Miracle-dz/UniFAR-FTUs huggingface dataset:
Plant stem cell research is uncovering the secrets of longevity and persistent growth

Summary Plant stem cells have several extraordinary features: they are generated de novo during development and regeneration, maintain their pluripotency, and produce another stem cell niche in an orderly manner. This enables plants to survive for an extended period and to continuously make new organs, representing a clear difference in their developmental program from animals. To uncover regulatory principles governing plant stem cell characteristics, our research project ‘Principles of pluripotent stem cells underlying plant vitality’ was launched in 2017, supported by a Grant‐in‐Aid for Scientific Research on Innovative Areas from the Japanese government. Through a collaboration involving 28 research groups, we aim to identify key factors that trigger epigenetic reprogramming and global changes in gene networks, and thereby contribute to stem cell generation. Pluripotent stem cells in the shoot apical meristem are controlled by cytokinin and auxin, which also play a crucial role in terminating stem cell activity in the floral meristem; therefore, we are focusing on biosynthesis, metabolism, transport, perception, and signaling of these hormones. Besides, we are uncovering the mechanisms of asymmetric cell division and of stem cell death and replenishment under DNA stress, which will illuminate plant‐specific features in preserving stemness. Our technology support groups expand single‐cell omics to describe stem cell behavior in a spatiotemporal context, and provide correlative light and electron microscopic technology to enable live imaging of cell and subcellular dynamics at high spatiotemporal resolution. In this perspective, we discuss future directions of our ongoing projects and related research fields.
A dark quencher genetically encodable voltage indicator (dqGEVI) exhibits high fidelity and speed

Significance Voltage sensing with genetically expressed optical probes is highly desirable for large-scale recordings of neuronal activity and detection of localized voltage signals in single neurons. Here we describe a method for a two-component (hybrid) genetically encodable fluorescent voltage sensing in neurons. The approach uses a glycosylphosphatidylinositol-tagged fluorescent protein (enhanced green fluorescent protein) that ensures the fluorescence to be specifically confined to the outside of the plasma membrane and D3, a voltage-dependent quencher. Previous hybrid genetically encoded voltage sensing approaches relied on a single quenching molecule, dipycrilamine (DPA), which is toxic, increases membrane capacitance, interferes with neurotransmitters, and is explosive. Our method uses a nontoxic and nonexplosive compound that performs better than DPA in all aspects of fluorescent voltage sensing. Voltage sensing with genetically expressed optical probes is highly desirable for large-scale recordings of neuronal activity and detection of localized voltage signals in single neurons. Most genetically encodable voltage indicators (GEVI) have drawbacks including slow response, low fluorescence, or excessive bleaching. Here we present a dark quencher GEVI approach (dqGEVI) using a Förster resonance energy transfer pair between a fluorophore glycosylphosphatidylinositol–enhanced green fluorescent protein (GPI-eGFP) on the outer surface of the neuronal membrane and an azo-benzene dye quencher (D3) that rapidly moves in the membrane driven by voltage. In contrast to previous probes, the sensor has a single photon bleaching time constant of ∼40 min, has a high temporal resolution and fidelity for detecting action potential firing at 100 Hz, resolves membrane de- and hyperpolarizations of a few millivolts, and has negligible effects on passive membrane properties or synaptic events. The dqGEVI approach should be a valuable tool for optical recordings of subcellular or population membrane potential changes in nerve cells.
Time Course of Inflammatory and Procoagulant Markers in the Early Period After Total Hip Replacement

