Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Antibiotic Use on Saliva Antibody Content and Oral Microbiota in Sprague Dawley Rats

Antibiotics are often used to treat systemic diseases not associated with the oral cavity. This application of antibiotics may affect the healthy oral microbiota community, as it destroys the balance between specific bacterial populations throughout the ecosystem and may lead to dysbacteriosis. We hypothesized that the effects on antibiotics on oral microbiota regulation and function would affect antibody content in saliva, depending on the antibiotic type. To address this, a total of 24 Sprague Dawley rats (divided into 4 cages, 6 per pen) were administered amoxicillin (AMX), spiramycin (SP), metronidazole (MTZ), or water (control) daily for 14 days (gavage). After treatment was completed, high-throughput sequencing of 16S rRNA genes was used to determine changes in the composition, metabolic function, and diversity of oral microbiota in the rats. Enzyme-linked immunosorbent assay was used to detect antibodies in saliva, including SIgA, IgG, and IgM. Results showed that AMX, MTZ, and SP significantly affected oral microbiota composition, diversity, and metabolic function in rats. AMX induced substantial changes in the rat salivary antibody concentrations. At the genus level, the relative abundance of Rothia and Haemophilus was higher in the AMX group than in the other groups. In conclusion, antibiotics-induced changes in oral microbiota populations may be associated with changes in salivary antibody concentrations. However, the specific interaction mechanisms remain unknown, and it is still unclear whether significant changes in the oral microbiota cause changes in salivary antibody concentrations or vice versa.
The P4 Study: Postpartum Maternal and Infant Faecal Microbiome 6 Months After Hypertensive Versus Normotensive Pregnancy

Objective/Hypothesis To explore potential differences in faecal microbiome between women, and their infants, who had normotensive pregnancies (NP) and those who had a hypertensive pregnancy (HP), either gestational hypertension (GH) or preeclampsia (PE). Methods This is a sub study of P4 (Postpartum Physiology, Psychology, and Paediatrics Study) and includes 18 mother-infant pairs: 10 NP and 8 HP (HP as defined by blood pressure > 140/90mmHg; of which 6 had PE, and 2 GH), six months postpartum. The participating mothers collected stool samples from themselves and their infants. 16S rRNA V3-V4 amplicons were used to study the faecal microbiome. Results The sample of women and their infants were mostly primiparous (n =16) with vaginal birth (n = 14). At the time of faecal sampling 8 women were using hormonal contraception, and one HP woman remained on an antihypertensive. All women had blood pressure < 130/80mmHg, and 10 had high BMI (> 30). All infants had started solids, 8 were exclusively breastfed, 1 exclusively formula fed and 9 both. Three infants had been exposed to a course of antibiotics. Six months postpartum, there were no significant differences in alpha or beta diversity between the gut microbiota of HP and NP women (P > 0.05). However, a statistically significant difference was detected in alpha diversity between infants following HP and NP, with lower diversity levels in HP infants (P < 0.05). It was also found that at a genus and species level, the gut microbiota of HP women was enriched with Bifidobacterium and Bifididobacterium sp. and depleted in Barnisiella and Barnesiella intestinihominis when compared to NP women (P < 0.05). Similarly, the gut microbiota of infants born from HP was enriched in Streptococcus infantis and depleted in Sutterella, Sutterella sp. , Bacteroides sp. and Clostridium aldenense compared to infants born from NP (P < 0.05). Discussion While our findings are at best preliminary, due to the very small sample size, they do suggest that the presence of hypertension in pregnancy may adversely affect the maternal microbiota post-partum, and that of their infants. Further analysis of postpartum microbiome data from future studies will be important to validate these early findings and provide further evidence about the changes in the microbiota in the offspring of women following hypertensive disorders of pregnancy (HDP), including possible links to the causes of long-term cardiovascular disease, the prevalence of which is increased in women who have experienced HDP.
Hinokiflavone Inhibits Growth of Esophageal Squamous Cancer By Inducing Apoptosis via Regulation of the PI3K/AKT/mTOR Signaling Pathway

