Miracle-dz/UniFAR-FTUs huggingface dataset:
Complexities of Inferring Symbiont Function: Paraburkholderia Symbiont Dynamics in Social Amoeba Populations and Their Impacts on the Amoeba Microbiota

The functions of symbionts in natural populations can be difficult to completely discern. The three Paraburkholderia bacterial farming symbionts of the social amoeba Dictyostelium discoideum have been shown in the laboratory environment to allow the amoebas to carry, rather than fully digest, food bacteria. ABSTRACT The relationship between the social amoeba Dictyostelium discoideum and its endosymbiotic bacteria Paraburkholderia provides a model system for studying the development of symbiotic relationships. Laboratory experiments have shown that any of three species of the Paraburkholderia symbiont allow D. discoideum food bacteria to persist through the amoeba life cycle and survive in amoeba spores rather than being fully digested. This phenomenon is termed “farming,” as it potentially allows spores dispersed to food-poor locations to grow their own. The occurrence and impact of farming in natural populations, however, have been a challenge to measure. Here, we surveyed natural D. discoideum populations and found that only one of the three symbiont species, Paraburkholderia agricolaris, remained prevalent. We then explored the effect of Paraburkholderia on the amoeba microbiota, expecting that by facilitating bacterial food carriage, it would diversify the microbiota. Contrary to our expectations, Paraburkholderia tended to infectiously dominate the D. discoideum microbiota, in some cases decreasing diversity. Similarly, we found little evidence for Paraburkholderia facilitating the carriage of particular food bacteria. These findings highlight the complexities of inferring symbiont function in nature and suggest the possibility that Paraburkholderia could be playing multiple roles for its host. IMPORTANCE The functions of symbionts in natural populations can be difficult to completely discern. The three Paraburkholderia bacterial farming symbionts of the social amoeba Dictyostelium discoideum have been shown in the laboratory environment to allow the amoebas to carry, rather than fully digest, food bacteria. This potentially provides a fitness benefit to the amoebas upon dispersal to food-poor environments, as they could grow their food. We expected that meaningful food carriage would manifest as a more diverse microbiota. Surprisingly, we found that Paraburkholderia tended to infectiously dominate the D. discoideum microbiota rather than diversifying it. We determined that only one of the three Paraburkholderia symbionts has increased in prevalence in natural populations in the past 20 years, suggesting that this symbiont may be beneficial, however. These findings suggest that Paraburkholderia may have an alternative function for its host, which drives its prevalence in natural populations.
Reconstructing the biogeography of a hunter-gatherer planet using machine-learning

Estimating the total human population size (i.e., abundance) of the preagricultural planet is important for setting the baseline expectations for human-environment interactions if all energy and material requirements to support growth, maintenance, and well-being were foraged from local environments. However, demographic parameters and biogeographic distributions do not preserve directly in the archaeological record. Rather than attempting to estimate human abundance at some specific time in the past, a principled approach to making inferences at this scale is to ask what the human demography and biogeography of a hypothetical planet Earth would look like if populated by ethnographic hunter-gatherer societies. Given ethnographic hunter-gatherer societies likely include the largest, densest, and most complex foraging societies to have existed, we suggest population inferences drawn from this sample provide an upper bound to demographic estimates in prehistory. Our goal in this paper is to produce principled estimates of hunter-gatherer abundance, diversity, and biogeography. To do this we trained an extreme gradient boosting algorithm (XGBoost) to learn ethnographic hunter-gatherer population densities from a large matrix of climatic, environmental, and geographic data. We used the predictions generated by this model to reconstruct the hunter-gatherer biogeography of the rest of the planet. We find the human abundance of this world to be 6.1±2 million with an ethnolinguistic diversity of 8,330±2,770 populations, most of whom would have lived near coasts and in the tropics. Significance Statement Understanding the abundance of humans on planet Earth prior to the development of agriculture and the industrialized world is essential to understanding human population growth. However, the problem is that these features of human populations in the past are unknown and so must be estimated from data. We developed a machine learning approach that uses ethnographic and environmental data to reconstruct the demography and biogeography of planet Earth if populated by hunter-gatherers. Such a world would house about 6 million people divided into about 8,330 populations with a particular concentration in the tropics and along coasts.
Poly(A)-binding protein is an ataxin-2 chaperone that emulsifies biomolecular condensates

