bluuebunny/crossref_metadata_2025 huggingface dataset:
Epigenetic Deregulation of Telomere-Related Genes in Newly Diagnosed Multiple Myeloma Patients
Authors: Roy Choudhury Samrat , Ashby Cody , Zhan Fenghuang , van Rhee Frits
Published: December 2021

High-risk Multiple Myeloma (MM) patients were found to maintain telomere length (TL), below the margin of short critical length, consistent with proactive overexpression of telomerase. Previously, DNA methylation has been shown as a determinant of telomere-related gene (TRG) expression and TL to assess risk in different types of cancer. We mapped genome-wide DNA methylation in a cohort of newly diagnosed MM (NDMM; n = 53) patients of major molecular subgroups, compared to age-matched healthy donors (n = 4). Differential methylation and expression at TRG-loci were analyzed in combination with overlapping chromatin marks and underlying DNA-sequences. We observed a strong correlation (R2 ≥ 0.5) between DNA methylation and expression amongst selective TRGs, such that demethylation at the promoters of DDX1 and TERF1 were associated to their oncogenic upregulation, while demethylation at the bodies of two key tumor suppressors ZNF208 and RAP1A led to downregulation of the genes. We demonstrated that TRG expression may be controlled by DNA methylation alone or in cooperation with chromatin modifications or CCCTC-binding factor at the regulatory regions. Additionally, we showed that hypomethylated DMRs of TRGs in NDMM are stabilized with G-quadruplex forming sequences, suggesting a crucial role of these epigenetically vulnerable loci in MM pathogenesis. We have identified a panel of five TRGs, which are epigenetically deregulated in NDMM patients and may serve as early detection biomarkers or therapeutic targets in the disease.
Impact of Immune Cell Heterogeneity on HER2+ Breast Cancer Prognosis and Response to Therapy
Authors: Perrone Milena , Talarico Giovanna , Chiodoni Claudia , Sangaletti Sabina
Published: December 2021

Breast cancer is a heterogeneous disease with a high degree of diversity among and within tumors, and in relation to its different tumor microenvironment. Compared to other oncotypes, such as melanoma or lung cancer, breast cancer is considered a “cold” tumor, characterized by low T lymphocyte infiltration and low tumor mutational burden. However, more recent evidence argues against this idea and indicates that, at least for specific molecular breast cancer subtypes, the immune infiltrate may be clinically relevant and heterogeneous, with significant variations in its stromal cell/protein composition across patients and tumor stages. High numbers of tumor-infiltrating T cells are most frequent in HER2-positive and basal-like molecular subtypes and are generally associated with a good prognosis and response to therapies. However, effector immune infiltrates show protective immunity in some cancers but not in others. This could depend on one or more immunosuppressive mechanisms acting alone or in concert. Some of them might include, in addition to immune cells, other tumor microenvironment determinants such as the extracellular matrix composition and stiffness as well as stromal cells, like fibroblasts and adipocytes, that may prevent cytotoxic T cells from infiltrating the tumor microenvironment or may inactivate their antitumor functions. This review will summarize the state of the different immune tumor microenvironment determinants affecting HER2+ breast tumor progression, their response to treatment, and how they are modified by different therapeutic approaches. Potential targets within the immune tumor microenvironment will also be discussed.
Orai1 Boosts SK3 Channel Activation
Authors: Tiffner Adéla , Hopl Valentina , Schober Romana , Sallinger Matthias , Grabmayr Herwig , Höglinger Carmen , Fahrner Marc , Lunz Victoria , Maltan Lena , Frischauf Irene , Krivic Denis , Bhardwaj Rajesh , Schindl Rainer , Hediger Matthias A. , Derler Isabella
Published: December 2021

The interplay of SK3, a Ca2+ sensitive K+ ion channel, with Orai1, a Ca2+ ion channel, has been reported to increase cytosolic Ca2+ levels, thereby triggering proliferation of breast and colon cancer cells, although a molecular mechanism has remained elusive to date. We show in the current study, via heterologous protein expression, that Orai1 can enhance SK3 K+ currents, in addition to constitutively bound calmodulin (CaM). At low cytosolic Ca2+ levels that decrease SK3 K+ permeation, co-expressed Orai1 potentiates SK3 currents. This positive feedback mechanism of SK3 and Orai1 is enabled by their close co-localization. Remarkably, we discovered that loss of SK3 channel activity due to overexpressed CaM mutants could be restored by Orai1, likely via its interplay with the SK3–CaM binding site. Mapping for interaction sites within Orai1, we identified that the cytosolic strands and pore residues are critical for a functional communication with SK3. Moreover, STIM1 has a bimodal role in SK3–Orai1 regulation. Under physiological ionic conditions, STIM1 is able to impede SK3–Orai1 interplay by significantly decreasing their co-localization. Forced STIM1–Orai1 activity and associated Ca2+ influx promote SK3 K+ currents. The dynamic regulation of Orai1 to boost endogenous SK3 channels was also determined in the human prostate cancer cell line LNCaP.
Sequential Isolation and Characterization of Single CTCs and Large CTC Clusters in Metastatic Colorectal Cancer Patients
Authors: Francescangeli Federica , Magri Valentina , De Angelis Maria Laura , De Renzi Gianluigi , Gandini Orietta , Zeuner Ann , Gazzaniga Paola , Nicolazzo Chiara
Published: December 2021

