bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computer-aided diagnosis of primary membranous nephropathy using expert system
Authors: Gao Jie , Wang Siyang , Xu Liang , Wang Jinyan , Guo Jiao , Wang Haiping , Sun Jing 
Published: February 2023

Abstract
Background
The diagnosis of primary membranous nephropathy (PMN) often depends on invasive renal biopsy, and the diagnosis based on clinical manifestations and target antigens may not be completely reliable as it could be affected by uncertain factors. Moreover, different experts could even have different diagnosis results due to their different experiences, which could further impact the reliability of the diagnosis. Therefore, how to properly integrate the knowledge of different experts to provide more reliable and comprehensive PMN diagnosis has become an urgent issue.

Methods
This paper develops a belief rule-based system for PMN diagnosis. The belief rule base is constructed based on the knowledge of the experts, with 9 biochemical indicators selected as the input variables. The belief rule-based system is developed of three layers: (1) input layer; (2) belief rule base layer; and (3) output layer, where 9 biochemical indicators are selected as the input variables and the diagnosis result is provided as the conclusion. The belief rule base layer is constructed based on the knowledge of the experts. The final validation was held with gold pattern clinical cases, i.e., with known and clinically confirmed diagnoses.

Results
134 patients are used in this study, and the proposed method is defined by its sensitivity, specificity, accuracy and area under curve (AUC), which are 98.0%, 96.9%, 97.8% and 0.93, respectively. The results of this study present a novel and effective way for PMN diagnosis without the requirement of renal biopsy.

Conclusions
Through analysis of the diagnosis results and comparisons with other methods, it can be concluded that the developed system could help diagnose PMN based on biochemical indicators with relatively high accuracy.

Graphical Abstract
Comparing socio-economic inequalities in self-reported and undiagnosed hypertension among adults 45 years and over in India: what explains these inequalities?
Authors: Bhatia Mrigesh , Dixit Priyanka , Kumar Manish , Dwivedi Laxmi Kant 
Published: February 2023

Abstract
Background
Hypertension (HTN) is a leading cause of mortality and morbidity in developing countries. For India, the hidden burden of undiagnosed hypertension is a major concern. This study aims to assess and explain socio-economic inequalities among self-reported and undiagnosed hypertensives in India.

Methods
The study utilized data from the Longitudinal Aging Study in India (LASI), a nationally-representative survey of more than 72,000 older adults. The study used funnel plots, multivariable logistic regression, concentration indices, and decomposition analysis to explain the socio-economic gap in the prevalence of self-reported and undiagnosed hypertension between the richest and the poorest groups.

Results
The prevalence of self-reported and undiagnosed hypertension was 27.4 and 17.8% respectively. Monthly per capita consumption expenditure (MPCE) quintile was positively associated with self-reported hypertension but negatively associated with undiagnosed hypertension. The concentration index for self-reported hypertension was 0.133 (p < 0.001), whereas it was − 0.047 (p < 0.001) for undiagnosed hypertension. Over 50% of the inequalities in self-reported hypertension were explained by the differences in the distribution of the characteristics whereas inequalities remained unexplained for undiagnosed hypertension. Obesity and diabetes were key contributors to pro-rich inequality.

Conclusions
Results imply that self-reported measures underestimate the true prevalence of hypertension and disproportionately affect the poorer MPCE groups. The prevalence of self-reported HTN was higher in the richest group, whereas socio-economic inequality in undiagnosed hypertension was significantly concentrated in the poorest group. As majority of the inequalities remain unexplained in case of undiagnosed hypertension, broader health systems issues including barriers to access to health care may be contributing to inequalities.
Associations of home and neighborhood environments with children’s physical activity in the U.S.-based Neighborhood Impact on Kids (NIK) longitudinal cohort study
Authors: Carver Alison , Cerin Ester , Akram Muhammad , Sallis James F. , Cain Kelli L. , Frank Lawrence D. , Geremia Carrie M. , Conway Terry L. , Glanz Karen , Saelens Brian E. 
Published: February 2023

Abstract
Introduction
Physical activity is important for children’s health and well-being. Supportiveness for physical activity of home and neighborhood environments may affect children’s PA, but most studies are cross-sectional. We examined environmental predictors of change in children’s physical activity over two years.

