bluuebunny/crossref_metadata_2025 huggingface dataset:
Reduced Immunosenescence of Peripheral Blood T Cells in Parkinson’s Disease with CMV Infection Background
Authors: Vavilova Julia D. , Boyko Anna A. , Ponomareva Natalya V. , Fokin Vitaly F. , Fedotova Ekaterina Y. , Streltsova Maria A. , Kust Sofya A. , Grechikhina Maria V. , Bril Ekaterina V. , Zimnyakova Olga S. , Kovalenko Elena I. , Sapozhnikov Alexander M.
Published: December 2021

Immunosenescence is a process of remodeling the immune system under the influence of chronic inflammation during aging. Parkinson’s disease (PD) is a common age-associated neurodegenerative disorder and is frequently accompanied by neuroinflammation. On the other hand, cytomegalovirus (CMV), one of the most spread infections in humans, may induce chronic inflammation which contributes to immunosenescence, differentiation and the inflation of T cells and NK cells. Currently, there is no clear understanding of immunosenescence severity in PD patients infected with CMV. In this study, we analyzed differentiation stages and immunosenescence characteristics of T cells and NK cells in 31 patients with mild and moderate PD severity, 33 age-matched and 30 young healthy donors. The PD patients were 100% CMV-seropositive compared to 76% age-matched and 73% young CMV-infected healthy donors. The proportion of effector memory T cells re-expressing CD45RA, CD57+CD56− T cells and CD57+CD56+ T cells was significantly reduced in PD patients compared with CMV-seropositive age-matched healthy individuals. The CD57+CD56− T cell proportion in PD patients was similar to that of CMV-seropositive young healthy donors. Thus, PD is characterized by reduced peripheral blood T cell immunosenescence, even against the background of CMV infection.
Genomic Features and Clinical Implications of Intraductal Carcinoma of the Prostate
Authors: Kang Minyong , Lee Hyunwoo , Byeon Sun-Ju , Kwon Ghee Young , Jeon Seong Soo
Published: December 2021

Intraductal carcinoma of the prostate (IDC-P) is a rare and unique form of aggressive prostate carcinoma, which is characterized by an expansile proliferation of malignant prostatic epithelial cells within prostatic ducts or acini and the preservation of basal cell layers around the involved glands. The vast majority of IDC-P tumors result from adjacent high-grade invasive cancer via the retrograde spreading of tumor cells into normal prostatic ducts or acini. A subset of IDC-P tumors is rarely derived from the de novo intraductal proliferation of premalignant cells. The presence of IDC-P in biopsy or surgical specimens is significantly associated with aggressive pathologic features, such as high Gleason grade, large tumor volume, and advanced tumor stage, and with poor clinical courses, including earlier biochemical recurrence, distant metastasis, and worse survival outcomes. These architectural and behavioral features of IDC-P may be driven by specific molecular properties. Notably, IDC-P possesses distinct genomic profiles, including higher rates of TMPRSS2–ERG gene fusions and PTEN loss, increased percentage of genomic instability, and higher prevalence of germline BRCA2 mutations. Considering that IDC-P tumors are usually resistant to conventional therapies for prostate cancer, further studies should be performed to develop optimal therapeutic strategies based on distinct genomic features, such as treatment with immune checkpoint blockades or poly (adenosine diphosphate–ribose) polymerase inhibitors for patients harboring increased genomic instability or BRCA2 mutations, as well as genetic counseling with genetic testing. Patient-derived xenografts and tumor organoid models can be the promising in vitro platforms for investigating the molecular features of IDC-P tumor.
Nucleolar Proteins and Non-Coding RNAs: Roles in Renal Cancer
Authors: Popławski Piotr , Bogusławska Joanna , Hanusek Karolina , Piekiełko-Witkowska Agnieszka
Published: December 2021

Renal cell cancer is the most frequent kidney malignancy. Most RCC cases are classified as clear cell renal cell carcinoma (ccRCC), characterized by high aggressiveness and poor prognosis for patients. ccRCC aggressiveness is defined by classification systems based on changes in morphology of nucleoli, the membraneless substructures of nuclei. The latter act as the sites of ribosome biogenesis as well as the hubs that trap and immobilize proteins, preventing their action in other cellular compartments. Thereby, nucleoli control cellular functioning and homeostasis. Nucleoli are also the sites of activity of multiple noncoding RNAs, including snoRNAs, IGS RNA, and miRNAs. Recent years have brought several remarkable discoveries regarding the role of nucleolar non-coding RNAs, in particular snoRNAs, in ccRCC. The expression of snoRNAs is largely dysregulated in ccRCC tumors. snoRNAs, such as SNHG1, SNHG4 and SNHG12, act as miRNA sponges, leading to aberrant expression of oncogenes and tumor suppressors, and directly contributing to ccRCC development and progression. snoRNAs can also act without affecting miRNA functioning, by altering the expression of key oncogenic proteins such as HIF1A. snoRNAs are also potentially useful biomarkers of ccRCC progression. Here, we comprehensively discuss the role of nucleolar proteins and non-coding RNAs in ccRCC.
Peptidome: Chaos or Inevitability
Authors: Lyapina Irina , Ivanov Vadim , Fesenko Igor
Published: December 2021