Circulating tumor cells (CTCs) detach from a primary tumor or its metastases and circulate in the bloodstream. The vast majority of CTCs are deemed to die into the bloodstream, with only few cells representing viable metastatic precursors. Particularly, single epithelial CTCs do not survive long in the circulation due to the loss of adhesion-dependent survival signals. In metastatic colorectal cancer, the generation of large CTC clusters is a very frequent occurrence, able to increase the aptitude of CTCs to survive in the bloodstream. Although a deepened analysis of large-sized CTC clusters might certainly offer new insights into the complexity of the metastatic cascade, most CTC isolation techniques are unfortunately not compatible with large-sized CTC clusters isolation. The inappropriateness of standard CTC isolation devices for large clusters isolation and the scarce availability of detection methods able to specifically isolate and characterize both single CTCs and CTC clusters finally prevented in-depth studies on the prognostic and predictive value of clusters in clinical practice, unlike that which has been described for single CTCs. In the present study, we validated a new sequential filtration method for the simultaneous isolation of large CTC clusters and single CTCs in patients with metastatic colorectal cancer at failure of first-line treatments. The new method might allow differential downstream analyses for single and clustered CTCs starting from a single blood draw, opening new scenarios for an ever more precise characterization of colorectal cancer metastatic cascade.
Efficacy of Superselective Conventional Transarterial Chemoembolization Using Guidance Software for Hepatocellular Carcinoma within Three Lesions Smaller Than 3 cm
Authors: Miyayama Shiro , Yamashiro Masashi , Ikeda Rie , Matsumoto Junichi , Takeuchi Kiyotaka , Sakuragawa Naoko , Ueda Teruyuki , Sanada Taku , Notsumata Kazuo , Terada Takuro
Published: December 2021

The indication of transarterial chemoembolization (TACE) has advanced to hepatocellular carcinoma (HCC) of Barcelona Clinic Liver Cancer (BCLC) stage A when surgical resection (SR), thermal ablation, and bridging to transplantation are contraindicated; however, TACE for small HCC is frequently difficult and ineffective because of less hypervascularity and the presence of tumor portions receiving a dual blood supply. Here, we report outcomes of superselective conventional TACE (cTACE) for 259 patients with HCCs within three lesions smaller than 3 cm using guidance software. Automated tumor feeder detection (AFD) functionality was applied to identify tumor feeders on cone-beam computed tomography during hepatic arteriography (CBCTHA) data. When it failed, the feeder was identified by manual feeder detection functionality and/or selective angiography and CBCTHA. Regarding the technical success in 382 tumors (mean diameter, 17.2 ± 5.9 mm), 310 (81.2%) were completely embolized with a safety margin (5 mm wide for HCC ≤25 mm and 10 mm wide for HCC >25 mm). In 61 (16.0%), the entire tumor was embolized but the safety margin was not uniformly obtained. The entire tumor was not embolized in 11 (2.9%). Regarding the tumor response at 2–3 months after cTACE in 303 tumors excluding those treated with combined radiofrequency ablation (RFA) or SR and lost to follow-up, 287 (94.7%) were classified into complete response, seven (2.3%) into partial response, and nine (3.0%) into stable disease. The mean follow-up period was 44.9 ± 27.6 months (range, 1–109) and the cumulative local tumor progression rates at 1, 3, 5, and 7 years were 17.8, 27.8, 32.0, and 36.0%, respectively. The 1-, 3-, 5-, and 7-year overall and recurrence-free survival rates in 175 patients, excluding those with Child–Pugh C class, who died of other malignancies, or who underwent combined RFA or hepatic resection, were 97.1 and 68.7, 82.8 and 34.9, 64.8 and 20.2, and 45.3 and 17.3%, respectively. Our results indicate the efficacy of superselective cTACE using guidance software for HCC within three lesions smaller than 3 cm.
Population Pharmacokinetic Model-Based Evaluation of Intact Oxaliplatin in Rats with Acute Kidney Injury
Authors: Kobuchi Shinji , Kai Miyu , Ito Yukako
Published: December 2021

Acute kidney injury (AKI) complicates the dosing strategies of oxaliplatin (L-OHP) and the requirement for L-OHP dose reduction in patients with renal failure remains controversial. The objective of this study is to assess the impact of AKI on the pharmacokinetics (PK) of intact L-OHP and simulate the relationship between the degree of renal function and intact L-OHP exposures using a population PK model. Intact L-OHP concentrations in plasma and urine after L-OHP administration were measured in mild and severe AKI models established in rats through renal ischemia-reperfusion. Population PK modeling and simulation were performed. There were no differences among rats in the area under the plasma concentration–time curve of intact L-OHP after intravenous L-OHP administrations. Nevertheless, the amount of L-OHP excretion after administration of 8 mg/kg L-OHP in mild and severe renal dysfunction rats was 63.5% and 37.7%, respectively, and strong correlations were observed between biochemical renal function markers and clearance of intact L-OHP. The population PK model simulated well the observed levels of intact L-OHP in AKI model rats. The population PK model-based simulation suggests that dose reduction is unnecessary for patients with mild to moderate AKI.
hsa_circ_0001275 Is One of a Number of circRNAs Dysregulated in Enzalutamide Resistant Prostate Cancer and Confers Enzalutamide Resistance In Vitro
Authors: Lim Marvin C. J. , Baird Anne-Marie , Greene John , McNevin Ciara , Ronan Karine , Podlesniy Petar , Sheils Orla , Gray Steven G. , McDermott Ray S. , Finn Stephen P.
Published: December 2021

