bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhanced seagull optimization for enhanced accuracy in CUDA-accelerated Levenberg–Marquardt backpropagation neural networks for earthquake forecasting
Authors: Kollam Manoj , Joshi Ajay
Published: September 2024

Hyperparameter tuning is crucial for enhancing the accuracy and reliability of artificial neural networks (ANNs). This study presents an optimization of the Levenberg–Marquardt backpropagation neural network (LM-BPNN) by integrating an improved seagull optimization algorithm (ISOA). The proposed ISOA-LM-BPNN model is designed to forecast earthquakes in the Caribbean region. The study further explores the impact of data and model parallelism, revealing that hybrid parallelism effectively mitigates the limitations of both. This leads to substantial gains in throughput and overall performance. To address computational demands, this model leverages the compute unified device architecture (CUDA) framework, enabling hybrid parallelism on graphics processing units (GPUs). This approach significantly enhances the model’s computational speed. The experimental results demonstrate that the ISOA-LM-BPNN model achieves a 20% improvement in accuracy compared to four baseline algorithms across three diverse datasets. The integration of ISOA with LM-BPNN refines the neural network’s hyperparameters, leading to more precise earthquake predictions. Additionally, the model’s computational efficiency is evidenced by a 56% speed increase when utilizing a single GPU, and an even greater acceleration with dual GPUs connected via NVLink compared to traditional CPU-based computations. The findings underscore the potential of ISOA-LM-BPNN as a robust tool for earthquake forecasting, combining high accuracy with enhanced computational speed, making it suitable for real-time applications in seismic monitoring and early warning systems.
Emerging fatal gout disease in Chinese goslings linked to acute kidney injury induced by novel goose astrovirus infection
Authors: Bi Zhuangli , Lv Xuan , Zhang Zicheng , Cai Linying , Zhang Miao , Li Wanxiao , Ding Yingying , Liu Huiwen , Yang Kang , Zhu Yingqi , Liu Guangqing , Wang Guijun
Published: September 2024

A novel goose astrovirus (GAstV) has broken out across China in recent years, causing widespread damage to the poultry industry. In goslings infected with GAstV, the leading cause of death is visceral gout. However, our understanding of the mechanism of gout formation in GAstV infection is largely inadequate. The aim of this study was to examine the pathogenicity of a GAstV strain and explore the molecular mechanisms of visceral gout caused by viral infection in goslings. The virulent GAstV strain HR2105/1 was effectively isolated from the visceral tissue of goslings in gout-affected areas. The whole genome of the HR2105/1 strain was sequenced and analyzed. Subsequently, we established a gosling gout models with experimental GAstV infection. Finally, we conducted a study on the mechanism of GAstV induced acute kidney injury. Phylogenetic analysis of the complete genome sequence showed that it was closely related to the strain circulating in China since 2016, and it was grouped within the GAstV-1 cluster. The clinical signs were reproduced by experimental infection of healthy goslings with the isolated strain and were found to be similar to those reported in clinical cases. Moreover, the virus exhibits strong renal tropism. Infection with the GAstV strain HR2105/1 was found to cause acute kidney injury, as evidenced by increased levels of uric acid and creatinine as well as severe pathological damage. Mechanistic experiments with Masson and Picrosirius Red staining revealed fibrosis in renal tissues after GAstV infection. Furthermore, TUNEL staining revealed that GAstV infection triggered renal cell apoptosis. Additionally, RT-qPCR revealed that GAstV infection caused an excessive inflammatory response by upregulating the expression of IL-1β, IL-6, IL-10, TGF-β, and iNOS in renal tissues. Overall, our findings demonstrate that GAstV infection causes renal damage by inducing renal cell apoptosis, fibrosis, and excessive inflammatory response, which subsequently leads to hyperuricemia and lethal visceral gout formation. This is the first systematic study on the etiology of lethal gout in goslings caused by GAstV infection, and we believe that the findings can guide vaccine development and therapeutic targets for GAstV-associated renal diseases.
Genomic signature for oligometastatic disease in non-small cell lung cancer patients with brain metastases
Authors: Choi Ariel R. , D’Agostino Ralph B. , Farris Michael K. , Abdulhaleem Mohammed , Hunting John C. , Wang Yuezhu , Smith Margaret R. , Ruiz Jimmy , Lycan Thomas W. , Petty W. Jeffrey , Cramer Christina K. , Tatter Stephen B. , Laxton Adrian W. , White Jaclyn J. , Li Wencheng , Su Jing , Whitlow Christopher , Xing Fei , Chan Michael D.
Published: September 2024

Purpose/objective(s)

Biomarkers for extracranial oligometastatic disease remain elusive and few studies have attempted to correlate genomic data to the presence of true oligometastatic disease.

Methods

Patients with non-small cell lung cancer (NSCLC) and brain metastases were identified in our departmental database. Electronic medical records were used to identify patients for whom liquid biopsy-based comprehensive genomic profiling (Guardant Health) was available. Extracranial oligometastatic disease was defined as patients having ≤5 non-brain metastases without diffuse involvement of a single organ. Widespread disease was any spread beyond oligometastatic. Fisher’s exact tests were used to screen for mutations statistically associated (p<0.1) with either oligometastatic or widespread extracranial disease. A risk score for the likelihood of oligometastatic disease was generated and correlated to the likelihood of having oligometastatic disease vs widespread disease. For oligometastatic patients, a competing risk analysis was done to assess for cumulative incidence of oligometastatic progression. Cox regression was used to determine association between oligometastatic risk score and oligoprogression.

