bluuebunny/crossref_metadata_2025 huggingface dataset:
The Use of Enamel Matrix Derivative during Surgical Therapy for Peri-Implantitis: A Case Series
Authors: Wilson Thomas G. , Harrel Stephen K. , Nunn Martha E.
Published: December 2023

Peri-implantitis is a growing concern and currently, there is no agreement on the best method for treating this condition. This study looked at surgical intervention with the use of enamel matrix derivative (EMD) for treating this condition. A cohort of 25 (34 implants) consecutive patients treated with EMD for peri-implantitis was followed for up to 6.4 years. The survival of the implants as well as changes in clinical parameters are reported. Statistical analysis was performed using paired t tests and general estimating equations. The mean length of time implants were followed post-surgery was 3.05 ± 1.53 years. All but two of the treated implants survived in function (94%). Both failed implants were lost in the same patient, who was a heavy smoker. The changes in mean probing depth (1.94 ± 1.18 mm), change in deepest probing depth (3.12 ± 1.45 mm), and reduction in bleeding on probing (73.6 ± 43.9%) according to patient means were all highly significant (p < 0.001 for all changes). When EMD is used during surgical treatment of peri-implantitis, there is a high survival rate of implants and significant improvements in clinical parameters.
Multi-Robot Coverage Path Planning for the Inspection of Offshore Wind Farms: A Review
Authors: Foster Ashley J. I. , Gianni Mario , Aly Amir , Samani Hooman , Sharma Sanjay
Published: December 2023

Offshore wind turbine (OWT) inspection research is receiving increasing interest as the sector grows worldwide. Wind farms are far from emergency services and experience extreme weather and winds. This hazardous environment lends itself to unmanned approaches, reducing human exposure to risk. Increasing automation in inspections can reduce human effort and financial costs. Despite the benefits, research on automating inspection is sparse. This work proposes that OWT inspection can be described as a multi-robot coverage path planning problem. Reviews of multi-robot coverage exist, but to the best of our knowledge, none captures the domain-specific aspects of an OWT inspection. In this paper, we present a review on the current state of the art of multi-robot coverage to identify gaps in research relating to coverage for OWT inspection. To perform a qualitative study, the PICo (population, intervention, and context) framework was used. The retrieved works are analysed according to three aspects of coverage approaches: environmental modelling, decision making, and coordination. Based on the reviewed studies and the conducted analysis, candidate approaches are proposed for the structural coverage of an OWT. Future research should involve the adaptation of voxel-based ray-tracing pose generation to UAVs and exploration, applying semantic labels to tasks to facilitate heterogeneous coverage and semantic online task decomposition to identify the coverage target during the run time.
Seeing Is Believing: Brain-Inspired Modular Training for Mechanistic Interpretability
Authors: Liu Ziming , Gan Eric , Tegmark Max
Published: December 2023

We introduce Brain-Inspired Modular Training (BIMT), a method for making neural networks more modular and interpretable. Inspired by brains, BIMT embeds neurons in a geometric space and augments the loss function with a cost proportional to the length of each neuron connection. This is inspired by the idea of minimum connection cost in evolutionary biology, but we are the first the combine this idea with training neural networks with gradient descent for interpretability. We demonstrate that BIMT discovers useful modular neural networks for many simple tasks, revealing compositional structures in symbolic formulas, interpretable decision boundaries and features for classification, and mathematical structure in algorithmic datasets. Qualitatively, BIMT-trained networks have modules readily identifiable by the naked eye, but regularly trained networks seem much more complicated. Quantitatively, we use Newman’s method to compute the modularity of network graphs; BIMT achieves the highest modularity for all our test problems. A promising and ambitious future direction is to apply the proposed method to understand large models for vision, language, and science.
Neural Causal Information Extractor for Unobserved Causes
Authors: Leong Keng-Hou , Xiu Yuxuan , Chen Bokui , Chan Wai Kin (Victor)
Published: December 2023

Causal inference aims to faithfully depict the causal relationships between given variables. However, in many practical systems, variables are often partially observed, and some unobserved variables could carry significant information and induce causal effects on a target. Identifying these unobserved causes remains a challenge, and existing works have not considered extracting the unobserved causes while retaining the causes that have already been observed and included. In this work, we aim to construct the implicit variables with a generator–discriminator framework named the Neural Causal Information Extractor (NCIE), which can complement the information of unobserved causes and thus provide a complete set of causes with both observed causes and the representations of unobserved causes. By maximizing the mutual information between the targets and the union of observed causes and implicit variables, the implicit variables we generate could complement the information that the unobserved causes should have provided. The synthetic experiments show that the implicit variables preserve the information and dynamics of the unobserved causes. In addition, extensive real-world time series prediction tasks show improved precision after introducing implicit variables, thus indicating their causality to the targets.
State of Health Estimation Procedure for Lithium-Ion Batteries Using Partial Discharge Data and Support Vector Regression
Authors: Petkovski Emil , Marri Iacopo , Cristaldi Loredana , Faifer Marco
Published: December 2023

