Miracle-dz/UniFAR-FTUs huggingface dataset:
The enemy of my enemy is my friend: Nematode infection of pollinating and non-pollinating fig wasps has net benefits for the fig-fig wasp pollination mutualism

Mutualistic associations between species pairs are ubiquitous in nature but are also components of broader organismal community networks. These community-level associations have shaped the evolution of individual mutualisms through interspecific interactions ranging from secondarily mutualistic to intensely antagonistic. Our understanding of this complex context remains limited because identifying species interacting with focal mutualists and assessing their associated fitness benefits and costs is difficult, especially over space and through time. Here, we focus on a community comprised of a fig and fig wasp mutualist, eight non-pollinating fig wasp (NPFW) commensals/antagonists, and a nematode previously believed to be associated only with the pollinator wasp mutualist. Through repeated sampling and field experiments, we identified that all NPFWs are targets for infection by this nematode. Further, this infection can impact NPFWs more severely than either mutualistic partner, suggesting a novel role of density-dependent facultative mutualism between fig and wasp mutualists and the nematode.
Characteristics of Microsatellites in Brassica rapa Genome and their Potential Utilization for Comparative Genomics in Cruciferae

We evaluated the nature of microsatellites in Brassica rapa in order to develop an informative and reliable DNA marker system for Brassica genetic analysis. Microsatellites were isolated by hybridization screening of an unconcentrated small-insert genomic library using tri-and dinucleotide probes. Of 45,000 clones screened, 210 had repeat sequences, in which 228 microsatellites were identified. The most frequent microsatellite motif was (GA)n at a frequency of one every 4.8 × 105 bp, followed by (CAA)n at one every 5.0 × 105 bp. The frequency of the tri- and dinucleotide microsatellites throughout the B. rapa genome was estimated to be one every 120 Kb. The number of repeats and the polymorphism information content of the dinucleotide microsatellites were higher than those of the trinucleotide microsatellites. More than 90 % of the primer pairs successfully amplified the corresponding microsatellite regions in other Brassica species. Furthermore, a considerable portion of them could be used in other Cruciferous species, 78.5 % in Raphanus sativus, 68.6 % in Sinapis alba and 39.8 % in Arabidopsis thaliana. Based on these results, we concluded that B. rapa microsatellites have a high potential for the development of DNA markers that could contribute to the genetic analysis of Brassica and other Cruciferae.
Applicability of ERA-Interim High-resolution Significant Wave Height Data in Global Sea Areas

ABSTRACT Wan, Y. ; Zhang, X. ; Dai, Y. ; Li, W. ; Li, L. , and Qu, X. , 2020. Applicability of ERA-Interim high-resolution significant wave height data in global sea areas. In: Zheng, C.W. ; Wang, Q. ; Zhan, C. , and Yang, S.B. (eds.), Air-Sea Interaction and Coastal Environments of the Maritime and Polar Silk Roads. Journal of Coastal Research, Special Issue No. 99, pp. 1-8. Coconut Creek (Florida), ISSN 0749-0208. In this paper, ERA-Interim high-resolution ocean wave reanalysis data provided by the European Center for Medium-range Weather Forecasts (ECMWF) are matched with time-space data from buoys in the China Sea, the United States East and West Coast, the Central Pacific Ocean and European seas. Taking the significant wave height (SWH) as an example, ERA-Interim wave field data are verified, and their applicabilities in sea areas around the world are analyzed. The results show that the means of the correlation coefficients (CCs) obtained by fitting in each sea area are greater than 0.7. Furthermore, in all areas except for the European waters, the root mean square errors (RMSEs) are less than 0.4 m. The linear regression method is used to correct the data in the European sea area, and the corrected results are significantly better than the uncorrected results. The corrected CC is reduced by 3.23% compared to the uncorrected CC. The corrected RMSE is increased by 24.24% compared to the uncorrected RMSE. This shows that corrected data better reflect the real situation of the ocean surface than uncorrected data.
Pain- and Fatigue-Related Functional and Structural Changes in Ankylosing Spondylitis: An fRMI Study

