bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular Evolution and Inheritance Pattern of Sox Gene Family among Bovidae
Authors: Akinyemi Mabel O. , Finucan Jessica , Grytsay Anastasia , Osaiyuwu Osamede H. , Adegbaju Muyiwa S. , Ogunade Ibukun M. , Thomas Bolaji N. , Peters Sunday O. , Morenikeji Olanrewaju B.
Published: October 2022

Sox genes are an evolutionarily conserved family of transcription factors that play important roles in cellular differentiation and numerous complex developmental processes. In vertebrates, Sox proteins are required for cell fate decisions, morphogenesis, and the control of self-renewal in embryonic and adult stem cells. The Sox gene family has been well-studied in multiple species including humans but there has been scanty or no research into Bovidae. In this study, we conducted a detailed evolutionary analysis of this gene family in Bovidae, including their physicochemical properties, biological functions, and patterns of inheritance. We performed a genome-wide cataloguing procedure to explore the Sox gene family using multiple bioinformatics tools. Our analysis revealed a significant inheritance pattern including conserved motifs that are critical to the ability of Sox proteins to interact with the regulatory regions of target genes and orchestrate multiple developmental and physiological processes. Importantly, we report an important conserved motif, EFDQYL/ELDQYL, found in the SoxE and SoxF groups but not in other Sox groups. Further analysis revealed that this motif sequence accounts for the binding and transactivation potential of Sox proteins. The degree of protein–protein interaction showed significant interactions among Sox genes and related genes implicated in embryonic development and the regulation of cell differentiation. We conclude that the Sox gene family uniquely evolved in Bovidae, with a few exhibiting important motifs that drive several developmental and physiological processes.
Bta-miR-6531 Regulates Calcium Influx in Bovine Leydig Cells and Is Associated with Sperm Motility
Authors: Ding Qiang , Ding Xiuhu , Xia Shuwen , Zhao Fang , Chen Kunlin , Qian Yong , Cao Shaoxian , Lin Zhiping , Gao Yundong , Wang Huili , Zhong Jifeng
Published: October 2022

MicroRNAs (miRNAs) play key roles in sperm as the regulatory factors involved in fertility and subsequent early embryonic development. Bta-miR-6531 is specifically a highly enriched miRNA in low-motility sperms in previous study. To investigate the mechanism of bta-miR-6531, 508 shared target genes of bta-miR-6531 were predicted using two miRNA target databases (TargetScan7 and miRWalk). According to the Kyoto Encyclopedia of Genes and Genomes (KEGG), the calcium and cAMP signaling pathways were the most enriched of the target genes. A dual-luciferase assay indicated that bta-miR-6531 targeted ATP2A2 mRNA by binding to the coding sequence region. In bovine Leydig cells, bta-miR-6531 overexpression affected the intracellular calcium concentration by restraining ATP2A2 expression. Moreover, we observed high calcium concentrations and high ATP2A2 protein levels in high-motility sperm compared with those in low-motility sperms. Furthermore, high-linkage single-nucleotide polymorphisms (SNPs) of the pre-bta-miR-6531 sequence were identified that related to sperm traits. Genotype TCTC of bta-miR-6531 showed high sperm motility and density and low deformity rate in Holstein bulls. However, the mutation in pre-miR-6531 did not significantly affect mature bta-miR-6531 expression in the sperm or cell models. Our results demonstrate that bta-miR-6531 might involve in sperm motility regulation by targeting ATP2A2 of the calcium signaling pathway in bovine spermatozoa.
Genetic Diversity and Population Structure of Hemiculter leucisculus (Basilesky, 1855) in Xinjiang Tarim River
Authors: Sun Siyuan , Hu Zhenyi , Lu Zhengyi , Liu Lu , Liu Xuan , Zhou Qiong , Huo Bin , Li Dapeng , Tang Rong
Published: October 2022

Hemiculter leucisculus is an invasive fish and widely distributed in the Xinjiang Tarim River. In this study, RAD-seq was used to explore the genetic diversity and population subgroup structure of H. leucisculus in the Tarim River and develop relevant Simple Sequence Repeat (SSR) markers. The study collected 40 samples distributed at four different sites of the Tarim River. A total of 7,291,260 single nucleotide polymorphisms (SNPs) were obtained. The genetic diversity results showed that the population genetic diversity level of H. leucisculus was low. The population pairwise FST values ranged from 0.231 to 0.258, indicating that there was moderate genetic differentiation among these populations. AMOVA showed that the genetic variation within populations accounted for 92.31% of the total variation. The principal component analysis (PCA) and neighbor joining (NJ) tree revealed that the four populations could be separated into two clusters (upper-middle and downstream populations) and the individuals from Taitema Lake (TTMH) showed differences and had a bigger geographic distance than the others. There is the probability that the H. leucisculus from Bosten Lake entered Taitema Lake to breed and then expanded into the Tarim River due to the water diversion projects in location. In addition, 147,705 SSRs loci were detected and 22,651 SSR primer pairs were developed. This study will contribute to providing valuable molecular data for the management of wild populations, marker-assisted selection and resource exploitation of H. leucisculus.
Phenotypic Spectrum and Molecular Findings in 17 ATR-X Syndrome Italian Patients: Some New Insights
Authors: Vaisfeld Alessandro , Taormina Sara , Simonati Alessandro , Neri Giovanni
Published: October 2022

