bluuebunny/crossref_metadata_2025_split huggingface dataset:
The spatial patterns of diversity and their relationships with environments in rhizosphere microorganisms and host plants differ along elevational gradients
Authors: Xu Shijia , Yuan Yan , Song Pengfei , Cui Mufeng , Zhao Rensheng , Song Xiaoyang , Cao Min , Zhang Yazhou , Yang Jie 
Published: February 2023

IntroductionIdentifying spatial patterns of biodiversity along elevational gradients provides a unified framework for understanding these patterns and predicting ecological responses to climate change. Moreover, microorganisms and plants are closely interconnected (e.g., via the rhizosphere) and thus may share spatial patterns of diversity and show similar relationships with environments.MethodsThis study compared diversity patterns and relationships with environments in host plants and rhizosphere microorganisms (including various functional groups) along elevational gradients across three climatic zones.ResultsWe found that above-and belowground diversity decreased monotonically or showed a hump-shaped or U-shaped pattern along elevation gradients. However, the diversity patterns of plants, bacteria, and fungi varied depending on the taxon and climatic zone. Temperature and humidity strongly contribute to above-and belowground diversity patterns and community composition along elevational gradients. Nonetheless, soil factors might be important regulators of diversity patterns and the community composition of plants and microorganisms along these gradients. Structural equation modeling revealed that environmental factors had a stronger direct effect on rhizosphere microbial diversity than host plant diversity.DiscussionIn sum, spatial patterns of diversity and their relationships with environments in rhizosphere microorganisms and their host plants differed at the regional scale. Different functional groups (e.g., pathogen, mycorrhiza and nitrifier) of soil microorganisms may have divergent elevational patterns and environmental responses. These data improve our understanding of elevational diversity patterns, and provide new insights into the conservation of biodiversity and ecosystem management, especially under climate change.
Current evidence and clinical relevance of drug-microbiota interactions in inflammatory bowel disease
Authors: Becker Heike E. F. , Demers Karlijn , Derijks Luc J. J. , Jonkers Daisy M. A. E. , Penders John 
Published: February 2023

BackgroundInflammatory bowel disease (IBD) is a chronic relapsing-remitting disease. An adverse immune reaction toward the intestinal microbiota is involved in the pathophysiology and microbial perturbations are associated with IBD in general and with flares specifically. Although medical drugs are the cornerstone of current treatment, responses vary widely between patients and drugs. The intestinal microbiota can metabolize medical drugs, which may influence IBD drug (non-)response and side effects. Conversely, several drugs can impact the intestinal microbiota and thereby host effects. This review provides a comprehensive overview of current evidence on bidirectional interactions between the microbiota and relevant IBD drugs (pharmacomicrobiomics).MethodsElectronic literature searches were conducted in PubMed, Web of Science and Cochrane databases to identify relevant publications. Studies reporting on microbiota composition and/or drug metabolism were included.ResultsThe intestinal microbiota can both enzymatically activate IBD pro-drugs (e.g., in case of thiopurines), but also inactivate certain drugs (e.g., mesalazine by acetylation via N-acetyltransferase 1 and infliximab via IgG-degrading enzymes). Aminosalicylates, corticosteroids, thiopurines, calcineurin inhibitors, anti-tumor necrosis factor biologicals and tofacitinib were all reported to alter the intestinal microbiota composition, including changes in microbial diversity and/or relative abundances of various microbial taxa.ConclusionVarious lines of evidence have shown the ability of the intestinal microbiota to interfere with IBD drugs and vice versa. These interactions can influence treatment response, but well-designed clinical studies and combined in vivo and ex vivo models are needed to achieve consistent findings and evaluate clinical relevance.
Soil bacterial communities associated with multi-nutrient cycling under long-term warming in the alpine meadow
Authors: Zhou Xiaorong , Chen Xianke , Qi Xiangning , Zeng Yiyuan , Guo Xiaowei , Zhuang Guoqiang , Ma Anzhou 
Published: February 2023

