bluuebunny/crossref_metadata_2025 huggingface dataset:
Research on the Ignition Process and Flame Stabilization of a Combination of Step and Strut: Experimental and Numerical Study
Authors: Zhao Shilong , Xiao Hui , Li Yafan
Published: March 2023

A combined application of step and strut was put forward to achieve reliable ignition and flame stabilization. In this work, the ignition process and temperature distribution have been tested, and a new reduction approach applied to jet fuel oxidation mechanism was developed to present a flow map via tracking C and H reaction paths, then the minor and major reactions were verified according to relative occurrence probabilities. With the half decrease of mechanism size, bias occurred and was controlled within 1.8%. This reduction method had such characteristics as universality, intuition, and quantification, due to its inherent simplification theory. This simulation of ignition process was always consistent with experimental results, which depicted kernel generation, flamelet breakup and flame propagation. Also, the influence of inlet temperature on outlet temperature and component distribution was performed, the biases of experimental and numerical results were within 5%. Chemical characteristics of Kerosene/air premixed combustible had changed and side reactions occurred to jet fuel above 900 K, which led to a converse effect on flame spreading. The side reactions aggravated the increasing coproducts of CO and CH4, which caused the decrease of volumetric heat production.
Excess Anisotropy: A Method to Predict Frequency of Resistive Fractures in the Wolfcamp Shale
Authors: Walker Joanna M. , Castagna John P.
Published: March 2023

A horizontal well in the Wolfcamp Formation within the Delaware Basin exhibits cross-dipole sonic log anisotropy varying from 0.0% to 29.7% over the reservoir interval. Massive limestones exhibit little anisotropy while shales and intervals with high fracture counts have high anisotropy. Integrated analysis of acoustic, image and triple combo open-hole log data indicates that the computed volume of shale log is a strong predictor of anisotropy with a simple linear relationship. However, there is much anisotropy that is not accounted for by this lithologically related linear relationship. We refer to the residual obtained by subtracting the predicted anisotropy using this relationship from the measured anisotropy from a cross-dipole sonic tool as the excess anisotropy. The excess anisotropy is the remaining anisotropy that is not accounted for by linear regression between the volume of shale log and the measured anisotropy. We find that the excess anisotropy is linearly correlated to the resistive fracture density. Linear regression between the two variables yields a statistically significant relationship that enables a rough estimation of the resistive fracture frequency from the excess anisotropy. Validation in a second well produces a similar correlation to fracture frequency.
Cooling of Concentrated Photovoltaic Cells—A Review and the Perspective of Pulsating Flow Cooling
Authors: Ibrahim Khalifa Aliyu , Luk Patrick , Luo Zhenhua
Published: March 2023

This article presents a review to provide up-to-date research findings on concentrated photovoltaic (CPV) cooling, explore the key challenges and opportunities, and discuss the limitations. In addition, it provides a vision of a possible future trend and a glimpse of a promising novel approach to CPV cooling based on pulsating flow, in contrast to existing cooling methods. Non-concentrated photovoltaics (PV) have modest efficiency of up to around 20% because they utilise only a narrow spectrum of solar irradiation for electricity conversion. Therefore, recent advances employed multi-junction PV or CPV to widen the irradiation spectrum for conversion. CPV systems concentrate solar irradiation on the cell’s surface, producing high solar flux and temperature. The efficient cooling of CPV cells is critical to avoid thermal degradation and ensure optimal performance. Studies have shown that pulsating flow can enhance heat transfer in various engineering applications. The advantage of pulsating flow over steady flow is that it can create additional turbulence and mixing in the fluid, resulting in a higher heat transfer coefficient. Simulation results with experimental validation demonstrate the enhancement of this new cooling approach for future CPV systems. The use of pulsating flow in CPV cooling has shown promising results in improving heat transfer and reducing temperature gradients.
A Novel Energy Accounting Model Using Fuzzy Restricted Boltzmann Machine—Recurrent Neural Network
Authors: Sorguli Sarhang , Rjoub Husam
Published: March 2023

Energy accounting is a system for regularly measuring, analyzing, and reporting the energy use of various activities. This is done to increase energy efficiency and monitor the impact of energy usage on the environment. Primary energy accounting is now done by determining the amount of fossil fuel energy required to generate it. However, if fossil fuels become scarcer, this strategy becomes less viable. Instead, a new energy accounting approach will be required, one that takes into consideration the intermittent character of the two most prevalent renewable energy sources, wind and solar power. Furthermore, estimation of the energy consumption data collected from household surveys, whether using a recall-based approach or a meter-based one, remains a difficult task. Hence, this paper proposes a novel energy accounting model using Fuzzy Restricted Boltzmann Machine-Recurrent Neural Network (FRBM-RNN). The energy consumption dataset is preprocessed using linear-scaling normalization. The proposed model is optimized using the Adaptive Fuzzy Adam Optimization Algorithm (AFAOA). The performance metrics like Mean Square Error (MSE), Root Mean Square Error (RMSE), Mean Absolute Error (MAE), and Mean Absolute Percentage Error (MAPE) are estimated. The estimated results for our proposed technique are MSE (0.19), RMSE (0.44), MAE (0.2), and MAPE (3.5).
Design and Implementation of Predictive Controllers for a 36-Slot 12-Pole Outer-Rotor SPMSM/SPMSG System with Energy Recovery
Authors: Liu Tian-Hua , Lu Wen-Rui , Cheng Sheng-Hsien
Published: March 2023

