Miracle-dz/UniFAR-FTUs huggingface dataset:
Inflammatory cytokine responses in children with asymptomatic malaria infection living in rural, semi‐urban and urban areas in south‐eastern Gabon

Cytokines are soluble mediators of the immune response, and their evolution influences the disease outcome. Gaining knowledge on cytokines has become important, as they can constitute biomarkers allowing the diagnosis of malaria and preventing severe forms of the disease. Here, we investigated 10 cytokines and their circulating levels in asymptomatic Gabonese children with Plasmodium falciparum infection living in urban, semi‐urban and rural areas. Blood samples were collected from 273 schoolchildren (153 uninfected and 120 infected) aged 6 to 192 months. Hematological parameters were determined and P. falciparum diagnosis was performed using a rapid diagnosis test, microscopy and nested polymerase chain reaction (PCR). Plasma pro‐ [interferon (IFN)‐γ, tumor necrosis factor (TNF)‐α, interleukin (IL)‐6, IL‐12p70, IL‐17A and IL‐22] and anti‐inflammatory [IL‐10, IL‐4, IL‐13 and transforming growth factor (TGF)‐β] cytokine levels were measured by enzyme‐linked immunosorbent assay (ELISA) and compared between asymptomatic‐infected and uninfected children. Results revealed that without distinction of area, IL‐10 and IL‐6 levels were higher in infected compared to uninfected children; however, the pro‐ and anti‐inflammatory ratios (IL‐6/IL‐10 and TNF‐α/IL‐10) were similar. Furthermore, with area distinction significantly elevated levels of IL‐10 in these asymptomatic children were always accompanied by either significantly low or high levels of a proinflammatory cytokine. Also, comparison between asymptomatic‐infected children from the three areas showed significantly lower IL‐17A, IL‐22 and TGF‐β levels in urban area compared to semi‐urban and rural areas. These results suggest that asymptomatic malaria infections induce significantly high inflammatory cytokine levels without modifying the balanced between pro‐ and anti‐inflammatory cytokines and underline the higher exposure to infections of children in rural areas.
Loss of Krüppel‐like factor 9 facilitates stemness in ovarian cancer ascites‐derived multicellular spheroids via Notch1/slug signaling

The ascites that develops in advanced OC, both at diagnosis and upon recurrence, is a rich source of multicellular spheroids/aggregates (MCSs/MCAs), which are the major seeds of tumor cell dissemination within the abdominal cavity. However, the molecular mechanism by which specific ascites‐derived tumor cells survive and metastasize remains largely unknown. In this study, we elucidated cancer stem cell (CSC) properties of ascites‐derived MCSs, concomitant with enhanced malignancy, induced EMT, and low KLF9 (Krüppel‐like factor 9) expression, compared with PTCs. KLF9 was also downregulated in OC cell line‐derived spheroids and the CD117+CD44+ subpopulation in MCSs. Functional experiments demonstrated that KLF9 negatively modulated stem‐like properties in OC cells. Mechanistic studies revealed that KLF9 reduced the transcriptional expression of Notch1 by directly binding to the Notch1 promoter, thereby inhibiting the function of slug in a CSL‐dependent manner. Clinically, expression of KLF9 was associated with histological grade and loss of KLF9 predicts poor prognosis in OC.
The role of hippocampal glial glutamate transporter (GLT‐1) in morphine‐induced behavioral responses

Opioid abuse modifies synaptic plasticity, which leads to behavioral changes, such as morphine dependence, but the mechanism remains poorly understood. Glial cells play an important role in the modulation of synaptic plasticity and are involved in addictive‐like behaviors. The indisputable role of glutamate in opiate addiction has been shown. Astrocytes, a type of glial cells, which are integral functional elements of synapses, modulate the concentration of glutamate in the synaptic space. One of the most important mechanisms for glutamate concentration regulation is its uptake from the synaptic cleft. In this study, we evaluated the role of hippocampal glial glutamate transporter (GLT‐1) in morphine dependence. Male rats received subcutaneous (s.c.) morphine sulfate (10 mg/kg) at an interval of 12 h for 9 days. In order to activate GLT‐1, animals received an intrahippocampal injection of ceftriaxone (0.5 mmol/0.5 μl) in the CA1 region of the hippocampus, 30 min before each morphine administration. Rats were assessed for morphine dependence by monitoring naloxone hydrochloride‐induced morphine withdrawal. Our results showed that hippocampal microinjection of ceftriaxone, as an activator of GLT‐1, reduced some signs of morphine withdrawal, such as activity, diarrhea, head tremor, freezing, and ptosis. It seems that hippocampal GLT‐1 can be affected by chronic morphine administration and involved in morphine dependence. Therefore, its activation may reduce morphine side effects by reducing hippocampal glutamate.
Supplementary material to "Mangrove sediment organic carbon storage and sources in relation to forest age and position along a deltaic salinity gradient"

