Machine Learning-based Cerebral Venous Thrombosis Diagnosis with Clinical Data.

OBJECTIVES: Cerebral Venous Thrombosis (CVT) poses diagnostic challenges due to the variability in disease course and symptoms. The prognosis of CVT relies on early diagnosis. Our study focuses on developing a machine learning-based screening algorithm using clinical data from a large neurology referral center in southern Iran. METHODS: The Iran Cerebral Venous Thrombosis Registry (ICVTR code: 9001013381) provided data on 382 CVT cases from Namazi Hospital. The control group comprised of adult headache patients without CVT as confirmed by neuroimaging and was retrospectively selected from those admitted to the same hospital. We collected 60 clinical and demographic features for model development and validation. Our modeling pipeline involved imputing missing values and evaluating four machine learning algorithms: generalized linear model, random forest, support vector machine, and extreme gradient boosting. RESULTS: A total of 314 CVT cases and 575 controls were included. The highest AUROC was reached when imputation was used to estimate missing values for all the variables, combined with the support vector machine model (AUROC=0.910, Recall=0.73, Precision=0.88). The best recall was achieved also by the support vector machine model when only variables with less than 50% missing rate were included (AUROC=0.887, Recall=0.77, Precision=0.86). The random forest model yielded the best precision by using variables with less than 50% missing rate (AUROC=0.882, Recall=0.61, Precision=0.94). CONCLUSION: The application of machine learning techniques using clinical data showed promising results in accurately diagnosing CVT within our study population. This approach offers a valuable complementary assistive tool or an alternative to resource-intensive imaging methods.

A translational model of chronic diabetic nephropathy in the Nile grass rat.

Diabetic nephropathy (DN) is a major healthcare challenge for individuals with diabetes and associated with increased cardiovascular morbidity and mortality. The existing rodent models do not fully represent the complex course of the human disease. Hence, developing a translational model of diabetes that reproduces both the early and the advanced characteristics of DN and faithfully recapitulates the overall human pathology is an unmet need. Here, we introduce the Nile grass rat (NGR) as a novel model of DN and characterize key pathologies underlying DN. NGRs spontaneously developed insulin resistance, reactive hyperinsulinemia, and hyperglycemia. Diabetic NGRs evolved DN and the key histopathological aspects of the human advanced DN, including glomerular hypertrophy, infiltration of mononuclear cells, tubular dilatation, and atrophy. Enlargement of the glomerular tufts and the Bowman's capsule areas accompanied the expansion of the Bowman's space. Glomerular sclerosis, renal arteriolar hyalinosis, Kimmelsteil-Wilson nodular lesions, and protein cast formations in the kidneys of diabetic NGR occurred with DN. Diabetic kidneys displayed interstitial and glomerular fibrosis, key characteristics of late human pathology as well as thickening of the glomerular basement membrane and podocyte effacement. Signs of injury included glomerular lipid accumulation, significantly more apoptotic cells, and expression of KIM-1. Diabetic NGRs became hypertensive, a known risk factor for kidney dysfunction, and showed decreased glomerular filtration rate. Diabetic NGRs recapitulate the breadth of human DN pathology and reproduce the consequences of chronic kidney disease, including injury and loss of function of the kidney. Hence, NGR represents a robust model for studying DN-related complications and provides a new foundation for more detailed mechanistic studies of the genesis of nephropathy, and the development of new therapeutic approaches.

Structure-guided design and cloning of peptide inhibitors targeting CDK9/cyclin T1 protein-protein interaction.