IntroductionThe functions of terrestrial ecosystems are mainly maintained by bacteria, as a key component of microorganisms, which actively participate in the nutrient cycling of ecosystems. Currently, there are few studies have been carried out on the bacteria contributing to the soil multi-nutrient cycling in responding to climate warming, which hampers our obtainment of a comprehensive understanding of the ecological function of ecosystems as a whole.MethodsIn this study, the main bacteria taxa contributing to the soil multi-nutrient cycling under the long-term warming in an alpine meadow was determined based onphysichemical properties measurement and high-throughput sequencing, and the potential reasons that warming altered the main bacteria contributing to the soil multi-nutrient cycling were further analyzed.ResultsThe results confirmed that the bacterial β-diversity was crucial to the soil multi-nutrient cycling. Furthermore, Gemmatimonadetes, Actinobacteria, and Proteobacteria were the main contributors to the soil multi-nutrient cycling, and played pivotal roles as keystone nodes and biomarkers throughout the entire soil profile. This suggested that warming altered and shifted the main bacteria contributing to the soil multi-nutrient cycling toward keystone taxa.DiscussionMeanwhile, their relative abundance was higher, which could make them have the advantage of seizing resources in the face of environmental pressures. In summary, the results demonstrated the crucial role of keystone bacteria in the multi-nutrient cycling under the climate warming in the alpine meadow. This has important implications for understanding and exploring the multi-nutrient cycling of alpine ecosystems under the global climate warming.
Ligand-based pharmacophore modeling and QSAR approach to identify potential dengue protease inhibitors
Authors: Poola Anushka A. , Prabhu Prithvi S. , Murthy T. P. Krishna , Murahari Manikanta , Krishna Swati , Samantaray Mahesh , Ramaswamy Amutha 
Published: February 2023

The viral disease dengue is transmitted by the Aedes mosquito and is commonly seen to occur in the tropical and subtropical regions of the world. It is a growing public health concern. To date, other than supportive treatments, there are no specific antiviral treatments to combat the infection. Therefore, finding potential compounds that have antiviral activity against the dengue virus is essential. The NS2B-NS3 dengue protease plays a vital role in the replication and viral assembly. If the functioning of this protease were to be obstructed then viral replication would be halted. As a result, this NS2B-NS3 proves to be a promising target in the process of anti-viral drug design. Through this study, we aim to provide suggestions for compounds that may serve as potent inhibitors of the dengue NS2B-NS3 protein. Here, a ligand-based pharmacophore model was generated and the ZINC database was screened through ZINCPharmer to identify molecules with similar features. 2D QSAR model was developed and validated using reported 4-Benzyloxy Phenyl Glycine derivatives and was utilized to predict the IC50 values of unknown compounds. Further, the study is extended to molecular docking to investigate interactions at the active pocket of the target protein. ZINC36596404 and ZINC22973642 showed a predicted pIC50 of 6.477 and 7.872, respectively. They also showed excellent binding with NS3 protease as is evident from their binding energy of −8.3and −8.1 kcal/mol, respectively. ADMET predictionsofcompounds have shown high drug-likeness. Finally, the molecular dynamic simulations integrated with MM-PBSA binding energy calculations confirmedboth identified ZINC compounds as potential hit moleculeswith good stability.
Analysis of gene expression profiles in Alzheimer’s disease patients with different lifespan: A bioinformatics study focusing on the disease heterogeneity
Authors: Zhang Ji , Li Xiaojia , Xiao Jun , Xiang Yang , Ye Fang 
Published: February 2023

