Detecting language network alterations in mild cognitive impairment using task-based fMRI and resting-state fMRI: A comparative study

OBJECTIVE

The objective of this study was to investigate the functional changes associated with mild cognitive impairment (MCI) using independent component analysis (ICA) with the word generation task functional magnetic resonance imaging (fMRI) and resting-state fMRI.

METHODS

In this study 17 patients with MCI and age and education-matched 17 healthy individuals as control group are investigated. All participants underwent resting-state fMRI and task-based fMRI while performing the word generation task. ICA was used to identify the appropriate independent components (ICs) and their associated networks. The Dice Coefficient method was used to determine the relevance of the ICs to the networks of interest.

RESULTS

IC-14 was found relevant to language network in both resting-state and task-based fMRI, IC-4 to visual, and IC-28 to dorsal attention network (DAN) in word generation task-based fMRI by Sorento-Dice Coefficient. ICA showed increased activation in language network, which had a larger voxel size in resting-state functional MRI than word generation task-based fMRI in the bilateral lingual gyrus. Right temporo-occipital fusiform cortex, right hippocampus, and right thalamus were also activated in the task-based fMRI. Decreased activation was found in DAN and visual network MCI patients in word generation task-based fMRI.

CONCLUSION

Task-based fMRI and ICA are more sophisticated and reliable tools in evaluation cognitive impairments in language processing. Our findings support the neural mechanisms of the cognitive impairments in MCI.

Molecular characterization of the complete genome of a novel ormycovirus infecting the ectomycorrhizal fungus Hortiboletus rubellus

Advancements in high-throughput sequencing and the development of new bioinformatics tools for large-scale data analysis play a crucial role in uncovering virus diversity and enhancing our understanding of virus evolution. The discovery of the ormycovirus clades, a group of RNA viruses that are phylogenetically distinct from all known Riboviria members and are found in fungi, highlights the value of these tools for the discovery of novel viruses. The aim of this study was to examine viral populations in fungal hosts to gain insights into the diversity, evolution, and classification of these viruses. Here, we report the molecular characterization of a newly discovered ormycovirus, which we have named "Hortiboletus rubellus ormycovirus 1" (HrOMV1), that was found in the ectomycorrhizal fungus Hortiboletus rubellus. The bipartite genome of HrOMV1, whose nucleotide sequence was determined by HTS and RLM-RACE, consists of two RNA segments (RNA1 and RNA2) that exhibit similarity to those of previously studied ormycoviruses in their organization and the proteins they encode. The presence of upstream, in-frame AUG triplets in the 5' termini of both RNA segments suggests that HrOMV1, like certain other ormycoviruses, employs a non-canonical translation initiation strategy. Phylogenetic analysis showed that HrOMV1 is positioned within the gammaormycovirus clade. Its putative RNA-dependent RNA polymerase (RdRp) exhibits sequence similarity to those of other gammaormycovirus members, the most similarity to that of Termitomyces ormycovirus 1, with 33.05% sequence identity. This protein was found to contain conserved motifs that are crucial for RNA replication, including the distinctive GDQ catalytic triad observed in gammaormycovirus RdRps. The results of this study underscore the significance of investigating the ecological role of mycoviruses in mycorrhizal fungi. This is the first report of an ormycovirus infecting a member of the ectomycorrhizal genus Hortiboletus.

Study of the effect of sFRP1 protein on molecules involved in the regulation of DNA methylation in CML cell line

Wnt-signaling pathway plays a crucial role in the pathogenesis and progression of Chronic Myeloid Leukemia (CML). sFRP1 is involved in the suppression of the Wnt-signaling pathway and has been shown to be epigenetically silenced by promoter hypermethylation during CML progression. DNMT3A plays a crucial role in promoter hypermethylation and is responsible for establishing methylation patterns. We aimed to analyze the relationship between sFRP1 expression and DNMT3A, TET1, TET2 and TET3 proteins that are responsible for maintaining cellular methylation patterns; along with miRNAs miR144-3p and miR-767-5p that are known to be associated with these proteins. CML cell lines K562 and K562S which stably expresses sFRP1, were used to compare the changes in miR144-3p and miR-767-5p expression. DNMT3A, TET1, TET2 and TET3 protein levels were analyzed by Western blot. In K562S cells the expression of miR-144-3p and miR-767-5p were decreased along with DNMT3A and TET1 protein levels. On the contrary, TET2 protein was increased. Our results support other reports involving sFRP1 and methylation dynamics; as well as opening new avenues of exploration. Our data supports the conclusion that re-expression of sFRP1 protein alters the expression of factors that play important roles in the overall methylation patterns in the leukemic cell line K562.