Background Globally, esophageal cancer ranks as the seventh most common cancer. Esophageal squamous cell carcinoma (ESCC) is one of its major histological types. ESCC accounts for the vast majority of cases in China, and the mortality rate is high. Cisplatin, the standard adjuvant chemotherapy drug for ESCC, has a modest response rate due to the development of drug resistance. Hinokiflavone (HF) is a natural biflavonoid compound with anti-melanoma activity. However, its anti-tumor effect on ESCC and the underlying mechanisms remain largely unknown. Methods The ESCC cell lines KYSE150 and TE14 were used. The cell counting kit-8 assay and flow cytometry analysis, along with colony formation, EdU, wound healing, and Transwell migration assays, were performed to assess cell characteristics (viability, migration, invasion, and apoptosis) following treatment with HF. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), western blotting, and molecular docking were used to investigate the pathways potentially modulated by HF. In vivo anti-tumor effects of HF were also investigated using a mouse xenograft model. Results Our findings revealed that HF inhibited ESCC cell proliferation. Hoechst 33342 staining, annexin V-FITC/PI staining, and western blotting confirmed that HF causes caspase-dependent apoptosis. KEGG pathway enrichment analysis and western blotting indicated that the PI3K/AKT/mTOR pathway played an important role in the process of HF-induced apoptosis. Furthermore, HF effectively impaired the migration and invasion abilities of KYSE150 cells and downregulated the expression of the matrix metalloproteinases (MMP) MMP2 and MMP9. HF inhibited tumor growth and exhibited minimal toxicity in the organs of the KYSE150 xenograft model. Conclusion This is the first study to demonstrate the inhibition of ESCC growth and progression by HF. The underlying mechanism is through blocking the PI3K/AKT/mTOR signaling pathway, thereby inhibiting cell proliferation and inducing apoptosis. HF can be used as a complementary/alternative agent for ESCC therapy.
Burden Imposed by Heterologous Protein Production in Two Major Industrial Yeast Cell Factories: Identifying Sources and Mitigation Strategies

Production of heterologous proteins, especially biopharmaceuticals and industrial enzymes, in living cell factories consumes cellular resources. Such resources are reallocated from normal cellular processes toward production of the heterologous protein that is often of no benefit to the host cell. This competition for resources is a burden to host cells, has a negative impact on cell fitness, and may consequently trigger stress responses. Importantly, this often causes a reduction in final protein titers. Engineering strategies to generate more burden resilient production strains offer sustainable opportunities to increase production and profitability for this growing billion-dollar global industry. We review recently reported impacts of burden derived from resource competition in two commonly used protein-producing yeast cell factories: Saccharomyces cerevisiae and Komagataella phaffii (syn. Pichia pastoris). We dissect possible sources of burden in these organisms, from aspects related to genetic engineering to protein translation and export of soluble protein. We also summarize advances as well as challenges for cell factory design to mitigate burden and increase overall heterologous protein production from metabolic engineering, systems biology, and synthetic biology perspectives. Lastly, future profiling and engineering strategies are highlighted that may lead to constructing robust burden-resistant cell factories. This includes incorporation of systems-level data into mathematical models for rational design and engineering dynamical regulation circuits in production strains.
The Characterization of Structure and Prediction for Aquaporin in Tumour Progression by Machine Learning

