Miracle-dz/UniFAR-FTUs huggingface dataset:
Transgenerational effects of egg nutrients on the early development of Chinook salmon (Oncorhynchus tshawytscha) across a thermal gradient

The transgenerational effect of maternal diet, expressed as variation in the composition and quantity of egg nutrients available to offspring during endogenous development (i.e., prior to free-feeding), has the potential to greatly influence the response of offspring phenotypes to varying environmental conditions. For this study, we examined how natural variation in the fatty acid and proximate composition of eggs from three Chinook salmon (Oncorhynchus tshawytscha) populations influenced early development across a thermal gradient using a common garden hatchery experiment. We found that the relative quantity of fat, lean mass, and water in the eggs was similar among populations. However, the fatty acid composition of the eggs differed among all populations. After controlling for egg mass, egg fatty acid and proximate composition influenced hatch length, swim-up length, and hatch to swim-up growth. Importantly, the magnitude and direction of these egg quality effects depended on the population of origin and temperature. Overall, our results demonstrate that natural variation in egg nutrient composition, likely driven by maternal diet, has transgenerational effects on offspring development under varying thermal conditions.
Evaluation of Dittrichia viscosa performance in substrates with moderately low levels of As and Cd contamination

Abstract We evaluated the ability of Dittrichia viscosa to extract cadmium (Cd) and arsenic (As) from agarized substrates with moderately low levels of contamination. This plant species spontaneously colonizes contaminated soils and has already been recognized as suitable for metal phytoremediation. D. viscosa retains As mainly in the roots and translocates it in limited amount to the aerial parts. We compared D. viscosa subpopulations to other plant species (Solalun lycopersicum L., Nicotiana tabacum L. and Daucus carota L.) and observed that their minor cultural needs not always accompanied higher phytoextraction performances. Different subpopulations exhibited different behavior. Based on the results obtained on the analyzed plants, we suggest that D. viscosa is a promising candidate for the phytoextraction of Cd and As from soils with relatively low contamination, cautioning that specific genetic improvements have to be pursued in order to prepare D. viscosa for widespread adoption.
Multiple-Tissue Integrative Transcriptome-Wide Association Studies Discovered New Genes Associated With Amyotrophic Lateral Sclerosis

Genome-wide association studies (GWAS) have identified multiple causal genes associated with amyotrophic lateral sclerosis (ALS); however, the genetic architecture of ALS remains completely unknown and a large number of causal genes have yet been discovered. To full such gap in part, we implemented an integrative analysis of transcriptome-wide association study (TWAS) for ALS to prioritize causal genes with summary statistics from 80,610 European individuals and employed 13 GTEx brain tissues as reference transcriptome panels. The summary-level TWAS analysis with single brain tissue was first undertaken and then a flexible p-value combination strategy, called summary data-based Cauchy Aggregation TWAS (SCAT), was proposed to pool association signals from single-tissue TWAS analysis while protecting against highly positive correlation among tests. Extensive simulations demonstrated SCAT can produce well-calibrated p-value for the control of type I error and was often much more powerful to identify association signals across various scenarios compared with single-tissue TWAS analysis. Using SCAT, we replicated three ALS-associated genes (i.e., ATXN3, SCFD1, and C9orf72) identified in previous GWASs and discovered additional five genes (i.e., SLC9A8, FAM66D, TRIP11, JUP, and RP11-529H20.6) which were not reported before. Furthermore, we discovered the five associations were largely driven by genes themselves and thus might be new genes which were likely related to the risk of ALS. However, further investigations are warranted to verify these results and untangle the pathophysiological function of the genes in developing ALS.
Electroacupuncture Protects Cognition by Regulating Tau Phosphorylation and Glucose Metabolism via the AKT/GSK3β Signaling Pathway in Alzheimer’s Disease Model Mice