ATR-X syndrome is a rare X-linked congenital disorder caused by hypomorphic mutations in the ATRX gene. A typical phenotype is well defined, with cognitive impairment, characteristic facial dysmorphism, hypotonia, gastrointestinal, skeletal, urogenital, and hematological anomalies as characteristic features. With a few notable exceptions, general phenotypic differences related to specific ATRX protein domains are not well established and should not be used, at least at the present time, for prognostic purposes. The phenotypic spectrum and genotypic correlations are gradually broadening, mainly due to rapidly increasing accessibility to NGS. In this scenario, it is important to continue describing new patients, illustrating the mode and age of onset of the typical and non-typical features, the classical ones and those tentatively added more recently. This report of well-characterized and mostly unreported patients expands the ATR-X clinical spectrum and emphasizes the importance of better clinical delineation of the condition. We compare our findings to those of the largest ATR-X series reported so far, discussing possible explanations for the different drawn conclusions.
QTL Mapping of Stem Rust Resistance in Populations of Durum Wheat
Authors: Marone Daniela , Mazzucotelli Elisabetta , Matny Oadi , Desiderio Francesca , Sciara Giuseppe , Maccaferri Marco , Marcotuli Ilaria , Gadaleta Agata , Steffenson Brian , Mastrangelo Anna Maria
Published: October 2022

Stem rinfectionust, caused by the fungus Puccinia graminis f. sp. tritici (Pgt), is one of the most devastating fungal diseases of durum and common wheat worldwide. The identification of sources of resistance and the validation of QTLs identified through genome-wide association studies is of paramount importance for reducing the losses caused by this disease to wheat grain yield and quality. Four segregating populations whose parents showed contrasting reactions to some Pgt races were assessed in the present study, and 14 QTLs were identified on chromosomes 3A, 4A, 6A, and 6B, with some regions in common between different segregating populations. Several QTLs were mapped to chromosomal regions coincident with previously mapped stem rust resistance loci; however, their reaction to different Pgt races suggest that novel genes or alleles could be present on chromosomes 3A and 6B. Putative candidate genes with a disease-related functional annotation have been identified in the QTL regions based on information available from the reference genome of durum cv. ‘Svevo’.
Mitochondrial tRNAGln 4394C>T Mutation May Contribute to the Clinical Expression of 1555A>G-Induced Deafness
Authors: Ding Yu , Teng Yaoshu , Guo Qinxian , Leng Jianhang
Published: October 2022

The mitochondrial 1555A>G mutation plays a critical role in aminoglycoside-induced and non-syndromic hearing loss (AINSHL). Previous studies have suggested that mitochondrial secondary variants may modulate the clinical expression of m.1555A>G-induced deafness, but the molecular mechanism has remained largely undetermined. In this study, we investigated the contribution of a deafness-associated tRNAGln 4394C>T mutation to the clinical expression of the m.1555A>G mutation. Interestingly, a three-generation family with both the m.1555A>G and m.4394C>T mutations exhibited a higher penetrance of hearing loss than another family harboring only the m.1555A>G mutation. At the molecular level, the m.4394C>T mutation resides within a very conserved nucleotide of tRNAGln, which forms a new base-pairing (7T-66A) and may affect tRNA structure and function. Using trans-mitochondrial cybrid cells derived from three subjects with both the m.1555A>G and m.4394C>T mutations, three patients with only the m.1555A>G mutation and three control subjects without these primary mutations, we observed that cells with both the m.1555A>G and m.4394C>T mutations exhibited more severely impaired mitochondrial functions than those with only the m.1555A>G mutation. Furthermore, a marked decrease in mitochondrial RNA transcripts and respiratory chain enzymes was observed in cells harboring both the m.1555A>G and m.4394C>T mutations. Thus, our data suggest that the m.4394C>T mutation may play a synergistic role in the m.1555A>G mutation, enhancing mitochondrial dysfunctions and contributing to a high penetrance of hearing loss in families with both mtDNA pathogenic mutations.
Phenotypic Impact of Rare Potentially Damaging Copy Number Variation in Obsessive-Compulsive Disorder and Chronic Tic Disorders
Authors: Mahjani Behrang , Birnbaum Rebecca , Buxbaum Grice Ariela , Cappi Carolina , Jung Seulgi , Avila Marina Natividad , Reichenberg Abraham , Sandin Sven , Hultman Christina M. , Buxbaum Joseph D. , Grice Dorothy E.
Published: October 2022

Background: Recent studies report an important—and previously underestimated—role of rare variation in risk of obsessive-compulsive disorder (OCD) and chronic tic disorders (CTD). Using data from a large epidemiological study, we evaluate the distribution of potentially damaging copy number variation (pdCNV) in OCD and CTD, examining associations between pdCNV and the phenotypes of probands, including a consideration of early- vs. late-diagnoses. Method: The Obsessive-Compulsive Inventory-Revised (OCI-R) questionnaire was used to ascertain psychometric profiles of OCD probands. CNV were identified genome-wide using chromosomal microarray data. Results: For 993 OCD cases, 86 (9%) were identified as pdCNV carriers. The most frequent pdCNV found was at the 16p13.11 region. There was no significant association between pdCNV and the OCI-R total score. However, pdCNV was associated with Obsessing and Checking subscores. There was no significant difference in pdCNV frequency between early- vs. late-diagnosed OCD probands. Of the 217 CTD cases, 18 (8%) were identified as pdCNV carriers. CTD probands with pdCNV were significantly more likely to have co-occurring autism spectrum disorder (ASD). Conclusions: pdCNV represents part of the risk architecture for OCD and CTD. If replicated, our findings suggest pdCNV impact some OCD symptoms. Genes within the 16p13.11 region are potential OCD risk genes.
Association of Gene Variants for Mechanical and Metabolic Muscle Quality with Cardiorespiratory and Muscular Variables Related to Performance in Skiing Athletes
Authors: Gasser Benedikt , Flück Martin , Frey Walter O. , Valdivieso Paola , Spörri Jörg
Published: October 2022