Thousands of naturally occurring peptides differing in their origin, abundance and possible functions have been identified in the tissue and biological fluids of vertebrates, insects, fungi, plants and bacteria. These peptide pools are referred to as intracellular or extracellular peptidomes, and besides a small proportion of well-characterized peptide hormones and defense peptides, are poorly characterized. However, a growing body of evidence suggests that unknown bioactive peptides are hidden in the peptidomes of different organisms. In this review, we present a comprehensive overview of the mechanisms of generation and properties of peptidomes across different organisms. Based on their origin, we propose three large peptide groups—functional protein “degradome”, small open reading frame (smORF)-encoded peptides (smORFome) and specific precursor-derived peptides. The composition of peptide pools identified by mass-spectrometry analysis in human cells, plants, yeast and bacteria is compared and discussed. The functions of different peptide groups, for example the role of the “degradome” in promoting defense signaling, are also considered.
The Curious Case of the HepG2 Cell Line: 40 Years of Expertise
Authors: Arzumanian Viktoriia A. , Kiseleva Olga I. , Poverennaya Ekaterina V.
Published: December 2021

Liver cancer is the third leading cause of cancer death worldwide. Representing such a dramatic impact on our lives, liver cancer is a significant public health concern. Sustainable and reliable methods for preventing and treating liver cancer require fundamental research on its molecular mechanisms. Cell lines are treated as in vitro equivalents of tumor tissues, making them a must-have for basic research on the nature of cancer. According to recent discoveries, certified cell lines retain most genetic properties of the original tumor and mimic its microenvironment. On the other hand, modern technologies allowing the deepest level of detail in omics landscapes have shown significant differences even between samples of the same cell line due to cross- and mycoplasma infection. This and other observations suggest that, in some cases, cell cultures are not suitable as cancer models, with limited predictive value for the effectiveness of new treatments. HepG2 is a popular hepatic cell line. It is used in a wide range of studies, from the oncogenesis to the cytotoxicity of substances on the liver. In this regard, we set out to collect up-to-date information on the HepG2 cell line to assess whether the level of heterogeneity of the cell line allows in vitro biomedical studies as a model with guaranteed production and quality.
Comparative Transcriptome Profiling of Young and Old Brown Adipose Tissue Thermogenesis
Authors: Kim Yumin , Kang Baeki E. , Ryu Dongryeol , Oh So Won , Oh Chang-Myung
Published: December 2021

Brown adipose tissue (BAT) is a major site for uncoupling protein 1 (UCP1)-mediated non-shivering thermogenesis. BAT dissipates energy via heat generation to maintain the optimal body temperature and increases energy expenditure. These energetic processes in BAT use large amounts of glucose and fatty acid. Therefore, the thermogenesis of BAT may be harnessed to treat obesity and related diseases. In mice and humans, BAT levels decrease with aging, and the underlying mechanism is elusive. Here, we compared the transcriptomic profiles of both young and aged BAT in response to thermogenic stimuli. The profiles were extracted from the GEO database. Intriguingly, aging does not cause transcriptional changes in thermogenic genes but upregulates several pathways related to the immune response and downregulates metabolic pathways. Acute severe CE upregulates several pathways related to protein folding. Chronic mild CE upregulates metabolic pathways, especially related to carbohydrate metabolism. Our findings provide a better understanding of the effects of aging and metabolic responses to thermogenic stimuli in BAT at the transcriptome level.
A Cancer-Related microRNA Signature Shows Biomarker Utility in Multiple Myeloma
Authors: Papanota Aristea-Maria , Karousi Paraskevi , Kontos Christos K. , Artemaki Pinelopi I. , Liacos Christine-Ivy , Papadimitriou Maria-Alexandra , Bagratuni Tina , Eleutherakis-Papaiakovou Evangelos , Malandrakis Panagiotis , Ntanasis-Stathopoulos Ioannis , Gavriatopoulou Maria , Kastritis Efstathios , Avgeris Margaritis , Dimopoulos Meletios-Athanasios , Scorilas Andreas , Terpos Evangelos
Published: December 2021

Multiple myeloma (MM) is the second most common hematological malignancy, arising from terminally differentiated B cells, namely plasma cells. miRNAs are small non-coding RNAs that participate in the post-transcriptional regulation of gene expression. In this study, we investigated the role of nine miRNAs in MM. CD138+ plasma cells were selected from bone marrow aspirates from MM and smoldering MM (sMM) patients. Total RNA was extracted and in vitro polyadenylated. Next, first-strand cDNA synthesis was performed using an oligo-dT–adapter primer. For the relative quantification of the investigated miRNAs, an in-house real-time quantitative PCR (qPCR) assay was developed. A functional in silico analysis of the miRNAs was also performed. miR-16-5p and miR-155-5p expression was significantly lower in the CD138+ plasma cells of MM patients than in those of sMM patients. Furthermore, lower levels of miR-15a-5p, miR-16-5p, and miR-222-3p were observed in the CD138+ plasma cells of MM patients with osteolytic bone lesions, compared to those without. miR-125b-5p was also overexpressed in the CD138+ plasma cells of MM patients with bone disease that presented with skeletal-related events (SREs). Furthermore, lower levels of miR-223-3p were associated with significantly worse overall survival in MM patients. In conclusion, we propose a miRNA signature with putative clinical utility in MM.
Antimicrobial Properties and Cytotoxic Effect of Imidazolium Geminis with Tunable Hydrophobicity
Authors: Amerkhanova Syumbelya K. , Voloshina Alexandra D. , Mirgorodskaya Alla B. , Lyubina Anna P. , Kuznetsova Darya A. , Kushnazarova Rushana A. , Mikhailov Vasilii A. , Zakharova Lucia Ya.
Published: December 2021

