backgrounds, such as extratropical systems (with large-scale moisture transport), monsoon systems, landfalling tropical cyclones, and supercell storms, the impact of the dynamic effects of cities cannot lead to the bifurcation of the weather system, nor can it change the horizontal distribution characteristics of the whole precipitation field, but it can have an impact on the local precipitation intensity and distribution. However, currently, people do not agree on the impact of cities on precipitation, especially regarding tropical cyclones. Hence, we provide a review and provide insights into the dynamic effects of cities on precipitation.
Atmospheric Deposition on the Southwest Coast of the Southern Basin of Lake Baikal
Authors: Golobokova Liudmila , Netsvetaeva Olga , Khodzher Tamara , Obolkin Vladimir , Khuriganova Olga
Published: October 2021

A precipitation monitoring station in Listvyanka was set up to determine the potential impact of the coastal area on the state of the adjacent air environment above Lake Baikal on its southwest coast. This article presents the results of studying the chemical composition of atmospheric deposition (aerosols and precipitation) at this station in 2020, and of their comparison with the data from previous years (from 2000 to 2019). In 2020, the ionic composition of atmospheric aerosols and precipitation had changed compared to previous years. In the modern period, the total amount of ions in aerosols, accounting for 0.46 ± 0.40 μg∙m−3, was lower by an order of magnitude than between 2000 and 2004. The average annual total amount of ions in precipitation in Listvyanka was almost unchanged from the average values in 2000–2010 and was 10% lower than that from 2011 to 2019 (7.3 mg/L). The ratio of major ions of sulphates and ammonium changed in the aerosol composition: compared to the period from 2000 to 2004, in 2020, the contribution of ammonium ions had decreased significantly, from 32% to 24%; the contribution of sulphates had increased to 43%, and the contribution of calcium had increased from 8 to 13%. Since 2010, the contribution of K+ ions has increased to 8–10%, indicating the effect of smoke aerosols from wildfires. In precipitation, despite the dominance of sulphates (26%) and calcium (18%) throughout the year, the contribution of nitrates increases to 19% during the cold season (from October to March), while the contribution of ammonium ions and hydrogen ions increases to 13% and 17%, respectively, in the warm season (from April to September). In 2020, as in previous research years, the acidity of precipitation at the Listvyanka station was elevated (pH 5.1 ± 0.5); 50% of precipitation in 2020 had pH ˂ 5. We quantified ions in atmospheric aerosols and precipitation on the underlying surface of the coastal southwestern part of Lake Baikal. Ion fluxes with precipitation were the highest in the warm season, which corresponds to the annual maximum precipitation. Unlike previous years (from 2000 to 2010 and from 2011 to 2019), wet deposition of most ions—especially calcium, ammonium and nitrates—had decreased in 2020. There was a 35-fold decrease in nitrogen fluxes and a 5-fold decrease in sulphur fluxes in aerosols, as well as 1.6-fold and 1.3-fold decreases, respectively, in precipitation.
Diagnosis of Atmospheric Drivers of High-Latitude Evapotranspiration Using Structural Equation Modeling
Authors: Thunberg Sarah M. , Euskirchen Eugénie S. , Walsh John E. , Redilla Kyle M.
Published: October 2021

Evapotranspiration (ET) is a relevant component of the surface moisture budget and is associated with different drivers. The interrelated drivers cause variations at daily to interannual timescales. This study uses structural equation modeling to diagnose the drivers over an ensemble of 45 high-latitude sites, each of which provides at least several years of in situ measurements, including latent heat fluxes derived from eddy covariance flux towers. The sites are grouped by vegetation type (tundra, forest) and the presence or absence of permafrost to determine how the relative importance of different drivers depends on land surface characteristics. Factor analysis is used to quantify the common variance among the variables, while a path analysis procedure is used to assess the independent contributions of different variables. The variability of ET at forest sites generally shows a stronger dependence on relative humidity, while ET at tundra sites is more temperature-limited than moisture-limited. The path analysis shows that ET has a stronger direct correlation with solar radiation than with any other measured variable. Wind speed has the largest independent contribution to ET variability. The independent contribution of solar radiation is smaller because solar radiation also affects ET through various other drivers. The independent contribution of wind speed is especially apparent at forest wetland sites. For both tundra and forest vegetation, temperature loads higher on the first factor when permafrost is present, implying that ET will become less sensitive to temperature as permafrost thaws.
Possible Linkages of Hydrological Variables to Ocean–Atmosphere Signals and Sunspot Activity in the Upstream Yangtze River Basin
Authors: Yang Ruting , Xing Bing
Published: October 2021