This paper investigates a drive system with energy recovery which uses a 3-phase 1-kW 36-slot 12-pole distributed winding outer-rotor surface-mounted permanent-magnet synchronous motor (SPMSM) and surface-mounted permanent-magnet synchronous generator (SPMSG), which can be used in indoor exercise bicycles. In order to extend drive system operating speed range, the constant torque control, flux-weakening control, and maximum torque/voltage control are used to extend its operation speed up to 1.75 times rated speed. In addition, a predictive speed controller and a predictive current controller are proposed to improve transient responses, load disturbance responses, and tracking responses. A digital signal processor, type TMS-320F-28035, manufactured by Texas Instruments, is used as a control center for the proposed SPMSM/SPMSG drive system. Experimental results validate the feasibility and correctness of the proposed methods.
Life Cycle Assessment of a Three-Storey Terrace of Three Timber-Framed Residential Workplace Units
Authors: Clancy Michael A. , Starbuck Sally , O’Dwyer Jean , Byrne Kenneth A.
Published: March 2023

There is an urgent need to evaluate the environmental impacts of both traditional and more recent innovations in sustainable building materials. This study conducted a life cycle assessment (LCA) of a single three-storey (aboveground) terrace in Ireland composed of three timber-framed residential workplace units. The supply of raw materials, their transport to the manufacturing site, and the manufacturing processes for the materials used in the building account for 58% of the GWP during the production stage. The horizontal elements of the An Corrán building and roof account for the largest contribution (29.3%) to the GWP environmental impact. The LCA results show that the building’s 469 m2 gross internal floor area (GIFA) produced life cycle carbon emissions of 220 t CO2e and has an embodied carbon value of 398 kg CO2e m−2 and 6.63 kg CO2e m−2 a−1 for the building’s 60-year estimated cradle-to-grave life cycle. When compared to conventional (i.e., masonry) and timber-framed buildings in Europe, the An Corrán building shows that substantial GWP savings occurred during the Use Stage with a GWP footprint of 50.5 kg CO2e m2 compared to 375.65 and 386.6 kg CO2e m2 for previously reported masonry and timber-framed houses, respectively.
Transcriptome Analysis of Pecan (Carya illinoinensis) Differentially Expressed Genes in Response to Drought Stress
Authors: Zhu Kaikai , Wei Lu , Ma Wenjuan , Hu Xiaoli , Zhao Juan , Tan Pengpeng , Liu Hui , Feng Gang , Fan Pinghua , Peng Fangren
Published: March 2023

Pecan (Carya illinoinensis) is an economically important nut tree that is greatly affected by drought, limiting its production and distribution. Although the complete genome of the pecan was published several years ago, the molecular basis of the pecan’s response to drought remains unclear. In this study, we analyzed the high-throughput transcriptome data for pecans under 3, 6, 9, 12, and 15 days of drought stress compared with the controls. A total of 12,893 differentially expressed genes (DEGs) were identified under drought stress, with 11,684 of them showing significant changes after 15 d of drought treatment. Among these, 4448 genes were up-regulated while 7226 were down-regulated. The trend analysis revealed that DEGs could be classified into 20 clusters. Surprisingly, the majority of genes (6148) showed a gradual down-regulation, and 3683 genes showed a gradual up-regulation in response to drought. Gene ontology enrichment analysis showed that the DEGs were mainly enriched in biological processes. The KEGG pathway enrichment results indicated that the DEGs were mainly enriched in several pathways, including metabolic pathways, the biosynthesis of secondary metabolites, and plant hormone signal transduction processes. Among the DEGs, 457 protein kinase and 734 transcription factor genes were shown to be drought-responsive and may play key roles in the response to drought, and the expression patterns of selected candidate genes were further validated using quantitative real-time PCR. Collectively, these findings highlighted the multiple processes in pecans under drought stress and provided valuable insights into the further investigation of the functions of drought stress-responsive genes and the molecular basis of the pecan drought stress response.
Assessing Seasonal Concentrations of Airborne Potentially Toxic Elements in Tropical Mountain Areas in Thailand Using the Transplanted Lichen Parmotrema Tinctorum (Despr. ex Nyl.) Hale
Authors: Boonpeng Chaiwat , Sangiamdee Duangkamon , Noikrad Sutatip , Boonpragob Kansri
Published: March 2023

The atmosphere of mountain areas may be contaminated by pollutants originating mainly from road traffic, as well as tourist and community activities within such areas. This study mainly aimed to assess the concentrations of airborne potentially toxic elements (PTEs) in two mountain areas in Thailand using lichen biomonitoring. Thalli of the lichen Parmotrema tinctorum from the relatively unpolluted area in Khao Yai National Park (KYNP) were prepared and exposed at nine sites in the KYNP and nine sites in Doi Inthanon National Park (DINP) during the rainy and dry seasons. The lichen transplants were collected and analyzed for 15 PTEs, including Al, As, Cd, Co, Cr, Cu, Fe, Mn, Mo, Ni, Pb, Sb, Ti, V, and Zn, using inductively coupled plasma-mass spectrometry. The result clearly showed that the atmosphere of many monitoring sites in both mountains were contaminated by the investigated PTEs. The contamination factors (CFs) revealed that several PTEs heavily contaminated the atmosphere at many monitoring sites. The pollution load indices (PLIs) clearly illustrated that the atmosphere of all sites had higher pollution loads in the dry season than in the rainy season, which was likely due to the higher numbers of motor vehicles and visitors. The highest pollution loads were observed at sites that had higher traffic density and human activities, including the park entrance site in the KYNP and the community site in the DINP. The lowest air pollution loads were discovered at the summit sites in both mountains. This study indicates that the atmosphere of mountain areas can be contaminated by some PTEs that are mainly produced by road traffic and local communities. It also confirms the ability of the transplanted lichen P. tinctorum to be an effective biomonitoring tool for airborne PTEs in natural environments.
Subarctic Vegetation under the Mixed Warming and Air Pollution Influence
Authors: Kharuk Viacheslav I. , Petrov Il’ya A. , Im Sergei T. , Golyukov Alexey S. , Dvinskaya Maria L. , Shushpanov Alexander S. , Savchenko Alexander P. , Temerova Victoria L.
Published: March 2023

