The mainstream adoption of chickpea proteins and lipids requires a thorough understanding of the impact of critical extraction parameters (enzyme use, reaction time, and solids-to-liquid ratio—SLR) and modes of extraction (single-stage extraction—SSE and countercurrent extraction—CCE) on the simultaneous extraction of lipids and proteins from full-fat chickpea flour and economic process feasibility. A kinetics study revealed that 68.5% oil and 87% protein extraction yields can be achieved using 0.5% protease at pH 9.0, 50 °C, 60 min, and 1:10 SLR, highlighting the role of proteolysis and an adequate incubation time on overall extractability. An increased gradient concentration between the matrix and aqueous media solutes at a lower SLR (1:15), and reduced slurry viscosity increased oil and protein extractability to 80 and 91%, respectively. The high-water usage in the SSE was addressed by the development of a two-stage CCE that reduced water usage by 47% while increasing oil and protei... [more]

Stephaniae Tetrandrae Radix (STR) is a commonly used herb with a history of thousands of years. Accumulating evidence shows the therapeutic effect on breast cancer (BC) of STR. Here, we aimed to elucidate the active components and mechanisms of STR against BC. The active components and targets were retrieved and screened from the corresponding databases. A target protein−protein interaction (PPI) network was built and Ingenuity Pathway Analysis (IPA) used to analyze and screen key targets and pathways. Subsequently, molecular docking was performed to visualize the patterns of interactions between components and targets. Finally, the main active components of STR in treating BC were confirmed by in vitro experiments, and 34 common targets were obtained. The PPI network and IPA showed that the key targets were TP53, JUN, CASP3, and so on. Additionally, signaling pathways were enriched. Docking verified that the active components have good binding potential with the key targets, especiall... [more]

As an agroindustrial waste product, potato peels contain valuable phenolic compounds that can be extracted before they are sent to the landfill. Based on previous work, this study focused on determining the efficacies of phenolic compound extraction from potato peels using conventional shaking extraction (CSE) and both direct ultrasound-assisted extraction (DUAE), and indirect ultrasound-assisted extraction (IUAE). The yield curve associated with each extraction method was measured and characterized. The maximum yield of phenolic compounds and its dependence on processing parameters were evaluated. The applicability of the Peleg model for describing the yield curve was evaluated. Based on the Peleg model, a recovery ratio was defined to calculate its corresponding extraction rate. This extraction rate, combined with the yield, can be used for describing the efficacy of an extraction method. Our results indicate that the ultrasound-assisted extraction methods were capable of extracting... [more]

In this study, pomegranate peel extract was used to dye cotton fabrics. Generally, natural dyes have low affinity for cellulosic fibers and therefore need treatment for attachment. Air atmospheric plasma was applied to lower the concentrations of mordants needed and enhance dyeability. The outcomes showed that the residual concentrations of metallic ions decreased when applying the plasma treatment. ATR-FTIR and SEM analysis were performed to evaluate the effect of plasma modification on the surface chemistry and topography of the cellulosic fibers. The traces of metals released from finished fabric were quantified using ICP OES spectrometry. Color fastnesses (wash, rubbing and light) were evaluated to assess the mordanting step effect and the durability of the color. All tested fastnesses were good to very good. The concentrations of metal ions in finished fabrics were 32.4 for Fe, 0.28 for Al, 0.29 for Cr and 1.21 for Cu. Plasma treatment can be considered an efficient strategy to re... [more]

This work utilizes the anthraquinone (AQ) database to identify potential inhibitors of the RIPK1 protein for developing medicines targeting AP-associated necroptosis. Screening for necroptosis-related genes that play a crucial role in AP is based on the GEO and GSEA databases. An optimum AQ for receptor-interacting protein kinase 1 (RIPK1) inhibition was virtually screened using the Discovery Studio 2019 tool, with a previously described RIPK1 inhibitor (necrostatin-1) as a reference ligand. Using LibDock and CDOCKER molecular docking, an AQ that robustly binds to RIPK1 was identified. The DOCKTHOR web server was used to calculate the ligand−receptor binding energy. The pharmacological properties and toxicity of potential AQ were evaluated using the ADME module and ProTox-II web server. The stability of ligand−receptor complexes was examined using molecular dynamics (MD) simulation. All 12 AQs showed solid binding activity to RIPK1, 5 of which were superior to necrostatin-1. Rheochrysi... [more]