Background: Enzalutamide is part of the treatment regimen for metastatic castration-resistant prostate cancer (MCRPC). However, both intrinsic and acquired resistance to the drug remain substantial clinical quandaries. circRNAs, a novel type of non-coding RNA, have been identified in a number of cancers including prostate cancer and have been associated with cancer development and progression. circRNAs have shown great potential as clinically useful blood-based ‘liquid biopsies’ and as therapeutic targets in prostate cancer. The aim of this study was to examine the role of circRNA transcripts in enzalutamide-resistant prostate cancer cells and assess their utility as biomarkers. Methods: An isogenic cell line model of enzalutamide resistance was subjected to circRNA microarray profiling. Several differentially expressed circRNAs, along with their putative parental genes were validated using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). circRNAs of interest were stably overexpressed in the control cell line and drug sensitivity was assessed using an ELISA-based proliferation assay. The candidate circRNA, hsa_circ_0001275, was measured in patient plasma samples using RT-droplet digital PCR (RT-ddPCR). Results: hsa_circ_0001275 and its parental gene, PLCL2, were significantly up-regulated in strongly resistant clones vs. control (p < 0.05). Overexpression of hsa_circ_0001275 in the control cell line resulted in increased resistance to enzalutamide (p < 0.05). While RT-ddPCR analysis of hsa_circ_0001275 expression in plasma samples of 44 clinical trial participants showed a trend that mirrored the stages of disease activity (as defined by PSA level), the association did not reach statistical significance. Conclusions: Our data suggest that increased levels of hsa_circ_0001275 contribute to enzalutamide resistance. hsa_circ_0001275 plasma expression showed a trend that mirrors the PSA level at specific disease time points, indicating that circRNAs mirror disease recurrence and burden and may be associated with enzalutamide resistance.
Artificial Neural Networks Predicted the Overall Survival and Molecular Subtypes of Diffuse Large B-Cell Lymphoma Using a Pancancer Immune-Oncology Panel
Authors: Carreras Joaquim , Hiraiwa Shinichiro , Kikuti Yara Yukie , Miyaoka Masashi , Tomita Sakura , Ikoma Haruka , Ito Atsushi , Kondo Yusuke , Roncador Giovanna , Garcia Juan F. , Ando Kiyoshi , Hamoudi Rifat , Nakamura Naoya
Published: December 2021

Diffuse large B-cell lymphoma (DLBCL) is one of the most frequent subtypes of non-Hodgkin lymphomas. We used artificial neural networks (multilayer perceptron and radial basis function), machine learning, and conventional bioinformatics to predict the overall survival and molecular subtypes of DLBCL. The series included 106 cases and 730 genes of a pancancer immune-oncology panel (nCounter) as predictors. The multilayer perceptron predicted the outcome with high accuracy, with an area under the curve (AUC) of 0.98, and ranked all the genes according to their importance. In a multivariate analysis, ARG1, TNFSF12, REL, and NRP1 correlated with favorable survival (hazard risks: 0.3–0.5), and IFNA8, CASP1, and CTSG, with poor survival (hazard risks = 1.0–2.1). Gene set enrichment analysis (GSEA) showed enrichment toward poor prognosis. These high-risk genes were also associated with the gene expression of M2-like tumor-associated macrophages (CD163), and MYD88 expression. The prognostic relevance of this set of 7 genes was also confirmed within the IPI and MYC translocation strata, the EBER-negative cases, the DLBCL not-otherwise specified (NOS) (High-grade B-cell lymphoma with MYC and BCL2 and/or BCL6 rearrangements excluded), and an independent series of 414 cases of DLBCL in Europe and North America (GSE10846). The perceptron analysis also predicted molecular subtypes (based on the Lymph2Cx assay) with high accuracy (AUC = 1). STAT6, TREM2, and REL were associated with the germinal center B-cell (GCB) subtype, and CD37, GNLY, CD46, and IL17B were associated with the activated B-cell (ABC)/unspecified subtype. The GSEA had a sinusoidal-like plot with association to both molecular subtypes, and immunohistochemistry analysis confirmed the correlation of MAPK3 with the GCB subtype in another series of 96 cases (notably, MAPK3 also correlated with LMO2, but not with M2-like tumor-associated macrophage markers CD163, CSF1R, TNFAIP8, CASP8, PD-L1, PTX3, and IL-10). Finally, survival and molecular subtypes were successfully modeled using other machine learning techniques including logistic regression, discriminant analysis, SVM, CHAID, C5, C&R trees, KNN algorithm, and Bayesian network. In conclusion, prognoses and molecular subtypes were predicted with high accuracy using neural networks, and relevant genes were highlighted.
N, S, P-Codoped Graphene-Supported Ag-MnFe2O4 Heterojunction Nanoparticles as Bifunctional Oxygen Electrocatalyst with High Efficiency
Authors: Dong Hongzhou , Chen Yingjie , Gong Chong , Sui Lina , Sun Qiong , Lv Kangle , Dong Lifeng
Published: December 2021

Due to slow kinetics of oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) during discharging and charging processes, it is essential to rationally design and synthesize non-precious metal bifunctional electrocatalysts with good performance for metal-air batteries. Herein, Ag-MnFe2O4 heterojunction nanoparticles supported on N, S, P-codoped graphene (NSPG) are developed with enhanced ORR and OER bifunctional electrocatalytic activities and stability. In contrast, S, P-doped graphene (SPG) and N, P-doped graphene (NPG) show less stabilization for the heterojunction particles. For example, under alkaline conditions, the ORR half-wave potential of Ag-MnFe2O4/NSPG can reach 0.831 V, and the over potential for OER is 0.56 V at the current density 10 mA·cm−2. Furthermore, Ag-MnFe2O4/NSPG shows better methanol resistance and durability than Pt/C catalysts.
The Potency of Fungal-Fabricated Selenium Nanoparticles to Improve the Growth Performance of Helianthus annuus L. and Control of Cutworm Agrotis ipsilon
Authors: Amin Mohamed A. , Ismail Mohamed A. , Badawy Ali A. , Awad Mohamed A. , Hamza Mohammed F. , Awad Mohamed F. , Fouda Amr
Published: December 2021