Background Alzheimer’s disease (AD) is mainly manifested as a continuous and progressive decline in cognitive ability. Neurofibrillary tangles (NFTs) are pathological hallmarks of AD and due to accumulated phosphorylated Tau. Glycogen synthase kinase-3β (GSK3β), as a major Tau kinase and a downstream target of the serine protein kinase B (AKT) signaling pathway, can regulate Tau phosphorylation in AD. Importantly, the AKT/GSK3β signaling pathway is involved in glucose metabolism, and abnormal glucose metabolism is found in the AD brain. Numerous studies have shown that electroacupuncture (EA), which is thought to be a potential complementary therapeutic approach for AD, can protect cognitive ability to a certain extent. Objective The purpose of this experiment was to investigate whether the protective and beneficial mechanism of EA on cognition was mediated by the AKT/GSK3β signaling pathway, thereby improving glucose metabolism and Tau phosphorylation in the brain. Methods EA was applied to the Baihui (GV20) and Yintang (GV29) acupoints of 6-month-old amyloid precursor protein (APP)/presenilin-1 (PS1) mice for 20 min, and then quickly prick Shuigou (GV26) acupoint. The intervention was performed once every other day for 28 days. The Morris water maze (MWM) test was performed on C57BL/6N (Non-Tg) mice, APP/PS1 (Tg) mice and EA-treated Tg (Tg + EA) mice to evaluate the effect of EA therapy on cognitive function. 18F-FDG positron emission tomography (PET), immunohistochemistry, and western blotting (WB) were used to investigate the possible mechanism underlying the effect of EA on AD. Results EA treatment significantly improved the cognition of APP/PS1 mice and the glucose uptake rate in the hippocampus. Furthermore, EA inhibited the phosphorylation of Tau (Ser199 and Ser202) proteins by inducing AKT (Ser473) and GSK3β (Ser9) phosphorylation. Conclusion These results demonstrate that EA intervention protects cognition by enhancing glucose metabolism and inhibiting abnormal phosphorylation of Tau protein in the AD model mice, and the AKT/GSK3β pathway might play an irreplaceable role in the regulation process.
A Random Shuffle Method to Expand a Narrow Dataset and Overcome the Associated Challenges in a Clinical Study: A Heart Failure Cohort Example

Heart failure (HF) affects at least 26 million people worldwide, so predicting adverse events in HF patients represents a major target of clinical data science. However, achieving large sample sizes sometimes represents a challenge due to difficulties in patient recruiting and long follow-up times, increasing the problem of missing data. To overcome the issue of a narrow dataset cardinality (in a clinical dataset, the cardinality is the number of patients in that dataset), population-enhancing algorithms are therefore crucial. The aim of this study was to design a random shuffle method to enhance the cardinality of an HF dataset while it is statistically legitimate, without the need of specific hypotheses and regression models. The cardinality enhancement was validated against an established random repeated-measures method with regard to the correctness in predicting clinical conditions and endpoints. In particular, machine learning and regression models were employed to highlight the benefits of the enhanced datasets. The proposed random shuffle method was able to enhance the HF dataset cardinality (711 patients before dataset preprocessing) circa 10 times and circa 21 times when followed by a random repeated-measures approach. We believe that the random shuffle method could be used in the cardiovascular field and in other data science problems when missing data and the narrow dataset cardinality represent an issue.
Biological Guided Carbon-Ion Microporous Radiation to Tumor Hypoxia Area Triggers Robust Abscopal Effects as Open Field Radiation

Recently, a growing number of studies focus on partial tumor irradiation to induce the stronger non-target effects. However, the value of partial volume carbon ion radiotherapy (CIRT) targeting hypoxic region of a tumor under imaging guidance as well as its effect of inducing radiation induced abscopal effects (RIAEs) have not been well investigated. Herein, we developed a technique of carbon ion microporous radiation (CI-MPR), guided by 18F-FMISO PET/computerized tomography (CT), for partial volume radiation targeting the hypoxia area of a tumor and investigated its capability of inducing abscopal effects. Tumor-bearing mice were inoculated subcutaneously with breast cancer 4T1 cells into the flanks of both hind legs of mouse. Mice were assigned to three groups: group I: control group with no treatment; group II: carbon ion open field radiation (CI-OFR group) targeting the entire tumor; group III: partial volume carbon ion microporous radiation (CI-MPR group) targeting the hypoxia region. The tumors on the left hind legs of mice were irradiated with single fraction of 20 Gy of CIRT. Mice treated with CI-MPR or CI-OFR showed that significant growth delay on both the irradiated and unirradiated of tumor as compared to the control groups. Tumor regression of left tumor irradiated with CI-OFR was more prominent as compared to the tumor treated with CI-MPR, while the regression of the unirradiated tumor in both CI-MPR and CI-OFR group was similar. Biological-guided CIRT using the newly developed microporous technique targeting tumor hypoxia region could induce robust abscopal effects similar to CIRT covering the entire tumor.
Extended Pelagic Life in a Bathybenthic Octopus