Despite the development of many antibiotics, excessive inflammation caused by endotoxins is still a subject of interest to biomedical researchers. The hyper-inflammatory response of macrophages activated by endotoxins is an important topic in the development of natural product-based anti-inflammatory drugs. Conioselinum tenuissimum, a perennial herb of the family Apiaceae, contains levistolide A, demethylsuberosin, and fraxetin. One of the synonyms of Conioselinum tenuissimum is Angelica tenuissima. The objective of this study was to determine the effects of Conioselinumtenuissimum root water extract (AT) on the hyper-inflammatory responses of macrophages activated by endotoxin (lipopolysaccharide; LPS) and the mechanisms involved in such effects. Levels of cytokines, nitric oxide (NO), hydrogen peroxide, and cytosolic calcium in LPS-activated RAW 264.7 murine macrophages were evaluated by the multiplex cytokine assay (MCA), Griess reagent assay (GRA), dihydrorhodamine 123 assay (DHR),... [more]

Airborne fungi emitted from livestock manure composting plants are one of the major harmful factors causing respiratory disease for workers and nearby residents. Their generation of emissions is relatively high compared to other workplaces. This study investigated the emission characteristics of airborne fungi generated in livestock manure composting plants and utilized them as basic data to prevent workers’ health. The livestock manure composting plants selected for the survey in this study were according to the fermentation mode, including screw type, rotary type and natural dry type. The field evaluation period was from September 2019 to August 2020 and was surveyed monthly. The equipment for collecting airborne fungi was a six-stage cascade impactor. An analysis of the quantification and qualification of airborne fungi was conducted through a culture method and identification technique, respectively. The mean levels of airborne fungi in livestock manure composting plants were 1143... [more]

Photodynamic therapy and photoacoustic (PA) imaging are emerging therapeutic modalities for the diagnosis and treatment of various types of cancer or other diseases. In this study, the second-generation photosensitizer Chlorin e6 was prepared on a pilot scale by using the rapid, simple, and green synthetic method as compared to a conventional protocol. In the modified method, the extraction/reaction time and volume of solvents were significantly reduced. The dark and photodynamic cytotoxicity of Ce6 was measured against B16F10 melanoma cell line. Ce6 did not affect cancer cells in the dark up to 192 µM, ensuring their safety in the absence of light. After PDT, it displayed significant cytotoxicity at lower concentrations (IC50: 18.9 µM). For in vivo study, B16F10 allograft mice were treated with Ce6 at 2.5 mg/kg and then exposed to red light (660 nm) after 3 h. The Ce6-PDT caused the inhibition of tumor growth. Furthermore, Ce6 was also used as a photoacoustic imaging agent in ICR mice... [more]

The status quo of a high-fat diet can impair the integrity of the intestinal barrier and promote inflammatory bowel diseases. The exploration of natural products as sources of new lead compounds that control such diseases becomes essential. Sweetpotato leaves (SPLs) have strong biological activity, and their phenolic acids were recently reported to be able to impart antioxidative, anti-inflammatory, and neuroprotection. The aim of this study was to investigate the effects and mechanisms of sweetpotato leaf phenolic acids (SPLPAs) extract on interleukin 1 beta (IL-1β)-induced barrier injury of Caco-2 monolayers. The safety from 0.02 to 0.2 mg/mL SPLPA extracts were demonstrated using the 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) method and Trypan blue staining. The 0.2 mg/mL SPLPA extract significantly decreased the release of Nitric oxide (NO) generation and its contribution to the expression of inflammation-related nitric oxide synthase (iNOS), tumor necro... [more]

We assessed a reactivity of chloroacetyl-modified tripeptides consisting of various amino acid residues (Cl-3X) and mercaptoundecahydrododecaborate (BSH) by converting Cl-3X to its reactant (BS-3X). We showed that the Cl-3X consisting of basic amino acid residues (e.g., Arg) reacted with BSH effectively and its conversion decreased as the number of Arg residues in the Cl-3X decreased. Furthermore, a reactivity of the peptides with introduction of an alkyl linker between the triarginine and the chloroacetyl group (Cl-Cn-3R) with BSH decreased with increasing alkyl linker length. These results indicate that an electrostatic attraction of positively charged amino acid residues in the tripeptides and negatively charged BSH causes BSH to gather in a vicinity of the chloroacetyl group, resulting in an accelerated reaction. This work should aid a development of new boron agents using BSH in boron neutron capture therapy.