Methods
Data were from the longitudinal, observational cohort study, ‘Neighborhood Impact on Kids’. Participants were children (initially aged 6–12 years) and their parent/caregiver (n = 727 dyads) living in neighborhoods throughout San Diego County, California and King County (Seattle area), Washington, USA. Children’s moderate-to-vigorous physical activity (MVPA) was measured using accelerometers at T1 (Time 1 or baseline, 2007–2009) and T2, the two-year follow-up. At T1, parents survey-reported on physical activity (PA) equipment at home and demographics. Neighborhood environment was measured using spatial data in Geographic Information Systems (intersection density; park availability) and in-person audits (informal play space near home; park-based PA facilities; land use; support for walking/cycling). Generalized additive mixed models estimated total effects, then direct effects, of environmental attributes on MVPA at T1. Two-way moderating effects of child’s sex and age were examined at T1. To examine associations of environmental exposures with changes in MVPA, we estimated interaction effects of environmental attributes on the association between time and MVPA.

Results
On average, children accumulated 146 min/day (standard deviation or SD = 53) of MVPA at T1, and 113 (SD = 58) min/day at T2. There were no significant total or direct effects of environmental attributes on MVPA at T1, and no significant two-way interaction effects of child’s age and sex for T1 MVPA. Having informal play spaces proximal to home with more amenities was associated with less MVPA decline from T1 to T2. Higher residential density, higher land use mix, and higher number of PA facilities in nearby parks were unexpectedly associated with greater MVPA decline.

Conclusion
Higher quality informal play spaces close to home may help offset declines in MVPA during middle childhood, as they may promote unstructured active play with opportunities for parental or neighbor surveillance. Unexpectedly, environmental factors consistent with higher walkability were associated with greater declines in children’s MVPA. As physical activity differs across the lifespan, so may environmental factors that facilitate it.
The soluble epoxide hydrolase inhibitor TPPU improves comorbidity of chronic pain and depression via the AHR and TSPO signaling
Authors: Luo Ailin , Wu Zifeng , Li Shan , McReynolds Cindy B. , Wang Di , Liu Hanyu , Huang Chaoli , He Teng , Zhang Xinying , Wang Yuanyuan , Liu Cunming , Hammock Bruce D. , Hashimoto Kenji , Yang Chun 
Published: February 2023

Abstract
Background
Patients suffering from chronic pain often also exhibit depression symptoms. Soluble epoxide hydrolase (sEH) inhibitors can decrease blood levels of inflammatory cytokines. However, whether inhibiting sEH signaling is beneficial for the comorbidity of pain and depression is unknown.

Methods
According to a sucrose preference test (SPT), spared nerve injury (SNI) mice were classified into pain with or without an anhedonia phenotype. Then, sEH protein expression and inflammatory cytokines were assessed in selected tissues. Furthermore, we used sEH inhibitor TPPU to determine the role of sEH in chronic pain and depression. Importantly, agonists and antagonists of aryl hydrocarbon receptor (AHR) and translocator protein (TSPO) were used to explore the pathogenesis of sEH signaling.

Results
In anhedonia-susceptible mice, the tissue levels of sEH were significantly increased in the medial prefrontal cortex (mPFC), hippocampus, spinal cord, liver, kidney, and gut. Importantly, serum CYP1A1 and inflammatory cytokines, such as interleukin 1β (IL-1β) and the tumor necrosis factor α (TNF-α), were increased simultaneously. TPPU improved the scores of mechanical withdrawal threshold (MWT) and SPT, and decreased the levels of serum CYP1A1 and inflammatory cytokines. AHR antagonist relieved the anhedonia behaviors but not the algesia behaviors in anhedonia-susceptible mice, whereas an AHR agonist abolished the antidepressant-like effect of TPPU. In addition, a TSPO agonist exerted a similar therapeutic effect to that of TPPU, whereas pretreatment with a TSPO antagonist abolished the antidepressant-like and analgesic effects of TPPU.