In the Siberian Arctic, worldwide largest forest mortality was caused by chronical (since the 1940s) influence of SO2 emissions on the larch-dominant communities. We hypothesized that warming might mitigate SO2 influence by increasing trees’ vigor and growth. We studied trees (larch, Larix sibirica; spruce, Picea obovate; birch, Betula pendula) and bushes (willow, Salix sp., alder, Duschekia fruticosa) growth dependence on SO2, air temperature, soil temperature and moisture, and precipitation. We sampled woods in severely damaged larch and moderately damaged mixed larch, spruce and birch forests. We generated tree ring chronologies and growth indices (GI). We used Terra/MODIS satellite data for mapping trends of vegetation (NDVI) and productivity (GPP, NPP) indexes. In the larch forest, we found a strong decrease in GI and tree mortality, which lasted until the end of 1990s. In the mixed forest, larch and birch were more resistant to SO2 influence compared to spruce. SO2, air and soil temperatures were mediators of all woody species growth. Winter precipitation stimulated trees growth by mitigating spring water stress. Warming onset in the 2000s led to a pronounced increase of all woody species growth. June–July air and soil temperatures, together with a moderate decrease in SO2 emissions, were the primary drivers of that phenomenon. Increasing trends of GPP, NPP, and NDVI were observed within the large part of earlier damaged forests, which was attributed to trees GI increase together with the expansion of SO2-resistant grasses and bushes.
Visual Simulation Research on Growth Polymorphism of Chinese Fir Stand Based on Different Comprehensive Grade Models of Spatial Structure Parameters
Authors: Hu Xingtao , Zhang Huaiqing , Yang Guangbin , Qiu Hanqing , Lei Kexin , Yang Tingdong , Liu Yang , Zuo Yuanqing , Wang Jiansen , Cui Zeyu
Published: March 2023

Since tree morphological structure is strongly influenced by internal genetic and external environmental factors, accurate simulation of individual morphological–structural changes in trees is the premise of forest management and 3D simulation. However, existing studies have few descriptions, and the research on the impact of growth environments and stand spatial structures on tree morphological structure and growth is still limited. In our study, we constructed a comprehensive grade model of spatial structure (CGMSS) to comprehensively evaluate individual tree growth states of the stands and grade them from 0 to 10 correspondingly. In addition, we developed a Chinese fir morphological structure growth model based on CGMSS, and dynamically simulate the growth variations of Chinese fir stands. The results showed that the overall stand prediction accuracy of CGMSS-based Chinese fir diameter at breast height, tree height, crown width and under-living branch height growth models was more than 94%. According to the analysis of the comprehensive grade of spatial structure (CGSS) of trees in the stand, except for the prediction accuracy and systematic error of the under-living branch height growth model at the CGSS = 3–5 levels, the systematic error of the Chinese fir growth model at each level was lower than 21.2%, and the prediction accuracy was greater than 73%. Compared with the spatial structural unit (SSU)-based Chinese fir growth model proposed by Ma et al., all growth models fit better at all levels, except for the CGMSS-based Chinese fir tree height and under-living branch height growth models that fit significantly lower than the SSU-based Chinese fir growth model at CGSS = 3–5 levels. In this study, the main conclusion is that the simulation results of CGMSS’s Chinese fir morphological structure growth model are closer to the real growth state of trees, achieving accurate simulation of differential growth of trees in different growth dominance degrees and spatial structure states in forest stands, making visualized forest management more effective and realistic.
Total Streamflow Variation for the Upper Catchment of Bosten Lake Basin in China Inferred from Tree-Ring Width Records
Authors: Liu Kexiang , Zhang Tongwen , Shang Huaming , Fan Yuting , Yu Shulong , Jiang Shengxia , Mao Weiyi , Liu Xinchun
Published: March 2023