CDK9 (cyclin-dependent kinase 9) plays a significant role in numerous pathological conditions, such as HIV-1 infection and cancer. The interaction between CDK9 and cyclin T1 is crucial for maintaining the kinase's active state. Therefore, targeting this protein-protein interaction offers a promising strategy for inhibiting CDK9. In this study, we aimed to design and characterize a library of mutant peptides based on the binding region of cyclin T1 to CDK9. Using Osprey software, a total of 7,776 mutant peptides were generated. After conducting a comprehensive analysis, three peptides, namely, mp3 (RAADVEGQRKRRE), mp20 (RAATVEGQRKRRE), and mp29 (RAADVEGQDKRRE), were identified as promising inhibitors that possess the ability to bind to CDK9 with high affinity and exhibit low free binding energy. These peptides exhibited favorable safety profiles and displayed promising dynamic behaviors. Notably, our findings revealed that the mp3 and mp29 peptides interacted with a conserved sequence in CDK9 (residues 60-66). In addition, by designing the structure of potential peptides in the plasmid vector pET28a (+), we have been able to pave the way for facilitating the process of their recombinant production in an Escherichia coli expression system in future studies. Predictions indicated good solubility upon overexpression, further supporting their potential for downstream applications. While these results demonstrate the promise of the designed peptides as blockers of CDK9 with high affinity, additional experimental studies are required to validate their biological activity and assess their selectivity. Such investigations will provide valuable insights into their therapeutic potential and pave the way for the future development of peptide-based inhibitors targeting the CDK9-cyclin T1 complex.

Gut-Lung Microbiota Characterization in Patients with Non-Small Cell Lung Carcinoma and COVID-19 Coinfection.

BACKGROUND: Non-small cell lung cancer (NSCLC) patients with COVID-19 have an excessive chance of morbidity and mortality. The fecal-nasopharyngeal microbiota compositions of NSCLC patients were assessed in this study. METHODS: In total, 234 samples were collected from 17 NSCLC patients infected with COVID-19, 20 NSCLC patients without confirmed COVID-19, 40 non NSCLC patients with COVID-19, and 40 healthy individuals. RESULTS: In lung microbiota, the abundance of Streptococcus spp. in NSCLC patients with confirmed COVID-19 was significantly higher than the two control groups. Pseudomonas aeruginosa and Staphylococcus aureus were listed as the most frequent pulmonary bacterial groups that colonized COVID-19 patients. In fecal specimens, the numbers of Bacteroidetes, Firmicutes, and Actinobacteria phyla were significantly higher amongst NSCLC patients with COVID-19. NSCLC patients infected with COVID-19 showed lower levels of Lactobacillus spp., Akkermansia muciniphila, and Bifidobacterium spp. The counts of Streptococcus spp., in NSCLC patients with COVID-19 were significantly higher than those of healthy individuals (8.49±0.70 log CFU/g wet feces vs 8.49±0.70 log CFU/g wet feces). Prevotella spp. were enriched in the gut and respiratory tracts of COVID-19 patient groups. The unbiased analysis showed an increment in Enterococcus spp., Streptococcus spp., and Prevotella spp. CONCLUSION: Eventually, it was found that compared to control groups, COVID-19 patients with NSCLC showed diminished gut bacteria diversity and increase in Lactobacillus spp., A. muciniphila, and Bifidobacterium spp. The overgrowth of Enterococcus spp., Streptococcus spp., and Prevotella spp. could be potential predictive biomarkers in the gut-lung axis of NSCLC patients with COVID-19.

Efficient Expression of Functionally Active Aflibercept with Designed N-glycans.

Aflibercept is a therapeutic recombinant fusion protein comprising extracellular domains of human vascular endothelial growth factor receptors (VEGFRs) and IgG1-Fc. It is a highly glycosylated protein with five N-glycosylation sites that might impact it structurally and/or functionally. Aflibercept is produced in mammalian cells and exhibits large glycan heterogeneity, which hampers glycan-associated investigations. Here, we report the expression of aflibercept in a plant-based system with targeted N-glycosylation profiles. Nicotiana benthamiana-based glycoengineering resulted in the production of aflibercept variants carrying designed carbohydrates, namely, N-glycans with terminal GlcNAc and sialic acid residues, herein referred to as AFLIGnGn and AFLISia, respectively. Both variants were transiently expressed in unusually high amounts (2 g/kg fresh leaf material) in leaves and properly assembled to dimers. Mass spectrometric site-specific glycosylation analyses of purified aflibercept showed the presence of two to four glycoforms in a consistent manner. We also demonstrate incomplete occupancy of some glycosites. Both AFLIGnGn and AFLISia displayed similar binding potency to VEGF165, with a tendency of lower binding to variants with increased sialylation. Collectively, we show the expression of functionally active aflibercept in significant amounts with controlled glycosylation. The results provide the basis for further studies in order to generate optimized products in the best-case scenario.

