bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple paths to rumination within a network analytical framework
Authors: Tamm Gerly , Koster Ernst H. W. , Hoorelbeke Kristof 
Published: May 2024

AbstractTheories of rumination have proposed different psychological factors to place one at risk for repetitive negative thinking. A comprehensive empirical test that captures the most relevant contributors to rumination is lacking. Building on influential self-regulatory and metacognitive frameworks, we modeled how key constructs in this context relate to ruminative thinking. 498 participants completed online questionnaires including indicators of rumination, metacognition, promotion goal orientation, effortful control, and depression. We estimated regularized partial correlation networks to investigate unique associations between the different constructs and followed these analyses up with directed acyclic graphs to identify potential pathways towards rumination. Results demonstrated that: (1) both self-regulatory and metacognitive factors were directly linked to rumination, amongst these were (2) positive beliefs, negative beliefs about uncontrollability and harm, cognitive self-consciousness, depression, effortful control, perfectionism, and (lack of) cognitive confidence, and (3) we identified multiple directed pathways, suggesting three direct contributors to rumination while controlling for the influence of all other variables: diminished effortful control, positive beliefs, and cognitive self-consciousness. This study is the first to comprehensively assess metacognitive and self-regulatory frameworks of rumination in a data-driven manner. Our findings suggest that there are multiple pathways towards rumination, which should be incorporated in clinical case conceptualization of rumination and related disorders.
RNA-Seq transcriptome profiling of immature grain wheat is a technique for understanding comparative modeling of baking quality
Authors: Ahmadi-Ochtapeh Hossein , Soltanloo Hassan , Ramezanpour Seyyede Sanaz , Yamchi Ahad , Shariati Vahid 
Published: May 2024

AbstractImproving the baking quality is a primary challenge in the wheat flour production value chain, as baking quality represents a crucial factor in determining its overall value. In the present study, we conducted a comparative RNA-Seq analysis on the high baking quality mutant “O-64.1.10” genotype and its low baking quality wild type "Omid" cultivar to recognize potential genes associated with bread quality. The cDNA libraries were constructed from immature grains that were 15 days post-anthesis, with an average of 16.24 and 18.97 million paired-end short-read sequences in the mutant and wild-type, respectively. A total number of 733 transcripts with differential expression were identified, 585 genes up-regulated and 188 genes down-regulated in the “O-64.1.10” genotype compared to the “Omid”. In addition, the families of HSF, bZIP, C2C2-Dof, B3-ARF, BES1, C3H, GRF, HB-HD-ZIP, PLATZ, MADS-MIKC, GARP-G2-like, NAC, OFP and TUB were appeared as the key transcription factors with specific expression in the “O-64.1.10” genotype. At the same time, pathways related to baking quality were identified through Kyoto Encyclopedia of Genes and Genomes. Collectively, we found that the endoplasmic network, metabolic pathways, secondary metabolite biosynthesis, hormone signaling pathway, B group vitamins, protein pathways, pathways associated with carbohydrate and fat metabolism, as well as the biosynthesis and metabolism of various amino acids, have a great deal of potential to play a significant role in the baking quality. Ultimately, the RNA-seq results were confirmed using quantitative Reverse Transcription PCR for some hub genes such as alpha-gliadin, low molecular weight glutenin subunit and terpene synthase (gibberellin) and as a resource for future study, 127 EST-SSR primers were generated using RNA-seq data.
Dynamic changes in extracellular vesicle-associated miRNAs elicited by ultrasound in inflammatory bowel disease patients
Authors: Tran Florian , Scharmacher Alena , Baran Nathan , Mishra Neha , Wozny Marek , Chavez Samuel Pineda , Bhardwaj Archana , Hinz Sophia , Juzenas Simonas , Bernardes Joana P. , Sievers Laura Katharina , Lessing Matthias , Aden Konrad , Lassen Arne , Bergfeld Arne , Weber Hauke Jann , Neas Lennart , Vetrano Stefania , Schreiber Stefan , Rosenstiel Philip 
Published: May 2024