Results

130 patients met study criteria and were included in the analysis. 51 patients (39%) had extracranial oligometastatic disease. Genetic mutations included in the Guardant panel that were associated (p<0.1) with the presence of oligometastatic disease included ATM, JAK2, MAP2K2, and NTRK1, while ARID1A and CCNE1 were associated with widespread disease. Patients with a positive, neutral and negative risk score for oligometastatic disease had a 78%, 41% and 11.5% likelihood of having oligometastatic disease, respectively (p<0.0001). Overall survival for patients with positive, neutral and negative risk scores for oligometastatic disease was 86% vs 82% vs 64% at 6 months (p=0.2). Oligometastatic risk score was significantly associated with the likelihood of oligoprogression based on the Wald chi-square test. Patients with positive, neutral and negative risk scores for oligometastatic disease had a cumulative incidence of oligometastatic progression of 77% vs 35% vs 33% at 6 months (p=0.03).

Conclusions

Elucidation of a genomic signature for extracranial oligometastatic disease derived from non-invasive liquid biopsy appears feasible for NSCLC patients. Patients with this signature exhibited higher rates of early oligoprogression. External validation could lead to a biomarker that has the potential to direct local therapies in oligometastatic patients.
Demand-side management scenario analysis for the energy-efficient future of Pakistan: Bridging the gap between market interests and national priorities
Authors: Chughtai Arshad , Uqaili Mohammad Aslam , Hussain Mirjat Nayyar , Shaikh Faheemullah , Khatri Shoaib Ahmed
Published: September 2024

Pakistan is facing the worst level of energy and economic crisis of its history. The underlying reason of the economic crisis is basically due to the energy crisis. Various approaches have been adopted to tackle the energy crises which the country is facing for over 2 decades. Demand-side management (DSM) is the most potent and cost-effective option to redress the energy crisis, which, unfortunately, has been the most neglected strategy in Pakistan. DSM has the potential to save up to 10.0%–15.0% of primary energy to ensure the country’s future energy security. Laws and codes do exist, but ironically, the most vital element of DSM’s policy framework and implementation mechanism is missing. Hence, the main objective of this research is to develop a DSM model for Pakistan and analyze the reference and DSM scenarios. Low-emission analysis platform (LEAP) is used to develop Pakistan’s DSM model for the study period 2021–2050. The three alternative DSM scenarios developed include energy efficiency (EEF), energy conservation (EC), and load management (LOM), and they are all analyzed. The model results estimate the electricity demand forecast of 1009.8 TWh under the reference scenario in 2050, whereas DSM tends to result in a 26.38% decreased electricity demand compared to the reference scenario. The alternative DSM scenarios also outperform the reference scenario. In 2050, the EC scenario reduces consumption by 178.0 TWh and GHG emissions by 19.20 million metric tons, the EEF scenario reduces consumption by 110.30 TWh and GHG emissions by 10.04 million metric tons, and the LOM scenario suggests reduced consumption by 101.0 TWh and GHG emissions by 6.20 million metric tons. This study concluded that the DSM must be institutionalized in Pakistan by building a robust regulatory framework and execution mechanism at the government and utility levels.
Grid-integrated solutions for sustainable EV charging: a comparative study of renewable energy and battery storage systems
Authors: Rehman Anis ur , Khalid Haris M. , Muyeen S. M.
Published: September 2024

Introduction

The integration of electric vehicles (EVs) into the power network challenges the 1) grid capacity, 2) stability, and 3) management. This is due to the 1) increased peak demand, 2) infrastructure strain, and 3) intermittent charging patterns. Previous studies lack comprehensive integration of renewable energy and battery storage with EV charging.

Methods

To address these challenges, this study explores the effectiveness of incorporating renewable energy resources (RERs) and battery energy storage systems (BESS) alongside the traditional grid. The proposed study utilizes the HOMER Grid® and conducted a comprehensive analysis.

Results

The proposed study compares two grid integrated scenarios: 1) Case-1 (grid and photovoltaic (PV) systems), and 2) Case-2 (grid, PV systems, and BESS). Both these scenarios are compared against a Base case relying solely on grid power. The evaluation employed techno-economic analysis while focusing on 1) net present cost (NPC), 2) cost of energy, and 3) annualized savings. Additionally, the proposed study analyzed 4) seasonal variations in EV charging demand, 5) grid interactions, 6) PV production, and 7) the operation of BESS in both summer and winter. The comparative analysis reveals that the Base case incurs a net present cost (NPC) of $546,977 and a cost of energy (COE) of $0.354 per kWh. In contrast, Case-1, which integrates a 100 kW PV system, shows a significantly lower NPC of -$122,962 and a reduced COE of -$0.043 per kWh, with annualized savings of $61,492. Case-2, incorporating both the 100 kW PV system and a BESS with a capacity of 9.8 kWh, has a higher NPC of $309,667 but a COE of $0.112 per kWh and provides annual savings of $51,233 compared to the Base case.