Evaluation of the expression level of microRNA-21, microRNA-15a, microRNA-372 in human follicular fluid stem cells-derived oocyte-like cells (OLCs).

OBJECTIVE: Today, researchers have succeeded in achieving oocyte-like cells through the in vitro differentiation of stem cells. MicroRNAs are key regulators of oocyte development. In this study we decided to evaluate the expression pattern of microRNA-21, microRNA-15a, and microRNA-372 in oocyte-like cells, to determine the maturation stage of oocyte-like cells. METHODS: Human follicular fluid samples were collected and centrifuged, and their cells were divided into 3 groups; day 7 as control group, days 14 and 21. During this period, the cells were evaluated for their morphological appearance and viability by inverted microscopy. RNA isolation was performed and cDNA was reversely transcribed by specific stem-loop RT primers. Real-time RT-PCR was used to detect microRNA expression. RESULTS: The relative expression of microRNA-21 and microRNA-15a on day 21 was significantly down-regulated compared to the control group (day 7), but microRNA-372 did not show a significant difference. Also, on day 14 compared to the control group (day 7), microRNA-21 did not show a significant difference; but microRNA-15a and microRNA-372 were significantly down-regulated. MicroRNA-21 and microRNA-15a on day 21 compared to day 14 revealed down-regulated levels, but microRNA-372 revealed up-regulated levels. CONCLUSIONS: Our results showed significant decreases in the expression of microRNA-21 and microRNA-15a in oocyte-like cells, as well as in oocytes, which may lead to cytoplasmic maturation, germinal vesicle break down and the completion of meiosis І. In addition, down-regulation expression of microRNA-372 maybe a confirmation that mesenchymal stem cells have differentiated into germ cells, and these cells were differentiated into oocyte-like cells.

Transcriptome analysis in Aegilops tauschii unravels further insights into genetic control of stripe rust resistance.

MAIN CONCLUSION: The Aegilops tauschii resistant accession prevented the pathogen colonization by controlling the sugar flow and triggering the hypersensitive reaction. This study suggested that NBS-LRRs probably induce resistance through bHLH by controlling JA- and SA-dependent pathways. Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst) is one of wheat's most destructive fungal diseases that causes a severe yield reduction worldwide. The most effective and economically-friendly strategy to manage this disease is genetic resistance which can be achieved through deploying new and effective resistance genes. Aegilops tauschii, due to its small genome and co-evolution with Pst, can provide detailed information about underlying resistance mechanisms. Hence, we used RNA-sequencing approach to identify the transcriptome variations of two contrasting resistant and susceptible Ae. tauschii accessions in interaction with Pst and differentially expressed genes (DEGs) for resistance to stripe rust. Gene ontology, pathway analysis, and search for functional domains, transcription regulators, resistance genes, and protein-protein interactions were used to interpret the results. The genes encoding NBS-LRR, CC-NBS-kinase, and phenylalanine ammonia-lyase, basic helix-loop-helix (bHLH)-, basic-leucine zipper (bZIP)-, APETALA2 (AP2)-, auxin response factor (ARF)-, GATA-, and LSD-like transcription factors were up-regulated exclusively in the resistant accession. The key genes involved in response to salicylic acid, amino sugar and nucleotide sugar metabolism, and hypersensitive response contributed to plant defense against stripe rust. The activation of jasmonic acid biosynthesis and starch and sucrose metabolism pathways under Pst infection in the susceptible accession explained the colonization of the host. Overall, this study can fill the gaps in the literature on host-pathogen interaction and enrich the Ae. tauschii transcriptome sequence information. It also suggests candidate genes that could guide future breeding programs attempting to develop rust-resistant cultivars.

A comprehensive meta-analysis of transcriptome data to identify signature genes associated with pancreatic ductal adenocarcinoma.

