Miracle-dz/UniFAR-FTUs huggingface dataset:
Nanoscale Zero-Valent Iron Modified by Bentonite with Enhanced Cr(VI) Removal Efficiency, Improved Mobility, and Reduced Toxicity

The aggregation of nanoscale zero-valent iron (nZVI) particles and their limited transport ability in environmental media hinder their application in environmental remediation. In this study, the Cr(VI) removal efficiency, transport performance, and toxicity of nZVI and bentonite-modified nZVI (B-nZVI) were investigated. Compared with nZVI, B-nZVI improved the removal efficiency of Cr(VI) by 10%, and also significantly increased the transport in quartz sand and soil. Increasing the flow rate can enhance the transport of nZVI and B-nZVI in the quartz sand columns. The transport of the two materials in different soils was negatively correlated with the clay composition. Besides, modification of nZVI by bentonite could reduce toxicity to luminous bacteria (Photobacterium phosphereum T3) and ryegrass (Lolium perenne L.). Compared with Fe-EDTA, the transfer factors of nZVI and B-nZVI were 65.0% and 66.4% lower, respectively. This indicated that although iron nanoparticles accumulated in the roots of ryegrass, they were difficult to be transported to the shoots. The results of this study indicate that B-nZVI has a strong application potential in in situ environmental remediation.
A Potential-Induced Transformation in the Double Electrical Layer on the Rhenium Electrode in Alkali Chloride Melts

Structural transformations in the adsorption layer caused by an electric potential are investigated using the experimental data on the capacitance of a double electric layer for a rhenium electrode in molten sodium, potassium and cesium chlorides at 1093 K. Likening the double electric layer to a flat capacitor, as well as the effective length of the shielding of the electrode charge and changes in the charge sign depending on the applied potential are estimated. It is found that near the minimum potential of the capacitance curve, the shielding length decreases proportionally to the square of the potential due to the deformation of the double layer. The deformation reaches critical values at the potentials of −0.65, −0.38 and −0.40 V for the Re|NaCl, Re|KCl and Re|CsCl systems respectively, and decreases sharply at more positive potentials. The analysis of the dependence of the charge density on the electrode revealed the effect of shielding of potential-induced rhenium cations by salt phase anions. The strong Raman-active Re–Cl stretching mode was observed at 292 cm−1. This can be explained by the transfer of anions across the interface resulting in the formation of ordered layers of ion associations (possibly, ReXn(n − 1)−) on a positively charged surface.
Mechanisms, Pathophysiology and Currently Proposed Treatments of Chronic Obstructive Pulmonary Disease

Chronic obstructive pulmonary disease (COPD) is one of the leading global causes of morbidity and mortality. A hallmark of COPD is progressive airflow obstruction primarily caused by cigarette smoke (CS). CS exposure causes an imbalance favoring pro- over antioxidants (oxidative stress), leading to transcription factor activation and increased expression of inflammatory mediators and proteases. Different cell types, including macrophages, epithelial cells, neutrophils, and T lymphocytes, contribute to COPD pathophysiology. Alteration in cell functions results in the generation of an oxidative and inflammatory microenvironment, which contributes to disease progression. Current treatments include inhaled corticosteroids and bronchodilator therapy. However, these therapies do not effectively halt disease progression. Due to the complexity of its pathophysiology, and the risk of exacerbating symptoms with existing therapies, other specific and effective treatment options are required. Therapies directly or indirectly targeting the oxidative imbalance may be promising alternatives. This review briefly discusses COPD pathophysiology, and provides an update on the development and clinical testing of novel COPD treatments.
Integrating advances in population and evolutionary ecology with conservation strategy through long-term studies of red-billed choughs.

Conceptual and methodological advances in population and evolutionary ecology are often pursued with the ambition that they will help identify demographic, ecological and genetic constraints on population growth rate (λ), and ultimately facilitate evidence-based conservation. However, such advances are often decoupled from conservation practice, impeding translation of scientific understanding into effective conservation, and of conservation-motivated research into wider conceptual understanding. We summarise key outcomes from long-term studies of a red-billed chough (Pyrrhorcorax pyrrhocorax) population of conservation concern, where we pro-actively aimed to achieve the dual and interacting objectives of advancing population and evolutionary ecology and advancing effective conservation. Estimation of means, variances and covariances in key vital rates from individual-based demographic data identified temporal and spatial variation in sub-adult survival as key constraints on λ, and simultaneously provided new insights into how vital rates can vary as functions of demographic structure, natal conditions and parental life-history. Targeted analyses showed that first-year survival increased with prey abundance, implying that food limitation may constrain λ. First-year survival then decreased dramatically, threatening population viability and prompting emergency supplementary feeding interventions. Detailed evaluations suggested that the interventions successfully increased first-year survival in some years, and additionally increased adult survival and successful reproduction, thereby feeding back to inform intervention refinements and understanding of complex ecological constraints on λ. Genetic analyses revealed novel evidence of expression of a lethal recessive allele, and demonstrated how critically small effective population size can arise, thereby increasing inbreeding and loss of genetic variation. Population viability analyses parameterised with all available demographic and genetic data showed how ecological and genetic constraints can interact to limit population viability, and identified ecological management as of primacy over genetic management to ensure short-term persistence of the focal population. This case study demonstrates a full iteration through the sequence of primary science, evidence-based intervention, quantitative evaluation and feedback that is advocated in conservation science but still infrequently achieved. It thereby illustrates how pure science advances informed conservation actions to ensure (short-term) stability of the target population, and how conservation-motivated analyses fed back to advance fundamental understanding of population processes.
Long‐term bisphosphonate therapy and atypical femoral fracture: Can you have too much of a good thing?