Battery aging is a complex phenomenon, and precise state of health (SoH) monitoring is essential for effective battery management. This paper presents a data-driven method for SoH estimation based on support vector regression (SVR), utilizing features built from both full and partial discharge capacity curves, as well as battery temperature data. It provides an in-depth discussion of the novel features constructed from different voltage intervals. Moreover, three combinations of features were analyzed, demonstrating how their efficacy changes across different voltage ranges. Successful results were obtained using the full discharge capacity curves, built from the full interval of 2 to 3.4 V and achieving a mean R2 value of 0.962 for the test set, thus showcasing the adequacy of the selected SVR strategy. Finally, the features constructed from the full voltage range were compared with ones built from 10 small voltage ranges. Similar success was observed, evidenced by a mean R2 value ranging between 0.939 and 0.973 across different voltage ranges. This indicates the practical applicability of the developed models in real-world scenarios. The tuning and evaluation of the proposed models were carried out using a substantial dataset created by Toyota, consisting of 124 lithium iron phosphate batteries.
Agricultural Research and Development Center Design with Building Integrated Photovoltaics in Fiji
Authors: Kim Sojung , Kim Sumin
Published: December 2023

Building-integrated photovoltaics (BIPVs) entail the use of photovoltaics as building materials, such as windows, roofs, and walls. Owing to their electricity-generation ability, BIPVs have become popular building materials for green buildings. This study involves an economic feasibility analysis of BIPVs for an agricultural research and development center in Fiji. The computerized relative allocation of facilities technique (CRAFT) is extended for cost-efficient facility design, and the levelized cost of electricity (LCOE) of BIPVs is evaluated to identify feasible alternatives from among three options, namely roof-integrated, window, and rooftop BIPVs. From the experiments, the LCOE values of the roof-integrated, window, and rooftop BIPVs were USD 0.13/kWh, 0.17/kWh, and 0.09/kWh, respectively. Moreover, the profit for the window BIPV was negative when the discount rate was greater than 0.08 due to its inefficient productivity. Contrarily, the roof-integrated BIPV showed a reasonable LCOE even though it required the highest investment cost. Nevertheless, further efforts are needed to reduce the cost of BIPVs for practical implementation.
Energy Harvesting Opportunities in Geoenvironmental Engineering
Authors: Marchiori Leonardo , Morais Maria Vitoria , Studart André , Albuquerque António , Andrade Pais Luis , Ferreira Gomes Luis , Cavaleiro Victor
Published: December 2023

Geoenvironmental engineering involves defining solutions for complex problems, such as containment systems management, contaminant transport control, wastewater management, remediation of contaminated sites and valorization of geomaterials and wastes. In the last years, energy harvesting (EH)—or energy scavenging—methods and technologies have been developed to reduce the dependence on traditional energy sources, namely fossil fuels, and nuclear power, also responding to the increase in energy demands for human activities and to fulfill sustainable development goals. EH in geoenvironmental works and the surrounding soil and water environment includes a set of processes for capturing and accumulating energy from several sources considered wasted or unusable associated with soil dynamics; the stress and strain of geomaterials, hydraulic, vibrations, biochemical, light, heating and wind sources can be potential EH systems. Therefore, this work presents a review of the literature and critical analysis on the main opportunities for EH capturing, accumulating and use in geoenvironmental works, among basic electric concepts and mechanisms, analyzing these works in complex conditions involving biological-, chemical-, mechanical-, hydraulic- and thermal-coupled actions, concluding with the main investigation and challenges within geoenvironmental aspects for EH purposes.
The Quality of Virginia Fanpetals Biomass as an Energy Source, Depending on the Type of Propagating Material and Plantation Age
Authors: Kwiatkowski Jacek , Graban Łukasz , Stolarski Mariusz Jerzy
Published: December 2023

Plant biomass is still the main raw material in the production of energy from renewable sources. Virginia fanpetals may be an alternative and complementary source of solid biomass to that obtained from forests and the wood industry. In this respect, it is important to assess the variability of the qualitative characteristics of Sida biomass as a solid biofuel over a long period of use of a plantation of this species. Three types of propagating material were used to establish the plantation: seeds, root cuttings (rhizomes), and seedlings, at two sowing/planting densities. The quality of the biomass, obtained during 14 consecutive years of harvest, was tested, including the moisture content, ash content, higher heating value (HHV), lower heating value (LHV), and the carbon, hydrogen, sulfur, and nitrogen content. It was found that both thermophysical properties and elemental composition were mostly determined by the years of vegetation. An important role in this respect was played by the juvenile period of the plants’ development. The biomass obtained after 1 year of vegetation contained a larger concentration of ash, nitrogen, and sulfur and less carbon and hydrogen, which reduced its energy value. The results confirm the possibility of obtaining biomass with low moisture, which favorably places it from an energy point of view.
A Critical Review of the Environmental Performance of Bifacial Photovoltaic Panels
Authors: Maniscalco Manfredi , Longo Sonia , Miccichè Gabriele , Cellura Maurizio , Ferraro Marco
Published: December 2023

