Miracle-dz/UniFAR-FTUs huggingface dataset:
Soluble mediators of innate immunity in annelids and bivalve mollusks: A mini-review

Annelids and mollusks, both in the superphylum of Lophotrochozoa (Bilateria), are important ecological groups, widespread in soil, freshwater, estuarine, and marine ecosystems. Like all invertebrates, they lack adaptive immunity; however, they are endowed with an effective and complex innate immune system (humoral and cellular defenses) similar to vertebrates. The lack of acquired immunity and the capacity to form antibodies does not mean a lack of specificity: invertebrates have evolved genetic mechanisms capable of producing thousands of different proteins from a small number of genes, providing high variability and diversity of immune effector molecules just like their vertebrate counterparts. This diversity allows annelids and mollusks to recognize and eliminate a wide range of pathogens and respond to environmental stressors. Effector molecules can kill invading microbes, reduce their pathogenicity, or regulate the immune response at cellular and systemic levels. Annelids and mollusks are “typical” lophotrochozoan protostome since both groups include aquatic species with trochophore larvae, which unite both taxa in a common ancestry. Moreover, despite their extensive utilization in immunological research, no model systems are available as there are with other invertebrate groups, such as Caenorhabditis elegans or Drosophila melanogaster, and thus, their immune potential is largely unexplored. In this work, we focus on two classes of key soluble mediators of immunity, i.e., antimicrobial peptides (AMPs) and cytokines, in annelids and bivalves, which are the most studied mollusks. The mediators have been of interest from their first identification to recent advances in molecular studies that clarified their role in the immune response.
Co-targeting triple-negative breast cancer cells and endothelial cells by metronomic chemotherapy inhibits cell regrowth and migration via downregulation of the FAK/VEGFR2/VEGF axis and autophagy/apoptosis activation

High-dose standard-of-care chemotherapy is the only option for triple-negative breast cancer (TNBC) patients, which eventually die due to metastatic tumors. Recently, metronomic chemotherapy (mCHT) showed advantages in treating TNBCs leading us to investigate the anti-metastatic and anti-angiogenic potential of metronomic 5-Fluorouracil plus Vinorelbine (5-FU+VNR) on endothelial cells (ECs) and TNBCs in comparison to standard treatment (STD). We found that 10-fold lower doses of 5-FU+VNR given mCHT vs. STD inhibits cell proliferation and survival of ECs and TNBC cells. Both schedules strongly affect ECs migration and invasion, but in TNBC cells mCHT is significantly more effective than STD in impairing cell migration and invasion. The two treatments disrupt FAK/VEGFR/VEGF signaling in both ECs and TNBC cells. mCHT, and to a much lesser extent STD treatment, induces apoptosis in ECs, whereas it switches the route of cell death from apoptosis (as induced by STD) to autophagy in TNBC cells. mCHT-treated TNBCs-derived conditioned medium also strongly affects ECs’ migration, modulates different angiogenesis-associated proteins, and hampers angiogenesis in matrix sponge in vivo. In conclusion, mCHT administration of 5-FU+VNR is more effective than STD schedule in controlling cell proliferation/survival and migration/invasion of both ECs and TNBC cells and has a strong anti-angiogenic effect. Our data suggest that the stabilization of tumor growth observed in TNBC patients treated with mCHT therapy schedule is likely due not only to direct cytotoxic effects but also to anti-metastatic and anti-angiogenic effects.
Editorial: Affective self-regulation and mental disorders: A transdiagnostic disposition in psychopathology

COPYRIGHT © 2022 Hairston. 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: A ective self-regulation and mental disorders: A transdiagnostic disposition in psychopathology
Precision caffeine therapy for apnea of prematurity and circadian rhythms: New possibilities open up

Caffeine is the globally consumed psychoactive substance and the drug of choice for the treatment of apnea of prematurity (AOP), but its therapeutic effects are highly variable among preterm infants. Many of the molecular underpinnings of the marked individual response have remained elusive yet. Interestingly, the significant association between Clock gene polymorphisms and the response to caffeine therapy offers an opportunity to advance our understanding of potential mechanistic pathways. In this review, we delineate the functions and mechanisms of human circadian rhythms. An up-to-date advance of the formation and ontogeny of human circadian rhythms during the perinatal period are concisely discussed. Specially, we summarize and discuss the characteristics of circadian rhythms in preterm infants. Second, we discuss the role of caffeine consumption on the circadian rhythms in animal models and human, especially in neonates and preterm infants. Finally, we postulate how circadian-based therapeutic initiatives could open new possibilities to promote precision caffeine therapy for the AOP management in preterm infants.
The role of growth hormone in assisted reproduction