: The bacterial destructing activity toward pesticides has been the focus of research in the last few decades. Hexachlorobenzene is included in the organochlorine pesticides group that are prohibited for use. However, large hexachlorobenzene amounts are still concentrated in the soil, stressing the relevance of research on hexachlorobenzene-destroying bacteria.: The ability to destroy hexachlorobenzene by Comamonas testosteroni UCM B-400, B-401, B-213 strains was investigated and established. Bacteria were cultivated (7 days at 28 °C) in mineral Luria-Bertrani (LB) medium with three hexachlorobenzene doses: 10, 20, 50 mg/L. The hexachlorobenzene concentrations were recorded by a gas chromatography method.: The results showed that C. testosteroni UCM B-400, B-401 have high destructive activity toward hexachlorobenzene. The highest (50 mg/L) initial concentration decreased to 41.5 and 43.8%, respectively, for C. testosteroni UCM B-400, B-401. The unadapted C. testosteroni UCM B-213 was t... [more]

The recovery of metal resources from wastewater is very important for both resource recovery and wastewater treatment. Compared with traditional metal-polluted wastewater treatment technologies, advanced wastewater treatment technologies with the functions of both recovering metals and generating electricity have been developed rapidly in recent years. These advanced technologies include microbial fuel cells, photo fuel cells, coupled redox fuel cells, etc. In this paper, these advanced technologies are elaborated from their principles to their applications in wastewater treatment for metals recovery and electricity generation. The recent progress of these technologies was also reviewed. The effects of different metal ions, cell configurations, and various operating parameters on their performance were also discussed. Although these technologies are promising, the challenges and the efforts needed to overcome them are also highlighted.

Plain film X-ray scanners are indispensable for medical diagnostics and clinical procedures. This type of device typically produces two radiographic images of the human spine, including the anteroposterior and lateral views. However, these two photographs presented perspectives that were distinct. The proposed procedure consists of three fundamental steps. For automated cropping, the grayscale lumbar input image was initially projected vertically using its vertical pattern. Then, Delaunay triangulation was performed with the SURF features serving as the triangle nodes. The posture area of the vertebrae was calculated by utilizing the edge density of each node. The proposed method provided an automated estimation of the position of the human lumbar vertebrae, thereby decreasing the radiologist’s workload, computing time, and complexity in a variety of bone-clinical applications. Numerous applications can be supported by the results of the proposed method, including the segmentation of l... [more]

Aqueous two-phase systems (ATPS) based on ionic liquids (IL) and deep eutectic solvents (DES) are ecofriendly choices and can be used to selectively separate compounds of interest, such as bioactive compounds. Bioactive compounds are nutrients and nonnutrients of animal, plant, and microbial origin that benefit the human body in addition to their classic nutritional properties. They can also be used for technical purposes in food and as active components in the chemical and pharmaceutical industries. Because they are usually present in complex matrices and low concentrations, it is necessary to separate them in order to increase their availability and stability, and ATPS is a highlighted technique for this purpose. This review demonstrates the application of ATPS based on IL and DES as a tool for recovering nonprotein bioactive compounds, considering critical factors, results and the most recent advances in this field. In addition, the review emphasizes the perspectives for expanding t... [more]

Wound healing continues to pose a challenge in clinical settings. Moreover, wound management must be performed properly and efficiently. Acute wound healing involves multiple cell divisions, a new extracellular matrix, and the process of formation, such as growth factors and cytokines, which are released at the site of the wound to regulate the process. Any changes that disrupt the healing process could cause tissue damage and prolong the healing process. Various factors, such as microbial infection, oxidation, and inflammation, can delay wound healing. In order to counter these problems, utilizing natural products with wound-healing effects has been reported to promote this process. Several natural products have been associated with wound healing, most of which are from medicinal plants. However, secondary microbial metabolites have not been extensively studied for their wound-healing properties. Further, investigations on the wound-healing control of natural microbial products are re... [more]

