Miracle-dz/UniFAR-FTUs huggingface dataset:
Developing Clinical Prediction Models Using Primary Care Electronic Health Record Data: The Impact of Data Preparation Choices on Model Performance

Objective To quantify prediction model performance in relation to data preparation choices when using electronic health records (EHR). Study Design and Setting Cox proportional hazards models were developed for predicting the first-ever main adverse cardiovascular events using Dutch primary care EHR data. The reference model was based on a 1-year run-in period, cardiovascular events were defined based on both EHR diagnosis and medication codes, and missing values were multiply imputed. We compared data preparation choices based on (i) length of the run-in period (2- or 3-year run-in); (ii) outcome definition (EHR diagnosis codes or medication codes only); and (iii) methods addressing missing values (mean imputation or complete case analysis) by making variations on the derivation set and testing their impact in a validation set. Results We included 89,491 patients in whom 6,736 first-ever main adverse cardiovascular events occurred during a median follow-up of 8 years. Outcome definition based only on diagnosis codes led to a systematic underestimation of risk (calibration curve intercept: 0.84; 95% CI: 0.83–0.84), while complete case analysis led to overestimation (calibration curve intercept: −0.52; 95% CI: −0.53 to −0.51). Differences in the length of the run-in period showed no relevant impact on calibration and discrimination. Conclusion Data preparation choices regarding outcome definition or methods to address missing values can have a substantial impact on the calibration of predictions, hampering reliable clinical decision support. This study further illustrates the urgency of transparent reporting of modeling choices in an EHR data setting.
Traditional Chinese Medicine as a Promising Strategy for the Treatment of Alzheimer’s Disease Complicated With Osteoporosis

Alzheimer’s disease (AD) and osteoporosis (OP) are progressive degenerative diseases caused by multiple factors, placing a huge burden on the world. Much evidence indicates that OP is a common complication in AD patients. In addition, there is also evidence to show that patients with OP have a higher risk of AD than those without OP. This suggests that the association between the two diseases may be due to a pathophysiological link rather than one disease causing the other. Several in vitro and in vivo studies have also proved their common pathogenesis. Based on the theory of traditional Chinese medicine, some classic and specific natural Chinese medicines are widely used to effectively treat AD and OP. Current evidence also shows that these treatments can ameliorate both brain damage and bone metabolism disorder and further alleviate AD complicated with OP. These valuable therapies might provide effective and safe alternatives to major pharmacological strategies.
Transcriptomic Analysis of Long Non-coding RNA-MicroRNA-mRNA Interactions in the Nucleus Accumbens Related to Morphine Addiction in Mice

Recent research suggest that some non-coding RNAs (ncRNAs) are important regulators of chromatin dynamics and gene expression in nervous system development and neurological diseases. Nevertheless, the molecular mechanisms of long non-coding RNAs (lncRNAs), acting as competing endogenous RNAs (ceRNAs), underlying morphine addiction are still unknown. In this research, RNA sequencing (RNA-seq) was used to examine the expression profiles of lncRNAs, miRNAs and mRNAs on the nucleus accumbens (NAc) tissues of mice trained with morphine or saline conditioned place preference (CPP), with differential expression of 31 lncRNAs, 393 miRNAs, and 371 mRNAs found. A ceRNA network was established for reciprocal interactions for 9 differentially expressed lncRNAs (DElncRNAs), 10 differentially expressed miRNAs (DEmiRNAs) and 12 differentially expressed mRNAs (DEmRNAs) based on predicted miRNAs shared by lncRNAs and mRNAs. KEGG pathway enrichment analyses were conducted to explore the potential functions of DEmRNAs interacting with lncRNAs in the ceRNA network. These DEmRNAs were enriched in synaptic plasticity-related pathways, including pyrimidine metabolism, ECM-receptor interaction, and focal adhesion. The correlation between the relative expression of lncRNAs, miRNAs and mRNAs was analyzed to further validate predicted ceRNA networks, and the Lnc15qD3-miR-139-3p-Lrp2 ceRNA regulatory interaction was determined. These results suggest that the comprehensive network represents a new insight into the lncRNA-mediated ceRNA regulatory mechanisms underlying morphine addiction and provide new potential diagnostic and prognostic biomarkers for morphine addiction.
Microfluidic and Static Organotypic Culture Systems to Support Ex Vivo Spermatogenesis From Prepubertal Porcine Testicular Tissue: A Comparative Study

