bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic and structural insights into Jyvaskylavirus, the first giant virus isolated from Finland
Authors: de Freitas Almeida Gabriel Magno , Arriaga Iker , de Azevedo Bruna Luiza , Leppänen Miika , Abrahao Jonatas Santos , Andreani Julien , Zabeo Davide , Ravantti Janne , Abrescia Nicola GA , Sundberg Lotta-Riina
Published: December 2024

Giant viruses of protists are a diverse and likely ubiquitous group of organisms. Here, we describe Jyvaskylavirus, the first giant virus isolated from Finland. This clade B marseillevirus was found in
Acanthamoeba castellanii
from a composting soil sample in Jyväskylä, Central Finland. Its genome shares similarities with other marseilleviruses, including conserved Nucleocytoviricota genes, histone-like genes, and three unique ORFans. Helium ion microscopy and electron microscopy of infected cells unraveled stages of the Jyvaskylavirus lifecycle, such as single virions attached to the cell membrane, likely triggering endocytosis, and virus-rich vesicle formation within the cytoplasm. We also reconstructed the Jyvaskylavirus particle to 6.3 Å resolution using cryo-EM. The ∼2,500 Å diameter virion displays structural similarities to other
Marseilleviridae
giant viruses. The capsid comprises of 9,240 copies of the major capsid protein ORF184, which possesses a double jellyroll fold arranged in trimers forming pseudo-hexameric capsomers. Below the capsid shell, the internal membrane vesicle encloses the genome. Through cross-structural and -sequence comparisons with other
Marseilleviridae
using AI-based software in model building and prediction, we elucidated ORF142 as the penton protein, which plugs the twelve vertices of the capsid. Five additional ORFs were identified, with models predicted and fitted into densities that either cap the capsomers externally or stabilize them internally.The isolation of Jyvaskylavirus, along with other virus-like particles, not only suggests that these viruses may be widespread in the boreal environment but also provide insights extendable to other marseilleviruses, addressing the previously lacking structural data on minor capsid proteins.
Structure of the human CTF18 clamp loader bound to PCNA
Authors: Briola Giuseppina R , Tehseen Muhammad , Al-Amodi Amani , Nguyen Phong Quoc , Savva Christos G , Hamdan Samir M , De Biasio Alfredo
Published: December 2024

Sliding clamps like PCNA are crucial processivity factors for replicative polymerases, requiring specific clamp loaders for loading onto DNA. The human alternative clamp loader CTF18 interacts with the leading strand polymerase Pol ε and loads PCNA onto primer/template DNA using its RFC pentameric module. Here, we provide a structural characterization of the human CTF18 complex and its interaction with PCNA. Our cryo-EM data support that the Ctf8 and Dcc1 subunits of CTF18, which form the regulatory module interacting with Pol ε, are flexibly tethered to the RFC module. A 2.9 Å cryo-EM structure shows the RFC module bound to PCNA in an auto-inhibited conformation similar to the canonical RFC loader, marking the initial step of the clamp-loading reaction. The unique RFC1 (Ctf18) large subunit of CTF18, which shows high relative mobility, is anchored to PCNA through an atypical low-affinity PIP box in the AAA+ domain and engages the RFC5 subunit using a novel β-hairpin at the disordered N-terminus. We show that deletion of this β-hairpin impairs the CTF18−PCNA complex stability and decreases the rate of primer synthesis by Pol ε. Our research identifies distinctive structural characteristics of the human CTF18-RFC complex, providing insights into its role in PCNA loading and the stimulation of leading strand synthesis by Pol ε.
Rejuvenating aged osteoprogenitors for bone repair
Authors: Reeves Joshua , Tournier Pierre , Becquart Pierre , Carton Robert , Tang Yin , Vigilante Alessandra , Fang Dong , Habib Shukry J
Published: December 2024

Aging is marked by a decline in tissue regeneration, posing significant challenges to an increasingly older population. Here, we investigate age-related impairments in calvarial bone healing and introduce a novel two-part rejuvenation strategy to restore youthful repair. We demonstrate that aging negatively impacts the calvarial bone structure and its osteogenic tissues, diminishing osteoprogenitor number and function and severely impairing bone formation. Notably, increasing osteogenic cell numbers locally fails to rescue repair in aged mice, identifying the presence of intrinsic cellular deficits. Our strategy combines Wnt-mediated osteoprogenitor expansion with intermittent fasting, which leads to a striking restoration of youthful levels of bone healing. We find that intermittent fasting improves osteoprogenitor function, benefits that can be recapitulated by modulating NAD
+
dependent pathways or the gut microbiota, underscoring the multifaceted nature of this intervention. Mechanistically, we identify mitochondrial dysfunction as a key component in age-related decline in osteoprogenitor function and show that both cyclical nutrient deprivation and Nicotinamide mononucleotide rejuvenate mitochondrial health, enhancing osteogenesis. These findings offer a promising therapeutic avenue for restoring youthful bone repair in aged individuals, with potential implications for rejuvenating other tissues.
Commissureless acts as a substrate adapter in a conserved Nedd4 E3 ubiquitin ligase pathway to promote axon growth across the midline
Authors: Sullivan Kelly G , Bashaw Greg J
Published: December 2024