Antimicrobial, membranotropic and cytotoxic properties of dicationic imidazolium surfactants of n-s-n (Im) series with variable length of alkyl group (n = 8, 10, 12, 14, 16) and spacer fragment (s = 2, 3, 4) were explored and compared with monocationic analogues. Their activity against a representative range of Gram-positive and Gram-negative bacteria, and also fungi, is characterized. The relationship between the biological activity and the structural features of these compounds is revealed, with the hydrophobicity emphasized as a key factor. Among dicationic surfactants, decyl derivatives showed highest antimicrobial effect, while for monocationic analogues, the maximum activity is observed in the case of tetradecyl tail. The leading compounds are 2–4 times higher in activity compared to reference antibiotics and prove effective against resistant strains. It has been shown that the antimicrobial effect is not associated with the destruction of the cell membrane, but is due to specific interactions of surfactants and cell components. Importantly, they show strong selectivity for microorganism cells while being of low harm to healthy human cells, with a SI ranging from 30 to 100.
Functional Significance of Selective Expression of ERα and ERβ in Mammary Gland Organ Culture
Authors: Mehta Rajendra G.
Published: December 2021

Thoracic pair of mammary glands from steroid hormone-pretreated mice respond to hormones structurally and functionally in organ culture. A short exposure of glands for 24 h to 7,12 Dimethylbenz(a)anthracene (DMBA) during a 24-day culture period induced alveolar or ductal lesions. Methods: To differentiate the functional significance of ERα and ERβ, we employed estrogen receptor (ER) knockout mice. We compared the effects of DMBA on the development of preneoplastic lesions in the glands in the absence of ERα (αERKO) and ERβ (βERKO) using an MMOC protocol. Glands were also subjected to microarray analyses. We showed that estradiol can be replaced by EGF for pretreatment of mice. The carcinogen-induced lesions developed under both steroids and EGF pretreatment protocols. The glands from αERKO did not develop any lesions, whereas in βERKO mice in which ERα is intact, mammary alveolar lesions developed. Comparison of microarrays of control, αERKO and βERKO mice showed that ERα was largely responsible for proliferation and the MAP kinase pathways, whereas ERβ regulated steroid metabolism-related genes. The results indicate that ERα is essential for the development of precancerous lesions. Both subtypes, ERα and Erβ, differentially regulated gene expression in mammary glands in organ cultures.
Adsorption of 1,2-Dichlorobenzene from the Aqueous Phase onto Activated Carbons and Modified Carbon Nanotubes
Authors: Jurkiewicz Martyna , Pełech Robert
Published: December 2021

This study aimed to describe the adsorption process of ortho-dichlorobenzene (o-DCB) onto activated carbons (ACs) and modified carbon nanotubes (CNTs) from the aqueous phase. The starting material NC_7000 carbon nanotubes were modified by chlorination (NC_C) and then by the introduction of hydroxyl groups (NC_C_B). The concentration of o-DCB in solutions was performed by UV-VIS spectrophotometry. After adsorption, the activated carbons were regenerated by extraction with organic solvents such as acetone, methanol, ethanol, and 1-propanol; the carbon nanotubes were regenerated by methanol. The degree of adsorbate recovery was determined by gas chromatography (GC) with flame ionization detection, using ethylbenzene as an internal standard. The equilibrium isotherm data of adsorption were satisfactorily fitted by the Langmuir equations. The results indicate that carbon adsorbents are effective porous materials for removing o-DCB from the aqueous phase. Additionally, activated carbons are more regenerative adsorbents than carbon nanotubes. The recoveries of o-DCB from ACs were in the range of 76–85%, whereas the recoveries from CNTs were in the range of 23–46%. Modifications of CNTs affect the improvement of their adsorption properties towards o-DCB compared to unmodified CNTs. However, the introduction of new functional groups on carbon nanotube surfaces makes the regeneration process less effective.
Caulerpin Mitigates Helicobacter pylori-Induced Inflammation via Formyl Peptide Receptors
Authors: Cuomo Paola , Medaglia Chiara , Allocca Ivana , Montone Angela Michela Immacolata , Guerra Fabrizia , Cabaro Serena , Mollo Ernesto , Eletto Daniela , Papaianni Marina , Capparelli Rosanna
Published: December 2021

The identification of novel strategies to control Helicobacter pylori (Hp)-associated chronic inflammation is, at present, a considerable challenge. Here, we attempt to combat this issue by modulating the innate immune response, targeting formyl peptide receptors (FPRs), G-protein coupled receptors that play key roles in both the regulation and the resolution of the innate inflammatory response. Specifically, we investigated, in vitro, whether Caulerpin—a bis-indole alkaloid isolated from algae of the genus Caulerpa—could act as a molecular antagonist scaffold of FPRs. We showed that Caulerpin significantly reduces the immune response against Hp culture filtrate, by reverting the FPR2-related signaling cascade and thus counteracting the inflammatory reaction triggered by Hp peptide Hp(2–20). Our study suggests Caulerpin to be a promising therapeutic or adjuvant agent for the attenuation of inflammation triggered by Hp infection, as well as its related adverse clinical outcomes.
Modulation of Prostanoids Profile and Counter-Regulation of SDF-1α/CXCR4 and VIP/VPAC2 Expression by Sitagliptin in Non-Diabetic Rat Model of Hepatic Ischemia-Reperfusion Injury
Authors: Krzystek-Korpacka Małgorzata , Fleszar Mariusz G. , Fortuna Paulina , Gostomska-Pampuch Kinga , Lewandowski Łukasz , Piasecki Tomasz , Kosyk Bogna , Szeląg Adam , Trocha Małgorzata
Published: December 2021