PURPOSE: Pancreatic ductal adenocarcinoma (PDAC) has a five-year survival rate of less than 5%. Absence of symptoms at primary tumor stages, as well as high aggressiveness of the tumor can lead to high mortality in cancer patients. Most patients are recognized at the advanced or metastatic stage without surgical symptom, because of the lack of reliable early diagnostic biomarkers. The objective of this work was to identify potential cancer biomarkers by integrating transcriptome data. METHODS: Several transcriptomic datasets comprising of 11 microarrays were retrieved from the GEO database. After pre-processing, a meta-analysis was applied to identify differentially expressed genes (DEGs) between tumor and nontumor samples for datasets. Next, co-expression analysis, functional enrichment and survival analyses were used to determine the functional properties of DEGs and identify potential prognostic biomarkers. In addition, some regulatory factors involved in PDAC including transcription factors (TFs), protein kinases (PKs), and miRNAs were identified. RESULTS: After applying meta-analysis, 1074 DEGs including 539 down- and 535 up-regulated genes were identified. Pathway enrichment analyzes using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that DEGs were significantly enriched in the HIF-1 signaling pathway and focal adhesion. The results also showed that some of the DEGs were assigned to TFs that belonged to 23 conserved families. Sixty-four PKs were identified among the DEGs that showed the CAMK family was the most abundant group. Moreover, investigation of corresponding upstream regions of DEGs identified 11 conserved sequence motifs. Furthermore, weighted gene co-expression network analysis (WGCNA) identified 8 modules, more of them were significantly enriched in Ras signaling, p53 signaling, MAPK signaling pathways. In addition, several hubs in modules were identified, including EMP1, EVL, ELP5, DEF8, MTERF4, GLUP1, CAPN1, IGF1R, HSD17B14, TOM1L2 and RAB11FIP3. According to survival analysis, it was identified that the expression levels of two genes, EMP1 and RAB11FIP3 are related to prognosis. CONCLUSION: We identified several genes critical for PDAC based on meta-analysis and system biology approach. These genes may serve as potential targets for the treatment and prognosis of PDAC.

Role of Interleukin-21 in retinal ischemia-reperfusion injury: Unveiling the impact on retinal ganglion cell apoptosis.

BACKGROUND: Retinal ischemia-reperfusion (I/R) serves as a significant contributor to ocular diseases, triggering a cascade of pathological processes. The interplay between neuroinflammation and the apoptosis of retinal ganglion cell (RGC) is a well-explored aspect of retinal I/R-induced tissue damage. Within this intricate landscape, the inflammatory cytokine Interleukin-21 (IL21) emerges as a potent mediator of neuroinflammation with known detrimental effects on neuronal integrity. However, its specific impact on RGC apoptosis in the context of retinal I/R has remains to be uncovered. This study aims to unravel the potential anti-apoptotic effects of IL21 siRNA on RGC, shedding light on the neuroprotection of retinal I/R. METHODS: Sprague-Dawley (SD) rats underwent a controlled elevation of intraocular pressure (IOP) to 110 mmHg for 60 min to simulate retinal I/R conditions. To explore the influence of IL21 on RGC apoptosis and its underlying molecular mechanisms, a comprehensive array of techniques such immunohistochemistry, immunofluorescence, TUNEL, Hematoxylin-eosin (H&E), immunoblotting, and qRT-PCR were carried out. RESULTS: The landscape of retinal I/R injury revealed an increase in the expression of IL21, reaching its peak at 72 h. Notably, IL21 markedly induced RGC apoptosis within the retinal I/R milieu. The introduction of IL21 siRNA showed promising outcomes, manifesting as an amelioration of neurological function deficits, a reduction in RGC loss, and an increase in the thickness of the inner retinal layer at the 72-hour reperfusion. Additionally, IL21 siRNA demonstrated its ability to hinder the release of proteins associated with apoptosis via the JAK/STAT signaling pathway. In the in vitro setting, IL21 siRNA efficiently reduced R28 cell apoptosis by suppressing the production of proteins associated with apoptosis by regulating the JAK/STAT signaling pathway. CONCLUSIONS: This study provides evidence for the pathogenic role of IL21 in retinal I/R. The findings underscore IL21 siRNA as a promising therapeutic target for ischemic retinal injury. Its efficacy lies in its ability to mitigate RGC apoptosis by suppressing the JAK/STAT signaling pathway. These findings not only enhance our comprehension of retinal I/R pathology but also suggests IL21 siRNA as a potential transformative factor in the development of targeted therapies for ischemic retinal injuries.

