bluuebunny/crossref_metadata_2025 huggingface dataset:
Patient Preferences for Long-Term Implant Care in Cochlear, Glaucoma and Cardiovascular Diseases
Authors: Schulz Sabine , Harzheim Laura , Hübner Constanze , Lorke Mariya , Jünger Saskia , Buchholz Annika , Frech Stefanie , Steffens Melanie , Woopen Christiane
Published: July 2023

In the process of developing and implementing innovative implant technologies the consideration of patient preferences can be beneficial for patients, doctors and developers. Nevertheless, in existing literature, there is still scarce knowledge of patients’ perspectives on long-term implant care. In this study, three discrete choice experiments (DCEs) were conducted in the context of cochlear implants (CI, n = 92), glaucoma implants (GI, n = 21) and cardiovascular implants (CVI, n = 23), examining the relative importance of attributes of long-term implant care from the patients’ perspective. The participants chose between differently shaped options for implant-related care. The attributes of these care options were generated and selected based on previous literature reviews, group discussions and a diary study with patients. The choice data were analyzed via binary logit regression. In CI-DCE, the technological compatibility of the implant with newer implant models, accessories or devices from other manufacturers was highly valued by participants, whereas in GI-DCE the (in)dependency on glaucoma medication post-implantation had the greatest influence on participants’ choice behavior. In CVI-DCE, the attribute with the highest relative importance related to the means of securing long-term treatment success. In all three DCE, shared decision making was relatively important for participants. Our results emphasized the importance of an adequate transfer of technological advancements in implant care for promoting patient benefits, such as the availability of comprehensible, understandable, high-quality information about current developments. Similarly, promoting technological health literacy and further pushing the technological compatibility, durability and safety of implants are directions for future implant development in accordance with patients’ preferences. Therefore, the participation of implant wearers in the development process is encouraged.
A Content Analysis of Persuasive Appeals Used in Media Campaigns to Encourage and Discourage Sugary Beverages and Water in the United States
Authors: Kraak Vivica I. , Holz Adrienne , Woods Chelsea L. , Whitlow Ann R. , Leary Nicole
Published: July 2023

The frequent consumption of sugary beverages is associated with many health risks. This study examined how persuasive appeals and graphics were used in different media campaigns to encourage and discourage sugary beverages and water in the United States (U.S.) The investigators developed a codebook, protocol and systematic process to conduct a qualitative content analysis for 280 media campaigns organized into a typology with six categories. SPSS version 28.0 was used to analyze rational and emotional appeals (i.e., positive, negative, coactive) for campaign slogans, taglines and graphic images (i.e., symbols, colors, audiences) for 60 unique campaigns across the typology. Results showed that positive emotional appeals were used more to promote sugary beverages in corporate advertising and marketing (64.7%) and social responsibility campaigns (68.8%), and less to encourage water in social marketing campaigns (30%). In contrast, public awareness campaigns used negative emotional appeals (48.1%), and advocacy campaigns combined rational (30%) and emotional positive (50%) and negative appeals (30%). Public policy campaigns used rational (82.6%) and positive emotional appeals (73.9%) to motivate support or opposition for sugary beverage tax legislation. Chi-square analyses assessed the relationships between the U.S. media campaign typology categories and graphic elements that revealed three variables with significant associations between the campaign typology and race/ethnicity (χ2(103) = 32.445, p = 0.039), content (χ2(103) = 70.760, p < 0.001) and product image (χ2(103) = 11.930, p = 0.036). Future research should examine how positive persuasive appeals in text and graphics can promote water to reduce sugary beverage health risks.
Lung and Colorectal Cancer Disparities in Appalachian Kentucky: Spatial Analysis on the Influence of Education and Literacy
Authors: Robertson Nicole M. , Burus Todd , Hudson Lauren , Hull Pamela C. , Park Lee , Vanderford Nathan L.
Published: July 2023

Low educational attainment and high cancer incidence and mortality rates have long been a challenge in Appalachian Kentucky. Prior studies have reported disparities in cancer incidence and mortality between Appalachian and non-Appalachian populations, but the influence of education on this disparity has not been extensively studied. Herein, all cancers and two cancer sites with available screenings (colorectal and lung) were joined with education indicators (educational attainment and literacy) and one geographic indicator across all 120 Kentucky counties. This dataset was used to build choropleth maps and perform simple linear and spatial regression to assess statistical significance and to measure the strength of the linear relationship between county-level education and cancer-related outcomes in Appalachian and non-Appalachian Kentucky. Among all cancer sites, age-adjusted cancer incidence and mortality was higher in Appalachian versus non-Appalachian Kentucky. The percentage of the population not completing high school was positively correlated with increased colorectal and lung cancer incidence and mortality in Appalachia. Similarly, counties with a higher percentage of the population lacking basic literacy had the strongest correlation with colorectal and lung cancer incidence and mortality, which were concentrated in Appalachian Kentucky. Our findings suggest a need for implementing interventions that increase educational attainment and enhance basic literacy as a means of improving cancer outcomes in Appalachia.
Mining Geomatics
Authors: Krawczyk Artur
Published: July 2023