The long‐term, continuous use of bisphosphonates (beyond 5 years) is not wholly without risk. Atypical femoral fracture is an uncommon but potentially very serious adverse event associated with the long‐term use of bisphosphonates. Here we consider the complexities of long‐term bisphosphonate prescribing, particularly in those that are low risk of osteoporotic fracture, wherein the duration of therapy should be reviewed regularly with individualised risk assessment to ensure the duration of treatment is appropriate.
Dendrite tapering actuates a self-organizing signaling circuit for stochastic filopodia initiation in neurons

Significance Cellular signaling pathways respond to a wide range of stimuli. How signaling circuits are activated without an instructive stimulus and what this is good for are less clear. Combining theoretical and experimental approaches, we show that curvature-sensing proteins stabilize stochastic membrane deformations to nucleate a self-organizing actin-regulatory signaling circuit. In neurons, these signaling hubs control the initiation of exploratory filopodia that sample the cell vicinity for appropriate synaptic partners. The extent and diversity of proteins capable of forming self-organizing circuits at stochastically deformed membranes indicates a general signaling mechanism. How signaling units spontaneously arise from a noisy cellular background is not well understood. Here, we show that stochastic membrane deformations can nucleate exploratory dendritic filopodia, dynamic actin-rich structures used by neurons to sample its surroundings for compatible transcellular contacts. A theoretical analysis demonstrates that corecruitment of positive and negative curvature-sensitive proteins to deformed membranes minimizes the free energy of the system, allowing the formation of long-lived curved membrane sections from stochastic membrane fluctuations. Quantitative experiments show that once recruited, curvature-sensitive proteins form a signaling circuit composed of interlinked positive and negative actin-regulatory feedback loops. As the positive but not the negative feedback loop can sense the dendrite diameter, this self-organizing circuit determines filopodia initiation frequency along tapering dendrites. Together, our findings identify a receptor-independent signaling circuit that employs random membrane deformations to simultaneously elicit and limit formation of exploratory filopodia to distal dendritic sites of developing neurons.
The Future of Stem Cells and Their Derivates in the Treatment of Glaucoma. A Critical Point of View

This review focuses on the clinical translation of preclinical studies, especially those that have used stem cells in the treatment of glaucoma, with an emphasis on optic nerve regeneration. The studies referred to in the review aim to treat optic nerve atrophy, while cell therapies targeting other sites in the eye, such as the trabecular meshwork, have not been addressed. Such complex and varied pathophysiological mechanisms that lead to glaucoma may explain the fact that although stem cells have a high capacity of neuronal regeneration, the treatments performed did not have the expected results and the promise offered by animal studies was not achieved. By analyzing the facts associated with failure, important lessons are to be learned: the type of stem cells that are used, the route of administration, the selection of patients eligible for these treatments, additional therapies that support stem cells transplantation and their mode of action, methods of avoiding the host’s immune response. Many of these problems could be solved using exosomes (EV), but also miRNA, which allows more targeted approaches with minimal side effects.
Powdery Mildew Resistance Genes in Single-Plant Progenies Derived from Accessions of a Winter Barley Core Collection