Genome-wide identification of the opsin protein in Leptosphaeria maculans and comparison with other fungi (pathogens of Brassica napus).

The largest family of transmembrane receptors are G-protein-coupled receptors (GPCRs). These receptors respond to perceived environmental signals and infect their host plants. Family A of the GPCR includes opsin. However, there is little known about the roles of GPCRs in phytopathogenic fungi. We studied opsin in Leptosphaeria maculans, an important pathogen of oilseed rape (Brassica napus) that causes blackleg disease, and compared it with six other fungal pathogens of oilseed rape. A phylogenetic tree analysis of 31 isoforms of the opsin protein showed six major groups and six subgroups. All three opsin isoforms of L. maculans are grouped in the same clade in the phylogenetic tree. Physicochemical analysis revealed that all studied opsin proteins are stable and hydrophobic. Subcellular localization revealed that most isoforms were localized in the endoplasmic reticulum membrane except for several isoforms in Verticillium species, which were localized in the mitochondrial membrane. Most isoforms comprise two conserved domains. One conserved motif was observed across all isoforms, consisting of the BACTERIAL_OPSIN_1 domain, which has been hypothesized to have an identical sensory function. Most studied isoforms showed seven transmembrane helices, except for one isoform of V. longisporum and four isoforms of Fusarium oxysporum. Tertiary structure prediction displayed a conformational change in four isoforms of F. oxysporum that presumed differences in binding to other proteins and sensing signals, thereby resulting in various pathogenicity strategies. Protein-protein interactions and binding site analyses demonstrated a variety of numbers of ligands and pockets across all isoforms, ranging between 0 and 13 ligands and 4 and 10 pockets. According to the phylogenetic analysis in this study and considerable physiochemically and structurally differences of opsin proteins among all studied fungi hypothesized that this protein acts in the pathogenicity, growth, sporulation, and mating of these fungi differently.

VEGFR-2 adhesive nanoprobes reveal early diabetic retinopathy in vivo.

Diabetic retinopathy (DR) is a debilitating organ manifestation of diabetes. Absent of early diagnosis and intervention, vision tends to drastically and irreversibly decline. Previously, we showed higher vascular endothelial growth factor receptor 2 (VEGFR-2) expression in diabetic microvessels, and the suitability of this molecule as a biomarker for early DR diagnosis. However, a hurdle to translation remained generation of biodegradable nanoprobes that are sufficiently bright for in vivo detection. Here, an adhesive fluorescent nanoprobe with high brightness was developed using biodegradable materials. To achieve that, a fluorophore with bulky hydrophobic groups was encapsulated in the nanoparticles to minimize fluorophore π-π stacking, which diminishes brightness at higher loading contents. The nanoprobe selectively targeted the VEGFR-2 under dynamic flow conditions. Upon systemic injection, the nanoprobes adhered in the retinal microvessels of diabetic mice and were visualized as bright spots in live retinal microscopy. Histology validated the in vivo results and showed binding of the nanoprobes to the microvascular endothelium and firmly adhering leukocytes. Leukocytes were found laden with nanoprobes, indicating the potential for payload transport across the blood-retinal barrier. Our results establish the translational potential of these newly generated nanoprobes in early diagnosis of DR.

Breath Biopsy Reveals Systemic Immunothrombosis and Its Resolution through Bioorthogonal Dendritic Nanoprobes.

