bluuebunny/crossref_metadata_2025 huggingface dataset:
BPAGS: a web application for bacteriocin prediction via feature evaluation using alternating decision tree, genetic algorithm, and linear support vector classifier
Authors: Akhter Suraiya , Miller John H.
Published: January 2024

The use of bacteriocins has emerged as a propitious strategy in the development of new drugs to combat antibiotic resistance, given their ability to kill bacteria with both broad and narrow natural spectra. Hence, a compelling requirement arises for a precise and efficient computational model that can accurately predict novel bacteriocins. Machine learning’s ability to learn patterns and features from bacteriocin sequences that are difficult to capture using sequence matching-based methods makes it a potentially superior choice for accurate prediction. A web application for predicting bacteriocin was created in this study, utilizing a machine learning approach. The feature sets employed in the application were chosen using alternating decision tree (ADTree), genetic algorithm (GA), and linear support vector classifier (linear SVC)-based feature evaluation methods. Initially, potential features were extracted from the physicochemical, structural, and sequence-profile attributes of both bacteriocin and non-bacteriocin protein sequences. We assessed the candidate features first using the Pearson correlation coefficient, followed by separate evaluations with ADTree, GA, and linear SVC to eliminate unnecessary features. Finally, we constructed random forest (RF), support vector machine (SVM), decision tree (DT), logistic regression (LR), k-nearest neighbors (KNN), and Gaussian naïve Bayes (GNB) models using reduced feature sets. We obtained the overall top performing model using SVM with ADTree-reduced features, achieving an accuracy of 99.11% and an AUC value of 0.9984 on the testing dataset. We also assessed the predictive capabilities of our best-performing models for each reduced feature set relative to our previously developed software solution, a sequence alignment-based tool, and a deep-learning approach. A web application, titled BPAGS (Bacteriocin Prediction based on ADTree, GA, and linear SVC), was developed to incorporate the predictive models built using ADTree, GA, and linear SVC-based feature sets. Currently, the web-based tool provides classification results with associated probability values and has options to add new samples in the training data to improve the predictive efficacy. BPAGS is freely accessible at https://shiny.tricities.wsu.edu/bacteriocin-prediction/.
Stable and efficient generation of functional iPSC-derived neural progenitor cell rosettes through regulation of collective cell-cell behavior
Authors: Kim Mee-Hae , Thanuthanakhun Naruchit , Kino-oka Masahiro
Published: January 2024

Although the potential of stem cells to differentiate into several cell types has shown promise in regenerative medicine, low differentiation efficiency and poor reproducibility significantly limit their practical application. We developed an effective and robust differentiation strategy for the efficient and robust generation of neural progenitor cell rosettes from induced pluripotent stem cells (iPSCs) incorporating botulinum hemagglutinin (HA). Treatment with HA suppressed the spontaneous differentiation of iPSCs cultured under undirected differentiation conditions, resulting in the preservation of their pluripotency. Moreover, treatment with HA during neural progenitor differentiation combined with dual SMAD inhibition generated a highly homogeneous population of PAX6-and SOX1-expressing neural progenitor cells with 8.4-fold higher yields of neural progenitor cells than untreated control cultures. These neural progenitor cells formed radially organized rosettes surrounding the central lumen. This differentiation method enhanced the generation of functional iPSC-derived neural progenitor cell rosettes throughout the culture vessel, suggesting that the regulation of collective cell-cell behavior using HA plays a morphogenetically important role in rosette formation and maturation. These findings show the significance of HA in the suppression of spontaneous differentiation through spatial homogeneity. The study proposes a novel methodology for the efficient derivation of functional iPSC-derived neural progenitor cell rosettes.
Green synthesis of gold and silver nanoparticles using crude extract of Aconitum violaceum and evaluation of their antibacterial, antioxidant and photocatalytic activities
Authors: Ahmad Shahbaz , Ahmad Shujaat , Xu Qianqian , Khan Idrees , Cao Xiaoyu , Yang Ruimin , Yan Hai
Published: January 2024

Green synthesis of metal nanoparticles (NPs) has received extensive attention over other conventional approaches due to their non-toxic nature and more biocompatibility. Herein we report gold and silver NPs (AuNPs@AV and AgNPs@AV) prepared by employing a green approach using crude extract of Aconitum violaceum Jacquem. ex Stapf. The synthesized NPs were characterized using Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), Energy Dispersive X-ray (EDX), X-ray Diffraction (XRD), UV/Visible spectroscopy, Fourier Transform Infrared (FTIR), X-ray Photoelectron Spectroscopy (XPS), and Zeta Potential. Morphological analysis showed spherical and triangular shapes of the NPs with average size of <100 nm. The AuNPs@AV and AgNPs@AV exhibited effective antibacterial activities, with minimum inhibitory concentrations (MICs) of 95 and 70 μg/mL against Lactobacillus acidophilus (L. acidophilus) and 90 and 65 μg/mL against Escherichia coli (E. coli), respectively. Strong antioxidant effect of AuNPs@AV and AgNPs@AV were reported against DPPH radical and PTIO within range of IC50 values; 161–80 μg/ml as compared to the standard (23–11 μg/mL) respectively. Moreover, the AuNPs@AV and AgNPs@AV showed efficient photocatalytic activity and degraded 89.88% and 93.7% methylene blue (MB) dye under UV light, respectively.
Dual COX-2/5-LOX inhibitors from Zanthoxylum simulans inhibit gastric cancer cells by cross-mediating thyroid, estrogen, and oxytocin signaling pathways
Authors: Tian Yong-Qiang , Liu Jing , Cheng Peng , Zou Jian , Xu Hui-Fang , Shi Xin-Hua , Zhang Yi-Sheng , Mei Ling
Published: January 2024