Bifacial photovoltaic (BPV) panels represent one of the main solar technologies that will be used in the near future for renewable energy production, with a foreseen market share in 2030 of 70% among all the photovoltaic (PV) technologies. Compared to monofacial panels, bifaciality can ensure a gain in energy production per unit panel area together with a competitive cost. However, it is of paramount importance to identify whether there is also an environmental benefit when adopting bifacial technologies as opposed to traditional monofacial ones. To obtain a proper insight into the environmental impact, this paper reviews the Life Cycle Assessment (LCA) studies of bifacial solar panels, identifying the most crucial processes and materials that raise environmental burdens. The analysis also contributes to determining whether the major aspects that influence energy production in real operation scenarios and, most of all, that can ensure the gain associated with bifaciality, are considered and how these can further affect the overall environmental impacts. In this sense, it was found that the installation parameters like the mounting structure, or the choice of ground material to raise the albedo as well as the diffuse irradiation that hits the rear surface of thepanel, are commonly not considered during LCA analysis. However, none of the analyzed studies address the issue in a comprehensive way, hampering an effective comparison between both the different works and traditional monofacial PV panels. Recommendations for future LCAs are finally proposed.
Reactive Power Compensation and Distortion Power Variation Identification in Extended Budeanu Power Theory for Single-Phase Systems
Authors: Sołjan Zbigniew , Zajkowski Maciej , Borusiewicz Andrzej
Published: December 2023

This article presents methods of reactive power compensation using passive elements in the form of a capacitor (C) or choke (L) and an LC structure selected in such a way as to lead to the minimization of the reactive current (reactive power) of a single-phase system. The adaptation of the parameters of a passive compensator, reducing reactive power and/or distortion power, was possible through the extended Budeanu theory. In addition, through the extended Budeanu theory and also through the knowledge of the equivalent parameters of the linear load, the obtained results of the increase in distortion power, depending on the structure of the passive compensator, were analyzed. The values listed in the tables, as well as the waveforms of the component currents of a single-phase linear load, were obtained based on calculations and simulation models in MATLAB/Simulink software R2023a.
Spatiotemporal Evolution and Market Dynamics of the International Liquefied Natural Gas Trade: A Multilevel Network Analysis
Authors: Hou Zeyu , Niu Xiaoyu , Yu Zhaoyuan , Chen Wei
Published: December 2023

Natural gas is considered a transitional energy source in the transition to clean energy owing to its clean, efficient, and ecologically beneficial properties. The trade of liquefied natural gas (LNG) serves as the backbone of the global natural gas trade and significantly influences the dynamics of the global energy trade system. This paper constructs long-term global LNG trade networks, and explores the spatiotemporal evolution and topological structures of the international LNG trade by utilizing multilevel network analysis methods, to provide insights for comprehensively understanding the market dynamics of the global LNG trade system. The findings indicate the following: (1) The global LNG trade volume shows an overall upward trend, and the global LNG trade network exhibits uneven spatial distribution, clear hierarchical differentiation, and an increasingly complicated structure. Global LNG trade is gradually changing from regionalization to globalization, and the international LNG market is undergoing structural reshaping. (2) The global LNG trade network continues to expand in size and density, and the rapidly growing LNG supply and trade relations are driving the formation of the global natural gas market. (3) Global LNG trade is still in a phase of rapid change, with the global efficiency of the network increasing and then decreasing. The trade network has traditionally been centered on ten countries, including Japan, South Korea, the United States, and Qatar. (4) The global LNG trade network exhibits clear core-periphery structures with considerable polarization effects, and the trade network structure is continuously evolving and is growing unbalanced. Finally, we put forward relevant policy suggestions to promote global LNG trade interconnectivity and enhance environmental protection and respond to global climate change.
Long-Term Monitoring Studies of the Mycorrhizal Colonization of Aesculus hippocastanum L. Roots and the Vitality of Soil Microorganisms in Urban and Non-Urban Environments
Authors: Tyburska-Woś Jolanta , Kieliszewska-Rokicka Barbara
Published: December 2023

Stress factors typical in urban environments adversely affect the productivity and vigor of trees and may limit the development of tree roots with associated soil fungi and bacteria. Studies on mycorrhizal symbiosis and the activity of soil microorganisms are important in monitoring the adaptation of trees to urban conditions. We compared the symbiotic activity of arbuscular mycorrhizal fungi (AMF) living in the rhizosphere of mature white chestnut trees (Aesculus hippocastanum L.) in an urban ecosystem at sites with varying degrees of anthropopressure and in a rural area. We used two methods: (1) direct analysis of the root samples, (2) assessment of the colonization of trap plants grown in the soil taken from under selected white horse chestnut trees. The seasonality of mycorrhizal colonization and soil microbial respiration based on the enzyme activity of nonspecific dehydrogenase (DHA) was studied over several growing seasons. The concentrations of macronutrients in the soil from all study sites were in the ranges accepted as normal for the upper soil layer. However, the C/N ratio indicated carbon limitation in the soil at urban and rural study sites. The results showed that arbuscular mycorrhizal fungi indigenous in the rhizosphere of A. hippocastanum developed a functioning mycorrhizal symbiosis at all research sites, including at highly disturbed urban locations, and that the mycorrhizal colonization varied between the study sites and the research term. The trap culture method confirmed the high biological potential of the soil microbial community, including AMF in urban ecosystems, which was comparable to that at the reference site in the rural environment. Soil moisture strongly affected the overall soil microbial vitality. This research showed that the mycorrhizal status of A. hippocastanum is more strongly influenced by climatic conditions and seasonal rhythms of trees than by urban/non-urban locations.
Advances in Droplet-Based Microfluidic High-Throughput Screening of Engineered Strains and Enzymes Based on Ultraviolet, Visible, and Fluorescent Spectroscopy
Authors: Hu Shunyang , Wang Bangxu , Luo Qing , Zeng Rumei , Zhang Jiamin , Cheng Jie
Published: December 2023

