Miracle-dz/UniFAR-FTUs huggingface dataset:
Habitual low carbohydrate high fat diet compared with omnivorous, vegan, and vegetarian diets

Background Dietary patterns which exclude whole food groups, such as vegetarian, vegan and low carbohydrate high fat diet (LCHF), are increasingly popular in general public. When carefully planned, all these diets have some known benefits for health, but concerns are also raised in particular for LCHF. The quality of LCHF diet which individuals follow in real life without supervision is not known. Methods One hundred thirty healthy individuals with stable body mass following LCHF, vegan, vegetarian and omnivorous diet for at least six months, were compared in a cross-sectional study. Diet was analyzed through 3-day food records and FFQ, anthropometric measurements were performed and serum metabolic biomarkers determined from fasting blood. Results Participants on LCHF diet had the intakes of micronutrients comparable to other groups, while the intakes of macronutrients differed in line with the definition of each diet. The intakes of saturated fats, cholesterol and animal proteins were significantly higher and the intakes of sugars and dietary fibers were lower compared to other groups. Healthy eating index 2015 in this group was the lowest. There were no differences in the levels of glucose, triacylglycerols and CRP among groups. Total and LDL cholesterol levels were significantly higher in LCHF group, in particular in participants with higher ketogenic ratio. Fatty acids intakes and intakes of cholesterol, dietary fibers and animal proteins explained 40% of variance in total cholesterol level, with saturated fatty acids being the strongest positive predictor and monounsaturated fatty acids a negative predictor. Conclusion None of the self-advised diets provided all the necessary nutrients in optimal levels. Due to the detected increased levels of serum cholesterols, selection of healthy fat sources, higher intake of dietary fibers and partial replacing of animal sources with plant sources of foods should be recommended to the individuals selecting LCFH dietary pattern. Clinical Trial Registration: ClinicalTrials.gov, identifier NCT04347213.
Plasma lipid profiles and homocysteine levels in anti-N-methyl-D-aspartate receptor encephalitis

Introduction We aimed to investigate whether lipid profiles and homocysteine levels in patients with anti-N-methyl-D-aspartate receptor encephalitis are related to clinical presentation and prognosis, which may contribute to further research on the pathogenesis and treatment of this disease. Methods This study included a total of 43 patients with anti-N-methyl-D-aspartate receptor encephalitis and 43 sex–age-matched healthy controls. Baseline demography, clinical data, patient outcomes, and ancillary examination results were recorded. Patients were followed up every 2–3 months during the first year. The modified Rankin Scale score was used to evaluate the therapeutic effect and clinical outcome. Results Among the 43 patients included in this study, 55.81% were male, the mean age of onset was 27 years old, and the median modified Rankin Scale score on admission was 3.0. Apolipoprotein A-1 was significantly lower in patients with anti-N-methyl-D-aspartate receptor encephalitis compared with healthy controls (p = 0.004). Compared with healthy controls, homocysteine (p = 0.002), apolipoprotein B (p = 0.004), Lpa (p = 0.045), and apolipoprotein B/apolipoprotein A-1 (p = 0.001) were significantly increased in patients with anti-N-methyl-D-aspartate receptor encephalitis. According to the modified Rankin Scale scores, 6 months after discharge, 72.09% of patients had a good prognosis and 27.91% had a poor prognosis. In the good prognosis group, age (p = 0.031), lipoprotein a (p = 0.023), apolipoprotein A-1 (p = 0.027) at baseline, and the modified Rankin Scale score on admission (p = 0.019) were significantly higher than those in the poor prognosis group. Conclusion This study suggests the possibility that serum lipid profile and homocysteine play an important role in the pathogenesis of anti-N-methyl-D-aspartate receptor encephalitis, providing support for lipid-lowering treatment of anti-N-methyl-D-aspartate receptor encephalitis patients.
Fitness costs of resistance to insecticide pymetrozine combined with antimicrobial zhongshengmycin in Nilaparvata lugens (Stål)