Planktonic stages of benthic octopuses can reach relatively large sizes in some species, usually in oceanic, epipelagic waters while living as part of the macroplankton. These young octopuses appear to delay settlement on the seabed for an undetermined period of time that is probably longer than for those octopus paralarvae living in coastal, neritic waters. The reason for this delay is unknown and existing information about their biology is very scarce. Here we report on the presence of juvenile and subadult forms of the bathybenthic octopus Pteroctopus tetracirrhus in oceanic waters of the South and North Atlantic and its association with the pyrosomid species Pyrosoma atlanticum, apparently used by the octopus as a refuge or shelter. The relatively large size of the P. tetracirrhus living in oceanic waters as the individuals reported here, together with the morphological characteristics of this bathybenthic species including its gelatinous body, minute suckers embedded in swollen skin and the deep interbrachial web, indicates that P. tetracirrhus may be considered a model of a transitional octopus species that is colonizing the pelagic environment by avoiding descending to the bathyal benthos. This process seems to occur in the same way as in the supposed origin of the ctenoglossan holopelagic octopods of the families Amphitretidae, Bolitaenidae, and Vitreledonellidae, which have arisen via neoteny from the planktonic paralarval stages of benthic octopuses.
Incorporating a Fresh Mixed Annual Ryegrass and Berseem Clover Forage Into the Winter Diet of Dairy Cows Resulted in Reduced Milk Yield, but Reduced Nitrogen Excretion and Reduced Methane Yield

The winter diet of dairy cows in Mediterranean climate regions is usually a total mixed ration with a base of conserved summer crops such as corn silage and alfalfa hay. However, there is increased labor and financial cost related to this kind of feeding, which could be reduced if fresh forages were used in place of some of the conserved forage in the cow diet. The objective of our study was to evaluate the effect of including fresh mixed annual ryegrass and berseem clover into the diet of dairy cows on milk, nitrogen utilization, and methane emission. Twenty-four lactating dairy cows were split into two groups and offered either a diet similar to that usually offered to the cows (CON) or one where a mixture of fresh annual ryegrass and berseem clover was used to partially substitute the corn silage and alfalfa hay in the diet (MIX). Milk yield was recorded automatically, and methane emissions were estimated using the SF6 tracer technique. The MIX diet had lower crude protein concentration (148 vs. 170 g/kg DM) but higher DM digestibility (81.6 vs. 78.6%) than the CON diet. Compared to the cows offered the CON diet, milk yield was reduced when cows were fed the MIX diet (36.4 vs. 31.9 kg/d), but methane emissions (381 vs. 332 g/d) and nitrogen excretion were also reduced (238 vs. 180 g/d). Nitrogen use efficiency was unaffected (30.8%). In addition, milk from cows fed the MIX diet had a fatty acid profile considered to be more beneficial to human health than that of the milk from cows fed the CON diet. Increasing the protein concentration in the MIX diet, either by direct supplementation or increasing the proportion of legume in the mixed herbage, could overcome the reduction on milk and positively affect methane emission and N use efficiency.
AI-Blue-Carba: A Rapid and Improved Carbapenemase Producer Detection Assay Using Blue-Carba With Deep Learning