Molecular mechanisms underlying the beneficial effect of sitagliptin repurposed for hepatic ischemia-reperfusion injury (IRI) are poorly understood. We aimed to evaluate the impact of IRI and sitagliptin on the hepatic profile of eicosanoids (LC-MS/MS) and expression/concentration (RTqPCR/ELISA) of GLP-1/GLP-1R, SDF-1α/CXCR4 and VIP/VPAC1, VPAC2, and PAC1 in 36 rats. Animals were divided into four groups and subjected to ischemia (60 min) and reperfusion (24 h) with or without pretreatment with sitagliptin (5 mg/kg) (IR and SIR) or sham-operated with or without sitagliptin pretreatment (controls and sitagliptin). PGI2, PGE2, and 13,14-dihydro-PGE1 were significantly upregulated in IR but not SIR, while sitagliptin upregulated PGD2 and 15-deoxy-12,14-PGJ2. IR and sitagliptin non-significantly upregulated GLP-1 while Glp1r expression was borderline detectable. VIP concentration and Vpac2 expression were downregulated in IR but not SIR, while Vpac1 was significantly downregulated solely in SIR. IRI upregulated both CXCR4 expression and concentration, and sitagliptin pretreatment abrogated receptor overexpression and downregulated Sdf1. In conclusion, hepatic IRI is accompanied by an elevation in proinflammatory prostanoids and overexpression of CXCR4, combined with downregulation of VIP/VPAC2. Beneficial effects of sitagliptin during hepatic IRI might be mediated by drug-induced normalization of proinflammatory prostanoids and upregulation of PGD2 and by concomitant downregulation of SDF-1α/CXCR4 and reinstating VIP/VCAP2 signaling.
The Important Role of Endothelium and Extracellular Vesicles in the Cellular Mechanism of Aortic Aneurysm Formation
Authors: Mikołajczyk Klaudia , Spyt Dominika , Zielińska Wioletta , Żuryń Agnieszka , Faisal Inaz , Qamar Murtaz , Świniarski Piotr , Grzanka Alina , Gagat Maciej
Published: December 2021

Homeostasis is a fundamental property of biological systems consisting of the ability to maintain a dynamic balance of the environment of biochemical processes. The action of endogenous and exogenous factors can lead to internal balance disorder, which results in the activation of the immune system and the development of inflammatory response. Inflammation determines the disturbances in the structure of the vessel wall, connected with the change in their diameter. These disorders consist of accumulation in the space between the endothelium and the muscle cells of low-density lipoproteins (LDL), resulting in the formation of fatty streaks narrowing the lumen and restricting the blood flow in the area behind the structure. The effect of inflammation may also be pathological dilatation of the vessel wall associated with the development of aneurysms. Described disease entities strongly correlate with the increased migration of immune cells. Recent scientific research indicates the secretion of specific vesicular structures during migration activated by the inflammation. The review focuses on the link between endothelial dysfunction and the inflammatory response and the impact of these processes on the development of disease entities potentially related to the secretion of extracellular vesicles (EVs).
Field Demonstration of Heat Technology to Mitigate Heat Sinks for Drywood Termite (Blattodea: Kalotermitidae) Management
Authors: Tay Jia-Wei , James Devon
Published: December 2021

With heat treatments to control drywood termites (Blattodea: Kalotermitidae), the presence of heat sinks causes heat to be distributed unevenly throughout the treatment areas. Drywood termites may move to galleries in heat sink areas to avoid exposure to lethal temperatures. Our studies were conducted in Crytotermes brevis-infested condominiums in Honolulu, Hawaii to reflect real-world condominium scenarios; either a standard heat treatment performed by a heat remediation company, or an improved heat treatment was used. For improved treatments, heated air was directed into the toe-kick voids of C. brevis infested cabinets to reduce heat sink effects and increase heat penetration into these difficult-to-heat areas. Eight thermistor sensors placed inside the toe-kick voids, treatment zone, embedded inside cabinets’ sidewalls, and in a wooden cube recorded target temperatures of above 46 °C or 50 °C for 120 min. Pre-treatment and follow-up inspections were performed at 6 months posttreatment to monitor termite inactivity using visual observations and by recording the numbers of spiked peaks on a microwave technology termite detection device (Termatrac). In improved treatment condominiums, significantly higher numbers of spiked peaks were recorded at pre-treatment as compared to 6 months posttreatment. Efficacious heat treatment protocols using the improved methods are proposed.
High Soluble Endoglin Levels Affect Aortic Vascular Function during Mice Aging
Authors: Nejmanová Iveta , Vitverová Barbora , Eissazadeh Samira , Tripská Katarina , Igreja Sa Ivone Cristina , Hyšpler Radomír , Němečkova Ivana , Pericacho Miguel , Nachtigal Petr
Published: December 2021

