Miracle-dz/UniFAR-FTUs huggingface dataset:
Patterns of mesozooplankton community composition and vertical fluxes in the global ocean

Vertical variations in physical and chemical conditions drive changes in marine zooplankton community diversity and composition. In turn, zooplankton communities play a critical role in regulating the transfer of organic matter produced in the surface ocean to deeper layers. Yet, the links between zooplankton community composition and the strength of vertical fluxes of particles remain elusive, especially on a global scale. Here, we provide a comprehensive analysis of variations in zooplankton community composition and vertical particle flux in the upper kilometer of the global ocean. Zooplankton samples were collected across five depth layers and vertical particle fluxes were assessed using continuous profiles of the Underwater Vision Profiler (UVP5) at 57 stations covering seven ocean basins. Zooplankton samples were analysed using a Zooscan and individual organisms were classified into 19 groups for the quantitative analyses. Zooplankton abundance, biomass and vertical particle flux decreased from the surface to 1000m depth at all latitudes. The zooplankton abundance decrease rate was stronger at sites characterised by oxygen minima (< 5µmol O2.kg−1) where most zooplankton groups showed a marked decline in abundance, except the jellyfishes, molluscs, annelids, large protists and a few copepod families. The attenuation rate of vertical particle fluxes was weaker at such oxygen-depleted sites. Canonical redundancy analyses showed that the epipelagic zooplankton community composition depended on the community structure of surface phytoplankton and the quantity and the quality of the produced particulate organic matter. We provide a consistent baseline of plankton community structure together with estimates of vertical flux and a contribution to our understanding of global zooplankton dynamics in the upper kilometer of the global ocean. Our results further suggest that future changes in surface phytoplankton composition and mesopelagic oxygen loss might lead to profound changes in zooplankton abundance and community structure in both the euphotic and mesopelagic ocean. These changes may affect the vertical export and hereby the strength of the biological carbon pump
Hierarchical clustering optimizes the tradeoff between compositionality and expressivity of task structures for flexible reinforcement learning

A hallmark of human intelligence, but challenging for reinforcement learning (RL) agents, is the ability to compositionally generalise, that is, to recompose familiar knowledge components in novel ways to solve new problems. For instance, when navigating in a city, one needs to know the location of the destination and how to operate a vehicle to get there, whether it be pedalling a bike or operating a car. In RL, these correspond to the reward function and transition function, respectively. To compositionally generalize, these two components need to be transferable independently of each other: multiple modes of transport can reach the same goal, and any given mode can be used to reach multiple destinations. Yet there are also instances where it can be helpful to learn and transfer entire structures, jointly representing goals and transitions, particularly whenever these recur in natural tasks (e.g., given a suggestion to get ice cream, one might prefer to bike, even in new towns). Prior theoretical work has explored how, in model-based RL, agents can learn and generalize task components (transition and reward functions). But a satisfactory account for how a single agent can simultaneously satisfy the two competing demands is still lacking. Here, we propose a hierarchical RL agent that learns and transfers individual task components as well as entire structures (particular compositions of components) by inferring both through a non-parametric Bayesian model of the task. It maintains a factorised representation of task components through a hierarchical Dirichlet process, but it also represents different possible covariances between these components through a standard Dirichlet process. We validate our approach on a variety of navigation tasks covering a wide range of statistical correlations between task components and show that it can also improve generalisation and transfer in more complex, hierarchical tasks with goal/subgoal structures. Finally, we end with a discussion of our work including how this clustering algorithm could conceivably be implemented by cortico-striatal gating circuits in the brain.
Sex differences in tissue gene regulation -- contributions of three classes of sex-biasing factors