Profiling the hydrological response of watershed precipitation and streamflow to large-scale circulation patterns and astronomical factors provides novel information into the scientific management and prediction of regional water resources. Possible contacts of El Niño–Southern Oscillation (ENSO), Pacific Decadal Oscillation (PDO), sunspot activity to precipitation and streamflow in the upper Yangtze River basin (UYRB) were investigated in this work. Monthly precipitation and streamflow were utilized as well as contemporaneous same-scale teleconnections time series spanning a total of 70 years from 1951 to 2020 in precipitation and 121 years from 1900 to 2020 in streamflow. The principal component analysis (PCA) method was applied so as to characterize the dominant variability patterns over UYRB precipitation time series, with the temporal variability of first two modes explaining more than 80% of total variance. Long-term evolutionary pattern and periodic variation characteristics of precipitation and streamflow are explored by applying continuous wavelet transform (CWT), cross-wavelet transform (XWT) and wavelet coherence (WTC), analyzing multi-scale correlation between hydrological variables and teleconnections in the time-frequency domain. The results manifest that ENSO exhibits multiple interannual period resonance with precipitation and streamflow, while correlations are unstable in time and phase. PDO and sunspot effects on precipitation and streamflow at interannual scales vary with time-frequency domains, yet significant differences are exhibited in their effects at interdecadal scales. PDO exhibits a steady negative correlation with streamflow on interdecadal scales of approximately 10 years, while the effect of sunspot on streamflow exhibits extremely steady positive correlation on longer interdecadal scales of approximately 36 years. Analysis reveals that both PDO and sunspot have significantly stronger effects on streamflow variability than precipitation, which might be associated with the high spatiotemporal variability of precipitation.
Hemodynamic Investigation of the Effectiveness of a Two Overlapping Flow Diverter Configuration for Cerebral Aneurysm Treatment
Authors: Uchiyama Yuya , Fujimura Soichiro , Takao Hiroyuki , Suzuki Takashi , Hayakawa Motoharu , Ishibashi Toshihiro , Karagiozov Kostadin , Fukudome Koji , Murayama Yuichi , Yamamoto Makoto
Published: October 2021

Flow diverters (FDs) are widely employed as endovascular treatment devices for large or wide-neck cerebral aneurysms. Occasionally, overlapped FDs are deployed to enhance the flow diversion effect. In this study, we investigated the hemodynamics of overlapping FDs via computational fluid dynamics (CFD) simulations. We reproduced the arterial geometry of a patient who had experienced the deployment of two overlapping FDs. We utilized two stent patterns, namely the patterns for one FD and two overlapping FDs. We calculated the velocity, mass flow rate, wall shear stress, and pressure loss coefficient as well as their change rates for each pattern relative to the no-FD pattern results. The CFD simulation results indicated that the characteristics of the blood flow inside the aneurysm were minimally affected by the deployment of a single FD; in contrast, the overlapping FD pattern results revealed significant changes in the flow. Further, the velocity at an inspection plane within the aneurysm sac decreased by up to 92.2% and 31.0% in the cases of the overlapping and single FD patterns, respectively, relative to the no-FD pattern. The simulations successfully reproduced the hemodynamics, and the qualitative and quantitative investigations are meaningful with regard to the clinical outcomes of overlapped FD deployment.
Sugarcane Ratooning Ability: Research Status, Shortcomings, and Prospects
Authors: Xu Fu , Wang Zhoutao , Lu Guilong , Zeng Rensen , Que Youxiong
Published: October 2021