Background: Skiing is a popular outdoor sport posing different requirements on musculoskeletal and cardiorespiratory function to excel in competition. The extent to which genotypic features contribute to the development of performance with years of ski-specific training remains to be elucidated. We therefore tested whether prominent polymorphisms in genes for angiotensin converting enzyme (ACE-I/D, rs1799752), tenascin-C (TNC, rs2104772), actinin-3 (ACTN3, rs1815739) and PTK2 (rs7460 and rs7843014) are associated with the differentiation of cellular hallmarks of muscle metabolism and contraction in high level skiers. Material & Methods: Forty-three skiers of a world-leading national ski team performed exhaustive cardiopulmonary exercise testing as well as isokinetic strength testing for single contractions, whereby 230 cardiopulmonary measurements were performed in the period from 2015–2018. A total of 168 and 62 data measurements were from the Alpine and Nordic skiing squads, respectively. Ninety-five and one hundred thirty-five measurements, respectively, were from male and female athletes. The average (±SD) age was 21.5 ± 3.0 years, height 174.0 ± 8.7 cm, and weight 71.0 ± 10.9 kg for the analysed skiers. Furthermore, all skiers were analysed concerning their genotype ACE-I/D, Tenascin C, ACTN3, PTK2. Results: The genotype distribution deviated from Hardy–Weinberg equilibrium for the ACTN3 genotype, where rs1815739-TT genotypes (corresponding to the nonsense mutation) were overrepresented in world-class skiers, indicating a slow muscle fibre phenotype. Furthermore, the heterozygous rs2104772-AT genotypes of TNC also demonstrated the best scaled peak power output values during ramp exercise to exhaustion. The highest values under maximum performance for heart rate were associated with the rs1799752-II and rs1815739-CC genotypes. The lowest values for peak power of single contractions were achieved for rs1815739-CC, rs1799752-II and rs7843014-CT genotypes. The skiing discipline demonstrated a main influence on cardiorespiratory parameters but did not further interact with genotype-associated variability in performance. Discussion: Classically, it is pointed out that muscles of, for example, alpine skiers do not possess a distinct fibre type composition, but that skiers tend to have a preponderance of slow-twitch fibres. Consequently, our findings of an overrepresentation of ACTN3-TT genotypes in a highly selective sample of elite world class skiers support the potential superiority of a slow fibre type distribution. Conclusions: We suggest that one competitive advantage that results from a slow, typically fatigue-resistant fibre type distribution might be that performance during intense training days is better preserved, whereby simply a higher technical training volume can be performed, yielding to a competitive advantage.
Parent-Reported Social-Communicative Skills of Children with 22q11.2 Copy Number Variants and Siblings
Authors: Verbesselt Jente , Van Den Heuvel Ellen , Breckpot Jeroen , Zink Inge , Swillen Ann
Published: October 2022

22q11.2 deletion (22q11.2DS) and 22q11.2 duplication (22q11.2Dup) confer risk for neurodevelopmental difficulties, but the characterization of speech-language and social skills in 22q11.2Dup is still limited. Therefore, this study aims to delineate social-communicative skills in school-aged children with 22q11.2Dup (n = 19) compared to their non-carrier siblings (n = 11) and age-matched children with 22q11.2DS (n = 19). Parents completed two standardized questionnaires: the Children’s Communication Checklist (CCC-2), screening speech, language, and social skills, and the Social Responsiveness Scales (SRS-2), assessing deficits in social behavior. Parents report that both children with 22q11.2Dup and 22q11.2DS show more social-communicative deficits than the general population; children with 22q11.2Dup seem to take an intermediate position between their siblings and children with 22q11.2DS. Compared to 22q11.2DS, they demonstrate less frequent and less severe problems, and more heterogeneous social-communicative profiles, with fewer restricted interests and repetitive behaviors. In siblings of 22q11Dup, milder social-communicative difficulties and equally heterogeneous profiles are reported, which might indicate that-in addition to the duplication-other factors such as the broader genetic context play a role in social-communicative outcomes.
DNA Barcoding and Species Classification of Morchella
Authors: Sa Wei , Qiao Jinxia , Gao Qiyuan , Li Zhonghu , Shang Qianhan
Published: October 2022