Endoglin is a 180 kDa transmembrane glycoprotein that was demonstrated to be present in two different endoglin forms, namely membrane endoglin (Eng) and soluble endoglin (sEng). Increased sEng levels in the circulation have been detected in atherosclerosis, arterial hypertension, and type II diabetes mellitus. Moreover, sEng was shown to aggravate endothelial dysfunction when combined with a high-fat diet, suggesting it might be a risk factor for the development of endothelial dysfunction in combination with other risk factors. Therefore, this study hypothesized that high sEng levels exposure for 12 months combined with aging (an essential risk factor of atherosclerosis development) would aggravate vascular function in mouse aorta. Male transgenic mice with high levels of human sEng in plasma (Sol-Eng+) and their age-matched male transgenic littermates that do not develop high soluble endoglin (Control) on a chow diet were used. The aging process was initiated to contribute to endothelial dysfunction/atherosclerosis development, and it lasted 12 months. Wire myograph analysis showed impairment contractility in the Sol-Eng+ group when compared to the control group after KCl and PGF2α administration. Endothelium-dependent responsiveness to Ach was not significantly different between these groups. Western blot analysis revealed significantly decreased protein expression of Eng, p-eNOS, and ID1 expression in the Sol-Eng+ group compared to the control group suggesting reduced Eng signaling. In conclusion, we demonstrated for the first time that long-term exposure to high levels of sEng during aging results in alteration of vasoconstriction properties of the aorta, reduced eNOS phosphorylation, decreased Eng expression, and altered Eng signaling. These findings suggest that sEng can be considered a risk factor for the development of vascular dysfunction during aging and a potential therapeutical target for pharmacological intervention.
Micro- and Nano-Scales Three-Dimensional Characterisation of Softwood
Authors: Patera Alessandra , Bonnin Anne , Mokso Rajmund
Published: December 2021

Understanding the mechanical response of cellular biological materials to environmental stimuli is of fundamental importance from an engineering perspective in composites. To provide a deep understanding of their behaviour, an exhaustive analytical and experimental protocol is required. Attention is focused on softwood but the approach can be applied to a range of cellular materials. This work presents a new non-invasive multi-scale approach for the investigation of the hygro-mechanical behaviour of softwood. At the TOMCAT beamline of the Paul Scherrer Institute, in Switzerland, the swelling behaviour of softwood was probed at the cellular and sub-cellular scales by means of 3D high-resolution phase-contrast X-ray imaging. At the cellular scale, new findings in the anisotropic and reversible swelling behaviour of softwood and in the origin of swelling hysteresis of porous materials are explained from a mechanical perspective. However, the mechanical and moisture properties of wood highly depend on sub-cellular features of the wood cell wall, such as bordered pits, yielding local deformations during a full hygroscopic loading protocol.
Skeleton-Based Attention Mask for Pedestrian Attribute Recognition Network
Authors: Sooksatra Sorn , Rujikietgumjorn Sitapa
Published: December 2021

This paper presents an extended model for a pedestrian attribute recognition network utilizing skeleton data as a soft attention model to extract a local feature corresponding to a specific attribute. This technique helped keep valuable information surrounding the target area and handle the variation of human posture. The attention masks were designed to focus on the partial and the whole-body regions. This research utilized an augmented layer for data augmentation inside the network to reduce over-fitting errors. Our network was evaluated in two datasets (RAP and PETA) with various backbone networks (ResNet-50, Inception V3, and Inception-ResNet V2). The experimental result shows that our network improves overall classification performance with a mean accuracy of about 2–3% in the same backbone network, especially local attributes and various human postures.
Coupling with the Embedded Boundary Method in a Runge-Kutta Discontinuous-Galerkin Direct Ghost-Fluid Method (RKDG-DGFM) Framework for Fluid-Structure Interaction Simulations of Underwater Explosions
Authors: Si Nan , Lu Zhaokuan , Brown Alan
Published: December 2021

Solution of near-field underwater explosion (UNDEX) problems frequently require the modeling of two-way coupled fluid-structure interaction (FSI). This paper describes the addition of an embedded boundary method to an UNDEX modeling framework for multiphase, compressible and inviscid fluid using the combined algorithms of Runge-Kutta, discontinuous-Galerkin, level-set and direct ghost-fluid methods. A computational fluid dynamics (CFD) solver based on these algorithms has been developed as described in previous work. A fluid-structure coupling approach was required to perform FSI simulation interfacing with an external structural mechanics solver. Large structural deformation and possible rupture and cracking characterize the FSI phenomenon in an UNDEX, so the embedded boundary method (EBM) is more appealing for this application in comparison to dynamic mesh methods such as the arbitrary Lagrangian-Eulerian (ALE) method to enable the fluid-structure coupling algorithm in the fluid. Its limitation requiring a closed interface that is fully submerged in the fluid domain is relaxed by an adjustment described in this paper so that its applicability is extended. Two methods of implementing the fluid-structure wall boundary condition are also compared. The first solves a local 1D fluid-structure Riemann problem at each intersecting point between the wetted elements and fluid mesh. In this method, iterations are required when the Tait equation of state is utilized. A second method that does not require the Riemann solution and iterations is also implemented and the results are compared.
Comment on Dimou et al. Profile of Membrane Cargo Trafficking Proteins and Transporters Expressed under N Source Derepressing Conditions in Aspergillus nidulans. J. Fungi 2021, 7, 560
Authors: Bravo-Plaza Ignacio , Hernández-González Miguel , Peñalva Miguel Á.
Published: December 2021