Cyclooxygenase 2 (COX-2) and 5-lipoxygenase (5-LOX) are overexpressed in gastric cancer cells, the dual inhibitors of which exhibit potential against metastasis and invasion with fewer side effects. To discover inhibitors targeting COX-2 and 5-LOX, we conducted ultrafiltration and enrichment calculation to screen candidates in quaternary alkaloids (QAs) from Zanthoxylum simulans through LC and LC-Q-TOF. For intensive peaks, peaks 19 (berberine) and 21 (chelerythrine) were observed as the most potent dual candidates and showed selective affinity to 5-LOX over COX-2. Peak 19 showed an enrichment at 4.36 for COX-2 and 22.81 for 5-LOX, while peak 21 showed an enrichment at 7.81 for COX-2 and 24.49 for 5-LOX. Molecular docking results revealed chelerythrine as a better dual inhibitor, showing time- and dose-dependent anti-proliferation against AGS cells. Bio-informatics strategies, such as Gene Expression Omnibus (GEO), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG), suggested that hormone pathways in gastric cancer cells might be mediated by chelerythrine. Further reviews and summaries helped outline the mechanisms by which COX-2/5-LOX inhibitors might promote apoptosis in gastric cancer cells via estrogen, thyroid, and oxytocin signaling pathways. Chelerythrine was also added to gastric cancer cells to verify the regulation of these three signaling pathways. As a result, significant calling back of thyroid-stimulating hormone receptor (TSHR), thyroid hormone α3 (TRα3), and thyroid hormone receptor β1 (TRβ1) and suppressing estrogen receptor α36 (ER-α36)–Src could benefit the anti-proliferation of chelerythrine. However, it was disappointing that regulation of estrogen receptor α66 (ER-α66), estrogen receptor β (ER-β), and oxytocin receptor (OTR) contributed inversely negative effects on anti-gastric cancer cells. At present, the integrative study not only revealed chelerythrine as the most potent dual COX-2/5-LOX inhibitor from QAs but also generally highlighted that comprehensive regulation of the estrogen, thyroid, and oxytocin pathway should be noted once gastric cancer cells were treated with inflammatory inhibitors.
Mushroom tyrosinase enzyme catalysis: synthesis of larvicidal active geranylacetone derivatives against Culex quinquesfasciatus and molecular docking studies
Authors: Mullaivendhan Janani , Ahamed Anis , Arif Ibrahim A. , Raman Gurusamy , Akbar Idhayadhulla
Published: January 2024

The grindstone process, which uses tyrosinase as a catalyst, was used to create analogues of geranylacetone. Tyrosinase was used to prepare the Mannich base under favourable reaction conditions, resulting in a high yield. All synthesized compounds were characterized using FTIR, Nuclear magnetic resonance, and mass spectral analyses. The active geranylacetone derivatives (1a-l) were investigated for larvicidal activity against Culex quinquefasciatus; compound 1b (LD50:20.7 μg/mL) was noticeably more effective than geranylacetone (LD50: >100 μg/mL) and permethrin (LD50: 24.4 μg/mL) lead compounds because of their ability to kill larvae and use them as pesticides. All compounds (1a-1l) were found to be low toxic, whereas compounds 1b, 1d, and 1k were screened for antifeedant screening of non -aquatic target for the toxicity measurement against marine fish Oreochromis mossambicus at 100 μg/mL caused 0% mortality in within 24 h. Molecular docking studies of synthesised compound 1b and permethrin docked with 3OGN, compound 1b demonstrated a greater binding affinity (−9.6 kcal/mol) compared to permethrin (−10.5 kcal/mol). According to these results, the newly synthesised geranylacetone derivatives can serve as lead molecules of larvicides agents.
Stenotrophomonas maltophilia complex: insights into evolutionary relationships, global distribution and pathogenicity
Authors: Li Kun , Yu Keyi , Huang Zhenzhou , Liu Xiao , Mei Li , Ren Xiaodong , Bai Xuemei , Gao He , Sun Zhiwen , Liu Xiaoning , Wang Duochun
Published: January 2024

Introduction

Stenotrophomonas maltophilia complex (Smc) comprises opportunistic Gram-negative bacilli responsible for various nosocomial infections. Limited data exists concerning its evolutionary lineage, global prevalence and pathogenicity.

Methods

We conducted an extensive genomic analysis on 734 Smc genomes, of which 90 were newly sequenced and isolated from different patients. The species composition and evolutionary relationships of Smc were examined using core protein sequence analysis. Pathogenicity evaluation was used by assays for swimming motility, biofilm formation and identification of virulence factors. The broth microdilution method was used to evaluate the drug resistance spectrum of clinical isolates.