An endoscopic approach providing near-infrared laser-induced coagulation with accurate depth limits

This article investigates an endoscopic approach that utilizes negative pressure to achieve laser-induced thermal coagulation limited to the esophageal wall's mucosal and superficial submucosal layers. The study was built upon a series of studies combining numerical simulation based on the Monte-Carlo technique and ex vivo porcine tissue experiments, including apparatus design and histology analysis. An endoscopy apparatus was developed using 3D printing to validate the tissue stretching-based approach. A fiber-pigtailed diode was used as the near-infrared source, emitting 208.8 W/cm2 laser irradiance at 1.5 μm. Simulation results suggested that the approach successfully created a local heat well to prevent residual thermal effects (>65°C) from penetrating the deeper submucosal layer. Histology analysis of ex vivo tissues showed that at a fluence of 5.22 kJ/cm2, the depth of thermal coagulation was reduced by half compared to the control. With further preclinical studies, including endoscopy apparatus design, the approach can be applied to the larger esophageal surface.

Full-length genome characterization of a novel mitovirus isolated from the root rot fungus Armillaria mellea

Members of the genus Armillaria belong to the group of pathogenic and facultative saprotrophic fungi that are generally known as one of the causative agents of white root rot in infected plants including deciduous and evergreen trees and shrubs. Although several single-stranded RNA mycoviruses were previously described in different Armillaria species, there is no report on mitoviruses (one of the simplest RNA viruses of fungal hosts) known to infect Armillaria taxa. In this study, a new mitovirus denominated "Armillaria mellea mitovirus 1" (AmMV1) was identified in the sporophore samples of Armillaria mellea, commonly known as honey mushroom. AmMV1 has a genome length of 4440 nucleotides and a G + C content of 48%. It encompasses a single open reading frame (ORF) that encodes an RNA-dependent RNA polymerase (RdRp). Comparison through BLASTp analysis revealed that the RdRp domain of AmMV1 shares a sequence identity ranging from 33.43% to 43.27% with RdRp domains of Duamitovirus genus members, having the highest similarity (43.27%) to Rhizoctonia solani mitovirus 94. According to phylogenetic analysis, AmMV1 is classified as a member of the genus Duamitovirus belonging to the Mitoviridae family. This marks the initial instance of a mitovirus identified in Armillaria spp..

Functional magnetic resonance imaging study during resting state and visual oddball task in mild cognitive impairment

BACKGROUND

Amnestic mild cognitive impairment (aMCI) is a transitional state between normal aging and dementia, and identifying early biomarkers is crucial for disease detection and intervention. Functional magnetic resonance imaging (fMRI) has the potential to identify changes in neural activity in MCI.

METHODS

We investigated neural activity changes in the visual network of the aMCI patients (n:20) and healthy persons (n:17) using resting-state fMRI and visual oddball task fMRI. We used independent component analysis to identify regions of interest and compared the activity between groups using a false discovery rate correction.

RESULTS

Resting-state fMRI revealed increased activity in the areas that have functional connectivity with the visual network, including the right superior and inferior lateral occipital cortex, the right angular gyrus and the temporo-occipital part of the right middle temporal gyrus (p-FDR = 0.008) and decreased activity in the bilateral thalamus and caudate nuclei, which are part of the frontoparietal network in the aMCI group (p-FDR = 0.002). In the visual oddball task fMRI, decreased activity was found in the right frontal pole, the right frontal orbital cortex, the left superior parietal lobule, the right postcentral gyrus, the right posterior part of the supramarginal gyrus, the right superior part of the lateral occipital cortex, and the right angular gyrus in the aMCI group.