This paper attempts to define a name for an area of science and technology that encompasses the acquisition, processing and application of spatial data in the mining industry. A comparative study of the evolution of spatial data exchange methods between Geographic Information Systems (GISs) and General Mining Planning (GMP) software is carried out to define the problem and name it. Subsequent modifications of the acronym GIS towards the specialisation of its application in mining are then reviewed. This is followed by the identification of three terminological postulates designed to formulate constraints and rules for the creation of a new definition. The subsequent analysis identifies the nomenclatural basis of the research area of geomatics and determines its applicability in the context of mining. The results of the research made it possible to formulate a new definition of “mining geomatics”. The final section of the article presents an initial proposal for an inventory of the basic concepts of mining geomatics in the form of a Body of Knowledge for mining geomatics.
Deep Characterization and Comparison of Different Retrovirus-like Particles Preloaded with CRISPR/Cas9 RNPs
Authors: Wichmann Max , Maire Cecile L. , Nuppenau Niklas , Habiballa Moataz , Uhde Almut , Kolbe Katharina , Schröder Tanja , Lamszus Katrin , Fehse Boris , Głów Dawid
Published: July 2023

The CRISPR/Cas system has a broad range of possible medical applications, but its clinical translation has been hampered, particularly by the lack of safe and efficient vector systems mediating the short-term expression of its components. Recently, different virus-like particles (VLPs) have been introduced as promising vectors for the delivery of CRISPR/Cas genome editing components. Here, we characterized and directly compared three different types of retrovirus-based (R) VLPs, two derived from the γ-retrovirus murine leukemia virus (gRVLPs and “enhanced” egRVLPs) and one from the lentivirus human immunodeficiency virus, HIV (LVLPs). First, we unified and optimized the production of the different RVLPs. To ensure maximal comparability of the produced RVLPs, we adapted several assays, including nanoparticle tracking analysis (NTA), multi-parametric imaging flow cytometry (IFC), and Cas9-ELISA, to analyze their morphology, surface composition, size, and concentration. Next, we comparatively tested the three RVLPs targeting different genes in 293T model cells. Using identical gRNAs, we found egRVLPs to mediate the most efficient editing. Functional analyses indicated better cargo (i.e., Cas9) transfer and/or release as the underlying reason for their superior performance. Finally, we compared on- and off-target activities of the three RVLPs in human-induced pluripotent stem cells (hiPSC) exploiting the clinically relevant C-C motif chemokine receptor 5 (CCR5) as the target. Again, egRVLPs facilitated the highest, almost 100% knockout rates, importantly with minimal off-target activity. In conclusion, in direct comparison, egRVLPs were the most efficient RVLPs. Moreover, we established methods for in-depth characterization of VLPs, facilitating their validation and thus more predictable and safe application.
Inhibitors of Endocannabinoids’ Enzymatic Degradation as a Potential Target of the Memory Disturbances in an Acute N-Methyl-D-Aspartate (NMDA) Receptor Hypofunction Model of Schizophrenia in Mice
Authors: Kruk-Slomka Marta , Adamski Bartlomiej , Slomka Tomasz , Biala Grazyna
Published: July 2023

Treating schizophrenia with the available pharmacotherapy is difficult. One possible strategy is focused on the modulation of the function of the endocannabinoid system (ECS). The ECS is comprised of cannabinoid (CB) receptors, endocannabinoids and enzymes responsible for the metabolism of endocannabinoids (fatty acid hydrolase (FAAH) and monoacylglycerol lipase (MAGL)). Here, the aim of the experiments was to evaluate the impact of inhibitors of endocannabinoids’ enzymatic degradation in the brain: KML-29 (MAGL inhibitor), JZL-195 (MAGL/FAAH inhibitor) and PF-3845 (FAAH inhibitor), on the memory disturbances typical for schizophrenia in an acute N-methyl-D-aspartate (NMDA) receptor hypofunction animal model of schizophrenia (i.e., injection of MK-801, an NMDA receptor antagonist). The memory-like responses were assessed in the passive avoidance (PA) test. A single administration of KML-29 or PF-3845 had a positive effect on the memory processes, but an acute administration of JZL-195 impaired cognition in mice in the PA test. Additionally, the combined administration of a PA-ineffective dose of KML-29 (5 mg/kg) or PF-3845 (3 mg/kg) attenuated the MK-801-induced cognitive impairment (0.6 mg/kg). Our results suggest that the indirect regulation of endocannabinoids’ concentration in the brain through the use of selected inhibitors may positively affect memory disorders, and thus increase the effectiveness of modern pharmacotherapy of schizophrenia.
Development of a Simple Direct and Hot-Start PCR Using Escherichia coli-Expressing Taq DNA Polymerase
Authors: Lee Sun Ju , Park Sang-Yong , Lee Kwang-Ho , Lee Min-Woo , Yu Chae-Yeon , Maeng Jaeyoung , Kim Hyeong-Dong , Kim Suhng Wook
Published: July 2023

Taq DNA polymerases have played an important role in molecular biology for several years and are frequently used for polymerase chain reaction (PCR); hence, there is an increasing interest in developing a convenient method for preparing Taq DNA polymerase for routine use in laboratories. We developed a method using Escherichia coli (E. coli) that expresses thermostable Taq DNA polymerase directly in the PCR without purification. The Taq gene was transformed into E. coli and expressed. After overnight incubation and washing, E. coli-expressing Taq DNA polymerase (EcoliTaq) was used as the DNA polymerase without purification. EcoliTaq showed activity comparable to that of commercial DNA polymerase and remained stable for 3 months. With a high-pH buffer containing 2% Tween 20 and 0.4 M trehalose, EcoliTaq facilitated direct PCR amplification from anticoagulated whole blood samples. EcoliTaq exhibited good performance in allele-specific PCR using both purified DNA and whole blood samples. Furthermore, it proved to be useful as a DNA polymerase in hot-start PCR by effectively minimizing non-specific amplification. We developed a simple and cost-effective direct and hot-start PCR method in which EcoliTaq was used directly as a PCR enzyme, thus eliminating the laborious and time-consuming steps of polymerase purification.
Canonical and Alternative Auxin Signaling Systems in Mono-, Di-, and Tetraploid Potatoes
Authors: Lomin Sergey N. , Kolachevskaya Oksana O. , Arkhipov Dmitry V. , Romanov Georgy A.
Published: July 2023