Genetic engineering and directed evolution are effective methods for addressing the low yield and poor industrialization level of microbial target products. The current research focus is on how to efficiently and rapidly screen beneficial mutants from constructed large-scale mutation libraries. Traditional screening methods such as plate screening and well-plate screening are severely limited in their development and application due to their low efficiency and high costs. In the past decade, microfluidic technology has become an important high-throughput screening technology due to its fast speed, low cost, high automation, and high screening throughput, and it has developed rapidly. Droplet-based microfluidic high-throughput screening has been widely used in various fields, such as strain/enzyme activity screening, pathogen detection, single-cell analysis, drug discovery, and chemical synthesis, and has been widely applied in industries such as those involving materials, food, chemicals, textiles, and biomedicine. In particular, in the field of enzyme research, droplet-based microfluidic high-throughput screening has shown excellent performance in discovering enzymes with new functions as well as improved catalytic efficiency or stability, acid-base tolerance, etc. Currently, droplet-based microfluidic high-throughput screening technology has achieved the high-throughput screening of enzymes such as glycosidase, lipase, peroxidase, protease, amylase, oxidase, and transaminase as well as the high-throughput detection of products such as riboflavin, coumarin, 3-dehydroquinate, lactic acid, and ethanol. This article reviews the application of droplet-based microfluidics in high-throughput screening, with a focus on high-throughput screening strategies based on UV, visible, and fluorescence spectroscopy, including labeled optical signal detection screening, as well as label-free electrochemical detection, mass spectrometry, Raman spectroscopy, nuclear magnetic resonance, etc. Furthermore, the research progress and development trends of droplet-based microfluidic technology in enzyme modification and strain screening are also introduced.
Time Series Classification with Multiple Wavelength Scattering Signals for Nuisance Alarm Mitigation
Authors: Han Kyuwon , Kim Soocheol , Yang Hoesung , Cho Kwangsoo , Lee Kangbok
Published: December 2023

Smoke detectors are the most widely used fire detectors due to their high sensitivity. However, they have persistently faced issues with false alarms, known as nuisance alarms, as they cannot distinguish smoke particles, and their responsiveness varies depending on the particle size and concentration. Although technologies for distinguishing smoke particles have shown promising results, the hardware limitations of smoke detectors necessitate an intelligent approach to analyze scattering signals of various wavelengths and their temporal changes. In this paper, we propose a pipeline that can distinguish smoke particles based on scattering signals of various wavelengths as input. In the data extraction phase, we propose methods for extracting datasets from time series data. We propose a method that combines traditional approaches, early detection methods, and a Dynamic Time Warping technique that utilizes only the shape of the signal without preprocessing. In the learning model and classification phase, we present a method to select and compare various architectures and hyperparameters to create a model that achieves the best classification performance for time series data. We create datasets for six different targets in our presented sensor and smoke particle test environment and train classification models. Through performance comparisons, we identify architecture and parameter combinations that achieve up to 98.7% accuracy. Ablation studies under various conditions demonstrate the validity of the chosen architecture and the potential of other models.
Thermal Transpiration Flow: Molecular Dynamics Study from Dense to Dilute Gas
Authors: Yamaguchi Hiroki , Kikugawa Gota
Published: December 2023

Thermal transpiration flow, a flow from cold to hot, driven by a temperature gradient along a wall under a high Knudsen number condition, was studied using the molecular dynamics method with a two-dimensional channel consisting of infinite parallel plates with nanoscale clearance based on our previous study. To accelerate the numerical analysis, a dense gas was employed in our previous study. In this study, the influence of the number density of gas was investigated by varying the height of the channel while keeping the number of molecules to achieve the flow ranging from dense to dilute gas while maintaining a constant Knudsen number. From the flow velocity profile compared to the number density profile, the thermal transpiration flow was observed for all number density conditions from dense to dilute gas. A similar flow structure was exhibited regardless of the number density. Thus, the numerical analysis in a dense gas condition is considered to be valid and useful for analyzing the thermal transpiration flow.
Computational Fluid Dynamics Modeling of Concrete Flows in Drilled Shafts
Authors: Jeyaraj Jesudoss Aservitham , Perez Anthony , Zayed Abla , Mullins Austin Gray , Tejada-Martinez Andres E.
Published: December 2023