CONCLUSION

Our results suggest the alterations in the visual network are present in aMCI patients, both during resting-state and task-based fMRI. These changes may represent early biomarkers of aMCI and highlight the importance of assessing visual processing in cognitive impairment. However, future studies with larger sample sizes and longitudinal designs are needed to confirm these findings.

New palladium complexes with N-heterocyclic carbene and morpholine ligands: Synthesis, characterization, crystal structure, molecular docking, and biological activities

This work includes the synthesis of a new series of palladium-based complexes containing both morpholine and N-heterocyclic carbene (NHC) ligands. The new complexes were characterized using NMR (1 H and 13 C), FTIR spectroscopic, and elemental analysis techniques. The crystal structure of complex 1b was obtained by utilizing the single-crystal X-ray diffraction method. X-ray studies show that the coordination environment of palladium atom is completed by the carbene carbon atom of the NHC ligand, the nitrogen atom of the morpholine ring, and a pair of bromide ligand, resulting in the formation of slightly distorted square planar geometry. All complexes were determined for some metabolic enzyme activities. Results indicated that all the synthetic complexes exhibited powerful inhibitory actions against all aims as compared to the control molecules. Ki values of new morpholine-liganded complexes bearing 4-hydroxyphenylethyl group 1a-e for hCA I, hCA II, AChE, BChE, and α-glycosidase enzymes were obtained in the ranges 0.93-2.14, 1.01-2.03, 4.58-10.27, 7.02-13.75, and 73.86-102.65 µM, respectively. Designing of reported complexes is impacted by molecular docking study, and interaction with the current enzymes also proclaimed that compounds 1e (-12.25 kcal/mol for AChE and -11.63 kcal/mol for BChE), 1c (-10.77 kcal/mol and -9.26 kcal/mol for α-Gly and hCA II, respectively), and 1a (-8.31 kcal/mol for hCA I) are showing binding affinity and interaction from the synthesized five novel complexes.

Understanding water characteristics and arsenic contamination of Lower Bakırçay Basin (LBB) and its coastal wetland (Western Turkiye): from Bergama (Pergamum) to Çandarlı (Elaia) by hydrogeochemical tools and stable isotope signatures

Bakırçay Basin is one of the largest and most productive basins in Turkey in terms of geothermal energy, history, mining, agriculture, and tourism. In this study, the lower part of the Bakırçay Basin was extensively examined using hydrogeochemical tools, encompassing 27 different water sample points in the basin, in alignment with the United Nations' 2030 sustainable development goals that focus on access to safe drinking water for all and climate action for carbon emissions. From the higher zones of the basin towards the coastal wetland, EC values increase from 212 to 26500 µS/cm. Again in the same direction, water types are Ca-Mg-HCO3 in hilly areas and Na-Cl at the coastal wetland. Salt marshes, which are the silent heroes of carbon sequestration, are the most important element of the Bakırçay coastal wetland. Irrigation water evaluation has also been made for agriculture, which is widespread in the basin. Except for the salty waters in the wetland, waters are suitable for irrigation. A contamination investigation was conducted in the waters with the aim of clean drinking water. As and Mn contamination, which exceeds the standard values, has been detected in the Bakırçay river and its tributaries, especially from the mining sites in LBB. The arsenic content of water in the study area varies between 2 and 62.2 ppb. Additionally, the study identified As(III) species, which is 60 times more toxic than As(V), in the study area. Stable isotope values (δ18O and δD) of waters in the basin are from - 6.66 to 1.43‰ and - 36.4 to 5.8‰, respectively, and all waters are of meteoric origin. It is essential to emphasize the importance of controlling mining activities in the basin, halting the construction of the port that will destroy the carbon sequestration coastal wetland, and instead, transforming it into a recreation area, the significance of which is now understood during the COVID-19 pandemic.

Comparing Tribbles Homolog 3 (TRIB3) Protein Expression Levels with Clinicopathological Characteristics and Survival Among Neuroblastoma Patients

Background

Tribbles Homolog 3 (TRIB3) is a member of the pseudokinase family of tribbles and acts as an adaptor protein to regulate different cellular processes. Upregulation of TRIB3 expression was shown either as a favorable or an adverse prognostic factor in various adult malignancies. However, TRIB3 expression has not been examined in pediatric cancers. Neuroblastoma is the most common malignant solid tumor of childhood, which affects mostly children under 5 years old. Risk stratification of patients defined by International Neuroblastoma Risk Group was used to determine prognosis and treatment of the disease. This study aimed to examine the relationship between TRIB3 protein expression levels and clinicopathological features and survival of patients.