It has long been known that the phytohormone auxin plays a promoting role in tuber formation and stress tolerance in potatoes. Our study aimed to identify and characterize the complete sets of auxin-related genes that presumably constitute the entire auxin signaling system in potato (Solanum tuberosum L.). The corresponding genes were retrieved from sequenced genomes of the doubled monoploid S. tuberosum DM1-3-516-R44 (DM) of the Phureja group, the heterozygous diploid line RH89-039-16 (RH), and the autotetraploid cultivar Otava. Both canonical and noncanonical auxin signaling pathways were considered. Phylogenetic and domain analyses of deduced proteins were supplemented by expression profiling and 3D molecular modeling. The canonical and ABP1-mediated pathways of auxin signaling appeared to be well conserved. The total number of potato genes/proteins presumably involved in canonical auxin signaling is 46 and 108 in monoploid DM and tetraploid Otava, respectively. Among the studied potatoes, spectra of expressed genes obviously associated with auxin signaling were partly cultivar-specific and quite different from analogous spectrum in Arabidopsis. Most of the noncanonical pathways found in Arabidopsis appeared to have low probability in potato. This was equally true for all cultivars used irrespective of their ploidy. Thus, some important features of the (noncanonical) auxin signaling pathways may be variable and species-specific.
Expression of Hairpin-Enriched Mitochondrial DNA in Two Hairworm Species (Nematomorpha)
Authors: Nikolaeva Olga V. , Beregova Aleksandra M. , Efeykin Boris D. , Miroliubova Tatiana S. , Zhuravlev Andrey Yu. , Ivantsov Andrey Yu. , Mikhailov Kirill V. , Spiridonov Sergei E. , Aleoshin Vladimir V.
Published: July 2023

Nematomorpha (hairworms) is a phylum of parasitic ecdysozoans, best known for infecting arthropods and guiding their hosts toward water, where the parasite can complete its life cycle. Over 350 species of nematomorphs have been described, yet molecular data for the group remain scarce. The few available mitochondrial genomes of nematomorphs are enriched with long inverted repeats, which are embedded in the coding sequences of their genes—a remarkably unusual feature exclusive to this phylum. Here, we obtain and annotate the repeats in the mitochondrial genome of another nematomorph species—Parachordodes pustulosus. Using genomic and transcriptomic libraries, we investigate the impact of inverted repeats on the read coverage of the mitochondrial genome. Pronounced drops in the read coverage coincide with regions containing long inverted repeats, denoting the ‘blind spots’ of short-fragment sequencing libraries. Phylogenetic inference with the novel data reveals multiple disagreements between the traditional system of Nematomorpha and molecular data, rendering several genera paraphyletic, including Parachordodes.
Early Splicing Complexes and Human Disease
Authors: Nagasawa Chloe K. , Garcia-Blanco Mariano A.
Published: July 2023

Over the last decade, our understanding of spliceosome structure and function has significantly improved, refining the study of the impact of dysregulated splicing on human disease. As a result, targeted splicing therapeutics have been developed, treating various diseases including spinal muscular atrophy and Duchenne muscular dystrophy. These advancements are very promising and emphasize the critical role of proper splicing in maintaining human health. Herein, we provide an overview of the current information on the composition and assembly of early splicing complexes—commitment complex and pre-spliceosome—and their association with human disease.
Effects of Normobaric Hypoxia and Adrenergic Blockade over 72 h on Cardiac Function in Rats
Authors: Neubert Elias , Rassler Beate , Hoschke Annekathrin , Raffort Coralie , Salameh Aida
Published: July 2023

In rats, acute normobaric hypoxia depressed left ventricular (LV) inotropic function. After 24 h of hypoxic exposure, a slight recovery of LV function occurred. We speculated that prolonged hypoxia (72 h) would induce acclimatization and, hence, recovery of LV function. Moreover, we investigated biomarkers of nitrosative stress and apoptosis as possible causes of hypoxic LV depression. To elucidate the role of hypoxic sympathetic activation, we studied whether adrenergic blockade would further deteriorate the general state of the animals and their cardiac function. Ninety-four rats were exposed over 72 h either to normal room air (N) or to normobaric hypoxia (H). The rodents received infusion (0.1 mL/h) with 0.9% NaCl or with different adrenergic blockers. Despite clear signs of acclimatization to hypoxia, the LV depression continued persistently after 72 h of hypoxia. Immunohistochemical analyses revealed significant increases in markers of nitrosative stress, adenosine triphosphate deficiency and apoptosis in the myocardium, which could provide a possible explanation for the absence of LV function recovery. Adrenergic blockade had a slightly deteriorative effect on the hypoxic LV function compared to the hypoxic group with maintained sympathetic efficacy. These findings show that hypoxic sympathetic activation compensates, at least partially, for the compromised function in hypoxic conditions, therefore emphasizing its importance for hypoxia adaptation.
Prognostic Role of Neutrophil, Monocyte and Platelet to Lymphocyte Ratios in Advanced Ovarian Cancer According to the Time of Debulking Surgery
Authors: Plaja Andrea , Teruel Iris , Ochoa-de-Olza Maria , Cucurull Marc , Arroyo Álvaro Javier , Pardo Beatriz , Ortiz Irene , Gil-Martin Marta , Piulats Josep María , Pla Helena , Fina Claudia , Carbó Anna , Barretina-Ginesta Maria-Pilar , Martínez-Román Sergio , Carballas Elvira , González Andrea , Esteve Anna , Romeo Margarita
Published: July 2023

