bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ising-like model replicating time-averaged spiking behaviour of in vitro neuronal networks
Authors: Sampaio Filho Cesar I. N. , de Arcangelis Lucilla , Herrmann Hans J. , Plenz Dietmar , Kells Patrick , Ribeiro Tiago Lins , Andrade José S. 
Published: March 2024

AbstractWe analyze time-averaged experimental data from in vitro activities of neuronal networks. Through a Pairwise Maximum-Entropy method, we identify through an inverse binary Ising-like model the local fields and interaction couplings which best reproduce the average activities of each neuron as well as the statistical correlations between the activities of each pair of neurons in the system. The specific information about the type of neurons is mainly stored in the local fields, while a symmetric distribution of interaction constants seems generic. Our findings demonstrate that, despite not being directly incorporated into the inference approach, the experimentally observed correlations among groups of three neurons are accurately captured by the derived Ising-like model. Within the context of the thermodynamic analogy inherent to the Ising-like models developed in this study, our findings additionally indicate that these models demonstrate characteristics of second-order phase transitions between ferromagnetic and paramagnetic states at temperatures above, but close to, unity. Considering that the operating temperature utilized in the Maximum-Entropy method is $$T_{o}=1$$

T
o

=
1

, this observation further expands the thermodynamic conceptual parallelism postulated in this work for the manifestation of criticality in neuronal network behavior.
Integrated image and location analysis for wound classification: a deep learning approach
Authors: Patel Yash , Shah Tirth , Dhar Mrinal Kanti , Zhang Taiyu , Niezgoda Jeffrey , Gopalakrishnan Sandeep , Yu Zeyun 
Published: March 2024

AbstractThe global burden of acute and chronic wounds presents a compelling case for enhancing wound classification methods, a vital step in diagnosing and determining optimal treatments. Recognizing this need, we introduce an innovative multi-modal network based on a deep convolutional neural network for categorizing wounds into four categories: diabetic, pressure, surgical, and venous ulcers. Our multi-modal network uses wound images and their corresponding body locations for more precise classification. A unique aspect of our methodology is incorporating a body map system that facilitates accurate wound location tagging, improving upon traditional wound image classification techniques. A distinctive feature of our approach is the integration of models such as VGG16, ResNet152, and EfficientNet within a novel architecture. This architecture includes elements like spatial and channel-wise Squeeze-and-Excitation modules, Axial Attention, and an Adaptive Gated Multi-Layer Perceptron, providing a robust foundation for classification. Our multi-modal network was trained and evaluated on two distinct datasets comprising relevant images and corresponding location information. Notably, our proposed network outperformed traditional methods, reaching an accuracy range of 74.79–100% for Region of Interest (ROI) without location classifications, 73.98–100% for ROI with location classifications, and 78.10–100% for whole image classifications. This marks a significant enhancement over previously reported performance metrics in the literature. Our results indicate the potential of our multi-modal network as an effective decision-support tool for wound image classification, paving the way for its application in various clinical contexts.
High-throughput homogenous assay for the direct detection of Listeria monocytogenes DNA
Authors: Armstrong Cheryl M. , Capobianco Joseph A. , Nguyen Sarah , Guragain Manita , Liu Yanhong 
Published: March 2024

AbstractThe Amplified Luminescent Proximity Homogenous Assay-linked Immunosorbent Assay (AlphaLISA) is known for detecting various protein targets; however, its ability to detect nucleic acid sequences is not well established. Here, the capabilities of the AlphaLISA technology were expanded to include direct detection of DNA (aka: oligo-Alpha) and was applied to the detection of Listeria monocytogenes. Parameters were defined that allowed the newly developed oligo-Alpha to differentiate L. monocytogenes from other Listeria species through the use of only a single nucleotide polymorphism within the 16S rDNA region. Investigations into the applicability of this assay with different matrices demonstrated its utility in both milk and juice. One remarkable feature of the oligo-Alpha is that greater sensitivity could be achieved through the use of multiple acceptor oligos compared to only a single acceptor oligo, even when only a single donor oligo was employed. Additional acceptor oligos were easily incorporated into the assay and a tenfold change in the detection limit was readily achieved, with detection limits of 250 attomole of target being recorded. In summary, replacement of antibodies with oligonucleotides allows us to take advantage of genotypic difference(s), which both expands its repertoire of biological markers and furthers its use as a diagnostic tool.
Digital finance, innovation transformation, and resilient city growth
Authors: Zhang Wenwu , Wang Jinguo , Jin Hongkui 
Published: March 2024