Immunothrombosis, an inflammation-dependent activation of the coagulation cascade, leads to microthrombi formations in small vessels. It is a dreaded complication of COVID-19 and a major cause of respiratory failure. Due to their size and disseminated nature, microthrombi are currently undetectable. Here, noninvasive detection of a volatile reporter in the exhaled air is introduced for assessment of systemic immunothrombosis. A dendritic nanoprobe, containing high loading of a thrombin-sensitive substrate, is selectively cleaved by thrombin, resulting in release of a synthetic bioorthogonal volatile organic compound (VOC). The VOC is quantitated in the exhaled air biopsies via gas chromatography-mass spectrometry (GC-MS), allowing near real-time assessment of systemic immunothrombosis. The VOC detection can be further improved with more rapid and sensitive MS-based technologies. The amount of the VOC in the exhaled air decreases with resolution of the microvascular inflammation and intravascular fibrin depositions. Through conjugation of the thrombin-sensitive peptide with a rhodol derivative, a novel thrombin-sensitive fluorescent nanoprobe is developed for intravital visualization of thrombin activity in actively growing thrombi. These results establish unprecedented detection of thrombin activity in vivo, addressing this unmet medical need. This novel approach facilitates diagnosis of immunothrombosis in diseases such as diabetic complications, disseminated intravascular coagulation, and COVID-19.

Neglected cervical meningocele in an adult: illustrative case.

BACKGROUND: Posterior cervical meningoceles are rare in adults because most are surgically excised early in life. Such meningoceles in adults are mostly presented as a cystic mass and their presentation as a solid mass is very rare. OBSERVATIONS: An asymptomatic adult with cervical meningocele presented as a congenital midline skin covered solid mass in the posterior aspect of the neck is presented. Neuroradiological surveys showed attachment of the mass to intradural spinal cord. With diagnosis of a cervical meningocele, after excision of the solid sac, the stalk extending from the core of the mass to the dura was isolated. This was followed by intradural spinal cord detethering. The mass was compatible with rudimentary meningocele in pathology. LESSONS: Neglected cervical meningocele is quite rare in adults. Surgical removal of the mass in adults is usually for cosmetic reasons rather than neurological impairment. However, surgical removal of the mass without intradural cord detethering is not sufficient. In such cases, late onset quadriparesis may be appear due to the spinal cord tethering scenario.

microRNA-96 targets the INS/AKT/GLUT4 signaling axis: Association with and effect on diabetic retinopathy.

Background: miR-96-5p is a highly expressed microRNA in the retina of subjects with diabetes. The INS/AKT/GLUT4 signaling axis is the main cell signaling pathway of glucose uptake in cells. Here, we investigated the role of miR-96-5p in this signaling pathway. Methods: Expression levels of miR-96-5p and its target genes were measured under high glucose conditions, in the retina of streptozotocin-induced diabetic mice, in the retina of AAV-2-eGFP-miR-96 or GFP intravitreal injected mice and in the retina of human donors with diabetic retinopathy (DR). MTT, wound healing, tube formation, Western blot, TUNEL, angiogenesis assays and hematoxylin-eosin staining of the retinal sections were performed. Results: miR-96-5p expression was increased under high glucose conditions in mouse retinal pigment epithelial (mRPE) cells, in the retina of mice receiving AAV-2 carrying miR-96 and STZ-treated mice. Expression of the miR-96-5p target genes related to the INS/AKT/GLUT4 signaling pathway was reduced following miR-96-5p overexpression. mmu-miR-96-5p expression decreased cell proliferation and thicknesses of retinal layers. Cell migration, tube formation, vascular length, angiogenesis, and TUNEL-positive cells were increased. Conclusions: In in vitro and in vivo studies and in human retinal tissues, miR-96-5p regulated the expression of the PIK3R1, PRKCE, AKT1, AKT2, and AKT3 genes in the INS/AKT axis and some genes involved in GLUT4 trafficking, such as Pak1, Snap23, RAB2a, and Ehd1. Because disruption of the INS/AKT/GLUT4 signaling axis causes advanced glycation end product accumulation and inflammatory responses, the inhibition of miR-96-5p expression could ameliorate DR.

Mannosylated preactivated hyaluronic acid-based nanostructures for bacterial infection treatment.