Results

Phylogenetic analyses delineated 24 species-level clades, dominated by S. maltophilia (42.8%), S. sepilia (13.6%) and S. geniculata (9.9%). Geographically, strains were primarily distributed in Europe (34.2%), Asia (33.7%) and North America (24.0%), with intricate global distribution patterns. Meanwhile, 154 virulence-associated genes and 46 antimicrobial resistance genes within Smc were identified. These genes encoded span various functions, including motility, adherence, toxin, RND antibiotic efflux pumps, beta-lactamases and aminoglycoside-modifying enzymes. Moreover, significant variations were indicated in swimming motility and biofilm-forming capability across the different species, with S. sepilia exhibiting superior levels of both traits. Additionally, no statistically significant discrepancy was detected among Smc species to other antibiotics, despite the fact that all S. geniculata isolates were resistant to Ceftazidime and much higher than other species.

Conclusion

Our findings indicate the need to pay increased attention to other mainstream species of Smc besides S. maltophilia in order to better manage Smc-related infections and tailor effective treatment strategies.
Prevalence and resistance characteristics of multidrug-resistant Streptococcus pneumoniae isolated from the respiratory tracts of hospitalized children in Shenzhen, China
Authors: Shi Xing , Patil Sandip , Wang Qing , Liu Zihao , Zhu Chunqin , Wang Heping , Chen Yunshen , Li Liqiang , Yang Liang , Zheng Yuejie , Dong Shaowei , Bao Yanmin
Published: January 2024

Background

PCV13 introduction in China has led to a significant reduction of vaccine serotype Streptococcus pneumoniae. However, non-vaccine serotypes with highly resistance and invasiveness were often reported in the post-pneumococcal conjugate vaccine era and there was regional differences.

Methods

A total of 669 S. pneumoniae strains were collected from the respiratory tracts of hospitalized children at Shenzhen Children’s Hospital in 2021 and 2022. Antimicrobial resistance (AMR) characteristics were assessed through antibiotic susceptibility testing performed with the VITEK 2 compact system. AMR genes and single nucleotide polymorphisms (SNPs) in pbp1a, pbp2b, and pbp2x were identified via analysis of whole genome sequencing data. Statistical examination of the data was conducted employing chi-square and Fisher’s exact tests.

Results

We found that non-vaccine serotypes strains had accounted for 46.6% of all the pneumococcal isolated strains. The most common non-vaccine serotype is 23A, with a prevalence rate of 8.9%, followed by 15A (6.6%), 6E (5.7%), 34 (3.2%), and 15B (2.9%). The multidrug resistance rates (MDR) of vaccine serotypes were 19F (99.36%), 19A (100%), 23F (98.08%), 6B (100%), and 6C (100%). Meanwhile, the MDR of non-vaccine serotypes were 15B (100.00%), 6E (100%), 15C (100%), 34 (95.24%), and 23A (98.31%). Resistance rates of 6E to more than six antibiotic classes reached 89.47%, which is similar to 19F (83.33%) and 19A (90%). Unique resistance profiles were also identified for non-vaccine serotypes, including significantly higher resistance to chloramphenicol in 6E, 15B, and 15C than in 19F and 19A. Furthermore, through genome sequencing, we revealed strong correlation of cat-TC with chloramphenicol resistance, patA/patB with tetracycline resistance, ermB and pmrA with erythromycin resistance.

Conclusion

The introduction of PCV13 into China from 2017 has led to a shift in the dominant composition of pneumococcal strains. There has been a notable rise and spread of multidrug-resistant non-vaccine serotypes among children. Specifically, the non-vaccine serotype 6E, which was not widely reported in China previously, has emerged. To comprehend the resistance mechanisms, it is crucial to further investigate the molecular and genetic characteristics of these non-vaccine serotypes.
Getting clues from nature: the impact of grass hay on suckling piglets’ gastrointestinal growth and colonic microbiota
Authors: Yao Renjie , Cools An , van Hees Hubèrt M. J. , Chiers Koen , Mebratu Awot Teklu , Aluwé Marijke , Maes Dominiek , Janssens Geert P. J.
Published: January 2024

Introduction

The effect of dietary fiber on pig production has been extensively evaluated. Inspired by observations of the diet of wild, young piglets, this study aimed to examine the possibility of feeding grass hay to suckling piglets besides concentrated creep feed.

Methods

The sow-nursed piglets in this study were divided into two groups based on balanced sow parities. The control group (CON, n = 7 sows) only received a regular, concentrated creep feed, while the treatment piglets (GH, n = 8 sows) were also provided with chopped grass hay from 2 days of age until weaning (28 days). At weaning, one piglet with a median weight was selected from each litter for post-mortem evaluation. Subsequently, six pigs around median weight per sow were grouped into nursery pens and monitored for their feed intake and body weight gain until 9 weeks of age.