AbstractBlood-based biomarkers that reliably indicate disease activity in the intestinal tract are an important unmet need in the management of patients with IBD. Extracellular vesicles (EVs) are cell-derived membranous microparticles, which reflect the cellular and functional state of their site of site of origin. As ultrasound waves may lead to molecular shifts of EV contents, we hypothesized that application of ultrasound waves on inflamed intestinal tissue in IBD may amplify the inflammation-specific molecular shifts in EVs like altered EV-miRNA expression, which in turn can be detected in the peripheral blood. 26 patients with IBD were included in the prospective clinical study. Serum samples were collected before and 30 min after diagnostic transabdominal ultrasound. Differential miRNA expression was analyzed by sequencing. Candidate inducible EV-miRNAs were functionally assessed in vitro by transfection of miRNA mimics and qPCR of predicted target genes. Serum EV-miRNA concentration at baseline correlated with disease severity, as determined by clinical activity scores and sonographic findings. Three miRNAs (miR-942-5p, mir-5588, mir-3195) were significantly induced by sonography. Among the significantly regulated EV-miRNAs, miR-942-5p was strongly induced in higher grade intestinal inflammation and correlated with clinical activity in Crohn’s disease. Prediction of target regulation and transfection of miRNA mimics inferred a role of this EV-miRNA in regulating barrier function in inflammation. Induction of mir-5588 and mir-3195 did not correlate with inflammation grade. This proof-of-concept trial highlights the principle of induced molecular shifts in EVs from inflamed tissue through transabdominal ultrasound. These inducible EVs and their molecular cargo like miRNA could become novel biomarkers for intestinal inflammation in IBD.
Exploring the geometry of the bifurcation sets in parameter space
Authors: Barrio Roberto , Ibáñez Santiago , Pérez Lucía 
Published: May 2024

AbstractBy studying a nonlinear model by inspecting a p-dimensional parameter space through $$(p-1)$$

(
p
-
1
)

-dimensional cuts, one can detect changes that are only determined by the geometry of the manifolds that make up the bifurcation set. We refer to these changes as geometric bifurcations. They can be understood within the framework of the theory of singularities for differentiable mappings and, in particular, of the Morse Theory. Working with a three-dimensional parameter space, geometric bifurcations are illustrated in two models of neuron activity: the Hindmarsh–Rose and the FitzHugh–Nagumo systems. Both are fast-slow systems with a small parameter that controls the time scale of a slow variable. Geometric bifurcations are observed on slices corresponding to fixed values of this distinguished small parameter, but they should be of interest to anyone studying bifurcation diagrams in the context of nonlinear phenomena.
Mortality among extrapulmonary tuberculosis patients in the HIV endemic setting: lessons from a tertiary level hospital in Mbeya, Tanzania
Authors: Grønningen Erlend , Nanyaro Marywinnie , Blomberg Bjørn , Hassan Shoaib , Ngadaya Esther , Mustafa Tehmina 
Published: May 2024

AbstractExtrapulmonary tuberculosis (EPTB) has received less attention than pulmonary tuberculosis due to its non-contagious nature. EPTB can affect any organ and is more prevalent in people living with HIV. Low- and middle-income countries are now facing the double burden of non-communicable diseases (NCDs) and HIV, complicating the management of patients with symptoms that could be compatible with both EPTB and NCDs. Little is known about the risk of death of patients presenting with symptoms compatible with EPTB. We included patients with a clinical suspicion of EPTB from a tertiary level hospital in Mbeya, Tanzania, to assess their risk of dying. A total of 113 (61%) patients were classified as having EPTB, and 72 (39%) as having non-TB, with corresponding mortality rates of 40% and 41%. Associated factors for mortality in the TB groups was hospitalization and male sex. Risk factors for hospitalization was having disease manifestation at any site other than lymph nodes, and comorbidities. Our results imply that NCDs serve as significant comorbidities amplifying the mortality risk in EPTB. To strive towards universal health coverage, focus should be on building robust health systems that can tackle both infectious diseases, such as EPTB, and NCDs.
Integrated single-cell and bulk RNA-Seq analysis enhances prognostic accuracy of PD-1/PD-L1 immunotherapy response in lung adenocarcinoma through necroptotic anoikis gene signatures
Authors: Sui Ping , Liu Xueping , Zhong Cheng , Sha Zhanming 
Published: May 2024