Background: Chronic pain and fatigue are two cardinal features of ankylosing spondylitis (AS) and how to effectively treat these conditions continues to be a challenge. The underlying mechanisms and the relationship between AS-related pain and fatigue remain poorly understood. The present study was conducted, therefore, to explore the brain functional and structural changes associated with pain and fatigue in AS. Methods: A total of 65 AS patients (48 men and 17 women; 32.33 ± 8.6 years) and 53 age- and sex-matched controls were enrolled in the study. The patients underwent clinical assessment based on Total Back Pain scores, Fatigue Severity Scale, Bath Ankylosing Spondylitis Disease Activity Index, (BASDAI), high-sensitivity C-reactive Protein (hsCRP), erythrocyte sedimentation rate (ESR), and Beck Depression Inventory (BDI). Using 3T magnetic resonance imaging (3T-MRI), we analyzed the brain functional (connectivity and nodal properties) and structural (covariance and gray matter volumes) differences between AS patients and controls. Furthermore, we extracted the values of the significantly changed regions in the AS cohort and explored their association with pain and fatigue. Results: In AS patients, there were functional and structural abnormalities distributed in the default mode network (DMN), salience network (SN), sensory/somatomotor network (SMN), dorsal attention network (DAN), task control network (TCN), and visual network, and some regions showed both types of changes. Among these, the functional connectivity (FC) between the left insula and medial prefrontal cortex, the betweenness centrality of the left medial prefrontal cortex and the gray matter volume of the right putamen tracked both pain and fatigue. In addition, pain was related to within-DMN FC disruption and nodal function / gray matter volumes changes in DMN, SN, and the visual network, while fatigue mainly involved the SMN, DAN, and TCN. Moreover, certain changes were also related to BASDAI and inflammation level. Conclusion: This study offers new insights into understanding the neural mechanism of AS-related pain and fatigue, and could help to stratify patients based on the correlation features and ultimately move towards a personalized therapy.
Experiential Neurorehabilitation: A Neurological Therapy Based on the Enactive Paradigm

With the arrival of the cognitive paradigm during the latter half of the last century, the theoretical and scientific bases of neurorehabilitation have been linked to the knowledge developed in cognitive neuropsychology and cognitive neuroscience. Although the knowledge generated by these disciplines has made relevant contributions to neurological therapy, their theoretical premises may create limitations in therapeutic processes. The present manuscript has two main objectives: first, to explicitly set forth the theoretical bases of cognitive neurorehabilitation and critically analyze the repercussions that these premises have produced in clinical practice; and second, to propose the enactive paradigm to reinterpret perspectives on people with brain damage and their therapy (assessment and treatment). This analysis will show that (1) neurorehabilitation as a therapy underutilizes body-originated resources that aid in recovery from neurological sequelae (embrained therapy); (2) the therapeutic process is based exclusively on subpersonal explanation models (subpersonal therapy); and (3), neurorehabilitation does not take subjectivity of each person in their own recovery processes into account (anti-subjective therapy). Subsequently, and in order to attenuate or resolve the conception of embrained, subpersonal and anti-subjective therapy, I argue in support of incorporating the enactive paradigm in rehabilitation of neurological damage. It is proposed here under a new term, “experiential neurorehabilitation. ” This proposal approaches neurological disease and its sequelae as alterations in dynamic interaction between the body structure and the environment in which the meaning of the experience is also altered. Therefore, when a person is not able to walk, remember the past, communicate a thought, or maintain efficient self-care, their impairments are not only a product of an alteration in a specific cerebral area or within information processing; rather, the sequelae of their condition stem from alterations in the whole living system and its dynamics with the environment. The objective of experiential neurorehabilitation is the recovery of the singular and concrete experience of the person, composed of physical and subjective life attributes.
Fire behaviour and fuel reduction burning: Bemm River wildfire, October 1988