Despite a multimodal radical treatment, mortality of advanced epithelial ovarian cancer (AEOC) remains high. Host-related factors, such as systemic inflammatory response and its interplay with the immune system, remain underexplored. We hypothesized that the prognostic impact of this response could vary between patients undergoing primary debulking surgery (PDS) and those undergoing interval debulking surgery (IDS). Therefore, we evaluated the outcomes of two surgical groups of newly diagnosed AEOC patients according to the neutrophil, monocyte and platelet to lymphocyte ratios (NLR, MLR, PLR), taking median ratio values as cutoffs. In the PDS group (n = 61), low NLR and PLR subgroups showed significantly better overall survival (not reached (NR) vs. 72.7 months, 95% confidence interval [CI]: 40.9–95.2, p = 0.019; and NR vs. 56.1 months, 95% CI: 40.9–95.2, p = 0.004, respectively) than those with high values. Similar results were observed in progression free survival. NLR and PLR-high values resulted in negative prognostic factors, adjusting for residual disease, BRCA1/2 status and stage (HR 2.48, 95% CI: 1.03–5.99, p = 0.043, and HR 2.91, 95% CI: 1.11–7.64, p = 0.03, respectively). In the IDS group (n = 85), ratios were not significant prognostic factors. We conclude that NLR and PLR may have prognostic value in the PDS setting, but none in IDS, suggesting that time of surgery can modulate the prognostic impact of baseline complete blood count (CBC).
An Engineered Heat-Inducible Expression System for the Production of Casbene in Nicotiana benthamiana
Authors: Forestier Edith C. F. , Cording Amy C. , Loake Gary J. , Graham Ian A.
Published: July 2023

Plants respond to heat stress by producing heat-shock proteins. These are regulated by heat-shock promoters containing regulatory elements, which can be harnessed to control protein expression both temporally and spatially. In this study, we designed heat-inducible promoters to produce the diterpene casbene in Nicotiana benthamiana, through a multi-step metabolic pathway. To potentially increase gene transcription, we coupled heat-shock elements from Arabidopsis thaliana Hsp101 or Glycine max GmHsp17.3-B promoters, CAAT and TATA boxes from CaMV 35S, and the 5′UTR from the tobacco mosaic virus. The resulting four chimeric promoters fused to a green fluorescent protein (GFP) reporter showed that the variant Ara2 had the strongest fluorescent signal after heat shock. We next created a 4-gene cassette driven by the Ara2 promoter to allow for exogenous synthesis of casbene and transformed this multigene construct along with a selectable marker gene into Nicotiana benthamiana. Metabolic analysis on the transgenic lines revealed that continuous heat outperforms heat shock, with up to 1 μg/mg DW of casbene detected after 32 h of uninterrupted 40 °C heat. These results demonstrate the potential of heat-inducible promoters as synthetic biology tools for metabolite production in plants.
Enzymatic Characterization of the Isocitrate Dehydrogenase with Dual Coenzyme Specificity from the Marine Bacterium Umbonibacter marinipuiceus
Authors: Bian Mingjie , Zhao Jiaxin , Xu Wenqiang , Han Xueyang , Chen Xuefei , Wang Peng , Zhu Guoping
Published: July 2023

Isocitrate dehydrogenase (IDH) can be divided into NAD+-dependent and NADP+-dependent types based on the coenzyme specificity. It is worth noting that some IDHs exhibit dual coenzyme specificity characteristics. Herein, a dual coenzyme-dependent IDH from Umbonibacter Marinipuiceus (UmIDH) was expressed, purified, and identified in detail for the first time. SDS-PAGE and Gel filtration chromatography analyses showed that UmIDH is an 84.7 kDa homodimer in solution. The Km values for NAD+ and NADP+ are 1800.0 ± 64.4 μM and 1167.7 ± 113.0 μM in the presence of Mn2+, respectively. Meanwhile, the catalytic efficiency (kcat/Km) of UmIDH is only 2.3-fold greater for NADP+ than NAD+. The maximal activity for UmIDH occurred at pH 8.5 (with Mn2+) or pH 8.7 (with Mg2+) and at 35 °C (with Mn2+ or Mg2+). Heat inactivation assay revealed that UmIDH sustained 50% of maximal activity after incubation at 57 °C for 20 min with either Mn2+ or Mg2+. Moreover, three putative core coenzyme binding residues (R345, L346, and V352) of UmIDH were evaluated by site-directed mutagenesis. This recent work identified a unique dual coenzyme-dependent IDH and achieved the groundbreaking bidirectional modification of this specific IDH’s coenzyme dependence for the first time. This provides not only a reference for the study of dual coenzyme-dependent IDH, but also a basis for the investigation of the coenzyme-specific evolutionary mechanisms of IDH.
Obesity Associated with Prediabetes Increases the Risk of Breast Cancer Development and Progression—A Study on an Obese Rat Model with Impaired Glucose Tolerance
Authors: Kallamadi Prathap Reddy , Esari Deepshika , Addi Utkarsh Reddy , Kesavan Rushendhiran , Putcha Uday Kumar , Nagini Siddavaram , Reddy Geereddy Bhanuprakash
Published: July 2023

