bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a three-dimensional organoid model to explore early retinal phenotypes associated with Alzheimer’s disease
Authors: Lavekar Sailee S. , Harkin Jade , Hernandez Melody , Gomes Cátia , Patil Shruti , Huang Kang-Chieh , Puntambekar Shweta S. , Lamb Bruce T. , Meyer Jason S. 
Published: August 2023

AbstractAlzheimer’s disease (AD) is a progressive neurodegenerative disorder characterized by the accumulation of Aβ plaques and neurofibrillary tangles, resulting in synaptic loss and neurodegeneration. The retina is an extension of the central nervous system within the eye, sharing many structural similarities with the brain, and previous studies have observed AD-related phenotypes within the retina. Three-dimensional retinal organoids differentiated from human pluripotent stem cells (hPSCs) can effectively model some of the earliest manifestations of disease states, yet early AD-associated phenotypes have not yet been examined. Thus, the current study focused upon the differentiation of hPSCs into retinal organoids for the analysis of early AD-associated alterations. Results demonstrated the robust differentiation of retinal organoids from both familial AD and unaffected control cell lines, with familial AD retinal organoids exhibiting a significant increase in the Aβ42:Aβ40 ratio as well as phosphorylated Tau protein, characteristic of AD pathology. Further, transcriptional analyses demonstrated the differential expression of many genes and cellular pathways, including those associated with synaptic dysfunction. Taken together, the current study demonstrates the ability of retinal organoids to serve as a powerful model for the identification of some of the earliest retinal alterations associated with AD.
Belatacept inhibit human B cell germinal center development in immunodeficient mice
Authors: Samson Chloé , Thiolat Allan , Moktefi Anissa , Cohen José L. , Pilon Caroline , Grimbert Philippe 
Published: August 2023

AbstractThe humoral response mediated by alloantibodies directed against donor HLA molecules (DSAs) is one of the main causes of graft loss in kidney transplantation. Understanding the pathophysiology leading to humoral kidney rejection as the development of therapeutic tools is therefore a main objective in the field of solid organ transplantation and necessitate adapted experimental models. Among the immunosuppressive agents used in renal transplantation, belatacept, a fusion protein targeting T costimulatory molecules has shown its ability to prevent more efficiently the secretion of DSA by different mechanisms including a direct action on plasma cells but also on B lymphocytes and follicular helper T lymphocytes (Tfh) cooperation. This cellular cooperation occurs within germinal centers (GC), the seat of B lymphocytes differentiation. Here, we aimed to develop a dedicated mouse model in which human GC would be functional to study the effect of belatacept on GC formation and the ability of B lymphocytes to secrete immunoglobulin. We next demonstrate that belatacept inhibits the formation of these GCs, by inhibiting the frequency of Tfh and B lymphocytes. This alters the B maturation and therefore the generation of plasma cells and consequently, immunoglobulin secretion.
The understanding of the impact of efficiently optimized underlap length on analog/RF performance parameters of GNR-FETs
Authors: Ahmad Md Akram , Kumar Jitendra 
Published: August 2023

AbstractThe aim of this study is to examine the analog/RF performance characteristics of graphene nanoribbon (GNR) field-effect transistors (FETs) using a novel technique called underlap engineering. The study employs self-consistent atomistic simulations and the non-equilibrium Green's function (NEGF) formalism. Initially, the optimal underlap length for the GNR-FET by device has been determined evaluating the ON-current (ION) to OFF-current (IOFF) ratio, which is a critical parameter for digital applications. Subsequently, the impact of underlap engineering on analog/RF performance metrics has been analyzed and conducting a comprehensive trade-off analysis considering parameters such as intrinsic-gain, transistor efficiency, and device cut-off frequency. The results demonstrate that the device incorporating the underlap mechanism exhibits superior performance in terms of the ION/IOFF ratio, transconductance generation factor (TGF), output resistance (r0), intrinsic gain (gmr0), gain frequency product (GFP), and gain transfer frequency product (GTFP). However, the device without the underlap effect demonstrates the highest transconductance (gm) and cut-off frequency (fT). Finally, a linearity analysis has been conducted to compare the optimized GNR-FET device with the conventional GNR-FET device without the underlap effect.
Using machine learning to predict protein–protein interactions between a zombie ant fungus and its carpenter ant host
Authors: Will Ian , Beckerson William C. , de Bekker Charissa 
Published: August 2023