Results and discussion

Piglets in GH consumed, on average, 57 g of grass hay per piglet during the entire lactation period. The emptied weight of the small and large intestine was significantly greater in GH (280 vs. 228 g, 88.8 vs. 79.3 g, respectively, p < 0.05), and the length of the large intestine was stimulated by the grass hay (164 vs. 150 cm, p < 0.05). Morphologically, the villus height in the jejunum was higher in GH (p < 0.05). In the large intestine, the crypt depth of the mid-colon was lower in GH. Moreover, the short-chain fatty acid (SCFA) concentrations in the cecum were increased in GH compared to CON (1,179 vs. 948 µmol/g dry matter, p < 0.05), whereas in the colon, SCFA concentrations were lower in CON (341 vs. 278 µmol/g dry matter, p < 0.05). There was no major impact of grass hay inclusion on the colonic microbiota composition. Only a trend was observed for a lower inverse of the classical Simpson (InvSimpon) index and a higher abundance of Lactobacillus genera in GH. After weaning, no significant differences in feed intake and body weight gain were observed. In conclusion, supplementing the grass hay to suckling piglets led to alterations in intestinal morphology, increased SCFA fermentation in proximal sections of large intestine, stimulation of gastrointestinal tract growth, and subtle modifications in colonic microbiota.
Non-alcoholic fatty liver disease increases the risk of cardiovascular disease in young adults and children: a systematic review and meta-analysis of cohort studies
Authors: Liao Yan-Lin , Zhu Gen-Yuan , Chang Cheng
Published: January 2024

Background and aims

It is uncertain if there is a link between non-alcoholic fatty liver disease (NAFLD) and cardiovascular diseases (CVD) in young adults and children. To evaluate the potential link between these two conditions, we conducted a systematic review and meta-analysis of cohort studies.

Methods

A comprehensive search was conducted in PubMed, Web of Science and Embase in order to locate all relevant cohort studies published until August 2023. Random effects meta-analyses were conducted using the generic inverse variance method, with additional subgroup and sensitivity analyses. The Newcastle-Ottawa Scale was employed to evaluate the methodological quality.

Results

Four cohort studies (eleven datasets) involving 10,668,189 participants were included in this meta-analysis. This meta-analysis demonstrated that NAFLD increases the risk of CVD in young adults and children (HR = 1.63, 95% CI: 1.46–1.82, P < 0.00001). Further subgroup analyses showed that individuals with NAFLD were at a heightened risk of coronary heart disease (CHD) (HR = 3.10, 95% CI: 2.01–4.77, P < 0.00001), myocardial infarction (MI) (HR = 1.69, 95% CI: 1.61–1.78, P < 0.00001), atrial fibrillation (AF) (HR = 2.00, 95% CI: 1.12–3.57, P = 0.02), congestive heart failure (CHF) (HR = 3.89, 95% CI: 1.20–12.61, P = 0.02), and stroke (HR = 1.47, 95% CI: 1.39–1.55, P < 0.00001). The results of subgroup analyses based on the study location, NAFLD definition, and follow-up time also showed consistency with the overall results. Sensitivity analyses showed that our results were robust. All of the included studies were judged to be of medium to high quality.

Conclusion

Current evidence reveals that NAFLD is linked to an increased risk of major CVD (including CHD, MI, AF, CHF and stroke) in young adults and children. Further research is needed to strengthen this association and provide stronger evidence for primary prevention of CVD in young adults and children with NAFLD.

Systematic Review Registration

https://www.crd.york.ac.uk/PROSPERO/, PROSPERO registration number: CRD42023457817.
The importance of visual acuity screening in dental education amongst undergraduate dental students: a straightforward method
Authors: Pindoria Jaya , Abela Stefan , Maguire Matthew , Sherriff Martyn , Bister Dirk
Published: January 2024

Background

Visual acuity plays a pivotal role in a dental professional's daily performance and screening the students' field of vision in their early formative years ensures successful undergraduate programmes.

Aims

To compare near and distance visual acuity and stereopsis in first-year and final-year dental students and investigate students' perception of their vision.

Method

This was a cross-sectional study involving 100 KCL first- and final-year dental students who underwent assessment of their vision and completed a self-perception questionnaire. Near visual acuity was assessed using a standardised near vision test chart, distance visual acuity using COMPlog (Clinical Vision Measurement Systems Ltd, London, UK) computerised software and stereopsis using the Frisby Stereotest. Based on the Mann–Whitney test, no statistical differences were found between the first-year and final-year students’ near and distance visual acuity, nor in stereopsis difference at a significance level of α = 0.05. The null hypothesis was accepted.

Results

84% of first-year students and 94% of final-year students attained the highest binocular near visual acuity score of 0.50M. Distance visual acuity scores showed a median ETDRS (Early Treatment Diabetic Retinopathy Study) Letters score 94 in the first-year group and 95 in the final-year group. 8% of students were found to have correctable refractive errors in distance visual acuity. The majority of students across both year groups were able to discern 20 s arc of the smallest disparity. The final-year students reported worrying about their eyesight significantly more than the first-year students.

Conclusions

No statistically significant differences were found in near and distance visual acuity, and stereopsis, between first-year and final-year dental students. However, 8% of students were identified with undiagnosed, correctable refractive errors. The importance of students' vision in clinical dentistry is highlighted, and regular eye examination is recommended.
GIS analysis of urban ground collapse susceptibility: a case study of eastern Hangzhou, China
Authors: Zhou Liling , Zhang Xiaoyi , Shen Huizhen , Zhang Dazheng , Bao Haijun
Published: January 2024

Introduction: In cities, the intensity of integrated development, both above and below ground, has been continuously increasing. Unfortunately, associated events such as surface cracking and ground collapse are common, and research into the susceptibility of urban ground collapse (UGC) has consequently, also been increasing.