Biomolecular condensation underlies the biogenesis of an expanding array of membraneless assemblies, including stress granules (SGs) which form under a variety of cellular stresses. Advances have been made in understanding the molecular grammar that dictates the behavior of a few key scaffold proteins that make up these phases but how the partitioning of hundreds of other SG proteins is regulated remains largely unresolved. While investigating the rules that govern the condensation of ataxin-2, a SG protein implicated in neurodegenerative disease, we unexpectedly identified a short 14aa sequence that acts as an ataxin-2 condensation switch and is conserved across the eukaryote lineage. We identify poly(A)-binding proteins as unconventional RNA-dependent chaperones that control this regulatory switch. Our results uncover a hierarchy of cis and trans interactions that fine-tune ataxin-2 condensation and reveal a new molecular function for ancient poly(A)-binding proteins as emulsifiers of biomolecular condensate proteins. These findings may inspire novel approaches to therapeutically target aberrant phases in disease.
Role of Decidual Natural Killer Cells in Human Pregnancy and Related Pregnancy Complications

Pregnancy is a unique type of immunological process. Healthy pregnancy is associated with a series of inflammatory events: implantation (inflammation), gestation (anti-inflammation), and parturition (inflammation). As the most abundant leukocytes during pregnancy, natural killer (NK) cells are recruited and activated by ovarian hormones and have pivotal roles throughout pregnancy. During the first trimester, NK cells represent up to 50–70% of decidua lymphocytes. Differently from peripheral-blood NK cells, decidual natural killer (dNK) cells are poorly cytolytic, and they release cytokines/chemokines that induce trophoblast invasion, tissue remodeling, embryonic development, and placentation. NK cells can also shift to a cytotoxic identity and carry out immune defense if infected in utero by pathogens. At late gestation, premature activation of NK cells can lead to a breakdown of tolerance of the maternal–fetal interface and, subsequently, can result in preterm birth. This review is focused on the role of dNK cells in normal pregnancy and pathological pregnancy, including preeclampsia, recurrent spontaneous abortion, endometriosis, and recurrent implantation failure. dNK cells could be targets for the treatment of pregnancy complications.
Contralateral Axon Sprouting but Not Ipsilateral Regeneration Is Responsible for Spontaneous Locomotor Recovery Post Spinal Cord Hemisection

Spinal cord injury (SCI) usually results in permanent functional impairment and is considered a worldwide medical problem. However, both motor and sensory functions can spontaneously recover to varying extents in humans and animals with incomplete SCI. This study observed a significant spontaneous hindlimb locomotor recovery in Sprague-Dawley rats at four weeks after post-right-side spinal cord hemisection at thoracic 8 (T8). To verify whether the above spontaneous recovery derives from the ipsilateral axonal or neuronal regeneration to reconnect the lesion site, we resected either the scar tissue or right side T7 spinal cord at five weeks post-T8 hemisected injury. The results showed that the spontaneously achieved right hindlimb locomotor function had little change after resection. Furthermore, when T7 left hemisection was performed five weeks after the initial injury, the spontaneously achieved right hindlimb locomotor function was dramatically abolished. A similar result could also be observed when T7 transection was performed after the initial hemisection. The results indicated that it might be the contralateral axonal remolding rather than the ipsilateral axonal or neuronal regeneration beyond the lesion site responsible for the spontaneous hindlimb locomotor recovery. The immunostaining analyses and corticospinal tracts (CSTs) tracing results confirmed this hypothesis. We detected no substantial neuronal and CST regeneration throughout the lesion site; however, significantly more CST fibers were observed to sprout from the contralateral side at the lumbar 4 (L4) spinal cord in the hemisection model rats than in intact ones. In conclusion, this study verified that contralateral CST sprouting, but not ipsilateral CST or neuronal regeneration, is primarily responsible for the spontaneous locomotor recovery in hemisection SCI rats.
Effect of TTN Mutations on Immune Microenvironment and Efficacy of Immunotherapy in Lung Adenocarcinoma Patients