True morels (Morchella) are a well-known edible fungi, with economically and medicinally important values. However, molecular identification and species taxonomy of the genus Morchella have long been controversial, due to numerous intermediate morphologies among species. In this study, we determined the identification efficiency of DNA barcoding and species classification of 260 individuals from 45 Morchella species, on the basis of multiple nuclear DNA markers. DNA barcoding analysis showed that the individual DNA fragment has a lower resolution of species identification than that of combined multiple DNA markers. ITS showed the highest level of species discrimination among the individual genetic markers. Interestingly, the combined DNA markers significantly increased the resolution of species identification. A combination of four DNA genes (EF1-α, RPB1, RPB2 and ITS) showed a higher species delimitation than that any combination of two or three markers. Phylogenetic analysis suggested that the species in genus Morchella could have been divided into two large genetic clades, the Elata Clade and Esculenta Clade lineages. The two lineages divided approximately 133.11 Mya [95% HPD interval: 82.77–197.95] in the early Cretaceous period. However, some phylogenetic species of Morchella showed inconsistent evolutionary relationships with the traditional morphological classifications, which may have resulted from incomplete lineage sorting and/or introgressive hybridization among species. These findings demonstrate that the interspecific gene introgression may have affected the species identification of true morels, and that the combined DNA markers significantly improve the resolution of species discrimination.
Identification and Registration for High-Yielding Strain through ST and MLT of Curcuma caesia Roxb. (Jor Lab KH-2): A High-Value Medicinal Plant
Authors: Lal Mohan , Munda Sunita , Begum Twahira , Gupta Tanmita , Paw Manabi , Chanda Sanjoy Kumar , Lekhak Himangshu
Published: October 2022

(1) Background: Curcuma caesia Roxb. is a high valued crop which is extensively used in pharmaceuticals, flavour and fragrances. C. caesia is recognised as an endangered species due to its extensive collection from the wild through human intervention. Therefore, to prevent the species from extinction, it is very necessary to conserve and cultivate this plant species for the sustainable availability of the raw material. (2) Methods: In the present plant breeding programme, a multi-year study was performed for the identification of superior genotypes which will help in conservation. To fulfil this objective, a total of 135 accessions of C. caesia were collected from different regions of India and were set up for experimental selection trial for three years (2016–2018). After proper evaluation of the genotypes based on six agronomical traits, five high-yielding genotypes were identified which underwent multilocation trial for two years (2019 and 2020). The stability analysis using the Eberhart–Russell method, AMMI and GGE biplot were used to study the consistency of the genotypes in varied environments compared with the check variety. (3) Results: Analysis of variance indicated significant genotype and environment interaction for the yield traits, i.e., dry rhizome recovery, rhizome yield and essential oil yield. The coefficient of variation (CV) was highest for tillers per plant (21.76) and lowest for the plant height (4.93). All the results clearly demonstrated Jor Lab KH-2 as the highest yielding and stable genotype in varied environments compared with the check variety and other selected genotypes. (4) Conclusions: This genotype was then submitted to ICAR-NBPGR, New Delhi, for germplasm registration and received its confirmation vide registration number INGR 21159. This genotype will greatly benefit the breeders and will also help in the conservation of this endangered species. This is the first report on the identification and registration of a high-yielding variety of C. caesia.
PyunBBX18 Is Involved in the Regulation of Anthocyanins Biosynthesis under UV-B Stress
Authors: Zhang Qin , Ma Dongxiao , Hu Zhixu , Zong Dan , He Chengzhong
Published: October 2022

(1) Background: Populus yunnanensis Dode (P. yunnanensis) grows in the low-latitude and high-altitude areas of southwest China. In low-latitude and high-altitude areas, plants suffer from the high intensity of UV-B (ultraviolet-b) radiation, and they have a complete regulation system to adapt to the environment of the high UV-B radiation. As natural antioxidants, anthocyanins play an important role in scavenging free radicals. BBX (B-box) genes are involved in anthocyanins biosynthesis. (2) Methods: By exploring the gene structure and motifs of PyunBBX genes (genes of P. yunnanensis BBX family) and the evolutionary relationship between PyunBBX genes and other species BBX genes, six PyunBBX genes that responded to UV-B and participated in anthocyanins biosynthesis were screened. BBX, with the potential to regulate anthocyanins biosynthesis, was further investigated by anthocyanins content determination and RT-qPCR (real-time quantitative polymerase chain reaction); (3) Results: After 7 days of UV-B treatment, anthocyanins were significantly accumulated, and the expression of PyunBBX18 was up-regulated for 7 days. The expression of PyunBBX12 was inhibited by UV-B treatment. By analyzing the RNA-seq data of leaves and bark of P. yunnanensis, we found that PyunBBX18 was highly expressed in leaves and young bark; (4) Conclusions: These results showed that PyunBBX18 and PyunBBX12 may be involved in the response process of UV-B stress, in which PyunBBX18 may regulate the anthocyanins biosynthesis to resist UV damage.
Transcriptome Analysis Provides Insights into Copulation, Fertilization, and Gestation in Sebastes schlegelii
Authors: Wang Xueying , Zhao Ning , Wang Tao , Du Shuran , Liu Qinghua , Li Jun
Published: October 2022