Drilled shafts are cylindrical, cast-in-place concrete deep foundation elements. During construction, anomalies in drilled shafts can occur due to the kinematics of concrete, flowing radially from the center of the shaft to the concrete cover region at the peripheral edge. This radial component of concrete flow develops veins or creases of poorly cemented or high water-cement ratio material, as the concrete flows around the reinforcement cage of rebars and ties, jeopardizing the shaft integrity. This manuscript presents a three-dimensional computational fluid dynamics (CFD) model of the non-Newtonian concrete flow in drilled shaft construction developed using the finite volume method with interface tracking based on the volume of fluid (VOF) method. The non-Newtonian behavior of the concrete is represented via the Carreau constitutive model. The model results are encouraging as the flow obtained from the simulations shows patterns of both horizontal and vertical creases in the concrete cover region, consistent with previously reported field and laboratory experiments. Moreover, the flow exhibits the concrete head differential developed between the inside and the outside of the reinforcement cage, as exhibited in the physical experiments. This head differential induces the radial component of the concrete flow responsible for the creases that develop in the concrete cover region. Results show that the head differential depends on the flowability of the concrete, consistent with field observations. Less viscous concrete tends to reduce the head differential and the formation of creases of poorly cemented material. The model is unique, making use of state-of-the-art numerical techniques and demonstrating the capability of CFD to model industrially relevant concrete flows.
Rheological Characteristics of Wheat Dough Containing Powdered Hazelnuts or Walnuts Oil Cakes
Authors: Pycia Karolina , Juszczak Lesław
Published: December 2023

This study assessed edible oil industry byproducts, oil cakes (OC) based on hazelnuts and walnuts (HOC, WOC), to replace wheat flour dough (WD) based on farinograph and extensograph parameters and rheological measurements. The research hypothesis of this work is that replacing part of wheat flour with ground nut oil cakes modifies the rheological characteristics of the dough. WF was replaced at the level of 5%, 10% and 15%. It was shown that use of OC in flour mixtures at various levels significantly influenced the rheological properties of the dough. The water absorption of wheat flour and oil cake mixtures was higher than that of the control sample, and the average value of this indicator was 53.4%. The control sample had the lowest dough development time (DDT), and the presence of HOC or WOC in the system resulted in a significant increase in this parameter (p < 0.05). The average DDT of WDHOC cakes was 4.7 min and was lower compared to WDWOC which was 5.9 min. The WDWOC10% and WDWOC15% samples were characterized by the highest dough stability value and the lowest degree of softening (p < 0.05). The presence of OC in the flour mixtures increased the values of the storage and loss moduli, which was reflected in the K′ and K″ values. The values of these parameters also increased as the level of OC addition increased. WDHOC doughs were characterized by higher values of the K′ and K″ parameters compared to WDWOC. The results of the creep and recovery test showed that the dough with the addition of nut OC was less susceptible to deformation compared to the control dough (p < 0.05). The resistance to deformation increased with the increasing share of HOC or WOC in the mixtures. The average value of viscoelastic compliance (J1) of this parameter for WDHOC dough was on average 1.8 × 10−4 Pa−1, and for WDWOC 2.0 × 10−4 Pa−1. Nut oil cakes are an interesting technological addition to the dough. Their use may have a positive impact on the characteristics of the finished product and expand their application possibilities in the food industry. This is because the dough with the addition of nut cakes was more stiff and less flexible and susceptible to deformation.
Equilibrium Selection in Hawk–Dove Games
Authors: Blázquez de Paz Mario , Koptyug Nikita
Published: December 2023

We apply three equilibrium selection techniques to study which equilibrium is selected in a hawk–dove game with a multiplicity of equilibria. By using a uniform-price auction as an illustrative example, we find that when the demand in the auction is low or intermediate, the tracing procedure method of Harsanyi and Selten (1988) and the quantal response method of McKelvey and Palfrey (1998) select the same equilibrium. When the demand is high, the tracing procedure method does not select any equilibrium, but the quantal response method still selects the same equilibrium as when the demand is low or intermediate. The robustness to strategic uncertainty method of Andersson, Argenton and Weibull (2014) selects two of the multiple equilibria irrespective of the demand size. We also analyze the impact of an increase in the minimum bid allowed by the auctioneer in the equilibrium selection.
Phase Inversion Gelation Process and Additive Effects on Hydrogel Film Properties of Cotton Cellulose
Authors: Ibaraki Ayano , Kobayashi Takaomi
Published: December 2023

During the preparation of cotton cellulose hydrogels using the phase inversion gelation method of N,N-dimethylacetamide/LiCl solution under ethanol vapor, acetone (AC), methyl ethyl ketone (MEK), or diethyl ketone (DEK) were added as additives, and their gelation state and the properties of the resulting hydrogels were evaluated. Adding the ketones to the cellulose solution caused an increase in the gelation time, but the solution viscosity decreased, indicating that the cellulose tended to aggregate in the solution. Among the hydrogels prepared by adding ketones, the water content was as high as 2050%, especially for AC and MEK. In these hydrogels, cellulose formed an agglomerated fibrous network of a few micron widths, forming a tuft-like entrapment space of about 10 to 100 μm size. The structure surrounded water and held it in the hydrogels. The FTIR results showed that the water, which formed hydrogen bonds, was retained within the hydrogel network. This structural configuration was determined to be conducive to maintaining the gel state against external deformation forces, especially in the case of the addition of MEK.
A Comprehensive Metabolism-Related Gene Signature Predicts the Survival of Patients with Acute Myeloid Leukemia
Authors: Zhai Yujia , Shen Heng , Wei Hui
Published: December 2023