Immune checkpoint inhibitors (ICIs) effectively treat lung adenocarcinoma (LUAD) with fewer side effects. However, for LUAD patients, the lack of predictive markers for ICIs makes their clinical benefits less than ideal. Despite reports suggesting that a TTN (titin) mutation plays an important role in immunotherapy of solid tumors and gastric cancer, the relationship between the TTN mutation and LUAD immunotherapy has not been determined. We collected a LUAD cohort with whole-exome sequencing (WES) and immunotherapy prognosis. The ICI cohort was used to explore the relationship between TTN mutation status and prognosis. Then, the Cancer Genome Atlas (TCGA)-LUAD and Chen-LUAD cohorts were downloaded from the cbioportal website. We also used CIBERSORT, gene-set enrichment analysis (GSEA), and single-sample GSEA (ssGSEA) to evaluate the proportion of immune cells and the degree of pathway activation in LUAD patients, respectively. DDR signaling pathways obtained from the Molecular Signatures Database (MSigDB), tumor mutation burden (TMB), and NAL were used to evaluate the immunogenicity of LUAD patients. In the ICI cohort, TTN-mutant (TTN-MT) had significantly longer overall survival (OS) than TTN-wildtype (TTN-WT) (P = 0.009). Univariate and multivariate COX models showed that TTN mutation status can independently predict immunotherapy prognosis. Notably, the results of tumor immune microenvironment (TIME) analysis showed that TTN-MT patients had inflammatory TIME, which showed enriched activated immune cells and higher immune scores. Immunogenicity analysis showed higher immunogenicity in TTN-MT patients, which indicated high levels of gene mutations in TMB, NAL, and DDR pathways. GSEA and ssGSEA results showed that TTN-MT was substantially enriched in chemokine secretion, inflammatory factor secretion, and antigen presentation. Some pathways related to immunosuppression and immune depletion were significantly downregulated. TTN-MT is associated with significantly prolonged OS in LUAD patients. Additionally, TTN-MT is related to high immunogenicity and inflammatory TIME, suggesting that TTN-MT may be a potential predictive marker for patients with LUAD to accept ICIs.
Research on Psychache in Suicidal Population: A Bibliometric and Visual Analysis of Papers Published During 1994–2020

Background: Psychache is a negative introspective experience, which is positively associated with the risk of suicide, independently of depression. It is undeniable that psychache is an important influencing factor to trigger suicide, which can also mediate the effect between depression and suicide variables. Nevertheless, the research tendency and current hotspots on psychache of suicide population have not been systematically investigated based on bibliometric analysis. Aim: The aim of the study was to analyze the research status, hotspots, and frontiers of psychological pain in the field of suicidology, so as to provide reference for domestic clinical research. Methods: The literature related to psychache in suicide individuals published from 1994 to 2020 was included and selected from the Web of Science Core Collection database on May 28, 2021. CiteSpace (version 5.7.R2) software was used to visualize and analyze highly cited journals, authors, and articles as well as co-occurrence analysis for countries, institution, authors, and keywords. Results: A total of 230 articles from the WoS database were included. The number of papers over the years showed an overall upward trend. The United States has made the largest contribution, with the majority of publications (89, 38.70%), followed by Canada (48, 20.87%), Israel (31, 13.48%), China (20, 8.80%), and Portugal (17, 7.39%). The most productive institution was Queen's University. Edwin S. Shneidman has the largest achievement and profound influence, and the most prolific author is Ronald R. Holden. However, the cooperation between institutions and authors was comparatively weak. The current hotspots in this field focus on the studies on the relationships between depression, despair, psychache, and suicide, the risk assessments of psychological pain, and the development of psychological pain scales. Suicide and Life-Threatening Behavior was the most frequently cited journal in this field. Conclusions: This analysis not only reveals the current research trend and hotspots but also provides some instructive suggestions on the development of psychache in the suicidology. Future work should pay more attention to develop effective psychological pain intervention programs for diverse suicide population. Additionally, longitudinal study can also be conducted to grasp the trajectory changes of psychological pain among suicide individuals.
Entrepreneurial Learning, Self-Efficacy, and Firm Performance: Exploring Moderating Effect of Entrepreneurial Orientation