Sex differences in physiology and disease in mammals result from the effects of three classes of factors that are inherently unequal in males and females: reversible (activational) effects of gonadal hormones, permanent (organizational) effects of gonadal hormones, and cell-autonomous effects of sex chromosomes, as well as genes driven by these classes of factors. Often, these factors act together to cause sex differences in specific phenotypes, but the relative contribution of each and the interactions among them remain unclear. Here, we used the Four Core Genotypes (FCG) mouse model with or without hormone replacement to distinguish the effects of each class of sex-biasing factors on transcriptome regulation in liver and adipose tissues. We found that the activational hormone levels have the strongest influence on gene expression, followed by the organizational gonadal sex effect and, lastly, sex chromosomal effect, along with interactions among the three factors. Tissue specificity was prominent, with a major impact of estradiol on adipose tissue gene regulation, and of testosterone on the liver transcriptome. The networks affected by the three sex-biasing factors include development, immunity and metabolism, and tissue-specific regulators were identified for these networks. Furthermore, the genes affected by individual sex-biasing factors and interactions among factors are associated with human disease traits such as coronary artery disease, diabetes, and inflammatory bowel disease. Our study offers a tissue-specific account of the individual and interactive contributions of major sex-biasing factors to gene regulation that have broad impact on systemic metabolic, endocrine, and immune functions.
Electrochemical Performances of Layered Polypyrrole/Chemically Reduced Graphene Oxide Nanocomposites as Supercapacitor Electrodes

Nanocomposites of polypyrrole(Ppy) and chemically reduced graphene oxide(CRGO),Ppy/CRGO,have been fabricated through in-situ polymerization of pyrrole on graphene oxide(GO) sheets.The as-synthesized Ppy/CRGO composites were characterized complementarily using scanning electron microscopy(SEM),thermogravimetric analysis(TGA) and Fourier transformed infrared spectroscopy(FT-IR). By controlling the initial ratio of the GO to pyrrole,the layered composites could be obtained and their thickness could be tuned properly.The Ppy/CRGO electrodes were prepared using a mechanical compressing technique and their electrical conductivity and electrochemical properties were characterized systematically.We demonstrated that as electrodes for supercapacitor,the Ppy/CRGO composites with Ppy to CRGO mass ratio of 10∶ 1 showed a competitive capacitance of 421 F·g-1 that could be further increased to 509 F·g-1 by introducing pores in it,which is higher than that of Ppy alone.Given the manifest electrical and electrochemical properties,we envisage that the Ppy/CRGO composites should find applications in supercapacitors.
Synthetic Portnet Generation with Controllable Complexity for Testing and Benchmarking

There are many classes of Petri nets for describing communicating systems. Some of these guarantee important properties, such as termination in the case of portnets. There are also many methods and tools available for their analysis and synthesis. However, when developing new methods, or benchmarking against existing ones, it is often helpful to quickly generate large sets of random models satisfying certain properties and user-defined rules. This paper presents a heuristic-driven method for synthetic generation of random portnets based on refinement rules. The method considers three user-specified complexity parameters: the expected number input and output places, and the prevalence of non-determinism in the skeleton of the generated net. An implementation of this method is available as an open-source Python tool. Experiments demonstrate the relations between the three complexity parameters and investigate the boundaries of the proposed method.
Magnesium sulphate as a treatment of acute attack of multiple sclerosis

The blood-brain barrier (BBB) is a complex organization of cerebral endothelial cells. Deregulation of the BBB is among the earliest cerebrovascular abnormalities seen in multiple sclerosis (MS). Magnesium sulfate has been shown to have a protective effect on BBB integrity in multiple experimental models. Magnesium sulphate attenuates BBB permeability. Also, results of light microscopy and electron microscopy verified that magnesium sulfate can attenuate BBB injury. I suggest using of MgSO4 which attenuates BBB permeability during acute relapses of MS. The hypothesis should be assessed in several experimental and clinical trials. If my hypothesis can be verified experimentally and clinically, then using Mg sulphate to treat MS disease could be achieved.
Digital Tools for the Treatment of Borderline Personality Disorder: A Critical Review of Smartphone Applications