A rapid and accurate detection of carbapenemase-producing Gram-negative bacteria (CPGNB) has an immediate demand in the clinic. Here, we developed and validated a method for rapid detection of CPGNB using Blue-Carba combined with deep learning (designated as AI-Blue-Carba). The optimum bacterial suspension concentration and detection wavelength were determined using a Multimode Plate Reader and integrated with deep learning modeling. We examined 160 carbapenemase-producing and non-carbapenemase-producing bacteria using the Blue-Carba test and a series of time and optical density values were obtained to build and validate the machine models. Subsequently, a simplified model was re-evaluated by descending the dataset from 13 time points to 2 time points. The best suitable bacterial concentration was determined to be 1.5 optical density (OD) and the optimum detection wavelength for AI-Blue-Carba was set as 615 nm. Among the 2 models (LRM and LSTM), the LSTM model generated the higher ROC-AUC value. Moreover, the simplified LSTM model trained by short time points (0–15 min) did not impair the accuracy of LSTM model. Compared with the traditional Blue-Carba, the AI-Blue-Carba method has a sensitivity of 95.3% and a specificity of 95.7% at 15 min, which is a rapid and accurate method to detect CPGNB.
Gender Difference in the Prevalence of Insomnia: A Meta-Analysis of Observational Studies

Objective: Insomnia is a major health challenge in the general population, but the results of the gender differences in the epidemiology of insomnia have been mixed. This is a meta-analysis to examine the gender difference in the prevalence of insomnia among the general population. Methods:Two reviewers independently searched relevant publications in PubMed, EMBASE, PsycINFO, Web of Science from their inception to 16 April 2019. Studies that reported the gender-based prevalence of insomnia according to the international diagnostic criteria were included for analyses using the random-effects model. Results:Eventually 13 articles were included in the meta-analysis. The pooled prevalence of insomnia in the general population was 22.0% [n = 22,980, 95% confidence interval (CI): 17.0–28.0%], and females had a significantly higher prevalence of insomnia compared with males (OR = 1.58, 95% CI: 1.35, 1.85, Z = 5.63, p < 0.0001). Subgroup analyses showed that greater gender difference was associated with the use of case-control study design and consecutive sampling method. Meta-regression analyses also revealed that higher proportion of females and better study quality were significantly associated with greater gender difference. Conclusions:This meta-analysis found that the prevalence of insomnia in females was significantly higher than males in the included studies. Due to the negative effects of insomnia on health, regular screening, and effective interventions should be implemented in the general population particularly for females.
Mechanobiology of Epithelia From the Perspective of Extracellular Matrix Heterogeneity

Understanding the complexity of the extracellular matrix (ECM) and its variability is a necessary step on the way to engineering functional (bio)materials that serve their respective purposes while relying on cell adhesion. Upon adhesion, cells receive messages which contain both biochemical and mechanical information. The main focus of mechanobiology lies in investigating the role of this mechanical coordination in regulating cellular behavior. In recent years, this focus has been additionally shifted toward cell collectives and the understanding of their behavior as a whole mechanical continuum. Collective cell phenomena very much apply to epithelia which are either simple cell-sheets or more complex three-dimensional structures. Researchers have been mostly using the organization of monolayers to observe their collective behavior in well-defined experimental setups in vitro. Nevertheless, recent studies have also reported the impact of ECM remodeling on epithelial morphogenesis in vivo. These new concepts, combined with the knowledge of ECM biochemical complexity are of key importance for engineering new interactive materials to support both epithelial remodeling and homeostasis. In this review, we summarize the structure and heterogeneity of the ECM before discussing its impact on the epithelial mechanobiology.
Deficits in Prediction Ability Trigger Asymmetries in Behavior and Internal Representation

Predictive coding is an emerging theoretical framework for explaining human perception and behavior. The proposed underlying mechanism is that signals encoding sensory information are integrated with signals representing the brain's prior prediction. Imbalance or aberrant precision of the two signals has been suggested as a potential cause for developmental disorders. Computational models may help to understand how such aberrant tendencies in prediction affect development and behavior. In this study, we used a computational approach to test the hypothesis that parametric modifications of prediction ability generate a spectrum of network representations that might reflect the spectrum from typical development to potential disorders. Specifically, we trained recurrent neural networks to draw simple figure trajectories, and found that altering reliance on sensory and prior signals during learning affected the networks' performance and the emergent internal representation. Specifically, both overly strong or weak reliance on predictions impaired network representations, but drawing performance did not always reflect this impairment. Thus, aberrant predictive coding causes asymmetries in behavioral output and internal representations. We discuss the findings in the context of autism spectrum disorder, where we hypothesize that too weak or too strong a reliance on predictions may be the cause of the large diversity of symptoms associated with this disorder.
SSVEP BCI and Eye Tracking Use by Individuals With Late-Stage ALS and Visual Impairments