Although the impact entrepreneurial learning on firm performance has attracted significant attention, a comprehensive understanding by integrating entrepreneurial orientation and individual self-efficacy remain poorly understood. We fill this void by integrating the above variables into a model and examine these relations. Findings from a sample of 411 nascent entrepreneurs support that entrepreneurial learning is positively related to firm performance, and this relationship is fully mediated by entrepreneurial self-efficacy (ESE). We also found entrepreneurial orientation strengthens the positive impact of entrepreneurial learning on ESE. The findings indicate that ESE must be in place to maximize the effect of entrepreneurial learning on performance, and entrepreneurial orientation is an important contingency in shaping entrepreneurial learning's impact on nascent entrepreneur's self-efficacy.
Elevated Serum Inflammatory Markers in Subacute Stroke Are Associated With Clinical Outcome but Not Modified by Aerobic Fitness Training: Results of the Randomized Controlled PHYS-STROKE Trial

Background: Inflammatory markers, such as C-reactive Protein (CRP), Interleukin-6 (IL-6), tumor necrosis factor (TNF)-alpha and fibrinogen, are upregulated following acute stroke. Studies have shown associations of these biomarkers with increased mortality, recurrent vascular risk, and poor functional outcome. It is suggested that physical fitness training may play a role in decreasing long-term inflammatory activity and supports tissue recovery. Aim: We investigated the dynamics of selected inflammatory markers in the subacute phase following stroke and determined if fluctuations are associated with functional recovery up to 6 months. Further, we examined whether exposure to aerobic physical fitness training in the subacute phase influenced serum inflammatory markers over time. Methods: This is an exploratory analysis of patients enrolled in the multicenter randomized-controlled PHYS-STROKE trial. Patients within 45 days of stroke onset were randomized to receive either four weeks of aerobic physical fitness training or relaxation sessions. Generalized estimating equation models were used to investigate the dynamics of inflammatory markers and the associations of exposure to fitness training with serum inflammatory markers over time. Multiple logistic regression models were used to explore associations between inflammatory marker levels at baseline and three months after stroke and outcome at 3- or 6-months. Results: Irrespective of the intervention group, high sensitive CRP (hs-CRP), IL-6, and fibrinogen (but not TNF-alpha) were significantly lower at follow-up visits when compared to baseline (p all ≤ 0.01). In our cohort, exposure to aerobic physical fitness training did not influence levels of inflammatory markers over time. In multivariate logistic regression analyses, increased baseline IL-6 and fibrinogen levels were inversely associated with worse outcome at 3 and 6 months. Increased levels of hs-CRP at 3 months after stroke were associated with impaired outcome at 6 months. We found no independent associations of TNF-alpha levels with investigated outcome parameters. Conclusion: Serum markers of inflammation were elevated after stroke and decreased within 6 months. In our cohort, exposure to aerobic physical fitness training did not modify the dynamics of inflammatory markers over time. Elevated IL-6 and fibrinogen levels in early subacute stroke were associated with worse outcome up to 6-months after stroke. Clinical Trial Registration: ClinicalTrials.gov, NCT01953549.
Johne's Disease in Dairy Cattle: An Immunogenetic Perspective