(1) Background: Acute myeloid leukemia (AML) is a clonal malignancy with heterogeneity in genomics and clinical outcome. Metabolism reprogramming has been increasingly recognized to play an important role in the leukemogenesis and prognosis in AML. A comprehensive prognostic model based on metabolism signatures has not yet been developed. (2) Methods: We applied Cox regression analysis and the least absolute shrinkage and selection operator (LASSO) normalization to establish a metabolism-related prognostic gene signature based on glycolysis, fatty acid metabolism, and the tricarboxylic acid cycle gene signatures. The Cancer Genome Atlas-Acute Myeloid Leukemia-like (TCGA-LAML) cohort was set as the training dataset for model construction. Three independent AML cohorts (GSE37642, GSE10358, and GSE12417) combined from Gene Expression Omnibus (GEO) datasets and the Beat-AML dataset were retrieved as two validation sets to test the robustness of the model. The transcriptome data and clinic information of the cohorts were enrolled for the analysis. (3) Results: Divided by the median value of the metabolism risk score, the five-year overall survival (OS) of the high-risk and low-risk groups in the training set were 8.2% and 41.3% (p < 0.001), respectively. The five-year OS of the high-risk and low-risk groups in the combined GEO cohort were 25.5% and 37.3% (p = 0.002), respectively. In the Beat-AML cohort, the three-year OS of the high-risk and low-risk groups were 16.2% and 40.2% (p = 0.0035), respectively. The metabolism risk score showed a significantly negative association with the long-term survival of AML. Furthermore, this metabolism risk score was an independent unfavorable factor for OS by univariate analysis and multivariate analysis. (4) Conclusions: Our study constructed a comprehensive metabolism-related signature with twelve metabolism-related genes for the risk stratification and outcome prediction of AML. This novel signature might contribute to a better use of metabolism reprogramming factors as prognostic markers and provide novel insights into potential metabolism targets for AML treatment.
Diachronic Comparison of Three Historical Skeletal Series from Croatia with Regard to Mandibular Bone Quality
Authors: Savić Pavičin Ivana , Adamić Hadžić Anita , Čivljak Tadej , Dumančić Jelena , Šlaus Mario , Lauc Tomislav , Zymber Çeshko Ajla
Published: December 2023

The aim of this study was to assess the quality of mandibular bone using CBCT images in archeological populations that inhabited Croatia from the medieval to the Early Modern Period. A total of 88 human skulls (45 male and 43 female) from three samples (pre-Ottoman (N = 27), Ottoman (N = 32), and Vlach (N = 29)) were analyzed by using CBCT. The mental index, gonion index, antegonion index, panoramic mandibular index, degree of resorption of the alveolar ridge, and cortical index of the mandible were evaluated using the OnDemand3DApp. The results showed an expected higher value of cortex thickness in males when compared to females. Females in the younger groups had higher values of cortical thickness than those in the older age group. The Ottoman sample had significantly lower values of mandibular indices than the other two samples. There were no age-related differences in bone thickness in males, suggesting that hormonal changes have a stronger influence in females. Lower values of mandibular indices in the Ottoman sample may be an indicator of specific factors that influenced this population. Our study of bone changes in archeological populations with different living conditions may contribute to a better understanding of impact of biocultural factors on physiological and pathological processes, which are extremely complex in bone tissue.
Why Do We Agree to Disagree? Agreement and Reasons for Disagreement in Judgements of Intentional Self-Harm from Coroners and a Suicide Register in Queensland, Australia, from 2001 to 2015
Authors: Leske Stuart , Weir Bridget , Adam Ghazala , Kõlves Kairi
Published: December 2023

Suicides are likely to be underreported. In Australia, the National Coronial Information System (NCIS) provides information about suicide deaths reported to coroners. The NCIS represents the findings on the intent of the deceased as determined by coroners. We used the Queensland Suicide Register (QSR) to assess the direction, magnitude, and predictors of any differences in the reporting of suicide in Queensland. Therefore, we conducted a consecutive case series study to assess agreement and variation between linked data from the NCIS and QSR determinations of suicide for all suicide deaths (N = 9520) in the QSR from 2001 to 2015 recorded from routinely collected coronial data. The rate of concordance between the QSR and NCIS for cases of intentional self-harm was 92.7%. There was disagreement between the findings in the data, since 6.3% (n = 597) were considered as intentional self-harm in the QSR but not in the NCIS, and, less commonly, 0.9% (n = 87) were considered intentional self-harm in the NCIS but not in the QSR. Overall, the QSR reported 510 more suicides than the NCIS in 15 years. These findings indicate that using suicide mortality data from suicide registers may not underreport suicide as often.
RNA Pol II Assembly Affects ncRNA Expression
Authors: Garrido-Godino Ana I. , Gupta Ishaan , Pelechano Vicent , Navarro Francisco
Published: December 2023

RNA pol II assembly occurs in the cytoplasm before translocation of the enzyme to the nucleus. Affecting this assembly influences mRNA transcription in the nucleus and mRNA decay in the cytoplasm. However, very little is known about the consequences on ncRNA synthesis. In this work, we show that impairment of RNA pol II assembly leads to a decrease in cryptic non-coding RNAs (preferentially CUTs and SUTs). This alteration is partially restored upon overcoming the assembly defect. Notably, this drop in ncRNAs is only partially dependent on the nuclear exosome, which suggests a major specific effect of enzyme assembly. Our data also point out a defect in transcription termination, which leads us to propose that CTD phosphatase Rtr1 could be involved in this process.
Biotransformation of Δ1-Progesterone Using Selected Entomopathogenic Filamentous Fungi and Prediction of Its Products’ Bioactivity
Authors: Panek Anna , Wójcik Patrycja , Świzdor Alina , Szaleniec Maciej , Janeczko Tomasz
Published: December 2023