AbstractParasitic fungi produce proteins that modulate virulence, alter host physiology, and trigger host responses. These proteins, classified as a type of “effector,” often act via protein–protein interactions (PPIs). The fungal parasite Ophiocordyceps camponoti-floridani (zombie ant fungus) manipulates Camponotus floridanus (carpenter ant) behavior to promote transmission. The most striking aspect of this behavioral change is a summit disease phenotype where infected hosts ascend and attach to an elevated position. Plausibly, interspecific PPIs drive aspects of Ophiocordyceps infection and host manipulation. Machine learning PPI predictions offer high-throughput methods to produce mechanistic hypotheses on how this behavioral manipulation occurs. Using D-SCRIPT to predict host–parasite PPIs, we found ca. 6000 interactions involving 2083 host proteins and 129 parasite proteins, which are encoded by genes upregulated during manipulated behavior. We identified multiple overrepresentations of functional annotations among these proteins. The strongest signals in the host highlighted neuromodulatory G-protein coupled receptors and oxidation–reduction processes. We also detected Camponotus structural and gene-regulatory proteins. In the parasite, we found enrichment of Ophiocordyceps proteases and frequent involvement of novel small secreted proteins with unknown functions. From these results, we provide new hypotheses on potential parasite effectors and host targets underlying zombie ant behavioral manipulation.
Deciphering phenotyping, DNA barcoding, and RNA secondary structure predictions in eggplant wild relatives provide insights for their future breeding strategies
Authors: Mohanty Sansuta , Mishra Bandana Kumari , Dasgupta Madhumita , Acharya Gobinda Chandra , Singh Satyapriya , Naresh Ponnam , Bhue Shyamlal , Dixit Anshuman , Sarkar Arup , Sahoo Manas Ranjan 
Published: August 2023

AbstractEggplant or aubergine (Solanum melongena L.) and its wild cousins, comprising 13 clades with 1500 species, have an unprecedented demand across the globe. Cultivated eggplant has a narrow molecular diversity that hinders eggplant breeding advancements. Wild eggplants need resurgent attention to broaden eggplant breeding resources. In this study, we emphasized phenotypic and genotypic discriminations among 13 eggplant species deploying chloroplast–plastid (Kim matK) and nuclear (ITS2) short gene sequences (400–800 bp) at DNA barcode region followed by ITS2 secondary structure predictions. The identification efficiency at the Kim matK region was higher (99–100%) than in the ITS2 region (80–90%). The eggplant species showed 13 unique secondary structures with a central ring with various helical orientations. Principal component analysis (PCoA) provides the descriptor–wise phenotypic clustering, which is essential for trait–specific breeding. Groups I and IV are categorized under scarlet complexes S. aethiopicum, S. trilobatum, and S. melongena (wild and cultivated). Group II represented the gboma clade (S. macrocarpon, S. wrightii, S. sisymbriifolium, and S. aculeatissimum), and group III includes S. mammosum, and S. torvum with unique fruit shape and size. The present study would be helpful in genetic discrimination, biodiversity conservation, and the safe utilization of wild eggplants.
Hierarchical automated machine learning (AutoML) for advanced unconventional reservoir characterization
Authors: Mubarak Yousef , Koeshidayatullah Ardiansyah 
Published: August 2023