Bosten Lake Basin not only is a major source of drinking water for the residents of the surrounding area, but also maintains the ecological balance of the region. However, with the influence of climate change and human activities, the water level of Bosten Lake fluctuates sharply and has a great impact on the surrounding ecological environment. Therefore, the study of its historical water flow changes as a reference has become a focus of research. In this study, the radial growth of Schrenk spruces (Picea schrenkiana Fisch. et Mey.) significantly correlated with the tributary streamflow coming from the mountainous region near Bosten Lake Basin. On the basis of this good coherence, the tree-ring chronologies were used to reconstruct the streamflow for Huangshuigou River from the previous August to the present July (r = 0.766, p < 0.0001, n = 50). The reconstructed streamflow series matched observations well, explaining 63.3% of the variation in the observed streamflow of 1956–2005. Then, the sum of the streamflow reconstruction of Huangshuigou River and another two tree-ring-based streamflow reconstructions (Kaidu River and Qingshui River) was used to represent the hydrological variation of the upper catchment of Bosten Lake Basin, and the reconstruction sequence was 306 years. The 10.7, 5.5, and 2.1 year cycles of the power spectrum and wavelet analysis revealed that the runoff series reconstructed from tree-ring hydrometeorology was related to solar activity. Some dry and wet years in the reconstructed streamflow series of the upper catchment of Bosten Lake Basin corresponded to the historical record. During the wet years, the Indian Ocean was probably the main source of precipitation.
A Descriptive Study of Webpage Designs for Posting Privacy Policies for Different-Sized US Hospitals to Create an Assessment Framework
Authors: Schnell Karen , Roy Kaushik , Siddula Madhuri
Published: March 2023

In the United States, there are laws and standards guiding how people should be informed about the use of their private data. However, the challenge of communicating these guidelines to the naïve user is still at its peak. Research has shown that the willingness to read privacy statements is influenced by attitudes toward privacy risks and privacy benefits. Many websites publish privacy policies somewhere on their web pages, and it can be difficult to navigate to them. In the healthcare field, research has found that health information websites’ key information is presented poorly and inconsistently. For the policies to be legally binding, a person must be able to find them. In the healthcare industry, where sensitive data are being collected, research on how a user navigates to privacy policies for different size hospital websites is limited. Studies exist about privacy policies or website design and not both. This descriptive study involved ascertaining commonalities and differences among different-sized hospitals’ website designs for supporting privacy policies. A foundation framework was created using Web Content Accessibility Guidelines (WGAC) principles and the literature review findings for evaluating practices for website publishing of privacy policies. The results demonstrated a very low variance in the website design concepts employed by hospitals to publish their privacy policy.
CvAMoS—Event Abstraction Using Contextual Information
Authors: Di Federico Gemma , Burattin Andrea
Published: March 2023

Process mining analyzes events that are logged during the execution of a process, with the aim of gathering useful information and knowledge. Process discovery algorithms derive process models that represent these processes. The level of abstraction at which the process model is represented is reflected in the granularity of the event log. When a process is captured by the usage of sensor systems, process activities are recorded at the sensor-level in the form of sensor readings, and are therefore too fine-grained and non-explanatory. To increase the understandability of the process model, events need to be abstracted into higher-level activities that provide a more meaningful representation of the process. The abstraction becomes more relevant and challenging when the process involves human behavior, as the flexible nature of human actions can make it harder to identify and abstract meaningful activities. This paper proposes CvAMoS, a trace-based approach for event abstraction, which focuses on identifying motifs while taking context into account. A motif is a recurring sequence of events that represents an activity that took place under specific circumstances depicted by the context. Context information is logged in the event log in the form of environmental sensor readings (e.g., the temperature and light sensors). The presented algorithm uses a distance function to deal with the variability in the execution of activities. The result is a set of meaningful and interpretable motifs. The algorithm has been tested on both synthetic and real datasets, and compared to the state of the art. CvAMoS is implemented as a Java application and the code is freely available.
Meta-Analysis of 49 SNPs Covering 25,446 Cases and 41,106 Controls Identifies Polymorphisms in Hormone Regulation and DNA Repair Genes Associated with Increased Endometrial Cancer Risk
Authors: Das Agneesh Pratim , Chaudhary Nisha , Tyagi Shrishty , Agarwal Subhash M.
Published: March 2023

Endometrial cancer (EC) is among the most common gynecological disorders globally. As single nucleotide polymorphisms (SNPs) play an important role in the causation of EC, therefore, a comprehensive meta-analysis of 49 SNPs covering 25,446 cases and 41,106 controls was performed to identify SNPs significantly associated with increased EC risk. PubMed was searched to identify case control studies and meta-analysis was performed to compute the pooled odds ratio (OR) at 95% confidence interval (CI). Cochran’s Q-test and I2 were used to study heterogeneity, based on which either a random or a fixed effect model was implemented. The meta-analysis identified 11 SNPs (from 10 genes) to be significantly associated with increased EC risk. Among these, seven SNPs were significant in at least three of the five genetic models, as well as three of the polymorphisms (rs1801320, rs11224561, and rs2279744) corresponding to RAD51, PGR, and MDM2 genes, which contained more than 1000 EC cases each and exhibited increased risk. The current meta-analysis indicates that polymorphisms associated with various hormone related genes—SULT1A1 (rs1042028), PGR (rs11224561), and CYP19A1 (rs10046 and rs4775936); DNA repair genes—ERCC2 (rs1799793), OGG1 (rs1052133), MLH1 (rs1800734), and RAD51 (rs1801320) as well as genes like MDM2 (rs2279744), CCND1 (rs9344), and SERPINE1 (rs1799889), are significantly associated with increased EC risk.
Satellite DNAs—From Localized to Highly Dispersed Genome Components
Authors: Šatović-Vukšić Eva , Plohl Miroslav
Published: March 2023