Johne's disease (JD), also known as paratuberculosis, is a severe production-limiting disease with significant economic and welfare implications for the global cattle industry. Caused by infection with Mycobacterium avium subspecies paratuberculosis (MAP), JD manifests as chronic enteritis in infected cattle. In addition to the economic losses and animal welfare issues associated with JD, MAP has attracted public health concerns with potential association with Crohn's disease, a human inflammatory bowel disease. The lack of effective treatment options, such as a vaccine, has hampered JD control resulting in its increasing global prevalence. The disease was first reported in 1895, but in recognition of its growing economic impact, extensive recent research facilitated by a revolution in technological approaches has led to significantly enhanced understanding of the immunological, genetic, and pathogen factors influencing disease pathogenesis. This knowledge has been derived from a variety of diverse models to elucidate host-pathogen interactions including in vivo and in vitro experimental infection models, studies measuring immune parameters in naturally-infected animals, and by studies conducted at the population level to enable the estimation of genetic parameters, and the identification of genetic markers and quantitative trait loci (QTL) putatively associated with susceptibility or resistance to JD. The main objectives of this review are to summarize these recent developments from an immunogenetics perspective and attempt to extract the principal and common findings emerging from this wealth of recent information. Based on these analyses, and in light of emerging technologies such as gene-editing, we conclude by discussing potential future avenues for effectively mitigating JD in cattle.
A Review of the Potential Use of Pinene and Linalool as Terpene-Based Medicines for Brain Health: Discovering Novel Therapeutics in the Flavours and Fragrances of Cannabis

“Medicinal cannabis” is defined as the use of cannabis-based products for the treatment of an illness. Investigations of cannabis compounds in psychiatric and neurological illnesses primarily focus on the major cannabinoids, cannabidiol (CBD) and Δ9-tetrahydrocannabinol (Δ9-THC), which are hypothesised to benefit multiple illnesses manifesting cognitive impairment, neurodegeneration and neuro-inflammation, as well as chronic pain, epilepsy and post-traumatic stress disorder, respectively. The cannabis plant contains >500 compounds, including terpenes responsible for the flavour and fragrance profiles of plants. Recently, research has begun providing evidence on the potential use of certain plant-derived terpenes in modern medicine, demonstrating anti-oxidant, anti-inflammatory, and neuroprotective effects of these compounds. This review examined the effects of two key terpenes, pinene and linalool, on parameters relevant to neurological and psychiatric disorders, highlighting gaps in the literature and recommendations for future research into terpene therapeutics. Overall, evidence is mostly limited to preclinical studies and well-designed clinical trials are lacking. Nevertheless, existing data suggests that pinene and linalool are relevant candidates for further investigation as novel medicines for illnesses, including stroke, ischemia, inflammatory and neuropathic pain (including migraine), cognitive impairment (relevant to Alzheimer's disease and ageing), insomnia, anxiety, and depression. Linalool and pinene influence multiple neurotransmitter, inflammatory and neurotrophic signals as well as behaviour, demonstrating psycho-activity (albeit non-intoxicating). Optimising the phytochemical profile of cannabis chemovars to yield therapeutic levels of beneficial terpenes and cannabinoids, such as linalool, pinene and CBD, could present a unique opportunity to discover novel medicines to treat psychiatric and neurological illnesses; however, further research is needed.
Style change detection using Siamese neural networks

Style change detection focuses on the intrinsic characteristics of a document to determine the location of authorship changes. In this paper, we describe how style change detection can be interpreted as a one shot learning task, which is a type of classification task where a single example of each class is given. For example, one shot learning image classification aims to train classifiers over a dataset, where only one image per class is available. While a large number of classes can be handled in such an approach, it is very difficult to train a neural network using only one sample per class. Siamese neural networks are one of the popular approaches for one shot learning tasks because they can learn the similarity between two object representations. Siamese neural networks have been shown to be useful for learning image similarity and semantic similarity between two texts. In this paper, we propose an end-to-end Siamese neural network approach for learning the stylistic similarity between two texts, even when the size of the texts are relatively short (mean text size of 50 words).
CIC at CheckThat! 2021: Fake News detection Using Machine Learning And Data Augmentation

Disinformation in theform of fake news, phoney press releases and hoaxesmay be misleading, especially when they are not from their original sources and this fake news can cause significant harm to the people. In this paper, we report several machine learning classifiers on the CLEF2021 dataset for the tasks of news claim and topic classification using 𝑛 -grams. We achieve an F 1 score of 38.92% on news claim classification (task 3a) and an F 1 score of 78.96% on topic classification (task 3b). In addition, we augmented the dataset for news claim classification and we observed that insertion of alternative words was not beneficial for the fake news classification task.