In contemporary ART, the use of “add-ons” during ovarian stimulation has increased, especially in poor responders. Growth Hormone (GH) is an adjunctive therapy that has been studied extensively in the translational and clinical setting, with an ongoing scientific debate over its effectiveness and optimal use. In this review, we aim to provide an overview of the physiologic basis for the use of GH in ART, and to summarize the latest evidence regarding its clinical use, primarily as an adjunct to ovarian stimulation, but also in the IVF lab and with regards to its effects on the endometrium.
The association between physical activity and mental health in medical postgraduates in China during COVID-19 pandemic

Background Chinese medical postgraduates (CMPs) are a special subpopulation that has a great risk of mental health due to high workload, and heavy academic and clinical pressure during the COVID-19 pandemic. Physical activity has been demonstrated to be positive for the mental health of human being. However, little is known about the risks to mental health among CMPs as well as the potential effects of physical activity on mental health in CMPs during the COVID-19 pandemic. Aims In the present study, the aims are to (1) investigate the levels of PA and mental health that CMPs had; (2) to identify the potential factors that contribute to mental health among CMPs; (3) to explore the potential effects of PA on the mental health in CMPs. Methods The survey was conducted online across 25 provinces of mainland China in 28 medical colleges or universities with structured questionnaires. Physical Activity Rating Scale-3 (PARS-3), Depression, Anxiety, Stress Scales (DASS-21), and General Self-Efficacy Scale (GSES) were employed to assess the levels of PA, Negative emotional states, and self-efficacy of the participants, respectively. Resilience was evaluated using Connor-Davidson Resilience Scale (CD-RISC). The chi-square and Wilcoxon rank-sum tests were used to compare inter-group differences in demographic data and mental health conditions. Spearman's rank correlation test and partial correlation analysis were used to assess associations between exercise scores and mental health. Results We found some socio-demographic variables such as the location, education levels of parents and the levels of degrees they are training had potential effects on outcomes of mental health among 2,217 CMPs (P < 0.05); furthermore, we also found that PA was negatively correlated with the negative emotion (r = −0.045, P < 0.05) such as depression (r = −0.052, P < 0.05), anxiety and stress, (r = −0.051, P < 0.05) but positively correlated with the self-efficacy (r = 0.143, P < 0.001) and resilience (r = 0.192, P < 0.001) among Chinese postgraduate medical students. Conclusion We concluded that for Chinese postgraduate medical students, taking part in physical activity would depress negative emotions such as depression, anxiety, and stress, but improve their self-efficacy and resilience, which will benefit them in completing their studies and training.
Nitrogen-loss and associated microbial communities in sediments from the Yangtze Estuary and adjacent sea

Introduction Denitrification and anammox play the crucial role for N removal processes in coastal ecosystems, but the ecological distribution of denitrifying and anammox microorganisms and their N removal rates in the Yangtze Estuary and its adjacent sea are required in-depth analysis. Methods Here, we utilized high-throughput sequencing, qPCR, and 15N isotope to reveal the community structure and function of denitrifying and anammox microorganisms in the surface sediments from Yangtze Estuary and adjacent sea. Results The results suggested that the gene abundances of nirS and nirK for denitrifiers were higher than AMX 16S rRNA for anammox bacteria. The genera composition of nirS- and nirK-encoding denitrifiers communities showed different distribution patterns. Furthermore, Candidatus Anammoximicrobium dominated the anammox community, implying the anammox oxidation capacity of the other genera should be noted in marine sediments. Discussion Compared to anammox, denitrification was the dominant contributor of nitrogen removal process and contributed 73.5% on average. The sediment Chla was the key factor to regulate denitrification and anammox rates, indicating the fresh organic matter was more labile and easier to be utilized by NOx− removal processes.
An alternative method for computing mean and covariance matrix of some multivariate distributions

Computing the mean and covariance matrix of some multivariate distributions, in particular, multivariate normal distribution and Wishart distribution are considered in this article. It involves a matrix transformation of the normal random vector into a random vector whose components are independent normal random variables, and then integrating univariate integrals for computing the mean and covariance matrix of a multivariate normal distribution. Moment generating function technique is used for computing the mean and covariances between the elements of a Wishart matrix. In this article, an alternative method that uses matrix differentiation and differentiation of the determinant of a matrix is presented. This method does not involve any integration.
The contour effect: Differences in the aesthetic preference and stress response to photo-realistic living environments