Sugarcane is an important sugar crop and it can be subjected to ratooning for several years. The advantages of ratooning include quality improvement, efficiency enhancement, and reduced costs and energy use. The genotype, environment, cultivation management, and harvesting technology affect the productivity and longevity of ratoon cane, with the genetic basis being the most critical factor. However, the majority of research has been focused on only limited genotypes, and a few studies have evaluated up to 100 sugarcane germplasm resources. They mainly focus on the comparison among different genotypes or among plant cane, different selection strategies for the first and second ratoon crops, together with screening indicators for the selection of stronger ratooning ability. In this paper, previous studies are reviewed in order to analyze the importance of sugarcane ratooning, the indicative traits used to evaluate ratooning ability, the major factors influencing the productivity and longevity of ratooning, the genetic basis of variation in ratooning ability, and the underlying mechanisms. Furthermore, the shortcomings of the existing research on sugarcane ratooning are highlighted. We then discuss the focus of future ratoon sugarcane research and the technical methods that will shorten the selection cycle and increase the genetic gain of ratooning ability, particularly the development of linked markers. This review is expected to provide a reference for understanding the mechanisms underlying the formation of ratooning ability and for breeding sugarcane varieties with a strong ratooning ability.
Calcium-Dependent Pulmonary Inflammation and Pharmacological Interventions and Mediators
Authors: Shipman Jeffrey G. , Onyenwoke Rob U. , Sivaraman Vijay
Published: October 2021

Pulmonary diseases present a significant burden worldwide and lead to severe morbidity and mortality. Lung inflammation caused by interactions with either viruses, bacteria or fungi is a prominent characteristic of many pulmonary diseases. Tobacco smoke and E-cig use (“vaping”) are considered major risk factors in the development of pulmonary disease as well as worsening disease prognosis. However, at present, relatively little is known about the mechanistic actions by which smoking and vaping may worsen the disease. One theory suggests that long-term vaping leads to Ca2+ signaling dysregulation. Ca2+ is an important secondary messenger in signal transduction. Cellular Ca2+ concentrations are mediated by a complex series of pumps, channels, transporters and exchangers that are responsible for triggering various intracellular processes such as cell death, proliferation and secretion. In this review, we provide a detailed understating of the complex series of components that mediate Ca2+ signaling and how their dysfunction may result in pulmonary disease. Furthermore, we summarize the recent literature investigating the negative effects of smoking and vaping on pulmonary disease, cell toxicity and Ca2+ signaling. Finally, we summarize Ca2+-mediated pharmacological interventions that could potentially lead to novel treatments for pulmonary diseases.
Diversity in Sensing and Signaling of Bacterial Sensor Histidine Kinases
Authors: Ishii Eiji , Eguchi Yoko
Published: October 2021

Two-component signal transduction systems (TCSs) are widely conserved in bacteria to respond to and adapt to the changing environment. Since TCSs are also involved in controlling the expression of virulence, biofilm formation, quorum sensing, and antimicrobial resistance in pathogens, they serve as candidates for novel drug targets. TCSs consist of a sensor histidine kinase (HK) and its cognate response regulator (RR). Upon perception of a signal, HKs autophosphorylate their conserved histidine residues, followed by phosphotransfer to their partner RRs. The phosphorylated RRs mostly function as transcriptional regulators and control the expression of genes necessary for stress response. HKs sense their specific signals not only in their extracytoplasmic sensor domain but also in their cytoplasmic and transmembrane domains. The signals are sensed either directly or indirectly via cofactors and accessory proteins. Accumulating evidence shows that a single HK can sense and respond to multiple signals in different domains. The underlying molecular mechanisms of how HK activity is controlled by these signals have been extensively studied both biochemically and structurally. In this article, we introduce the wide diversity of signal perception in different domains of HKs, together with their recently clarified structures and molecular mechanisms.
Alternative Pre-mRNA Splicing of the Mu Opioid Receptor Gene, OPRM1: Insight into Complex Mu Opioid Actions
Authors: Liu Shan , Kang Wen-Jia , Abrimian Anna , Xu Jin , Cartegni Luca , Majumdar Susruta , Hesketh Patrick , Bekker Alex , Pan Ying-Xian
Published: October 2021