Methods: In this study, we calculated the spatial probability distribution of historical UGC events in Hangzhou, China as a case study. To avoid the influence of the subjectivity of expert opinions on the evaluation results, and to distinguish it from the first version of the UGC sensitivity map in 2021, collinearity and correlation analyses based on geo-detector were conducted, and the 11 most representative factors from 22 candidates were identified. Then, a GIS-based susceptibility assessment system was established and applied to eastern Hangzhou, China.

Results: The assessment results were divided into three grades. High-susceptibility areas accounted for 6.08% of the total area and were mainly distributed in the central area on both sides of the Qiantang River. Medium-susceptibility areas accounted for 23.92% of the total area and showed an expanding trend around the central area. Low-susceptibility areas accounted for 12.42% of the total area and were mainly distributed within the bedrock mountainous areas on the west side.

Discussion: The assessment model take more urban construction activies into consideration, which can fits better with the trigger factors of UGC itself, and has good applicability for other cities in Zhejiang Province to assess the susceptibility of UGC events.
Predictability of Duolingo English mock test for Chinese college-level EFLs: using assessment use argument
Authors: Ma Xinyi , Zhang Haomin
Published: January 2024

Online international language tests have been gaining popularity since the COVID-19 pandemic. This study explored the predictive ability of the mock test of Duolingo English Test (DET) for Chinese students. College-level EFLs (N = 42) participated in this study and completed the official online mock test. Through quantitative analysis, the findings demonstrated that mock scores were significantly correlated with TOEFL or IELTS results. However, given that the mock test scores are significantly lower than expected, the consequential validity needs further analysis. Using Assessment Use Argument in qualitative analysis, the study established the claim, warrants, evidence, and potential rebuttals regarding the consequential validity of Duolingo English mock test. With further analysis on test specification, the characterization of Target Language Use domain of DET reading test items were investigated. The results indicate that although the DET mock test is relatively more accessible, it needs modification to become more suitable for Chinese EFLs. Suggestions and limitations on Chinese students using DET and its mock test were also discussed.
Sex dimorphism in the effect and predictors of weight loss after sleeve gastrectomy
Authors: Shu Jiaxin , Zhu Tao , Xiong Sisi , Liu Teng , Zhao Yian , Huang Xin , Liu Shaozhuang
Published: January 2024

Background

No sex-specific guidelines for surgical anti-obesity strategies have been proposed, partially due to the controversy regarding sex-related differences in weight loss after bariatric metabolic surgery.

Objectives

To explore sex dimorphism in the effect and predictors of weight loss after sleeve gastrectomy (SG), thereby providing clinical evidence for the sex-specific surgical treatment strategy.

Methods

In a prospective cohort design, participants scheduled for SG at an affiliated hospital between November 2020 and January 2022 were assessed for eligibility and allocated to the Male or Female group with a 1-year follow-up after surgery. The primary outcome was the sex difference in the weight-loss effect after SG indicated by both percentage of total weight loss (TWL%) and excess weight loss (EWL%). The secondary outcome was the analysis of sex-specific preoperative predictors of weight loss after SG based on univariate and multivariate analyses. Independent predictors were obtained to construct a nomogram model. The discrimination, calibration, and clinical utility of the nomogram were based on receiver operating characteristic curve, concordance index, calibration curve, and decision curve analysis, respectively.

Results

Ninety-five male and 226 female patients were initially included. After propensity score matching by baseline body mass index (BMI), 85 male and 143 female patients achieved comparable TWL% and EWL% for 1 year after SG. For male patients, baseline BMI, area under the curve for insulin during oral glucose tolerance test, and progesterone were independent predictors of weight loss after SG. Baseline BMI, age, thyroid stimulating hormone, and Self-Rating Anxiety Scale score were independent predictors for female patients.

Conclusion

No obvious sex difference is detected in the weight-loss effect after SG. Sex dimorphism exists in the predictors of weight loss after SG. Further research with long-term and a multicenter design is needed to confirm the predictive model.
Archimedes optimization algorithm based parameter extraction of photovoltaic models on a decent basis for novel accurate RMSE calculation
Authors: Hussain Md Tahmid , Hussan Md Reyaz , Tariq Mohd , Sarwar Adil , Ahmad Shafiq , Poshtan Majid , Mahmoud Haitham A.
Published: January 2024

Solar photovoltaic (PV) technology stands as a promising alternative to conventional fossil fuel-based power generation, offering pollution-free and low-maintenance energy production. To harness its potential effectively, understanding the power generation process and accurately modeling solar PV systems are essential. Unfortunately, manufacturers often do not provide the necessary parameters for modeling solar cells, making it challenging for researchers. This research employs the Archimedes Optimization Algorithm (AOA), an optimization technique, to determine unknown parameters for the PVM752 GaAs thin film solar cell and the RTC France solar cell. The modeling of these solar cells utilizes both a Single Diode Model (SDM) and a Double Diode Model (DDM). Performance evaluations are conducted using the sum of individual absolute errors (SIAE) and a novel root mean square error (RMSE) method. Comparing the effectiveness of the AOA with other optimization methods, The RMSEs for the AOA applied to the SDM and DDM of RTC France solar cell were 3.7415 × 10–3 and 1.0033 × 10–3. Similarly, for PVM752 GaAs thin film solar cell were 1.6564 × 10–3, and 0.00106365, respectively. The SIAE values for both solar diode models of RTC France cells were 0.071845 and 0.021268, respectively. For the PVM752 GaAs thin film, the corresponding SIAE values were 0.031488 and 0.040224. The results highlight the efficiency of the AOA-based approach, showcasing consistent convergence and a high level of accuracy in obtained solutions. The suggested approach produces superior results with a lower RMSE compared to other algorithms, demonstrating its efficacy in determining solar PV parameters for modeling purposes.
Facebook and social representations of Filipino migrant life in Germany: a reflexive computational approach
Authors: Umel Audris
Published: January 2024