The application of green nanotechnology in agriculture has been receiving substantial attention, especially in the development of new nano-fertilizers and nano-insecticides. Herein, the metabolites secreted by the fungal strain Penicillium chrysogenum are used as a reducing agent for selenium ions to form selenium nanoparticles (Se-NPs). The synthesized Se-NPs were characterized using color change, UV-Vis spectroscopy, Fourier transform infrared (FT-IR) spectroscopy, transmission electron microscopy (TEM), energy dispersive X-ray (EDX), X-ray diffraction (XRD), and dynamic light scattering (DLS). The biomass filtrate of the fungal strain changed from colorless to a ruby red color after mixing with sodium selenite with a maximum surface plasmon resonance at 262 nm. Data exhibits the successful formation of spherical, amorphous Se-NPs with sizes ranging between 3–15 nm and a weight percentage of 38.52%. The efficacy of Se-NPs on the growth performance of sunflower (Helianthus annuus L.) and inhibition of cutworm Agrotis ipsilon was investigated. The field experiment revealed the potentiality of Se-NPs to enhance the growth parameters and carotenoid content in sunflower, especially at 20 ppm. The chlorophylls, carbohydrates, proteins, phenolic compounds, and free proline contents were markedly promoted in response to Se-NPs concentrations. The antioxidant enzymes (peroxidase, catalase, superoxide dismutase, and polyphenol oxidase) were significantly decreased compared with the control. Data analysis showed that the highest mortality for the 1st, 2nd, 3rd, 4th, and 5th instar larvae of Agrotis ipsilon was achieved at 25 ppm with percentages of 89.7 ± 0.3, 78.3 ± 0.3, 72.3 ± 0.6, 63.7 ± 0.3, and 68.7 ± 0.3 respectively after 72 h.
Insights into the Influence of Key Preparation Parameters on the Performance of MoS2/Graphene Oxide Composites as Active Materials in Supercapacitors
Authors: Salagean Catalin Alexandru , Costinas Codrut , Cotet Liviu Cosmin , Baia Lucian
Published: December 2021

Advances in energy storage and energy conversion play an essential role nowadays because the energy demands are becoming greater than ever. To overcome the actual performances of the materials used to build supercapacitors, a combination of transition metal dichalcogenides (TMDCs) and graphene oxide (GO) or reduced graphene oxide (rGO) as graphene-based structures are often studied for their excellent properties, such as high specific area and good electrical conductivity. Nevertheless, synthesis pathways and parameters play key roles in obtaining better materials as components for supercapacitors with higher technical performances. Driven by the desire to understand the influence of the structural and morphological particularities on the performances of supercapacitors based on MoS2/graphene oxide (GO) composites, a survey of the literature was performed by pointing out the alterations induced by different synthesis pathways and key parameters to the above-mentioned particularities.
Advances in Oxidative Desulfurization of Fuel Oils over MOFs-Based Heterogeneous Catalysts
Authors: Luo Hongsi , Gu Yulong , Liu Daqing , Sun Yinyong
Published: December 2021

Catalytic oxidative desulfurization (ODS) of fuel oils is considered one of the most promising non-hydrodesulfurization technologies due to the advantages of mild reaction conditions, low cost and easy removal of aromatic sulfur compounds. Based on this reason, the preparation of highly efficient ODS catalysts has been a hot research topic in this field. Recently, metal-organic frameworks (MOFs) have attracted extensive attention due to the advantages involving abundant metal centers, high surface area, rich porosity and varied pore structures. For this, the synthesis and catalytic performance of the ODS catalysts based on MOFs materials have been widely studied. Until now, many research achievements have been obtained along this direction. In this article, we will review the advances in oxidative desulfurization of fuel oils over MOFs-based heterogeneous catalysts. The catalytic ODS performance over various types of catalysts is compared and discussed. The perspectives for future work are proposed in this field.
LaFeO3 Modified with Ni for Hydrogen Evolution via Photocatalytic Glucose Reforming in Liquid Phase
Authors: Iervolino Giuseppina , Vaiano Vincenzo , Sannino Diana , Puga Felipe , Navío Josè Antonio , Hidalgo María C.
Published: December 2021

In this work, the optimization of Ni amount on LaFeO3 photocatalyst was studied in the photocatalytic molecular hydrogen production from glucose aqueous solution under UV light irradiation. LaFeO3 was synthesized via solution combustion synthesis and different amount of Ni were dispersed on LaFeO3 surface through deposition method in aqueous solution and using NaBH4 as reducing agent. The prepared samples were characterized with different techniques: Raman spectroscopy, UltraViolet-Visible Diffuse Reflectance Spettroscopy (UV–Vis-DRS), X-ray Diffraction (XRD), X-ray Photoelectron Spectroscopy (XPS), X-ray Fluorescence (XRF), Transmission Electron microscopy (TEM), and Scanning Electron microscopy (SEM) analyses. For all the investigated photocatalysts, the presence of Ni on perovskite surface resulted in a better activity compared to pure LaFeO3. In particular, it is possible to identify an optimal amount of Ni for which it is possible to obtain the best hydrogen production. Specifically, the results showed that the optimal Ni amount was equal to nominal 0.12 wt% (0.12Ni/LaFeO3), for which the photocatalytic H2 production was equal to 2574 μmol/L after 4 h of UV irradiation. The influence of different of photocatalyst dosage and initial glucose concentration was also evaluated. The results of the optimization of operating parameters indicated that the highest molecular hydrogen production was achieved on 0.12Ni/LaFeO3 sample with 1.5 g/L of catalyst dosage and 1000 ppm initial glucose concentration. To determine the reactive species that play the most significant role in the photocatalytic hydrogen production, photocatalytic tests in the presence of different radical scavengers were performed. The results showed that •OH radical plays a significant role in the photocatalytic conversion of glucose in H2. Moreover, photocatalytic tests carried out with D2O instead of H2O evidenced the role of water molecules in the photocatalytic production of molecular hydrogen in glucose aqueous solution.
Finding Aquaporins in Annelids: An Evolutionary Analysis and a Case Study
Authors: Mucciolo Serena , Desiderato Andrea , Salonna Marika , Mamos Tomasz , Prodocimo Viviane , Di Domenico Maikon , Mastrototaro Francesco , Lana Paulo , Gissi Carmela , Calamita Giuseppe
Published: December 2021