In both vertebrates and invertebrates, commissural neurons prevent premature responsiveness to the midline repellant Slit by downregulating surface levels of its receptor Roundabout1 (Robo1). In
Drosophila
, Commissureless (Comm) plays a critical role in this process; however, there is conflicting data on the underlying molecular mechanism. Here, we demonstrate that the conserved PY motifs in the cytoplasmic domain of Comm are required allow the ubiquitination and lysosomal degradation of Robo1. Disruption of these motifs prevents Comm from localizing to Lamp1 positive late endosomes and to promote axon growth across the midline
in vivo
. In addition, we conclusively demonstrate a role for Nedd4 in midline crossing. Genetic analysis shows that
nedd4
mutations result in midline crossing defects in the Drosophila embryonic nerve cord, which can be rescued by introduction of exogenous Nedd4. Biochemical evidence shows that Nedd4 incorporates into a three-member complex with Comm and Robo1 in a PY motif-dependent manner. Finally, we present genetic evidence that Nedd4 acts with Comm in the embryonic nerve cord to downregulate Robo1 levels. Taken together, these findings demonstrate that Comm promotes midline crossing in the nerve cord by facilitating Robo1 ubiquitination by Nedd4, ultimately leading to its degradation.
Ciliary length regulation by intraflagellar transport in zebrafish
Authors: Sun Yi , Chen Zhe , Jin Minjun , Xie Haibo , Zhao Chengtian
Published: December 2024

How cells regulate the size of their organelles remains a fundamental question in cell biology. Cilia, with their simple structure and surface localization, provide an ideal model for investigating organelle size control. However, most studies on cilia length regulation are primarily performed on several single-celled organisms. In contrast, the mechanism of length regulation in cilia across diverse cell types within multicellular organisms remains a mystery. Similar to humans, zebrafish contain diverse types of cilia with variable lengths. Taking advantage of the transparency of zebrafish embryos, we conducted a comprehensive investigation into intraflagellar transport (IFT), an essential process for ciliogenesis. By generating a transgenic line carrying Ift88-GFP transgene, we observed IFT in multiple types of cilia with varying lengths. Remarkably, cilia exhibited variable IFT speeds in different cell types, with longer cilia exhibiting faster IFT speeds. This increased IFT speed in longer cilia is likely not due to changes in common factors that regulate IFT, such as motor selection, BBSome proteins, or tubulin modification. Interestingly, longer cilia in the ear cristae tend to form larger IFT compared to shorter spinal cord cilia. Reducing the size of IFT particles by knocking down Ift88 slowed IFT speed and resulted in the formation of shorter cilia. Our study proposes an intriguing model of cilia length regulation via controlling IFT speed through the modulation of the size of the IFT complex. This discovery may provide further insights into our understanding of how organelle size is regulated in higher vertebrates.
Fluid mechanics of luminal transport in actively contracting endoplasmic reticulum
Authors: Htet Pyae Hein , Avezov Edward , Lauga Eric
Published: December 2024

The endoplasmic reticulum (ER), the largest cellular compartment, harbours the machinery for the biogenesis of secretory proteins and lipids, calcium storage/mobilisation, and detoxification. It is shaped as layered membranous sheets interconnected with a network of tubules extending throughout the cell. Understanding the influence of the ER morphology dynamics on molecular transport may offer clues to rationalising neuro-pathologies caused by ER morphogen mutations. It remains unclear, however, how the ER facilitates its intra-luminal mobility and homogenises its content. It has been recently proposed that intra-luminal transport may be enabled by active contractions of ER tubules. To surmount the barriers to empirical studies of the minuscule spatial and temporal scales relevant to ER nanofluidics, here we exploit the principles of viscous fluid dynamics to generate a theoretical physical model emulating in silico the content motion in actively contracting nanoscopic tubular networks. The computational model reveals the luminal particle speeds, and their impact in facilitating active transport, of the active contractile behaviour of the different ER components along various time–space parameters. The results of the model indicate that reproducing transport with velocities similar to those reported experimentally in single-particle tracking would require unrealistically high values of tubule contraction site length and rate. Considering further nanofluidic scenarios, we show that width contractions of the ER’s flat domains (perinuclear sheets) generate local flows with only a short-range effect on luminal transport. Only contractions of peripheral sheets can reproduce experimental measurements, provided they are able to contract fast enough.
A Memory Model of Rodent Spatial Navigation: Place Cells are Memories Arranged in a Grid and Grid Cells are Non-spatial
Authors: Huber David E
Published: December 2024