Among the viviparous marine teleosts of China, the black rockfish (Sebastes schlegelii Hilgendorf) is one of the most economically important. In addition to copulation and internal fertilization, it features lengthy sperm storage in the female ovary as well as a high rate of abortion. A network of gene regulation is necessary for these processes. To elucidate the mechanisms of copulation, fertilization, and gestation, it is essential to determine the genetic basis of viviparous teleost oogenesis and embryogenesis. In this study, we analyzed the transcriptome of the ovary during different developmental phases to investigate the dynamic changes that occur. We constructed 24 ovary transcriptomes. In order to investigate the regulation of embryogenesis, differentially expressed genes (DEGs) with specific expression patterns were subjected to gene ontology annotation, pathway analyses, and weighted gene co-expression network analysis (WGCNA). The up-regulated genes were significantly enriched in focal adhesion, regulation of the actin cytoskeleton, Wnt, and ECM-receptor interaction signaling pathways. As a result of our study, we provide omics evidence for copulation, fertilization, and gestation in viviparous marine teleosts. Decoding the S. schlegelii gene regulation network, as well as providing new insights into embryogenesis, is highly valuable to researchers in the marine teleost reproduction sciences.
Establishment of an Efficient In Vitro Propagation of Cnidium officinale Makino and Selection of Superior Clones through Flow Cytometric Assessment of DNA Content
Authors: Kim Hyung-Eun , Han Jong-Eun , Lee Hyoshin , Murthy Hosakatte Niranjana , Kwon Hyuk-Joon , Lee Gun-Myung , Park So-Young
Published: October 2022

Cnidium officinale is a valuable medicinal plant cultivated in Asia for its rhizomes. This study reports the in vitro regeneration of Cnidium officinale plants and the induction of rhizomes from microshoots. The rhizomatous buds of Cnidium officinale induced multiple shoots on Murashige and Skoog (MS) medium supplemented with 0.5 mg L−1 BA, which led to the regeneration of plants within four weeks of culture. After four weeks of culture, the plants were assessed for fresh weight, the number of leaves, the number of roots, and the length of roots to compare the performance of the different clones. The clones with good growth characteristics were selected with the aid of a flow cytometric analysis of 2C nuclear DNA content. The plants bearing high DNA values showed better growth characteristics. Various factors, namely, sucrose concentration (30, 50, 70, and 90 g L−1), ABA (0, 0.5, 1.0, and 2.0 mg L−1), the synergistic effects of BA (1.0 mg L−1) + NAA (0.5 mg L−1) and BA (1.0 mg L−1) + NAA (0.5 mg L−1) + ABA (1.0 mg L−1) with or without activated charcoal (1 g L−1), and light and dark incubation were tested on rhizome formation from microshoots. The results of the above experiments suggest that MS medium supplemented with 50 g L−1 sucrose, 1.0 mg L−1 ABA, and 1 g L−1 AC is good for the induction of rhizomes from the shoots of Cnidium officinale. Plantlets with rhizomes were successfully transferred to pots, and they showed 100% survival.
Bioinformatics Identification of Aberrantly Methylated Differentially Expressed Genes Associated with Arteriosclerosis by Integrative Analysis of Gene Expression and DNA Methylation Datasets
Authors: Cheng Jin , Hou Yuli , Wang Cong , Guo Lianrui
Published: October 2022

The prognosis of patients with advanced arteriosclerosis is bleak due to the lack of understanding of arteriosclerosis. Epigenetics-based DNA methylation plays an important role in the pathogenesis of arteriosclerosis. Hence, we aimed to identify the epigenetics-related aberrantly methylated differentially expressed genes (AMDEGs) in arteriosclerosis. A gene expression dataset and DNA methylation dataset were downloaded from the Gene Expression Omnibus database, and AMDEGs were identified on the basis of the relationship between methylation and expression. Subsequently, the expression levels of candidate hub genes were detected in human peripheral blood mononuclear cells (PBMCs) from atherosclerotic patients and control subjects by RT-qPCR and Western blot. Lastly, the methylation level of the target gene was detected using the MassARRAY method. In the present study, the hypermethylated and downregulated genes were mainly involved in vascular smooth muscle contraction. The hypomethylated and upregulated genes were markedly associated with immune-inflammatory processes. Following validation, LMOD1 was identified as the target gene, which was hypermethylated and downregulated in arteriosclerosis. The methylation levels of CpG sites in LMOD1 promoter were detected to be elevated in the PBMCs of atherosclerotic patients. In conclusion, AMDEGs identified in the present study may assist in understanding the pathogenesis of arteriosclerosis. LMOD1 exhibits potential as a promising diagnostic and therapeutic biomarker for arteriosclerosis.
Projection of Expression Profiles to Transcription Factor Activity Space Provides Added Information
Authors: Bornshten Rut , Danilenko Michael , Rubin Eitan
Published: October 2022

Acute myeloid leukemia (AML) is an aggressive type of leukemia, characterized by the accumulation of highly proliferative blasts with a disrupted myeloid differentiation program. Current treatments are ineffective for most patients, partly due to the genetic heterogeneity of AML. This is driven by genetically distinct leukemia stem cells, resulting in relapse even after most of the tumor cells are destroyed. Thus, personalized treatment approaches addressing cellular heterogeneity are urgently required. Reconstruction of Transcriptional regulatory Networks (RTN) is a tool for inferring transcriptional activity in patients with various diseases. In this study, we applied this method to transcriptome profiles of AML patients to test if it provided additional information for the interpretation of transcriptome data. We showed that when RTN results were added to RNA-seq results, superior clusters were formed, which were more homogenous and allowed the better separation of patients with low and high survival rates. We concluded that the external knowledge used for RTN analysis improved the ability of unsupervised machine learning to find meaningful patterns in the data.
Alternative Splicing in Human Physiology and Disease
Authors: Artemaki Pinelopi I. , Kontos Christos K.
Published: October 2022