Background: In vitro maturation of immature testicular tissue (ITT) cryopreserved for fertility preservation is a promising fertility restoration strategy. Organotypic tissue culture proved successful in mice, leading to live births. In larger mammals, including humans, efficiently reproducing spermatogenesis ex vivo remains challenging. With advances in biomaterials technology, culture systems are becoming more complex to better mimic in vivo conditions. Along with improving culture media components, optimizing physical culture conditions (e.g., tissue perfusion, oxygen diffusion) also needs to be considered. Recent studies in mice showed that by using silicone-based hybrid culture systems, the efficiency of spermatogenesis can be improved. Such systems have not been reported for ITT of large mammals. Methods: Four different organotypic tissue culture systems were compared: static i.e., polytetrafluoroethylene membrane inserts (OT), agarose gel (AG) and agarose gel with polydimethylsiloxane chamber (AGPC), and dynamic i.e., microfluidic (MF). OT served as control. Porcine ITT fragments were cultured over a 30-day period using a single culture medium. Analyses were performed at days (d) 0, 5, 10, 20 and 30. Seminiferous tubule (ST) integrity, diameters, and tissue core integrity were evaluated on histology. Immunohistochemistry was used to identify germ cells (PGP9.5, VASA, SYCP3, CREM), somatic cells (SOX9, INSL3) and proliferating cells (Ki67), and to assess oxidative stress (MDA) and apoptosis (C-Caspase3). Testosterone was measured in supernatants using ELISA. Results: ITT fragments survived and grew in all systems. ST diameters, and Sertoli cell (SOX9) numbers increased, meiotic (SYCP3) and post-meiotic (CREM) germ cells were generated, and testosterone was secreted. When compared to control (OT), significantly larger STs (d10 through d30), better tissue core integrity (d5 through d20), higher numbers of undifferentiated spermatogonia (d30), meiotic and post-meiotic germ cells (SYCP3: d20 and 30, CREM: d20) were observed in the AGPC system. Apoptosis, lipid peroxidation (MDA), ST integrity, proliferating germ cell (Ki67/VASA) numbers, Leydig cell (INSL3) numbers and testosterone levels were not significantly different between systems. Conclusions: Using a modified culture system (AGPC), germ cell survival and the efficiency of porcine germ cell differentiation were moderately improved ex vivo. We assume that further optimization can be obtained with concomitant modifications in culture media components.
Retrospective Analysis of Task-Specific Effects on Brain Activity After Stroke: A Pilot Study

Background Evidence supports cortical reorganization in sensorimotor areas induced by constraint-induced movement therapy (CIMT). However, only a few studies examined the neural plastic changes as a function of task specificity. This retrospective analysis aims to evaluate the functional brain activation changes during a precision and a power grasp task in chronic stroke survivors who received 2-weeks of CIMT compared to a no-treatment control group. Methods Fourteen chronic stroke survivors, randomized to CIMT (n = 8) or non-CIMT (n = 6), underwent functional MRI (fMRI) before and after a 2-week period. Two behavioral measures, the 6-item Wolf Motor Function Test (WMFT-6) and the Motor Activity Log (MAL), and fMRI brain scans were collected before and after a 2-week period. During scan runs, participants performed two different grasp tasks (precision, power). Pre to post changes in laterality index (LI) were compared by group and task for two predetermined motor regions of interest: dorsal premotor cortex (PMd) and primary motor cortex (MI). Results In contrast to the control group, the CIMT group showed significant improvements in the WMFT-6. For the MAL, both groups showed a trend toward greater improvements from baseline. Two weeks of CIMT resulted in a relative increase in activity in a key region of the motor network, PMd of the lesioned hemisphere, under precision grasp task conditions compared to the non-treatment control group. No changes in LI were observed in MI for either task or group. Conclusion These findings provide preliminary evidence for task-specific effects of CIMT in the promotion of recovery-supportive cortical reorganization in chronic stroke survivors.
Increased Resting-State Functional Connectivity of the Hippocampus in Rats With Sepsis-Associated Encephalopathy