AbstractRecent advances in machine learning (ML) have transformed the landscape of energy exploration, including hydrocarbon, CO2 storage, and hydrogen. However, building competent ML models for reservoir characterization necessitates specific in-depth knowledge in order to fine-tune the models and achieve the best predictions, limiting the accessibility of machine learning in geosciences. To mitigate this issue, we implemented the recently emerged automated machine learning (AutoML) approach to perform an algorithm search for conducting an unconventional reservoir characterization with a more optimized and accessible workflow than traditional ML approaches. In this study, over 1000 wells from Alberta’s Athabasca Oil Sands were analyzed to predict various key reservoir properties such as lithofacies, porosity, volume of shale, and bitumen mass percentage. Our proposed workflow consists of two stages of AutoML predictions, including (1) the first stage focuses on predicting the volume of shale and porosity by using conventional well log data, and (2) the second stage combines the predicted outputs with well log data to predict the lithofacies and bitumen percentage. The findings show that out of the ten different models tested for predicting the porosity (78% in accuracy), the volume of shale (80.5%), bitumen percentage (67.3%), and lithofacies classification (98%), distributed random forest, and gradient boosting machine emerged as the best models. When compared to the manually fine-tuned conventional machine learning algorithms, the AutoML-based algorithms provide a notable improvement on reservoir property predictions, with higher weighted average f1-scores of up to 15–20% in the classification problem and 5–10% in the adjusted-R2 score for the regression problems in the blind test dataset, and it is achieved only after ~ 400 s of training and testing processes. In addition, from the feature ranking extraction technique, there is a good agreement with domain experts regarding the most significant input parameters in each prediction. Therefore, it is evidence that the AutoML workflow has proven powerful in performing advanced petrophysical analysis and reservoir characterization with minimal time and human intervention, allowing more accessibility to domain experts while maintaining the model’s explainability. Integration of AutoML and subject matter experts could advance artificial intelligence technology implementation in optimizing data-driven energy geosciences.
Identification of glutathione metabolic genes from a dimorphic fungus Talaromyces marneffei and their gene expression patterns under different environmental conditions
Authors: Wangsanut Tanaporn , Sukantamala Panwarit , Pongpom Monsicha 
Published: August 2023

AbstractTalaromyces marneffei is a human fungal pathogen that causes endemic opportunistic infections, especially in Southeast Asia. The key virulence factors of T. marneffei are the ability to survive host-derived heat and oxidative stress, and the ability to convert morphology from environmental mold to fission yeast forms during infection. Glutathione metabolism plays an essential role in stress response and cellular development in multiple organisms. However, the role of the glutathione system in T. marneffei is elusive. Here, we identified the genes encoding principal enzymes associated with glutathione metabolism in T. marneffei, including glutathione biosynthetic enzymes (Gcs1 and Gcs2), glutathione peroxidase (Gpx1), glutathione reductase (Glr1), and a family of glutathione S-transferase (Gst). Sequence homology search revealed an extended family of the TmGst proteins, consisting of 20 TmGsts that could be divided into several classes. Expression analysis revealed that cells in conidia, mold, and yeast phases exhibited distinct expression profiles of glutathione-related genes. Also, TmGst genes were highly upregulated in response to hydrogen peroxide and xenobiotic exposure. Altogether, our findings suggest that T. marneffei transcriptionally regulates the glutathione genes under stress conditions in a cell-type-specific manner. This study could aid in understanding the role of glutathione in thermal-induced dimorphism and stress response.
Exploring the spatio-temporal clusters of closed restaurants after the COVID-19 outbreak in Seoul using relative risk surfaces
Authors: Park Sungjae , Seo Hyunil , Koo Hyeongmo 
Published: August 2023

AbstractThis study explores the clusters of closed restaurants in Seoul in response to the COVID-19 pandemic using the relative risk surface (RRS). The RRS developed based on kernel density estimation provides alternative perspectives for finding the cluster by combining different control and case events. Specifically, the varying impacts on diverse types of restaurants are examined by comparing the densities of closed casual restaurants and cafes. The clusters of closed businesses following the COVID-19 outbreak are subsequently explored through a comparison of the densities of the closed businesses preceding the outbreak. Furthermore, this analysis estimates the clusters of declined commercial areas after the pandemic outbreak based on the comparison between the densities of opened and closed restaurants. Finally, the specific time and region of the clusters are explored using space–time RRS. The analysis results effectively demonstrate various aspects of the closed restaurant clusters. For example, in the central business areas, the densities of closed cafes have decreased after the pandemic outbreak, and the density of closed cafes is significantly higher than that of opened cafes. This study would contribute to the literature on spatial data analysis and urban policy support in response to future epidemics.
Enhanced photocatalytic and antibacterial activities of novel Ag-HA bioceramic nanocatalyst for waste-water treatment
Authors: Elbasuney Sherif , El-Khawaga Ahmed M. , Elsayed Mohamed A. , Elsaidy Amir , Correa-Duarte Miguel A. 
Published: August 2023