Patients with comorbidities of obesity and diabetes are recognized to be at high risk of breast cancer development and face worse breast cancer outcomes. Though several reports showed the reinforced link between obesity, diabetes, and prediabetes with breast cancer, the underlying molecular mechanisms are still unknown. The present study aimed to investigate the underlying molecular link between increased risks of breast cancer due to coincident diabetes or obesity using a spontaneous obese rat model with impaired glucose tolerance (WNIN/GR-Ob rat). A single dose of solubilized DMBA suspension (40 mg/kg body weight) was orally administered to the animals at the age of 60 days to induce breast tumors. The tumor incidence, latency period, tumor frequency, and tumor volume were measured. Histology, immunohistochemistry, and immunoblotting were performed to evaluate the tumor morphology and expression levels of signal molecules. The development of mammary tumors in GR-Ob rats was characterized by early onset and shorter latency periods compared to control lean rats. While 62% of obese rats developed breast tumors, tumor development in lean rats was only 21%. Overexpression of ER, PR, Ki67, and p53 markers was observed in tumor tissues of obese rats in comparison with lean rats. The levels of the hallmarks of cell proliferation and angiogenesis involved in IGF-1/PI3K/Akt/GSK3β/β-catenin signaling pathway molecules were upregulated in obese rat breast tumors compared to lean rats. Furthermore, obesity with prediabetes is associated with changes in IGF-1 signaling and acts on PI3K/Akt/GSK3β/β-catenin signaling, which results in rapid cell proliferation and development of breast tumors in obese rats than the lean rats. These results indicate that tumor onset and development were faster in spontaneous obese rat models with impaired glucose tolerance than in their lean counterparts.
Myocardial Infarction Susceptibility and the MTNR1B Polymorphisms
Authors: Škrlec Ivana , Biloglav Zrinka , Talapko Jasminka , Džijan Snježana , Daus-Šebeđak Danijela , Cesar Vera
Published: July 2023

Melatonin is a circadian hormone with antioxidant properties that protects against myocardial ischemia-reperfusion injury. Genetic variations of the melatonin receptor 1B gene (MTNR1B) play an important role in the development of type 2 diabetes, a risk factor for cardiovascular diseases. Accordingly, MTNR1B polymorphisms are crucial in numerous disorders of the cardiovascular system. Therefore, the aim of the present study was to investigate a possible association of MTNR1B polymorphisms with chronotype and susceptibility to myocardial infarction. The present case-control study included 199 patients with myocardial infarction (MI) (57% men) and 198 control participants (52% men) without previous cardiovascular diseases who underwent genotyping for the MTNR1B polymorphisms rs10830963, rs1387153, and rs4753426 from peripheral blood samples. Chronotype was determined using the Morningness-Eveningness Questionnaire (MEQ). As estimated by the chi-square test, no significant association was found in the distribution of alleles and genotypes between myocardial infarction patients and controls. In addition, there was no association between MTNR1B polymorphisms and chronotype in MI patients. As some previous studies have shown, the present negative results do not exclude the role of the MTNR1B polymorphisms studied in the development of myocardial infarction. Rather, they may indicate that MTNR1B polymorphisms are a minor risk factor for myocardial infarction.
IgGκ Signal Peptide Enhances the Efficacy of an Influenza Vector Vaccine against Respiratory Syncytial Virus Infection in Mice
Authors: Pulkina Anastasia , Vasilyev Kirill , Muzhikyan Arman , Sergeeva Mariia , Romanovskaya-Romanko Ekaterina , Shurygina Anna-Polina , Shuklina Marina , Vasin Andrey , Stukova Marina , Egorov Andrej
Published: July 2023

Intranasal vaccination using influenza vectors is a promising approach to developing vaccines against respiratory pathogens due to the activation of the mucosa-associated immune response. However, there is no clear evidence of a vector design that could be considered preferable. To find the optimal structure of an influenza vector with a modified NS genomic segment, we constructed four vector expressing identical transgene sequences inherited from the F protein of the respiratory syncytial virus (RSV). Two vectors were designed aiming at transgene accumulation in the cytosol. Another two were supplemented with an IgGκ signal peptide prior to the transgene for its extracellular delivery. Surprisingly, adding the IgGκ substantially enhanced the T-cell immune response to the CD8 epitope of the transgene. Moreover, this strategy allowed us to obtain a better protection of mice from the RSV challenge after a single intranasal immunization. Protection was achieved without antibodies, mediated by a balanced T-cell immune response including the formation of the RSV specific effector CD8+ IFNγ+/IL10+-producing cells and the accumulation of Treg cells preventing immunopathology in the lungs of infected mice. In addition to the presented method for optimizing the influenza vector, our results highlight the possibility of achieving protection against RSV through a respiratory-associated T-cell immune response alone.
Ancient Horizontal Gene Transfers from Plastome to Mitogenome of a Nonphotosynthetic Orchid, Gastrodia pubilabiata (Epidendroideae, Orchidaceae)
Authors: Kim Young-Kee , Jo Sangjin , Cheon Se-Hwan , Hong Ja-Ram , Kim Ki-Joong
Published: July 2023