Abstract. Mangroves are widely recognised as key ecosystems for climate change mitigation as they capture and store significant amounts of sediment organic carbon (SOC). Yet, there is incomplete knowledge on how sources of SOC and their differential preservation vary between mangrove sites in relation to environmental gradients. To address this, sediment depth profiles were sampled from mangrove sites ranging from river-dominated to marine-dominated sites and including old and young mangrove sites, in the Guayas delta (Ecuador). The stable carbon isotope ratios (δ13C) and the elemental composition (OC%, C : N) of sediment profiles, local vegetation (i.e., autochthonous carbon) and externally-supplied suspended particulate matter (i.e., allochthonous carbon) were obtained to assess variations in the amount and sources of SOC at different locations throughout the delta. In general, across all sites, we found increasing SOC contents and stocks are associated with decreasing δ13C and increasing C / N ratios, indicating that SOC stocks and sources are intrinsically related. The SOC stocks (down to 0.64 m deep profiles) are significantly lower in young mangrove sites (46–55 Mg C ha−1) than in old sites (78–92 Mg C ha−1). The SOC in the young mangrove sites is mainly of allochthonous origin (estimated on average at 79 %) whereas in the old sites there is a slight dominance of autochthonous OC (on average 59 %). Moreover, from river- to marine-dominated sites, a pattern was found of increasing SOC stocks and increasing autochthonous SOC contribution. These observed differences along the two studied gradients are hypothesized to be mainly driven by (1) expected higher sedimentation rates in the river-dominated and lower-elevation younger sites, thereby “diluting” the SOC content and decreasing the relative autochthonous contribution; and (2) potential differences in preservation of the different SOC sources. Our finding of high contributions of allochthonous SOC, especially in young mangroves, implies that this carbon is not originating from CO2 sequestration by the mangrove ecosystem itself, but is externally supplied from other terrestrial, marine or estuarine ecosystems. We argue that accounting for lower SOC stocks and higher contribution of allochthonous SOC in young and river-dominated mangrove sites, as compared to old and marine-dominant sites, is particularly relevant for designing and valuing nature-based climate mitigation programs based on mangrove reforestation.
Review on Theory of Computation

: Automata theory that is also considered as theory computation is defined as a branch of the theory of computer science and mathematics that generally focuses on the logic of computation in respect to easy machines which are referred to as automata. The philosophy of computation in theoretical computer science is the field that utilizes an algorithm to decide whether something how questions can easily be solved on a mathematical model. The sciences are classified into three major groups: theory of technology, programming science and science of machine sophistication. Computer scientists use a conceptual representation of machines called the numerical model to perform a systematic analysis of computing. Various methods are being implemented, but the Turing machine is the most frequently studied. This paper presents a comprehensive review of the theory of computation along with its applications.
Soil-derived Nature's Contributions to People and their contribution to the UN Sustainable Development Goals