AbstractIn addition to presenting significant diagnostic and treatment challenges, lung adenocarcinoma (LUAD) is the most common form of lung cancer. Using scRNA-Seq and bulk RNA-Seq data, we identify three genes referred to as HMR, FAM83A, and KRT6A these genes are related to necroptotic anoikis-related gene expression. Initial validation, conducted on the GSE50081 dataset, demonstrated the model's ability to categorize LUAD patients into high-risk and low-risk groups with significant survival differences. This model was further applied to predict responses to PD-1/PD-L1 blockade therapies, utilizing the IMvigor210 and GSE78220 cohorts, and showed strong correlation with patient outcomes, highlighting its potential in personalized immunotherapy. Further, LUAD cell lines were analyzed using quantitative PCR (qPCR) and Western blot analysis to confirm their expression levels, further corroborating the model's relevance in LUAD pathophysiology. The mutation landscape of these genes was also explored, revealing their broad implication in various cancer types through a pan-cancer analysis. The study also delved into molecular subclustering, revealing distinct expression profiles and associations with different survival outcomes, emphasizing the model’s utility in precision oncology. Moreover, the diversity of immune cell infiltration, analyzed in relation to the necroptotic anoikis signature, suggested significant implications for immune evasion mechanisms in LUAD. While the findings present a promising stride towards personalized LUAD treatment, especially in immunotherapy, limitations such as the retrospective nature of the datasets and the need for larger sample sizes are acknowledged. Prospective clinical trials and further experimental research are essential to validate these findings and enhance the clinical applicability of our prognostic model.
SNPs in microRNA seed region and impact of miR-375 in concurrent regulation of multiple lipid accumulation-related genes
Authors: Lee Jiyeon , Hong Inpyo , Lee Chanwoo , Kim Daehyun , Kim Sunghak , Lee Yoonseok 
Published: May 2024

AbstractBovine intramuscular fat (IMF), commonly referred to as marbling, is regulated by lipid metabolism, which includes adipogenesis, lipogenesis, glycerolipid synthesis, and lipolysis. In recent years, breeding researchers have identified single nucleotide polymorphisms (SNPs) as useful marker-assisted selection tools for improving marbling scores in national breeding programs. These included causal SNPs that induce phenotypic variation. MicroRNAs (miRNAs) are small highly conserved non-coding RNA molecules that bind to multiple non-coding regions. They are involved in post-transcriptional regulation. Multiple miRNAs may regulate a given target. Previously, three SNPs in the GPAM 3ʹ UTR and four miRNAs were identified through in silico assays. The aim of this study is to verify the binding ability of the four miRNAs to the SNPs within the 3ʹUTR of GPAM, and to identify the regulatory function of miR-375 in the expression of genes related to lipid metabolism in mammalian adipocytes. It was verified that the four miRNAs bind to the GPAM 3ʹUTR, and identified that the miR-375 sequence is highly conserved. Furthermore, it was founded that miR-375 upregulated the GPAM gene, C/EBPα, PPARγ and lipid metabolism-related genes and promoted lipid droplet accumulation in 3T3-L1 cells. In conclusion, these results suggest that miR-375 is a multifunctional regulator of multiple lipid metabolism-related genes and may aid in obesity research as a biomarker.
Optimization of off-grid hybrid renewable energy systems for cost-effective and reliable power supply in Gaita Selassie Ethiopia
Authors: Agajie Elsabet Ferede , Agajie Takele Ferede , Amoussou Isaac , Fopah-Lele Armand , Nsanyuy Wirnkar Basil , Khan Baseem , Bajaj Mohit , Zaitsev Ievgen , Tanyi Emmanuel 
Published: May 2024