Computational approaches have grown in prominence amidst advancements in new media and technologies and ever-increasing amounts of digital data. This article critically examines these automated techniques, especially the analytical affordances and concerns that such methods introduce to the study of online migrant and mobility discourses. The paper further argues for a mixed methodology anchored on social representations theory—a contextually sensitive framework that enables reflexive use of computational approaches, i.e., quantitatively analyze but also explore different layers of cultural and linguistic meanings in online diasporic interactions. With Filipino migrants in Germany as a case study and partner community, the study then demonstrates the combined application of topic modeling and ethnographically inspired qualitative analysis on migrant posts in Facebook. The findings are discussed in the form of a cultural reflection on Filipino values and expectations and an advocacy for mixed methodologies grounded on critical, social, and practice-oriented theories.
Identification and validation of platelet-related diagnostic markers and potential drug screening in ischemic stroke by integrating comprehensive bioinformatics analysis and machine learning
Authors: Geng Yifei , Liu Yuchen , Wang Min , Dong Xi , Sun Xiao , Luo Yun , Sun Xiaobo
Published: January 2024

Background

Ischemic stroke (IS), caused by blood and oxygen deprivation due to cerebral thrombosis, has links to activated and aggregated platelets. Discovering platelet-related biomarkers, developing diagnostic models, and screening antiplatelet drugs are crucial for IS diagnosis and treatment.

Methods and results

Combining and normalizing GSE16561 and GSE22255 datasets identified 1,753 upregulated and 1,187 downregulated genes. Fifty-one genes in the platelet-related module were isolated using weighted gene co-expression network analysis (WGCNA) and other analyses, including 50 upregulated and one downregulated gene. Subsequent enrichment and network analyses resulted in 25 platelet-associated genes and six diagnostic markers for a risk assessment model. This model’s area under the ROC curve outperformed single genes, and in the peripheral blood of the high-risk group, immune infiltration indicated a higher proportion of CD4, resting CD4 memory, and activated CD4 memory T cells, along with a lower proportion of CD8 T cells in comparison to the low-risk group. Utilizing the gene expression matrix and the CMap database, we identified two potential drugs for IS. Finally, a rat MACO/R model was used to validate the diagnostic markers’ expression and the drugs’ predicted anticoagulant effects.

Conclusion

We identified six IS platelet-related biomarkers (APP, THBS1, F13A1, SRC, PPBP, and VCL) for a robust diagnostic model. The drugs alpha-linolenic acid and ciprofibrate have potential antiplatelet effects in IS. This study advances early IS diagnosis and treatment.
Advances on adaptive immune responses affected by infectious bursal disease virus in chicken
Authors: Zhang Tao , Wang Suyan , Liu Yongzhen , Qi Xiaole , Gao Yulong
Published: January 2024

Infectious bursal disease (IBD) is an acute, highly infectious, and immunosuppressive disease caused by the infectious bursal disease virus (IBDV), which interferes with the immune system, causes hypoimmunity and seriously threatens the healthy development of the poultry industry. Adaptive immune response, an important defense line of host resistance to pathogen infection, is the host-specific immune response mainly mediated by T and B lymphocytes. As an important immunosuppressive pathogen in poultry, IBDV infection is closely related to the injury of the adaptive immune system. In this review, we focus on recent advances in adaptive immune response influenced by IBDV infection, especially the damage on immune organs, as well as the effect on humoral immune response and cellular immune response, hoping to provide a theoretical basis for further exploration of the molecular mechanism of immunosuppression induced by IBDV infection and the establishment of novel prevention and control measures for IBD.
Deciphering decidual leukocyte traffic with serial intravascular staining
Authors: Vazquez Jessica , Mohamed Mona A. , Banerjee Soma , Keding Logan T. , Koenig Michelle R. , Leyva Jaimes Fernanda , Fisher Rachel C. , Bove Emily M. , Golos Thaddeus G. , Stanic Aleksandar K.
Published: January 2024