Global warming is one of the most serious problems leading to changes in the distribution areas of species and biodiversity. Rhodiola quadrifida is a rare plant with adaptogenic properties and grows in the highlands in a narrow temperature range of 2−15 °C. The aim of our work was to study the growth and content of the main metabolites in two in vitro cultures of Rhodiola quadrifida at temperatures of 5, 15 and 25 °C. Hairy roots and calli were cultivated on agar medium for 28 days. The maximum values of the growth index were observed at 25 °C (2.32 and 2.12 for calli and hairy roots, respectively). HPLC-MS showed the absence of tyrosol and rosarin in both cultures, and rosin in the root culture. The content of salidroside changed slightly in calli and roots. Cultivation at 5 °C significantly stimulated the formation of rosin in calli. Only a residual amount of rosavin was noted in the roots, regardless of temperature. The content of rosin was higher in calli at 15 °C with a maximum co... [more]

The use of photogrammetry provides an inexpensive, alternative method that can simplify the processes traditionally carried out in the orthotics workshop. The objectives of this study are to develop a method based on photogrammetry to obtain 3D-printed positive foot casts for fabricating thermoconformed orthoses from a negative cast in phenolic foam. Using a basic Smartphone, a photo capture protocol for feet, free software and a 3D printer, we tested the suitability of the positive cast obtained to fabricate custom foot orthoses using thermoconformed 3 mm polypropylene in the orthotics laboratory. The results show that digitally fabricated casts provide a very close replicate of the positive casts obtained traditionally through plaster casting (maximum dimension discrepancy between casts of 2 mm in length and 0.4 mm in forefoot, midfoot and rearfoot measurements). They are also suitable for the process of fabricating 2- and 3-mm polypropylene thermoconformed plantar orthoses. Photogra... [more]

In the upcoming years, the world will face societal challenges arising, in particular, from the impact of climate change and the inefficient use of natural resources, in addition to an exponential growth of the world population, which according to the United Nations (UN) estimations will be 9.8 billion in 2050. This increasing trend requires optimized management of natural resources with the use of value-added waste and a significant reduction in food loss and food waste. Moreover, the recent pandemic situation, COVID-19, has contributed indisputably. Along with the agri-food supply chain, several amounts of waste or by-products are generated. In most cases, these biomass wastes cause serious environmental concerns and high costs to enterprises. The valorisation of the agri-food loss and food industry wastes emerged as a useful strategy to produce certain value-added compounds with several potential applications, namely in the food, health, pharmaceutical, cosmetic, and environmental f... [more]

This is the source code for the STORE (STochasic Omentum REsponse) model. The model is used to simulate how naive T-cells in the omentum will prime and multiply during the expansion period (8 days) after a T-cell vaccination in a mouse.

This is the matlab source code used in the following paper:

Christian DA, Adams TA II, Smith TA, Shallberg LA, Theisen DJ, Phan AT, Abraha M, Perry J, Ruthel G, Clark JT, Murphy KM, Kedl, RM, Hunter CA. cDC1 coordinate innate and adaptive responses in the omentum required for T cell priming and memory. Science Immunology 7, eabq7432 (2022).

This is fixed legacy code used for the paper for scientific auditing and reproduction purposes. See paper for documentation.

Proprotein Convertase Subtilisin Kexin type 9 (PCSK9), comprises 12 exons, encoded for an enzyme which plays a critical role in the regulation of circulating low density lipoprotein. The gain-of-function (GOF) mutations aggravate the degradation of LDL receptors, resulting in familial hypercholesterolemia (FH), while loss-of-function (LOF) mutations lead to higher levels of the LDL receptors, lower the levels of LDL cholesterol, and preventing from cardiovascular diseases. It is noted that, previous publications related to the mutations of PCSK9 were not always unification. Therefore, this study aims to present the spectrum and distribution of PCSK9 gene mutations by a meta-analysis. A systematic literature analysis was conducted based on previous studies published by using different keywords. The weighted average frequency of PCSK9 mutation was calculated and accessed by MedCalc®. A total of 32 cohort studies, that included 19,725 familial hypercholesterolemia blood samples, were enro... [more]