According to the established classical view, satellite DNAs are defined as abundant non-coding DNA sequences repeated in tandem that build long arrays located in heterochromatin. Advances in sequencing methodologies and development of specialized bioinformatics tools enabled defining a collection of all repetitive DNAs and satellite DNAs in a genome, the repeatome and the satellitome, respectively, as well as their reliable annotation on sequenced genomes. Supported by various non-model species included in recent studies, the patterns of satellite DNAs and satellitomes as a whole showed much more diversity and complexity than initially thought. Differences are not only in number and abundance of satellite DNAs but also in their distribution across the genome, array length, interspersion patterns, association with transposable elements, localization in heterochromatin and/or in euchromatin. In this review, we compare characteristic organizational features of satellite DNAs and satellitomes across different animal and plant species in order to summarize organizational forms and evolutionary processes that may lead to satellitomes’ diversity and revisit some basic notions regarding repetitive DNA landscapes in genomes.
Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs
Authors: Alvarez-Estape Marina , Pawar Harvinder , Fontsere Claudia , Trujillo Amber E. , Gunson Jessica L. , Bergl Richard A. , Bermejo Magdalena , Linder Joshua M. , McFarland Kelley , Oates John F. , Sunderland-Groves Jacqueline L. , Orkin Joseph , Higham James P. , Viaud-Martinez Karine A. , Lizano Esther , Marques-Bonet Tomas
Published: March 2023

The critically endangered western gorillas (Gorilla gorilla) are divided into two subspecies: the western lowland (G. g. gorilla) and the Cross River (G. g. diehli) gorilla. Given the difficulty in sampling wild great ape populations and the small estimated size of the Cross River gorilla population, only one whole genome of a Cross River gorilla has been sequenced to date, hindering the study of this subspecies at the population level. In this study, we expand the number of whole genomes available for wild western gorillas, generating 41 new genomes (25 belonging to Cross River gorillas) using single shed hairs collected from gorilla nests. By combining these genomes with publicly available wild gorilla genomes, we confirm that Cross River gorillas form three population clusters. We also found little variation in genome-wide heterozygosity among them. Our analyses reveal long runs of homozygosity (>10 Mb), indicating recent inbreeding in Cross River gorillas. This is similar to that seen in mountain gorillas but with a much more recent bottleneck. We also detect past gene flow between two Cross River sites, Afi Mountain Wildlife Sanctuary and the Mbe Mountains. Furthermore, we observe past allele sharing between Cross River gorillas and the northern western lowland gorilla sites, as well as with the eastern gorilla species. This is the first study using single shed hairs from a wild species for whole genome sequencing to date. Taken together, our results highlight the importance of implementing conservation measures to increase connectivity among Cross River gorilla sites.
A Missense Mutation c.1132G > A in Fumarate Hydratase (FH) Leads to Hereditary Leiomyomatosis and Renal Cell Cancer (HLRCC) Syndrome and Insights into Clinical Management in Uterine Leiomyomata
Authors: Shi Yue , Xu Yan , Wang Chao , Chen Yiqing , Ren Xiaojun , Kang Yu , Wang Chao
Published: March 2023

Background: HLRCC syndrome is a hereditary cancer predisposition syndrome caused by heterozygous germline pathogenic variant of the fumarate hydratase (FH) gene and characterized by cutaneous leiomyomas (CL), uterine leiomyomas (UL), and renal cell carcinoma (RCC). Loss of function variant of FH gene inactivates the Kreb’s cycle enzyme activity and predisposes individuals with such variant to the development of HLRCC. Methods: Next-generation sequencing (NGS) and Sanger confirmation were given to family members accessible. Following that, a functional study in vitro was performed to further confirm the pathogenicity of the variant. FH-Wild type (FH-WT) and FH-mutant (FH-MUT) (E378K) plasmid were constructed and transfected into 293T and uterine leiomyoma cell lines, respectively. Proliferation assessment was executed to show how this mutation affects the growth of uterine leiomyoma. qPCR and Western blotting were performed to investigate the change of transcription and translation of FH with mutation (E378K), and FH enzyme assay activity were tested in 293T cells with mutation and wild-type plasmids. Results: Here, we presented two families with the same missense variant (c.1132G > A) that has not been reported as a germline mutation in hereditary uterine leiomyomas before and classified as VUS in gene databases. Our in vitro experiments supported the pathogenicity of this missense variant, especially in uterine leiomyomata. Conclusions: According to the American College of Medical Genetics (ACMG) guideline, the E378K variant was classified as likely pathogenic (with evidence PS4_support, PS3_support, PM2_support, PP1, PP3 and PP4 evidence). Further insights into clinical management in uterine leiomyomata were discussed and should be practiced in gynecological clinical settings.
Integration of Stemness Gene Signatures Reveals Core Functional Modules of Stem Cells and Potential Novel Stemness Genes
Authors: Barata Tânia , Duarte Isabel , Futschik Matthias E.
Published: March 2023

Stem cells encompass a variety of different cell types which converge on the dual capacity to self-renew and differentiate into one or more lineages. These characteristic features are key for the involvement of stem cells in crucial biological processes such as development and ageing. To decipher their underlying genetic substrate, it is important to identify so-called stemness genes that are common to different stem cell types and are consistently identified across different studies. In this meta-analysis, 21 individual stemness signatures for humans and another 21 for mice, obtained from a variety of stem cell types and experimental techniques, were compared. Although we observed biological and experimental variability, a highly significant overlap between gene signatures was identified. This enabled us to define integrated stemness signatures (ISSs) comprised of genes frequently occurring among individual stemness signatures. Such integrated signatures help to exclude false positives that can compromise individual studies and can provide a more robust basis for investigation. To gain further insights into the relevance of ISSs, their genes were functionally annotated and connected within a molecular interaction network. Most importantly, the present analysis points to the potential roles of several less well-studied genes in stemness and thus provides promising candidates for further experimental validation.
Proteome and Ubiquitylome Analyses of Maize Endoplasmic Reticulum under Heat Stress
Authors: Gao Chunyan , Peng Xiaohui , Zhang Luoying , Zhao Qi , Ma Liguo , Yu Qi , Lian Xuechun , Gao Lei , Xiong Langyu , Li Shengben
Published: March 2023