Conclusions
sEH underlies the mechanisms of the comorbidity of chronic pain and depression and that TPPU exerts a beneficial effect on anhedonia behaviors in a pain model via AHR and TSPO signaling.
TNEA therapy promotes the autophagic degradation of NLRP3 inflammasome in a transgenic mouse model of Alzheimer’s disease via TFEB/TFE3 activation
Authors: Lin Wenjia , Li Zhao , Liang Guangfeng , Zhou Runjin , Zheng Xiaoyan , Tao Rongrong , Huo Qingwei , Su Chengfu , Li Min , Xu Nenggui , Tang Chunzhi , Song Ju-Xian 
Published: February 2023

Abstract
Background
The impairment in the autophagy-lysosomal pathway (ALP) and the activation of NLR family pyrin domain containing 3 (NLRP3) inflammasome represent two molecular events leading to neurodegeneration and neuroinflammation in Alzheimer’s disease (AD), a devastating neurodegenerative disorder without a cure. Previously we demonstrated the cognitive-enhancing effect of a combined electroacupuncture (EA) therapy termed TNEA in a transgenic mouse model of AD, involving activation of transcription factor EB (TFEB), a master regulator of ALP. However, whether and how TNEA inhibits NLRP3 inflammasome via TFEB-mediated ALP in AD remains to be investigated.

Methods
5xFAD mice overexpressing amyloid-β (Aβ) were treated with TNEA or EA on its composing acupoints (GB13 and GV24). The changes in the signaling pathways regulating NLRP3 inflammasome, the association of NLRP3 inflammasome with ALP, and the roles of TFEB/TFE3 in mice brains were determined by immunoblots, immunohistochemistry and AAV-mediated knockdown assays.

Results
TNEA inhibits the activation of NLRP3 inflammasome and the release of active interleukin 1β (IL1B) in the hippocampi of 5xFAD mice. Mechanistically, TNEA promoted the autophagic degradation of inflammasome components via activating both TFEB and TFE3 by modulating kinases including AMPK and AKT. The composing acupoints in TNEA showed synergistic effects on regulating these molecular events and memory improvement.

Conclusion
Our findings suggest that TNEA attenuates AD-associated memory impairment via promoting TFEB/TFE3-mediated autophagic clearance of Aβ and NLRP3 inflammasome, and partially reveal the molecular basis of combined acupoints therapy originated from ancient wisdom.
The maturation of iPS cell-derived brain microvascular endothelial cells by inducible-SOX18 expression
Authors: Zhang Hongyan , Yamaguchi Tomoko , Kawabata Kenji 
Published: February 2023

Abstract
Background
Brain microvascular endothelial cells (BMECs) play a major role in the blood–brain barrier (BBB), and are critical for establishing an in vitro BBB model. Currently, iPSC-derived BMECs (iBMECs) have been used to construct in vitro BBB models with physiological barrier functions, such as high trans-endothelial electrical resistance (TEER) and expression of transporter proteins. However, the relatively low p-glycoprotein (P-gp) level and a decrease in the efflux ratio of its substrates in iBMECs suggest their immature nature. Therefore, more mature iBMECs by optimizing the differentiation induction protocol is beneficial for establishing a more reliable in vitro BBB model for studying central nervous system (CNS) drug transport.

Methods
To identify human brain endothelial cell fate-inducing factors, HUVEC was transfected with Zic3A-, Zic3B-, and Sox18-expressing lentivirus vector. Since SOX18 was found to induce BMEC properties, we used a Dox-inducible Tet-on system to express SOX18 during iBMEC differentiation and explored the impact of SOX18 expression on iBMEC maturation.

Results
Sox18-mediated iBMECs achieved a higher TEER value than normal iBMECs (> 3000 Ω cm2). From day 6 to day 10 (d6–10 group), the iBMECs with SOX18 expression expressed a series of tight junction markers and showed upregulation of Mfsd2a, a specific marker of the BBB. The d6–10 group also expressed SLC2A1/Glut1 at levels as high as normal iBMECs, and upregulated ABCB1/P-gp and ABCC1/MRP1 expression. Moreover, Sox18-mediated iBMECs showed higher viability than normal iBMECs after puromycin treatment, indicating that SOX18 expression could upregulate P-gp activity in iBMECs.

Conclusions
Inducible SOX18 expression in iBMECs gained BBB phenotypes, including high TEER values and upregulation of tight junction-related genes, endothelial cell (EC) markers, BBB transporters, and higher cell viability after treatment with puromycin. Collectively, we provide a differentiation method for the maturation of human iPS cell-derived BMECs with SOX18 expression, describing its contribution to form an in vitro BBB model for CNS drug transport studies.
LoFTK: a framework for fully automated calculation of predicted Loss-of-Function variants and genes
Authors: Alasiri Abdulrahman , Karczewski Konrad J. , Cole Brian , Loza Bao-Li , Moore Jason H. , van der Laan Sander W. , Asselbergs Folkert W. , Keating Brendan J. , van Setten Jessica 
Published: February 2023

Abstract
Background
Loss-of-Function (LoF) variants in human genes are important due to their impact on clinical phenotypes and frequent occurrence in the genomes of healthy individuals. The association of LoF variants with complex diseases and traits may lead to the discovery and validation of novel therapeutic targets. Current approaches predict high-confidence LoF variants without identifying the specific genes or the number of copies they affect. Moreover, there is a lack of methods for detecting knockout genes caused by compound heterozygous (CH) LoF variants.