Gastrodia pubilabiata is a nonphotosynthetic and mycoheterotrophic orchid belonging to subfamily Epidendroideae. Compared to other typical angiosperm species, the plastome of G. pubilabiata is dramatically reduced in size to only 30,698 base pairs (bp). This reduction has led to the loss of most photosynthesis-related genes and some housekeeping genes in the plastome, which now only contains 19 protein coding genes, three tRNAs, and three rRNAs. In contrast, the typical orchid species contains 79 protein coding genes, 30 tRNAs, and four rRNAs. This study decoded the entire mitogenome of G. pubilabiata, which consisted of 44 contigs with a total length of 867,349 bp. Its mitogenome contained 38 protein coding genes, nine tRNAs, and three rRNAs. The gene content of G. pubilabiata mitogenome is similar to the typical plant mitogenomes even though the mitogenome size is twice as large as the typical ones. To determine possible gene transfer events between the plastome and the mitogenome individual BLASTN searches were conducted, using all available orchid plastome sequences and flowering plant mitogenome sequences. Plastid rRNA fragments were found at a high frequency in the mitogenome. Seven plastid protein coding gene fragments (ndhC, ndhJ, ndhK, psaA, psbF, rpoB, and rps4) were also identified in the mitogenome of G. pubilabiata. Phylogenetic trees using these seven plastid protein coding gene fragments suggested that horizontal gene transfer (HGT) from plastome to mitogenome occurred before losses of photosynthesis related genes, leading to the lineage of G. pubilabiata. Compared to species phylogeny of the lineage of orchid, it was estimated that HGT might have occurred approximately 30 million years ago.
Genome-Wide Association Study Identifies a Plant-Height—Associated Gene OsPG3 in a Population of Commercial Rice Varieties
Authors: Peng Shasha , Liu Yanchen , Xu Yuchen , Zhao Jianhua , Gao Peng , Liu Qi , Yan Shuangyong , Xiao Yinghui , Zuo Shi-Min , Kang Houxiang
Published: July 2023

Plant height is one of the most crucial components of plant structure. However, due to its complexity, the genetic architecture of rice plant height has not been fully elucidated. In this study, we performed a genome-wide association study (GWAS) to determine rice plant height using 178 commercial rice varieties and identified 37 loci associated with rice plant height (LAPH). Among these loci, in LAPH2, we identified a polygalacturonase gene, OsPG3, which was genetically and functionally associated with rice plant height. The rice plant exhibits a super dwarf phenotype when the knockout of the OsPG3 gene occurs via CRISPR-Cas9 gene-editing technology. RNA-Seq analysis indicated that OsPG3 modulates the expression of genes involved in phytohormone metabolism and cell-wall-biosynthesis pathways. Our findings suggest that OsPG3 plays a vital role in controlling rice plant height by regulating cell wall biosynthesis. Given that rice architecture is one of the most critical phenotypes in rice breeding, OsPG3 has potential in rice’s molecular design breeding toward an ideal plant height.
AhRR and PPP1R3C: Potential Prognostic Biomarkers for Serous Ovarian Cancer
Authors: Ardizzoia Alessandra , Jemma Andrea , Redaelli Serena , Silva Marco , Bentivegna Angela , Lavitrano Marialuisa , Conconi Donatella
Published: July 2023

The lack of effective screening and successful treatment contributes to high ovarian cancer mortality, making it the second most common cause of gynecologic cancer death. Development of chemoresistance in up to 75% of patients is the cause of a poor treatment response and reduced survival. Therefore, identifying potential and effective biomarkers for its diagnosis and prognosis is a strong critical need. Copy number alterations are frequent in cancer, and relevant for molecular tumor stratification and patients’ prognoses. In this study, array-CGH analysis was performed in three cell lines and derived cancer stem cells (CSCs) to identify genes potentially predictive for ovarian cancer patients’ prognoses. Bioinformatic analyses of genes involved in copy number gains revealed that AhRR and PPP1R3C expression negatively correlated with ovarian cancer patients’ overall and progression-free survival. These results, together with a significant association between AhRR and PPP1R3C expression and ovarian cancer stemness markers, suggested their potential role in CSCs. Furthermore, AhRR and PPP1R3C’s increased expression was maintained in some CSC subpopulations, reinforcing their potential role in ovarian cancer. In conclusion, we reported for the first time, to the best of our knowledge, a prognostic role of AhRR and PPP1R3C expression in serous ovarian cancer.
Low-Dose Non-Targeted Effects and Mitochondrial Control
Authors: Averbeck Dietrich
Published: July 2023

Non-targeted effects (NTE) have been generally regarded as a low-dose ionizing radiation (IR) phenomenon. Recently, regarding long distant abscopal effects have also been observed at high doses of IR) relevant to antitumor radiation therapy. IR is inducing NTE involving intracellular and extracellular signaling, which may lead to short-ranging bystander effects and distant long-ranging extracellular signaling abscopal effects. Internal and “spontaneous” cellular stress is mostly due to metabolic oxidative stress involving mitochondrial energy production (ATP) through oxidative phosphorylation and/or anaerobic pathways accompanied by the leakage of O2− and other radicals from mitochondria during normal or increased cellular energy requirements or to mitochondrial dysfunction. Among external stressors, ionizing radiation (IR) has been shown to very rapidly perturb mitochondrial functions, leading to increased energy supply demands and to ROS/NOS production. Depending on the dose, this affects all types of cell constituents, including DNA, RNA, amino acids, proteins, and membranes, perturbing normal inner cell organization and function, and forcing cells to reorganize the intracellular metabolism and the network of organelles. The reorganization implies intracellular cytoplasmic-nuclear shuttling of important proteins, activation of autophagy, and mitophagy, as well as induction of cell cycle arrest, DNA repair, apoptosis, and senescence. It also includes reprogramming of mitochondrial metabolism as well as genetic and epigenetic control of the expression of genes and proteins in order to ensure cell and tissue survival. At low doses of IR, directly irradiated cells may already exert non-targeted effects (NTE) involving the release of molecular mediators, such as radicals, cytokines, DNA fragments, small RNAs, and proteins (sometimes in the form of extracellular vehicles or exosomes), which can induce damage of unirradiated neighboring bystander or distant (abscopal) cells as well as immune responses. Such non-targeted effects (NTE) are contributing to low-dose phenomena, such as hormesis, adaptive responses, low-dose hypersensitivity, and genomic instability, and they are also promoting suppression and/or activation of immune cells. All of these are parts of the main defense systems of cells and tissues, including IR-induced innate and adaptive immune responses. The present review is focused on the prominent role of mitochondria in these processes, which are determinants of cell survival and anti-tumor RT.
Towards Machine Learning in Heterogeneous Catalysis—A Case Study of 2,4-Dinitrotoluene Hydrogenation
Authors: Jakab-Nácsa Alexandra , Garami Attila , Fiser Béla , Farkas László , Viskolcz Béla
Published: July 2023