Background Sepsis-associated encephalopathy (SAE) has been identified as a frequent complication of sepsis, featured by an aberrant level of cognitive and affective functions. The present study is designed to explore the changes in functional connectivity (FC) of the hippocampus in rats with SAE utilizing resting-state functional magnetic resonance imaging (rs-fMRI). Methods Sprague-Dawley rats were randomly assigned to the SAE and control groups. We acquired rs-fMRI data using a 7T MRI to evaluate hippocampal network functional differences between the two groups with a seed-based approach. Behavioral performance was assessed using the open field test and forced swimming test. Statistical analysis was undertaken to evaluate the correlation between the hippocampal FC and behavioral findings. Results Compared with the control group, the SAE group showed increased FC between the bilateral hippocampus and thalamus, septum, bed nuclei stria terminalis (BNST), left primary forelimb somatosensory cortex (S1FL), primary motor cortex (M1), and inferior colliculus. Increased FC between the left hippocampus and thalamus, septum, BNST, left S1FL, and inferior colliculus was observed. While with the right hippocampus, FC in thalamus, septum, left S1FL and inferior colliculus was enhanced. Additionally, positive correlations were found between the hippocampal FC and the immobility time in the forced swimming test. Conclusion Hippocampus-related brain networks have significant alterations in rats with SAE, and the elevated hippocampal resting-state FC was positively related to affective deficits. Changes in FC between the hippocampus and other brain regions could be a potential neuroimaging biomarker of cognitive or mental disorders triggered by SAE.
Structure and Pattern Formation in Biological Liquid Crystals: Insights From Theory and Simulation of Self-Assembly and Self-Organization

This review presents theory and simulation of liquid crystal phase ordering in biological fibrous materials, solutions, and composites in the presence of elastic fields, second phase inclusions, and transport phenomena, including complex shear-extensional flow and mass transfer. Liquid crystal self-assembly through phase ordering on elastic deformable membranes is first applied to characterize the mechanisms that control the structures in plant cell walls, highlighting how curvophobic and curvophilic effects introduce new structuring fields beyond hard-core repulsion. Then chiral nematic self-assembly is simulated in a mesophase containing fibrillar colloidal inclusions (liquid crystal-fibre composites) to demonstrate how the inclusion positional order generates defects and disclinations as shown in the plant cell wall. Coupling phase ordering to tuned transport phenomena is shown how and why it leads to self-organization such as paranematic states of dilute acidic aqueous collagen solutions. Further directed dehydration of well-organized paranematic collagen leads to defect free cholesteric films only when directed dehydration is synchronized with chirality formation. In addition, the ubiquitous surface nanowrinkling of cholesterics is captured with surface anchoring. In these four representative systems, the new mechanisms that enhance the well-known exclude volume interactions are identified quantified and validated with experimental data. Future directions to create new advanced multifunctional materials based on principles of self-assembly and self-organization are identified by leveraging the new couplings between material structure, geometry, and transport phenomena.
Differential Urinary Microbiota Composition Between Women With and Without Recurrent Urinary Tract Infection