This special issue provides an assessment of the contribution of soils to Nature's Contributions to People (NCP). Here, we combine this assessment and previously published relationships between NCP and delivery on the UN Sustainable Development Goals (SDGs) to infer contributions of soils to the SDGs. We show that in addition to contributing positively to the delivery of all NCP, soils also have a role in underpinning all SDGs. While highlighting the great potential of soils to contribute to sustainable development, it is recognized that poorly managed, degraded or polluted soils may contribute negatively to both NCP and SDGs. The positive contribution, however, cannot be taken for granted, and soils must be managed carefully to keep them healthy and capable of playing this vital role. A priority for soil management must include: (i) for healthy soils in natural ecosystems, protect them from conversion and degradation; (ii) for managed soils, manage in a way to protect and enhance soil biodiversity, health and sustainability and to prevent degradation; and (iii) for degraded soils, restore to full soil health. We have enough knowledge now to move forward with the implementation of best management practices to maintain and improve soil health. This analysis shows that this is not just desirable, it is essential if we are to meet the SDG targets by 2030 and achieve sustainable development more broadly in the decades to come. This article is part of the theme issue ‘The role of soils in delivering Nature's Contributions to People’.
Digital social innovation: An overview and research framework

Taking OSS as an example of DSI, Dong and Götz (2021) present a new perspective on understanding the role of project leaders as boundary spanners in the development of DSI. They investigate the impacts of size and tenure of project leaders on project performance from a social viewpoint — the quantity of software being used by users and the quality of software to users' satisfaction. To tease out the theoretical mechanism of project leaders as boundary spanners, they further examine the moderating effects of project leaders' network ties across different projects in which they are involved. This study contributes a novel resource dependence perspective, suggesting project leaders as boundary spanners and their social network embeddedness as a key contingency condition. It contributes to our understanding of how to better develop DSI through leveraging project leaders' boundary-spanning role. Practically, it identifies key success factors related to project leaders with useful guidance for organising a larger, experienced and well-embedded leader team that can improve project performance. This study views OSS as a notable type of DSI, as OSS is developed by mass collaboration (crowdsourcing) within digital communities to provide digital innovation (i.e., software) as free alternatives to commercial products (Qureshi & Fang, 2011). Such digital innovation has clear social value and is particularly useful for economically disadvantaged users for whom proprietary software is not affordable. There are many examples of OSS that help address the UN's SDG#4 quality education (e.g., Moodle), SDG#8 decent work and economic growth (e.g., OpenOffice, FileZilla and Tor Browser) and SDG#9 industry, innovation and infrastructure (e.g., Code::Blocks and Scribus). This study demonstrates that the resource dependence perspective is a powerful theoretical lens for DSI research, highlighting the boundary-spanning role of project leaders in facilitating social value creation regarding quantity and quality. Future research can adopt this novel theoretical perspective to investigate other success factors associated with project leaders in developing different types of DSI and deepen our understanding of organising for DSI.
Distinct Roles of Dopamine D1 and D2 Receptor-expressing Neurons in the Nucleus Accumbens for a Strategy Dependent Decision Making

To optimize decision making, animals need to execute not only a strategy to choose a good option but sometimes also one to avoid a bad option. A psychological study indicates that positive and negative information is processed in a different manner in the brain. The nucleus accumbens (NAc) contains two different types of neurons, dopamine D1 and D2 receptor-expressing neurons which are implicated in reward-based decision making and aversive learning. However, little is known about the neural mechanisms by which D1 or D2 receptor-expressing neurons in the NAc contribute to the execution of the strategy to choose a good option or one to avoid a bad option under decision making. Here, we have developed two novel visual discrimination tasks for mice to assess the strategy to choose a good option and one to avoid a bad option. By chemogenetically suppressing the subpopulation of the NAc neurons, we have shown that dopamine D2 receptor-expressing neurons in the NAc selectively contribute to the strategy to avoid a bad option under reward-based decision making. Furthermore, our optogenetic and calcium imaging experiments indicate that dopamine D2 receptor-expressing neurons are activated by error choices and the activation following an error plays an important role in optimizing the strategy in the next trial. Our findings suggest that the activation of D2 receptor-expressing neurons by error choices through learning enables animals to execute the appropriate strategy.
Multi-layered chromatin proteomics identifies cell vulnerabilities in DNA repair