Contrary to the opinion recently offered by Dimou et al., our previously published biochemical, subcellular and genetic data supported our contention that AN11127 corresponds to the A. nidulans gene encoding Sec12, which is the guanine nucleotide exchange factor (GEF) specific for SAR1. We add here additional bioinformatics evidence that fully disprove the otherwise negative evidence reported by Dimou et al., highlighting the dangers associated with the lax interpretation of genomic data. On the positive side, we establish guidelines for the identification of this key secretory gene in other species of Ascomycota and Basidiomycota, including species of medical and applied interest.
Sequential Production of ᴅ-xylonate and Ethanol from Non-Detoxified Corncob at Low-pH by Pichia kudriavzevii via a Two-Stage Fermentation Strategy
Authors: Ji Hao , Xu Ke , Dong Xiameng , Sun Da , Jin Libo
Published: December 2021

Improving the comprehensive utilization of sugars in lignocellulosic biomass is a major challenge for enhancing the economic viability of lignocellulose biorefinement. A robust yeast Pichia kudriavzevii N-X showed excellent performance in ethanol production under high temperature and low pH conditions and was engineered for ᴅ-xylonate production without xylitol generation. The recombinant strain P. kudriavzevii N-X/S1 was employed for sequential production of ᴅ-xylonate and ethanol from ᴅ-xylose, feeding on ᴅ-glucose without pH control in a two-stage strategy of aerobic and shifting micro-aerobic fermentation. Acid-pretreated corncob without detoxification and filtration was used for ᴅ-xylonate production, then simultaneous saccharification and ethanol fermentation was performed with cellulase added at pH 4.0 and at 40 °C. By this strategy, 33.5 g/L ᴅ-xylonate and 20.8 g/L ethanol were produced at yields of 1.10 g/g ᴅ-xylose and 84.3% of theoretical value, respectively. We propose a promising approach for the sequential production of ᴅ-xylonate and ethanol from non-detoxified corncob using a single microorganism.
The CWI Pathway: A Versatile Toolbox to Arrest Cell-Cycle Progression
Authors: Quilis Inma , Gomar-Alba Mercè , Igual Juan Carlos
Published: December 2021

Cell-signaling pathways are essential for cells to respond and adapt to changes in their environmental conditions. The cell-wall integrity (CWI) pathway of Saccharomyces cerevisiae is activated by environmental stresses, compounds, and morphogenetic processes that compromise the cell wall, orchestrating the appropriate cellular response to cope with these adverse conditions. During cell-cycle progression, the CWI pathway is activated in periods of polarized growth, such as budding or cytokinesis, regulating cell-wall biosynthesis and the actin cytoskeleton. Importantly, accumulated evidence has indicated a reciprocal regulation of the cell-cycle regulatory system by the CWI pathway. In this paper, we describe how the CWI pathway regulates the main cell-cycle transitions in response to cell-surface perturbance to delay cell-cycle progression. In particular, it affects the Start transcriptional program and the initiation of DNA replication at the G1/S transition, and entry and progression through mitosis. We also describe the involvement of the CWI pathway in the response to genotoxic stress and its connection with the DNA integrity checkpoint, the mechanism that ensures the correct transmission of genetic material and cell survival. Thus, the CWI pathway emerges as a master brake that stops cell-cycle progression when cells are coping with distinct unfavorable conditions.
Multilocus Genotyping of Pneumocystis jirovecii from Deceased Cuban AIDS Patients Using Formalin-Fixed and Paraffin-Embedded Tissues
Authors: Friaza Vicente , de Armas Yaxsier , Capó Virginia , Morilla Rubén , Plascencia-Hernández Arturo , Pérez-Gómez Héctor R. , Iglesias Enrique , Fonte Luis , de la Horra Carmen , Calderón Enrique J.
Published: December 2021

The results of the genotypic characterization of Pneumocystis jirovecii are described in lung tissue samples from 41 Cubans who died of AIDS with pneumocystosis between 1995 and 2008. Histological sections of the lung preserved as formalin-fixed and paraffin-embedded tissue were examined. PCR amplification and nucleotide sequencing of the two mitochondrial genes (large and small) of the pathogen allowed verification of a predominance of genotype 3 (85T/248C) of the large mitochondrial gene and genotype 3 (160A/196T) of the small mitochondrial gene over a period of 14 years (1995–2008). These results suggest that the 85T/248C//160A/196T genotype circulates with the highest frequency (81.3%) among AIDS patients in Cuba. Multilocus analysis indicates a limited circulation of pathogen genotypes on the island with the existence of a clonal genotype with an epidemic structure. Furthermore, it appears that circulating strains of P. jirovecii have not developed mutations related to sulfonamide resistance. Taken together, the data in this study revealed important elements about pneumocystosis in Cuban patients dying of AIDS and the usefulness of formalin-fixed and paraffin-embedded samples to carry out molecular epidemiology studies of P. jirovecii.
Race-Specific Genetic Profiles of Homologous Recombination Deficiency in Multiple Cancers
Authors: Hsiao Yi-Wen , Lu Tzu-Pin
Published: December 2021