Recurrence and new cases of cancer constitute a challenging human health problem. Aquaporins (AQPs) can be expressed in many types of tumours, including the brain, breast, pancreas, colon, skin, ovaries, and lungs, and the histological grade of cancer is positively correlated with AQP expression. Therefore, the identification of aquaporins is an area to explore. Computational tools play an important role in aquaporin identification. In this research, we propose reliable, accurate and automated sequence predictor iAQPs-RF to identify AQPs. In this study, the feature extraction method was 188D (global protein sequence descriptor, GPSD). Six common classifiers, including random forest (RF), NaiveBayes (NB), support vector machine (SVM), XGBoost, logistic regression (LR) and decision tree (DT), were used for AQP classification. The classification results show that the random forest (RF) algorithm is the most suitable machine learning algorithm, and the accuracy was 97.689%. Analysis of Variance (ANOVA) was used to analyse these characteristics. Feature rank based on the ANOVA method and IFS strategy was applied to search for the optimal features. The classification results suggest that the 26th feature (neutral/hydrophobic) and 21st feature (hydrophobic) are the two most powerful and informative features that distinguish AQPs from non-AQPs. Previous studies reported that plasma membrane proteins have hydrophobic characteristics. Aquaporin subcellular localization prediction showed that all aquaporins were plasma membrane proteins with highly conserved transmembrane structures. In addition, the 3D structure of aquaporins was consistent with the localization results. Therefore, these studies confirmed that aquaporins possess hydrophobic properties. Although aquaporins are highly conserved transmembrane structures, the phylogenetic tree shows the diversity of aquaporins during evolution. The PCA showed that positive and negative samples were well separated by 54D features, indicating that the 54D feature can effectively classify aquaporins. The online prediction server is accessible at http://lab.malab. cn/∼acy/iAQP.
Putting an Explanatory Understanding into a Predictive Perspective: An Exemplary Study on School Track Enrollment

Complementing widely used explanatory models in the educational sciences that pinpoint the resources and characteristics for explaining students’ distinct educational transitions, this paper departs from methodological traditions and evaluates the predictive power of established concepts: to what extent can we actually predict school track enrollment based on a plethora of well-known explanatory factors derived from previous research? Predictive models were established using recursive partitioning adopted from machine learning. The basis for the analyses was the unique Zurich Learning Progress Study in Switzerland, a longitudinal study that followed a sample of 2000 students throughout compulsory education. This paper presents an exemplary examination of predictive modeling, and encourages educational sciences in general to explore beyond the horizon of their disciplinary methodological standards, which may help to consider the limits of an exclusive focus on explanatory approaches. The results provide an insight into the predictive capacity of well-established educational measures and concepts in predicting school track enrollment. The results show that there is quite a bit we cannot explain in educational navigation at the very end of elementary education. Yet, predictive misclassifications mainly occur between adjacent school tracks. Very few misclassifications in the future enrollment of academic-track and basic-track students, i.e., those pursuing the most- and least-prestigious tracks, respectively, occur.
A Review of Combined Training Studies in Older Adults According to a New Categorization of Conventional Interventions

Physical and cognitive training are effective to attenuate age-related declines of brain and cognition. Accordingly, interest in interventions that combine physical, motor, and cognitive exercises has recently grown. In the present review, we aimed to determine whether and under which conditions combined training could be more effective than separated cognitive and physical training, thanks to a structured framework build around seven interacting constructs (stimuli, settings, targets, markers, outcomes, moderators, and mechanisms), which collectively afford a global picture of the determining factors of combined training. We concluded that the general principles underlying the effectiveness of combined training were still difficult identify, due to the heterogeneity of the available studies. However, our analysis also suggested that, when they are well-designed and well-conducted, combined training interventions are more effective than separated physical and cognitive training to improve brain and cognition in older adults. Also, we identified still not answered questions, which could be addressed in futures studies. Finally, we showed that the new categorization of combined training could be also applied to review the literature on training with exergames.
Endoplasmic Reticulum Stress: An Emerging Therapeutic Target for Intervertebral Disc Degeneration