Access to communication is critical for individuals with late-stage amyotrophic lateral sclerosis (ALS) and minimal volitional movement, but they sometimes present with concomitant visual or ocular motility impairments that affect their performance with eye tracking or visual brain-computer interface (BCI) systems. In this study, we explored the use of modified eye tracking and steady state visual evoked potential (SSVEP) BCI, in combination with the Shuffle Speller typing interface, for this population. Two participants with late-stage ALS, visual impairments, and minimal volitional movement completed a single-case experimental research design comparing copy-spelling performance with three different typing systems: (1) commercially available eye tracking communication software, (2) Shuffle Speller with modified eye tracking, and (3) Shuffle Speller with SSVEP BCI. Participant 1 was unable to type any correct characters with the commercial system, but achieved accuracies of up to 50% with Shuffle Speller eye tracking and 89% with Shuffle Speller BCI. Participant 2 also had higher maximum accuracies with Shuffle Speller, typing with up to 63% accuracy with eye tracking and 100% accuracy with BCI. However, participants’ typing accuracy for both Shuffle Speller conditions was highly variable, particularly in the BCI condition. Both the Shuffle Speller interface and SSVEP BCI input show promise for improving typing performance for people with late-stage ALS. Further development of innovative BCI systems for this population is needed.
Investigation of Clay Type on Low Salinity Water Flooding Using a Glass Micromodel

Clay minerals are usually regarded as an important factor affecting the results of low salinity water (LSW) flooding. However, experiments on clay minerals are mainly in qualitative stage, the mechanism of clay minerals has not been studied completely. In this paper, Zeta potential of four kinds of clay minerals (montmorillonite; chlorite; illite; kaolinite) in different brine was measured, microscopic models of these clay minerals were made to measured wetting angle in different brine, and montmorillonite and kaolinite were chosen to conduct microscopic displacement experiments through customized micro-glass etching models. From experiment results, the following conclusions can be get: 1). With the decrease of salinity of injected water, the negative zeta potential of clay minerals increases and the wetting angle decreases. 2). Clay minerals are more sensitive to monovalent Na+ than bivalent Ca2+. 3). The results of microscopic experiments show that LSW can effectively improve oil recovery, whether kaolinite or montmorillonite. The recovery of montmorillonite is better with a relatively high salinity of LSW and kaolinite is better with a relatively low salinity of LSW. The mechanism of LSW improves kaolinite recovery factor is the change of wettability while that of montmorillonite is the increase of water phase wettability. However, a lot of droplet-like residual oil cannot be displaced in the montmorillonite throat. In filed production, both kaolinite-rich and montmorillonite-rich reservoirs are suitable for LSW flooding to improve oil recovery. However, for kaolinite reservoirs, a lower salinity of injected water would produce a better result, while for montmorillonite reservoirs, residual oil droplets in the throat are noteworthy.
Functional Characterization of the Cnidarian Antiviral Immune Response Reveals Ancestral Complexity

Animals developed a broad repertoire of innate immune sensors and downstream effector cascades for defense against RNA viruses. Yet, this system highly varies between different bilaterian animals, masking its ancestral state. In this study we aimed to characterize the antiviral immune response of the cnidarian Nematostella vectensis and decipher the function of the retinoic acid-inducible gene I-like receptors (RLRs) known to detect viral double-stranded RNA (dsRNA) in bilaterians, but activate different antiviral pathways in vertebrates and nematodes. We show that a mimic of long viral dsRNA triggers a complex antiviral immune response bearing features distinctive for both vertebrate and invertebrate systems. Furthermore, the results of affinity assays and knockdown experiments provide functional evidence for the conserved role of RLRs in initiating immune response to dsRNA that originated before the cnidarian-bilaterian split and lay a strong foundation for future research on the evolution of the immune responses to RNA viruses.