Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbial roles in cave biogeochemical cycling

Among fundamental research questions in subterranean biology, the role of subterranean microbiomes playing in key elements cycling is a top-priority one. Karst caves are widely distributed subsurface ecosystems, and cave microbes get more and more attention as they could drive cave evolution and biogeochemical cycling. Research have demonstrated the existence of diverse microbes and their participance in biogeochemical cycling of elements in cave environments. However, there are still gaps in how these microbes sustain in caves with limited nutrients and interact with cave environment. Cultivation of novel cave bacteria with certain functions is still a challenging assignment. This review summarized the role of microbes in cave evolution and mineral deposition, and intended to inspire further exploration of microbial performances on C/N/S biogeocycles.
Acute, chronic, and genotoxic studies on the protopine total alkaloids of the Macleaya cordata (willd.) R. Br. in rodents

The protopine alkaloids are widely distributed within the opium poppy family and have a wide range of pharmacological effects. MPTA is a product of the protopine total alkaloids extracted from the Macleaya cordata (Willd.) R. Br. Previously, we reported good anti-inflammatory activity of MPTA as well as oral acute and sub-chronic toxicity studies in rats. In order to perform a systematic toxicological safety assessment of MPTA, oral acute toxicity, genotoxicity (bone marrow cell chromosome aberration test, sperm abnormality test, bone marrow cell micronucleus test, and rat teratogenicity test), and chronic toxicity in mice were performed in this study. In the oral acute toxicity test, the LD50 in ICR mice was 481.99 mg/kg, with 95% confidence limits ranging from 404.27 to 574.70 mg/kg. All three mutagenicity tests tested negative in the range of 60.25–241.00 mg/kg. The results of the teratogenicity test in rats showed no reproductive or embryonic developmental toxicity at only 7.53 mg/kg, which can be considered as a no observed effect level (NOEL) for the teratogenicity test. Therefore, MPTA is safe for use at the doses tested, but attention should be paid to the potential risk to pregnant animals and the safety evaluation and toxicity mechanisms in target animals should be further investigated.
An analysis of trends and policies supporting alternative fuels for road freight transport in Europe

A significant proportion of transport greenhouse gas emissions originates from the activity of light-duty trucks and heavy-duty vehicles. The overarching aim of this study is to assess road freight transport decarbonization in Europe by analyzing relevant trends (recent developments and future estimates) and policies. Specifically, the paper investigates the policy measures in place or introduced in the European Union Member States plus the United Kingdom between 2016 and 2018, as reported in their submissions to the European Commission, the market progress and status until 2020/1 and the techno-economic barriers that slow down further emissions mitigation. The study focuses on electric vehicles (battery electric and plug-in hybrid), fuel cell electric vehicles and natural gas-powered vehicles. We find wide differences in the strength of policy support by country, mode and fuel. Our analysis is constrained by data availability and we highlight the need for improvements in data reporting by countries, including the communication of future vehicle estimates and infrastructure targets. We reach the conclusion that, despite some progress, stronger action is needed to timely decarbonize road freight transport in Europe.
Influence of particle characteristics on dynamic characteristics of tail beam under coal rock caving impact

In order to improve the accuracy of simulation parameters used in the discrete element simulation test of a fully mechanized top-coal caving process and further explore the intelligent fully mechanized coal caving technology, this research work studies the influence of particle characteristics on the dynamic response of tail beams under the impact of caving coal rock in the process of coal caving. Based on the interface technology, the EDEM–RecurDyn–AMESim multi-domain collaborative simulation top-coal caving support is a built-model of a hydraulic mechanical integration system for scraper conveyors, which is used to simulate the coal caving process of the top-coal caving support to obtain the vibration signal of the tail beam of the top-coal caving support. This model can also be used to convert it into a two-dimensional time-spectrum image using the short-time Fourier transform (STFT) algorithm. Several groups of simulation tests were carried out on different particle radii, standard deviation of particle normal distribution, and particle slenderness ratio. The time-domain information and frequency-domain information obtained from the simulation were analyzed and compared. Combined with the vibration signal of the tail beam measured on the spot, the optimal setting parameters of the multi-field collaborative virtual prototype simulation were obtained. Compared with the data measured in the coal mine, the relative error of the maximum vibration value of the tail beam is only 3.8%, the minimum relative error is 5.5%, and the relative error of the root mean square value is 14%, which verifies the method and simulation results. This method solves the problems of difficult on-site sampling, high risk coefficient, and high test cost and promotes the development of an intelligent process of coal mining.
Olfactory loss is a predisposing factor for depression, while olfactory enrichment is an effective treatment for depression