Low back pain (LBP) is a global health issue. Intervertebral disc degeneration (IDD) is a major cause of LBP. Although the explicit mechanisms underpinning IDD are unclear, endoplasmic reticulum (ER) stress caused by aberrant unfolded or misfolded proteins may be involved. The accumulation of unfolded/misfolded proteins may result in reduced protein synthesis and promote aberrant protein degradation to recover ER function, a response termed the unfolded protein response. A growing body of literature has demonstrated the potential relationships between ER stress and the pathogenesis of IDD, indicating some promising therapeutic targets. In this review, we summarize the current knowledge regarding the impact of ER stress on the process of IDD, as well as some potential therapeutic strategies for alleviating disc degeneration by targeting different pathways to inhibit ER stress. This review will facilitate understanding the pathogenesis and progress of IDD and highlights potential therapeutic targets for treating this condition.
Expressed Emotion in the Family: A Meta-Analytic Review of Expressed Emotion as a Mechanism of the Transgenerational Transmission of Mental Disorders

Background High Expressed Emotion (HEE) has been identified as a risk factor for the exacerbation and course of mental illness. EE has been investigated as a caregiver's response to an offspring's problem behavior and pathology. The present meta-analysis regards EE from a transgenerational perspective and as one mechanism that might explain the transgenerational transmission of mental disorders. Method We identified a total of 13 studies relying on 16 independent samples of parent-child dyads of parents with a mental illness and healthy controls; these were included in our analysis. Results were synthesized into one effect size per sample; meta-regression on additional effects of parental diagnostic category, child mental illness, and child age were also applied. Results Parents with a mental illness are classified as HEE significantly more often. Effects were established for high criticism, albeit of small size (OR = 1.45), although they become stronger whenever offspring exhibit mental illness themselves (OR = 2.82). Conclusion The current study highlights the dearth of studies on EE in families in which a parent has a mental illness and its effects on their children. Our findings highlight EE as a potential mechanism for attributing the transgenerational transmission of mental disorders, especially for the EE-variable criticism, indicating dysfunctional parent-child interactions. Systematic Review Registration http://www.crd. york.ac. uk/PROSPERO/display_record. php? ID=CRD42019117609, identifier: CRD42019117609.
Re-polarisation of Macrophages Within Collective Tumour Cell Migration: A Multiscale Moving Boundary Approach

Cancer invasion of the surrounding tissue is a multiscale process of collective cell movement that involves not only tumour cells but also other immune cells in the environment, such as the tumour-associated macrophages (TAMs). The heterogeneity of these immune cells, with the two extremes being the pro-inflammatory and anti-tumour M1 cells, and the anti-inflammatory and pro-tumour M2 cells, has a significant impact on cancer invasion as these cells interact in different ways with the tumour cells and with the ExtraCellular Matrix (ECM). Experimental studies have shown that cancer cells co-migrate with TAMs, but the impact of these different TAM sub-populations (which can change their phenotype and re-polarise depending on the microenvironment) on this co-migration is not fully understood. In this study, we extend a previous multi-scale moving boundary mathematical model, by introducing the M1-like macrophages alongside with their exerted multi-scale effects on the tumour invasion process. With the help of this model we investigate numerically the impact of re-polarising the M2 TAMs into the anti-tumoral M1 phenotype and how such a strategy affects the overall tumour progression. In particular, we investigate numerically whether the M2→M1 re-polarisation could depend on time and/or space, and what would be the macroscopic effects of this spatial- and temporal-dependent re-polarisation on tumour invasion.
Preventive Vitamin A Supplementation Improves Striatal Function in 6-Hydroxydopamine Hemiparkinsonian Rats