AbstractDigital finance is a pivotal catalyst for a contemporary economic system and assumes a significant auxiliary function in the establishment of resilient urban centers. This study empirically examines the enabling influence of digital finance on resilient cities using panel data from 287 prefecture-level cities and above in China between 2011 and 2020. The analysis is based on the mechanisms of innovation and transformation. The importance of digital finance in facilitating the development of resilient cities has been observed, with a specific emphasis on its impact on enhancing the adaptive capacity and growth resilience of urban areas. The utilization of digital finance has the potential to expedite the process of transforming urban industrial structures, invigorating innovation and entrepreneurial activities, and serving as a significant catalyst for the development of resilient cities. The analysis of heterogeneity reveals that various aspects of digital finance have varying degrees of influence on urban resilience. Specifically, the depth of utilization of digital finance exerts the most significant impact, followed by the level of digitalization, while the extent of coverage has the least effect. Furthermore, when considering regional distribution, the promotion effect of digital finance on resilient cities diminishes gradually from the eastern to the central and western regions.
Role of Rad18 in B cell activation and lymphomagenesis
Authors: Kalweit Kevin , Gölling Vanessa , Kosan Christian , Jungnickel Berit 
Published: March 2024

AbstractMaintenance of genome integrity is instrumental in preventing cancer. In addition to DNA repair pathways that prevent damage to DNA, damage tolerance pathways allow for the survival of cells that encounter DNA damage during replication. The Rad6/18 pathway is instrumental in this process, mediating damage bypass by ubiquitination of proliferating cell nuclear antigen. Previous studies have shown different roles of Rad18 in vivo and in tumorigenesis. Here, we show that B cells induce Rad18 expression upon proliferation induction. We have therefore analysed the role of Rad18 in B cell activation as well as in B cell lymphomagenesis mediated by an Eµ–Myc transgene. We find no activation defects or survival differences between Rad18 WT mice and two different models of Rad18 deficient tumour mice. Also, tumour subtypes do not differ between the mouse models. Accordingly, functions of Rad18 in B cell activation and tumorigenesis may be compensated for by other pathways in B cells.
Association among childhood adversity and susceptibility to interference during varying salience: two studies in healthy males
Authors: Amedick Greta , Krylova Marina , Mayer Kathrin , Izyurov Igor , Herrmann Luisa , Martens Louise , Kasties Vanessa , Heller Johanna , Li Meng , van der Meer Johan , Croy Ilona , Engert Veronika , Walter Martin , Colic Lejla 
Published: March 2024

AbstractChildhood adversity, a prevalent experience, is related to a higher risk for externalizing and internalizing psychopathology. Alterations in the development of cognitive processes, for example in the attention-interference domain may link childhood adversity and psychopathology. Interfering stimuli can vary in their salience, i.e. ability to capture attentional focus, and valence. However, it is not known if interference by salience or valence is associated with self-reported adversity. In two independent study samples of healthy men (Study 1: n = 44; mean age [standard deviation (SD)] = 25.9 [3.4] years; Study 2: n = 37; 43.5 [9.7] years) we used the attention modulation task (AMT) that probed interference by two attention-modulating conditions, salience and valence separately across repeated target stimuli. The AMT measures the effects of visual distractors (pictures) on the performance of auditory discrimination tasks (target stimuli). We hypothesized that participants reporting higher levels of childhood adversity, measured with the childhood trauma questionnaire, would show sustained interference in trials with lower salience. Due to conflicting reports on the valence-modulation, we tested the valence condition in an exploratory manner. Linear mixed models revealed an interaction between reported childhood adversity and the salience condition across tone presentations in both study samples (Sample 1: p = .03; Sample 2: p = .04), while there were no effects for the valence condition across both studies. Our study suggests that higher self-reported childhood adversity is related to faster processing of target cues during high salience, but slower during low salience conditions. These results hint to the mechanisms linking childhood adversity and psychopathological symptoms in the attentional domain.
Voluntary exercise preserves visual function and reduces inflammatory response in an adult mouse model of autosomal dominant retinitis pigmentosa
Authors: Bales Katie L. , Karesh Austin M. , Hogan Kelleigh , Chacko Alicia S. , Douglas GianMarco L. , Feola Andrew J. , Nickerson John M. , Pybus Alyssa , Wood Levi , Boatright Jeffrey H. , Pardue Machelle T. 
Published: March 2024