Discussion

Seasonal analysis highlights that Case-2 achieves the lowest carbon emissions in summer, ranging from 2.0 to 2.5 tons, while Case-1 shows the lowest emissions in winter, ranging from 3.2 to 3.4 tons. This model 1) reduces operational costs, 2) minimizes carbon emissions, while 3) making it compelling for future energy systems in increasing EV adoption.
Multi-objective-based economic and emission dispatch with integration of wind energy sources using different optimization algorithms
Authors: Lalhmachhuana R. , Deb Subhasish , Datta Subir , Singh Ksh. Robert , Cali Umit , Ustun Taha Selim
Published: September 2024

In this work, a study of economic and emission dispatch issues based on the multi-objective optimization is solved, and generation costs and emissions are reduced by utilizing multi-objective optimization techniques. This optimization is carried out in an IEEE-30 bus system, with and without the integration of wind energy sources, with equality and inequality constraints. The equality constraints are the power balance constraints, stipulating that to have an optimal solution, the generated power must be adequate to satisfy the load demand plus losses. The inequality constraints are a collection of limitations for active power generation, reactive power generation, generator bus voltage, and load bus voltage. To track the hourly load demand, a daily load profile is established using the IEEE-30 bus system. The generation costs and emissions in the system are optimized using multi-objective particle swarm optimization and multi-objective Ant–Lion Optimization approaches. In order to determine the goals’ minimum values, a fuzzy min–max technique is applied. The values that have been minimized are then compared to determine how well wind energy integration has reduced the generation costs and emissions. Two case studies are performed in this work. For Case 1, the total generation costs and emissions using MOPSO are less, with a difference of $42.763, while MOALO has lower emissions, with a difference of 157.337 tons. For Case 2, with the implementation of wind energy, MOPSO has lower total generation costs, with a difference of $51.678, and lower emissions, with a difference of 459.446 tons.
A combined transcriptomics and proteomics approach reveals S100A4 as a potential biomarker for Graves’ orbitopathy
Authors: Chng Chiaw-Ling , Lai Oi Fah , Seah Lay-Leng , Yong Kai-Ling , Chung Yvonne Hsi-Wei , Goh Rochelle , Lim Che Kang
Published: September 2024

Background

There are no reliable biomarkers to identify Graves’ disease patients who will develop severe Graves’ orbitopathy (GO). We hypothesize that integrating various omics platforms can enhance our understanding of disease mechanisms and uncover potential biomarkers. This study aimed to (1) elucidate the differential gene expression profile of orbital fibroblasts in GO during early adipogenesis to better understand disease mechanisms and (2) compare tear protein profiles from our earlier study and the transcriptome profiles of orbital fibroblasts (OFs) to identify possible biomarkers of the disease.

Methods

OFs were grown from orbital adipose tissue obtained from nine GO patients (three for discovery and six for validation experiments). Total RNA was extracted from OFs on day 0 as the baseline for each sample and from differentiated OFs on days 4 and 8. Protein–protein interaction (PPI) analysis and functional enrichment analysis were also carried out. The differentially expressed genes (DEGs) from the RNA sequencing experiments were then compared to the full tear proteome profile from the author’s previous study, which examined the tear protein changes of GO patients based on fold change > 1.6 or < −1.6. FDR < 0.05 was applied within all datasets. Further validation of S100 calcium-binding protein A4 (S100A4) downregulation in GO was performed via quantitative real-time PCR (qPCR).

Results

The whole transcriptomic analysis revealed 9 upregulated genes and 15 downregulated genes in common between the discovery and validation experiments. From the PPI network analysis, an interaction network containing six identified DEGs (ALDH2, MAP2K6, MT2A, SOCS3, S100A4, and THBD) was observed. The functional enrichment network analysis identified a set of genes related to oxysterol production. S100A4 was found to be consistently downregulated in both our transcriptome studies and the full-tear proteome profile from the author’s previous study.

Conclusion

Our study identified several DEGs and potential gene pathways in GO patients, which concurred with the results of other studies. Tear S100A4 may serve as a biomarker for the propensity to develop thyroid eye disease (TED) in patients with autoimmune thyroid disease (AITD) before clinical manifestation and should be confirmed in future studies.
Genetic characterization of cashmere goat (Capra hircus) populations in Mongolia
Authors: Baldan Sergelen , Sölkner Johann , Gebre Kahsa Tadel , Mészáros Gábor , Crooijmans Richard , Periasamy Kathiravan , Pichler Rudolf , Manaljav Bayarjargal , Baatar Narantuya , Purevdorj Myagmarsuren
Published: September 2024

Objective

Characterization studies of the phenotypic and genetic diversity of Mongolian goats are limited, despite several goat breeds being registered in the country. This study aimed to evaluate the phenotypic and genetic diversity of 14 cashmere goat populations in Mongolia, consisting largely of identified goat breeds.

Methods

Body weight, cashmere quality, and coat color were the phenotypic traits considered in this study. A linear model was used to fit body weight and cashmere traits, and least squares means (LSMs) were estimated for the region and location classes. Genetic diversity and structure were assessed using a goat 50K SNP array.

Results

The studied populations exhibited greater phenotypic diversity at the regional level. A very small overall differentiation index (Fst: 0.017) was revealed by Wright’s Fst and a very small overall inbreeding index (FROH1:0.019) was revealed based on runs of homozygosity. Genetic clustering of populations by principal components showed large variances for the two goat populations of the Russian admixture (Gobi Gurvan Saikhan and Uuliin Bor), and smaller but differentiated clusters for the remaining populations. Similar results were observed in the admixture analysis, which identified populations with the highest (Govi Gurvan Saikhan and Uuliin Bor) and lowest (Tsagaan Ovoo Khar) exotic admixtures. A genomewide association study (GWAS) of body weight and cashmere traits identified a few significant variants on chromosomes 2, 4, 5, 9, and 15, with the strongest variant for cashmere yield on chromosome 4. The GWAS on coat color yielded nine significant variants, with the strongest variants located on chromosomes 6, 13, and 18 and potential associations with KIT, ASIP, and MC1R genes. These signals were also found in other studies on coat color and patterns in goats.