The main problems of crop gene banks comprise heterogeneity of accessions, resulting from mechanical admixtures or out-crossing during their multiplication, and especially the mislabeling of accessions. These discrepancies can adversely affect the results of many expensive research and breeding projects that are based on the use of gene bank resources. To tackle these problems, 860 single-plant progenies (SPPs) of 172 accessions of the Czech winter barley core collection were grown and tested with a set of 53 isolates representing the global virulence/avirulence diversity of powdery mildew. Seventy-one resistance phenotypes encompassed the diversity of known specific resistances and their combinations. Based on testing groups of five SPPs, 94 accessions had one phenotype found in all five SPPs (homogeneous accessions), whereas in 78 accessions (45.3%) more than one phenotype was identified (heterogeneous accessions). In three varieties, specific resistances against the whole set of isolates were detected, but due to high adaptability of the pathogen, they are not recommended for breeding resistant cultivars. Selected SPPs were integrated in the gene bank and are now a reliable source of genotypically pure seed with defined powdery mildew resistance genes that can be used by breeders and researchers. The results obtained can be used to verify authenticity of accession genotype and pedigree, particularly for older varieties for which no other original criteria are available.
MMV-db: vaccinomics and RNA-based therapeutics database for infectious hemorrhagic fever-causing mammarenaviruses

Abstract The recent viral outbreaks and the current pandemic situation urges us to timely address any emerging viral infections by designing therapeutic strategies. Multi-omics and therapeutic data are of great interest to develop early remedial interventions. This work provides a therapeutic data platform (Mammarenavirus (MMV)-db) for pathogenic mammarenaviruses with potential catastrophic effects on human health around the world. The database integrates vaccinomics and RNA-based therapeutics data for seven human pathogenic MMVs associated with severe viral hemorrhagic fever and lethality in humans. Protein-specific cytotoxic T lymphocytes, B lymphocytes, helper T-cell and interferon-inducing epitopes were mapped using a cluster of immune-omics-based algorithms and tools for the seven human pathogenic viral species. Furthermore, the physiochemical and antigenic properties were also explored to guide protein-specific multi-epitope subunit vaccine for each species. Moreover, highly efficacious RNAs (small Interfering RNA (siRNA), microRNA and single guide RNA (sgRNA)) after extensive genome-based analysis with therapeutic relevance were explored. All the therapeutic RNAs were further classified and listed on the basis of predicted higher efficacy. The online platform (http://www.mmvdb.dqweilab-sjtu.com/index.php) contains easily accessible data sets and vaccine designs with potential utility in further computational and experimental work. Conclusively, the current study provides a baseline data platform to secure better future therapeutic interventions against the hemorrhagic fever causing mammarenaviruses. Database URL: http://www.mmvdb. dqweilab-sjtu.com/index.php
On Analyzing Capnogram as a Novel Method for Screening COVID-19: A Review on Assessment Methods for COVID-19

In November 2019, the novel coronavirus disease COVID-19 was reported in Wuhan city, China, and was reported in other countries around the globe. COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Strategies such as contact tracing and a vaccination program have been imposed to keep COVID-19 under control. Furthermore, a fast, noninvasive and reliable testing device is needed urgently to detect COVID-19, so that contact can be isolated and ringfenced before the virus spreads. Although the reverse transcription polymerase chain reaction (RT-PCR) test is considered the gold standard method for the diagnosis of SARS-CoV-2 infection, this test presents some limitations which cause delays in detecting the disease. The antigen rapid test (ART) test, on the other hand, is faster and cheaper than PCR, but is less sensitive, and may limit SARS-CoV-2 detection. While other tests are being developed, accurate, noninvasive and easy-to-use testing tools are in high demand for the rapid and extensive diagnosis of the disease. Therefore, this paper reviews current diagnostic methods for COVID-19. Following this, we propose the use of expired carbon dioxide (CO2) as an early screening tool for SARS-CoV-2 infection. This system has already been developed and has been tested on asthmatic patients. It has been proven that expired CO2, also known as capnogram, can help differentiate between respiratory conditions and, therefore, could be used to detect SARS-CoV-2 infection, as it causes respiratory tract-related diseases.
Key Global Actions for Mycotoxin Management in Wheat and Other Small Grains

Mycotoxins in small grains are a significant and long-standing problem. These contaminants may be produced by members of several fungal genera, including Alternaria, Aspergillus, Fusarium, Claviceps, and Penicillium. Interventions that limit contamination can be made both pre-harvest and post-harvest. Many problems and strategies to control them and the toxins they produce are similar regardless of the location at which they are employed, while others are more common in some areas than in others. Increased knowledge of host-plant resistance, better agronomic methods, improved fungicide management, and better storage strategies all have application on a global basis. We summarize the major pre- and post-harvest control strategies currently in use. In the area of pre-harvest, these include resistant host lines, fungicides and their application guided by epidemiological models, and multiple cultural practices. In the area of post-harvest, drying, storage, cleaning and sorting, and some end-product processes were the most important at the global level. We also employed the Nominal Group discussion technique to identify and prioritize potential steps forward and to reduce problems associated with human and animal consumption of these grains. Identifying existing and potentially novel mechanisms to effectively manage mycotoxin problems in these grains is essential to ensure the safety of humans and domesticated animals that consume these grains.
Multi-Organs-on-Chips for Testing Small-Molecule Drugs: Challenges and Perspectives