A theory and neurocomputational model are presented that explain grid cell responses as the byproduct of equally dissimilar hippocampal memories. On this account, place and grid cells are best understood as the natural consequence of memory encoding and retrieval. In the proposed memory model, place cells represent memories that are conjunctions of both spatial and non-spatial attributes, and grid cells primarily represent the non-spatial attributes (e.g., sounds, surface texture, etc.) found throughout the two-dimensional recording enclosure. Place cells support memories of the locations where non-spatial attributes can be found (e.g., positions with a particular sound), which are arranged in a hexagonal lattice owing to memory encoding and consolidation processes (pattern separation) as applied to situations in which the non-spatial attributes are found at all locations of a two-dimensional surface. Grid cells exhibit their spatial firing pattern owing to feedback from hippocampal place cells (i.e., a hexagonal pattern of remembered locations for the non-spatial attribute represented by a grid cell). The model explains: 1) grid fields that appear to be centered outside the box; 2) the toroidal nature of grid field representations; 3) grid field alignment with the enclosure borders; 4) modules in which grid cells have the same orientation and spacing but different phases; 5) head direction conjunctive grid cells that become simple head direction cells in the absence of hippocampal feedback; 6) the instant existence of grid fields in a novel environment; 7) the slower learning of place cells; 8) the manner in which head direction sensitivity of place cells changes near borders and in narrow passages; 9) the kinds of changes that underlie remapping of place cells; and 10) grid-like responses for two-dimensional coordinate systems other than navigation.
A human forebrain organoid model reveals the essential function of GTF2IRD1-TTR-ERK axis for the neurodevelopmental deficits of Williams syndrome
Authors: Zhao Xingsen , Sun Qihang , Shou Yikai , Chen Weijun , Wang Mengxuan , Qu Wenzheng , Huang Xiaoli , Li Ying , Wang Chao , Gu Yan , Ji Chai , Shu Qiang , Li Xuekun
Published: December 2024

Williams syndrome (WS; OMIM#194050) is a rare disorder, which is caused by the microdeletion of one copy of 25–27 genes, and WS patients display diverse neuronal deficits. Although remarkable progresses have been achieved, the mechanisms for these distinct deficits are still largely unknown. Here, we have shown that neural progenitor cells (NPCs) in WS forebrain organoids display abnormal proliferation and differentiation capabilities, and synapse formation. Genes with altered expression are related to neuronal development and neurogenesis. Single cell RNA-seq (scRNA-seq) data analysis revealed 13 clusters in healthy control and WS organoids. WS organoids show an aberrant generation of excitatory neurons. Mechanistically, the expression of transthyretin (TTR) are remarkably decreased in WS forebrain organoids. We have found that GTF2IRD1 encoded by one WS associated gene GTF2IRD1 binds to TTR promoter regions and regulates the expression of TTR. In addition, exogenous TTR can activate ERK signaling and rescue neurogenic deficits of WS forebrain organoids. Gtf2ird1-deficient mice display similar neurodevelopmental deficits as observed in WS organoids. Collectively, our study reveals critical function of GTF2IRD1 in regulating neurodevelopment of WS forebrain organoids and mice through regulating TTR-ERK pathway.
Nitric oxide modulates contrast suppression in a subset of mouse retinal ganglion cells
Authors: Gonschorek Dominic , Goldin Matías A , Oesterle Jonathan , Schwerd-Kleine Tom , Arlinghaus Ryan , Zhao Zhijian , Schubert Timm , Marre Olivier , Euler Thomas
Published: December 2024

Neuromodulators have major influences on the regulation of neural circuit activity across the nervous system. Nitric oxide (NO) has been shown to be a prominent neuromodulator in many circuits and has been extensively studied in the retina. Here, it has been associated with the regulation of light adaptation, gain control, and gap junctional coupling, but its effect on the retinal output, specifically on the different types of retinal ganglion cells (RGCs), is still poorly understood. In this study, we used two-photon Ca
2+
imaging and multi-electrode array (MEA) recordings to measure light-evoked activity of RGCs in the ganglion cell layer in the
ex vivo
mouse retina. This approach allowed us to investigate the neuromodulatory effects of NO on a cell type-level. Our findings reveal that NO selectively modulates the suppression of temporal responses in a distinct subset of contrast-suppressed RGC types, increasing their activity without altering the spatial properties of their receptive fields. Given that under photopic conditions, NO release is triggered by quick changes in light levels, we propose that these RGC types signal fast contrast changes to higher visual regions. Remarkably, we found that about one-third of the RGC types, recorded using two-photon Ca
2+
imaging, exhibited consistent, cell type-specific adaptational response changes throughout an experiment, independent of NO. By employing a sequential-recording paradigm, we could disentangle those additional adaptational response changes from drug-induced modulations. Taken together, our research highlights the selective neuromodulatory effects of NO on RGCs and emphasizes the need of considering non-pharmacological activity changes, like adaptation, in such study designs.
Long non-coding RNA Malat1 fine-tunes bone homeostasis and repair by orchestrating cellular crosstalk and the β-catenin-OPG/Jagged1 pathway
Authors: Qin Yongli , Shirakawa Jumpei , Xu Cheng , Chen Ruge , Yang Xu , Courtney Ng , Nakano Shinichi , Elguindy Mahmoud , Deng Zhonghao , Prasanth Kannanganattu V , Eissmann Moritz F , Nakagawa Shinichi , Ricci William M , Zhao Baohong
Published: December 2024