Conclusion

Mongolian cashmere goats showed relatively low genetic differentiation and low inbreeding levels, possibly caused by the traditional pastoral livestock management system and the practice of trading breeding bucks across provinces, along with a recent increase in the goat population. Further investigation of cashmere traits using larger samples and alternative methods may help identify the genes or genomic regions underlying cashmere quality in goats.
FCGR2/3 polymorphisms are associated with susceptibility to Kawasaki disease but do not predict intravenous immunoglobulin resistance and coronary artery aneurysms
Authors: Uittenbogaard Paula , Netea Stejara A. , Tanck Michael W. T. , Geissler Judy , Buda Piotr , Kowalczyk-Domagała Monika , Okarska-Napierała Magdalena , van Stijn Diana , Tacke Carline E. ,   US Kawasaki Disease Genetics Consortium, Burgner David P. , Shimizu Chisato , Burns Jane C. , Kuipers Irene M. , Kuijpers Taco W. , Nagelkerke Sietse Q.
Published: September 2024

Introduction

Kawasaki disease (KD) is a pediatric vasculitis that can result in coronary artery aneurysm (CAA) formation, which is a dangerous complication. Treatment with intravenous immunoglobulin (IVIg) significantly decreases the risk of CAA, possibly through competitive binding to Fc-gamma receptors (FcγRs), which reduces the binding of pathological immune complexes. However, ~20% of children have recrudescence of fever and have an increased risk of CAA. Therefore, we aimed to identify genetic markers at the FCGR2/3 locus associated with susceptibility to KD, IVIg resistance, or CAA.

Materials and methods

We investigated the association of single-nucleotide polymorphisms (SNPs) and copy number variations (CNVs) at the FCGR2/3 locus with KD susceptibility, IVIg resistance, and CAA risk using a family-based test (KD susceptibility) and case–control analyses (IVIg resistance and CAA risk) in different cohorts, adding up to a total of 1,167 KD cases. We performed a meta-analysis on IVIg resistance and CAA risk including all cohorts supplemented by previous studies identified through a systematic search.

Results

FCGR2A-p.166His was confirmed to be strongly associated with KD susceptibility (Z = 3.17, p = 0.0015). In case–control analyses, all of the investigated genetic variations at the FCGR2/3 locus were generally not associated with IVIg resistance or with CAA risk, apart from a possible association in a Polish cohort for the FCGR3B-NA2 haplotype (OR = 2.15, 95% CI = 1.15–4.01, p = 0.02). Meta-analyses of all available cohorts revealed no significant associations of the FCGR2/3 locus with IVIg resistance or CAA risk.

Discussion

FCGR2/3 polymorphisms are associated with susceptibility to KD but not with IVIg resistance and CAA formation. Currently known genetic variations at the FCGR2/3 locus are not useful in prediction models for IVIg resistance or CAA risk.
Obstetrical and perinatal outcomes of women with preeclampsia at Woldia Comprehensive Specialized Hospital, Northeast Ethiopia
Authors: Kumsa Henok , Mergiyaw Desalew
Published: September 2024

Background

Preeclampsia is a multisystem disorder that affects pregnant women. Preeclampsia and its complications are the leading causes of maternal and perinatal morbidity and mortality in developing countries. Studies conducted in Ethiopia have primarily concentrated on preeclampsia’s trends and prevalence rather than its obstetrical and perinatal consequences. Thus, this study aimed to determine the risk of adverse obstetric and perinatal outcomes among women with preeclampsia at Woldia Comprehensive Specialized Hospital, Northeast Ethiopia.

Methods

A retrospective cohort study was conducted among 140 preeclamptic women and 280 normotensive women who gave birth at Woldia Comprehensive Specialized Hospital between 30 December 2020 and 29 December 2022. Maternal records were retrieved using data-extraction tools. The data were entered into EpiData version 4.6.0.6 and analyzed using SPSS version 26. Binary and multivariable logistic regression models were used to test the associations between independent and outcome variables. The adjusted odds ratio (OR) with a 95% confidence interval (CI) and p-values <0.05 were used to measure the strength of the association and declare the level of statistical significance.

Results

The odds of at least one adverse obstetric outcome among preeclamptic women were 2.25 times higher than those among normotensive women [AOR: 2.25, 95% CI: (1.06, 4.77)]. In addition, babies born to preeclamptic women were at a higher risk of perinatal death [AOR: 2.90, 95% CI: (1.10, 8.17)], low birth weight [AOR: 3.11, 95% CI: (1.43, 6.7)], birth asphyxia [AOR: 2.53, 95% CI: (1.15, 5.5)], and preterm birth [AOR: 2.21, 95% CI: (1.02, 4.8)] than babies born to normotensive women.

Conclusion

More adverse obstetric and perinatal outcomes were observed in women with preeclampsia than those in normotensive women. This study highlights the significantly elevated level of at least one adverse obstetric outcome associated with preeclampsia, low hemoglobin level, and rural residents. Moreover, perinatal death, low birth weight, asphyxia, and preterm birth were significantly associated with preeclampsia.
Comparative effectiveness of combined biologic agents versus standard therapies in the treatment of plaque psoriasis: a retrospective analysis
Authors: Wu Bo , Chen Qian , Cao Rong , Zhu Lei , Zhu Hongyan
Published: September 2024

Introduction

Plaque psoriasis is a persistent skin disorder that necessitates efficient management. This study investigates the therapeutic effectiveness and timeline for skin lesion resolution in plaque psoriasis patients treated with combined biologic agents compared to standard therapies.