AbstractHydroxyapatite (HA), the most common bioceramic material, offers attractive properties as a catalyst support. Highly crystalline mono-dispersed silver doped hydroxyapatite (Ag-HA) nanorods of 60 nm length was developed via hydrothermal processing. Silver dopant offered enhanced chemisorption for crystal violet (CV) contaminant. Silver was found to intensify negative charge on the catalyst surface; in this regard enhanced chemisorption of positively charged contaminants was accomplished. Silver dopant experienced decrease in the binding energy of valence electron for oxygen, calcium, and phosphorous using X-ray photoelectron spectroscopy XPS/ESCA; this finding could promote electron–hole generation and light absorption. Removal efficiency of Ag-HA nanocomposite for CV reached 88% after the synergistic effect with 1.0 mM H2O2; silver dopant could initiate H2O2 cleavage and intensify the release of active ȮH radicals. Whereas HA suffers from lack of microbial resistance; Ag-HA nanocomposite demonstrated high activity against Gram-positive (S. aureus) bacteria with zone of inhibition (ZOI) mm value of 18.0 mm, and high biofilm inhibition of 91.1%. Ag-HA nanocompsite experienced distinctive characerisitcs for utilization as green bioceramic photocatalyst for wastewater treatment.
Development and validation of a questionnaire for assessing parents’ health literacy regarding vision screening for children: a Delphi study
Authors: Ravid-Saffir Ahuva , Sella Shulamit , Ben-Eli Hadas 
Published: August 2023

AbstractPreschool vision screening is recommended to reduce the incidence of amblyopia that persists into adulthood. However, parent’s perceptions regarding the importance of screening and early intervention may constitute a significant barrier to seeking vision exams and pursuing treatment. The aim of this study is to develop and validate a questionnaire for assessing parent’s awareness, perception and health literacy of children's vision tests. The questionnaire was developed using the Delphi method with experts from the fields of pediatric ophthalmology, optometry, orthoptics, pediatric medicine, social sciences and Mother and Child Health Care centers. Experts were provided with drafts of the questions iteratively in three rounds until a consensus was reached independently on the relevant items, coherently language and redundancies. For the first, second and third stages of the Delphi process, 17, 15 and 13 experts participated in the panel respectively. Validity was achieved by wide consensus among the panel on the relevance of each question, of 75%, 85% and 90%, for the three rounds respectively. Here we describe the final questionnaire, EYES: Evaluating Young-Children Eye health Survey, which includes 31 questions regarding demographics, ocular history, parental health literacy, and perceptions of vision and vison exams.
Methodological challenges and new perspectives of shifting vegetation phenology in eddy covariance data
Authors: Panwar Annu , Migliavacca Mirco , Nelson Jacob A. , Cortés José , Bastos Ana , Forkel Matthias , Winkler Alexander J. 
Published: August 2023