The IncRNA Malat1 was initially believed to be dispensable for physiology due to the lack of observable phenotypes in Malat1 knockout (KO) mice. However, our study challenges this conclusion. We found that both Malat1 KO and conditional KO mice in the osteoblast lineage exhibit significant osteoporosis. Mechanistically, Malat1 acts as an intrinsic regulator in osteoblasts to promote osteogenesis. Interestingly, Malat1 does not directly affect osteoclastogenesis but inhibits osteoclastogenesis in a non-autonomous manner
in vivo
via integrating crosstalk between multiple cell types, including osteoblasts, osteoclasts and chondrocytes. Our findings substantiate the existence of a novel remodeling network in which Malatl serves as a central regulator by binding to β-catenin and functioning through the β-catenin-OPG/Jagged1 pathway in osteoblasts and chondrocytes. In pathological conditions, Malat1 significantly promotes bone regeneration in fracture healing. Bone homeostasis and regeneration are crucial to well-being. Our discoveries establish a previous unrecognized paradigm model of Malat1 function in the skeletal system, providing novel mechanistic insights into how a lncRNA integrates cellular crosstalk and molecular networks to fine tune tissue homeostasis, remodeling and repair.
Template switching during DNA replication is a prevalent source of adaptive gene amplification
Authors: Chuong Julie N , Nun Nadav Ben , Suresh Ina , Matthews Julia Cano , De Titir , Avecilla Grace , Abdul-Rahman Farah , Brandt Nathan , Ram Yoav , Gresham David
Published: December 2024

Copy number variants (CNVs)—gains and losses of genomic sequences—are an important source of genetic variation underlying rapid adaptation and genome evolution. However, despite their central role in evolution little is known about the factors that contribute to the structure, size, formation rate, and fitness effects of adaptive CNVs. Local genomic sequences are likely to be an important determinant of these properties. Whereas it is known that point mutation rates vary with genomic location and local DNA sequence features, the role of genome architecture in the formation, selection, and the resulting evolutionary dynamics of CNVs is poorly understood. Previously, we have found that the
GAP1
gene in
Saccharomyces cerevisiae
undergoes frequent and repeated amplification and selection under long-term experimental evolution in glutamine-limiting conditions. The
GAP1
gene has a unique genomic architecture consisting of two flanking long terminal repeats (LTRs) and a proximate origin of DNA replication (autonomously replicating sequence, ARS), which are likely to promote rapid
GAP1
CNV formation. To test the role of these genomic elements on CNV-mediated adaptive evolution, we performed experimental evolution in glutamine-limited chemostats using engineered strains lacking either the adjacent LTRs, ARS, or all elements. Using a CNV reporter system and neural network simulation-based inference (nnSBI) we quantified the formation rate and fitness effect of CNVs for each strain. We find that although
GAP1
CNVs repeatedly form and sweep to high frequency in strains with modified genome architecture, removal of local DNA elements significantly impacts the rate and fitness effect of CNVs and the rate of adaptation. We performed genome sequence analysis to define the molecular mechanisms of CNV formation for 177 CNV lineages. We find that across all four strain backgrounds, between 26% and 80% of all
GAP1
CNVs are mediated by Origin Dependent Inverted Repeat Amplification (ODIRA) which results from template switching between the leading and lagging strand during DNA synthesis. In the absence of the local ARS, a distal ARS can mediate CNV formation via ODIRA. In the absence of local LTRs, homologous recombination mechanisms still mediate gene amplification following
de novo
insertion of retrotransposon elements at the locus. Our study demonstrates the remarkable plasticity of the genome and reveals that template switching during DNA replication is a frequent source of adaptive CNVs.
Quantum-inspired seagull optimised deep belief network approach for cardiovascular disease prediction
Authors: Banumathy D. , Vetriselvi T. , Venkatachalam K. , Cho Jaehyuk
Published: December 2024

The early detection and accurate diagnosis of cardiovascular diseases is vital to reduce global morbidity and death rates. In this work, the quantum-inspired seagull optimization algorithm (QISOA) combined with a deep belief network (DBN) is proposed to improve the identification of cardiovascular disorders. As part of preprocessing, cleaning, transformation, and standardization are performed to eliminate noise, inconsistencies, and scaling issues in the data. QISOA is used to optimize the weights and biases of the DBN model, enhancing its prediction efficiency. The algorithm incorporates quantum mechanics concepts to develop its exploration potential further, leading to faster convergence and increased global search efficiency. Optimized DBN provides efficient acquisition of hierarchical representations of the data, which results in improved feature learning and classification accuracy. The publicly accessible Cleveland Heart Disease dataset is used to assess the performance of the suggested model. Extensive experiments are conducted to demonstrate the superior performance of the QISOA-optimized DBN model compared to traditional machine learning and other metaheuristic-based models. Initially, machine learning models such as support vector machines, decision trees, Random Forests, multi-layer perceptrons, and fully connected networks were considered for comparison with the cardiovascular predictive performance of the DBN model. Further, meta-heuristic optimization algorithms such as particle swarm optimization, genetic algorithm, grey wolf optimization, cuckoo search optimization and crow search algorithm are combined with the machine learning models and the classification efficiency is evaluated. Additionally, few state-of-the-art techniques proposed in the existing literature are investigated and compared against the proposed model. It was evident from the comprehensive performance assessment of the proposed model that it yields a higher accuracy of 98.6% with precision, recall, and F1-scores of 97.6%, 96.8%, and 97.1%, respectively, compared to other traditional and existing models for cardiovascular disease prediction.
Cluster channel equalization using adaptive sensing and reinforcement learning for UAV communication
Authors: Liu Xin , Zhao Shanghong , Liang Yanxia , Karim Shahid
Published: December 2024