Methods

Conducted retrospectively between March 2020 and March 2023, the study included 162 patients with moderate to severe plaque psoriasis. Participants were divided into two groups: the Control Group, which received standard treatments, and the Combined Biologic Agent Group, which received additional biologic therapy with secukinumab. Participants in the Control Group received standard treatments, while those in the Combined Biologic Agent Group received standard treatments plus secukinumab.

Results

The results showed that the Combined Biologic Agent Group experienced a significantly faster onset of therapeutic effects, with an average time of 3.04 ± 2.25 days compared to 6.12 ± 2.06 days in the Control Group. Additionally, skin lesion resolution occurred more rapidly in the biologic agent group (7.04 ± 2.13 days) than in the control group (14.56 ± 4.73 days). By week 24, the Psoriasis Area and Severity Index (PASI) scores demonstrated a more substantial reduction in the biologic agent group, decreasing from 26.98 ± 11.28 to 2.48 ± 3.01, whereas the control group showed a reduction from 25.82 ± 10.47 to 10.40 ± 7.63. The overall effectiveness rate was higher in the biologic agent group, with no cases of ineffectiveness, compared to a 20.99% ineffectiveness rate in the control group. Furthermore, there was no recurrence of the disease in the biologic agent group, while the control group experienced an 11.11% recurrence rate. Both groups had a similar incidence of adverse reactions, indicating that the addition of biologic agents does not significantly increase the risk of adverse events.

Discussion

These findings suggest that combined biologic agent therapy offers a more effective and faster treatment option for plaque psoriasis without compromising safety. However, larger-scale clinical trials are necessary to validate these results and establish the long-term benefits and safety of this treatment approach in diverse patient populations.
Solubilization and enhanced degradation of benzene phenolic derivatives—Bisphenol A/Triclosan using a biosurfactant producing white rot fungus Hypocrea lixii S5 with plant growth promoting traits
Authors: Chaturvedi Mridula , Kaur Navpreet , Rahman Pattanathu K. S. M. , Sharma Shashi
Published: September 2024

Introduction

Endocrine disrupting chemicals (EDCs) as benzene phenolic derivatives being hydrophobic partition to organic matter in sludge/soil sediments and show slow degradation rate owing to poor bioavailability to microbes.

Methods

In the present study, the potential of a versatile white rot fungal isolate S5 identified as Hypocrea lixii was monitored to degrade bisphenol A (BPA)/triclosan (TCS) under shake flask conditions with concomitant production of lipopeptide biosurfactant (BS) and plant growth promotion.

Results

Sufficient growth of WRF for 5 days before supplementation of 50 ppm EDC (BPA/TCS) in set B showed an increase in degradation rates by 23% and 29% with corresponding increase in secretion of lignin-modifying enzymes compared to set A wherein almost 84% and 97% inhibition in fungal growth was observed when BPA/TCS were added at time of fungal inoculation. Further in set B, EDC concentration stimulated expression of laccase and lignin peroxidase (Lip) with 24.44 U/L of laccase and 281.69 U/L of Lip in 100 ppm BPA and 344 U/L Lip in 50 ppm TCS supplemented medium compared to their respective controls (without EDC). Biodegradation was also found to be correlated with lowering of surface tension from 57.02 mN/m (uninoculated control) to 44.16 mN/m in case of BPA and 38.49 mN/m in TCS, indicative of biosurfactant (BS) production. FTIR, GC-MS, and LC-ESI/MSMS confirmed the presence of surfactin lipopeptide isoforms. The WRF also displayed positive plant growth promoting traits as production of ammonia, indole acetic acid, siderophores, Zn solubilization, and 1-1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, reflecting its soil restoration ability.

Discussion

The combined traits of biosurfactant production, EDC degradation and plant growth promotion displayed by WRF will help in emulsifying the hydrophobic pollutants favoring their fast degradation along with restoration of contaminated soil in natural conditions.
Gastrointestinal microbiota and metabolites responses to dietary cereal grains in an adult pig model
Authors: Feng Ganyi , Deng Menglong , Li Rui , Hou Gaifeng , Ouyang Qing , Jiang Xianji , Liu Xiaojie , Tang Hui , Chen Fengming , Pu Shihua , Wan Dan , Yin Yulong
Published: September 2024

Corn (C), wheat (W), and paddy rice (PR) are important energy sources and are commonly used in feed production for swine. This study mainly focuses on the variation and regularities of microbiota and metabolites in the gastrointestinal tract (GIT) of pigs in response to C, W, and PR. A total of 18 pigs were allotted into three dietary groups with six replicated pigs and received diets containing C, W, or PR as the sole energy source, respectively. The results showed that digestive parts significantly affected the diversity of microbial communities. Cereal grain sources significantly influenced the β-diversity of microbial communities in the colon and rectum. Campylobacterota and Proteobacteria are mainly distributed in the duodenum, Lactobacillus in the jejunum, and Bacteroidota in the colon and rectum. The W diet increased the Bacteroidota, Spirochaetota, and Prevotellaceae_NK3B31_group abundances and showed the highest concentrations of all short-chain fatty acids (SCFAs) in the hindgut. Fibrobacterota, Bacteroidota, Spirochaetota, Prevotellaceae_NK3B31_group, Prevotella, and Treponema in the colon or rectum were positively correlated with acetate, propionate, butyrate, and total SCFAs. These findings suggested that aerobic bacteria and facultative anaerobes in the foregut will gradually be replaced by anaerobes in the hindgut. The W diet had the best fermentability and was beneficial to the colonization of microbial communities that mainly used carbohydrates. The hindgut flora of the PR diet group may be more balanced with fewer potential pathogenic bacteria. Many microbial communities have been identified to contribute positively to the SCFA production of the hindgut. Collectively, our study revealed the spatial variation regularities of GIT microbial communities in an adult pig model and provided new insights into GIT microbiota and responses of metabolites to cereal grain diets.
Co-expression of endoglucanase and cellobiohydrolase from yak rumen in lactic acid bacteria and its preliminary application in whole-plant corn silage fermentation
Authors: Wan Xuerui , SunKang Yongjie , Chen Yijun , Zhang Zhao , Gou Huitian , Xue Yu , Wang Chuan , Wei Yaqin , Yang Yuze
Published: September 2024