Background The mechanisms leading to a loss of dopaminergic (DA) neurons from the substantia nigra pars compacta (SNc) in Parkinson's disease (PD) have multifactorial origins. In this context, nutrition is currently investigated as a modifiable environmental factor for the prevention of PD. In particular, initial studies revealed the deleterious consequences of vitamin A signaling failure on dopamine-related motor behaviors. However, the potential of vitamin A supplementation itself to prevent neurodegeneration has not been established yet. Objective The hypothesis tested in this study is that preventive vitamin A supplementation can protect DA neurons in a rat model of PD. Methods The impact of a 5-week preventive supplementation with vitamin A (20 IU/g of diet) was measured on motor and neurobiological alterations induced by 6-hydroxydopamine (6-OHDA) unilateral injections in the striatum of rats. Rotarod, step test and cylinder tests were performed up to 3 weeks after the lesion. Post-mortem analyses (retinol and monoamines dosages, western blots, immunofluorescence) were performed to investigate neurobiological processes. Results Vitamin A supplementation improved voluntary movements in the cylinder test. In 6-OHDA lesioned rats, a marked decrease of dopamine levels in striatum homogenates was measured. Tyrosine hydroxylase labeling in the SNc and in the striatum was significantly decreased by 6-OHDA injection, without effect of vitamin A. By contrast, vitamin A supplementation increased striatal expression of D2 and RXR receptors in the striatum of 6-OHDA lesioned rats. Conclusions Vitamin A supplementation partially alleviates motor alterations and improved striatal function, revealing a possible beneficial preventive approach for PD.
Predicting Dishonesty When the Stakes Are High: Physiologic Responses During Face-to-Face Interactions Identifies Who Reneges on Promises to Cooperate

Trust is risky. The mere perception of strategically deceptive behavior that disguises intent or conveys unreliable information can inhibit cooperation. As gregariously social creatures, human beings would have evolved physiologic mechanisms to identify likely defectors in cooperative tasks, though these mechanisms may not cross into conscious awareness. We examined trust and trustworthiness in an ecological valid manner by (i) studying working-age adults, (ii) who make decisions with meaningful stakes, and (iii) permitting participants to discuss their intentions face-to-face prior to making private decisions. In order to identify why people fulfill or renege on their commitments, we measured neurophysiologic responses in blood and with electrodermal activity while participants interacted. Participants (mean age 32) made decisions in a trust game in which they could earn up to $530. Nearly all interactions produced promises to cooperate, although first decision-makers in the trust game reneged on 30.7% of their promises while second decision-makers reneged on 28%. First decision-makers who reneged on a promise had elevated physiologic stress using two measures (the change in adrenocorticotropin hormone and the change in skin conductance levels) during pre-decision communication compared to those who fulfilled their promises and had increased negative affect after their decisions. Neurophysiologic reactivity predicted who would cooperate or defect with 86% accuracy. While self-serving behavior is not rare, those who exhibit it are stressed and unhappy.
FATE: An Industrial Grade Platform for Collaborative Learning With Data Protection

Collaborative and federated learning has become an emerging solution to many industrial applications where data values from diﬀerent sites are exploit jointly with privacy protection. We introduce FATE, an industrial-grade project that supports enterprises and institutions to build machine learning models collaboratively at large-scale in a distributed manner. FATE supports a variety of secure computation protocols and machine learning algorithms, and features out-of-box usability with end-to-end building modules and visualization tools. Documentations are available at https://github.com/FederatedAI/FATE . Case studies and other information are available at https://www.fedai. org .
Meta-Governance Framework to Guide the Establishment of Mass Collaborative Learning Communities

The application of mass collaboration in different areas of study and work has been increasing over the last few decades. For example, in the education context, this emerging paradigm has opened new opportunities for participatory learning, namely, “mass collaborative learning (MCL)”. The development of such an innovative and complementary method of learning, which can lead to the creation of knowledge-based communities, has helped to reap the benefits of diversity and inclusion in the creation and development of knowledge. In other words, MCL allows for enhanced connectivity among the people involved, providing them with the opportunity to practice learning collectively. Despite recent advances, this area still faces many challenges, such as a lack of common agreement about the main concepts, components, applicable structures, relationships among the participants, as well as applicable assessment systems. From this perspective, this study proposes a meta-governance framework that benefits from various other related ideas, models, and methods that together can better support the implementation, execution, and development of mass collaborative learning communities. The proposed framework was applied to two case-study projects in which vocational education and training respond to the needs of collaborative education–enterprise approaches. It was also further used in an illustration of the MCL community called the “community of cooks”. Results from these application cases are discussed.