The brown planthopper, Nilaparvata lugens (Stål), is a major pest of rice crops, and its control is critical for food security. Pymetrozine has been recommended as an alternative to imidacloprid for controlling N. lugens, but the pest has developed high resistance to it, making its prohibition and restriction urgent. To address this issue, we conducted a study using a mixture of pymetrozine and zhongshengmycin with the effective ratio of 1:40, to evaluate the fitness costs in N. lugens. Our results showed that N. lugens had a relative fitness of 0.03 under this ratio, with significantly reduced longevity, female and male adult periods, total pre-oviposition days, and fecundity. Moreover, the expression levels of the uricase gene (EC1.7.3.3) and farnesyl diphosphate farnesyl transferase gene (EC2.5.1.21) were reduced in N. lugens. These genes are involved in urea metabolism and steroid biosynthesis pathway, respectively, and their suppression can interfere with the normal nutritional function of N. lugens. Our study demonstrates that the combination of chemical insecticides and antimicrobials can delay the development of resistance and improve the efficiency of pest control. This information is valuable for researchers developing management strategies to delay the development of pymetrozine resistance in N. lugens.
Mock circulatory loop applications for testing cardiovascular assist devices and in vitro studies

The mock circulatory loop (MCL) is an in vitro experimental system that can provide continuous pulsatile flows and simulate different physiological or pathological parameters of the human circulation system. It is of great significance for testing cardiovascular assist device (CAD), which is a type of clinical instrument used to treat cardiovascular disease and alleviate the dilemma of insufficient donor hearts. The MCL installed with different types of CADs can simulate specific conditions of clinical surgery for evaluating the effectiveness and reliability of those CADs under the repeated performance tests and reliability tests. Also, patient-specific cardiovascular models can be employed in the circulation of MCL for targeted pathological study associated with hemodynamics. Therefore, The MCL system has various combinations of different functional units according to its richful applications, which are comprehensively reviewed in the current work. Four types of CADs including prosthetic heart valve (PHV), ventricular assist device (VAD), total artificial heart (TAH) and intra-aortic balloon pump (IABP) applied in MCL experiments are documented and compared in detail. Moreover, MCLs with more complicated structures for achieving advanced functions are further introduced, such as MCL for the pediatric application, MCL with anatomical phantoms and MCL synchronizing multiple circulation systems. By reviewing the constructions and functions of available MCLs, the features of MCLs for different applications are summarized, and directions of developing the MCLs are suggested.
Predicting near-term glaucoma progression: An artificial intelligence approach using clinical free-text notes and data from electronic health records

Purpose The purpose of this study was to develop a model to predict whether or not glaucoma will progress to the point of requiring surgery within the following year, using data from electronic health records (EHRs), including both structured data and free-text progress notes. Methods A cohort of adult glaucoma patients was identified from the EHR at Stanford University between 2008 and 2020, with data including free-text clinical notes, demographics, diagnosis codes, prior surgeries, and clinical information, including intraocular pressure, visual acuity, and central corneal thickness. Words from patients’ notes were mapped to ophthalmology domain-specific neural word embeddings. Word embeddings and structured clinical data were combined as inputs to deep learning models to predict whether a patient would undergo glaucoma surgery in the following 12 months using the previous 4-12 months of clinical data. We also evaluated models using only structured data inputs (regression-, tree-, and deep-learning-based models) and models using only text inputs. Results Of the 3,469 glaucoma patients included in our cohort, 26% underwent surgery. The baseline penalized logistic regression model achieved an area under the receiver operating curve (AUC) of 0.873 and F1 score of 0.750, compared with the best tree-based model (random forest, AUC 0.876; F1 0.746), the deep learning structured features model (AUC 0.885; F1 0.757), the deep learning clinical free-text features model (AUC 0.767; F1 0.536), and the deep learning model with both the structured clinical features and free-text features (AUC 0.899; F1 0.745). Discussion Fusion models combining text and EHR structured data successfully and accurately predicted glaucoma progression to surgery. Future research incorporating imaging data could further optimize this predictive approach and be translated into clinical decision support tools.
Assessment of anti-HIV-1 guide RNA efficacy in cells containing the viral target sequence, corresponding gRNA, and CRISPR/Cas9