High temperatures severely affect plant growth and pose a threat to global crop production. Heat causes the accumulation of misfolded proteins in the endoplasmic reticulum(ER), as well as triggering the heat-shock response (HSR) in the cytosol and the unfolded protein response (UPR) in the ER. Excessive misfolded proteins undergo further degradation through ER-associated degradation (ERAD). Although much research on the plant heat stress response has been conducted, the regulation of ER-localized proteins has not been well-studied thus far. We isolated the microsome fraction from heat-treated and untreated maize seedlings and performed proteome and ubiquitylome analyses. Of the 8306 total proteins detected in the proteomics analysis, 1675 proteins were significantly up-regulated and 708 proteins were significantly down-regulated. Global ubiquitination analysis revealed 1780 proteins with at least one ubiquitination site. Motif analysis revealed that alanine and glycine are the preferred amino acids upstream and downstream of ubiquitinated lysine sites. ERAD components were found to be hyper-ubiquitinated after heat treatment, implying the feedback regulation of ERAD activity through protein degradation.
Effect of Rainfall Intensity on Landslide Initiation: Flume Tests and Numerical Analysis
Authors: Tang Qianhao , Gratchev Ivan , Ravindran Sinnappoo
Published: March 2023

This paper seeks to investigate the effect of rainfall intensity on the occurrence of shallow landslides by means of a series of flume tests. Coarse-grained material was used to build a slope, and several rainfall events with an intensity of either 40 mm/h, 70 mm/h, or 100 mm/h were simulated to initiate slope failure. A set of pore water pressure and moisture content sensors was installed in the slope to monitor changes in the water conditions during each test. Different initial moisture contents of 5% and 10% of the soil mass were used to better understand the effect of moisture on slope stability during rainfall. It was found that the slope failed when intensities of 70 mm/h and 100 mm/h were used; however, no failure was observed with a rainfall intensity of 40 mm/h. The failure patterns were found to be similar, with progressive slides occurring as more water infiltrated the slope. A numerical procedure to estimate the factor of safety over the period of the rainfall event was proposed and validated against the laboratory data. The results of the numerical analysis yielded the failure time, which was close to the time observed in the flume tests.
Reduced-Cost Production of Sophorolipids by Starmerella bombicola CGMCC1576 Grown on Cottonseed Molasses and Cottonseed Oil-Based Medium
Authors: Qin Zehua , Guo Wei , Liu Jun , Zhao Guoqin , Liu Mingxin , Song Xin
Published: March 2023

A large-scale application of sophorolipids (SLs) was blocked by their high production cost. One feasible way to reduce the cost of SL production is to develop cheap feedstocks as the substrates for SL fermentation. In the present work, cottonseed molasses (CM), a waste from raffinose production, was used as the hydrophilic substrate;, and cottonseed oil (CO) was used as a hydrophobic substrate for SL production by Starmerella bombicola CGMCC 1576. The primary optimization of carbon sources, nitrogen source and inorganic salts, produced 57.6 ± 2.3 g/L of total SLs and 24.0 ± 1.2 g/L of lactonic SLs on CM and CO, almost equal to the titer of SLs produced from glucose and oleic. A response surface method was applied to optimize the fermentation medium for growth and SL production of S. bombicola. The production of total SLs reached 58.4 ± 3.4 g/L, and lactonic SLs were elevated to more than 25.0 ± 1.9 g/L. HPLC–MS analysis showed that the compositions of SLs produced by S. bombicola on CM and CO were very similar to those on glucose and oleic acid. These results suggested that cottonseed molasses and cottonseed oil can be used as renewable cheap substrates for the reduced-cost production of SLs.
Genome-Wide Identification and Expression Analysis of Cysteine-Rich Polycomb-like Protein (CPP) Gene Family in Tomato
Authors: Sun Yaoguang , Jia Xinyi , Chen Dexia , Fu Qingjun , Chen Jinxiu , Yang Wenhui , Yang Huanhuan , Xu Xiangyang
Published: March 2023