Salmonella Typhi is an intracellular bacterium causing a variety of enteric diseases, being typhoid fever the most common. Current modalities for treating S. typhi infection are subjected to multi-drug resistance. Herein, a novel macrophage targeting approach was developed via coating bioinspired mannosylated preactivated hyaluronic acid (Man-PTHA) ligands on a self-nanoemulsifying drug delivery system (SNEDDS) loaded with the anti-bacterial drug ciprofloxacin (CIP). The shake flask method was used to determine the drug solubility in the different excipients (oil, surfactants and co-surfactants). Man-PTHA were characterized by physicochemical, in vitro, and in vivo parameters. The mean droplet size was 257 nm, with a PDI of 0.37 and zeta potential of -15 mV. In 72 h, 85 % of the drug was released in a sustained manner, and the entrapment efficiency was 95 %. Outstanding biocompatibility, mucoadhesion, muco-penetration, anti-bacterial action and hemocompatibility were observed. Intra-macrophage survival of S. typhi was minimal (1 %) with maximum nanoparticle uptake, as shown by their higher fluorescence intensity. Serum biochemistry evaluation showed no significant changes or toxicity, and histopathological evaluation confirmed the entero-protective nature of the bioinspired polymers. Overall, results confirm that Man-PTHA SNEDDS can be employed as novel and effective delivery systems for the therapeutic management of S. typhi infection.

Integrating sustainability into production scheduling in hybrid flow-shop environments.

Global energy consumption is projected to grow by nearly 50% as of 2018, reaching a peak of 910.7 quadrillion BTU in 2050. The industrial sector accounts for the largest share of the energy consumed, making energy awareness on the shop floors imperative for promoting industrial sustainable development. Considering a growing awareness of the importance of sustainability, production planning and control require the incorporation of time-of-use electricity pricing models into scheduling problems for well-informed energy-saving decisions. Besides, modern manufacturing emphasizes the role of human factors in production processes. This study proposes a new approach for optimizing the hybrid flow-shop scheduling problems (HFSP) considering time-of-use electricity pricing, workers' flexibility, and sequence-dependent setup time (SDST). Novelties of this study are twofold: to extend a new mathematical formulation and to develop an improved multi-objective optimization algorithm. Extensive numerical experiments are conducted to evaluate the performance of the developed solution method, the adjusted multi-objective genetic algorithm (AMOGA), comparing it with the state-of-the-art, i.e., strength Pareto evolutionary algorithm (SPEA2), and Pareto envelop-based selection algorithm (PESA2). It is shown that AMOGA performs better than the benchmarks considering the mean ideal distance, inverted generational distance, diversification, and quality metrics, providing more versatile and better solutions for production and energy efficiency.

Integrative systems biology analysis of barley transcriptome ─ hormonal signaling against biotic stress.

Biotic stresses are pests and pathogens that cause a variety of crop diseases and damages. In response to these agents, crops trigger specific defense signal transduction pathways in which hormones play a central role. To recognize hormonal signaling, we integrated barley transcriptome datasets related to hormonal treatments and biotic stresses. In the meta-analysis of each dataset, 308 hormonal and 1232 biotic DEGs were identified respectively. According to the results, 24 biotic TFs belonging to 15 conserved families and 6 hormonal TFs belonging to 6 conserved families were identified, with the NF-YC, GNAT, and WHIRLY families being the most prevalent. Additionally, gene enrichment and pathway analyses revealed that over-represented cis-acting elements were recognized in response to pathogens and hormones. Based on the co-expression analysis, 6 biotic and 7 hormonal modules were uncovered. Finally, the hub genes of PKT3, PR1, SSI2, LOX2, OPR3, and AOS were candidates for further study in JA- or SA-mediated plant defense. The qPCR confirmed that the expression of these genes was induced from 3 to 6 h following exposure to 100 µM MeJA, with peak expression occurring between 12 h and 24 h and decreasing after 48 h. Overexpression of PR1 was one of the first steps toward SAR. As well as regulating SAR, NPR1 has also been shown to be involved in the activation of ISR by the SSI2. LOX2 catalyzes the first step of JA biosynthesis, PKT3 plays an important role in wound-activated responses, and OPR3 and AOS are involved in JA biosynthesis. In addition, many unknown genes were introduced that can be used by crop biotechnologists to accelerate barley genetic engineering.