AbstractThis paper explores scenarios for powering rural areas in Gaita Selassie with renewable energy plants, aiming to reduce system costs by optimizing component numbers to meet energy demands. Various scenarios, such as combining solar photovoltaic (PV) with pumped hydro-energy storage (PHES), utilizing wind energy with PHES, and integrating a hybrid system of PV, wind, and PHES, have been evaluated based on diverse criteria, encompassing financial aspects and reliability. To achieve the results, meta-heuristics such as the Multiobjective Gray wolf optimization algorithm (MOGWO) and Multiobjective Grasshopper optimization algorithm (MOGOA) were applied using MATLAB software. Moreover, optimal component sizing has been investigated utilizing real-time assessment data and meteorological data from Gaita Sillasie, Ethiopia. Metaheuristic optimization techniques were employed to pinpoint the most favorable loss of power supply probability (LPSP) with the least cost of energy (COE) and total life cycle cost (TLCC) for the hybrid system, all while meeting operational requirements in various scenarios. The Multi-Objective Grey Wolf Optimization (MOGWO) technique outperformed the Multi-Objective Grasshopper Optimization Algorithm (MOGOA) in optimizing the problem, as suggested by the results. Furthermore, based on MOGWO findings, the hybrid solar PV-Wind-PHES system demonstrated the lowest COE (0.126€/kWh) and TLCC (€6,897,300), along with optimal satisfaction of the village's energy demand and LPSP value. In the PV-Wind-PHSS scenario, the TLCC and COE are 38%, 18%, 2%, and 1.5% lower than those for the Wind-PHS and PV-PHSS scenarios at LPSP 0%, according to MOGWO results. Overall, this research contributes valuable insights into the design and implementation of sustainable energy solutions for remote communities, paving the way for enhanced energy access and environmental sustainability.
Micro- and nano-Illite to improve strength of untreated-soil as a nano soil-improvement (NSI) technique
Authors: Cheraghalikhani Mohadeseh , Niroumand Hamed , Balachowski Lech 
Published: May 2024

AbstractSoil stabilization is a technique of improving the geotechnical properties of soils for various engineering applications. However, conventional stabilizers such as cement and lime have some limitations, such as high cost, environmental impact, and durability issues. Therefore, there is a need for alternative and innovative stabilizers that can overcome these challenges. This study introduces nano-Illite, a type of clay mineral, as a novel and effective soil stabilizer. Nano-Illite can form nano-cementation (NC) in soil, which is a process of enhancing the durability of various building materials. NC is also known as nano soil-improvement (NSI), a technique that has been developed in recent years. Four formulations of micro- and nano-Illite with concentrations of 0, 1, 2, and 3% were separately added to soil samples. The unconfined compressive strength (UCS) and the secant modulus at 50% of peak stress (E50) of the treated samples were measured and compared with the untreated samples. The results showed that 3% nano-Illite increased the UCS of soil by more than 2.2 times and the E50 by more than 1.5 times after 7 days of curing. Micro-Illite also improved the UCS and E50 of soil, but to a lesser extent. X-ray fluorescence (XRF), scanning electron microscopy (SEM), and X-ray diffraction (XRD) analyses revealed the micro- and nano-structures of the soil specimens and the performance of Illite as a nano-additive. This research demonstrates the effectiveness of nano-Illite in soil improvement as a NSI technique, and its potential to replace or reduce the use of conventional stabilizers. This study also contributes to the understanding of the mechanisms and factors that influence the NC process in soil.
Analysis of vertical differentiation of vegetation in Taishan World Heritage site based on cloud model
Authors: Wang Zhe , Han Fang , Li Chuanrong , Shen Weixing , Yang Zhijun , Li Kun , Yao Qi 
Published: May 2024