The cysteine-rich polycomb-like protein (CPP) gene family is a class of transcription factors containing conserved cysteine-rich CRC structural domains that is involved in the regulation of plant growth and stress tolerance to adversity. Relative to other gene families, the CPP gene family has not received sufficient attention. In this study, six SlCPPs were identified for the first time using the most recent genome-wide identification data of tomato. Subsequently, a phylogenetic analysis classified SlCPPs into four subfamilies. The analysis of cis-acting elements in the promoter indicates that SlCPPs are involved in plant growth and development and also stress response. We present for the first time the prediction of the tertiary structure of these SlCPPs proteins using the AlphaFold2 artificial intelligence system developed by the DeepMind team. Transcriptome data analysis showed that SlCPPs were differentially expressed in different tissues. Gene expression profiling showed that all SlCPPs except SlCPP5 were up-regulated under drought stress; SlCPP2, SlCPP3 and SlCPP4 were up-regulated under cold stress; SlCPP2 and SlCPP5 were up-regulated under salt stress; all SlCPPs were up-regulated under inoculation with Cladosporium fulvum; and SlCPP1, SlCPP3, and SlCPP4 were up-regulated under inoculation with Stemphylium lycopersici. We performed a virus-induced gene silencing experiment on SlCPP3, and the results indicated that SlCPP3 was involved in the response to drought stress. Finally, we predicted the interaction network of the key gene SlCPP3, and there was an interaction relationship between SlCPP3 and 10 genes, such as RBR1 and MSI1. The positive outcome showed that SlCPPs responded to environmental stress. This study provides a theoretical and empirical basis for the response mechanisms of tomato in abiotic stresses.
Novel Aspects of the Immune Response Involved in the Peritoneal Damage in Chronic Kidney Disease Patients under Dialysis
Authors: Trionfetti Flavia , Marchant Vanessa , González-Mateo Guadalupe T. , Kawka Edyta , Márquez-Expósito Laura , Ortiz Alberto , López-Cabrera Manuel , Ruiz-Ortega Marta , Strippoli Raffaele
Published: March 2023

Chronic kidney disease (CKD) incidence is growing worldwide, with a significant percentage of CKD patients reaching end-stage renal disease (ESRD) and requiring kidney replacement therapies (KRT). Peritoneal dialysis (PD) is a convenient KRT presenting benefices as home therapy. In PD patients, the peritoneum is chronically exposed to PD fluids containing supraphysiologic concentrations of glucose or other osmotic agents, leading to the activation of cellular and molecular processes of damage, including inflammation and fibrosis. Importantly, peritonitis episodes enhance peritoneum inflammation status and accelerate peritoneal injury. Here, we review the role of immune cells in the damage of the peritoneal membrane (PM) by repeated exposure to PD fluids during KRT as well as by bacterial or viral infections. We also discuss the anti-inflammatory properties of current clinical treatments of CKD patients in KRT and their potential effect on preserving PM integrity. Finally, given the current importance of coronavirus disease 2019 (COVID-19) disease, we also analyze here the implications of this disease in CKD and KRT.
The Benefits of the Post-Transplant Cyclophosphamide in Both Haploidentical and Mismatched Unrelated Donor Setting in Allogeneic Stem Cells Transplantation
Authors: Dybko Jarosław , Sobczyk-Kruszelnicka Małgorzata , Makuch Sebastian , Agrawal Siddarth , Dudek Krzysztof , Giebel Sebatian , Gil Lidia
Published: March 2023

Allogeneic hematopoietic cell transplantation (alloHSCT) is a standard therapeutic approach for acute leukemias and many other hematologic malignancies. The proper choice of immunosuppressants applicable to different types of transplantations still requires strict and careful consideration, and data in this regard are divergent. For this reason, in this single-centered, retrospective study, we aimed to compare the outcome of 145 patients who received post-transplant cyclophosphamide (PTCy) for MMUD and haplo-HSCT or GvHD prophylaxis for MMUD-HSCT alone. We attempted to verify if PTCy is an optimal strategy in MMUD setting. Ninety-three recipients (93/145; 64.1%) underwent haplo-HSCT while 52 (52/145; 35.9%) underwent MMUD-HSCT. There were 110 patients who received PTCy (93 in haplo and 17 in MMUD group) and 35 patients received conventional GvHD prophylaxis based on antithymocyte globulin (ATG), cyclosporine (CsA), and methotrexate (Mtx) in the MMUD group only. Our study revealed that patients receiving post-transplant cyclophosphamide (PTCy) show decreased acute GvHD rates and CMV reactivation as well as a statistically lower number of CMV copies before and after antiviral treatment compared to the CsA + Mtx + ATG group. Taking into account chronic GvHD, the main predictors are donor age, ≥40 years, and haplo-HSCT administration. Furthermore, the survival rate of patients following MMUD-HSCT and receiving PTCy with tacrolimus and mycophenolate mofetil was more than eight times greater in comparison to patients receiving CsA + Mtx + ATG (OR = 8.31, p = 0.003). These data taken together suggest that the use of PTCy displays more benefits in terms of survival rate compared to ATG regardless of the type of transplantation performed. Nevertheless, more studies with a larger sample size are required to confirm the conflicting results in the literature studies.
Long Non-Coding RNA lncWOX11a Suppresses Adventitious Root Formation of Poplar by Regulating the Expression of PeWOX11a
Authors: Ran Na , Liu Sian , Qi Haoran , Wang Jiali , Shen Tengfei , Xu Wenlin , Xu Meng
Published: March 2023