Introduction

Endoglucanase (EG) and cellobiohydrolase (CBH) which produced by microorganisms, have been widely used in industrial applications.

Methods

In order to construct recombinant bacteria that produce high activity EG and CBH, in this study, eg (endoglucanase) and cbh (cellobiohydrolase) were cloned from the rumen microbial genome of yak and subsequently expressed independently and co-expressed within Lactococcus lactis NZ9000 (L. lactis NZ9000).

Results

The recombinant strains L. lactis NZ9000/pMG36e-usp45-cbh (L. lactis-cbh), L. lactis NZ9000/pMG36e-usp45-eg (L. lactis-eg), and L. lactis NZ9000/pMG36e-usp45-eg-usp45-cbh (L. lactis-eg-cbh) were successfully constructed and demonstrated the ability to secrete EG, CBH, and EG-CBH. The sodium carboxymethyl cellulose activity of the recombinant enzyme EG was the highest, and the regenerated amorphous cellulose (RAC) was the specific substrate of the recombinant enzyme CBH, and EG-CBH. The optimum reaction temperature of the recombinant enzyme CBH was 60°C, while the recombinant enzymes EG and EG-CBH were tolerant to higher temperatures (80°C). The optimum reaction pH of EG, CBH, and EG-CBH was 6.0. Mn2+, Fe2+, Cu2+, and Co2+ could promote the activity of CBH. Similarly, Fe2+, Ba2+, and higher concentrations of Ca2+, Cu2+, and Co2+ could promote the activity of EG-CBH. The addition of engineered strains to whole-plant corn silage improved the nutritional quality of the feed, with the lowest pH, acid detergent fiber (ADF), and neutral detergent fiber (NDF) contents observed in silage from the L. lactis-eg group (p < 0.05), and the lowest ammonia nitrogen (NH3-N), and highest lactic acid (LA) and crude protein (CP) contents in silage from the L. lactis-eg + L. lactis-cbh group (p < 0.05), while the silage quality in the L. lactis-cbh group was not satisfactory.

Discussion

Consequently, the recombinant strains L. lactis-cbh, L. lactis-eg, and L. lactis-eg-cbh were successfully constructed, which could successfully expressed EG, CBH, and EG-CBH. L. lactis-eg promoted silage fermentation by degrading cellulose to produce sugar, enabling the secretory expression of EG, CBH, and EG-CBH for potential industrial applications in cellulose degradation.
Clear zone formation in microdroplets for high-throughput screening for lactic acid bacteria
Authors: Mori Koji , Watanabe Mizuki , Nanri Keiko , Matsukura Satoko , Ota Yuri , Homma Nobuyuki , Noda Naohiro
Published: September 2024

Droplet microfluidic-based technology is a powerful tool for biotechnology, and it is also expected that it will be applied to culturing and screening methods. Using this technology, a new high-throughput screening method for lactic acid bacteria was developed. In this study, the conventional culture of lactic acid bacteria that form clear zones on an agar medium was reproduced in water-in-oil droplets, and only the droplets in which lactic acid bacteria grew were collected one by one. Using this method, the specific recovery of Lactiplantibacillus plantarum from a mixture of L. plantarum and Escherichia coli and the acquirement of lactic acid bacteria from an environmental sample were successful. This method could be applied to various conventional screening methods using the clear zone as a microbial growth indicator. This has expanded the possibilities of applying droplet microfluidic-based technology to microbial cultivations.
Genomic surveillance reveals low-level circulation of two subtypes of genogroup C coxsackievirus A10 in Nanchang, Jiangxi Province, China, 2015–2023
Authors: He Fenglan , Zhu Chunlong , Wu Xuan , Yi Liu , Lin Ziqi , Wen Weijie , Zhu Chunhui , Tu Junling , Qian Ke , Li Qingxiang , Ma Guangqiang , Li Hui , Wang Fang , Zhou Xianfeng
Published: September 2024

Introduction

In recent years, coxsackievirus (CV) A10 has been associated with increasing sporadic hand, foot, and mouth disease (HFMD) cases and outbreaks globally. In addition to mild symptoms such as pharyngitis and herpangina, CVA10-related complications or even fatality can occur. Currently, systematic phylogenetic studies of CVA10 are limited.

Methods

In this study, we first explored the epidemiological and genetic characteristics of CVA10 in Nanchang, an inland southeastern city of China, based on the HFMD surveillance network from 2015-2023.