Summary On 14 October 1988 a major wildfire occurred in the Bemm River area, 33 km east of Orbost in the East Gippsland region of Victoria. The weather was dominated by wind speeds of gale force strength. The fire burnt under “very high” to “extreme” fire danger conditions with a maximum McArthur fire danger index of 82, a maximum mean forward rate of spread between 3.5 and 4.0 km/h and a maximum mean fireline intensity in the range 31,200 to 35,500 kW/m. The final area of the wildfire was 5,670 ha and the perimeter was 80 km. A highly significant influence on fire behaviour was the layer of aerated, highly flammable shrub fuel. This was combined in the coastal forests of the Bemm River area with high quantities of litter and the high spotting potential of the stringybark eucalypts. Total fine fuel loads averaged about 20 t/ha. The rate of spread predicted by the McArthur Mk 5 Forest Fire Danger Meter during the initial two hour period of the wildfire was 2.0 km/h and the observed mean rate of spread was .
Online COVID-19 diagnosis with chest CT images: Lesion-attention deep neural networks

Chest (computed tomography) CT scanning is one of the most important technologies for COVID-19 diagnosis in the current clinical practice, which motivates more concerted efforts in developing AI-based diagnostic tools to alleviate the enormous burden on the medical system. We develop a lesion-attention deep neural network (LA-DNN) to predict COVID-19 positive or negative with a richly annotated chest CT image dataset. The CT image dataset contains 746 public chest CT images of COVID-19 patients collected from over 760 preprints, and the data annotations are accompanied with the textual radiology reports. We extract two types of important information from these annotations: One is the flag of whether an image indicates a positive or negative case of COVID-19, and the other is the description of five lesions on the CT images associated with the positive cases. The proposed data-driven LA-DNN model focuses on the primary task of binary classification for COVID-19 diagnosis, while an auxiliary multi-label learning task is implemented simultaneously to draw the model's attention to the five lesions of COVID-19 during the training. The joint task learning process makes it a highly sample-efficient deep model that can learn COVID-19 radiology features effectively with very limited samples. The experimental results show that the area under the curve (AUC) and sensitivity (recall) for the diagnosis of COVID-19 patients are 91.2% and 85.7% respectively, which reach the clinical standards for practical use. An online system has been developed for fast online diagnoses using CT images at the web address https://www.covidct. cn/.
Concentration and Delivery of Abscisic Acid in Xylem Sap are Greater at the Shoot Base than at a Target Leaf Nearer to the Shoot Apex

: Samples of xylem sap from 5-week-old Ricinus corn-munis L. were obtained after severing a lamina, or shoot, from plants pressurized at the roots with air to raise hydrostatic xylem water potentials to atmospheric. In situ sap flow gauges, and mass flow measurements, showed that removing the lamina approximately doubted sap flow rate through the petiole stub that remained attached to the plant. This was a consequence of flow out of the roots being diverted along this low-resistance pathway and away from leaves higher in the canopy. Leaf and whole shoot excision temporarily released extra solutes in to sap as it discharged from the cut petiole or from the hypo-cotyl stump. This contamination prevented the use of sap extracted from detached lamina by overpressurizing in a Scholan-der bomb. To minimise distortions to sap flow and wound-induced contamination, estimates of in planta concentration and delivery (concentration × sap flow rate) of ABA and osmolality in xylem sap were made using sap flow rates measured before excision and concentrations in flowing sap collected approximately 30 mm after excision. At this time, effects of excision on solute contamination had subsided. The approach revealed that withholding water from upper roots increased ABA delivery from roots into the shoot base 3-fold. However, approximately half this ABA was lost en route to the youngest fully open leaf. This loss of ABA may explain the slow stomatal response to drying of upper roots shown by R. communis.
The Multilocus Multispecies Coalescent: A Flexible New Model of Gene Family Evolution