AbstractWhile numerous studies report shifts in vegetation phenology, in this regard eddy covariance (EC) data, despite its continuous high-frequency observations, still requires further exploration. Furthermore, there is no general consensus on optimal methodologies for data smoothing and extracting phenological transition dates (PTDs). Here, we revisit existing methodologies and present new prospects to investigate phenological changes in gross primary productivity (GPP) from EC measurements. First, we present a smoothing technique of GPP time series through the derivative of its smoothed annual cumulative sum. Second, we calculate PTDs and their trends from a commonly used threshold method that identifies days with a fixed percentage of the annual maximum GPP. A systematic analysis is performed for various thresholds ranging from 0.1 to 0.7. Lastly, we examine the relation of PTDs trends to trends in GPP across the years on a weekly basis. Results from 47 EC sites with long time series (> 10 years) show that advancing trends in start of season (SOS) are strongest at lower thresholds but for the end of season (EOS) at higher thresholds. Moreover, the trends are variable at different thresholds for individual vegetation types and individual sites, outlining reasonable concerns on using a single threshold value. Relationship of trends in PTDs and weekly GPP reveal association of advanced SOS and delayed EOS to increase in immediate primary productivity, but not to the trends in overall seasonal productivity. Drawing on these analyses, we emphasise on abstaining from subjective choices and investigating relationship of PTDs trend to finer temporal trends of GPP. Our study examines existing methodological challenges and presents approaches that optimize the use of EC data in identifying vegetation phenological changes and their relation to carbon uptake.
Anti-inflammation-based treatment of atherosclerosis using Gliclazide-loaded biomimetic nanoghosts
Authors: Karami Zahra , Mehrzad Jalil , Akrami Mohammad , Hosseinkhani Saman 
Published: August 2023

AbstractIn the study, a biomimetic platform for anti-inflammatory-based treatment of atherosclerotic plaque was developed. Gliclazide (GL) as an anti-inflammasome agent was encapsulated in PLGA nanoparticles (NP), which were coated by monocyte membrane using an extrusion procedure. The size and zeta potential of the nanoghost (NG) changed to 292 and – 10 nm from 189.5 to −34.1 in the core NP. In addition, the actual size of 62.5 nm with a coating layer of 5 nm was measured using TEM. The NG was also showed a sustained release profile with the drug loading content of about 4.7%. Beside to attenuated TNFα, decrease in gene expression levels of NLRP3, MyD88, NOS, IL-1β, IL-18 and caspases 1/3/8/9 in LPS-primed monocytes exposed to NG strongly indicated remarkable inflammation control. After systemic toxicity evaluation and pharmacokinetic analysis of NP and NG, intravenous NG treatment of rabbits with experimentally induced atherosclerosis revealed remarkably less plaque lesions, foam cells, lipid-laden macrophages, and pathological issues in tunica media of aorta sections. Higher expression of CD163 than CD68 in aorta of NG-treated rabbits strongly reveals higher M2/M1 macrophage polarization. The bio/hemocompatible, biomimetic and anti-inflammatory NG can be considered as a potential platform for immunotherapy of particularly atherosclerosis in the field of personalized medicine.
Pediatric Hearing Aid Management: Experiences and Perspectives of Spanish-Speaking Parents
Authors: Muñoz Karen , Guillen Diego , Muñoz Carlos , Twohig Michael P. 
Published: August 2023

Purpose:
The purpose of the study was twofold: (a) to explore hearing aid management experiences of Spanish-speaking parents who have young children using hearing aids and (b) to explore parents' access to the Internet and perceptions about remote audiology services.

Method:
The study used a mixed methods design. Data were collected through a phone interview.

Results:
Eleven mothers of children aged 14–60 months participated. Most of the children (9/11) had a bilateral hearing loss, and two had an additional disability. Three themes emerged for hearing aid management experiences: audiology services, routines, and emotional challenges/supports. Parents had variable levels of confidence in their skills ranging from no confidence to complete confidence, with the greatest variability for three items: (a) using the listening tube to make sure that the sound quality of the hearing aid is good, (b) removing moisture from the earmold tubing, and (c) troubleshooting problems when your child's hearing aids are not working. All participants reported having consistent Internet access and had positive perceptions about the possibility of remote audiology services.

Conclusions:
This study provided insights into hearing aid management experiences and perceptions of Spanish-speaking parents. Parents described variability for audiology services, routines for hearing aid use and care, and access to other parents of children with hearing loss. Spanish-speaking parents present additional elements in the hearing care process that need to be incorporated in planning. Remote services may be an opportunity to enhance access to support that could improve effectiveness of hearing aid management.