Our study aimed to investigate the levels and time-course of systemic inflammatory and hemostasis markers in the early postoperative period in patients undergoing total hip replacement (THR). The study included 70 patients of both sexes, average age 68.4 ± 10.9 years. Levels of inflammatory and hemostasis markers were measured before surgery (POD 0), a day after the surgery (POD 1) and 5 days after surgery (POD 5). In the postoperative period inflammatory markers increased. The operation provoked a significant increase of CRP on POD 1 in comparison to POD 0 (68.5 ± 5.4 vs 6.8 ± 2.2 μg/mL, p < 0.001) and the additional increase was registered on POD 5 (87.5 ± 8.1 vs 68.5 ± 5.4 μg/mL, p < 0.001). Interleukin-6 significantly increased on POD 1 (251.5 ± 21.6 vs 14.6 ± 7.1 μg/mL, p < 0.001) and after that (POD 5) decreased. After surgery leukocyte count, neutrophil/lymphocyte ratio and platelet/lymphocyte ratio were significantly higher compared to POD 0. Activation of coagulation in the postoperative period was shown by increased peak thrombin on POD 5 in comparison to POD 0 (185 ± 27 vs. 124 ± 31 nM, p < 0.001). D-dimer was increased on POD 1 and an additional rise was observed on POD 5. vWF also progressively increased in the observed period. Results of our study showed that after THR systemic inflammatory markers increased and coagulation function was enhanced. Determination of inflammatory and procoagulant markers could help identify patients at risk for cardiovascular thromboembolic events.
Anharmonic Vibrational Spectroscopy of the F-(H2O)n Complexes, n = 1, 2

We report anharmonic vibrational spectra (fundamentals, first overtones) for the F-(H2O) and F-(H2O)2 clusters computed at the MP2 and CCSD(T) levels of theory with basis sets of triple-ζ quality. Anharmonic corrections were estimated via the correlation-corrected vibrational self-consistent field (CC−VSCF) method. The CC−VSCF anharmonic spectra obtained on the potential energy surfaces evaluated at the CCSD(T) level of theory are the first ones reported at a correlated level beyond MP2. We have found that the average basis set effect (TZP vs aug-cc-pVTZ) is on the order of 30−40 cm-1, whereas the effects of different levels of electron correlation [MP2 vs CCSD(T)] are smaller, 20−30 cm-1. However, the basis set effect is much larger in the case of the H-bonded O−H stretch of the F-(H2O) cluster amounting to 100 cm-1 for the fundamentals and 200 cm-1 for the first overtones. Our calculations are in agreement with the limited available set of experimental data for the F-(H2O) and F-(H2O)2 systems and provi.
Partial Inhibition of Calcineurin Activity by Rcn2 as a Potential Remedy for Vps13 Deficiency

Regulation of calcineurin, a Ca2+/calmodulin-regulated phosphatase, is important for the nervous system, and its abnormal activity is associated with various pathologies, including neurodegenerative disorders. In yeast cells lacking the VPS13 gene (vps13Δ), a model of VPS13-linked neurological diseases, we recently demonstrated that calcineurin is activated, and its downregulation reduces the negative effects associated with vps13Δ mutation. Here, we show that overexpression of the RCN2 gene, which encodes a negative regulator of calcineurin, is beneficial for vps13Δ cells. We studied the molecular mechanism underlying this effect through site-directed mutagenesis of RCN2. The interaction of the resulting Rcn2 variants with a MAPK kinase, Slt2, and subunits of calcineurin was tested. We show that Rcn2 binds preferentially to Cmp2, one of two alternative catalytic subunits of calcineurin, and partially inhibits calcineurin. Rcn2 ability to bind to and reduce the activity of calcineurin was important for the suppression. The binding of Rcn2 to Cmp2 requires two motifs in Rcn2: the previously characterized C-terminal motif and a new N-terminal motif that was discovered in this study. Altogether, our findings can help to better understand calcineurin regulation and to develop new therapeutic strategies against neurodegenerative diseases based on modulation of the activity of selected calcineurin isoforms.
Polylysine-immobilized Affinity Nylon Membrane used for Bilirubin Adsorption

Microporous polyamide membranes were activated by epibromohydrin and subsequently bound with hydroxyethylcellulose (HEC) to amplify reactive groups. Then polylysine (PLL) as ligand was also immobilized onto the nylon membranes by epibromohydrin activation. Such PLL-HEC affinity membranes are used to adsorb bilirubin from the phosphate buffer solutions. The adsorption mechanism of bilirubin and the effects of temperature and ionic strength on adsorption were investigated by batch experiments. These membranes were also set in stack and used to adsorb bilirubin. The results showed that the quicker adsorption equilibrium was attained and these membranes exhibited high binding affinity capacities for bilirubin.
A transcriptomic analysis of sugarcane response to Leifsonia xyli subsp. xyli infection