Aquaporins (AQPs) are a family of membrane channels facilitating diffusion of water and small solutes into and out of cells. Despite their biological relevance in osmoregulation and ubiquitous distribution throughout metazoans, the presence of AQPs in annelids has been poorly investigated. Here, we searched and annotated Aqp sequences in public genomes and transcriptomes of annelids, inferred their evolutionary relationships through phylogenetic analyses and discussed their putative physiological relevance. We identified a total of 401 Aqp sequences in 27 annelid species, including 367 sequences previously unrecognized as Aqps. Similar to vertebrates, phylogenetic tree reconstructions clustered these annelid Aqps in four clades: AQP1-like, AQP3-like, AQP8-like and AQP11-like. We found no clear indication of the existence of paralogs exclusive to annelids; however, several gene duplications seem to have occurred in the ancestors of some Sedentaria annelid families, mainly in the AQP1-like clade. Three of the six Aqps annotated in Alitta succinea, an estuarine annelid showing high salinity tolerance, were validated by RT-PCR sequencing, and their similarity to human AQPs was investigated at the level of “key” conserved residues and predicted three-dimensional structure. Our results suggest a diversification of the structures and functions of AQPs in Annelida comparable to that observed in other taxa.
hnRNP Q and hnRNP A1 Regulate the Translation of Cofilin in Response to Transient Oxygen–Glucose Deprivation in Hippocampal Neurons
Authors: Kim Sung Wook , Hong In Kyung , Kim Mingee , Song Yun Seon , Kim Kyong-Tai
Published: December 2021

Protein aggregates of cofilin and actin have been found in neurons under oxygen–glucose deprivation. However, the regulatory mechanism behind the expression of Cfl1 during oxygen–glucose deprivation remains unclear. Here, we found that heterogeneous nuclear ribonucleoproteins (hnRNP) Q and hnRNP A1 regulate the translation of Cfl1 mRNA, and formation of cofilin–actin aggregates. The interaction between hnRNP A1 and Cfl1 mRNA was interrupted by hnRNP Q under normal conditions, while the changes in the expression and localization of hnRNP Q and hnRNP A1 increased such interaction, as did the translation of Cfl1 mRNA under oxygen–glucose deprived conditions. These findings reveal a new translational regulatory mechanism of Cfl1 mRNA in hippocampal neurons under oxygen–glucose deprivation.
Differential Dose- and Tissue-Dependent Effects of foxo on Aging, Metabolic and Proteostatic Pathways
Authors: Manola Maria S. , Gumeni Sentiljana , Trougakos Ioannis P.
Published: December 2021

Aging is the gradual deterioration of physiological functions that culminates in death. Several studies across a wide range of model organisms have revealed the involvement of FOXO (forkhead box, class O) transcription factors in orchestrating metabolic homeostasis, as well as in regulating longevity. To study possible dose- or tissue-dependent effects of sustained foxo overexpression, we utilized two different Drosophila transgenic lines expressing high and relatively low foxo levels and overexpressed foxo, either ubiquitously or in a tissue-specific manner. We found that ubiquitous foxo overexpression (OE) accelerated aging, induced the early onset of age-related phenotypes, increased sensitivity to thermal stress, and deregulated metabolic and proteostatic pathways; these phenotypes were more intense in transgenic flies expressing high levels of foxo. Interestingly, there is a defined dosage of foxo OE in muscles and cardiomyocytes that shifts energy resources into longevity pathways and thus ameliorates not only tissue but also organismal age-related defects. Further, we found that foxo OE stimulates in an Nrf2/cncC dependent-manner, counteracting proteostatic pathways, e.g., the ubiquitin-proteasome pathway, which is central in ameliorating the aberrant foxo OE-mediated toxicity. These findings highlight the differential dose- and tissue-dependent effects of foxo on aging, metabolic and proteostatic pathways, along with the foxo-Nrf2/cncC functional crosstalk.
Development of a 3-Dimensional Model to Study Right Heart Dysfunction in Pulmonary Arterial Hypertension: First Observations
Authors: Llucià-Valldeperas Aida , Smal Rowan , Bekedam Fjodor T. , Cé Margaux , Pan Xiaoke , Manz Xue D. , Wijnker Paul J. M. , Vonk-Noordegraaf Anton , Bogaard Harm J. , Goumans Marie-Jose , Man Frances S. de
Published: December 2021