The interest in the response to contours has recently re-emerged, with various studies suggesting a universal preference for curved over angular stimuli. Although no consensus has yet been reached on the reasons for this preference, similar effects have been proposed in interior environments. However, the scarcely available research primarily depends on schematic or unmatched stimuli and faces heterogeneity in the reported results. In a within-subject design, we investigated the claimed contour effect in photo-realistic indoor environments using stimulus material previously tested in virtual reality (VR). A total of 198 online participants rated 20 living room images, exclusively manipulated on the contours (angular vs. curved) and style (modern vs. classic) levels. The scales represented aesthetic (beauty and liking) and stress (rest and stress) responses. Beyond our main focus on contours, we additionally examined style and sex effects to account for potential interactions. Results revealed a significant main effect of contours on both aesthetic (η2g = 1–2%) and stress (η2g = 8–12%) ratings. As expected, images of curved (vs. angular) contours scored higher on beauty, liking, and rest scales, and lower on stress. Regarding interactions with style, curvature was aesthetically preferred over angularity only within images depicting modern interiors, however, its positive effect on stress responses remained significant irrespective of style. Furthermore, we observed sex differences in aesthetic but not in stress evaluations, with curvature preference only found in participants who indicated female as their sex. In sum, our study primarily confirms positive effects of curvature, however, with multiple layers. First, the impact on aesthetic preference seems to be influenced by individual and contextual factors. Second, in terms of stress responses, which might be especially relevant for designs intended to promote mental-health, the consistent effects suggest a more generalizable, potentially biophilic characteristic of curves. To the best of our knowledge, this is the first study to demonstrate these effects in fully-matched, photo-realistic, and multi-perspective interior design stimuli. From the background of a previous VR trial from our research group, whereby the same rooms did not elicit any differences, our findings propose that static vs. immersive presentations might yield different results in the response to contours.
The increasing incidence and high body mass index-related burden of gallbladder and biliary diseases–A results from global burden of disease study 2019

Background Gallbladder and biliary diseases are common gastrointestinal conditions associated with huge socioeconomic costs and are considered risk factors for cardiovascular diseases and digestive system cancers. The prevalence and incidence of gallbladder and biliary diseases have not received enough attention from 1990 to 2019. Several non-communicable diseases were associated with the incidence of gallbladder and biliary diseases. It is necessary to clarify the change in the incidence and disability burden of gallbladder and biliary diseases worldwide. Methods Data on high body mass index (BMI)-related disease burden and incidence, years of life lost prematurely, and years lived with disability (YLDs) due to gallbladder and biliary diseases were obtained from the Global Burden of Disease 2019. The estimated annual percentage change was calculated to qualify the gallbladder and biliary disease burden change. Results The global age-standardized incidence rate has increased from 585.35 per 100,000 (95% UI: 506.05–679.86) in 1990 to 634.32 per 100,000 (95% UI: 540.21–742.93) in 2019. And the increase in incidence was positively correlated with rising high BMI-related summary exposure value. The high BMI-related YLDs of gallbladder and biliary diseases have increased worldwide over time. Globally, the 25–49 age group suffered a rapid rise in incidence and high BMI attributable to the YLDs rate of gallbladder and biliary diseases. Conclusion The global incidence and high BMI-related YLDs of gallbladder and biliary diseases remain prominent to increase over the past 30 years. Notably, the incidence and high BMI-related YLDs among people aged 25–49 years have rapidly increased over time. Therefore, high BMI should be emphasized in strategic priorities for controlling gallbladder and biliary diseases.
Associations of metal exposure with hyperuricemia and gout in general adults

Background Epidemiological evidence of the associations between metal exposure and gout-related outcomes (including serum uric acid [SUA], hyperuricemia and gout) is scarce. The aim of the study is to investigate the associations of metal exposure with SUA, hyperuricemia and gout in general adults. Methods In this study, the exposure to five blood metals (mercury, manganese, lead, cadmium and selenium) of general adults was analyzed based on the National Health and Nutrition Examination Survey (NHANES) from 2011 to 2018 (n = 14,871). Linear, logistic and weighted quantile sum (WQS) regression models were applied to examine the associations of blood metals with gout-related outcomes. Possible dose-response relationships were analyzed through restricted cubic spline regression. Results Compared with the lowest quartile of blood metals, mercury (quartile 2 and 4), lead (quartile 2, 3, and 4) and selenium (quartile 2 and 4) were found to be positively correlated with SUA and hyperuricemia. Higher levels of mercury and lead were associated with gout, but only those in the fourth quartile had statistical significance (OR [95%CI]: 1.39 [1.10-1.75] and 1.905 [1.41-2.57]) respectively). The WQS index of the blood metals was independently correlated with SUA (β [95%CI]: 0.17 [0.13-0.20]), hyperuricemia (OR [95%CI]: 1.29 [1.16-1.42]) and gout (OR [95%CI]: 1.35 [1.15-1.58]). Among them, lead was the most heavily weighted component (weight = 0.589 for SUA, 0.482 for hyperuricemia, and 0.527 for gout). In addition, restricted cubic spline regression models showed a linear association of lead with the prevalence of hyperuricemia and gout. Conclusion Our results suggested that blood metal mixtures were positively associated with gout-related outcomes, with the greatest effect coming from lead.
Multimode minimum uncertainty squeezed states