Background Recurrent urinary tract infection (RUTI) is common and burdensome in women. Due to the low concentration or slow-growing of uropathogens in RUTI, standard urine cultures (SUCs) are often negative. Next-generation sequencing (NGS) of bacterial 16S rRNA gene is more sensitive and could be used to reveal the differential microbiota between patients with RUTI and asymptomatic controls. Methods Women (aged ≥ 18 years) with clinically diagnosed RUTI with negative SUC and age-matched women asymptomatic controls with normal urinalysis were enrolled. Their midstream voided urine specimens were collected and processed for NGS (Illumina MiSeq) targeting the bacterial 16S rRNA gene V3-V4 region. The dataset was clustered into operational taxonomic units (OTUs) using QIIME. Taxonomic analysis, alpha diversity, beta diversity, multivariate statistical analysis, and linear discriminant analysis effect size (LEfSe) for differential analysis were performed and compared between patients with RUTI and asymptomatic controls. Results A total of 90 patients with RUTI and 62 asymptomatic controls were enrolled in this study. Among them, 74.4% (67/90) and 71.0% (44/62) were successfully amplified and sequenced their bacterial 16S rRNA gene. In the alpha diversity analysis, the chao1 index and observed species index were significantly lower in the RUTI group than in the control group (P = 0.015 and 0.028, respectively). In the beta diversity analysis, there was a significant difference between the 2 groups [Analysis of similarities (ANOSIM), R = 0.209, P = 0.001]. The relative abundance of 36 bacterial taxa was significantly higher, and another 24 kinds of bacteria were significantly lower in the RUTI group compared with the control group [LEfSe analysis, P < 0.05, linear discriminative analysis (LDA) score > 3], suggesting that Ralstonia, Prevotella, Dialister, and Corynebacterium may play an important role in RUTI. Conclusion The urinary microbiota of women with clinically diagnosed RUTI were significantly different from age-matched asymptomatic controls.
Maternal Immune Dysregulation and Autism–Understanding the Role of Cytokines, Chemokines and Autoantibodies

Autism spectrum disorder (ASD) is acknowledged as a highly heterogeneous, behaviorally defined neurodevelopmental disorder with multiple etiologies. In addition to its high heritability, we have come to recognize a role for maternal immune system dysregulation as a prominent risk factor for the development of ASD in the child. Examples of these risk factors include altered cytokine/chemokine activity and the presence of autoantibodies in mothers that are reactive to proteins in the developing brain. In addition to large clinical studies, the development of pre-clinical models enables the ability to evaluate the cellular and molecular underpinnings of immune-related pathology. For example, the novel animal models of maternal autoantibody-related (MAR) ASD described herein will serve as a preclinical platform for the future testing of targeted therapeutics for one ‘type’ of ASD. Identification of the cellular targets will advance precision medicine efforts toward tailored therapeutics and prevention. This minireview highlights emerging evidence for the role of maternal immune dysregulation as a potential biomarker, as well as a pathologically relevant mechanism for the development of ASD in offspring. Further, we will discuss the current limitations of these models as well as potential avenues for future research.
Macroscopic averaging of electrical properties inside grains of polycrystalline materials

The polycrystalline material film consists of various size crystalline grains that have properties of crystalline material. The grains are usually randomly spatially oriented thus affecting the magnitude of orientation dependent properties. Here we considered resistive and piezoresistive properties of polycrystalline silicon. Depending on the dopant concentration within the grains the depleted regions originated owing to carrier trapping on the grain boundary can have various lengths. As the carrier concentration within depletion region is lower the resistance and piezoresistance can be higher than in the rest of the grain. Results of the calculation show that the deviation of the average parameters such as concentration of free carriers, specific resistivity, piezoresistance coefficient, can be significantly different from that obtained on assumption of uniform free carrier distribution in the crystallite.
Recognition of Gallotannins and the Physiological Activities: From Chemical View

Gallotannins, characterized with the glycosidic core and galloyl unit, are seemed as vital components of hydrolyzable tannins. Benefit from the more and more discoveries of their bioactivities and edibility, application of gallotannins in food industry, pharmacy industry, and other fields is increasing. Inheriting previous study achievements, chemical structure of gallotannins was illustrated and degradation as well as synthetic routes to gallotannins were summarized. On this basis, distribution in the nature also including the distinction of gallotannins was discussed. More than that, activities involving in antioxidant, anti-inflammatory, enzyme inhibitions, protein binding, and so on, as well as applications in the field of food industry, biopharmaceutical science, agricultural production, etc., were combed. Finally, improvement of bioavailability, chemical modification of the structure, and accurate determination of new gallotannins were pointed out to be the orientation in the future.
Expression Analysis of TCP Transcription Factor Family in Autopolyploids of Chrysanthemum nankingense