Homologous recombination deficiency (HRD) has been used to predict both cancer prognosis and the response to DNA-damaging therapies in many cancer types. HRD has diverse manifestations in different cancers and even in different populations. Many screening strategies have been designed for detecting the sensitivity of a patient’s HRD status to targeted therapies. However, these approaches suffer from low sensitivity, and are not specific to each cancer type and population group. Therefore, identifying race-specific and targetable HRD-related genes is of clinical importance. Here, we conducted analyses using genomic sequencing data that was generated by the Pan-Cancer Atlas. Collapsing non-synonymous variants with functional damage to HRD-related genes, we analyzed the association between these genes and race within cancer types using the optimal sequencing kernel association test (SKAT-O). We have identified race-specific mutational patterns of curated HRD-related genes across cancers. Overall, more significant mutation sites were found in ATM, BRCA2, POLE, and TOP2B in both the ‘White’ and ‘Asian’ populations, whereas PTEN, EGFG, and RIF1 mutations were observed in both the ‘White’ and ‘African American/Black’ populations. Furthermore, supported by pathogenic tendency databases and previous reports, in the ‘African American/Black’ population, several associations, including BLM with breast invasive carcinoma, ERCC5 with ovarian serous cystadenocarcinoma, as well as PTEN with stomach adenocarcinoma, were newly described here. Although several HRD-related genes are common across cancers, many of them were found to be specific to race. Further studies, using a larger cohort of diverse populations, are necessary to identify HRD-related genes that are specific to race, for guiding gene testing methods.
A Prospective Study on the Association between Oxidative Stress and Duration of Symptoms in Allergic Rhinitis
Authors: Moon Hyun , Sim Changsun , Lee Jiho , Oh Inbo , An Taehoon , Lee Jongcheol
Published: December 2021

Oxidative stress has been known to play an important role in inflammatory responses of allergic rhinitis. We investigated the association between degree of oxidative stress and severity of allergic rhinitis. A total 226 allergic rhinitis students were classified by a history of allergic rhinitis into groups according to number and duration of symptoms within the previous year. The total antioxidant status (TAS) and total oxidant status (TOS) levels were compared among groups. Mean TAS level (14.03 ± 9.09 mmol/L) in the group with more than six months of symptoms had a tendency to be higher (p = 0.068) than that of the group with fewer than six months (12.33 ± 8.83 mmol/L). There was no statistically significant difference in mean TAS or TOS level with number of symptoms (nasal congestion, itching, sneezing and watery rhinorrhea). A multivariate logistic regression showed that the adjusted odds ratio of TAS was 1.655 and the adjusted odds ratio of TOS was 0.972 in more than a six-month duration group. The TAS level was significantly associated with a more than six-month symptom duration (p = 0.034). Our results suggest that antioxidant activity increased when allergic rhinitis became chronic and further research will be needed considering the disease severity.
Central Counterparties and Liquidity Provision in Cash Markets
Authors: Richter Thomas
Published: December 2021

This paper investigates increased liquidity provision by market makers resulting from their ability to reduce balance sheet encumbrance through the use of central counterparties (CCPs). The introduction of the Basel III leverage rule constitutes a shock to market makers’ balance sheets and thus affects their capacity to intermediate trades. Using trade-by-trade data from sovereign bond markets, we show that liquidity provision by CCP members decreased to a lesser extent following the rule change. We attribute these findings to balance sheet reductions due to the netting enabled by CCPs, thereby highlighting their importance in cash markets.
Business Data Sharing through Data Marketplaces: A Systematic Literature Review
Authors: Abbas Antragama Ewa , Agahari Wirawan , van de Ven Montijn , Zuiderwijk Anneke , de Reuver Mark
Published: December 2021

Data marketplaces are expected to play a crucial role in tomorrow’s data economy, but such marketplaces are seldom commercially viable. Currently, there is no clear understanding of the knowledge gaps in data marketplace research, especially not of neglected research topics that may advance such marketplaces toward commercialization. This study provides an overview of the state-of-the-art of data marketplace research. We employ a Systematic Literature Review (SLR) approach to examine 133 academic articles and structure our analysis using the Service-Technology-Organization-Finance (STOF) model. We find that the extant data marketplace literature is primarily dominated by technical research, such as discussions about computational pricing and architecture. To move past the first stage of the platform’s lifecycle (i.e., platform design) to the second stage (i.e., platform adoption), we call for empirical research in non-technological areas, such as customer expected value and market segmentation.
E-Commerce in Agri-Food Sector: A Systematic Literature Review Based on Service-Dominant Logic
Authors: Zhang Mengzhen , Berghäll Sami
Published: December 2021

Agricultural e-commerce (AE) has attracted substantial attention within various research disciplines for several years. In this paper, we present a literature review of the recent state of AE research published from 2000 through to 2021 in 83 journals. Based on Service-Dominant Logic (S-D logic) and Qualitative Comparative Analysis (QCA), we identify six research themes, and a theoretical continuum is applied to reveal how research themes and scholarly approaches fit into the S-D logic framework. A general increasing trend in the number of articles confirms the escalating interest in AE research; however, different themes perform unevenly with S-D logic. Even though research themes such as Consumer Willingness are getting closer to S-D logic premises, and ideologies that are increasingly approaching S-D logic have been applied to analyzing AE topics, unfortunately, there remains a paucity of papers that wield S-D logic in the AE field. Our research focuses on an innovative emerging AE field and, simultaneously, provides an approach of integrating S-D logic into analyzing academic papers in the AE domain. This research may shed some light on future possibilities that S-D logic could support the co-creation of value between consumers and agribusiness managers, and other broader disciplines such as management and marketing.
Thermal and Optical Properties of the Sunspace Casing as Factors Influencing Temperature Rise in Greenhouse Systems
Authors: Grudzińska Magdalena
Published: December 2021