Aiming to address the need for dynamic sensing and channel equalization in UAV cluster communication environments, this article introduces an equalization algorithm based on a U-Net model and fuzzy reinforcement Q-learning (U-FRQL-EA). This algorithm is designed to enhance the channel sensing and equalization capabilities of UAV communication systems. Initially, we develop a U-Net-based signal processing algorithm that effectively reduces acoustic noise in UAV communication channels and enables real-time, accurate perception of channel states by automatically learning channel features. Subsequently, we enhance fuzzy reinforcement Q-learning by incorporating a fuzzy neural network to approximate the Q-values and integrating this approach with the allocation strategy of wireless sensing nodes. This enhancement not only improves the accuracy of Q-value approximation but also increases the algorithm’s adaptability and decision-making ability in complex channel environments. Finally, we construct the U-FRQL-EA equalization algorithm by combining the improved U-Net model with fuzzy reinforcement Q-learning. This algorithm leverages the U-Net model to sense channel states in real time and intelligently adjusts data forwarding strategies based on fuzzy values generated by the fuzzy reinforcement Q-learning. Simulation results demonstrate that the U-FRQL-EA algorithm effectively reduces the system’s bit error rate, enhances communication quality, and optimizes network resource utilization, offering a novel solution for improving the performance of uncrewed aerial vehicle communication systems.
Computer vision syndrome and associated factors among urban and rural bankers in Trinidad and Tobago
Authors: Ekemiri Kingsley , McKnight Devonte , Ekemiri Chioma , Ezinne Ngozika , Ashang Henrietta , Victor Virginia , Okonedo Osaze , Shuaibu Ayishetu Oshoke , Seemongal-Dass Robin
Published: December 2024

Background

Modern workplace requirements in the banking sector require bankers to work on screens for more than 6 h a day, putting much stress and strain on their eyes, which leads to computer vision syndrome. Therefore, this study aimed to assess the prevalence of computer vision syndrome and associated factors among urban and rural bankers in Trinidad and Tobago.

Methods and materials

A cross-sectional design was applied to collect data from 399 bankers between April and June 2023. The collected data was entered into Excel worksheets and later uploaded to SPSS for further analysis. A variable with a P-value of 0.25 in binary logistic regression is a candidate for multi-variable logistic regression analysis. Finally, a variable with a P-value of 0.05 was used to declare statistical significance.

Results

A total of 371 participants were enrolled in this study, leading to a response rate of 92.9%. Of the total participants, 277 (74.7%) had computer vision syndrome. Working in rural areas (AOR = 2.69; 95% CI [1.41–5.13]) and using eyesight glasses (AOR = 0.57; 95% CI [0.33–0.97]) was associated with computer vision syndrome.

Conclusion

Despite being easily preventable, computer vision syndrome is substantially prevalent among bankers in Trinidad. The use of eye-sight glasses and the working area are significantly associated with computer vision syndrome. Therefore, it is necessary to improve workplace practices by encouraging the use of anti-glare screens and glasses for employees who work long hours on the computer.
Companion animal foster caregiving: a scoping review exploring animal and caregiver welfare, barriers to caregiver recruitment and retention, and best practices for foster care programs in animal shelters
Authors: Phillips Grace E. , Gunter Lisa M.
Published: December 2024

Each year, millions of animals enter animal shelters across the United States and are met with a variety of potential stressors that can negatively impact their experience, including noise, confinement, and social isolation. Foster care, a unique form of human–animal interaction, is increasingly understood to be an effective tool for improving welfare by allowing animals to escape the stressors of the shelter, providing an environment that allows for greater social interaction, and offering opportunities for improved health and behavior. This review includes 42 published articles, reports, master’s theses, and doctoral dissertations that have previously evaluated companion animal foster care programs. While scientific literature in this area has increased over the last decade, no review of the research exploring companion animal fostering has been published. Here, we examine foster care programs and their effects on human and animal welfare, evaluate the successes and challenges of supporting shelter foster care programs, recommend best practices for programmatic success, illuminate discrepancies in equity and diversity of caregiver engagement, and offer directions for future research in animal foster caregiving. The examinations in this review conclude that fostering provides both proximate (i.e., physiological and behavioral) and distal (i.e., length of stay and adoption outcomes) welfare benefits for shelter animals as well as their caregivers. Companion animal foster care programs may be further improved by providing greater caregiver support and increasing the diversity and extent of community engagement. Meanwhile, scientific investigations should explore lesser-researched components of foster care programs that are not yet well understood.
Development of machine learning models for the prediction of the skin sensitization potential of cosmetic compounds
Authors: Qiao Wu , Xie Tong , Lu Jing , Jia Tinghan
Published: December 2024

Background

To enhance the accuracy of allergen detection in cosmetic compounds, we developed a co-culture system that combines HaCaT keratinocytes (transfected with a luciferase plasmid driven by the AKR1C2 promoter) and THP-1 cells for machine learning applications.

Methods

Following chemical exposure, cell cytotoxicity was assessed using CCK-8 to determine appropriate stimulation concentrations. RNA-Seq was subsequently employed to analyze THP-1 cells, followed by differential expression gene (DEG) analysis and weighted gene co-expression net-work analysis (WGCNA). Using two data preprocessing methods and three feature extraction techniques, we constructed and validated models with eight machine learning algorithms.