System network analysis of Rosmarinus officinalis transcriptome and metabolome-Key genes in biosynthesis of secondary metabolites.

Medicinal plants contain valuable compounds that have attracted worldwide interest for their use in the production of natural drugs. The presence of compounds such as rosmarinic acid, carnosic acid, and carnosol in Rosmarinus officinalis has made it a plant with unique therapeutic effects. The identification and regulation of the biosynthetic pathways and genes will enable the large-scale production of these compounds. Hence, we studied the correlation between the genes involved in biosynthesis of the secondary metabolites in R. officinalis using proteomics and metabolomics data by WGCNA. We identified three modules as having the highest potential for the metabolite engineering. Moreover, the hub genes highly connected to particular modules, TFs, PKs, and transporters were identified. The TFs of MYB, C3H, HB, and C2H2 were the most likely candidates associated with the target metabolic pathways. The results indicated that the hub genes including Copalyl diphosphate synthase (CDS), Phenylalanine ammonia lyase (PAL), Cineole synthase (CIN), Rosmarinic acid synthase (RAS), Tyrosine aminotransferase (TAT), Cinnamate 4-hydroxylase (C4H), and MYB58 are responsible for biosynthesis of important secondary metabolites. Thus, we confirmed these results using qRT-PCR after treating R. officinalis seedlings with methyl jasmonate. These candidate genes may be employed for genetic and metabolic engineering research to increase R. officinalis metabolite production.

Identification of key genes involved in secondary metabolite biosynthesis in Digitalis purpurea.

The medicinal plant Digitalis purpurea produces cardiac glycosides that are useful in the pharmaceutical industry. These bioactive compounds are in high demand due to ethnobotany's application to therapeutic procedures. Recent studies have investigated the role of integrative analysis of multi-omics data in understanding cellular metabolic status through systems metabolic engineering approach, as well as its application to genetically engineering metabolic pathways. In spite of numerous omics experiments, most molecular mechanisms involved in metabolic pathways biosynthesis in D. purpurea remain unclear. Using R Package Weighted Gene Co-expression Network Analysis, co-expression analysis was performed on the transcriptome and metabolome data. As a result of our study, we identified transcription factors, transcriptional regulators, protein kinases, transporters, non-coding RNAs, and hub genes that are involved in the production of secondary metabolites. Since jasmonates are involved in the biosynthesis of cardiac glycosides, the candidate genes for Scarecrow-Like Protein 14 (SCL14), Delta24-sterol reductase (DWF1), HYDRA1 (HYD1), and Jasmonate-ZIM domain3 (JAZ3) were validated under methyl jasmonate treatment (MeJA, 100 µM). Despite early induction of JAZ3, which affected downstream genes, it was dramatically suppressed after 48 hours. SCL14, which targets DWF1, and HYD1, which induces cholesterol and cardiac glycoside biosynthesis, were both promoted. The correlation between key genes and main metabolites and validation of expression patterns provide a unique insight into the biosynthesis mechanisms of cardiac glycosides in D. purpurea.

Integration of mRNA and protein expression data for the identification of potential biomarkers associated with pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is one of the most death-dealing tumors, with a tremendously poor prognosis. Here, we, through interrogation of mRNA and protein data combined with a system biology approach, identified several key genes, functional processes, and pathways that can have critical roles in PDAC. We detected an interesting module related to the clinical traits that enriched in the ribosome, hematopoietic cell lineage, and cell adhesion molecules-related pathways. We also identified several hub genes in important modules that are associated with immune system processes. The results also indicated some lncRNAs, such as FAM30A, and MIR223HG with essential functions that are involved in PDAC. Additionally, five genes, including CD53, ITGAL, WDFY4, TLX1, and LMAN1L were screened by survival analysis and can be considered as candidate biomarkers or therapeutic targets. According to our strategy, the findings of this study may provide a better understanding of the molecular mechanisms and suggest potential prognostic and therapeutic targets for PDAC.