The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 gene editing system has been shown to be effective at inhibiting human immunodeficiency virus type 1 (HIV-1). Studies have not consistently used a trackable dual reporter system to determine what cells received the Cas9/gRNA to determine the overall knockdown of HIV. Some studies have used stably transduced cells under drug selection to accomplish this goal. Here a two-color system was used that allows tracking of viral protein expression and which cells received the CRISPR/Cas9 system. These experiments ensured that each gRNA used was a perfect match to the intended target to remove this variable. The data showed that gRNAs targeting the transactivation response element (TAR) region or other highly conserved regions of the HIV-1 genome were effective at stopping viral gene expression, with multiple assays demonstrating greater than 95 percent reduction. Conversely, gRNAs targeting conserved sites of the 5’ portion of the U3 region were largely ineffective, demonstrating that the location of edits in the long terminal repeat (LTR) matter with respect to function. In addition, it was observed that a gRNA targeting Tat was effective in a T-cell model of HIV-1 latency. Taken together, these studies demonstrated gRNAs designed to highly conserved functional regions have near 100% efficacy in vitro in cells known to have received the Cas9/gRNA pair.
Transcriptomic analysis identified SLC40A1 as a key iron metabolism-related gene in airway macrophages in childhood allergic asthma

Introduction: Asthma is the most common chronic condition in children, with allergic asthma being the most common phenotype, accounting for approximately 80% of cases. Growing evidence suggests that disruption of iron homeostasis and iron regulatory molecules may be associated with childhood allergic asthma. However, the underlying molecular mechanism remains unclear. Methods: Three childhood asthma gene expression datasets were analyzed to detect aberrant expression profiles of iron metabolism-related genes in the airways of children with allergic asthma. Common iron metabolism-related differentially expressed genes (DEGs) across the three datasets were identified and were subjected to functional enrichment analysis. Possible correlations between key iron metabolism-related DEGs and type 2 airway inflammatory genes were investigated. Single-cell transcriptome analysis further identified major airway cell subpopulations driving key gene expression. Key iron metabolism-related gene SLC40A1 was validated in bronchoalveolar lavage (BAL) cells from childhood asthmatics with control individuals by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and immunofluorescence. The intracellular iron content in BAL cells was assessed by Perls iron staining and the iron levels in BAL supernatant was measured by iron assay to assess airway iron metabolism status in childhood asthmatics. Results: Five common iron metabolism-related DEGs were identified, which were functionally related to iron homeostasis. Among these genes, downregulated SLC40A1 was strongly correlated with type 2 airway inflammatory markers and the gene signature of SLC40A1 could potentially be used to determine type 2-high and type 2-low subsets in childhood allergic asthmatics. Further single-cell transcriptomic analysis identified airway macrophages driving SLC40A1 expression. Immunofluorescence staining revealed colocalization of FPN (encoded by SLC40A1) and macrophage marker CD68. Down-regulation of SLC40A1 (FPN) was validated by qRT-PCR and immunofluorescence analysis. Results further indicated reduced iron levels in the BAL fluid, but increased iron accumulation in BAL cells in childhood allergic asthma patients. Furthermore, decreased expression of SLC40A1 was closely correlated with reduced iron levels in the airways of children with allergic asthma. Discussion: Overall, these findings reveal the potential role of the iron metabolism-related gene SLC40A1 in the pathogenesis of childhood allergic asthma.
Editorial: Functional neuroimaging in psychiatric practice: How far have we come?