Results

Our results demonstrated the effectiveness of this integrated approach. The best performing models were random forest (RF) and voom-based diagonal quadratic discriminant analysis (voomDQDA), both achieving 100% accuracy. Support vector machine (SVM) and voom based nearest shrunken centroids (voomNSC) showed excellent performance with 96.7% test accuracy, followed by voom-based diagonal linear discriminant analysis (voomDLDA) at 95.2%. Nearest shrunken centroids (NSC), Poisson linear discriminant analysis (PLDA) and negative binomial linear discriminant analysis (NBLDA) achieved 90.5% and 90.2% accuracy, respectively. K-nearest neighbors (KNN) showed the lowest accuracy at 85.7%.

Conclusion

This study highlights the potential of integrating co-culture systems, RNA-Seq, and machine learning to develop more accurate and comprehensive in vitro methods for skin sensitization testing. Our findings contribute to the advancement of cosmetic safety assessments, potentially reducing the reliance on animal testing.
Prognostic value of serum Mrp 8/14 in sepsis-induced acute respiratory distress syndrome patients: a retrospective cohort study
Authors: Sun Caizhi , Xie Yongpeng , Zhu Chenchen , Guo Lei , Xu Bowen , Qin Haidong , Li Xiaomin
Published: December 2024

Background

Mrp 8/14 is abundantly secreted by activated neutrophils during infection and inflammation. However, its prognostic value in acute respiratory distress dyndrome (ARDS) induced by sepsis is poorly understood. Our aim was to investigate the relationship between serum Mrp 8/14 and the prognosis in sepsis-induced ARDS patients admitted to the intensive care unit (ICU).

Methods

Serum Mrp 8/14 concentrations were analyzed in 118 ARDS patients induced by sepsis included in the analytical study. Patients were enrolled upon admission to the ICU of Nanjing Hospital affiliated to Nanjing Medical University. The baseline information and clinical outcomes were obtained. Patients were divided into survivor group and non-survivor group according to whether they died during ICU hospitalization.

Results

The serum Mrp 8/14 levels were significantly increased in the non-survivor group compared to the survivor group (P < 0.05). Logistic regression analysis showed that serum Mrp 8/14, albumin and APACHE II were the independent factors for predicting the prognosis of sepsis-induced ARDS during ICU hospitalization after adjustment. Additionally, the area under the receiver operating characteristic curve for Mrp 8/14 combined with albumin was associated with ICU mortality and was higher than that of Mrp 8/14, albumin, APACHE II and Mrp 8/14 combined with APACHE II (all P < 0.05). A nomogram was constructed to predict ICU mortality and the c-indexes of predictive accuracy was 0.830 in the cohort (P < 0.05).

Conclusions

The serum Mrp 8/14 upon ICU admission in septic patients may be useful for predicting mortality in sepsis-induced ARDS patients during ICU hospitalization.
Recycling photovoltaic modules: a sustainable approach to renewable energy
Authors: Hiranobe Márcia Ferreira , Souza Dener Silva , Filgueira Matheus da Silva , Kawall Samara Araújo , Ribeiro Gabriel Deltrejo , Hiranobe Carlos Toshiyuki
Published: December 2024

The growing demand for clean energy has driven the expansion of photovoltaic solar energy, leading to an increase in the number of installed solar panels. However, the improper disposal of solar panels can result in negative environmental impacts. Therefore, the recycling of photovoltaic panels emerges as a critical alternative to mitigate these effects. This review article aims to present the currently available solar panel recycling techniques and discuss the challenges and future perspectives of this practice. The methodology was based on searches in the Scopus, Web of Science, and Google Scholar databases to identify relevant articles on solar panel recycling. The findings highlight the necessity of combining mechanical methods with chemical and physical processes to achieve high-quality recycled materials. Furthermore, the study emphasizes the importance of implementing public policies and raising societal awareness about the significance of solar panel recycling to make this practice more widespread and effective.
Empreendedorismo e inovação: um estudo do impacto da pandemia do COVID-19 no comércio informal do município de Codó-MA
Authors: Façanha Neto Inácio Ferreira , Sousa Pedro da Silva
Published: December 2024

Em vista da crise sanitária causada pelo coronavírus e suas repercussões nas atividades econômicas, neste trabalho pesquisa-se sobre os impactos da pandemia de covid-19 na atuação de empreendedores do município de Codó-MA, em especial, nas atividades informais, com a finalidade de analisar as principais adversidades enfrentadas assim como as oportunidades surgidas nesse contexto. Para tanto, se faz necessário identificar a prática empreendedora e inovadora como fatores importantes para a continuidade do comércio municipal na pandemia, caracterizar no cenário pandêmico principais desafios enfrentados e oportunidades surgidas para os empreendedores e verificar principais implicações resultadas da pandemia no empreendedorismo informal de Codó-MA. Realiza-se, então, uma pesquisa bibliográfica juntamente com uma de campo através de questionário direcionado a empreendedores no município para coleta de dados primários, ambas com abordagem qualitativa. Diante disso, verifica-se que a maior parte dos participantes da pesquisa concorda, seja parcial ou totalmente, que as medidas para evitar aglomerações afetaram negativamente suas atividades e desempenho profissional, 40,9% afirmam ter sofrido mudanças de funcionamento no trabalho devido à crise sanitária e 88,3% disseram que investir em atividades online é uma das melhores formas de superar as dificuldades diante dessa crise.
Impact of Controlled Release NPK (16:16:16) Fertilizer on Soil Total Nitrogen Content, Nitrogen Uptake, and Growth of Sweet Corn (Zea mays saccharata L.) in Jatinangor Inceptisols
Authors: Sofyan Emma Trinurani , Herdiyantoro Diyan , Pratama Dea
Published: December 2024