Emerging evidence highlights the relevance of extracellular vesicles (EVs) in modulating human diseases including but not limited to cancer, inflammation, and neurological disorders. EVs can be found in almost all types of human body fluids, suggesting that their trafficking may allow for their targeting to remote recipient cells. While molecular processes underlying EV biogenesis and secretion are increasingly elucidated, mechanisms governing EV transportation, target finding and binding, as well as uptake into recipient cells remain to be characterized. Understanding the specificity of EV transport and uptake is critical to facilitating the development of EVs as valuable diagnostics and therapeutics. In this mini review, we focus on EV uptake mechanisms and specificities, as well as their implications in human diseases.

Recent years have witnessed a growing interest in the use of biocatalysts in flow reactors. This merging combines the high selectivity and mild operation conditions typical of biocatalysis with enhanced mass transfer and resource efficiency associated to flow chemistry. Additionally, it provides a sound environment to emulate Nature by mimicking metabolic pathways in living cells and to produce goods through the systematic organization of enzymes towards efficient cascade reactions. Moreover, by enabling the combination of enzymes from different hosts, this approach paves the way for novel pathways. The present review aims to present recent developments within the scope of flow chemistry involving multi-enzymatic cascade reactions. The types of reactors used are briefly addressed. Immobilization methodologies and strategies for the application of the immobilized biocatalysts are presented and discussed. Key aspects related to the use of whole cells in flow chemistry are presented. The... [more]

We previously reported that macropinocytosis (accompanied by actin reorganization, ruffling of the plasma membrane, and engulfment of large volumes of extracellular fluid) is an important process for the cellular uptake of extracellular vesicles, exosomes. Accordingly, we developed techniques to induce macropinocytosis by the modification of biofunctional peptides on exosomal membranes, thereby enhancing their cellular uptake. Arginine-rich cell-penetrating peptides have been shown to induce macropinocytosis via proteoglycans; accordingly, we developed peptide-modified exosomes that could actively induce macropinocytotic uptake by cells. In addition, the activation of EGFR induces macropinocytosis; based on this knowledge, we developed artificial leucine-zipper peptide (K4)-modified exosomes. These exosomes can recognize E3 sequence-fused EGFR (E3-EGFR), leading to the clustering and activation of E3-EGFR by coiled-coil formation (E3/K4), which induces cellular exosome uptake by macrop... [more]

A liposome-based artificial cell (LBAC) consists of a liposome encapsulating a cell-free protein expression system (CFPES) and protein-encoding DNA. It is surrounded by a lipid bilayer membrane and synthesizes proteins that resemble actual cells. Hence, they have been one of the most studied artificial cells. According to recent studies, they have been able to sense bio-functional molecules by synthesizing fluorescent proteins in response to target molecules. Therefore, they are expected to be used as biosensors. However, previously reported LBACs encapsulated the CFPES derived from Escherichia coli, resulting in the most productive protein expression at 20−40 °C. To broaden the range of their working temperatures to lower temperatures, in this study, we constructed LBACs using a CFPES derived from Pseudomonas fluorescens that grows at a temperature range of 4 °C to 30 °C. We then demonstrated that the constructed LBAC expressed proteins at 8 °C and that, the protein expression capabil... [more]

Nonalcoholic fatty liver disease (NAFLD) generally co-occurs with metabolic disorders, but it is unclear which genes have a pleiotripic effect on NAFLD and metabolic traits. We performed a large-scale cross-trait association analysis to identify the overlapping genes between NAFLD and nine metabolic traits. Among all the metabolic traits, we found that obesity and type II diabetes are associated with NAFLD. Then, a multitrait association analysis among NAFLD, obesity and type II diabetes was conducted to improve the overall statistical power. We identified 792 significant variants by a cross-trait meta-analysis involving 100 pleiotripic genes. Moreover, we detected another two common genes by a genome-wide gene test. The results from the pathway enrichment analysis show that the 102 shared risk genes are enriched in cancer, diabetes, insulin secretion, and other related pathways. This study can help us understand the molecular mechanisms underlying comorbid NAFLD and metabolic disorder... [more]