Utilization of multivariate data analysis in catalysis research has extraordinary importance. The aim of the MIRA21 (MIskolc RAnking 21) model is to characterize heterogeneous catalysts with bias-free quantifiable data from 15 different variables to standardize catalyst characterization and provide an easy tool to compare, rank, and classify catalysts. The present work introduces and mathematically validates the MIRA21 model by identifying fundamentals affecting catalyst comparison and provides support for catalyst design. Literature data of 2,4-dinitrotoluene hydrogenation catalysts for toluene diamine synthesis were analyzed by using the descriptor system of MIRA21. In this study, exploratory data analysis (EDA) has been used to understand the relationships between individual variables such as catalyst performance, reaction conditions, catalyst compositions, and sustainable parameters. The results will be applicable in catalyst design, and using machine learning tools will also be possible.
Realizing Eco-Friendly Water-Resistant Sodium-Alginate-Based Films Blended with a Polyphenolic Aqueous Extract from Grape Pomace Waste for Potential Food Packaging Applications
Authors: Gubitosa Jennifer , Rizzi Vito , Marasciulo Cosma , Maggi Filippo , Caprioli Giovanni , Mustafa Ahmed M. , Fini Paola , De Vietro Nicoletta , Aresta Antonella Maria , Cosma Pinalysa
Published: July 2023

Water-resistant and environmentally friendly sodium-alginate-based films have been investigated to develop functional materials to extend the food’s shelf-life. A water-stable alginate-based film was prepared, employing both the internal and external gelation approach in the presence of CaCl2. To apply this film to food packaging and thus preserve food quality, the aim of this work is to perform a chemical and physical characterization of the proposed materials, evidencing the main features and stability under different work conditions. Water contact angle measurements showed a value of 65°, suggesting an important reduced hydrophilic character of the obtained alginate films due to the novel CaCl2-induced compacted polymer network. The film’s stability was thus checked through swelling measurements in water after varying pH, temperature, and ionic strength. The film was stable at high temperatures and not pH-responsive. Only highly concentrated salt-based solutions negatively affected the proposed packaging, causing a large swelling. Furthermore, a water-based polyphenolic extract from grape (Vitis vinifera L.) pomace waste was embedded inside the films in different amounts in order to confer additional properties. The extract’s polyphenolic content (evaluated from HPLC/MS-MS measurements) endowed the films’ UV-light screening and enhanced antioxidant properties. These important findings suggest the additional potential role of these films in protecting food from light deterioration. The stability of these hybrid films was also checked by observation, as the polyphenols’ presence did not largely alter the alginate network that occurred yet was water-resistant under the described work conditions.
Effects of Angiotensin 1-7 and Mas Receptor Agonist on Renal System in a Rat Model of Heart Failure
Authors: Cohen-Segev Ravit , Nativ Omri , Kinaneh Safa , Aronson Doron , Kabala Aviva , Hamoud Shadi , Karram Tony , Abassi Zaid
Published: July 2023

Congestive heart failure (CHF) is often associated with impaired kidney function. Over- activation of the renin–angiotensin–aldosterone system (RAAS) contributes to avid salt/water retention and cardiac hypertrophy in CHF. While the deleterious effects of angiotensin II (Ang II) in CHF are well established, the biological actions of angiotensin 1-7 (Ang 1-7) are not fully characterized. In this study, we assessed the acute effects of Ang 1-7 (0.3, 3, 30 and 300 ng/kg/min, IV) on urinary flow (UF), urinary Na+ excretion (UNaV), glomerular filtration rate (GFR) and renal plasma flow )RPF) in rats with CHF induced by the placement of aortocaval fistula. Additionally, the chronic effects of Ang 1-7 (24 µg/kg/h, via intra-peritoneally implanted osmotic minipumps) on kidney function, cardiac hypertrophy and neurohormonal status were studied. Acute infusion of either Ang 1-7 or its agonist, AVE 0991, into sham controls, but not CHF rats, increased UF, UNaV, GFR, RPF and urinary cGMP. In the chronic protocols, untreated CHF rats displayed lower cumulative UF and UNaV than their sham controls. Chronic administration of Ang 1-7 and AVE 0991 exerted significant diuretic, natriuretic and kaliuretic effects in CHF rats, but not in sham controls. Serum creatinine and aldosterone levels were significantly higher in vehicle-treated CHF rats as compared with controls. Treatment with Ang 1-7 and AVE 0991 reduced these parameters to comparable levels observed in sham controls. Notably, chronic administration of Ang 1-7 to CHF rats reduced cardiac hypertrophy. In conclusion, Ang 1-7 exerts beneficial renal and cardiac effects in rats with CHF. Thus, we postulate that ACE2/Ang 1-7 axis represents a compensatory response to over-activity of ACE/AngII/AT1R system characterizing CHF and suggest that Ang 1-7 may be a potential therapeutic agent in this disease state.
Justification vs. Transparency: Why and How Visual Explanations in a Scientific Literature Recommender System
Authors: Guesmi Mouadh , Chatti Mohamed Amine , Joarder Shoeb , Ain Qurat Ul , Siepmann Clara , Ghanbarzadeh Hoda , Alatrash Rawaa
Published: July 2023