The potential for sweet corn in Indonesia is very high, however, its cultivation often experiences problems, one of which is that the planting land has a low fertility level. Optimizing the use of fertilizer is one way to increase soil fertility and increase the growth of sweet corn. Using controlled-release NPK fertilizer is the best way to ensure that nutrient availability meets plant nutrient needs. This experiment aims to obtain the best effect and treatment of coating and time on total soil N content and N uptake of sweet corn plants. The experiment was carried out from June to September 2021 at the Experimental Garden and Laboratory of Soil Chemistry and Plant Nutrition, Department of Soil Science and Land Resources, Faculty of Agriculture, Padjadjaran University, Jatinangor. This experiment used a Split Plot Repeated Observation Design experiment over time with 12 treatment combinations and 3 replications consisting of 3 levels of coating treatment, namely without coating (C0), 5-6% coating (C1) and 11-12% coating (C2); and 4 treatment time levels, namely 15 days after planting (W1), 30 days after planting (W2), 45 days after planting (W3), and 60 days after planting (W4). The research results show that; (1) there is no interaction between the coating factor and the time factor on total soil N content and plant N uptake; (2) There is an independent influence of the coating factor on soil N-total and plant N uptake. Coating treatments of 5-6% (C1) and 11-12% (C2) produced lower total soil N content and plant N uptake compared to the treatment without coating (C0); and (3) There is an independent influence of the time factor on the total N content of the soil, but it has no significant effect on plant N uptake. The longer the application time is followed the higher the total N content of the soil and plant N uptake.
Comparative Efficacy of Botanical Priming Agents on Germination Kinetics and Post-transplant Performance of Brassica rapa: A Correlation Analysis
Authors: Cuares Irish , Cordova Siony , Jr. Ratunil Virgilio , Feril Joanna , Bagaipo Bernadette
Published: December 2024

Aims: Short-duration crops like pechay (Brassica rapa) require rapid establishment and enhanced early vigor for optimal productivity, making seed quality improvement crucial. Seed priming with plant extracts offers a sustainable alternative to conventional priming methods, but their effectiveness and optimal application parameters still need to be explored. This study evaluated the efficacy of single-application seed priming using Ficus nota water extract, banana water extract, and coconut water on pechay seed performance and subsequent crop development.
Place and Duration of Study: Surigao del Norte Horticultural Garden (SNSU) on August to October, 2024.
Methodology: The experiment utilized a Completely Randomized Design with four treatments (distilled water, Ficus nota extract, banana water extract, and coconut water) replicated three times, examining germination parameters, vegetative growth characteristics, and final yield metrics under Type II climate conditions.
Results: Results revealed that distilled water and Ficus nota water extract emerged as the most effective priming agents. Distilled water achieved optimal germination timing (28.86 days) and emergence percentage (78.67%), while Ficus nota extract demonstrated comparable effectiveness with the highest survival rate (93.33%). Both treatments produced superior fresh weight yields, being 97.63 g and 86.40 g, respectively and dry matter content, being 37.96% and 35.31%, respectively. Correlation analyses established critical relationships between early development and final crop performance, with perfect positive correlation between germination timing and mortality (r = 1.000) and strong correlations between environmental factors and yield parameters.
Conclusion: The study concludes that while distilled water provides a cost-effective priming solution, Ficus nota extract offers promise as a locally-sourced alternative. Environmental factors significantly modulated plant responses to priming treatments, with temperature showing consistent negative correlations with survival (r = -0.488) and yield parameters (r = -0.531). These findings establish a framework for optimizing seed priming protocols in short-duration crop production, particularly emphasizing the need for concentration optimization in plant extract applications and considering environmental interactions for maximizing treatment effectiveness.
The Effect of the Project-Based Seamless Learning Model on Critical Thinking of Prospective Early Childhood Education Educator Students
Authors: Vicy  , Mustaji  , Mariono Andi , Arianto Fajar
Published: December 2024

Aims: The aim of this study was to identify the effect of the project-based seamless learning model on critical thinking of prospective early childhood education educator students.
Study Design:  The research used quantitative experimental design.
Methodology: The method used quasi experiment with research design nonequivalent pretest posttest group design, where there is an experimental group and a control group, the experimental group is given treatment and there is no treatment on the control group. The research subjects were 150 students, 75 students in the experimental group and 75 students in the control group. Data collection using tests conducted pretest and posttest. project-based seamless learning model on critical thinking skills of prospective educator students. Based on the results of hypothesis testing on the posttest, the value on the posttest of the experimental group and the control group obtained a significance value of 0.001 <0.050. And also the difference in the average value of the experimental group's posttest of 84.20, greater than the lower control group of 80.40. This proves that there are differences caused by the application of learning models in the two groups. The experimental group used a project-based seamless learning model while the control group used a conventional model.
Conclusion: There is an effectiveness of project-based seamless learning model on critical thinking skills of prospective early childhood education educator students. Hopefully, the project-based seamless learning model can be applied at various levels of educational institutions, various subject matter so that the quality of learning will be better. Can improve and develop various skills of students during learning.
Development and validation of a comprehensive patient‐specific quality assurance program for a novel stereotactic radiation delivery system for breast lesions
Authors: Becker Stewart J. , Niu Ying , Mutaf Yildirim , Chen Shifeng , Poirier Yannick , Nichols Elizabeth M. , Yi ByongYong
Published: December 2019

Purpose

The GammaPod is a dedicated prone breast stereotactic radiosurgery (SRS) machine composed of 25 cobalt‐60 sources which rotate around the breast to create highly conformal dose distributions for boosts, partial‐breast irradiation, or neo‐adjuvant SRS. We describe the development and validation of a patient‐specific quality assurance (PSQA) system for the GammaPod.