COPYRIGHT © 2023 Kundu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Editorial: Functional neuroimaging in psychiatric practice: How far have we come?
The serum soluble scavenger with 5 domains levels: A novel biomarker for individuals with heart failure

Background: We aimed to explore the relationship between the serum Soluble Scavenger with 5 Domains (SSC5D) levels and heart failure (HF). Methods and Results: We retrospectively enrolled 276 patients diagnosed with HF or normal during hospitalization in Shanghai General Hospital between September 2020 and December 2021. Previously published RNA sequencing data were re-analyzed to confirm the expression profile of SSC5D in failing and non-failing human and mouse heart tissues. Quantitative real-time polymerase chain reaction assay was used to quantify Ssc5d mRNA levels in murine heart tissue after myocardial infarction and transverse aortic constriction surgery. To understand the HF-induced secreted proteins profile, 1,755 secreted proteins were investigated using human dilated cardiomyopathy RNA-seq data, and the results indicated that SSC5D levels were significantly elevated in failing hearts compared to the non-failing. Using single-cell RNA sequencing data, we demonstrated that Ssc5d is predominantly expressed in cardiac fibroblasts. In a murine model of myocardial infarction or transverse aortic constriction, Ssc5d mRNA levels were markedly increased compared with those in the sham group. Similarly, serum SSC5D levels were considerably elevated in the HF group compared with the control group [15,789.35 (10,745.32–23,110.65) pg/mL, 95% CI (16,263.01–19,655.43) vs. 8,938.72 (6,154.97–12,778.81) pg/mL, 95% CI (9,337.50–11,142.93); p < 0.0001]. Moreover, serum SSC5D levels were positively correlated with N-terminal pro-B-type natriuretic peptide (R = 0.4, p = 7.9e-12) and inversely correlated with left ventricular ejection fraction (R = −0.46, p = 9.8e-16). Conclusion: We concluded that SSC5D was a specific response to HF. Serum SSC5D may function as a novel biomarker and therapeutic target for patients with HF.
Effects of human placenta cryopreservation on molecular characteristics of placental mesenchymal stromal cells

Cryopreservation of placenta tissue for long-term storage provides the opportunity in the future to isolate mesenchymal stromal cells that could be used for cell therapy and regenerative medicine. Despite being widely used, the established cryopreservation protocols for freezing and thawing still raise concerns about their impact on molecular characteristics, such as epigenetic regulation. In our study, we compared the characteristics of human placental mesenchymal stromal cells (hPMSCs) isolated from fresh (native) and cryopreserved (cryo) placenta tissue. We assessed and compared the characteristics of native and cryo hPMSCs such as morphology, metabolic and differentiation potential, expression of cell surface markers, and transcriptome. No significant changes in immunophenotype and differentiation capacity between native and cryo cells were observed. Furthermore, we investigated the epigenetic changes and demonstrated that both native and cryo hPMSCs express only slight variations in the epigenetic profile, including miRNA levels, DNA methylation, and histone modifications. Nevertheless, transcriptome analysis defined the upregulation of early-senescence state-associated genes in hPMSCs after cryopreservation. We also evaluated the ability of hPMSCs to improve pregnancy outcomes in mouse models. Improved pregnancy outcomes in a mouse model confirmed that isolated placental cells both from native and cryo tissue have a positive effect on the restoration of the reproductive system. Still, the native hPMSCs possess better capacity (up to 66%) in comparison with cryo hPMSCs (up to 33%) to restore fertility in mice with premature ovarian failure. Our study demonstrates that placental tissue can be cryopreserved for long-term storage with the possibility to isolate mesenchymal stromal cells that retain characteristics suitable for therapeutic use.
Editorial: Interactions between COVID-19 and malaria

COPYRIGHT © 2023 Yanow and Whittaker. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. TYPE Editorial PUBLISHED 13 April 2023 DOI 10.3389/fimmu.2023. 1193377
STGATE: Spatial-temporal graph attention network with a transformer encoder for EEG-based emotion recognition