ObjectiveAlzheimer’s disease (AD) as the most frequent neurodegenerative disease is featured by gradual decline of cognition and social function in the elderly. However, there have been few studies focusing on AD heterogeneity which exists both genetically and clinically, leading to the difficulties of AD researches. As one major kind of clinical heterogeneity, the lifespan of AD patients varies significantly. Aiming to investigate the potential driving factors, the current research identified the differentially expressed genes (DEGs) between longer-lived AD patients and shorter-lived ones via bioinformatics analyses.MethodsQualified datasets of gene expression profiles were identified in National Center of Biotechnology Information Gene Expression Omnibus (NCBI-GEO). The data of the temporal lobes of patients above 60 years old were used. Two groups were divided according to the lifespan: the group ≥85 years old and the group &lt;85 years old. Then GEO2R online software and R package of Robust Rank Aggregation (RRA) were used to screen DEGs. Bioinformatic tools were adopted to identify possible pathways and construct protein–protein interaction network.ResultSixty-seven AD cases from four qualified datasets (GSE28146, GSE5281, GSE48350, and GSE36980) were included in this study. 740 DEGs were identified with 361 upregulated and 379 downregulated when compared longer-lived AD patients with shorter-lived ones. These DEGs were primarily involved in the pathways directly or indirectly associated with the regulation of neuroinflammation and cancer pathogenesis, as shown by pathway enrichment analysis. Among the DEGs, the top 15 hub genes were identified from the PPI network. Notably, the same bioinformatic procedures were conducted in 62 non-AD individuals (serving as controls of AD patients in the four included studies) with distinctly different findings from AD patients, indicating different regulatory mechanisms of lifespan between non-AD controls and AD, reconfirming the necessity of the present study.ConclusionThese results shed some lights on lifespan-related regulatory mechanisms in AD patients, which also indicated that AD heterogeneity should be more taken into account in future investigations.
Scoping review of disease-modifying effect of drugs in experimental epilepsy
Authors: Ots Heather D. , Anderson Taylor , Sherrerd-Smith William , DelBianco John , Rasic Gordana , Chuprin Anthony , Toor Zeeshan , Fitch Elizabeth , Ahuja Kripa , Reid Faith , Musto Alberto E. 
Published: February 2023

ObjectiveEpilepsy affects ~50 million people worldwide causing significant medical, financial, and sociologic concerns for affected patients and their families. To date, treatment of epilepsy is primarily symptomatic management because few effective preventative or disease-modifying interventions exist. However, recent research has identified neurobiological mechanisms of epileptogenesis, providing new pharmacologic targets to investigate. The current scientific evidence remains scattered across multiple studies using different model and experimental designs. The review compiles different models of anti-epileptogenic investigation and highlights specific compounds with potential epileptogenesis-modifying experimental drugs. It provides a platform for standardization of future epilepsy research to allow a more robust compound analysis of compounds with potential for epilepsy prevention.MethodsPubMed, Ovid MEDLINE, and Web of Science were searched from 2007 to 2021. Studies with murine models of epileptogenesis and explicitly detailed experimental procedures were included in the scoping review. In total, 51 articles were selected from 14,983 and then grouped by five core variables: (1) seizure frequency, (2) seizure severity, (3) spontaneous recurrent seizures (SRS), (4) seizure duration, and (5) mossy fiber sprouting (MFS). The variables were differentiated based on experimental models including methods of seizure induction, treatment schedule and timeline of data collection. Data was categorized by the five core variables and analyzed by converting original treatment values to units of percent of its respective control.ResultsDiscrepancies in current epileptogenesis models significantly complicate inter-study comparison of potential anti-epileptogenic interventions. With our analysis, many compounds showed a potential to reduce epileptogenic characteristics defined by the five core variables. WIN55,212-2, aspirin, rapamycin, 1400W, and LEV + BQ788 were identified compounds with the potential of effective anti-epileptic properties.SignificanceOur review highlights the need for consistent methodology in epilepsy research and provides a novel approach for future research. Inconsistent experimental designs hinder study comparison, slowing the progression of treatments for epilepsy. If the research community can optimize and standardize parameters such as methods of seizure induction, administration schedule, sampling time, and aniMal models, more robust meta-analysis and collaborative research would follow. Additionally, some compounds such as rapamycin, WIN 55,212-2, aspirin, 1400W, and LEV + BQ788 showed anti-epileptogenic modulation across multiple variables. We believe they warrant further study both individually and synergistically.
Nitrous oxide-induced neurotoxicity: Clinical characteristics and impacts on overall neurological impairments
Authors: Gao Hui , Wang Ruihan , Zeng Yan , Qin Linyuan , Cai Hanlin , Zhou Dong , Chen Qin 
Published: February 2023