The loss of olfactory stimulation correlates well with at least 68 widely differing neurological disorders, including depression, and we raise the possibility that this relationship may be causal. That is, it seems possible that olfactory loss makes the brain vulnerable to expressing the symptoms of these neurological disorders, while daily olfactory enrichment may decrease the risk of expressing these symptoms. This situation resembles the cognitive reserve that is thought to protect people with Alzheimer’s neuropathology from expressing the functional deficit in memory through the cumulative effect of intellectual stimulation. These relationships also resemble the functional response of animal models of human neurological disorders to environmental enrichment, wherein the animals continue to have the induced neuropathology, but do not express the symptoms as they do in a standard environment with restricted sensorimotor stimulation.
Using fish to understand how cities affect sexual selection before and after mating

Urbanization transforms natural and agricultural areas into built landscapes. Such profound habitat alteration imposes strong pressure on phenotypic trait changes through processes related to natural and/or sexual selection. Evidence of how natural selection drives changes to traits in urban biota is increasing, but little is known about the role of sexual selection. In this study, we assessed the effect of urbanization on the expression and interaction of males' pre-mating traits (body size and color) and a post-mating trait (sperm load). We used a widespread invasive species, the guppy (Poecilia reticulata), which is a wellknown model for studying sexual selection, but have never been studied in urban systems for this purpose. We found that urbanization did not affect mean body size or condition, but it resulted in size-dependent reductions in the expression of orange and iridescent colors, as well as sperm load. The orange color was reduced in small urban guppies, while the iridescent colors were reduced in large urban guppies compared to non-urban guppies. The difference in sperm load was only found in large males, with lower sperm load in urban guppies. The relationship between orange color and sperm load was positive in urban guppies but negative in non-urban guppies, while the association between iridescent color and sperm load followed the opposite pattern. Our findings suggest that sexual selection on pre- and post-mating traits is weaker in urban than in non-urban systems and that interactions between such traits are context dependent. These responses can be related to the pollution and altered visual environment of urban systems and provide an opportunity to advance our understanding of the mechanisms determining adaptation in cities.
Skin-to-blood pH shift triggers metabolome and proteome global remodelling in Staphylococcus epidermidis

Staphylococcus epidermidis is one of the most common bacteria of the human skin microbiota. Despite its role as a commensal, S. epidermidis has emerged as an opportunistic pathogen, associated with 80% of medical devices related infections. Moreover, these bacteria are extremely difficult to treat due to their ability to form biofilms and accumulate resistance to almost all classes of antimicrobials. Thus new preventive and therapeutic strategies are urgently needed. However, the molecular mechanisms associated with S. epidermidis colonisation and disease are still poorly understood. A deeper understanding of the metabolic and cellular processes associated with response to environmental factors characteristic of SE ecological niches in health and disease might provide new clues on colonisation and disease processes. Here we studied the impact of pH conditions, mimicking the skin pH (5.5) and blood pH (7.4), in a S. epidermidis commensal strain by means of next-generation proteomics and 1H NMR-based metabolomics. Moreover, we evaluated the metabolic changes occurring during a sudden pH change, simulating the skin barrier break produced by a catheter. We found that exposure of S. epidermidis to skin pH induced oxidative phosphorylation and biosynthesis of peptidoglycan, lipoteichoic acids and betaine. In contrast, at blood pH, the bacterial assimilation of monosaccharides and its oxidation by glycolysis and fermentation was promoted. Additionally, several proteins related to virulence and immune evasion, namely extracellular proteases and membrane iron transporters were more abundant at blood pH. In the situation of an abrupt skin-to-blood pH shift we observed the decrease in the osmolyte betaine and changes in the levels of several metabolites and proteins involved in cellular redoxl homeostasis. Our results suggest that at the skin pH S. epidermidis cells are metabolically more active and adhesion is promoted, while at blood pH, metabolism is tuned down and cells have a more virulent profile. pH increase during commensal-to-pathogen conversion appears to be a critical environmental signal to the remodelling of the S. epidermidis metabolism toward a more pathogenic state. Targeting S. epidermidis proteins induced by pH 7.4 and promoting the acidification of the medical device surface or surrounding environment might be new strategies to treat and prevent S. epidermidis infections.
Trainability of novel person recognition based on brief exposure to form and motion cues