In sunspaces, there is an observable temperature rise above the external air temperature, caused by solar gains and the buffering effect of their enclosure. In addition, their external partitions form a barrier preventing the direct influence of the external environment and delaying the natural deterioration of elevation surface. In the paper, the temperature rise in a glazed balcony attached to a typical flat in a multifamily building, together with the energy demand in the living zone, were assessed with the use of dynamic computer simulations. Ten variants of the sunspace casing were analysed, with different thermal and solar energy transmittance of the glazing (which is a novel subject in the research area). This enabled us to evaluate average values of the temperature reduction factor during the year and to choose the most efficient variant of the sunspace external partitions. It turned out to be an insulated, double-glazed casing with a spectrally selective coating (type O 21), combining high insulative properties with high solar transmittance. These features allowed the temperature in the sunspace to rise by almost 10°C (compared with the external air) and lower total energy demand in the flat by 33% (compared with a flat with an open balcony).
Efficacy of Alkaline-Treated Soy Waste Biomass for the Removal of Heavy-Metal Ions and Opportunities for Their Recovery
Authors: Bulgariu Laura , Ferţu Daniela Ionela , Cara Irina Gabriela , Gavrilescu Maria
Published: December 2021

In this study, soy waste biomass (SW) resulting from oil extraction was treated with alkaline solution, and the obtained material (Na-SW) was used as biosorbent for the removal of Pb(II), Cd(II), and Zn(II) ions from aqueous media. The performance of this biosorbent was examined in batch systems, at different initial metal ion concentrations and contact times (pH 3.4; 5 g of biosorbent/L). Isotherm and kinetic modeling was used to calculate the equilibrium and kinetics of the biosorption processes. The maximum biosorption capacity, calculated from the Langmuir isotherm model, followed the order Zn(II) (0.49 mmol/g) > Cd(II) (0.41 mmol/g) ≈ Pb(II) (0.40 mmol/g), while the kinetics of biosorption processes fit the pseudo-second-order model. Three cycles of biosorption/desorption were performed to estimate the reusability of Na-SW biosorbent, and the regeneration efficiency was higher than 97% in all cases. The practical applicability of Na-SW biosorbent in treating of wastewater contaminated with Pb(II), Cd(II), and Zn(II) ions was examined using simulated wastewater samples, and the main quality characteristics of the effluents obtained after treatment were evaluated. All these aspects highlight the potential applicability of Na-SW for large-scale wastewater treatment.
High-Efficiency Ultrathin Si-Based Solar Cells by Cascading Dilute-Nitride GaNAsP
Authors: Lin Yen-Ju , Feng David Jui-Yang , Lin Tzy-Rong
Published: December 2021

Thin-film solar cells are currently an important research subject. In this study, a lattice-matched GaNAsP/Si tandem cell was designed. We adopted the drift-diffusion model to analyze the power conversion efficiency (PCE) of the solar cell. To find the maximum solar cell PCE, the recombination terms and the interlayer between subcells was omitted. For an optimal tandem cell PCE, this study analyzed the mole fraction combinations of GaNAsP and the thickness combinations between the GaNAsP and the Si subcells of the tandem cell. Our results showed the superiority of the tandem cell over the Si cell. The 4.5 μm tandem cell had a 12.5% PCE, the same as that of the 10.7 μm Si cell. The 11.5 μm tandem cell had 20.2% PCE, while the 11.5 μm Si cell processed 12.7% PCE. We also analyzed the Si subcell thickness ratio of sub-12 μm tandem cells for maximum PCE. The tandem cell with a thickness between 40% to 70% of a Si cell would have a max PCE. The ratio depended on the tandem cell thickness. We conclude that the lattice-matched GaNAsP/Si tandem cell has potential for ultrathin thin Si-based solar cell applications.
Surface Characterisation of Human Serum Albumin Layers on Activated Ti6Al4V
Authors: Hierro-Oliva Margarita , Gallardo-Moreno Amparo M. , González-Martín María Luisa
Published: December 2021

Adpsortion of protein layers on biomaterials plays an important role in the interactions between implants and the bio-environment. In this context, human serum albumin (HSA) layers have been deposited on modified Ti6Al4V surfaces at different ultraviolet (UV-C) irradiation times to observe possible changes in the adsorbed protein layer. Protein adsorption was done from solutions at concentraions lower than the serum protein concentration, to follow the surface modifications at the beginning of the albumin adhesion process. For this purpose, the surface of the protein-coated samples has been characterized by time of flight secondary ion mass spectrometry (ToF-SIMS), contact angle and zeta potential measurements. The results obtained show a reduction in the total surface tension and zeta potential of samples treated with UV-C light when coated with a protein layer. Furthermore, the UV-C light treatment applied to titanium alloy surfaces is able to modify the conformation, orientation and packing of the proteins arranged in the adsorbed layer. Low irradiation time generates an unstable surface with the lowest protein adsorption and the highest hydrophobic/hydrophilic protein ratio, indicating a possible denaturalization of the protein on these surfaces. However, surface changes are stabilized after 15 h or UV-C irradiation, favoring the protein adsorption through electrical interactions.