Methods

TRIB3 protein expression was analyzed using immunohistochemical staining on formalin-fixed paraffin-embedded tissue samples of neuroblastoma patients (n = 56). Survival analyses were performed with Kaplan-Meier method and log-rank tests. Association between TRIB3 expression and clinicopathological characteristics were analyzed with Spearman's correlation.

Results

Of the patients, 32.1% were in the low-risk group, 21.4% in the medium-risk group, and 46.4% in the high-risk group. Survival analysis was performed in the entire neuroblastoma patient group and sub-risk groups of neuroblastoma patients. In the entire patient group, there was no significant difference in overall survival (P = .202) and event-free survival (P = .172) between TRIB3-positive and -negative patients. However, when survival analyses were performed in each risk group, TRIB3 expression was significantly associated with higher overall survival (P = .034) and event-free survival (P = .032) in low-risk group neuroblastoma patients. Nevertheless, no association was found between TRIB3 expression and overall survival (P = .799) and event-free survival (P = .448) in high-risk neuroblastoma patients. Furthermore, a significant correlation was identified between 1p36 loss-of-heterozygosity and TRIB3 expression (P = .030). However, TRIB3 expression did not correlate with other clinicopathological features.

Conclusion

TRIB3 expression is a potential predictive biomarker for low-risk neuroblastoma patients.

Seasonal variability of airborne mold concentrations as related to dust in a coastal urban area in the Eastern Mediterranean

Recent studies have demonstrated that the amount of specific airborne mold types and their concentrations increase during dust events. This study investigates the seasonal variation of airborne mold concentrations before, during, and after the dust transport in an eastern Mediterranean coastal area, Izmir city, Turkey. A total of 136 airborne mold samples were collected between September 2020 and May 2021. Two different culture media, namely Potato Dextrose Agar (PDA) and Malt-Extract Agar (MEA), were used for enumeration and genus-based identification of the airborne mold. In addition to culture media, the influences of air temperature, relative humidity, and particulate matter equal to or less than 10 µm (PM10) were also investigated seasonally. The HYSPLIT trajectory model and web-based simulation results were mainly used to determine dusty days. The mean total mold concentrations (TMC) on dusty days (543 Colony Forming Unit (CFU)/m3 on PDA and 668 CFU/m3 on MEA) were approximately 2-2.5 times higher than those on non-dusty days (288 CFU/m3 on PDA and 254 CFU/m3 on MEA) for both culture media. TMC levels showed seasonal variations (p < 0.001), indicating that meteorological parameters influenced mold concentrations and compositions. Some mold genera, including Cladosporium sp., Chrysosporium sp., Aspergillus sp., Bipolaris sp., Alternaria sp., and yeast, were found higher during dusty days than non-dusty days. Thus, dust event impacts levels and types of airborne molds and has implications for regions where long-range dust transport widely occurs.

Is the clinical course of non-arteritic ischemic optic neuropathy associated with oxidative damage and the dynamics of the antioxidant response?

PURPOSE

Oxidative stress is known to be a decisive factor in the wide etiopathogenesis of optic neuropathy. This study aimed to comprehensively evaluate the interaction of optic neuropathy's clinical course with systemic oxidative damage and antioxidant response dynamics in a large series.

METHODS

This case-controlled clinical study included 33 non-arteritic anterior ischemic optic neuropathy (NAION) patients and 32 healthy individuals. Extensive systemic oxidation profiles were statistically compared between the two groups, and correlations between the clinical and biochemical data in the study group were analyzed.

RESULTS

Vitamin E and malondialdehyde (MDA) levels were significantly higher in the study group. Significant correlations were observed in the analyses between clinical findings and oxidative stress parameters. Correlations between vitamin E and intraocular pressure (IOP), between B12 and cup-to-disk ratio (c/d), between antioxidant glutathione and superoxide dismutase (SOD) enzyme systems, and between uric acid (UA) and age were found to be very significant. As significant correlations were found in either clinical and biochemical data or in oxidative stress parameters, correlations between vitamin E and cholesterol, MDA were found to be very significant.