Most opioid analgesics used clinically, including morphine and fentanyl, as well as the recreational drug heroin, act primarily through the mu opioid receptor, a class A Rhodopsin-like G protein-coupled receptor (GPCR). The single-copy mu opioid receptor gene, OPRM1, undergoes extensive alternative splicing, creating multiple splice variants or isoforms via a variety of alternative splicing events. These OPRM1 splice variants can be categorized into three major types based on the receptor structure: (1) full-length 7 transmembrane (TM) C-terminal variants; (2) truncated 6TM variants; and (3) single TM variants. Increasing evidence suggests that these OPRM1 splice variants are pharmacologically important in mediating the distinct actions of various mu opioids. More importantly, the OPRM1 variants can be targeted for development of novel opioid analgesics that are potent against multiple types of pain, but devoid of many side-effects associated with traditional opiates. In this review, we provide an overview of OPRM1 alternative splicing and its functional relevance in opioid pharmacology.
Integrative Multi-Omics in Biomedical Research
Authors: Hill Michelle M. , Gerner Christopher
Published: October 2021

Genome technologies have revolutionized biomedicine, but the complexity of biological systems cannot be explained by genomics alone [...]
Cdc42-Specific GTPase-Activating Protein Rga1 Squelches Crosstalk between the High-Osmolarity Glycerol (HOG) and Mating Pheromone Response MAPK Pathways
Authors: Patterson Jesse C. , Goupil Louise S. , Thorner Jeremy
Published: October 2021

Eukaryotes utilize distinct mitogen/messenger-activated protein kinase (MAPK) pathways to evoke appropriate responses when confronted with different stimuli. In yeast, hyperosmotic stress activates MAPK Hog1, whereas mating pheromones activate MAPK Fus3 (and MAPK Kss1). Because these pathways share several upstream components, including the small guanosine-5'-triphosphate phosphohydrolase (GTPase) cell-division-cycle-42 (Cdc42), mechanisms must exist to prevent inadvertent cross-pathway activation. Hog1 activity is required to prevent crosstalk to Fus3 and Kss1. To identify other factors required to maintain signaling fidelity during hypertonic stress, we devised an unbiased genetic selection for mutants unable to prevent such crosstalk even when active Hog1 is present. We repeatedly isolated truncated alleles of RGA1, a Cdc42-specific GTPase-activating protein (GAP), each lacking its C-terminal catalytic domain, that permit activation of the mating MAPKs under hyperosmotic conditions despite Hog1 being present. We show that Rga1 down-regulates Cdc42 within the high-osmolarity glycerol (HOG) pathway, but not the mating pathway. Because induction of mating pathway output via crosstalk from the HOG pathway takes significantly longer than induction of HOG pathway output, our findings suggest that, under normal conditions, Rga1 contributes to signal insulation by limiting availability of the GTP-bound Cdc42 pool generated by hypertonic stress. Thus, Rga1 action contributes to squelching crosstalk by imposing a type of “kinetic proofreading”. Although Rga1 is a Hog1 substrate in vitro, we eliminated the possibility that its direct Hog1-mediated phosphorylation is necessary for its function in vivo. Instead, we found first that, like its paralog Rga2, Rga1 is subject to inhibitory phosphorylation by the S. cerevisiae cyclin-dependent protein kinase 1 (Cdk1) ortholog Cdc28 and that hyperosmotic shock stimulates its dephosphorylation and thus Rga1 activation. Second, we found that Hog1 promotes Rga1 activation by blocking its Cdk1-mediated phosphorylation, thereby allowing its phosphoprotein phosphatase 2A (PP2A)-mediated dephosphorylation. These findings shed light on why Hog1 activity is required to prevent crosstalk from the HOG pathway to the mating pheromone response pathway.
Reversal of ABCG2/BCRP-Mediated Multidrug Resistance by 5,3′,5′-Trihydroxy-3,6,7,4′-Tetramethoxyflavone Isolated from the Australian Desert Plant Eremophila galeata Chinnock
Authors: Petersen Malene J. , Lund Xamuel L. , Semple Susan J. , Buirchell Bevan , Franzyk Henrik , Gajhede Michael , Kongstad Kenneth T. , Stenvang Jan , Staerk Dan
Published: October 2021