The DNA damage response (DDR) is essential to maintain genome stability, and its deregulation predisposes to carcinogenesis while encompassing attractive targets for cancer therapy. Chromatin governs the DDR via the concerted interplay among different layers, including DNA, histone post-translational modifications (hPTMs), and chromatin-associated proteins. Here we employ multi-layered proteomics to characterize chromatin-mediated functional interactions of repair proteins, signatures of hPTMs, and the DNA-bound proteome during DNA double-strand break (DSB) repair at high temporal resolution. Our data illuminate the dynamics of known and novel DDR-associated factors both at chromatin and at DSBs. We functionally attribute novel chromatin-associated proteins to repair by non-homologous end-joining (NHEJ), homologous recombination (HR) and DSB repair pathway choice. We reveal histone reader ATAD2, microtubule organizer TPX2 and histone methyltransferase G9A as regulators of HR and PARP-inhibitor sensitivity. Furthermore, we distinguish hPTMs that are globally induced by DNA damage from those specifically acquired at sites flanking DSBs (γH2AX foci-specific), and profiled their dynamics during the DDR. Integration of complementary chromatin layers implicates G9A-mediated monomethylation of H3K56 at DSBs in HR. Our data provide a dynamic chromatin-centered view of the DDR that can be further mined to identify novel mechanistic links and cell vulnerabilities in DSB repair.
3,3’-Diindolylmethane induces apoptosis and autophagy in fission yeast

3,3’-Diindolylmethane (DIM) is a compound derived from the digestion of indole-3-carbinol, found in the broccoli family. It induces apoptosis and autophagy in some types of human cancer. DIM extends lifespan in the fission yeast Schizosaccharomyces pombe. The mechanisms by which DIM induces apoptosis and autophagy in humans and expands lifespan in fission yeasts are not fully understood. Here, we show that DIM induces apoptosis and autophagy in log-phase cells, which is dose-dependent in fission yeast. A high concentration of DIM disrupted the nuclear envelope (NE) structure and induced chromosome condensation at an early time point. In contrast, a low concentration of DIM induced autophagy but did not disrupt NE structure. The mutant defective in autophagy was more sensitive to a low concentration of DIM, demonstrating that the autophagic pathway contributes to the survival of cells against DIM. Moreover, our results showed that the lem2 mutant is more sensitive to DIM. NE in the lem2 mutant was disrupted even at the low concentration of DIM. Our results demonstrate that the autophagic pathway and NE integrity are important to maintain viability in the presence of a low concentration of DIM. The mechanism of apoptosis and autophagy induction by DIM might be conserved in fission yeast and humans. Further studies will contribute to the understanding of the mechanism of apoptosis and autophagy by DIM in fission yeast and humans.
A study of spatio-temporal dynamics of emotion processing using DENS dataset ⋆,⋆⋆

The emotion research with artiﬁcial stimuli does not represent the dynamic processing of emotions in real-life situations. The lack of data on emotion with the ecologically valid naturalistic paradigm hinders the knowledge of emotion mechanisms in a real-world interaction. To this aim, we collected the emotional multimedia clips, validated them with the university students, recorded the neuro-physiological activities and self-assessment ratings for these stimuli. Participants localized their emotional feelings (in time) and were free to choose the best emotion for describing their feelings with minimum distractions and cognitive load. The obtained electrophysiological and self-assessment responses were analyzed with functional connectivity, machine learning and source localization techniques. We observed that the connectivity patterns in the theta and beta band could diﬀerentiate emotions better. Using machine learning, we observed that the classiﬁcation of aﬀective self-assessment features, namely dominance, familiarity, and self-relevance, involves midline brain regions responsible for mentalization and event construction activity compared to valence and arousal, which were mainly associated with lateral brain regions. This ﬁnding advocates the need for more than two dimensions for emotion representation. The channels with high predictability were source localized to the brain regions in DMN, sensorimotor and salience networks. Hence, in this naturalistic study, we ﬁnd that the domain-general systems contribute to emotion construction.
Local regulation of extracellular vesicle traffic by the synaptic endocytic machinery