AbstractWhole-body physical exercise has been shown to promote retinal structure and function preservation in animal models of retinal degeneration. It is currently unknown how exercise modulates retinal inflammatory responses. In this study, we investigated cytokine alterations associated with retinal neuroprotection induced by voluntary running wheel exercise in a retinal degeneration mouse model of class B1 autosomal dominant retinitis pigmentosa, I307N Rho. I307N Rho mice undergo rod photoreceptor degeneration when exposed to bright light (induced). Our data show, active induced mice exhibited significant preservation of retinal and visual function compared to inactive induced mice after 4 weeks of exercise. Retinal cytokine expression revealed significant reductions of proinflammatory chemokines, keratinocyte-derived chemokine (KC) and interferon gamma inducible protein-10 (IP-10) expression in active groups compared to inactive groups. Through immunofluorescence, we found KC and IP-10 labeling localized to retinal vasculature marker, collagen IV. These data show that whole-body exercise lowers specific retinal cytokine expression associated with retinal vasculature. Future studies should determine whether suppression of inflammatory responses is requisite for exercise-induced retinal protection.
Comparative efficacy of different types of exercise modalities on psychiatric symptomatology in patients with schizophrenia: a systematic review with network meta-analysis
Authors: Cui Wenlai , Liu Zhitao , Liang Cheng , Zhao Zhizhi 
Published: March 2024

AbstractThis network meta-analysis investigated the effects of 8 types of physical exercises on treating positive symptoms, negative symptoms, general psychopathology, and the Positive And Negative Syndrome Scale (PANSS) total score in patients with schizophrenia. The methods adhered to PRISMA guidelines and used the Cochrane risk of bias tool for quality assessment, and Stata software for data analysis. Data were sourced from PubMed, Embase, Web of Science, and the Cochrane database up to August 15, 2023, following PICOS principles. A total of 25 studies including 1441 participants were analyzed. Results showed that resistance exercise seems to be effective for improving positive symptoms, while Yoga was more effective for negative symptoms. Low-intensity aerobic exercise was optimal for general psychopathology, and Yoga was effective in improving the PANSS total score. The study concluded that yoga and aerobic exercise demonstrated superior performance, but the impact of exercise on patients with schizophrenia is also influenced by individual factors and intervention dosages. Therefore, a pre-assessment of patients considering factors such as interests, hobbies, and physical capabilities is crucial for selecting appropriate exercise modalities.
The reproduction process of Gram-positive protocells
Authors: Kanaparthi Dheeraj , Lampe Marko , Krohn Jan-Hagen , Zhu Baoli , Hildebrand Falk , Boesen Thomas , Klingl Andreas , Phapale Prasad , Lueders Tillmann 
Published: March 2024

AbstractProtocells are believed to have existed on early Earth prior to the emergence of prokaryotes. Due to their rudimentary nature, it is widely accepted that these protocells lacked intracellular mechanisms to regulate their reproduction, thereby relying heavily on environmental conditions. To understand protocell reproduction, we adopted a top–down approach of transforming a Gram-positive bacterium into a lipid-vesicle-like state. In this state, cells lacked intrinsic mechanisms to regulate their morphology or reproduction, resembling theoretical propositions on protocells. Subsequently, we grew these proxy-protocells under the environmental conditions of early Earth to understand their impact on protocell reproduction. Despite the lack of molecular biological coordination, cells in our study underwent reproduction in an organized manner. The method and the efficiency of their reproduction can be explained by an interplay between the physicochemical properties of cell constituents and environmental conditions. While the overall reproductive efficiency in these top-down modified cells was lower than their counterparts with a cell wall, the process always resulted in viable daughter cells. Given the simplicity and suitability of this reproduction method to early Earth environmental conditions, we propose that primitive protocells likely reproduced by a process like the one we described below.
Optimization by Box–Behnken design for environmental contaminants removal using magnetic nanocomposite
Authors: Buenaño Luis , Ali Eyhab , Jafer Ahmed , Zaki Shaima Haithem , Hammady Fathi Jihad , Khayoun Alsaadi Salima Baqir , Karim Manal Morad , Ramadan Montather F. , Omran Alaa A. , Alawadi Ahmed , Alsalamy Ali , Kazemi Ali 
Published: March 2024