Multidrug resistance (MDR) is a major challenge in cancer treatment, and the breast cancer resistance protein (BCRP) is an important target in the search for new MDR-reversing drugs. With the aim of discovering new potential BCRP inhibitors, the crude extract of leaves of Eremophila galeata, a plant endemic to Australia, was investigated for inhibitory activity of parental (HT29par) as well as BCRP-overexpressing HT29 colon cancer cells resistant to the chemotherapeutic SN-38 (i.e., HT29SN38 cells). This identified a fraction, eluted with 40% acetonitrile on a solid-phase extraction column, which showed weak growth-inhibitory activity on HT29SN38 cells when administered alone, but exhibited concentration-dependent growth inhibition when administered in combination with SN-38. The major constituent in this fraction was isolated and found to be 5,3′,5′-trihydroxy-3,6,7,4′-tetramethoxyflavone (2), which at a concentration of 25 μg/mL potentiated the growth-inhibitory activity of SN-38 to a degree comparable to that of the known BCRP inhibitor Ko143 at 1 μM. A dye accumulation experiment suggested that 2 inhibits BCRP, and docking studies showed that 2 binds to the same BCRP site as SN-38. These results indicate that 2 acts synergistically with SN-38, with 2 being a BCRP efflux pump inhibitor while SN-38 inhibits topoisomerase-1.
Changes of Metabolic Biomarker Levels upon One-Year Anti-TNF-α Therapy in Rheumatoid Arthritis and Ankylosing Spondylitis: Associations with Vascular Pathophysiology
Authors: Czókolyová Monika , Pusztai Anita , Végh Edit , Horváth Ágnes , Szentpéteri Anita , Hamar Attila , Szamosi Szilvia , Hodosi Katalin , Domján Andrea , Szántó Sándor , Kerekes György , Seres Ildikó , Harangi Mariann , Paragh György , Szekanecz Éva , Szekanecz Zoltán , Szűcs Gabriella
Published: October 2021

Background: Cardiovascular (CV) morbidity, mortality, and metabolic syndrome are associated with rheumatoid arthritis (RA) and ankylosing spondylitis (AS). Here, lipids and other metabolic markers in relation to vascular function and clinical markers were evaluated in RA and AS patients undergoing one-year anti-TNF therapy. Patients and methods: Fifty-three patients including 36 RA patients treated with either etanercept (ETN) or certolizumab pegol (CZP) and 17 AS patients treated with ETN were included in a 12-month follow-up study. Various lipids, paraoxonase (PON) and arylesterase (ARE) activities, myeloperoxidase (MPO) and adipokine levels were determined overtime. Ultrasonography was performed to determine flow-mediated vasodilation (FMD), common carotid intima-media thickness (ccIMT), and arterial pulse-wave velocity (PWV) in all patients. All assessments were performed at baseline and 6 and 12 months after treatment initiation. Results: Anti-TNF therapy decreased ARE activity, MPO, adiponectin, and chemerin levels after 12 months (p < 0.05). Lipids, PON activity, and leptin remained unchanged. Regression analyses suggested variable associations of IMT, PWV, and FMD with ARE, MPO, leptin, and lipids (p < 0.05). On the other hand, these metabolic parameters were significantly associated with disease duration, CV history, CRP, obesity, PWV, and IMT (p < 0.05). One-year anti-TNF treatment together with baseline leptin (p = 0.039) or CRP (p = 0.016) levels determined 12 months of lipid changes overtime. TNF inhibition together with baseline disease activity determined ARE activity changes (p = 0.046). Anti-TNF therapy and baseline chemerin levels determined IMT changes overtime (p = 0.003). Conclusions: Assessment of various metabolic parameters together with disease activity, CRP, and ultrasound-based techniques may exert additional value in determining CV burden and in monitoring the effects of biologics on preclinical vascular pathophysiology.
The Dynamic Change of Immune Checkpoints and CD14+ Monocytes in Latent Tuberculosis Infection
Authors: Wang Ping-Huai , Wu Ming-Fang , Hsu Chi-Yu , Lin Shu-Yung , Chang Ya-Nan , Lee Ho-Shen , Wei Yu-Feng , Shu Chin-Chung
Published: October 2021