Results

Among 3429 enterovirus-positive cases, 110 (3.04%) were associated with CVA10, with a male-to-female ratio of 1.62. The median age of the CVA10 patients was 2.3 years (interquartile range, IQR 1.0-4.0), with 94.55% (104/110) of the patients aged less than 5 years. Phylogenetic analyses using the full-length VP1, 5’UTR, P1, P2, P3 sequences and near full-length genomes indicated that CVA10 strains (n = 57) isolated in Nanchang belonged to genogroup C; two strains identified in 2017 belonged to C1 subtypes clustered with strains from Vietnam, Madagascar, France and Spain; and the others belonged to C2 subtypes interdigitating with CVA10 isolates from mainland China, the United States and Australia. Through extensive analysis, we identified a rare F168Y mutation in epitope 4 of VP1 in a Madagascar strain of genogroup F and a Chinese strain of genogroup C. Based on Bayesian evolutionary analyses, the average nucleotide substitution rate for the VP1 gene of CV10 strains was 3.07×10–3 substitutions/site/year. The most recent common ancestor (tMRCA) of genogroup C was dated 1990.84, and the tMRCA of CVA10 strains from Nanchang was dated approximately 2003.16, similar to strains circulating in other regions of China, suggesting that the viruses were likely introduced and cryptically circulated in China before the establishment of the HFMD surveillance network. Recombination analysis indicated intertypic recombination of the Nanchang strain with the genogroup G strain in the 3D region.

Discussion

Given the shifting dominance of viral genotypes and frequent recombination events, the existing surveillance system needs to be regulated to enhance genomic surveillance efforts on a more diverse spectrum of genotypes in the future.
Oral swabs as a proxy for direct ruminal microbiome sampling in Holstein dairy cows is correlated with sample color
Authors: Skarlupka Joseph H. , Cox Madison S. , Steinberger Andrew J. , Sbardellati Dino L. , McClure Jennifer C. , Bickhart Derek M. , Scheftgen Andrew J. , Zuniga-Chaves Ibrahim , Wolfe Luke A. , Paget Eric , Skadron Charles , Attipetty Nithya , Suen Garret
Published: September 2024

Using oral swabs to collect the remnants of stomach content regurgitation during rumination in dairy cows can replicate up to 70% of the ruminal bacterial community, offering potential for broad-scale population-based studies on the rumen microbiome. The swabs collected from dairy cows often vary widely with respect to sample quality, likely due to several factors such as time of sample collection and cow rumination behavior, which may limit the ability of a given swab to accurately represent the ruminal microbiome. One such factor is the color of the swab, which can vary significantly across different cows. Here, we hypothesize that darker-colored swabs contain more rumen contents, thereby better representing the ruminal bacterial community than lighter-colored swabs. To address this, we collected oral swabs from 402 dairy cows and rumen samples from 13 cannulated cows on a research farm in Wisconsin, United States and subjected them to 16S rRNA sequencing. In addition, given that little is known about the ability of oral swabs to recapitulate the ruminal fungal community, we also conducted ITS sequencing of these samples. To correlate swab color to the microbiota we developed and utilized a novel imaging approach to colorimetrically quantify each swab from a range of light to dark. We found that swabs with increasing darkness scores were significantly associated with increased bacterial alpha diversity (p < 0.05). Lighter swabs exhibited greater variation in their community structure, with many identified amplicon sequence variants (ASVs) categorized as belonging to known bovine oral and environmental taxa. Our analysis of the fungal microbiome found that swabs with increasing darkness scores were associated with decreased alpha diversity (p < 0.05) and were also significantly associated with the ruminal solids fungal community, but not with the ruminal liquid community. Our study refines the utility of oral swabs as a useful proxy for capturing the ruminal microbiome and demonstrates that swab color is an important factor to consider when using this approach for documenting both the bacterial and fungal communities.
GRB7-mediated enhancement of cell malignant characteristics induced by Helicobacter pylori infection
Authors: Zhao Huilin , Chen Si , Bai Xinfeng , Zhang Jianhui , Liu Shuzhen , Sun Zekun , Cao Xinying , Wang Jianping , Zhang Ying , Li Boqing , Ji Xiaofei
Published: September 2024

Growth factor receptor bound protein 7 (GRB7) is reportedly upregulated in human gastric cancer (GC), which is closely associated with tumor progression and prognosis. However, the mechanism underlying its dysregulation in GC remains poorly understood. In this study, we found that GRB7 overexpression was associated with Helicobacter pylori (H. pylori) infection. GC cells (AGS and MGC-803) infection assays revealed that this upregulation was mediated by the transcription factor STAT3, and activation of STAT3 by H. pylori promoted GRB7 expression in infected GC cells. Moreover, CagA, the key virulence factor of H. pylori, was found involved in STAT3-mediated GRB7 overexpression. The overexpressed GRB7 further promoted GC cell proliferation, migration, and invasion by activating ERK signaling. Mice infection was further used to investigate the action of GRB7. In H. pylori infection, GRB7 expression in mice gastric mucosa was elevated, and higher STAT3 and ERK activation were also detected. These results revealed GRB7-mediated pathogenesis in H. pylori infection, in which H. pylori activates STAT3, leading to increased GRB7 expression, then promotes activation of the ERK signal, and finally enhances malignant properties of infected cells. Our findings elucidate the role of GRB7 in H. pylori-induced gastric disorders, offering new prospects for the treatment and prevention of H. pylori-associated gastric carcinogenesis by targeting GRB7.
Disruptive and complementary effects of depression symptoms on spontaneous brain activity in the subcortical vascular mild cognitive impairment
Authors: Hu Liyu , Chen Jianxiang , Li Xinbei , Zhang Haoran , Zhang Jinhuan , Lu Yingqi , Lian Jie , Yu Haibo , Yang Nan , Wang Jianjun , Lyu Hanqing , Xu Jinping
Published: September 2024

Background

Although depression symptoms are commonly reported in patients with subcortical vascular mild cognitive impairment (svMCI), their impact on brain functions remains largely unknown, with diagnoses mainly dependent on behavioral assessments.