AbstractIn this study, a CoO–Fe2O3/SiO2/TiO2 (CIST) nanocomposite was synthesized and utilized as an adsorbent to remove methylene blue (MB), malachite green (MG), and copper (Cu) from aqueous environments. The synthesized nanocomposite was characterized using field emission scanning electron microscopy (FE-SEM), Fourier-transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), and X-ray diffraction (XRD). Input parameters included pH (3–10), contact time (10–30 min), adsorbent amount (0.01–0.03 g), and pollutant concentration (20–60 mg L−1). The effects of these parameters on the removal process efficiency were modeled and optimized using the response surface methodology (RSM) based on the Box–Behnken design (BBD). The RSM-BBD method demonstrated the capability to develop a second-degree polynomial model with high validity (R2 ˃ 0.99) for the removal process. The optimization results using the RSM-BBD method revealed a removal efficiency of 98.01%, 93.06%, and 88.26% for MB, MG, and Cu, respectively, under optimal conditions. These conditions were a pH of 6, contact time of 10 min, adsorbent amount of 0.025 g, and concentration of 20 mg L−1. The synthesized adsorbent was recovered through five consecutive adsorption–desorption cycles using hydrochloric acid. The results showed an approximately 12% reduction from the first to the seventh cycle. Also, MB, MG, and Cu removal from real water samples in optimal conditions was achieved in the range of 81.69–98.18%. This study demonstrates the potential use of CIST nanocomposite as an accessible and reusable option for removing MB, MG, and Cu pollutants from aquatic environments.
The complete mitochondrial genome of Chibiraga houshuaii (Lepidoptera, Limacodidae) and its phylogenetic implications
Authors: Cai Yanpeng , Yin Aihui 
Published: March 2024

AbstractChibiraga is a mall East Asian genus in the family Limacodidae (slug-moths). The latter includes many agricultural pests. Mitochondrial genome analysis is an important tool for studying insect molecular identification and phylogenetics. However, there are very few mitogenome sequences available for Limacodidae species, and none for the genus Chibiraga at all. To explore the mitogenome features of Chibiraga and verify its phylogenetic position, the complete mitogenome of Chibiraga houshuaii was sequenced and annotated. The complete 15,487 bp genome encoded 37 mitochondrial genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region (CR). Most of the PCGs had typical ATN start codons and terminated with TAA or a single T residue. UUA (Leu2), AUU (Ile), UUU (Phe), AUA (Met) and AAU (Asn) were the five most frequently used codons. All tRNAs were folded into cloverleaf secondary structure, except for trnS1, which lacked the DHU arm. Phylogenetic analyses within the superfamily Zygaenoidea were performed based on multiple datasets from mitochondrial genes. The results showed that the families Phaudidae, Limacodidae and Zygaenidae were respectively recovered as monophyly; C. houshuaii was clustered in a clade with nettle type larvae in Limacodidae.
Ketotifen directly modifies the fibrotic response of human skin fibroblasts
Authors: Leong Edwin , Al-Bitar Haya , Marshall Jean S. , Bezuhly Michael 
Published: March 2024