CONCLUSIONS

This study not only supplies significant information regarding oxidative damage and antioxidant response in NAION, but also points out the specific interactions of neuromodulators, like vitamin E, in intracellular signaling pathways and regulation mechanisms. A better reading of these connections may help improve diagnosis, follow-ups and treatment criteria and strategies.

Description of a new cellulosic natural fiber extracted from Helianthus tuberosus L. as a composite reinforcement material

Natural fiber-reinforced composites are generally known as eco-friendly, long-lasting, and recyclable materials. This study characterizes cellulosic Helianthus tuberosus L. fiber for polymer-based green composites for the first time. Helianthus tuberosus L. fiber has many advantages as a reinforcement material in polymer-based composites. For example, the high roughness of the fiber surface increases the locking into the composite body. One of the most critical advantages is its high thermal stability temperature of 247.3°C. Other advantages of the Helianthus tuberosus L. fiber are high cellulose content, high crystallinity, and high tensile strength. The hollow fiber structure allows its use in insulation materials. Finally, the high cellulose content of 62.65% supports its usage in various industries, including paper and paperboard manufacturing.

Anna Karenina principle in personalized treatment of bladder cancer according to oncogram: which drug for which patient?

Aim: To evaluate the ex vivo efficacy of chemotherapy, immunotherapy and targeted agents with the oncogram method in patients with bladder cancer and determine the most appropriate personalized treatment agent using immune markers. Materials & methods: Bladder cancer tissues were obtained from each patient. After cultivation, cell cultures were divided into 12 groups for each patient and 11 drugs were administered. Cell viability and immunohistochemistry expression were examined. Results: A good response rate was determined to be a 23% viability drop. The nivolumab good response rate was slightly better in PD-L1-positive patients and the ipilimumab good response rate was slightly better in tumoral CTLA-4-positive cases. Interestingly, the cetuximab response was worse in EGFR-positive cases. Conclusion: Although good responses of drug groups after their ex vivo application by using oncogram were found to be higher than control group, this outcome differed on a per patient basis.

Identification of ALK Mutation in Neuroblastoma on the Point of Molecular Heterogeneity

BACKGROUND AND AIM

In neuroblastoma, anaplastic lymphoma kinase mutations have recently received attention as molecular targets for the treatment of neuroblastoma, as 6% to 10% of patients with neuroblastoma have anaplastic lymphoma kinase mutations. There are little data from the cases in Turkey. We aimed to detect anaplastic lymphoma kinase mutations and molecular heterogeneity in neuroblastoma using next-generation sequencing. This study is the first one with this many cases in Turkey.

METHODS

Next-generation sequencing analysis was performed using an Illumina MiniSeq custom gene panel. Clinically important mutations were selected for the analysis. We also gathered clinical data of the patients from Turkish Pediatric Oncology Group cohorts to associate them with anaplastic lymphoma kinase mutations. This study is a retrospective cross-sectional study. We followed STROBE guideline (https://www.equator-network.org/reporting-guidelines/strobe/) on this study.

RESULTS

We analyzed anaplastic lymphoma kinase in 108 patients with neuroblastoma, with a mean age of 43.76 months. Pathogenic anaplastic lymphoma kinase mutations were detected in 13 patients (12.04%). We noted that anaplastic lymphoma kinase mutations were primarily observed in intermediate- and high-risk patients (P  =  .028). R1275Q and F1174-related mutations were predominant; I1171T, L1226F, S1189F, V1135A, and G1125S mutations were rare. Duplicate samples did not exhibit any heterogeneity.

CONCLUSIONS

We found that F1174 and R1275Q-related anaplastic lymphoma kinase mutations are the most common pathogenic mutations in neuroblastoma. Anaplastic lymphoma kinase mutation status did not show any heterogeneity, and the mutations were correlated with intermediate- or high-risk groups.