The decidual immunome is dynamic, dramatically changing its composition across gestation. Early pregnancy is dominated by decidual NK cells, with a shift towards T cells later in pregnancy. However, the degree, timing, and subset-specific nature of leukocyte traffic between the decidua and systemic circulation during gestation remains poorly understood. Herein, we employed intravascular staining in pregnant C57BL/6J mice and cynomolgus macaques (Macaca fascicularis) to examine leukocyte traffic into the decidual basalis during pregnancy. Timed-mated or virgin mice were tail-vein injected with labelled αCD45 antibodies 24 hours and 5 minutes before sacrifice. Pregnant cynomolgus macaques (GD155) were infused with labelled αCD45 at 2 hours or 5 mins before necropsy. Decidual cells were isolated and resulting suspensions analyzed by flow cytometry. We found that the proportion of intravascular (IVAs)-negative leukocytes (cells labeled by the 24h infusion of αCD45 or unlabeled) decreased across murine gestation while recent immigrants (24h label only) increased in mid- to late-gestation. In the cynomolgus model our data confirmed differential labeling of decidual leukocytes by the infused antibody, with the 5 min infused animal having a higher proportion of IVAs+ cells compared to the 2hr infused animal. Decidual tissue sections from both macaques showed the presence of intravascularly labeled cells, either in proximity to blood vessels (5min infused animal) or deeper into decidual stroma (2hr infused animal). These results demonstrate the value of serial intravascular staining as a sensitive tool for defining decidual leukocyte traffic during pregnancy.
Who said it? Native and non-native listeners' source memory for object-speaker associations
Authors: Beck Sara D. , Weber Andrea
Published: January 2024

Memory for who said what can help native and non-native listeners identify critical information for use in conversations. In two experiments, source memory for object-speaker associations was tested for listeners varying in language proficiency. Native and non-native participants of English first heard speakers name objects with prototypical color (e.g., broccoli) before they had to indicate who had previously named each object. Speakers either consistently named objects of one color, or they randomly named objects of different colors. While both listener groups associated objects with speakers successfully, in Experiment 1, with black and white images, native listeners showed an advantage in source memory in the color consistent condition over the random condition, while non-native listeners had no such advantage. The finding for non-native listeners was replicated in Experiment 2 with color images. The results confirm the role of source memory representations in communication, but also suggest that encoding object-speaker association in L2 may be less sensitive to consistent patterns in the input.
Large-scale bedrock outcrop mapping on the NE Atlantic Irish continental margin
Authors: Recouvreur Audrey , Wheeler Andrew J. , Strachan Ruaihri , Meere Patrick A. , Unitt Richard P. , Lim Aaron
Published: January 2024

The Irish continental margin (ICM) encompasses many complex sedimentary basins and diverse geomorphological features displaying bedrock outcrops where a large variety of habitats can be observed. This large area of seabed extends over >400,000 km2 and cannot be mapped manually or in a standardized way. Novel bedrock suitability mapping is applied to the entire ICM to determine potential bedrock outcrop from shallow to deep settings and to improve on the regional near-surface geology of the Irish margin. With the use of ROV video transects covering all the ICM and multibeam echosounder dataset, key terrain variables diagnostic of bedrock outcrop have been derived from bathymetry. A reclassification of each terrain variable was created by identifying the suitable ranges for outcrop occurrence in the variables, corresponding to the most common values occurring where the bedrock is located. Suitable bedrock location in non-surveyed areas have been calculated using these variables with map algebra to develop the novel Bedrock Suitability Index. This high-resolution (25 m2) model indicates that the main features where outcrop could be observed are canyon heads, terraces, or failure scarps, especially noticeable on the Whittard Canyon system. The Bedrock Suitability Index model is validated by video observations of bedrock exposures and is established with 58% level of confidence with 25 m2 resolution on the overall margin over >400,000 km2. The BSI mapping suggests a structural control on bedrock outcrop occurrences, with high BSI correlating with deep structural fabrics of the margin as bedrock outcrop can be found in areas where previously mapped faults have been identified. Bedrock and hard substratum mapping are important components to improve habitat identification and mapping. This less-invasive, low-cost method can be applied with open source software in a relatively simple way of determining where bedrock could be found. It can also be used to refine areas where there will be simply too much data for use to manually classify. Potential bedrock outcrop mapping can be included in a species distribution model.
Direct yaw moment control of eight-wheeled distributed drive electric vehicles based on super-twisting sliding mode control
Authors: Liao Zili , Cai Lichun , Li Jiaqi , Zhang Yunyin , Liu Chunguang
Published: January 2024

This paper proposed a novel direct yaw moment control (DYC) system to enhance vehicle stability and handling performance in various driving conditions and overcome the chattering problem of traditional sliding mode control. Accordingly, a DYC strategy is developed for eight-wheeled DDEVs by utilizing a super-twisting sliding mode (STSM) algorithm. Initially, a three-degrees-of-freedom model, nonlinear tire model, and motor model are established for vehicles. Subsequently, the reference yaw rate is obtained based on the reference model of the vehicle to serve as a control target. The DYC strategy is then established using the error between the actual yaw rate and the reference yaw rate as the input. Moreover, a traditional sliding mode (SM) controller is developed to enhance vehicle stability. A second-order SM controller is designed by incorporating a STSM control algorithm to address the chattering problem associated with traditional SM controllers. The algorithm adaptively adjusts the sliding surface and controls the gains based on the dynamic state of the vehicle. The effectiveness of the proposed control strategy is validated via hardware-in-the-loop simulations.
Frequently asked questions about the ISAPP postbiotic definition
Authors: Vinderola Gabriel , Sanders Mary Ellen , Cunningham Marla , Hill Colin
Published: January 2024