Digital tools provide an opportunity to increase access to and reduce costs of Dialectical Behavioral Therapy (DBT), the gold standard treatment for symptoms of Borderline Personality Disorder (BPD). Yet the integration of smartphone applications has been slow and fractured. This paper summarizes data on DBT digital intervention efficacy, and reviews the intelligent user interface (IUI) and user experience (UX) of four DBT-based smartphone applications. It concludes with suggestions for improved clinical-technology partnerships in order to address barriers to adoption, and presents considerations for expanding current offerings by leveraging passive monitoring, digital nudging and positive reinforcement.
Type I Interferon Induction in Cutaneous DNA Damage Syndromes

Type I interferons (IFNs) as part of the innate immune system have an outstanding importance as antiviral defense cytokines that stimulate innate and adaptive immune responses. Upon sensing of pattern recognition particles (PRPs) such as nucleic acids, IFN secretion is activated and induces the expression of interferon stimulated genes (ISGs). Uncontrolled constitutive activation of the type I IFN system can lead to autoinflammation and autoimmunity, which is observed in autoimmune disorders such as systemic lupus erythematodes and in monogenic interferonopathies. They are caused by mutations in genes which are involved in sensing or metabolism of intracellular nucleic acids and DNA repair. Many authors described mechanisms of type I IFN secretion upon increased DNA damage, including the formation of micronuclei, cytosolic chromatin fragments and destabilization of DNA binding proteins. Hereditary cutaneous DNA damage syndromes, which are caused by mutations in proteins of the DNA repair, share laboratory and clinical features also seen in autoimmune disorders and interferonopathies; hence a potential role of DNA-damage-induced type I IFN secretion seems likely. Here, we aim to summarize possible mechanisms of IFN induction in cutaneous DNA damage syndromes with defects in the DNA double-strand repair and nucleotide excision repair. We review recent publications referring to Ataxia teleangiectasia, Bloom syndrome, Rothmund–Thomson syndrome, Werner syndrome, Huriez syndrome, and Xeroderma pigmentosum. Furthermore, we aim to discuss the role of type I IFN in cancer and these syndromes.
Buffering by Transporters Can Spare Geometric Hindrance in Controlling Glutamate Escape

The surface of astrocyte processes that often surround excitatory synapses is packed with high-affinity glutamate transporters, largely preventing extrasynaptic glutamate escape. The shape and prevalence of perisynaptic astroglia vary among brain regions, in some cases providing a complete isolation of synaptic connections from the surrounding tissue. The perception has been that the geometry of perisynaptic environment is therefore essential to preventing extrasynaptic glutamate escape. To understand to what degree this notion holds, we modelled brain neuropil as a space filled with a scatter of randomly sized, overlapping spheres representing randomly shaped cellular elements and intercellular lumen. Simulating release and diffusion of glutamate molecules inside the interstitial gaps in this medium showed that high-affinity transporters would efficiently constrain extrasynaptic spread of glutamate even when diffusion passages are relatively open. We thus estimate that, in the hippocampal or cerebellar neuropil, the bulk of glutamate released by a synaptic vesicle is rapidly bound by transporters (or high-affinity target receptors) mainly in close proximity of the synaptic cleft, whether or not certain physiological or pathological events change local tissue geometry.
Anti-Obesity and Lipid Lowering Activity of Bauhiniastatin-1 is Mediated Through PPAR-γ/AMPK Expressions in Diet-Induced Obese Rat Model