Resveratrol Inhibits NLRP3 Inflammasome-Induced Pyroptosis and miR-155 Expression in Microglia Through Sirt1/AMPK Pathway

Resveratrol is a natural polyphenolic compound with a wide range of biological activities such as antioxidant, anti-carcinogenic, anti-obesity, anti-aging, anti-inflammatory, immunomodulatory properties. Accumulating evidence suggests that resveratrol has pharmacological benefits in life-threatening diseases, including cardiovascular disease, cancer, diabetes, and neurodegenerative diseases. Resveratrol is widely known for its anti-inflammatory properties; however, signaling mechanisms of anti-inflammatory action are still elusive. Studies have illustrated that resveratrol can control different regulatory pathways by altering the expression and consequently regulatory effects of microRNAs. Our study aims to clarify the regulatory mechanisms of resveratrol in its anti-inflammatory features in the N9 microglial cell line. Our results demonstrated that resveratrol inhibits LPS- and ATP-activated NLRP3 inflammasome and protects microglial cells upon oxidative stress, proinflammatory cytokine production, and pyroptotic cell death resulting from inflammasome activation. Additionally, resveratrol inhibits nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling and activates AMPK/Sirt1 pathways. Furthermore, our results indicated that resveratrol downregulated inflammasome-induced miR-155 expression. Then, inhibition of AMPK and Sirt1 pathways has significantly reversed protective effect of resveratrol on miR-155 expression. To sum up, our results suggest that resveratrol suppresses the NLRP3 inflammasome and miR-155 expression through AMPK and Sirt1 pathways in microglia.

Adaptive phenotypic modulations lead to therapy resistance in chronic myeloid leukemia cells

Tyrosine kinase inhibitor (TKI) resistance is a major problem in chronic myeloid leukemia (CML). We generated a TKI-resistant K562 sub-population, K562-IR, under selective imatinib-mesylate pressure. K562-IR cells are CD34-/CD38-, BCR-Abl-independent, proliferate slowly, highly adherent and form intact tumor spheroids. Loss of CD45 and other hematopoietic markers reveal these cells have diverged from their hematopoietic origin. CD34 negativity, high expression of E-cadherin and CD44; decreased levels of CD45 and β-catenin do not fully confer with the leukemic stem cell (LSC) phenotype. Expression analyses reveal that K562-IR cells differentially express tissue/organ development and differentiation genes. Our data suggest that the observed phenotypic shift is an adaptive process rendering cells under TKI stress to become oncogene independent. Cells develop transcriptional instability in search for a gene expression framework suitable for new environmental stresses, resulting in an adaptive phenotypic shift in which some cells partially display LSC-like properties. With leukemic/cancer stem cell targeted therapies underway, the difference between treating an entity and a spectrum of dynamic cellular states will have conclusive effects on the outcome.

Solid waste composition and the properties of biodegradable fractions in Izmir City, Turkey: an investigation on the influencing factors

BACKGROUND

Waste composition and characteristics are determinative in selecting technological alternatives to develop waste management strategies that can meet legislative requirements. The aim of this study is to identify the major factors influencing the municipal solid waste (MSW) composition and the properties of its biodegradable fraction in İzmir city, Turkey.

METHODS

MSW composition was determined in samples collected from different income level areas of the city. Water and organic matter contents, calorific value, and the total chlorine levels in seven biodegradable waste (Bio-MSW) size fractions (between >120 mm and > 10 mm) and in the fine fraction (<10 mm) were analyzed. The data on waste components and Bio-MSW properties were statistically investigated.

RESULTS

The average shares of biodegradables and recyclables in MSW were found as 50.2 and 40.3%, respectively. The organic matter content of Bio-MSW increased with waste size (r = 0.313, p < 0.05) and its calorific value were in the range of 2310-3686 kcal/kg. A link between the plastics' share in MSW and the Bio-MSW chlorine levels was recognized (r: 0.666, p < 0.1). PCA analysis identified the main factors degrading the Bio-MSW quality as the cross contamination due to the mixed collection (30.8%), compaction applied in waste trucks (27.5%), and the inert broken materials trapped in larger fractions (21.3%).

CONCLUSION

Strong negative impact of mixed collection on Bio-MSW quality indicated that implementation of source separated collection of MSW is crucial for Izmir city in order to develop an integrated waste management system that meets the legal requirements by means of end product quality.