Sugarcane ratoon stunting disease (RSD) caused by Leifsonia xyli subsp. xyli (Lxx) is a common destructive disease that occurs around the world. Lxx is an obligate pathogen of sugarcane, and previous studies have reported some physiological responses of RSD-affected sugarcane. However, the molecular understanding of sugarcane response to Lxx infection remains unclear. In the present study, transcriptomes of healthy and Lxx-infected sugarcane stalks and leaves were studied to gain more insights into the gene activity in sugarcane in response to Lxx infection. RNA-Seq analysis of healthy and diseased plants transcriptomes identified 107,750 unigenes. Analysis of these unigenes showed a large number of differentially expressed genes (DEGs) occurring mostly in leaves of infected plants. Sugarcane responds to Lxx infection mainly via alteration of metabolic pathways such as photosynthesis, phytohormone biosynthesis, phytohormone action-mediated regulation, and plant-pathogen interactions. It was also found that cell wall defense pathways and protein phosphorylation/dephosphorylation pathways may play important roles in Lxx pathogeneis. In Lxx-infected plants, significant inhibition in photosynthetic processes through large number of differentially expressed genes involved in energy capture, energy metabolism and chloroplast structure. Also, Lxx infection caused down-regulation of gibberellin response through an increased activity of DELLA and down-regulation of GID1 proteins. This alteration in gibberellic acid response combined with the inhibition of photosynthetic processes may account for the majority of growth retardation occurring in RSD-affected plants. A number of genes associated with plant-pathogen interactions were also differentially expressed in Lxx-infected plants. These include those involved in secondary metabolite biosynthesis, protein phosphorylation/dephosphorylation, cell wall biosynthesis, and phagosomes, implicating an active defense response to Lxx infection. Considering the fact that RSD occurs worldwide and a significant cause of sugarcane productivity, a better understanding of Lxx resistance-related processes may help develop tools and technologies for producing RSD-resistant sugarcane varieties through conventional and/or molecular breeding.
Regulators of commensal and pathogenic life‐styles of an opportunistic fungus—Candida albicans

The yeast Candida albicans is primarily a commensal of humans that colonizes the mucosal surfaces of the gastrointestinal and genital tracts. Yet, C. albicans can under certain circumstances undergo a shift from commensalism to pathogenicity. This transition is governed by fungal factors such as morphological transitions, environmental cues for instance relationships with gut microbiota and the host immune system. C. albicans utilizes distinct sets of regulatory programs to colonize or infect its host and to evade the host defense systems. Moreover, an orchestrated iron acquisition mechanism operates to adapt to specific niches with variable iron availability. Studies on regulatory networks and morphogenesis of these two distinct modes of C. albicans growth, suggest that both yeast and hyphal forms exist in both growth patterns and the regulatory circuits are inter‐connected. Here, we summarize current knowledge about C. albicans commensal‐to‐pathogen shift, its regulatory elements and their contribution to human disease.
Multi‐Constrained Catchment Scale Optimization of Groundwater Abstraction Using Linear Programming

Due to increasing water demands globally, freshwater ecosystems are under constant pressure. Groundwater resources, as the main source of accessible freshwater, are crucially important for irrigation worldwide. Over‐abstraction of groundwater leads to declines in groundwater levels; consequently, the groundwater inflow to streams decreases. The reduction in baseflow and alteration of the streamflow regime can potentially have an adverse effect on groundwater‐dependent ecosystems. A spatially distributed, coupled groundwater–surface water model can simulate the impacts of groundwater abstraction on aquatic ecosystems. A constrained optimization algorithm and a simulation model in combination can provide an objective tool for the water practitioner to evaluate the interplay between economic benefits of groundwater abstractions and requirements to environmental flow. In this study, a holistic catchment‐scale groundwater abstraction optimization framework has been developed that allows for a spatially explicit optimization of groundwater abstraction, while fulfilling a predefined maximum allowed reduction of streamflow (baseflow [Q95] or median flow [Q50]) as constraint criteria for 1484 stream locations across the catchment. A balanced K‐Means clustering method was implemented to reduce the computational burden of the optimization. The model parameters and observation uncertainties calculated based on Bayesian linear theory allow for a risk assessment on the optimized groundwater abstraction values. The results from different optimization scenarios indicated that using the linear programming optimization algorithm in conjunction with integrated models provides valuable information for guiding the water practitioners in designing an effective groundwater abstraction plan with the consideration of environmental flow criteria important for the ecological status of the entire system.
Epidemiology of Chronic Kidney Disease in Children: A Report from Lithuania