Since the discovery of alternative splicing in the late 1970s, a great number of alternatively spliced transcripts have emerged; this number has exponentially increased with the advances in transcriptomics and massive parallel sequencing technologies [...]
Should Anthropic Ridges Framed as Foredunes Be Considered Real Dunes?
Authors: de Carvalho Alexandre Medeiros , Claudino-Sales Vanda , Lima Junior Sergio Bezerra , Eduardo Leticia Mesquita , da Costa Gastão Francisco Gleidson , de Souza Pinheiro Lidriana
Published: October 2022

Aeolian features framed as foredunes worldwide, whose classification faces challenges to separate wave-formed from aeolian ridges, are relevant to the context of anthropic control. An example of this kind of morphology, previously classified as foredunes, is arranged along Brazil’s northeastern coast, and the pertinence of its classification as such or even as truly developed dunes was examined. To contribute to the debate on this issue, detailed geomorphological mapping was carried out through UAV and LIDAR surveys, in addition to the multitemporal study of satellite images and aerial photographs. Ground penetration radar sections, trenches, and particle size analysis were also conducted. Although the obliquity of wind direction to the coastline, this study’s main bedform of focus shows coast-parallel positioning conditioned by the exogenous vegetation previously inserted about 70 m from the high tide line. This morphology showed practically no migration for over 15 years; however, the wind breaks through the vegetation barrier and develops depositional lobes and V-shaped low crests protruding into the mainland. GPR sections reveal cross-strata sets with a high dip angle in only two aeolian sequences, one preceding exogenous vegetation introduction and the other in a contemporary layer, amidst the dominance of horizontal to sub-horizontal strata. The sediments are characteristically aeolian, with cross-strata and morphology resembling incipient protodunes and a few stretches at the lee slope highlighting characteristics of retention or precipitation dunes. There was little similarity to the foredunes compared to the other occurrences along the equatorial northeast coast; there was also an inconsistency in the correlation between the cross-strata and the morphological stage. In addition, the disconnection between the aeolian dynamics and morphogenetic process also differentiates it from regional foredunes. This morphology, therefore, presents aspects that are not characteristic of the classification of foredunes or the naturally formed dunes in the region and thus demands a classification to emphasize the anthropogenic character.
Soil Loss Potential Assessment for Natural and Post-Fire Conditions in Evia Island, Greece
Authors: Valkanou Kanella , Karymbalis Efthimios , Bathrellos George , Skilodimou Hariklia , Tsanakas Konstantinos , Papanastassiou Dimitris , Gaki-Papanastassiou Kalliopi
Published: October 2022

A devastating forest fire in August 2021 burned about 517 km2 of the northern part of Evia Island, affecting vegetation, soil properties, sediment delivery and the hydrological response of the catchments. This study focuses on the estimation of the annual soil loss in the study area under natural (pre-fire) and post-fire conditions. The assessment of the soil loss potential was conducted with the application of the Universal Soil Loss Equation (USLE), which is an empirical equation and an efficient way to predict soil loss. The USLE factors include rainfall erosivity (R), soil erodibility (K), the slope and slope length factor (LS), the cover management factor (C) and the erosion control practice factor (P). The USLE quantified the annual soil erosion (in t/ha/year) for both pre- and post-wildfire conditions, and the study area has been classified into various soil loss categories and soil erosion intensity types. The results showed that the annual soil loss before the forest fires ranged from 0 to 1747 t/ha, with a mean value of 253 t/ha, while after the fire the soil loss significantly increased (the highest annual soil loss was estimated at 3255 t/ha and the mean value was 543 t/ha). These values demonstrate a significant post-fire change in mean annual soil loss that corresponds to an increase of 114% compared to the pre-fire natural condition. The area that is undergoing high erosion rates after the extreme wildfire event increased by approximately 7%, while the area of moderate rates increased by 2%. The calculated maximum potential of soil erosion, before and after the 2021 extreme wildfire event, has been visualized on spatial distribution maps of the average annual soil loss for the study area. The present study underlines the significant post-fire increase in soil loss as part of the identification of the more vulnerable to erosion areas that demand higher priority regarding the protective/control measures.
Exploiting Ground-Penetrating Radar Signal Enhancements by Water-Saturated Bulb Surrounding Defective Waterpipes for Leak Detection
Authors: Carrive Pierre , Saintenoy Albane , Léger Emmanuel , Arcone Steven A. , Sailhac Pascal
Published: October 2022

The detection of water leakage along its transportation network has important societal impacts, such as avoiding a large volume of water wasted along the waterways or preventing water-related chemical or physical surrounding media deterioration. Among the vast domain of destructive techniques, Ground-Penetrating Radar (GPR) is a common and efficient tool used for detection in many near-surface contexts, and it is particularly efficient in civil engineering cases, such as utility detection, due to its fine resolution and the ease of data acquisition. A peculiar form of signal enhancement appears in GPR profiles recorded over spheres and cylinders where velocity contrasts exist between the body’s material and the surrounding medium. We used this enhancement to detect potential water leakages in water pipes. After exhibiting the signal enhancement effect in a laboratory sandbox experiment using a spherical glass ball, we verified the results with numerical experiments with varied sphere and cylinder sizes and dielectric properties. We then investigated field and numerical experiments of GPR transects above a “real life” water-leaking PVC pipe. Our results show that the water cylinder and water infiltration bulb produced a characteristic signal that could be used for detecting water leakages along water pipes. The largest amplitude in the GPR signal is caused by a bottom pipe reflection enhanced by the water bulb and not by the top of the pipe. We stress the risk of miscalculating the pipe’s depth during velocity estimation when amplitude enhancement conditions are met. Beyond civil-engineering impacts, knowledge on signal amplification phenomena can help GPR data interpretations in sedimentology and hydrogeology studies.
Using Mixed Reality for the Visualization and Dissemination of Complex 3D Models in Geosciences—Application to the Montserrat Massif (Spain)
Authors: Janeras Marc , Roca Joan , Gili Josep A. , Pedraza Oriol , Magnusson Gerald , Núñez-Andrés M. Amparo , Franklin Kathryn
Published: October 2022