Methods

We present two PSQA methods: measurement based and calculation based PSQA. The measurements are performed with a combination of absolute and relative dose measurements. Absolute dosimetry is performed in a single point using a 0.053‐cc pinpoint ionization chamber in the center of a polymethylmethacrylate (PMMA) breast phantom and a water‐filled breast cup. Relative dose distributions are verified with EBT3 film in the PMMA phantom. The calculation‐based method verifies point doses with a novel semi‐empirical independent‐calculation software.

Results

The average (± standard deviation) breast and target sizes were 1263 ± 335.3 cc and 66.9 ± 29.9 cc, respectively. All ion chamber measurements performed in water and the PMMA phantom agreed with the treatment planning system (TPS) within 2.7%, with average (max) difference of –1.3% (−1.9%) and −1.3% (−2.7%), respectively. Relative dose distributions measured by film showed an average gamma pass rate of 97.0 ± 3.2 when using a 3%/1 mm criteria. The lowest gamma analysis pass rate was 90.0%. The independent calculation software had average agreements (max) with the patient and QA plan calculation of 0.2% (2.2%) and −0.1% (2.0%), respectively.

Conclusion

We successfully implemented the first GammaPod PSQA program. These results show that the GammaPod can be used to calculate and deliver the predicted dose precisely and accurately. For routine PSQA performed prior to treatments, the independent calculation is recommended as it verifies the accuracy of the planned dose without increasing the risk of losing vacuum due to prolonged waiting times.
Searching for faces in crowd chokepoint videos
Authors: Kramer Robin S. S. , Hardy Sarah C. , Ritchie Kay L.
Published: December 2019

Investigations of face identification have typically focussed on matching faces to photographic IDs. Few researchers have considered the task of searching for a face in a crowd. In Experiment 1, we created the Chokepoint Search Test to simulate real‐time search for a target. Performance on this test was poor (39% accuracy) and showed moderate associations with tests of face matching and memory. In addition, trial‐level confidence predicted accuracy, and for those participants who were previously familiar with one or more targets, higher familiarity was associated with increased accuracy. In Experiment 2, we found improvements in performance on the test when three recent images of the target, but not three social media images, were displayed during searches. Taken together, our results highlight the difficulties inherent in real‐time searching for faces, with important implications for those security personnel who carry out this task on a daily basis.
Most family physicians report communicating the risks of adverse drug reactions in words (vs. numbers)
Authors: Juanchich Marie , Sirota Miroslav
Published: December 2019

Family physicians can communicate to patients the risk of adverse drug reactions using words or numbers, and this format has important implications for patients' ability to make informed decisions. The present study (a) assessed which formats family physicians preferred to communicate the risk of a given side effect, (b) tested whether the severity of this adverse drug reaction affected this preference, and (c) investigated the type of quantifiers physicians preferred to use in general (e.g., ratios, percentages). In a format selection task, a sample of 131 family physicians reported that they mostly use words to communicate to patients the risk of mild and severe adverse drug reactions, but the verbal preference was weaker for severe adverse drug reactions. The quantifier selection task showed that the most common quantifiers were verbal frequencies and verbal probabilities. Family physicians and patients should be aware of the implications of this preference.
In Situ Preparation of Thin and Rigid COF Film on Li Anode as Artificial Solid Electrolyte Interphase Layer Resisting Li Dendrite Puncture
Authors: Chen Dongdong , Huang Sheng , Zhong Lei , Wang Shuanjin , Xiao Min , Han Dongmei , Meng Yuezhong
Published: December 2019

Metallic Li is considered the most promising anode material for high‐energy density batteries due to its high theoretical capacity and low electrochemical potential. However, commercialization of the Li anode has been hampered by the safety issue associated with Li‐dendrite growth resulting from uneven Li‐ion deposition and an unstable solid electrolyte interphase (SEI). Herein, an in situ prepared 10 nm thin film of covalent organic framework (COF) uniformly covered on the Li anode (COF‐Li) is used as an artificial SEI layer for Li plating/striping stabilization and Li dendrite inhibition. Abundant microcellular structures in the COF can redistribute the Li‐ion flux and lead to the homogeneous plating/stripping process. Meanwhile, the superhard mechanical properties and mechanical behavior during needling of the ultrathin COF film is studied via the digital pulsed force mode equipped in atomic force microscopy, illustrating a high Young's modulus of 6.8 GPa that is strong enough to resist dendrite growth. As a result, stable cycling for 400 h is achieved in the COF‐Li symmetrical cell at a current density of 1 mA cm−2, and the internal short circuit is effectively blocked by COF‐Li in Li–S batteries.