Fast and accurate recognition of teammates is crucial in contexts as varied as fast-moving sports, the military, and law enforcement engagements; misrecognition can result in lost scoring opportunities in sport or friendly fire in combat contexts. Initial studies on teammate recognition in sport suggests that athletes are adept at this perceptual ability but still susceptible to errors. The purpose of the current proof-of-concept study was to explore the trainability of teammate recognition from very brief exposure to vision of the whole-body form and motion of a previously unknown individual. Participants were divided into three groups: a 4-week training group who were also the actors for the test and training footage, a 2-week training group, and a no-training group. Findings revealed significant differences between the training groups and their improvement from the pre-to post-test on Response Accuracy and Movement Time. The current study found the best performance in the 4-week Training group. The biggest improvement was found in the 2-week training group, whilst no significant improvement was made in the Control group. These results suggest that training was effective, but also indicate that having initially performed the movements as actors may have led to improvements in baseline testing and ultimately the best results, thus physical performance of skills combined with video-based training may reduce the amount of time needed to improve teammate identification.
Integrated metabolomic and transcriptomic analyses reveal different metabolite biosynthesis profiles of Juglans mandshurica in shade

Light is not only a very important source of energy for the normal growth and development of plants, but also a regulator of many development and metabolic processes. The mechanism of plant growth and development under low light conditions is an important scientific question. With the promulgation of the law to stop natural forest cutting, understory regeneration is an important method for artificial forest afforestation. Here, the growth and physiological indexes of Juglans mandshurica, an important hardwood species in Northeast China, were measured under different shade treatments. In addition, transcriptome and metabolome were compared to analyze the molecular mechanism of shade tolerance in J. mandshurica. The results showed that the seedling height of the shade treatment group was significantly higher than that of the control group, and the 50% light (L50) treatment was the highest. Compared with the control group, the contents of gibberellin, abscisic acid, brassinolide, chlorophyll a, and chlorophyll b in all shade treatments were significantly higher. However, the net photosynthetic rate and water use efficiency decreased with increasing shade. Furthermore, the transcriptome identified thousands of differentially expressed genes in three samples. Using enrichment analysis, we found that most of the differentially expressed genes were enriched in photosynthesis, plant hormone signal transduction and chlorophyll synthesis pathways, and the expression levels of many genes encoding transcription factors were also changed. In addition, analysis of differentially accumulated metabolites showed that a total of 470 differential metabolites were identified, and flavonoids were the major differential metabolites of J. mandshurica under light stress. These results improved our understanding of the molecular mechanism and metabolite accumulation under light stress in J. mandshurica.
Mapping species diversification metrics in macroecology: Prospects and challenges

The intersection of macroecology and macroevolution is one of today’s most active research in biology. In the last decade, we have witnessed a steady increment of macroecological studies that use metrics attempting to capture macroevolutionary processes to explain present-day biodiversity patterns. Evolutionary explanations of current species richness gradients are fundamental for understanding how diversity accumulates in a region. Although multiple hypotheses have been proposed to explain the patterns we observe in nature, it is well-known that the present-day diversity patterns result from speciation, extinction, colonization from nearby areas, or a combination of these macroevolutionary processes. Whether these metrics capture macroevolutionary processes across space is unknown. Some tip-rate metrics calculated directly from a phylogenetic tree (e.g., mean root distance -MRD-; mean diversification rate -mDR-) seem to return very similar geographical patterns regardless of how they are estimated (e.g., using branch lengths explicitly or not). Model-based tip-rate metrics —those estimated using macroevolutionary mixtures, e.g., the BAMM approach— seem to provide better net diversification estimates than only speciation rates. We argue that the lack of appropriate estimates of extinction and dispersal rates in phylogenetic trees may strongly limit our inferences about how species richness gradients have emerged at spatial and temporal scales. Here, we present a literature review about this topic and empirical comparisons between select taxa with several of these metrics. We implemented a simple null model approach to evaluate whether mapping of these metrics deviates from a random sampling process. We show that phylogenetic metrics by themselves are relatively poor at capturing speciation, extinction, and dispersal processes across geographical gradients. Furthermore, we provide evidence of how parametric biogeographic methods can improve our inference of past events and, therefore, our conclusions about the evolutionary processes driving biodiversity patterns. We recommend that further studies include several approaches simultaneously (e.g., spatial diversification modeling, parametric biogeographic methods, simulations) to disentangle the relative role of speciation, extinction, and dispersal in the generation and maintenance of species richness gradients at regional and global scales.
Salt stress resilience in plants mediated through osmolyte accumulation and its crosstalk mechanism with phytohormones