Electroencephalogram (EEG) is a crucial and widely utilized technique in neuroscience research. In this paper, we introduce a novel graph neural network called the spatial-temporal graph attention network with a transformer encoder (STGATE) to learn graph representations of emotion EEG signals and improve emotion recognition performance. In STGATE, a transformer-encoder is applied for capturing time-frequency features which are fed into a spatial-temporal graph attention for emotion classification. Using a dynamic adjacency matrix, the proposed STGATE adaptively learns intrinsic connections between different EEG channels. To evaluate the cross-subject emotion recognition performance, leave-one-subject-out experiments are carried out on three public emotion recognition datasets, i.e., SEED, SEED-IV, and DREAMER. The proposed STGATE model achieved a state-of-the-art EEG-based emotion recognition performance accuracy of 90.37% in SEED, 76.43% in SEED-IV, and 76.35% in DREAMER dataset, respectively. The experiments demonstrated the effectiveness of the proposed STGATE model for cross-subject EEG emotion recognition and its potential for graph-based neuroscience research.
Kinematics of base sphere as a segment of spheres kinematical chain: Gravitational acceleration as equivalent central acceleration

Assuming that the theory for differential geometry of curve is correct, this paper introduces a spheres kinematical chain of changeable radii positioned in such a fashion that the centre of the next sphere is firmly attached to the previous one within the chain. The kinematical chain consists of the base sphere and the rest of the chain which is inside the base sphere. The paper discusses the undisturbed and disturbed motion of the base sphere. Tha gravitational acceleration is interpreted as equivalent central acceleration during undisturbed rotation of the base sphere. The disturbed motion with respect to the undisturbed motion is described by increments of corresponding kinematical quantities. The relationship with the existing laws for translational motion in the classical mechanics is also established. And finally, a simple experiment for verification of the exposed theory is proposed in this paper.
Temperature and Precipitation Fluctuation of Madinah-Al-Munawara, Kingdom of Saudi Arabia (1959-2011)

The work discusses the temperature and precipitation fluctuation of Madinah-Al-Munawara, Saudi Arabia for a time period of 1959-2011. This is a city in the Hejaz region of western Saudi Arabia, the capital of Al Madinah Province and important religious place. For many years now, Royal Kingdom of Saudi Arabia is active on national as well as international levels to adopt a more suitable policy for the study of climate changes and reviews it periodically as per country economic desires. The main sectors that affect the temperature and precipitation fluctuations in Saudi Arabia are surface water, coastal management, overgrazing, forestry, livestock, drought, desertification, industrialization, landuse change, tourism, and aridity etc. The paper analyzes the temperature and precipitation fluctuations of Madinah-Al-Munawara in terms of general climatology, climate fluctuation/variation, seasonal distribution and extreme weather events. The mean monthly temperature of the city recorded during 1959-2011 is 28°C having mean maximum temperature of 34°C and mean minimum of 21°C. The mean monthly temperature of the city shows an increase of 1.7°C having 1.2°C increase in maximum temperature and decrease of -1.9°C in minimum temperature. Generally, there is a rise and fall in the temperature condition and shows irregular pattern throughout the period. The total precipitation of the city is 36 millimeters; having a decrease of -0.3 millimeters but in general the trend of precipitation at Madinah-Al-Munawara shows an increasing trend throughout the period. April and November are the wettest, while June, August, September and October are the hottest months of the city. The area is characterized by two main seasons that is winter (5 months) and summer (7 months), which can further be sub-divided into four rainy seasons namely winter, post-winter, summer, and post-summer seasons.
IWKM clustering algorithm for high dimensional multi view data based on chaos PSO

: Aiming at the problem that traditional clustering algorithm can't deal with multi view and high dimension data in big data, this paper proposed an intelligent weighted K-means clustering algorithm based on chaos particle swarm optimization algorithm. Firstly, it introduced the coupling degree between clusters to expand the similarity of clusters. Secondly, in order to eliminate the sensitivity of the initial clustering center, it used chaos particle swarm optimization algorithm to obtain the optimal initial clustering center, view weight and feature weight through global search. Then, it introduced an accurate perturbation strategy to improve the performance of chaos particle swarm optimization. Finally, experiments on Apache spark and single node show that the proposed method has better clustering performance under the condition of complex data sets with multiple views and high dimensions.