Significant attention has been paid to enhancing recommender systems (RS) with explanation facilities to help users make informed decisions and increase trust in and satisfaction with an RS. Justification and transparency represent two crucial goals in explainable recommendations. Different from transparency, which faithfully exposes the reasoning behind the recommendation mechanism, justification conveys a conceptual model that may differ from that of the underlying algorithm. An explanation is an answer to a question. In explainable recommendation, a user would want to ask questions (referred to as intelligibility types) to understand the results given by an RS. In this paper, we identify relationships between Why and How explanation intelligibility types and the explanation goals of justification and transparency. We followed the Human-Centered Design (HCD) approach and leveraged the What–Why–How visualization framework to systematically design and implement Why and How visual explanations in the transparent Recommendation and Interest Modeling Application (RIMA). Furthermore, we conducted a qualitative user study (N = 12) based on a thematic analysis of think-aloud sessions and semi-structured interviews with students and researchers to investigate the potential effects of providing Why and How explanations together in an explainable RS on users’ perceptions regarding transparency, trust, and satisfaction. Our study shows qualitative evidence confirming that the choice of the explanation intelligibility types depends on the explanation goal and user type.
Enhancing CSI-Based Human Activity Recognition by Edge Detection Techniques
Authors: Shahverdi Hossein , Nabati Mohammad , Fard Moshiri Parisa , Asvadi Reza , Ghorashi Seyed Ali
Published: July 2023

Human Activity Recognition (HAR) has been a popular area of research in the Internet of Things (IoT) and Human–Computer Interaction (HCI) over the past decade. The objective of this field is to detect human activities through numeric or visual representations, and its applications include smart homes and buildings, action prediction, crowd counting, patient rehabilitation, and elderly monitoring. Traditionally, HAR has been performed through vision-based, sensor-based, or radar-based approaches. However, vision-based and sensor-based methods can be intrusive and raise privacy concerns, while radar-based methods require special hardware, making them more expensive. WiFi-based HAR is a cost-effective alternative, where WiFi access points serve as transmitters and users’ smartphones serve as receivers. The HAR in this method is mainly performed using two wireless-channel metrics: Received Signal Strength Indicator (RSSI) and Channel State Information (CSI). CSI provides more stable and comprehensive information about the channel compared to RSSI. In this research, we used a convolutional neural network (CNN) as a classifier and applied edge-detection techniques as a preprocessing phase to improve the quality of activity detection. We used CSI data converted into RGB images and tested our methodology on three available CSI datasets. The results showed that the proposed method achieved better accuracy and faster training times than the simple RGB-represented data. In order to justify the effectiveness of our approach, we repeated the experiment by applying raw CSI data to long short-term memory (LSTM) and Bidirectional LSTM classifiers.
In Situ Techniques for Characterization of Layered Double Hydroxide-Based Oxygen Evolution Catalysts
Authors: Mavrič Andraž , Valant Matjaž
Published: July 2023

Functional layered double hydroxide (LDH) usually contains different cationic substitutes to increase the activity of the oxygen evolution reaction (OER). The intrinsic OER activity of LDH materials is connected with the chemical composition and dispersion of metal cations substitutions in the matrix phase. The potential induced phase transitions, in particular hydroxide-to-oxyhydroxide transitions, are a predisposition for the high OER activity of LDH materials and can be followed by coupling the electrochemical experiments with spectroscopic techniques. The understanding of LDH catalysts under electrochemical conditions also allows an understanding of the behavior of OER catalysts based on transition metals, metal-chalcogenides, -pnictides, -carbides, and metal–organic frameworks. The surfaces of those materials are intrinsically poor OER catalysts. However, they act as precursors to catalysts, which are oxidized into a metal (oxy)hydroxide. This review summarizes the use of in situ techniques for the characterization of LDH-based OER electrocatalysts and presents the influence of these techniques on the understanding of potential induced phase transitions, identification of active sites, and reaction mechanisms.
Hierarchical ZSM-5 Zeolite Synthesized Only with Simple Organic Templates
Authors: Zhao Ying , Li Yuanchen , Cheng Peng , Zhang Hongdan
Published: July 2023

Hierarchical zeolites have attracted more and more attention due to their excellent diffusion and mass transfer performance. However, synthesis of most hierarchical zeolites requires long-chain organic templates, which could increase preparation cost. Here, hierarchical ZSM-5 zeolites were successfully prepared with simple organic templates (triethylenetetramine) in a rotating oven. Besides hierarchical structure, the crystal size of ZSM-5 also decreased when they were synthesized under dynamic hydrothermal conditions. The samples were analyzed using various physicochemical characterizations, such as X-ray diffraction (XRD), X-ray fluorescence (XRF), scanning electron microscopy (SEM), Fourier transform infrared spectra (FT-IR), temperature-programmed desorption of ammonia (NH3-TPD) and N2 adsorption–desorption. The hierarchical ZSM-5 zeolites synthesized in a rotating oven presented better catalytic activity and stability in iso-butane cracking reaction than those synthesized under conventional static hydrothermal conditions.