In the last two decades, both the amount and quality of geoinformation in the geosciences field have improved substantially due to the increasingly more widespread use of techniques such as Laser Scanning (LiDAR), digital photogrammetry, unmanned aerial vehicles, geophysical reconnaissance (seismic, electrical, geomagnetic), and ground-penetrating radar (GPR), among others. Furthermore, the advances in computing, storage and visualization resources allow the acquisition of 3D terrain models (surface and underground) with unprecedented ease and versatility. However, despite these scientific and technical developments, it is still a common practice to simplify the 3D data in 2D static images, losing part of its communicative potential. The objective of this paper is to demonstrate the possibilities of extended reality (XR) for communication and sharing of 3D geoinformation in the field of geosciences. A brief review of the different variants within XR is followed by the presentation of the design and functionalities of headset-type mixed reality (MR) devices, which allow the 3D models to be investigated collaboratively by several users in the office environment. The specific focus is on the functionalities of Microsoft’s HoloLens 2 untethered holographic head mounted display (HMD), and the ADA Platform App by Clirio, which is used to manage model viewing with the HMD. We demonstrate the capabilities of MR for the visualization and dissemination of complex 3D information in geosciences in data rich and self-directed immersive environment, through selected 3D models (most of them of the Montserrat massif). Finally, we highlight the educational possibilities of MR technology. Today MR has an incipient and reduced use; we hope that it will gain popularity as the barriers of entry become lower.
Variable Response in Alpine Tree-Ring Stable Isotopes Following Volcanic Eruptions in the Tropics and Iceland
Authors: Arosio Tito , Affolter Stéphane , Nicolussi Kurt , Sigl Michael , Ziehmer-Wenz Malin Michelle , Schlüchter Christian , Schaad Emmanuel , Stähli Rafael , Leuenberger Markus Christian
Published: October 2022

The importance of the stable isotopes in tree rings for the study of the climate variations caused by volcanic eruptions is still unclear. We studied δ18O, δD, δ13C stable isotopes of larch and cembran pine cellulose around four major eruptions with annual resolution, along with a superposed epoch analysis of 34 eruptions with 5-year resolution. Initial analysis of the tropical Tambora (1815 CE) and Samalas (1257 CE) eruptions showed a post-eruption decrease in δ18O values attributed to post-volcanic cooling and increased summer precipitation in Southern Europe, as documented by observations and climate simulations. The post-volcanic cooling was captured by the δD of speleothem fluid inclusion. The δ18O decrease was also observed in the analysis of 34 major tropical eruptions over the last 2000 years. In contrast, the eruptions of c. 750, 756, and 764 CE attributed to Icelandic volcanoes left no significant responses in the cellulose isotopes. Further analysis of all major Icelandic eruptions in the last 2000 years showed no consistent isotopic fingerprints, with the exception of lower post-volcanic δ13C values in larch. In summary, the δ18O values of cellulose can provide relevant information on climatic and hydroclimatic variations following major tropical volcanic eruptions, even when using the 5-year resolution wood samples of the Alpine Tree-Ring Isotope Record database.
Conversion of Triaxial Compression Strain–Time Curves from Stepwise Loading to Respective Loading
Authors: Qu Haigang , Mu Dianrui , Nie Zhong , Tang Aiping
Published: October 2022

Numerous researchers of soil creep behavior adopt stepwise loading (SL) rather than respective loading (RL) to perform the triaxial creep tests. However, a complete continuous strain–time curve of SL needs to be converted into assumed curve clusters supposing obtained under RL before the deformation data are used to develop creep constitutive models. Classical methods realize the conversion mainly by focusing on the creep deformation parts and classifying them into linear and nonlinear compositions. Mostly, the linear parts are simply superposed while the nonlinear parts are complex to consider and so are neglected. Moreover, classical methods are not sufficiently valid to eliminate the stress history effect on the conversion. Here, a new method is proposed to achieve the conversion without neglecting the stress history effect. The method rebuilds the triaxial creep test mathematically and physically, adhering to the revising of energy. The method treats the tested deformation in its entirety, instead of distinguishing it into elastic, visco-elastic, plastic and creep (linear and nonlinear) deformation to convert respectively. The comparison among actual measured SL and RL strain–time curves and the curves converted by the new method proves the stress history effect should not be neglected. The higher the vertical load level, the larger the discrepancy between the RL and SL strain–time curve, and the disparity becomes larger with time. The new method highlights the necessity of considering the stress history effect in analysis and design for higher accuracy. The comparisons illustrate the conversion method at least produces more satisfactory results for clayey soil. Primarily examined, at the later stages of loading, the disparity in strain between the converted RL and measured RL decreases by 52.5%~53.5% compared with strain between the measured SL and measured RL.
Effectiveness of Nurses’ Training in Identifying, Reporting and Handling Elderly Abuse: A Systematic Literature Review
Authors: Ranabhat Pratibha , Nikitara Monica , Latzourakis Evangelos , Constantinou Costas S.
Published: October 2022