Autopolyploids often exhibit plant characteristics different from their diploid ancestors and are frequently associated with altered genes expression controlling growth and development. TCP is a unique transcription factor family in plants that is closely related to plant growth and development. Based on transcriptome sequencing of Chrysanthemum nankingense, 23 full-length TCP genes were cloned. The expression of CnTCP9 was most variable in tetraploids, at least threefold greater than diploids. Due to the lack of a C. nankingense transgenic system, we overexpressed CnTCP9 in Arabidopsis thaliana (Col-0) and Chrysanthemum morifolium. Overexpression of CnTCP9 caused enlargement of leaves in A. thaliana and petals in C. morifolium, and the expression of genes downstream of the GA pathway in C. morifolium were increased. Our results suggest that autopolyploidization of C. nankingense led to differential expression of TCP family genes, thereby affecting plant characteristics by the GA pathway. This study improves the understanding of enlarged plant size after autopolyploidization.
Neuroprotective Mechanisms of Ginsenoside Rb1 in Central Nervous System Diseases

Panax ginseng and Panax notoginseng, two well-known herbs with enormous medical value in Asian countries, have a long usage history in China for the therapy of some diseases, such as stroke. Ginsenoside Rb1 is one of most important active ingredients in Panax ginseng and Panax notoginseng. In the last two decades, more attention has focused on ginsenoside Rb1 as an antioxidative, anti-apoptotic and anti-inflammatory agent that can protect the nervous system. In the review, we summarize the neuroprotective roles of ginsenoside Rb1 and its potential mechanisms in central nervous system diseases (CNSDs), including neurodegenerative diseases, cerebral ischemia injury, depression and spinal cord injury. In conclusion, ginsenoside Rb1 has a potential neuroprotection due to its inhibition of oxidative stress, apoptosis, neuroinflammation and autophagy in CNSDs and may be a promising candidate agent for clinical therapy of CNSDs in the future.
Validation of Serological Methods for COVID-19 and Retrospective Screening of Health Employees and Visitors to the São Paulo University Hospital, Brazil

Reliable serological tests for the detection of SARS-CoV-2 antibodies among infected or vaccinated individuals are important for epidemiological and clinical studies. Low-cost approaches easily adaptable to high throughput screenings, such as Enzyme-Linked Immunosorbent Assays (ELISA) or electrochemiluminescence immunoassay (ECLIA), can be readily validated using different SARS-CoV-2 antigens. A total of 1,119 serum samples collected between March and July of 2020 from health employees and visitors to the University Hospital at the University of São Paulo were screened with the Elecsys® Anti-SARS-CoV-2 immunoassay (Elecsys) (Roche Diagnostics) and three in-house ELISAs that are based on different antigens: the Nucleoprotein (N-ELISA), the Receptor Binding Domain (RBD-ELISA), and a portion of the S1 protein (ΔS1-ELISA). Virus neutralization test (CPE-VNT) was used as the gold standard to validate the serological assays. We observed high sensitivity and specificity values with the Elecsys (96.92% and 98.78%, respectively) and N-ELISA (93.94% and 94.40%, respectively), compared with RBD-ELISA (90.91% sensitivity and 88.80% specificity) and the ΔS1-ELISA (77.27% sensitivity and 76% specificity). The Elecsys® proved to be a reliable SARS-CoV-2 serological test. Similarly, the recombinant SARS-CoV-2 N protein displayed good performance in the ELISA tests. The availability of reliable diagnostic tests is critical for the precise determination of infection rates, particularly in countries with high SARS-CoV-2 infection rates, such as Brazil. Collectively, our results indicate that the development and validation of new serological tests based on recombinant proteins may provide new alternatives for the SARS-CoV-2 diagnostic market.