This research aimed at obtaining new derivatives of pregn-1,4-diene-3,20-dione (Δ1-progesterone) (2) through microbiological transformation. For the role of catalysts, we used six strains of entomopathogenic filamentous fungi (Beauveria bassiana KCh J1.5, Beauveria caledonica KCh J3.3, Isaria fumosorosea KCh J2, Isaria farinosa KCh KW1.1, Isaria tenuipes MU35, and Metarhizium robertsii MU4). The substrate (2) was obtained by carrying out an enzymatic 1,2-dehydrogenation on an increased scale (3.5 g/L) using a recombinant cholest-4-en-3-one Δ1-dehydrogenase (AcmB) from Sterolibacterium denitrificans. All selected strains were characterized by the high biotransformation capacity for the used substrate. As a result of the biotransformation, six steroid derivatives were obtained: 11α-hydroxypregn-1,4-diene-3,20-dione (3), 6β,11α-dihydroxypregn-1,4-diene-3,20-dione (4), 6β-hydroxypregn-1,4-diene-3,11,20-trione (5), 6β,17α-dihydroxypregn-1,4-diene-3,20-dione (6), 6β,17β-dihydroxyandrost-1,4-diene-3-one (7), and 12β,17α-dihydroxypregn-1,4-diene-3,20-dione (8). The results show evident variability of the biotransformation process between strains of the tested biocatalysts from different species described as entomopathogenic filamentous fungi. The obtained products were tested in silico using cheminformatics tools for their pharmacokinetic and pharmacodynamic properties, proving their potentially high biological activities. This study showed that the obtained compounds may have applications as effective inhibitors of testosterone 17β-dehydrogenase. Most of the obtained products should, also with a high probability, find potential uses as androgen antagonists, a prostate as well as menopausal disorders treatment. They should also demonstrate immunosuppressive, erythropoiesis-stimulating, and anti-inflammatory properties.
The Functional Diversity of the High-Affinity Nitrate Transporter Gene Family in Hexaploid Wheat: Insights from Distinct Expression Profiles
Authors: Sigalas Petros P. , Buchner Peter , Kröper Alex , Hawkesford Malcolm J.
Published: December 2023

High-affinity nitrate transporters (NRT) are key components for nitrogen (N) acquisition and distribution within plants. However, insights on these transporters in wheat are scarce. This study presents a comprehensive analysis of the NRT2 and NRT3 gene families, where the aim is to shed light on their functionality and to evaluate their responses to N availability. A total of 53 NRT2s and 11 NRT3s were identified in the bread wheat genome, and these were grouped into different clades and homoeologous subgroups. The transcriptional dynamics of the identified NRT2 and NRT3 genes, in response to N starvation and nitrate resupply, were examined by RT-qPCR in the roots and shoots of hydroponically grown wheat plants through a time course experiment. Additionally, the spatial expression patterns of these genes were explored within the plant. The NRT2s of clade 1, TaNRT2.1-2.6, showed a root-specific expression and significant upregulation in response to N starvation, thus emphasizing a role in N acquisition. However, most of the clade 2 NRT2s displayed reduced expression under N-starved conditions. Nitrate resupply after N starvation revealed rapid responsiveness in TaNRT2.1-2.6, while clade 2 genes exhibited gradual induction, primarily in the roots. TaNRT2.18 was highly expressed in above-ground tissues and exhibited distinct nitrate-related response patterns for roots and shoots. The TaNRT3 gene expression closely paralleled the profiles of TaNRT2.1-2.6 in response to nitrate induction. These findings enhance the understanding of NRT2 and NRT3 involvement in nitrogen uptake and utilization, and they could have practical implications for improving nitrogen use efficiency. The study also recommends a standardized nomenclature for wheat NRT2 genes, thereby addressing prior naming inconsistencies.
Characterization of Progranulin Gene Mutations in Portuguese Patients with Frontotemporal Dementia
Authors: Almeida Maria Rosário , Tábuas-Pereira Miguel , Baldeiras Inês , Lima Marisa , Durães João , Massano João , Pinto Madalena , Cruto Catarina , Santana Isabel
Published: December 2023

In Portugal, heterozygous loss-of-function mutations in the progranulin (GRN) gene account for approximately half of the genetic mediated forms of frontotemporal dementia (FTD). GRN mutations reported thus far cause FTD through a haploinsufficiency disease mechanism. Herein, we aim to unveil the GRN mutation spectrum, investigated in 257 FTD patients and 19 family members from the central/north region of Portugal using sequencing methods. Seven different pathogenic variants were identified in 46 subjects including 40 patients (16%) and 6 relatives (32%). bvFTD was the most common clinical presentation among the GRN mutation patients, who showed a global pattern of moderate-to-severe frontotemporoparietal deficits in the neuropsychological evaluation. Interestingly, two mutations were novel (p.Thr238Profs*18, p.Leu354Profs*16), and five were previously described, although three of them only in the Portuguese population, suggesting a population-specific GRN mutational spectrum. The subjects harboring a GRN mutation showed a significant reduction in serum PGRN levels, supporting the pathogenic nature of these variants. This work broadens the mutation spectrum of GRN and the identification of the underlying GRN mutations provided an accurate genetic counselling and allowed the enrolment of subjects with GRN mutations (both asymptomatic and symptomatic) in ongoing clinical trials, which is essential to test new drugs for the disease.
Ganoderma adspersum (Ganodermataceae): Investigation of Its Secondary Metabolites and the Antioxidant, Antimicrobial, and Cytotoxic Potential of Its Extracts
Authors: Chafouz Raichan , Karavergou Sofia , Tsiftsoglou Olga St. , Maskovic Pavle , Lazari Diamanto
Published: December 2023