Objective: To evaluate the therapeutic efficacy and underlying molecular mechanisms of Bauhiniastatin-1 (BSTN1) to alleviate adiposity in diet-induced obese rodent model and in 3T3-L1 cells. Methods: BSTN1 was purified and confirmed through HPLC. In-vitro experiments such as MTT assay, Oil Red-O (ORO) stain, cellular lipid content, glycerol release and RT-PCR analysis were performed in 3T3-L1 cells in the presence and absence of BSTN1. In animal experiments, rats were divided into Group-I: normal pellet diet-fed, Group-II: HFD-fed, Groups-III, IV and V: HFD-fed BSTN1 (1.25, 2.5, and 5 mg/kg.b.wt./day/rat)-treated and Group-VI: HFD-fed Orlistat-treated. The rats were fed either normal diet or high fat diet (HFD) for 18 weeks and water ad-libitum. BSTN1 was orally administered from 13th week onwards to the selected HFD-fed groups. Body composition parameters, biochemical assays, histopathology examination and western blot analysis were performed to identify the predicted targets related to obesity. Molecular docking studies threw light on the binding interactions of BSTN1 against PPAR-γ, FAS and AMPK. Results: BSTN1 at 20 μM significantly (p < 0.001) inhibited adipocyte differentiation and lipid accumulation in 3T3-L1 cells. A conspicuous down-regulation in the mRNA expression levels of PPAR-γ, FAS and SREBP1 was observed but AMPK expression remained unchanged in BSTN1 treated 3T3-L1 cells. A substantial decrease in body weight gain, fat percent, total body fat, serum and liver lipid profile (except high-density lipoprotein), glucose, insulin and insulin resistance in BSTN1 treated rats was noticed in a dose dependent manner. In BSTN1 (5 mg/kg.b.wt.)-treated groups significantly (p < 0.01) elevated plasma adiponectin level but reduced leptin level as well as fall in serum AST and ALT were noticed. Further, the disturbed structural integrity and architecture of adipose and hepatic tissues due to high fat diet feeding were considerably recovered with BSTN1 treatment. Down-regulation in the protein expression level of PPAR-γ and activation of AMPK through phosphorylation was observed in BSTN1 treated rats than the untreated. Molecular docking studies revealed strong binding interactions of BSTN1 against PPAR-γ and AMPK and thus supported the experimental results. Conclusion: Taken together, the results suggest that BSTN1 could be a promising pharmacological molecule in the treatment of obesity and dyslipidemia.
A Multifunctional Solution for Wicked Problems: Value-Chain Wide Facilitation of Legumes Cultivated at Bioregional Scales Is Necessary to Address the Climate-Biodiversity-Nutrition Nexus

Well-managed legume-based food systems are uniquely positioned to curtail the existential challenge posed by climate change through the significant contribution that legumes can make toward limiting Green House Gas (GHG) emissions. This potential is enabled by the specific functional attributes offered only by legumes, which deliver multiple co-benefits through improved ecosystem functions, including reduced farmland biodiversity loss, and better human-health and -nutrition provisioning. These three critical societal challenges are referred to collectively here as the “climate-biodiversity-nutrition nexus. ” Despite the unparalleled potential of the provisions offered by legumes, this diverse crop group remains characterized as underutilized throughout Europe, and in many regions world-wide. This commentary highlights that integrated, diverse, legume-based, regenerative agricultural practices should be allied with more-concerted action on ex-farm gate factors at appropriate bioregional scales. Also, that this can be achieved whilst optimizing production, safeguarding food-security, and minimizing additional land-use requirements. To help avoid forfeiting the benefits of legume cultivation for system function, a specific and practical methodological and decision-aid framework is offered. This is based upon the identification and management of sustainable-development indicators for legume-based value chains, to help manage the key facilitative capacities and dependencies. Solving the wicked problems of the climate-biodiversity-nutrition nexus demands complex solutions and multiple benefits and this legume-focus must be allied with more-concerted policy action, including improved facilitation of the catalytic provisions provided by collaborative capacity builders—to ensure that the knowledge networks are established, that there is unhindered information flow, and that new transformative value-chain capacities and business models are established.
A Recurrent Cryptic MED14-HOXA9 Rearrangement in an Adult Patient With Mixed-Phenotype Acute Leukemia, T/myeloid, NOS