Results
We have developed the Loss-of-Function ToolKit (LoFTK), which allows efficient and automated prediction of LoF variants from genotyped, imputed and sequenced genomes. LoFTK enables the identification of genes that are inactive in one or two copies and provides summary statistics for downstream analyses. LoFTK can identify CH LoF variants, which result in LoF genes with two copies lost. Using data from parents and offspring we show that 96% of CH LoF genes predicted by LoFTK in the offspring have the respective alleles donated by each parent.

Conclusions
LoFTK is a command-line based tool that provides a reliable computational workflow for predicting LoF variants from genotyped and sequenced genomes, identifying genes that are inactive in 1 or 2 copies. LoFTK is an open software and is freely available to non-commercial users at https://github.com/CirculatoryHealth/LoFTK.
Semi-field evaluation of the space spray efficacy of Fludora Co-Max EW against wild insecticide-resistant Aedes aegypti and Culex quinquefasciatus mosquito populations from Abidjan, Côte d’Ivoire
Authors: Zahouli Julien Z. B. , Dibo Jean-Denis , Diakaridia Fofana , Yao Laurence V. A. , Souza Sarah D. , Horstmann Sebastian , Koudou Benjamin G. 
Published: February 2023

Abstract
Background
Space spraying of insecticides is still an important means of controlling Aedes and Culex mosquitoes and arboviral diseases. This study evaluated the space spray efficacy of Fludora Co-Max EW, (water-based insecticide space spray combining flupyradifurone and transfluthrin with film forming aqueous spray technology (FFAST)), against wild insecticide-resistant Aedes aegypti and Culex quinquefasciatus mosquitoes from Abidjan, Côte d’Ivoire, compared with K-Othrine EC (deltamethrin-only product), in small-scale field trials.

Methods
Wild Ae. aegypti and Cx. quinquefasciatus mosquito larvae were collected in Abidjan, Côte d’Ivoire from August to December 2020. Mosquito larvae were reared in the laboratory until the adult stage. Fludora Co-Max EW and K-Othrine EC were tested against emerged adult females (F0 generation) using ultra-low volume cold fogging (ULV) and thermal fogging (TF) delivery technology, both outdoors and indoors in Agboville, Côte d’Ivoire. Specifically, cages containing 20 mosquitoes each were placed at distances of 10, 25, 50, 75 and 100 m from the spraying line for outdoor spraying, and at ceiling, mid-height and floor levels for indoor house spraying. Knockdown and mortality were recorded at each checkpoint and compared by treatments.

Results
Overall, Fludora Co-Max EW induced significantly higher knockdown and mortality effects in the wild insecticide-resistant Ae. aegypti and Cx. quinquefasciatus compared with K-Othrine EC. In both species, mortality rates with Fludora Co-Max EW were > 80% (up to 100%) with the ULV spray outdoors at each distance checkpoint (i.e. 10–100 m), and 100% with the ULV and TF sprays indoors at all checkpoints (i.e. ceiling, mid-height and floor). K-Othrine EC induced high mortality indoors (97.9–100%), whereas mortality outdoors rapidly declined in Ae. aegypti from 96.7% (10 m) to 36.7% (100 m) with the ULV spray, and from 85.0% (10 m) to 38.3% (100 m) with the TF spray. Fludora Co-Max EW spray applied as ULV spray outdoors had higher knockdown and higher killing effects on Ae. aegypti and Cx. quinquefasciatus than when applied as TF spray. Fludora Co-Max EW performed better against Cx. quinquefasciatus than against Ae. aegypti.