AbstractWhile the forests on Mount Taishan are predominantly man-made, there is a notable vertical variation in vegetation. This study employs the method of cloud model, quantifying uncertainty (fuzziness and randomness) of things. Utilizing digital elevation model (DEM) and vegetation distribution data, we constructed elevation cloud models for Mount Taishan’s deciduous broad-leaved, temperate coniferous, and mixed coniferous-broadleaved forests. Using three numerical features of the cloud model—Expectation (EX), Entropy (EN), and Hyper-entropy (HE)—we quantitatively analyzed the macro regularity and local heterogeneity of Mount Taishan’s forests vertical distribution from the perspective of uncertainty theory. The results indicate: (1) The EX of the core zone elevation of deciduous broad-leaved forest is 716.65 m, temperate coniferous forest is 1053.51 m, and mixed coniferous-broadleaved forest is 1384.09 m. The variation range of the core zone distribution height is smaller in the mixed coniferous-broadleaved forest (EN: 53.74 m) compared to deciduous broad-leaved forest (EN: 99.63 m) and temperate coniferous forest (EN: 121.70 m). (2) The fuzziness and randomness of the distribution height of the lower extension zones of deciduous broad-leaved forest and temperate coniferous forest (EN: 75.15 m, 184.56 m; HE: 24.09 m, 63.54 m) are greater than those of the upper extension zones (EN: 44.75 m, 42.49 m; HE: 14.48 m, 13.23 m). (3) The distribution fuzziness and randomness within temperate coniferous forests exceed those of deciduous broad-leaved forests. Within the core zones, the uncertainty regarding the vertical distribution of vegetation across different aspects remains consistent, which retains the characteristic of man-made forests. However, in transition areas, there is significant disparity, reflecting the adaptive relationship between vegetation and its environment to some extent. In the upper and lower extension zones of deciduous broad-leaved forests, the EX values for the vertical distribution height of mixed coniferous and broad-leaved forests differ significantly from those of deciduous broad-leaved forests (the difference is 22.82–39.15 m), yet closely resemble those of temperate coniferous forests (the difference is 4.79–7.94 m). This suggests a trend wherein deciduous broad-leaved tree species exhibit a proclivity to encroach upon coniferous forest habitats. The elevation cloud model of vertical vegetation zones provides a novel perspective and method for the detailed analysis of Mount Taishan’s vegetation vertical differentiation.
Effects of porous structure and oxygen functionalities on electrochemical synthesis of hydrogen peroxide on ordered mesoporous carbon
Authors: Albashir Abdalazeez Ismail Mohamed , Lu Xingyu , Dai Xueya , Qi Wei 
Published: May 2024

AbstractTwo-electron oxygen reduction reaction (2e− ORR) is a promising alternative to energy-intensive anthraquinone process for hydrogen peroxide (H2O2) production. Metal-free nanocarbon materials have garnered intensive attention as highly prospective electrocatalysts for H2O2 production, and an in-depth understanding of their porous structure and active sites have become a critical scientific challenge. The present research investigates a range of porous carbon catalysts, including non-porous, microporous, and mesoporous structures, to elucidate the impacts of porous structures on 2e− ORR activity. The results highlighted the superiority of mesoporous carbon over other porous materials, demonstrating remarkable H2O2 selectivity. Furthermore, integration of X-ray photoelectron spectroscopy (XPS) data analysis with electrochemical assessment results unravels the moderate surface oxygen content is the key to increase 2e− ORR activity. These results not only highlight the intricate interplay between pore structure and oxygen content in determining catalytic selectivity, but also enable the design of carbon catalysts for specific electrochemical reactions.
Recovery of missing samples in Orthogonal Frequency Division Multiplexing signals with optimisation using data carriers
Authors: Haglund Anders , Frölind Per‐Olov , Ulander Lars M. H. 
Published: May 2024

AbstractA method is proposed for reconstructing an Orthogonal Frequency Division Multiplexing (OFDM) signal that contains data gaps, with the aim to improve demodulation. The main objective is to use the method in a passive radar application with missing data samples and to improve target detection. The OFDM signal is assumed to comply with the Digital Video Broadcasting Terrestrial standard. The proposed recovery method is based on optimisation of a novel objective function, which consists of two parts. The first part is a function of the energy in the out‐of‐band frequencies, whereas the second, and novel part, uses the location of data carriers in the constellation diagram. The method is evaluated using both simulations and real data. The authors show that the proposed method significantly improves the OFDM signal in just a few iteration steps. The proposed method improved the condition number more than a factor ten thousand millions compared to using the least square method on the out‐of‐band frequencies only. The authors also decode the symbols with the Viterbi decoding algorithm and show how the required number of iterations with the proposed algorithm depends on the amount of missing samples and on the Signal‐to‐Noise Ratio in order to achieve a Bit Error Rate of less than one in one hundred thousand millions.