The concept of the single mode 'squeezed state', a minimum uncertainty state with reduced fluctuations in either of the two canonically conjugate variables, is generalised to an arbitrary number of modes. It is shown that the n-mode squeezed states are a subset of the generalised coherent states of Sp(2n:R).
Predicting genetic interactions, cell line dependencies and drug sensitivities with variational graph auto-encoder

Large scale cancer genomics data provide crucial information about the disease and reveal points of intervention. However, systematic data have been collected in specific cell lines and their collection is laborious and costly. Hence, there is a need to develop computational models that can predict such data for any genomic context of interest. Here we develop novel models that build on variational graph auto-encoders and can integrate diverse types of data to provide high quality predictions of genetic interactions, cell line dependencies and drug sensitivities, outperforming previous methods. Our models, data and implementation are available at: https://github.com/aijag/drugGraphNet.
Transcriptomic and physiological analysis reveals the possible mechanism of ultrasound inhibiting strawberry (Fragaria × ananassa Duch.) postharvest softening

Ultrasound effectively inhibited strawberry softening but the mechanism was not clear. In this study, physical data including firmness, soluble pectin (SP) contents, pectin esterase (PE), polygalacturonase (PG) activity and transcriptome sequencing data were analyzed to explore the mechanism of strawberry response to ultrasonic treatment. After 24 days storage, the firmness reduction rate and soluble contents (SP) increased rate of the strawberry treated with ultrasound (25 kHz, 0.15 W/cm2) for 3 min decreased 41.70 and 63.12% compared with the control, respectively. While the PG and PE enzyme activities of ultrasound-treated strawberries were significantly lower than control after storage for 18 days. A total of 1,905 diferentially expressed genes (DEGs) were identified between ultrasound-treated and control, with 714 genes upregulated and 1,254 genes downregulated, including 56 genes in reactive oxygen species (ROS), auxin (AUX), ethylene (ETH) and jasmonic acid (JA) signaling pathways. At 0 h, 15 genes including LOX, JMT, ARP, SKP, SAUR, IAA, ARF, and LAX were significantly upregulated compared with the control group, which means reactive oxygen specie, auxin, ethylene and jasmonic acid-mediated signaling pathway respond to ultrasound immediately. ERF109, ERF110, and ACS1_2_6 downregulated before 2 days storage indicated ethylene signaling pathway was inhibited, while after 2 days, 9 genes including ERF027, ERF109, and ERF110 were significantly upregulated indicating that the response of the ethylene signaling pathway was lagging. Therefore, in strawberry ultrasound enhanced ROS scavenging and activated JA biosynthesis, which acts as a signal for delaying the activation of ET signaling pathway, thus suppressing the activity of pectin-degrading enzymes PE and PG, and ultimately inhibiting postharvest softening.
Regional organic matter and mineral dust are the main components of atmospheric aerosols over the Nam Co station on the central Tibetan Plateau in summer

The transport of air pollutants from areas surrounding the Tibetan Plateau (TP) has recently been studied. However, the major sources of atmospheric total suspended particulate matter (TSP) on the central TP remain unclear due to a lack of in-situ observations on aerosol physico-chemical properties. Therefore, to quantitatively investigate the physico-chemical properties and reveal the major sources of atmospheric aerosols, a comprehensive field campaign was conducted at the site of Nam Co from August 6 to September 11, 2020. Aerosol loading was low during the campaign with average TSP mass concentration, scattering coefficient at 550 nm, and absorption coefficient at 670 nm being 10.11 ± 5.36 μg m−3, 1.71 ± 1.36 Mm−1, and 0.26 ± 0.20 Mm−1, respectively. Organic matter (63.9%) and mineral dust (27.8%) accounted for most of the TSP mass concentrations. The average scattering Ångström exponent of 0.59 ± 0.14 reflected the influence of mineral dust, and the elemental fractions and the results of enrichment factor illustrated that crustal materials were the main contributors of mineral dust. The organic to elemental carbon ratio of 15.33 is probably caused by the aging that occurs during the transport of aerosols. The strong correlation between organic carbon and Ca2+ and the results of the electron microscopy analysis of single particles indicated that organic carbon and mineral dust had the same sources; however, the weak relation between mineral dust and wind speed indicated that local wind erosion was not the main contributor to the mineral dust. The potential source contribution function further illustrated that the summertime TSP in the central TP was mainly characterized by background biomass and mineral dust aerosols originating regionally from the ground within the TP.