Pulmonary arterial hypertension (PAH) patients eventually die of right heart failure (RHF). Currently, there is no suitable pre-clinical model to study PAH. Therefore, we aim to develop a right heart dysfunction (RHD) model using the 3-dimensional engineered heart tissue (EHT) approach and cardiomyocytes derived from patient-induced pluripotent stem cells (iPSCs) to unravel the mechanisms that determine the fate of a pressure-overloaded right ventricle. iPSCs from PAH and healthy control subjects were differentiated into cardiomyocytes (iPSC-CMs), incorporated into the EHT, and maintained for 28 days. In comparison with control iPSC-CMs, PAH-derived iPSC-CMs exhibited decreased beating frequency and increased contraction and relaxation times. iPSC-CM alignment within the EHT was observed. PAH-derived EHTs exhibited higher force, and contraction and relaxation times compared with control EHTs. Increased afterload was induced using 2× stiffer posts from day 0. Due to high variability, there were no functional differences between normal and stiffer EHTs, and no differences in the hypertrophic gene expression. In conclusion, under baseline spontaneous conditions, PAH-derived iPSC-CMs and EHTs show prolonged contraction compared with controls, as observed clinically in PAH patients. Further optimization of the hypertrophic model and profound characterization may provide a platform for disease modelling and drug screening.
Construction of Three High-Density Genetic Linkage Maps and Dynamic QTL Mapping of Growth Traits in Yellow River Carp (Cyprinus carpio haematopterus)
Authors: Wang Lei , Jia Songpeng , Zhang Yuxuan , Jiang Shuhong , Chen Yuhan , Chen Junping , Yu Miao , Zhang Lan , Qiao Zhigang , Li Xuejun
Published: December 2021

To provide the theoretical basis for researching growth, development, and molecular marker-assisted breeding of the economically important Yellow River carp (Cyprinus carpio haematopterus) using dynamic quantitative trait locus (QTL) mapping, we constructed three genetic linkage maps from 207 progeny using a new modified genotyping-by-sequencing method. The three maps contained 16,886, 16,548, and 7482 single nucleotide polymorphism markers, respectively, with an average interval of 0.36 cM, 0.45 cM, and 1.00 cM. We identified 148 QTLs related to four growth traits that were located on 25 chromosomes from three growth stages of Yellow River carp. A total of 32, 36, 43, and 37 QTLs were associated with body length, height, width, and weight, respectively. Among them, 47 QTLs were detected for only one growth trait in one stage, but all of the other QTLs were co-localized. Of the 14 main QTLs, 13 were located on chromosome 12, which suggests the presence of growth-related genes on this chromosome. We then detected 17 candidate genes within 50 K upstream and downstream of the 14 main QTLs. This is the first report of the dynamic QTL mapping of growth traits of Yellow River carp, and the results can be used in future studies of growth, development, and molecular-assisted breeding of this species.
Improved Production of Streptomyces sp. FA1 Xylanase in a Dual-Plasmid Pichia pastoris System
Authors: Xia Wei , Hu Mengkai , Pan Yang , Wu Dan , Wu Jing
Published: December 2021

Methanol is considered as a potential hazard in the methanol-induced yeast expression of food-related enzymes. To increase the production efficiency of recombinant proteins in Pichia pastoris without methanol induction, a novel dual-plasmid system was constructed, for the first time, by a combining the strategies of genomic integration and episomal expression. To obtain a high copy number of the target gene, the autonomously replicating sequence derived from Kluyveromyces lactis (PARS) was used to construct episomal vectors carrying the constitutive promoters PGAP and PGCW14. In addition, an integrative vector carrying the PGCW14 promoter was constructed by replacing the PGAP promoter sequence with a partial PGCW14 promoter. Next, using xylanase XynA from Streptomyces sp. FA1 as the model enzyme, recombination strains were transformed with different combinations of integrating and episomal vectors that were constructed to investigate the changes in the protein yield. Results in shake flasks indicated that the highest enzyme yield was achieved when integrated PGAP and episomal PGCW14 were simultaneously transformed into the host strain. Meanwhile, the copy number of xynA increased from 1.14 ± 0.46 to 3.06 ± 0.35. The yield of XynA was successfully increased to 3925 U·mL−1 after 102 h of fermentation in a 3.6 L fermenter, which was 16.7-fold and 2.86-fold of the yields that were previously reported for the constitutive expression and methanol-induced expression of the identical protein, respectively. Furthermore, the high-cell-density fermentation period was shortened from 132 h to 102 h compared to that of methanol-induced system. Since the risk of methanol toxicity is removed, this novel expression system would be suitable for the production of proteins related to the food and pharmaceutical industries.
Thermal Characterization of Coolant Maxwell Type Nanofluid Flowing in Parabolic Trough Solar Collector (PTSC) Used Inside Solar Powered Ship Application
Authors: Jamshed Wasim , Şirin Ceylin , Selimefendigil Fatih , Shamshuddin MD. , Altowairqi Yasir , Eid Mohamed R.
Published: December 2021

Parabolic trough solar collectors (PTSCs) are generally utilized to reach high temperatures in solar-thermal applications. The current work investigates entropy production analysis and the influence of nano solid particles on a parabolic trough surface collector (PTSC) installed within a solar powered ship (SPS). For the current investigation, the non-Newtonian Maxwell type, as well as a porous medium and Darcy–Forchheimer effects, were used. The flow in PTSC was produced by a nonlinear stretching surface, and the Cattaneo–Christov approach was used to assess the thermal boundary layer’s heat flux. Similarity transformation approach has been employed to convert partial differential equations into solvable ordinary differential equations allied to boundary conditions. Partial differential and the boundary conditions have been reduced into a group of non-linear ordinary differential equations. A Keller-box scheme applied to solve approximate solutions of the ordinary differential equations. Single-walled carbon nanotubes -engine oil (SWCNT-EO) and Multiwalled carbon nanotubes/engine oil (MWCNT-EO) nanofluids have been utilized as working fluid. According to the findings, the magnetic parameter led to a reduction in the Nusselt number, as well as an increment in skin friction coefficient. Moreover, total entropy variance over the domain enhanced for flow rates through Reynolds number and viscosity fluctuations were monitored by using Brinkman number. Utilizing SWCNT-EO nanofluid increased the thermal efficiency between 1.6–14.9% in comparison to MWCNT-EO.
Surface Acoustic Wave-Based Flexible Piezocomposite Strain Sensor
Authors: Srinivasaraghavan Govindarajan Rishikesh , Rojas-Nastrucci Eduardo , Kim Daewon
Published: December 2021