Long non-coding RNAs (lncRNAs), a class of poorly conserved transcripts without protein-encoding ability, are widely involved in plant organogenesis and stress responses by mediating the transmission and expression of genetic information at the transcriptional, posttranscriptional, and epigenetic levels. Here, we cloned and characterized a novel lncRNA molecule through sequence alignment, Sanger sequencing, transient expression in protoplasts, and genetic transformation in poplar. lncWOX11a is a 215 bp transcript located on poplar chromosome 13, ~50 kbp upstream of PeWOX11a on the reverse strand, and the lncRNA may fold into a series of complex stem–loop structures. Despite the small open reading frame (sORF) of 51 bp within lncWOX11a, bioinformatics analysis and protoplast transfection revealed that lncWOX11a has no protein-coding ability. The overexpression of lncWOX11a led to a decrease in the quantity of adventitious roots on the cuttings of transgenic poplars. Further, cis-regulatory module prediction and CRISPR/Cas9 knockout experiments with poplar protoplasts demonstrated that lncWOX11a acts as a negative regulator of adventitious rooting by downregulating the WUSCHEL-related homeobox gene WOX11, which is supposed to activate adventitious root development in plants. Collectively, our findings imply that lncWOX11a is essential for modulating the formation and development of adventitious roots.
The Gut Microbiome, Microsatellite Status and the Response to Immunotherapy in Colorectal Cancer
Authors: Sillo Toritseju O. , Beggs Andrew D. , Middleton Gary , Akingboye Akinfemi
Published: March 2023

There is increasing evidence in a range of cancer types that the microbiome plays a direct role in modulating the anti-cancer immune response both at the gut level and systemically. Differences in the gut microbiota have been shown to correlate with differences in immunotherapy responses in a range of non-gastrointestinal tract cancers. DNA mismatch repair-deficient (dMMR) colorectal cancer (CRC) is radically different to DNA mismatch repair-proficient (pMMR) CRC in clinical phenotype and in its very good responses to immunotherapy. While this has usually been thought to be due to the high mutational burden in dMMR CRC, the gut microbiome is radically different in dMMR and pMMR CRC in terms of both composition and diversity. It is probable that differences in the gut microbiota contribute to the varied responses to immunotherapy in dMMR versus pMMR CRC. Targeting the microbiome offers a way to boost the response and increase the selection of patients who might benefit from this therapy. This paper reviews the available literature on the role of the microbiome in the response to immunotherapy in dMMR and pMMR CRC, explores the potential causal relationship and discusses future directions for study in this exciting and rapidly changing field.
De Novo Transcriptome Sequencing of Codonopsis lanceolata for Identification of Triterpene Synthase and Triterpene Acetyltransferase
Authors: Choi Han-Bin , Shim Sangrea , Wang Myeong-Hyeon , Choi Yong-Eui
Published: March 2023

Codonopsis lanceolata (Campanulaceae) is a perennial plant commonly known as the bonnet bellflower. This species is widely used in traditional medicine and is considered to have multiple medicinal properties. In this study, we found that shoots and roots of C. lanceolata contained various types of free triterpenes (taraxerol, β-amyrin, α-amyrin, and friedelin) and triterpene acetates (taraxerol acetate, β-amyrin acetate, and α-amyrin acetate). The content of triterpenes and triterpene acetates by GC analysis was higher in the shoot than in the roots. To investigate the transcriptional activity of genes involved in triterpenes and triterpene acetate biosynthesis, we performed de novo transcriptome analysis of shoots and roots of C. lanceolata by sequencing using the Illumina platform. A total of 39,523 representative transcripts were obtained. After functional annotation of the transcripts, the differential expression of genes involved in triterpene biosynthetic pathways was investigated. Generally, the transcriptional activity of unigenes in the upstream region (MVA and MEP pathway) of triterpene biosynthetic pathways was higher in shoots than in roots. Various triterpene synthases (2,3-oxidosqualene cyclase, OSC) participate to produce triterpene skeletons by the cyclization of 2,3-oxidosqualene. A total of fifteen contigs were obtained in annotated OSCs in the representative transcripts. Functional characterization of four OSC sequences by heterologous expression in yeast revealed that ClOSC1 was determined as taraxerol synthase, and ClOSC2 was a mixed-amyrin synthase producing α-amyrin and β-amyrin. Five putative contigs of triterpene acetyltransferases showed high homology to the lettuce triterpene acetyltransferases. Conclusively, this study provides the basis of molecular information, particularly for the biosynthesis of triterpenes and triterpene acetates in C. lanceolata.
Improving Whole Tomato Transformation for Prostate Health: Benign Prostate Hypertrophy as an Exploratory Model
Authors: Natali Pier Giorgio , Piantelli Mauro , Minacori Marco , Eufemi Margherita , Imberti Luisa
Published: March 2023

It is well-established that the beneficial properties of single phytonutrients can be better attained when they are taken with the complex of the molecules present in their natural milieu. Tomato, the fruit providing the most comprehensive complex of prostate-health-preserving micronutrients, has been shown to be superior to its single-nutrient counterparts in decreasing the incidence of age-related prostate diseases. Herein, we describe a novel tomato food supplement enriched with olive polyphenols, containing cis-lycopene concentrations far exceeding those present in industry-produced tomato commodities. The supplement, endowed with antioxidant activity comparable to that of N-acetylcysteine, significantly reduced, in experimental animals, the blood levels of prostate-cancer-promoting cytokines. In prospective, randomized, double-blinded, placebo-controlled studies performed on patients affected by benign prostatic hyperplasia, its uptake significantly improved urinary symptoms and quality of life. Therefore, this supplement can complement and, in some cases, be an alternative to current benign prostatic hyperplasia management. Furthermore, the product suppressed carcinogenesis in the TRAMP mouse model of human prostate cancer and interfered with prostate cancer molecular signaling. Thus, it may offer a step forward in exploring the potential of tomato consumption to delay or prevent the onset of age-related prostate diseases in high-risk individuals.