To define the fusion genes in T/myeloid mixed-phenotype acute leukemia (T/M MPAL), we performed transcriptome sequencing of diagnostic bone marrow samples from 20 adult patients. Our analysis identified a second instance of a recurrent MED14-HOXA9 chimeric gene resulting from the in-frame fusion of exon 23 of MED14 and exon 1 of HOXA9, the first in an adult patient. The MED14-HOXA9 fusion gene was detected in both the diagnostic and relapsed blasts with reverse transcription-polymerase chain reaction and Sanger sequencing. The patient received combined conventional chemotherapy but suffered relapse at 11 months and died of disease progression one year after the initial diagnosis. Our data suggest that MED14-HOXA9 is a cryptic recurrent aberration in T/M MPAL, which might indicate an aggressive clinical course and inferior outcome after conventional chemotherapy. Further studies will be carried out to reveal the effects of the MED14-HOXA9 fusion on the differentiation and proliferation of leukemia stem cells, as well as suitable treatment strategies for this emerging entity.
Effects of Smoking on Inflammatory Markers in a Healthy Population as Analyzed via the Gut Microbiota

The number of people who smoke has increased in recent years, and the incidence of smoking-related diseases increases annually. This study was conducted to explore whether smoking affects diseases via changes in the gut microbiota. We enrolled 33 smokers and 121 non-smokers. We collected fecal samples from all participants and performed whole-genome sequencing. Smoking significantly affected the gut microbiota. At the phylum through genus levels, the smokers’ microbiotas showed slight changes compared with those of the non-smokers. The α- and β-diversities differed significantly between the smokers and non-smokers, and the smokers’ gut microbiota compositions differed significantly from those of the non-smokers. At the species level, the relative abundances of Ruminococcus gnavus (P=0.00197) and Bacteroides vulgatus (P=0.0468) were significantly greater in the smokers than in the non-smokers, while the relative abundances of Faecalibacterium prausnitzii (P=0.0000052) and Akkermansia muciniphila (P=0.0057) were significantly lower in the smokers. Smoking increases inflammation in the body by inducing an increased abundance of proinflammatory bacteria. Non-smokers had higher abundances of anti-inflammatory microorganisms than did smokers; these microorganisms can produce short-chain fatty acids, which inhibit inflammation.
Can Control Infections Slow Down the Progression of Alzheimer’s Disease? Talking About the Role of Infections in Alzheimer’s Disease

Alzheimer’s disease as the most common age-related dementia affects more than 40 million people in the world, representing a global public health priority. However, the pathogenesis of Alzheimer’s disease (AD) is complex, and it remains unclear. Over the past decades, all efforts made in the treatments of AD, with targeting the pathogenic amyloid β (Aβ), neurofibrillary tangles, and misfolded tau protein, were failed. Recently, many studies have hinted that infection, and chronic inflammation that caused by infection are crucial risk factors for AD development and progress. In the review, we analyzed the role of infections caused by bacteria, viruses, and other pathogens in the pathogenesis of AD and its animal models, and explored the therapeutic possibility with anti-infections for AD. However, based on the published data, it is still difficult to determine their causal relationship between infection and AD due to contradictory results. We think that the role of infection in the pathogenesis of AD should not be ignored, even though infection does not necessarily cause AD, it may act as an accelerator in AD at least. It is essential to conduct the longitudinal studies and randomized controlled trials in humans, which can determine the role of infection in AD and clarify the links between infection and the pathological features of AD. Finding targeting infection drugs and identifying the time window for applying antibacterial or antiviral intervention may be more promising for future clinical therapeutic strategies in AD.
The Role of the Medial Septum—Associated Networks in Controlling Locomotion and Motivation to Move

The Medial Septum and diagonal Band of Broca (MSDB) was initially studied for its role in locomotion. However, the last several decades were focussed on its intriguing function in theta rhythm generation. Early studies relied on electrical stimulation, lesions and pharmacological manipulation, and reported an inconclusive picture regarding the role of the MSDB circuits. Recent studies using more specific methodologies have started to elucidate the differential role of the MSDB’s specific cell populations in controlling both theta rhythm and behaviour. In particular, a novel theory is emerging showing that different MSDB’s cell populations project to different brain regions and control distinct aspects of behaviour. While the majority of these behaviours involve movement, increasing evidence suggests that MSDB-related networks govern the motivational aspect of actions, rather than locomotion per se. Here, we review the literature that links MSDB, theta activity, and locomotion and propose open questions, future directions, and methods that could be employed to elucidate the diverse roles of the MSDB-associated networks.