ObjectiveThe reports of the recreational use of nitrous oxide (N2O) and its related neuropathy are increasing. However, it is unclear whether specific clinical characteristics are associated with the overall neurological impairments among these individuals.MethodsWe retrospectively included 20 hospitalized patients with N2O-related neurological complaints between January 2016 and March 2021 at the West China Hospital of Sichuan University. Detailed demographic, clinical features, lab tests, and imaging data were collected. A functional disability rating score (FDRS) was calculated to determine the degree of neurological impairment. The relationships between the aforementioned factors and the FDRS sum score were explored.ResultsThese individuals were aged between 16 and 30 years (mean ± SD: 21.90 ± 4.06). At admission, unsteady gait (95%, nineteen of twenty), weakness (95%, nineteen of twenty), and limb paresthesia (70%, fourteen of twenty) were the most common symptoms; decreased deep tendon reflexes (100%, nineteen of nineteen), reduced muscle strength (95%, nineteen of twenty), and impaired coordination (95%, nineteen of twenty) were frequently found. The FDRS sum scores ranged from 3 to 12. Among all the factors, admission from the emergency room (p = 0.033), decreased hemoglobin (p = 0.004) (without previous VitB12 supplements), decreased red blood cell (RBC) count (p = 0.004) (without previous VitB12 supplements), and increased mean corpuscular volume (p = 0.036) (with previous VitB12 supplements) positively correlated with the FDRS sum score.ConclusionNitrous oxide (N2O) could lead to severe neurological impairments among users. Abnormal RBC indicators at admission may be associated with a worse clinical presentation and need further attention. Population education about the consequences of N2O consumption and control measures concerning access to N2O should be further emphasized.
Macular vessel density in the superficial plexus is not associated to cerebrospinal fluid core biomarkers for Alzheimer’s disease in individuals with mild cognitive impairment: The NORFACE cohort
Authors: Marquié Marta , García-Sánchez Ainhoa , Alarcón-Martín Emilio , Martínez Joan , Castilla-Martí Miguel , Castilla-Martí Luis , Orellana Adelina , Montrreal Laura , de Rojas Itziar , García-González Pablo , Puerta Raquel , Olivé Clàudia , Cano Amanda , Hernández Isabel , Rosende-Roca Maitée , Vargas Liliana , Tartari Juan Pablo , Esteban-De Antonio Ester , Bojaryn Urszula , Ricciardi Mario , Ariton Diana M. , Pytel Vanesa , Alegret Montserrat , Ortega Gemma , Espinosa Ana , Pérez-Cordón Alba , Sanabria Ángela , Muñoz Nathalia , Lleonart Núria , Aguilera Núria , Tárraga Lluís , Valero Sergi , Ruiz Agustín , Boada Mercè 
Published: February 2023

BackgroundOptical coherence tomography angiography (OCT-A) is a novel method in the dementia field that allows the detection of retinal vascular changes. The comparison of OCT-A measures with established Alzheimer’s disease (AD)-related biomarkers is essential to validate the former as a marker of cerebrovascular impairment in the AD continuum. We aimed to investigate the association of macular vessel density (VD) in the superficial plexus quantified by OCT-A with the AT(N) classification based on cerebrospinal fluid (CSF) Aβ1-42, p181-tau and t-tau measurements in individuals with mild cognitive impairment (MCI).Materials and methodsClinical, demographic, ophthalmological, OCT-A and CSF core biomarkers for AD data from the Neuro-ophthalmology Research at Fundació ACE (NORFACE) project were analyzed. Differences in macular VD in four quadrants (superior, nasal, inferior, and temporal) among three AT(N) groups [Normal, Alzheimer and Suspected non-Alzheimer pathology (SNAP)] were assessed in a multivariate regression model, adjusted for age, APOE ε4 status, hypertension, diabetes mellitus, dyslipidemia, heart disease, chronic obstructive pulmonary disease and smoking habit, using the Normal AT(N) group as the reference category.ResultsThe study cohort comprised 144 MCI participants: 66 Normal AT(N), 45 Alzheimer AT(N) and 33 SNAP AT(N). Regression analysis showed no significant association of the AT(N) groups with any of the regional macular VD measures (all, p &gt; 0.16). The interaction between sex and AT(N) groups had no effect on differentiating VD. Lastly, CSF Aβ1-42, p181-tau and t-tau measures were not correlated to VD (all r &lt; 0.13; p &gt; 0.13).DiscussionOur study showed that macular VD measures were not associated with the AT(N) classification based on CSF biomarkers in patients with MCI, and did not differ between AD and other underlying causes of cognitive decline in our cohort.
Presynaptic spike-driven plasticity based on eligibility trace for on-chip learning system
Authors: Gao Tian , Deng Bin , Wang Jiang , Yi Guosheng 
Published: February 2023