Controlling latent tuberculosis infection (LTBI) is important for preventing tuberculosis (TB). However, the immune regulation of LTBI remains uncertain. Immune checkpoints and CD14+ monocytes are pivotal for immune defense but have been scarcely studied in LTBI. We prospectively enrolled participants with LTBI and controls from January 2017 to December 2019. We measured their CD14+ monocytes and the expression of immune checkpoints, including programmed death-1 (PD-1), cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), and T cell immunoglobulin mucin domain-containing-3 (TIM3) on T lymphocytes in peripheral blood mononuclear cells before and after LTBI treatment. A total of 87 subjects were enrolled, including 29 IGRA-negative healthy controls (HC), 58 in the LTBI group (19 without chronic kidney disease (non-CKD), and 39 with end-stage renal disease (ESRD)). All PD-1, CTLA-4, and TIM3 on lymphocytes and monocytes were higher in the LTBI group than that in the HC group. Total CD14+ monocytes were higher and PD-L2+CD14+ over monocytes were lower in patients with LTBI-non-CKD than that in the HC group. After LTBI treatment, CD14+ monocytes, TIM3+ on CD4+ and monocytes, and CTLA-4 on lymphocytes decreased significantly. Multivariable logistic regression indicated that CD14+ monocytes was an independent factor for LTBI-non-CKD from the HC group, whereas PD-L2+CD14+ monocytes and TIM3+ monocytes were significant for LTBI-ESRD from the HC group. In conclusion, LTBI status was associated with increasing CD14+ monocytes plus low PD-L2 expression. By contrast, increased expression of immune checkpoints over all immune cells might be due to Mycobacterium tuberculosis related immune exhaustion, which decreased after treatment.
The Slower Antibody Response in Myelofibrosis Patients after Two Doses of mRNA SARS-CoV-2 Vaccine Calls for a Third Dose
Authors: Fiorino Fabio , Sicuranza Anna , Ciabattini Annalisa , Santoni Adele , Pastore Gabiria , Simoncelli Martina , Polvere Jacopo , Galimberti Sara , Auddino Stefano , Baratè Claudia , Montagnani Francesca , Sammartano Vincenzo , Bocchia Monica , Medaglini Donata
Published: October 2021

Immunization with mRNA SARS-CoV-2 vaccines has been highly recommended and prioritized in fragile subjects, including patients with myelofibrosis (MF). Available data on the vaccine immune response developed by MF patients and the impact of ruxolitinib treatment are still too fragmented to support an informed decision on a third dose for this category of subjects. Here, we show that 76% of MF patients develop spike-specific IgG after the second mRNA SARS-CoV-2 vaccine dose, but the response has a slower kinetics compared to healthy subjects, suggesting a reduced capability of their immune system to promptly react to vaccination. A reduced ACE2/RBD binding inhibition activity of spike-specific antibodies was also observed, especially in ruxolitinib-treated patients. Our results, showing slow kinetics of antibody responses in MF patients following vaccination with mRNA SARS-CoV-2 vaccines, support the need for a third vaccine dose.
Insights into Potential Pathogenesis and Treatment Options for Immune-Checkpoint Inhibitor-Related Pneumonitis
Authors: Ando Hiroyuki , Suzuki Kunihiro , Yanagihara Toyoshi
Published: October 2021