Salinity stress is one of the significant abiotic stresses that influence critical metabolic processes in the plant. Salinity stress limits plant growth and development by adversely affecting various physiological and biochemical processes. Enhanced generation of reactive oxygen species (ROS) induced via salinity stress subsequently alters macromolecules such as lipids, proteins, and nucleic acids, and thus constrains crop productivity. Due to which, a decreasing trend in cultivable land and a rising world population raises a question of global food security. In response to salt stress signals, plants adapt defensive mechanisms by orchestrating the synthesis, signaling, and regulation of various osmolytes and phytohormones. Under salinity stress, osmolytes have been investigated to stabilize the osmotic differences between the surrounding of cells and cytosol. They also help in the regulation of protein folding to facilitate protein functioning and stress signaling. Phytohormones play critical roles in eliciting a salinity stress adaptation response in plants. These responses enable the plants to acclimatize to adverse soil conditions. Phytohormones and osmolytes are helpful in minimizing salinity stress-related detrimental effects on plants. These phytohormones modulate the level of osmolytes through alteration in the gene expression pattern of key biosynthetic enzymes and antioxidative enzymes along with their role as signaling molecules. Thus, it becomes vital to understand the roles of these phytohormones on osmolyte accumulation and regulation to conclude the adaptive roles played by plants to avoid salinity stress.
Lacticaseibacillus rhamnosus R0011 secretome attenuates Salmonella enterica serovar Typhimurium secretome-induced intestinal epithelial cell monolayer damage and pro-inflammatory mediator production in intestinal epithelial cell and antigen-presenting cell co-cultures

Certain lactic acid bacteria (LAB) are associated with immune modulatory activities including down-regulation of pro-inflammatory gene transcription and expression. While host antigen-presenting cells (APCs) and intestinal epithelial cells (IEC) can interact directly with both pathogenic and commensal bacteria through innate immune pattern recognition receptors, recent evidence indicates indirect communication through secreted molecules is an important inter-domain communication mechanism. This communication route may be especially important in the context of IEC and APC interactions which shape host immune responses within the gut environment. We have previously shown that the Lacticaseibacillus rhamnosus R0011 secretome (LrS) dampens pro-inflammatory gene transcription and mediator production from Tumor Necrosis Factor-α and Salmonella enterica serovar Typhimurium secretome (STS)-challenged HT-29 IECs through the induction of negative regulators of innate immunity. However, many questions remain about interactions mediated through these bacterial-derived soluble components and the resulting host immune outcomes in the context of IEC and APC interactions. In the present study, we examined the ability of the LrS to down-regulate pro-inflammatory gene transcription and cytokine production from STS-challenged T84 human IEC and THP-1 human monocyte co-cultures. Cytokine and chemokine profiling revealed that apically delivered LrS induces apical secretion of macrophage inhibitory factor (MIF) and down-regulates STS-induced pro-inflammatory mediator secretion into the apical and basolateral chambers of the T84/THP-1 co-culture. Transcriptional profiling confirmed these results, as the LrS attenuated STS challenge-induced CXCL8 and NFκB1 expression in T84 IECs and THP-1 APCs. Interestingly, the LrS also reversed STS-induced damage to monolayer transepithelial resistance (TER) and permeability, results which were confirmed by ZO-1 gene expression and immunofluorescence visualization of ZO-1 expression in T84 IEC monolayers. The addition of a MIF-neutralizing antibody abrogated the ability of the LrS to reverse STS-induced damage to T84 IEC monolayer integrity, suggesting a novel role for MIF in maintaining IEC barrier function and integrity in response to soluble components derived from LAB. The results presented here provide mechanistic evidence for indirect communication mechanisms used by LAB to modulate immune responses to pathogen challenge, using in vitro approaches which allow for IEC and APC cell communication in a context which more closely mimics that which occurs in vivo.
Expansion of typical lakes in Xinjiang under the combined effects of climate change and human activities

Lakes are important guarantees of regional economic development and ecological security. Previous studies focused on trends of surface area and water level of lakes in Xinjiang, but paid less attention to nonlinear change and driving mechanisms of lake areas at annual and monthly scales. To address this issue, this study used a remote-sensing Big Data cloud platform and mathematical statistical methods to investigate the change in typical lakes and its attribution in Xinjiang during 1986–2020. The results showed that: 1) there was a significant linear trend in Xinjiang lakes: except for Jili Lake, the plains lakes showed an insignificant (p > 0.1) expansion trend, while the mountain lakes showed an significant expansion trend (p < 0.01). 2) There was a significant nonlinear trend in Xinjiang lakes: most of the plains lakes showed periodicity at 14 and 21 years, however most of the mountain lakes showed periodicity at 17 and 21 years. Most of the mutation trends of plains lakes were not significant, yet the mutation trends of mountain lakes showed significant expansion. 3) Human activities were the dominant factor leading to changes in the plains lakes: among the anthropogenic factors, farmland area, GDP, and population had significant effects on lake area (p < 0.1), and lake expansion was closely related to population and farmland area. Among climatic elements, precipitation mainly affected the changes in plains lakes. 4) Climate change was the dominant factor leading to changes in mountain lakes. The effects of temperature change on mountain lakes were all significantly positive (p < 0.05). In the future, it will be necessary to build lake protection schemes that adapt to climate change and human disturbances. This study can provide an important scientific basis for the rational development and utilization of lakes in Xinjiang.