A surface acoustic wave (SAW), device composed of polymer and ceramic fillers, exhibiting high piezoelectricity and flexibility, has a wide range of sensing applications in the aerospace field. The demand for flexible SAW sensors has been gradually increasing due to their small size, wireless capability, low fabrication cost, and fast response time. This paper discusses the structural, thermal, and electrical properties of the developed sensor, based on different micro- and nano-fillers, such as lead zirconate titanate (PZT), calcium copper titanate (CCTO), and carbon nanotubes (CNTs), along with polyvinylidene fluoride (PVDF) as a polymer matrix. The piezocomposite substrate of the SAW sensor is fabricated using a hot press, while interdigital transducers (IDTs) are deposited through 3D printing. The piezoelectric properties are also enhanced using a non-contact corona poling technique under a high electric field to align the dipoles. Results show that the developed passive strain sensor can measure mechanical strains by examining the frequency shifts of the detected wave signals.
Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography
Authors: Guven Omur , Gul Mehmet , Ayan Esra , Johnson J Austin , Cakilkaya Baris , Usta Gozde , Ertem Fatma Betul , Tokay Nurettin , Yuksel Busra , Gocenler Oktay , Buyukdag Cengizhan , Botha Sabine , Ketawala Gihan , Su Zhen , Hayes Brandon , Poitevin Frederic , Batyuk Alexander , Yoon Chun Hong , Kupitz Christopher , Durdagi Serdar , Sierra Raymond G. , DeMirci Hasan
Published: December 2021

Since early 2020, COVID-19 has grown to affect the lives of billions globally. A worldwide investigation has been ongoing for characterizing the virus and also for finding an effective drug and developing vaccines. As time has been of the essence, a crucial part of this research has been drug repurposing; therefore, confirmation of in silico drug screening studies have been carried out for this purpose. Here we demonstrated the possibility of screening a variety of drugs efficiently by leveraging a high data collection rate of 120 images/second with the new low-noise, high dynamic range ePix10k2M Pixel Array Detector installed at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Linac Coherent Light Source (LCLS). The X-ray Free-Electron Laser (XFEL) is used for remote high-throughput data collection for drug repurposing of the main protease (Mpro) of SARS-CoV-2 at ambient temperature with mitigated X-ray radiation damage. We obtained multiple structures soaked with nine drug candidate molecules in two crystal forms. Although our drug binding attempts failed, we successfully established a high-throughput Serial Femtosecond X-ray crystallographic (SFX) data collection protocol.
Facile Synthesis Sandwich-Structured Ge/NrGO Nanocomposite as Anodes for High-Performance Lithium-Ion Batteries
Authors: Autthawong Thanapat , Promanan Theeraporn , Chayasombat Bralee , Yu Ai-Shui , Uosaki Kohei , Yamaguchi Atsushi , Kurata Hiroki , Chairuangsri Torranin , Sarakonsri Thapanee
Published: December 2021

This work aimed to design a facile preparation of sandwich-liked Ge nanoparticles/nitrogen-doped reduced graphene oxide (Ge/NrGO) nanocomposites used as anode in lithium-ion batteries through the chemical solution route. The advanced electron microscopy, STEM-HAADF and STEM-EDS mapping, evidenced that the individual Ge particles with sizes ranging from 5 to 20 nm were distributed and wrapped as sandwiches within the multi-layered NrGO sheets, which were mainly composed of the pyridinic-N form (4.8%wt.). The battery performances of the 20Ge/NrGO nanocomposite anode exhibit a high reversible capacity (700 mAh g−1) and retained its outstanding stability during long-term cycling. The internal resistance (28.0 Ω) was also decreased after cycling, according to EIS measurement. The sandwiched structure of Ge-based nanocomposite with the interconnected NrGO layers discussed in this article possessed the high-performance LIBs with great potential application in energy storage technologies.
Surface-Passivated CsPbBr3 for Developing Efficient and Stable Perovskite Photovoltaics
Authors: Tak Hyeon Ju , Lee Ji Hyeon , Bae Seunghwan , Jo Jea Woong
Published: December 2021

All-inorganic perovskites consisting of only inorganic elements have been recently considered as highly stable semiconductors for photoactive layer of optoelectronics applications. However, the formation of high-quality thin film and trap-reduced interface has still remains an important task, which should be solved for improving the performances of all-inorganic perovskite-based photovoltaics. Here, we adopted facile method that could reduce charge-carrier recombination by depositing a passivation agent on the top surface of the CsPbBr3 all-inorganic perovskite layer. We also found that the CsPbBr3 perovskite photovoltaic prepared from surface treatment method using n-octylammonium bromide provides an improved stability in ambient environment and 1-sun illuminating condition. Therefore, the perovskite photovoltaics fabricated from our approach offered an improved power conversion efficiency of 5.44% over that of the control device without surface treatment (4.12%).
Titanium Dioxide Nanoparticles Are Toxic for the Freshwater Mussel Unio ravoisieri: Evidence from a Multimarker Approach
Authors: Smii Hanen , Khazri Abdelhafidh , Ben Ali Manel , Mezni Amine , Hedfi Amor , Albogami Bander , Almalki Mohammed , Pacioglu Octavian , Beyrem Hamouda , Boufahja Fehmi , Dellali Mohamed
Published: December 2021