Background and Objectives: The data on the prevalence of chronic kidney disease (CKD) in the pediatric population are limited. The prevalence of CKD ranges from 56 to 74.7 cases per million of the age-related population (pmarp). The most common cause of CKD among children is congenital anomalies of the kidney and urinary tract (CAKUT). With progressing CKD, various complications occur, and end-stage renal disease (ESRD) can develop. The aim of the study was to determine the causes, stage, prevalence, and clinical signs of CKD and demand for RRT (renal replacement therapy) among Lithuanian children in 2017 and to compare the epidemiological data of CKD with the data of 1997 and 2006. Materials and Methods: The data of 172 Lithuanian children who had a diagnosis of CKD (stage 2–5) in 1997 (n = 41), in 2006 (n = 65), and in 2017 (n = 66) were retrospectively analyzed. Physical development and clinical signs of children who had CKD (stage 2–5) in 2017 were assessed. Results: The prevalence of CKD stages 2–5 was 48.0 pmarp in 1997; 88.7 in 2006; and 132.1 in 2017 (p < 0.01). Congenital and hereditary diseases of the kidney in 1997 accounted for 66% of all CKD causes; in 2006, for 70%; and in 2017, for 79%. In 2017, children with CKD stages 4 or 5 (except transplanted children) had hypertension (87.5%) and anemia (50%) (p < 0.01). Children under ≤2 years with CKD were at a 3-fold greater risk of having elevated blood pressure (OR = 3.375, 95% CI: 1.186–9.904). Conclusions: There was no change in the number of children with CKD in Lithuania; however, the prevalence of CKD increased due to reduced pediatric population. CAKUT remains the main cause of CKD at all time periods. Among children with CKD stages 4 or 5, there were more children with hypertension and anemia. In children who were diagnosed with CKD at an early age hypertension developed at a younger age.
Reduction of the contents of carbon, phosphorus and nitrogen in waste products from the alcohol industry by the method of denitrification

This paper reports results of a study on the reduction of the COD in waste products from the alcohol industry based on the denitrification process, with the use of the laboratory culture of Bacillus licheniformis bacteria. The optimum conditions for the process have been established, taking into account the effect of the composition and dilution of the waste, temperature of the process, concentration of nitrates and phosphates, and aeration. In optimum conditions COD was reduced by over 70%, and phosphorus by about 60%. The total reduction of nitrates was obtained in 24 hours.
Temporo-Frontal Coherences and High-Frequency iEEG Responses during Spatial Navigation in Patients with Drug-Resistant Epilepsy

The prefrontal cortex and hippocampus function in tight coordination during multiple cognitive processes. During spatial navigation, prefrontal neurons are linked to hippocampal theta oscillations, presumably in order to enhance communication. Hippocampal ripples have been suggested to reflect spatial memory processes. Whether prefrontal-hippocampal-interaction also takes place within the ripple band is unknown. This intracranial EEG study aimed to investigate whether ripple band coherences can also be used to show this communication. Twelve patients with epilepsy and intracranial EEG evaluation completed a virtual spatial navigation task. We calculated ordinary coherence between prefrontal and temporal electrodes during retrieval, re-encoding, and pre-task rest. Coherences were compared between the conditions via permutation testing. Additionally, ripples events were automatically detected and changes in occurrence rates were investigated excluding ripples on epileptic spikes. Ripple-band coherences yielded no general effect of the task on coherences across all patients. Furthermore, we did not find significant effects of task conditions on ripple rates. Subsequent analyses pointed to rather short periods of synchrony as opposed to general task-related changes in ripple-band coherence. Specifically designed tasks and adopted measures might be necessary in order to map these interactions in future studies.
Purchase Intention for Organic Food Products in Mexico: The Mediation of Consumer Desire