The elderly population globally is estimated to grow by one-third of the world’s population by the year 2050. At the same time, elder abuse and neglect have been acknowledged as major growing concerns. With the growing elderly population and increasing concerns about elder abuse, understanding the ways to deal with elder abuse is important. The healthcare professionals, especially nurses, are among the first groups who come in contact with the elderly population and can identify and assess cases of elder abuse. There is evidence to suggest that nurses lack knowledge in the assessment, identification, management, and reporting of an elder abuse case. This study aims to explore the available literature in the effectiveness of training programs for nurses in elder abuse management. The search strategy included the electronic databases CINHAL, Medline, and Health Source. A total of 646 research articles published between 2010 and 2021 were screened against inclusion and exclusion criteria. After reviewing and removing duplicates and irrelevant studies, 14 articles were included in this review. The findings of this literature review revealed that providing education and training for nurses in elder abuse can enhance their knowledge and increase identification and reporting of elder abuse cases. It also indicated that mixed teaching methods, such as face-to-face lectures, simulation, or case scenarios and debriefings or feedback can strengthen the learning process of nurses. In conclusion, educational programs for nurses can significantly improve the identification, reporting, and handling skills of elder abuse incidents. This finding can help in developing accurate strategies for minimizing and preventing elder abuse cases. From the results of this systematic review, we propose the ECLiPSE pathway for the effective training of nurses and handling of elder abuse cases, eventually contributing to decreasing the incidents.
Creation of a Whole Health Age-Friendly Template and Dashboard Facilitates Implementation of 4Ms into Primary Care
Authors: Powers James S. , Penaranda Natalie
Published: October 2022

The Veterans Administration has joined the Age-Friendly Health Systems (AFHS) movement as part of its Whole Health initiative to provide safe, high-quality geriatric care using a set of evidence-based practices known as the “4Ms”—What Matters, Medication, Mentation, and Mobility—to provide care across all care settings. Two healthcare centers utilized an automated review of 4Ms care. For non-templated notes in the TVHS GeriPACT clinic over a 30-day period, all the 4Ms health factors (HFs) were addressed in only 1% of patients, and 16% had three HFs, 37% had two HFs, and 71% had one HF addressed. During the pilot of a new templated note and associated dashboard at the RICVAMC, GeriPACT and Home-Based Primary Care (HBPC) addressed all the age-friendly health factors in 41% of patients, while 24% had three health factors, 10% had two health factors, and 13% had one health factor addressed, and 10% were indeterminate by manual review. For both facilities, What Matters Most had the lowest prevalence, representing the most difficult individual health factor to address. The use of a templated note improves the reliable delivery of age-friendly care compared to non-templated notes and facilitates the dashboard display of practice- and provider-specific age-friendly encounter data, which may provide useful QI information to clinicians and health systems.
Understanding User Requirements for a Senior-Friendly Mobile Health Application
Authors: Tajudeen Farzana Parveen , Bahar Nurhidayah , Tan Maw Pin , Peer Mustafa Mumtaz Begum , Saedon Nor Izzati , Jesudass Jenifer
Published: October 2022

The advancement of mobile technologies has motivated countries around the world to aim for smarter health management to support senior citizens. However, the use of mobile health applications (mHealth apps) among senior citizens appears to be low. Thus, drawing upon user expectations, the present study examined user requirements for a senior-friendly mHealth application. A total of 74 senior citizens were interviewed to explore the difficulties they encounter when using existing mobile apps. This study followed Nielsen’s usability model to identify user requirements from five aspects, namely learnability, efficiency, memorability, error, and satisfaction. Based on the results, a guideline was proposed pertaining to usability and health management features. This guideline offers suggestions for mHealth app issues related to phrasing, menus, simplicity, error messages, icons and buttons, navigation, and layout, among others. The study also found that speech recognition technology can help seniors access information quickly. The proposed guideline and findings offer valuable input for software and app developers in building more engaging and senior-friendly mHealth apps.
Factors Associated with Physical Activity in a Diverse Older Population
Authors: Tappen Ruth M. , Newman David , Gropper Sareen S. , Horne Cassandre , Vieira Edgar R.
Published: October 2022

Physical activity is important for healthy aging, but few older adults achieve the goal of 150 min per week of moderate activity. The purpose of this study was to employ a robust statistical approach in the analysis of the factors related to physical activity in a diverse sample of older adults. A secondary analysis of factors associated with calculated MET-h/week was conducted in a sample of 601 African Americans, Afro-Caribbeans, European Americans, and Hispanic Americans age 59 to 96 living independently in the community. Age, education, social network, pain, and depression were the five variables that accounted for a statistically significant proportion of unique variance in the model. The strongest correlation to total MET-h/week was with depression. Directionality of the relationship between these variables and physical activity is complex: while pain and depression can reduce physical activity, activity may also help to reduce pain and depression. Additionally, of note is that many of these factors may be modified, calling for the design and testing of individual, group, and community level interventions to increase physical activity in the older population.