The current work investigated the ecotoxicological effects induced by Titanium Dioxide (TiO2) nanoparticles (NPs), used at three different concentrations (C1 = 10 μg·L−1, C2 = 100 μg·L−1 and C3 = 1000 μg·L−1) in a laboratory experiment, on the freshwater mussel Unio ravoisieri. Biochemical analyses of gills and digestive glands revealed a stress-related disruption of the antioxidant system. The catalase activity and the rates of malonedialdehyde and hydrogen peroxide production were significantly higher in both organs following the exposure to TiO2 NPs and was concentration-dependent. In addition, based on the observed changes in acetylcholinesterase activity, it can be concluded that the disturbance threshold for the cholinergic system was less than 1 mg·L−1 of TiO2. Overall, the results suggest that the mussel Unio ravoisieri could be used as a sentinel species in monitoring surveys assessing the environmental impact of metallic nanoparticles in freshwater systems.
Deep Radiotranscriptomics of Non-Small Cell Lung Carcinoma for Assessing Molecular and Histology Subtypes with a Data-Driven Analysis
Authors: Trivizakis Eleftherios , Souglakos John , Karantanas Apostolos , Marias Kostas
Published: December 2021

Radiogenomic and radiotranscriptomic studies have the potential to pave the way for a holistic decision support system built on genomics, transcriptomics, radiomics, deep features and clinical parameters to assess treatment evaluation and care planning. The integration of invasive and routine imaging data into a common feature space has the potential to yield robust models for inferring the drivers of underlying biological mechanisms. In this non-small cell lung carcinoma study, a multi-omics representation comprised deep features and transcriptomics was evaluated to further explore the synergetic and complementary properties of these diverse multi-view data sources by utilizing data-driven machine learning models. The proposed deep radiotranscriptomic analysis is a feature-based fusion that significantly enhances sensitivity by up to 0.174 and AUC by up to 0.22, compared to the baseline single source models, across all experiments on the unseen testing set. Additionally, a radiomics-based fusion was also explored as an alternative methodology yielding radiomic signatures that are comparable to several previous publications in the field of radiogenomics. Furthermore, the machine learning multi-omics analysis based on deep features and transcriptomics achieved an AUC performance of up to 0.831 ± 0.09/0.925 ± 0.04 for the examined molecular and histology subtypes analysis, respectively. The clinical impact of such high-performing models can add prognostic value and lead to optimal treatment assessment by targeting specific oncogenes, namely the response of tyrosine kinase inhibitors of EGFR mutated or predicting the chemotherapy resistance of KRAS mutated tumors.
Plethysmography System to Monitor the Jugular Venous Pulse: A Feasibility Study
Authors: Proto Antonino , Conti Daniele , Menegatti Erica , Taibi Angelo , Gadda Giacomo
Published: December 2021

Cerebral venous outflow is investigated in the diagnosis of heart failure through the monitoring of jugular venous pulse, an indicator to assess cardiovascular diseases. The jugular venous pulse is a weak signal stemming from the lying internal jugular vein and often invasive methodologies requiring surgery are mandatory to detect it. Jugular venous pulse can also be extrapolated via the ultrasound technique, but it requires a qualified healthcare operator to perform the examination. In this work, a wireless, user-friendly, wearable device for plethysmography is developed to investigate the possibility of monitoring the jugular venous pulse non-invasively. The proposed device can monitor the jugular venous pulse and the electrocardiogram synchronously. To study the feasibility of using the proposed device to detect physiological variables, several measurements were carried out on healthy subjects by considering three different postures: supine, sitting, and upright. Data acquired in the experiment were properly filtered to highlight the cardiac oscillation and remove the breathing contribution, which causes a considerable shift in the amplitude of signals. To evaluate the proper functioning of the wearable device for plethysmography, a comparison with the ultrasound technique was carried out. As a satisfactory result, the acquired signals resemble the typical jugular venous pulse waveforms found in literature.
Application of FTIR Spectroscopy for Quantitative Analysis of Blood Serum: A Preliminary Study
Authors: Bel’skaya Lyudmila V. , Sarf Elena A. , Solomatin Denis V.
Published: December 2021

The aim of this study was to analyze the possibility of simultaneous determination of the concentration of components from the characteristics of FTIR spectra using the example of a model blood serum. To prepare model solutions, a set of freeze-dried control sera based on bovine blood serum was used, certified for approximately 38 parameters. Based on the values of the absorbance and areas of absorption bands in the FTIR spectra of model solutions, a regression equation was constructed by solving a nonlinear problem using the generalized reduced gradient method. By using the absorbance of the absorption bands at 1717 and 3903 cm−1 and the areas of the absorption bands at 616, 3750, and 3903 cm−1, it is possible to simultaneously determine the concentrations of 38 components with an error of less than 0.1%. The results obtained confirm the potential clinical use of FTIR spectroscopy as a reagent-free express method for the analysis of blood serum. However, its practical implementation requires additional research, in particular, analysis of real blood serum samples and validation of the method.
The Patent Ductus Arteriosus in Adults with Special Focus on Role of CT
Authors: Lee Soo Jeong , Yoo Seung Min , Son Min Ji , White Charles S.
Published: December 2021

The primary imaging modality for the diagnosis of patent ductus arteriosus (PDA) is echocardiography. However, CT may be the technique on which an incidental PDA is first recognized because of the increasing number of chest CT scans performed for a variety of causes. Identification of PDA on CT may lead to earlier closure using a PDA occluder device. Immediate identification of incidental PDA is important, but a high rate of missed diagnosis of PDA has been reported due to its small size and anatomic location. In addition, echocardiography may overlook the presence of even a large PDA due to decrease in the amount of shunting through the PDA caused by high pulmonary artery pressures. This review provides the basic CT anatomy and clinical perspective of PDA, and discusses the role of CT in the evaluation of PDA as well as methods to avoid overlooking a small PDA on CT.