AbstractFibrosis is a destructive, end-stage disease process. In the skin, it is associated with systemic sclerosis and scarring with considerable health burden. Ketotifen is a clinical antihistamine and mast cell stabilizer. Studies have demonstrated mast cell-dependent anti-fibrotic effects of ketotifen but direct effects on fibroblasts have not been determined. Human dermal fibroblasts were treated with pro-fibrotic transforming growth factor-β1 (TGFβ) followed by ketotifen or control treatments to determine direct effects on fibrotic fibroblasts. Ketotifen impaired TGFβ-induced α-smooth muscle actin gene and protein responses and decreased cytoskeletal- and contractility-associated gene responses associated with fibrosis. Ketotifen reduced Yes-associated protein phosphorylation, transcriptional coactivator with PDZ binding motif transcript and protein levels, and phosphorylation of protein kinase B. In a fibroblast-populated collagen gel contraction assay, ketotifen reduced the contractile activity of TGFβ-activated fibroblasts. In a murine model of bleomycin-induced skin fibrosis, collagen density and dermal thickness were significantly decreased in ketotifen-treated mice supporting in vitro findings. These results support a novel, direct anti-fibrotic activity of ketotifen, reducing pro-fibrotic phenotypic changes in fibroblasts and reducing collagen fibres in fibrotic mouse skin. Together, these findings suggest novel therapeutic potential and a novel mechanism of action for ketotifen in the context of fibrosis.
A new index to measure the uniformity of remolded loess
Authors: Wang Haike , Howard Ken , Peng Jianbing , Qian Hui , Gao Yanyan , Xu Panpan 
Published: March 2024

AbstractThe uniformity of remolded loess is crucial for engineering stability and in laboratory testing, as it affects physical and mechanical properties. It is important to have an index which can accurately and conveniently evaluate the uniformity of remolded loess. This study demonstrated and verified the feasibility of using hydraulic conductivity (K) as an indicator for evaluating the uniformity of remolded loess through laboratory experiments and theoretical analysis. In laboratory research, nine loess samples under different preparation conditions were meticulously prepared in duplicate, which were divided into three sets according to the whole dry density (WDD) of approximately 1.3 g/cm3, 1.4 g/cm3, and 1.5 g/cm3 respectively. For the nine duplicate samples, two procedures were performed for each of the sample. One is the uniformity analysis by cutting the soil column and weighing. The other is the hydraulic conductivity experiment. Results showed that sample uniformity is affected by sample preparation conditions, and there are differences in the uniformity of the same WDD samples. The values of K positively correlate with the degree of sample uniformity. In theoretical analysis, based on Darcy’s Law and Kozeny-Carman equation, it is found K is inversely proportional to the variance ($$\sigma^{2}$$

σ
2

) of the sample dry density. That is, K is positively proportional to the sample uniformity. Since K can be easily determined in the laboratory, the application of this new index in the field of geotechnical engineering makes it very convenient and simple to evaluate the uniformity of remolded loess.
Mouse auditory cortex sub-fields receive neuronal projections from MGB subdivisions independently
Authors: Wang Chi , Jiang Zhen-yu , Chai Jian-yuan , Chen Hong-suo , Liu Li-xia , Dang Tong , Meng Xian-mei 
Published: March 2024

AbstractMouse auditory cortex is composed of six sub-fields: primary auditory field (AI), secondary auditory field (AII), anterior auditory field (AAF), insular auditory field (IAF), ultrasonic field (UF) and dorsoposterior field (DP). Previous studies have examined thalamo-cortical connections in the mice auditory system and learned that AI, AAF, and IAF receive inputs from the ventral division of the medial geniculate body (MGB). However, the functional and thalamo-cortical connections between nonprimary auditory cortex (AII, UF, and DP) is unclear. In this study, we examined the locations of neurons projecting to these three cortical sub-fields in the MGB, and addressed the question whether these cortical sub-fields receive inputs from different subsets of MGB neurons or common. To examine the distributions of projecting neurons in the MGB, retrograde tracers were injected into the AII, UF, DP, after identifying these areas by the method of Optical Imaging. Our results indicated that neuron cells which in ventral part of dorsal MGB (MGd) and that of ventral MGB (MGv) projecting to UF and AII with less overlap. And DP only received neuron projecting from MGd. Interestingly, these three cortical areas received input from distinct part of MGd and MGv in an independent manner. Based on our foundings these three auditory cortical sub-fields in mice may independently process auditory information.