Ganoderma is a genus of wood-degrading mushrooms with medicinal importance. Most Ganoderma species have been studied extensively for their secondary metabolites, biological activities, and ecological value. In this study, the biological activities of the extracts of G. adspersum growing wild on Morus alba trees in the region of Western Thrace (Greece) were evaluated, and the petroleum ether, dichloromethanolic, and methanolic extracts were studied further for their secondary metabolites. Six substances were isolated by chromatographic (Clumn Chromatography (C.C.), High Performance Liquid Chromatography (HPLC)) and spectroscopic methods (Nuclear Magnetic Resonance (NMR)), which were classified in the following categories: (a) unsaturated fatty acids: cis-oleic acid (1); (b) sterols: ergosta-7,22-dien-3-one (2), ergosta-7,22-dien-3-ol (3), and ergosta-5,7,22-trien-3-ol (4); and (c) lanostane-type triterpenoids: applanoxidic acid G (5) and applanoxidic acid A (6). Finally, the biological activities of the extracts were estimated for their antioxidant, antimicrobial, and cytotoxic potential. The methanolic extract of G. adspersum showed the highest total antioxidant activity. The results of the antimicrobial activities indicated that all of the extracts had a minimum inhibitory concentration (MIC) ranging between 39.1 and 312.5 μg/mL. The evaluation of the cytotoxic activity of the samples showed once again that the methanolic extract was the most potent among the examined extracts, with half-maximal inhibitory concentration (IC50) values of 19.22 μg/mL (Hep2c cells), 32.9 μg/mL (RD cells), and 8.94 μg/mL (L2OB cells). Moreover, the bioactivity scores of the isolated secondary metabolites were calculated using the online computer software program Molinspiration. The compounds showed promising bioactivity scores for drug targets.
Novel Polyelectrolytes Based on Naphthalene Diimide with Different Counteranions for Cathode Interlayers in Polymer Solar Cells
Authors: Nasrun Rahmatia Fitri Binti , Son Dong Hwan , Kim Joo Hyun
Published: December 2023

We synthesized novel polyelectrolytes based on naphthalene diimide with quaternary amine featuring hydroxyl groups at the side chain, along with different counteranions (PF-NDIN-Br-OH and PF-NDIN-I-OH) for polymer solar cell (PSC) application as the interlayer. The polyelectrolytes establish a beneficial interface dipole through the ionic moieties and synergistic effects arising from the hydroxyl groups located at the side chain. Incorporating polyelectrolytes as the cathode interlayer resulted in an enhancement of the power conversion efficiency (PCE). The PCE of the device with PF-NDIN-Br-OH increased from 8.96% to 9.51% compared to the ZnO-only device. The best PCE was obtained with the device based on PF-NDIN-I-OH, up to 9.59% resulting from the Jsc enhancement. This outcome implies a correlation between the performance of the device and the synergistic effects observed in polyelectrolytes containing hydroxyl groups in the side chain, along with larger anions when employed in PSCs.
Cellular and Enzymatic Determinants Impacting the Exolytic Action of an Anti-Staphylococcal Enzybiotic
Authors: Gouveia Ana , Pinto Daniela , Vítor Jorge M. B. , São-José Carlos
Published: December 2023

Bacteriophage endolysins are bacteriolytic enzymes that have been explored as potential weapons to fight antibiotic-resistant bacteria. Despite several studies support the application of endolysins as enzybiotics, detailed knowledge on cellular and enzymatic factors affecting their lytic activity is still missing. The bacterial membrane proton motive force (PMF) and certain cell wall glycopolymers of Gram-positive bacteria have been implicated in some tolerance to endolysins. Here, we studied how the anti-staphylococcal endolysin Lys11, a modular enzyme with two catalytic domains (peptidase and amidase) and a cell binding domain (CBD11), responded to changes in the chemical and/or electric gradients of the PMF (ΔpH and Δψ, respectively). We show that simultaneous dissipation of both gradients enhances endolysin binding to cells and lytic activity. The collapse of ΔpH is preponderant in the stimulation of Lys11 lytic action, while the dissipation of Δψ is mainly associated with higher endolysin binding. Interestingly, this binding depends on the amidase domain. The peptidase domain is responsible for most of the Lys11 bacteriolytic activity. Wall teichoic acids (WTAs) are confirmed as major determinants of endolysin tolerance, in part by severely hindering CBD11 binding activity. In conclusion, the PMF and WTA interfere differently with the endolysin functional domains, affecting both the binding and catalytic efficiencies.