Conclusions
Fludora Co-Max EW induced high mortality and knockdown effects against wild insecticide-resistant Ae. aegypti and Cx. quinquefasciatus Abidjan strains and performed better than K-Othrine EC. The presence of flupyradifurone and transfluthrin (with new and independent modes of action) and FFAST technology in the current Fludora Co-Max EW formulation appears to have broadened its killing capacity. Fludora Co-Max EW is thus an effective adulticide and may be a useful tool for Aedes and Culex mosquito and arbovirus control in endemic areas.

Graphical Abstract
State of nutrition amongst US college students: dataset of a national survey study
Authors: Gande Saipriya , Mangal Rohan K. , Stead Thor S. , Ganti Latha 
Published: February 2023

Abstract
Objective
This article presents the dataset titled “Nutrition habits amongst college students in the United States. [1]” The dataset contains the survey responses of 200 US college students aged 18–24 years regarding their knowledge, attitudes, and challenges with regard to nutrition. The recommended USDA (US daily allowance) is 200 calories, comprised of 2 cups fruits, 2.5 cups vegetables, 5.5 ounces of protein, 6 ounces of grains, and 3 cups of dairy [2]. Adhering to these nutritional guidelines however can be complicated by rising tuition prices, food insecurity, and inability to make one’s own food.

Data description
The data in the dataset attempt to estimate the incidence of these barriers. These data could be useful to understand the barriers to healthy eating amongst young adults, and design targeted solutions.
Models and data of AMPlify: a deep learning tool for antimicrobial peptide prediction
Authors: Li Chenkai , Warren René L. , Birol Inanc 
Published: February 2023

Abstract
Objectives
Antibiotic resistance is a rising global threat to human health and is prompting researchers to seek effective alternatives to conventional antibiotics, which include antimicrobial peptides (AMPs). Recently, we have reported AMPlify, an attentive deep learning model for predicting AMPs in databases of peptide sequences. In our tests, AMPlify outperformed the state-of-the-art. We have illustrated its use on data describing the American bullfrog (Rana [Lithobates] catesbeiana) genome. Here we present the model files and training/test data sets we used in that study. The original model (the balanced model) was trained on a balanced set of AMP and non-AMP sequences curated from public databases. In this data note, we additionally provide a model trained on an imbalanced set, in which non-AMP sequences far outnumber AMP sequences. We note that the balanced and imbalanced models would serve different use cases, and both would serve the research community, facilitating the discovery and development of novel AMPs.

Data description
This data note provides two sets of models, as well as two AMP and four non-AMP sequence sets for training and testing the balanced and imbalanced models. Each model set includes five single sub-models that form an ensemble model. The first model set corresponds to the original model trained on a balanced training set that has been described in the original AMPlify manuscript, while the second model set was trained on an imbalanced training set.
Hippocampus-centred grey matter covariance networks predict the development and reversion of mild cognitive impairment
Authors: Dang Mingxi , Yang Caishui , Chen Kewei , Lu Peng , Li He , Zhang Zhanjun ,   for the Beijing Aging Brain Rejuvenation Initiative, for the Alzheimer’s Disease Neuroimaging Initiative
Published: February 2023

Abstract
Background
Mild cognitive impairment (MCI) has been thought of as the transitional stage between normal ageing and Alzheimer’s disease, involving substantial changes in brain grey matter structures. As most previous studies have focused on single regions (e.g. the hippocampus) and their changes during MCI development and reversion, the relationship between grey matter covariance among distributed brain regions and clinical development and reversion of MCI remains unclear.

Methods
With samples from two independent studies (155 from the Beijing Aging Brain Rejuvenation Initiative and 286 from the Alzheimer’s Disease Neuroimaging Initiative), grey matter covariance of default, frontoparietal, and hippocampal networks were identified by seed-based partial least square analyses, and random forest models were applied to predict the progression from normal cognition to MCI (N-t-M) and the reversion from MCI to normal cognition (M-t-N).

Results
With varying degrees, the grey matter covariance in the three networks could predict N-t-M progression (AUC = 0.692–0.792) and M-t-N reversion (AUC = 0.701–0.809). Further analyses indicated that the hippocampus has emerged as an important region in reversion prediction within all three brain networks, and even though the hippocampus itself could predict the clinical reversion of M-t-N, the grey matter covariance showed higher prediction accuracy for early progression of N-t-M.

Conclusions
Our findings are the first to report grey matter covariance changes in MCI development and reversion and highlight the necessity of including grey matter covariance changes along with hippocampal degeneration in the early detection of MCI and Alzheimer’s disease.