Incomplete lineage sorting (ILS), the interaction between coalescence and speciation, can generate incongruence between gene trees and species trees, as can gene duplication (D), transfer (T) and loss (L). These processes are usually modelled independently, but in reality, ILS can affect gene copy number polymorphism, i.e., interfere with DTL. This has been previously recognised, but not treated in a satisfactory way, mainly because DTL events are naturally modelled forward-in-time, while ILS is naturally modelled backwards-in-time with the coalescent. Here we consider the joint action of ILS and DTL on the gene tree/species tree problem in all its complexity. In particular, we show that the interaction between ILS and duplications/transfers (without losses) can result in patterns usually interpreted as resulting from gene loss, and that the realised rate of D, T and L becomes non-homogeneous in time when ILS is taken into account. We introduce algorithmic solutions to these problems. Our new model, the multilocus multispecies coalescent (MLMSC), which also accounts for any level of linkage between loci, generalises the multispecies coalescent model and offers a versatile, powerful framework for proper simulation and inference of gene family evolution.
Application of Fused Organoid Models to Study Human Brain Development and Neural Disorders

Human brain organoids cultured from human pluripotent stem cells provide a promising platform to recapitulate histological features of the human brain and model neural disorders. However, unlike animal models, brain organoids lack a reproducible topographic organization, which limits their application in modeling intricate biology, such as the interaction between different brain regions. To overcome these drawbacks, brain organoids have been pre-patterned into specific brain regions and fused to form an assembloid that represents reproducible models recapitulating more complex biological processes of human brain development and neurological diseases. This approach has been applied to model interneuron migration, neuronal projections, tumor invasion, oligodendrogenesis, forebrain axis establishment, and brain vascularization. In this review article, we will summarize the usage of this technology to understand the fundamental biology underpinning human brain development and disorders.
Testing for context-dependent effects of maternal thyroid hormones on offspring survival and physiology: an experimental approach manipulating temperature in a wild bird species

Maternal effects via hormonal transfer from the mother to the offspring provide a tool to translate environmental cues to the offspring. Experimental manipulations of maternally transferred hormones have yielded increasingly contradictory results, which may be explained by environment-dependent effects of hormones. Yet context-dependent effects have rarely been experimentally tested. We therefore studied whether maternally transferred thyroid hormones (THs) exert context-dependent effects on offspring survival and physiology by manipulating both egg TH levels and post-hatching nest temperature in wild pied flycatchers (Ficedula hypoleuca) using a full factorial design. We found no clear evidence for context-dependent effects of prenatal THs related to postnatal temperature on growth, survival and potential underlying physiological responses (plasma TH levels, oxidative stress and mitochondrial density). We conclude that future studies should test for other key environmental conditions, such as food availability, to understand potential context-dependent effects of maternally transmitted hormones on offspring, and their role in adapting to changing environments.
Dihydroartemisinin Induces Growth Arrest and Overcomes Dexamethasone Resistance in Multiple Myeloma

The discovery of artemisinin (ART) for malaria treatment won the 2015 Nobel Prize in Medicine, which inspired the rediscovery and development of ART for the treatment of other diseases including cancer. In this study, we investigated the potential therapeutic effect of ART and dihydroartemisinin (DHA) on multiple myeloma (MM) cells including primary MM cells and in 5TMM3VT mouse model. Both in vitro and in vivo experiments showed that DHA might be a more promising anti-MM agent with significantly improved efficacy compared to ART. Mechanistic analyses suggested that DHA activated the mitochondrial apoptotic pathway by interacting with ferrous (Fe2+) ions and oxygen to produce reactive oxygen species (ROS). Intriguingly, DHA could reverse the upregulated expression of B-cell lymphoma 2 (Bcl-2) protein, a typical mitochondrial apoptotic marker, induced by dexamethasone (Dexa) in MM. We further demonstrated that DHA treatment could overcome Dexa resistance and enhance Dexa efficacy in MM. Additionally, DHA combined with Dexa resulted in increased ROS production and cytochrome C translocation from the mitochondria to the cytoplasm, resulting in alterations to the mitochondrial membrane potential and caspase-mediated apoptosis. In summary, our study demonstrated that DHA was superior to ART in MM treatment and overcame Dexa resistance both in vitro and in vivo, providing a promising therapeutic strategy for MM therapy.
Excess DHA Induces Cell Cycle Arrest by Activating the P53/Cycling Pathway in Blunt Snout Bream (Megalobrama amblycephala)