Immune-checkpoint inhibitors (ICIs) targeting cytotoxic T-lymphocyte antigen 4 (CTLA-4), programmed cell death-1 (PD-1), and programmed cell death-1-ligand 1 (PD-L1) have become new treatment options for various malignancies. ICIs bind to immune-checkpoint inhibitory receptors or to the foregoing ligands and block inhibitory signals to release the brakes on the immune system, thereby enhancing immune anti-tumor responses. On the other hand, unlike conventional chemotherapies, ICIs can cause specific side effects, called immune-related adverse events (irAEs). These toxicities may affect various organs, including the lungs. ICI-related pneumonitis (ICI-pneumonitis) is not the most frequent adverse event, but it is serious and can be fatal. In this review, we summarize recent findings regarding ICI-pneumonitis, with a focus on potential pathogenesis and treatment.
Surface Modification of Porous Polyethylene Implants with an Albumin-Based Nanocarrier-Release System
Authors: Eckrich Jonas , Hoormann Niklas , Kersten Erik , Piradashvili Keti , Wurm Frederik R. , Heller Martin , Becker Sven , Anusic Toni , Brieger Juergen , Strieth Sebastian
Published: October 2021

Background: Porous polyethylene (PPE) implants are used for the reconstruction of tissue defects but have a risk of rejection in case of insufficient ingrowth into the host tissue. Various growth factors can promote implant ingrowth, yet a long-term gradient is a prerequisite for the mediation of these effects. As modification of the implant surface with nanocarriers may facilitate a long-term gradient by sustained factor release, implants modified with crosslinked albumin nanocarriers were evaluated in vivo. Methods: Nanocarriers from murine serum albumin (MSA) were prepared by an inverse miniemulsion technique encapsulating either a low- or high-molar mass fluorescent cargo. PPE implants were subsequently coated with these nanocarriers. In control cohorts, the implant was coated with the homologue non-encapsulated cargo substance by dip coating. Implants were consequently analyzed in vivo using repetitive fluorescence microscopy utilizing the dorsal skinfold chamber in mice for ten days post implantation. Results: Implant-modification with MSA nanocarriers significantly prolonged the presence of the encapsulated small molecules while macromolecules were detectable during the investigated timeframe regardless of the form of application. Conclusions: Surface modification of PPE implants with MSA nanocarriers results in the alternation of release kinetics especially when small molecular substances are used and therefore allows a prolonged factor release for the promotion of implant integration.
Zoledronate Bound to Ceramics Increases Ectopic Bone Volume Induced by rhBMP6 Delivered in Autologous Blood Coagulum in Rats
Authors: Stokovic Nikola , Ivanjko Natalia , Erjavec Igor , Breski Anita , Peric Mihaela , Vukicevic Slobodan
Published: October 2021

Autologous bone graft substitute (ABGS) containing rhBMP6 in autologous blood coagulum (ABC) with synthetic ceramics is a novel therapeutic solution for bone repair. The aim of this study was to investigate whether the application of Zoledronate (ZOL) with ABGS might enhance the properties of newly formed bone. The effect of ZOL on bone induction was tested in a rat subcutaneous implant model. ZOL bound to synthetic ceramics was added into ABGS implants, and the quantity, quality, and longevity of the induced bone were assessed by micro-CT, histomorphometry, and histology over a period of 365 days. Local use of ZOL in the ABGS implants with ceramics had no influence on the bone volume (BV) on day 14 but subsequently significantly increased BV on days 35, 50, 105, 140, and 365 compared to the control implants. Locally applied ZOL had a similar effect in all of the applied doses (2–20 µg), while its systemic use on stimulating the BV of newly induced bone by ABGS depended on the time of application. BV was increased when ZOL was applied systemically on day 14 but had no effect when applied on day 35. The administration of ZOL bound to ceramics in ABGS increased and maintained the BV over a period of one year, offering a novel bone tissue engineering strategy for treating bone defects and spinal fusions.