Organ-on-a-chip technology has been used in testing small-molecule drugs for screening potential therapeutics and regulatory protocols. The technology is expected to boost the development of novel therapies and accelerate the discovery of drug combinations in the coming years. This has led to the development of multi-organ-on-a-chip (MOC) for recapitulating various organs involved in the drug–body interactions. In this review, we discuss the current MOCs used in screening small-molecule drugs and then focus on the dynamic process of drug absorption, distribution, metabolism, and excretion. We also address appropriate materials used for MOCs at low cost and scale-up capacity suitable for high-performance analysis of drugs and commercial high-throughput screening platforms.
The Trace Element Selenium Is Important for Redox Signaling in Phorbol Ester-Differentiated THP-1 Macrophages

Physiological selenium (Se) levels counteract excessive inflammation, with selenoproteins shaping the immunoregulatory cytokine and lipid mediator profile. How exactly differentiation of monocytes into macrophages influences the expression of the selenoproteome in concert with the Se supply remains obscure. THP-1 monocytes were differentiated with phorbol 12-myristate 13-acetate (PMA) into macrophages and (i) the expression of selenoproteins, (ii) differentiation markers, (iii) the activity of NF-κB and NRF2, as well as (iv) lipid mediator profiles were analyzed. Se and differentiation affected the expression of selenoproteins in a heterogeneous manner. GPX4 expression was substantially decreased during differentiation, whereas GPX1 was not affected. Moreover, Se increased the expression of selenoproteins H and F, which was further enhanced by differentiation for selenoprotein F and diminished for selenoprotein H. Notably, LPS-induced expression of NF-κB target genes was facilitated by Se, as was the release of COX- and LOX-derived lipid mediators and substrates required for lipid mediator biosynthesis. This included TXB2, TXB3, 15-HETE, and 12-HEPE, as well as arachidonic acid (AA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA). Our results indicate that Se enables macrophages to accurately adjust redox-dependent signaling and thereby modulate downstream lipid mediator profiles.
A Novel Effector Protein SsERP1 Inhibits Plant Ethylene Signaling to Promote Sclerotinia sclerotiorum Infection

Sclerotinia sclerotiorum is one of the most devastating pathogens in Brassica napus and causes huge economic loss worldwide. Though around one hundred putative effectors have been predicted in Sclerotinia sclerotiorum genome, their functions are largely unknown. In this study, we cloned and characterized a novel effector, SsERP1 (ethylene pathway repressor protein 1), in Sclerotinia sclerotiorum. SsERP1 is a secretory protein highly expressed at the early stages of Sclerotinia sclerotiorum infection. Ectopic overexpression of SsERP1 in plant leaves promoted Sclerotinia sclerotiorum infection, and the knockout mutants of SsERP1 showed reduced pathogenicity but retained normal mycelial growth and sclerotium formation, suggesting that SsERP1 specifically contributes to the pathogenesis of Sclerotinia sclerotiorum. Transcriptome analysis indicated that SsERP1 promotes Sclerotinia sclerotiorum infection by inhibiting plant ethylene signaling pathway. Moreover, we showed that knocking down SsERP1 by in vitro synthesized double-strand RNAs was able to effectively inhibit Sclerotinia sclerotiorum infection, which verifies the function of SsERP1 in Sclerotinia sclerotiorum pathogenesis and further suggests a potential strategy for Sclerotinia disease control.
Microarray Analysis of Paramylon, Isolated from Euglena Gracilis EOD-1, and Its Effects on Lipid Metabolism in the Ileum and Liver in Diet-Induced Obese Mice

We previously showed that supplementation of a high fat diet with paramylon (PM) reduces the postprandial glucose rise, serum total and LDL cholesterol levels, and abdominal fat accumulation in mice. The purpose of this study was to explore the underlying mechanism of PM using microarray analysis. Male mice (C57BL/BL strain) were fed an experimental diet (50% fat energy) containing 5% PM isolated from Euglena gracilis EOD-1 for 12 weeks. After confirming that PM had an improving effect on lipid metabolism, we assessed ileal and hepatic mRNA expression using DNA microarray and subsequent analysis by gene ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The results suggested that dietary supplementation with PM resulted in decreased abdominal fat accumulation and serum LDL cholesterol concentrations via suppression of the digestion and absorption pathway in the ileum and activation of the hepatic PPAR signaling pathway. Postprandial glucose rise was reduced in mice fed PM, whereas changes in the glucose metabolism pathway were not detected in GO classification and KEGG pathway analysis. PM intake might enhance serum secretory immunoglobulin A concentrations via promotion of the immunoglobulin production pathway in the ileum.