A previous study showed that diets with high levels of docosahexaenoic acid (DHA) cause growth retardation in Megalobrama amblycephala. In order to explore the mechanisms involved, a feeding trial and a primary hepatocyte culture experiment were designed. In vivo, fish (average weight 26.40 ± 0.11 g) were randomly divided into groups and were fed three levels of DHA (0, 0.2, and 1.6% diets, respectively.) for 8 weeks. The results showed that the final body weight and weight gain of fish fed 1.6% DHA were significantly lower than those of fish fed 0.2% DHA (P < 0.05). P53 gene and protein expression levels were significantly increased (P < 0.05), while expression of downstream Cyclin D1 and Cyclin E1 was significantly inhibited in the 1.6% DHA group when compared with the 0 and 0.2% DHA groups (P < 0.05). In vitro, primary hepatocytes isolated from Megalobrama amblycephala incubated with 500 μM DHA showed significantly increased cell cycle arrest and apoptosis (P < 0.05), significantly increased P53 gene and protein levels (P < 0.05), and significantly decreased Cyclin D1 and Cyclin E1 levels (P < 0.05) when compared with other groups. When primary hepatocytes were incubated with DHA and a P53 inhibitor (pifithrin-α), P53 expression and P53-mediated signaling were inhibited, cell cycle progression recovered, and apoptosis was reduced. In summary, high levels of DHA activated the P53/Cyclin pathway to induce cell cycle arrest. Inhibition of P53 activity may be a potential way of reducing the side effects of DHA on the growth of Megalobrama amblycephala.
Exercise: A Protective Measure or an “Open Window” for COVID-19? A Mini Review

The coronavirus disease 2019 (COVID-19) has spread to at least 115 countries and caused an alarming number of deaths. The current outbreak has lead authorities from many countries to adopt several protective measures, including lockdown and social distancing. Although being a reasonable measure to counteract the COVID-19 contamination, the restrictive measures have limited individual's ability to perform exercise outdoors or in gyms and similar facilities, thus raising the risks for chronic health conditions related to a sedentary lifestyle. The recent exercise recommendations to counteract the potential deleterious effects of COVID-19-related lockdown have not fully addressed resistance exercise interventions as potential home-based exercise strategies. Additionally, the following questions have been constantly raised: (1) Is training status capable of protecting an individual from COVID-19 infection? ; and (2) Can a single endurance or resistance exercise session acutely increase the risks for COVID-19 infection? Therefore, the current mini review aimed to focus on these two concerns, as well as to discuss the potential use of practical blood flow restriction and no load resistance training as possible resistance exercise strategies that could be performed during the current COVID-19 pandemic.
Meta-Signer: Metagenomic Signature Identifier based on Rank Aggregation of Features

Background The advance of metagenomic studies provides the opportunity to identify microbial taxa that are associated to human diseases. Multiple methods exist for the association analysis. However, the results could be inconsistent, presenting challenges in interpreting the host-microbiome interactions. To address this issue, we introduce Meta-Signer, a novel Metagenomic Signature Identifier tool based on rank aggregation of features identified from multiple machine learning models including Random Forest, Support Vector Machines, LASSO, Multi-Layer Perceptron Neural Networks, and our recently developed Convolutional Neural Network framework (PopPhy-CNN). Meta-Signer generates ranked taxa lists by training individual machine learning models over multiple training partitions and aggregates them into a single ranked list by an optimization procedure to represent the most informative and robust microbial features. Meta-Signer can rank taxa using two input forms of the data: the relative abundances of the original taxa and taxa from the populated taxonomic trees generated from the original taxa. The latter form allows the evaluation of the association of microbial features at different taxonomic levels to the disease, which is attributed to our novel model of PopPhy-CNN. Results We evaluate Mega-Signer on five different human gut-microbiome datasets. We demonstrate that the features derived from Meta-Signer were more informative compared to those obtained from other available feature ranking methods. The highly ranked features are strongly supported by published literature. Conclusion Meta-Signer is capable of deriving a robust set of microbial features at multiple taxonomic levels for the prediction of host phenotype. Meta-Signer is user-friendly and customizable, allowing users to explore their datasets quickly and efficiently.