Socially responsible consumption benefits the environment, the consumer, and the producer. In Mexico, smallholder farmers are vulnerable, and the consumption of organic food products is low. Analysing the purchase intention of organic food products contributes towards generating the most appropriate marketing strategies. Previous models provide evidence that the attitude of the consumer is the biggest predictor of purchase intention. However, little is known about the results of the mediating effect of desire on said relationship. The objective of the study is to analyse the mediating effect of desire on the relationship between attitude and purchase intention. 204 consumers of organic food products were surveyed using a structured, self-administrated questionnaire or through face-to-face interviews, in established retail stores, alternative street markets, and via the web. It was found that when the benefits of organic food products to the consumer, environment, and smallholder farmers are evaluated favourably, then consumer desire is higher, and thus also purchase intention. Consumers have the highest purchase intention for organic food products when their desire to buy them to achieve a goal related with social, personal, and environmental benefits intervenes.
Electrophilic substitution of organosilicon compounds. II: Synthesis of allyl-terminated polyisobutylenes by quantitative allylation of tert-chloro-polyisobutylenes with allyltrimethylsilane

Essentially quantitative allylation of linear and three-arm star tert-chloro capped polyisobutylenes [tCl–PIB–Clt and PIB(Clt)3] has been achieved by the use of allyltrimethylsilane (AllylSiMe3) and Friedel–Crafts acids. Quantitative allylation occurs under suitable conditions, e.g., slight molar excess of TiCl4 and AllySiMe3 polar media, −70°C. These conditions have been developed from quantitative model allylation experiments using 2,4,4-trimethyl-2-chloropentane. Essentially quantitative allylation occurs with long-chain or “once fired” tert-chloro-end groups. Complete allylation can also be effected in a “one-pot two-step” synthesis, i.e., by first preparing the tert-chloro-ended PIB by the inifer method and without isolating the product, completing the synthesis by allylation in the same reactor. Extensive but not quantitative allylation can also be obtained in situ, i. e. , during polymerization, by the use of the AllylSiMe3/cumyl chloride/BCI3/isobutylene combination. While allylation proceeds with great ease under the mildest conditions, e.g., −70°C, vinylation with vinyltrimethylsilane could not be achieved even under more forcing conditions.
Cross-effect of TRPV1 and EP3 receptor on coughs and bronchopulmonary C-neural activities

Prostaglandin E2 (PGE2)-induced coughs in vivo and vagal nerve depolarization in vitro are inhibited by systemic and local administration of prostaglandin EP3 receptor (L-798106) and TRPV1 antagonists (JNJ 17203212). These results indicate a modulating effect of TRPV1 on the EP3 receptor-mediated cough responses to PGE2 likely through the vagal sensory nerve. This study aimed to determine whether 1) inhalation of aerosolized JNJ 17203212 and L-798106 affected cough responses to citric acid (CA, mainly stimulating TRPV1) and PGE2; 2) TRPV1 and EP3 receptor morphologically are co-expressed and electrophysiologically functioned in the individual of vagal pulmonary C-neurons (cell bodies of bronchopulmonary C-fibers in the nodose/jugular ganglia); and 3) there was a cross-effect of TRPV1 and EP3 receptor on these neural excitations. To this end, aerosolized CA or PGE2 was inhaled by unanesthetized guinea pigs pretreated without or with each antagonist given in aerosol form. Immunofluorescence was applied to identify the co-expression of TRPV1 and EP3 receptor in vagal pulmonary C-neurons (retrogradely traced by DiI). Whole-cell voltage patch clamp approach was used to detect capsaicin (CAP)- and PGE2-induced currents in individual vagal pulmonary C-neurons and determine the effects of the TRPV1 and EP3 receptor antagonists on the evoked currents. We found that PGE2-induced cough was attenuated by JNJ 17203212 or L-798106 and CA-evoked cough greatly suppressed only by JNJ 17203212. Approximately 1/4 of vagal pulmonary C-neurons co-expressed EP3 with a cell size < 20 μm. Both CAP- and PGE2-induced currents could be recorded in the individuals of some vagal pulmonary C-neurons. The former was largely inhibited only by JNJ 17203212, while the latter was suppressed by JNJ 17203212 or L-798106. The similarity of the cross-effect of both antagonists on cough and vagal pulmonary C-neural activity suggests that a subgroup of vagal pulmonary C-neurons co-expressing TRPV1 and EP3 receptor is, at least in part, responsible for the cough response to PGE2.