Neuronal extracellular vesicles (EVs) can be locally released from presynaptic terminals, carrying cargoes that are important in intercellular signaling and disease. EVs are derived from endosomes, but it remains unclear how synaptic cargoes are directed to the EV pathway, rather than undergoing conventional retrograde endosomal transport and degradation. Here, we find that the clathrin-mediated endocytic machinery plays an unexpected role in maintaining a release-competent pool of synaptic EV cargoes. Endocytic mutants, including nervous wreck (nwk), Shibire/Dynamin, and AP-2, exhibit local depletion of multiple cargoes in EV donor terminals. Accordingly, nwk mutants phenocopy synaptic plasticity defects associated with loss of the EV cargo Synaptotagmin-4, and suppress lethality upon overexpression of the EV cargo Amyloid Precursor Protein. These EV defects are genetically separable from canonical functions of endocytic proteins in synaptic vesicle recycling and synaptic growth. This endocytic pathway opposes the endosomal retromer complex to regulate EV cargo levels, and acts upstream of synaptic cargo removal by retrograde axonal transport. Our data suggest a novel molecular mechanism that protects EV cargoes from local depletion at synapses.
Wild Wheat Introgression Promotes Temporal Water fluxes Dynamics under Terminal Drought Stress through Plant-Atmospheric Interrelations

The intensity of water stress experienced by plants depends upon soil moisture status as well as atmospheric variables such as temperature, radiation, and air vapour pressure deficit (VPD). Although the role of shoot architecture with these edaphic and atmospheric factors is well-studied, the extent to shoot and root dynamic interactions as a continuum are controlled by genotypic variation is less known. Here, we targeted these interactions using a wild emmer introgression line (IL20) with a distinct drought-induced shift in the shoot-to-root ratio and its drought-sensitive recurrent parent Svevo. Using a gravimetric platform, we show that IL20 maintained higher root water influx and gas exchange under terminal drought, which supported a greater growth. Interestingly, the advantage of IL20 in root influx and transpiration was expressed earlier during the daily diurnal cycle under lower VPD and therefore supported higher transpiration efficiency. Application of structural equation model indicates that under water-stress, VPD and radiation are antagonistic to transpiration rate, whereas the root water influx operates as feedback for the higher atmospheric responsiveness of leaves. Collectively, these results suggest that a drought-induced shift in root-to-shoot ratio can improve plant water uptake potential in a short preferable time window determined by both water and atmospheric parameters.
Active Sinking Particles: Sessile Suspension Feeders significantly alter the Flow and Transport to Sinking Aggregates

Sinking or sedimentation of biological aggregates plays a critical role in carbon sequestration in the ocean and in vertical material fluxes in waste-water treatment plants. In both these contexts, the sinking aggregates are “active,” since they are biological hot-spots and are densely colonized by microorganisms including bacteria and sessile protists, some of which generate feeding currents. However, the effect of these feeding currents on the sinking rates, trajectories, and mass transfer to these “active sinking particles,” has not previously been studied. Here we use a novel scale-free vertical-tracking microscope (a.k.a. Gravity Machine, Krishnamurthy et al. “Scale-free vertical tracking microscopy.” Nature Methods (2020)) to follow model sinking aggregates (agar spheres) with attached protists (Vorticella convallaria), sinking over long distances while simultaneously measuring local flows. We find that activity due to attached Vorticella cause substantial changes to the flow around aggregates in a dynamic manner and reshape mass transport boundary layers. Further, we find that activity-mediated local flows along with sinking significantly changes how aggregates interact with the water-column at larger scales by modifying the encounter and plume cross-sections and by inducing sustained aggregate rotations. In this way our work suggests an important role of biological activity in understanding the growth, degradation, composition and sinking speeds of aggregates with consequences for predicting vertical material fluxes in marine, freshwater and man-made environments. 1 Significance Statement Sinking aggregates are a critical part of aquatic ecosystems. Plentiful sinking aggregates account for the majority of carbon sequestration in the oceans. These aggregates are densely colonized by microorganisms, including many that generate feeding currents. Utilizing a novel instrument for high resolution imaging of sinking particles, we demonstrate that these feeding currents significantly change how water flows near the aggregates. We show that these changes in flow are likely to affect aquatic system processes, including aggregation rates, degradation rates, sinking speeds, and aggregate composition. Our work provides a starting point for exploring the larger-scale implications of attached organisms on these system processes, which, in turn, are critical for understanding carbon sequestration in the oceans or efficiency in waste-water treatment plants.