Methods

In this study, we analyzed resting-state fMRI data from a cohort of 34 svMCI patients, comprising 18 patients with depression symptoms (svMCI+D) and 16 patients without (svMCI-D), along with 34 normal controls (NC). The study used the fraction of the amplitude of low-frequency fluctuations (fALFF), resting-state functional connectivity, correlation analyses, and support vector machine (SVM) techniques.

Results

The fALFF of the right cerebellum (CERE.R) differed among the svMCI+D, svMCI-D, and NC groups. Specifically, the regional mean fALFF of CERE. R was lower in svMCI-D patients compared to NC but higher in svMCI+D patients compared to svMCI-D patients. Moreover, the adjusted fALFF of CERE. R showed a significant correlation with Montreal Cognitive Assessment (MOCA) scores in svMCI-D patients. The fALFF of the right orbital part of the superior frontal gyrus was significantly correlated with Hamilton Depression Scale scores in svMCI+D patients, whereas the fALFF of the right postcingulate cortex (PCC.R) showed a significant correlation with MOCA scores in svMCI-D patients. Furthermore, RSFC between PCC. R and right precuneus, as well as between CERE. R and the right lingual gyrus (LING.R), was significantly reduced in svMCI-D patients compared to NC. In regional analyses, the adjusted RSFC between PCC. R and PreCUN. R, as well as between CERE. R and LING. R, was decreased in svMCI-D patients compared to NC but increased in svMCI+D patients compared to svMCI-D. Further SVM analyses achieved good performances, with an area under the curve (AUC) of 0.82 for classifying svMCI+D, svMCI-D, and NC; 0.96 for classifying svMCI+D and svMCI-D; 0.82 for classifying svMCI+D and NC; and 0.92 for classifying svMCI-D and NC.

Conclusion

The study revealed disruptive effects of cognitive impairment, along with both disruptive and complementary effects of depression symptoms on spontaneous brain activity in svMCI. Moreover, these findings suggest that the identified features might serve as potential biomarkers for distinguishing between svMCI+D, svMCI-D, and NC, thereby guiding clinical treatments such as transcranial magnetic stimulation for svMCI.
Association between cerebral blood flow variation and cognitive decline in older patients undergoing hemodialysis
Authors: Guo Yidan , Cui Wei , Ye Pengpeng , Luo Yang
Published: September 2024

Background

The mechanism of cognitive impairment in hemodialysis patients is multifactorial. The relationship between cerebral blood flow and the decline of cognitive function is poorly understood.

Objective

To investigate the association between cerebral blood flow variation and decline of cognitive function in older patients undergoing hemodialysis.

Methods

In this prospective observational cohort study of 121 older patients undergoing hemodialysis, we used transcranial Doppler ultrasound (TCD) to measure cerebral arterial mean flow velocity (MFV) throughout dialysis, assessed cognitive function at baseline and 12-month follow-up, and then analyzed associations between MFV and changes on cognitive scores.

Results

TCD recordings demonstrated a significant reduction in MFV throughout dialysis, which were significantly correlated with cumulative ultrafiltration volume (rho 0.356, p < 0.001), ΔSBP (rho 0.251, p = 0.005), and ΔMAP (rho 0.194, p = 0.032). Compared with the baseline assessments, cognitive scores of participants at the 12-month follow-up were significantly worsened in global cognition (MOCA), some tests of memory (CFT-memory), executive function (TMT-B, SCWT-C, and SCWT-T), attention/processing speed (SDMT), and visuospatial function (CFT-copy) (p < 0.05). The worsening scores in global cognition (MOCA) (β = 0.066, 95% CI 0.018–0.113, p = 0.007) and some tests of memory (AVLT5) (β = 0.050, 95% CI 0.004–0.097, p = 0.035) and executive function (TMT-B, SCWT-C, SCWT-T) (β = 1.955, 95% CI 0.457–3.453, p = 0.011; β = 0.298, 95% CI 0.112–0.484, p = 0.002 and β = 1.371, 95% CI 0.429–2.303, p = 0.004, respectively) were significantly associated with the reduction of MFV.

Conclusion

Hemodialysis may significantly reduce cerebral blood flow in older patients; Repetitive intradialytic decreases in CBF may be one of the mechanisms underlying the decline of cognitive function.

Clinical trial registration

https://register.clinicaltrials.gov/prs/app/action/SelectProtocol?sid=S000C5B5&selectaction=Edit&uid=U0003QEL&ts=4&cx=-djoi2
RNA in axons, dendrites, synapses and beyond
Authors: Taylor Richard , Nikolaou Nikolas
Published: September 2024

In neurons, a diverse range of coding and non-coding RNAs localize to axons, dendrites, and synapses, where they facilitate rapid responses to local needs, such as axon and dendrite extension and branching, synapse formation, and synaptic plasticity. Here, we review the extent of our current understanding of RNA subclass diversity in these functionally demanding subcellular compartments. We discuss the similarities and differences identified between axonal, dendritic and synaptic local transcriptomes, and discuss the reported and hypothesized fates and functions of localized RNAs. Furthermore, we outline the RNA composition of exosomes that bud off from neurites, and their implications for the biology of neighboring cells. Finally, we highlight recent advances in third-generation sequencing technologies that will likely provide transformative insights into splice isoform and RNA modification diversity in local transcriptomes.