The term postbiotic was defined by the International Scientific Association of Probiotics and Prebiotics (ISAPP) as “a preparation of inanimate microorganisms and/or their components that confers a health benefit on the host.” Although the ISAPP definition is widely cited, some concerns were aired after publication, and alternative definitions of postbiotic, as well as different terms for inactivated microbes, have been previously suggested. This paper addresses questions about the ISAPP definition that have been raised in different forums, including scientific meetings, social media commentary and personal communications. We focus on the rationale, scope, wording, composition and commercial implementation, as well as what is expected of postbiotics regarding safety, efficacy, quantification and mechanisms of action. We hope that exploring these questions will further clarify the definition and its scope and support a common understanding of the concept of postbiotics.
Open field test for the assessment of anxiety-like behavior in Gnathonemus petersii fish
Authors: Horka Petra , Langova Veronika , Hubeny Jan , Vales Karel , Chrtkova Ivana , Horacek Jiri
Published: January 2024

The open field test (OFT) is a basic and most widely used test for investigation in animal studies of the neurobiological basis of anxiety and screening for novel drug targets. Here, we present the results of an OFT for weakly electric fish Gnathonemus petersii. This study aimed to describe the behavioral response of G. petersii exposed to an OFT, simultaneously with an evaluation of electrical organ discharges (EOD), to determine whether any association between EOD and patterns of motor behavior in the OFT exists. Treatment of OFT activity and its temporal patterning was assessed for the whole 6-min trial as well as per-minute distributions of activity using a near-infrared camera and an EOD data acquisition system. Our results demonstrated that the time spent, distance moved, and time of activity were significantly higher in the periphery of the OFT arena. The zone preference pattern over the 6-min test session showed that G. petersii prefer the outer zone (83.61%) over the center of the arena (16.39%). The motor behavior of fish measured as distance moved, active time, and swim speed were correlated with the number of EODs; however, no relationship was found between EOD and acceleration.
A reinforcement learning model with choice traces for a progressive ratio schedule
Authors: Ihara Keiko , Shikano Yu , Kato Sae , Yagishita Sho , Tanaka Kenji F. , Takata Norio
Published: January 2024

The progressive ratio (PR) lever-press task serves as a benchmark for assessing goal-oriented motivation. However, a well-recognized limitation of the PR task is that only a single data point, known as the breakpoint, is obtained from an entire session as a barometer of motivation. Because the breakpoint is defined as the final ratio of responses achieved in a PR session, variations in choice behavior during the PR task cannot be captured. We addressed this limitation by constructing four reinforcement learning models: a simple Q-learning model, an asymmetric model with two learning rates, a perseverance model with choice traces, and a perseverance model without learning. These models incorporated three behavioral choices: reinforced and non-reinforced lever presses and void magazine nosepokes, because we noticed that male mice performed frequent magazine nosepokes during PR tasks. The best model was the perseverance model, which predicted a gradual reduction in amplitudes of reward prediction errors (RPEs) upon void magazine nosepokes. We confirmed the prediction experimentally with fiber photometry of extracellular dopamine (DA) dynamics in the ventral striatum of male mice using a fluorescent protein (genetically encoded GPCR activation-based DA sensor: GRABDA2m). We verified application of the model by acute intraperitoneal injection of low-dose methamphetamine (METH) before a PR task, which increased the frequency of magazine nosepokes during the PR session without changing the breakpoint. The perseverance model captured behavioral modulation as a result of increased initial action values, which are customarily set to zero and disregarded in reinforcement learning analysis. Our findings suggest that the perseverance model reveals the effects of psychoactive drugs on choice behaviors during PR tasks.
Dietary supplementation of 3′-sialyllactose or 6′-sialyllactose elicits minimal influence on cognitive and brain development in growing pigs
Authors: Golden Rebecca K. , Sutkus Loretta T. , Donovan Sharon M. , Dilger Ryan N.
Published: January 2024

Sialylated human milk oligosaccharides (HMO), such as 3′-sialyllactose (3′-SL) and 6′-sialyllactose (6′-SL), are abundant throughout lactation and at much higher concentrations than are present in bovine milk or infant formulas. Previous studies have suggested that sialylated HMO may have neurocognitive benefits in early life. Recent research has focused on infant formula supplementation with key nutrients and bioactives to narrow the developmental gap between formula-fed and breastfed infants. Herein, we investigated the impact of supplemental 3′-SL or 6′-SL on cognitive and brain development at two time-points [postnatal days (PND) 33 and 61]. Two-day-old piglets (N = 75) were randomly assigned to commercial milk replacer ad libitum without or with 3′-SL or 6′-SL (added in a powdered form at a rate of 0.2673% on an as-is weight basis). Cognitive development was assessed via novel object recognition and results were not significant at both time-points (p > 0.05). Magnetic resonance imaging was used to assess structural brain development. Results varied between scan type, diet, and time-point. A main effect of diet was observed for absolute volume of white matter and 9 other regions of interest (ROI), as well as for relative volume of the pons on PND 30 (p < 0.05). Similar effects were observed on PND 58. Diffusion tensor imaging indicated minimal differences on PND 30 (p > 0.05). However, several dietary differences across the diffusion outcomes were observed on PND 58 (p < 0.05) indicating dietary impacts on brain microstructure. Minimal dietary differences were observed from myelin water fraction imaging at either time-point. Overall, sialyllactose supplementation had no effects on learning and memory as assessed by novel object recognition, but may influence temporally-dependent aspects of brain development.