IntroductionRecurrent spiking neural network (RSNN) performs excellently in spatio-temporal learning with backpropagation through time (BPTT) algorithm. But the requirement of computation and memory in BPTT makes it hard to realize an on-chip learning system based on RSNN. In this paper, we aim to realize a high-efficient RSNN learning system on field programmable gate array (FPGA).MethodsA presynaptic spike-driven plasticity architecture based on eligibility trace is implemented to reduce the resource consumption. The RSNN with leaky integrate-and-fire (LIF) and adaptive LIF (ALIF) models is implemented on FPGA based on presynaptic spike-driven architecture. In this architecture, the eligibility trace gated by a learning signal is used to optimize synaptic weights without unfolding the network through time. When a presynaptic spike occurs, the eligibility trace is calculated based on its latest timestamp and drives synapses to update their weights. Only the latest timestamps of presynaptic spikes are required to be stored in buffers to calculate eligibility traces.ResultsWe show the implementation of this architecture on FPGA and test it with two experiments. With the presynaptic spike-driven architecture, the resource consumptions, including look-up tables (LUTs) and registers, and dynamic power consumption of synaptic modules in the on-chip learning system are greatly reduced. The experiment results and compilation results show that the buffer size of the on-chip learning system is reduced and the RSNNs implemented on FPGA exhibit high efficiency in resources and energy while accurately solving tasks.DiscussionThis study provides a solution to the problem of data congestion in the buffer of large-scale learning systems.
Sociodemographic and lifestyle factors and the risk of metabolic syndrome in taxi drivers: A focus on street food
Authors: Sekgala Machoene Derrick , Opperman Maretha , Mpahleni Buhle , Mchiza Zandile June-Rose 
Published: February 2023

BackgroundIn South Africa, similar to other populous countries, the taxi industry is an important form of transportation that contributes to the country's development. As a result, minibus taxi driving is an occupation characterized by strenuous activities such as long hours of driving, limited rest, and challenges related to securing passengers, among several others. Consequently, to combat stress, some commercial drivers resort to smoking, overeating unhealthy food sold at transportation interchange areas (i.e., taxi ranks), and participating in sedentary behaviors. Most of these activities are risk factors for metabolic syndrome (MetS).AimTherefore, this study aimed to investigate the sociodemographic and lifestyle factors that predispose South African taxi drivers who work in the Cape Town Metropole area to the risk of developing MetS.MethodsThis cross-sectional study used a convenient sampling method that included 185 male minibus taxi drivers aged 20 years or above. The participants were interviewed using a validated questionnaire to gather information regarding their sociodemographic characteristics and lifestyle practices. They also underwent physical and metabolic assessments, and the International Diabetes Federation (IDF) criteria were used to diagnose people with MetS.ResultsOverall, the mean age and driving experience of the taxi drivers were 40.0 years (SD: 10.7) and 9.1 years (SD: 7.4), respectively, with those with MetS being significantly older and having more driving experience than those without. Older participants were 3 and 2.9 times more likely to be diagnosed with MetS than the younger participants. Most taxi drivers (70%) met the IDF diagnostic criteria for MetS. Smokers, those who spent more than 100 ZAR (USD 5.9) and those who spent less than 1.4 MET-minutes per week on physical activity were 1.96, 2.0, and 13.6 times more likely to suffer from MetS that those who were nonsmokers, those who spent less than 100 ZAR and those who spent &lt;1.4 MET-minutes per week on physical activity. Consumption of alcohol and sugar-sweetened beverages (SSBs), as well as takeaway and fried foods, snacks, and sold by the SF vendors, increased the likelihood of developing MetS, abnormal HDL-C, TG, and hypertension, while avoiding takeaway and fried foods decreased this likelihood. Taxi drivers who also avoided consuming fresh fruits had abnormal HDL-C.ConclusionThese findings have significant public health implications, highlighting the need for South African policymakers to adopt a system-level approach to promote lifestyle changes among taxi drivers within the taxi industry. This can help reduce the health risks faced by these drivers and improve their overall health profile.