Typical Sequence Research Articles

Distance Degree Sequence and Distance Neighborhood Degree Sequence of Vertices in Fuzzy Graphs and Some of Their Properties

Objectives: The objective of this study is to explore new types of sequences in fuzzy graphs namely distance degree sequence and distance neighborhood degree sequence of fuzzy graphs which may have various applications in the real world. Methods: In this paper, two unique sequences for each vertex of fuzzy graphs are given by means of its degree and neighborhood degree which are called as the distance degree sequence and distance neighborhood degree sequence of vertices of fuzzy graphs respectively. The n-tuple of the distance degree sequence of vertices of a fuzzy graph arranged in lexicographic order is called the distance degree sequence of the fuzzy graph and the n-tuple of distance neighborhood degree sequence of vertices of a fuzzy graph arranged in lexicographic order is called the distance neighborhood degree sequence of the fuzzy graph. Findings: The distance degree sequence and distance neighborhood degree sequence of fuzzy graphs are introduced. The properties of these sequences and the general forms of these sequences of various fuzzy graphs are given. The relationship between the distance degree sequence and distance neighborhood degree sequences is discussed. Novelty: The distance degree sequence of graphs has already been introduced. In fuzzy graph theory, the distance degree sequence and distance neighborhood degree sequence are introduced in this paper. Mathematics Subject Classification (202 0): 03E72, 05C72, 05C12. Keywords: Fuzzy graphs, Distance degree sequence, Distance neighborhood-degree sequence, Regular fuzzy graphs

Which factors predict teachers’ evaluation of the difficulty and usefulness of phrasal verbs in L2 contexts?

Abstract Research examining teachers’ cognition of lexical items has flourished in the past few years. However, most of these studies focused on individual words rather than formulaic sequences. The present study aims to fill this gap through eliciting teachers’ evaluation of one type of formulaic sequences: phrasal verbs (PVs). The aim is to examine factors (frequency, opacity, and learners’ receptive and productive knowledge) that might predict teachers’ evaluation of the difficulty and usefulness of 100 PV senses. For that purpose, a survey was administered to 174 teachers. Results of generalized mixed-effects modelling showed that teachers’ assessment of both the usefulness and difficulty of PVs was predicted by sense-specific corpus frequency and receptive knowledge of these PV senses. Moreover, difficulty ratings were additionally affected by opacity and productive knowledge of PVs. We discuss these findings in relation to previous research on L2 PV knowledge and implications for L2 teaching practice.

Genetic Variation and Population Structure of Clonorchis sinensis: An In Silico Analysis

Clonorchis sinensis is an important zoonotic parasite that is mainly prevalent in China, Korea, Vietnam and the Russian Far East. To explore the genetic variation and population structure of C. sinensis, an in silico analysis was conducted based on mitochondrial cytochrome c oxidase subunit 1 (COX1), ribosomal internal transcribed spacer 1 (ITS1) and ribosomal internal transcribed spacer 2 (ITS2) sequences. The sequences obtained from NCBI were truncated for further analyses, including haplotype network, phylogenetic, gene flow, diversity and neutrality analyses. The results showed that there were 20, 11 and 4 haplotypes for COX1, ITS1 and ITS2, respectively. The results of both the haplotype network and phylogenetic analyses indicated that the haplotypes for each type of sequence from the same country were not all clustered together. Haplotype diversity values were all lower than 0.5. Values of nucleotide diversity were higher than 0.005, except for ITS2. Tajima’s D and Fu’s Fs values were all negative, and p-values showed significant differences, indicating that the population of C. sinensis is growing. Fst values were all lower than 0.05. In conclusion, this study found that there are specific variations of C. sinensis in different countries, and the population of this parasite is growing with less genetic variation. The findings provide a crucial foundation for understanding the molecular epidemiology and population dynamics of C. sinensis.

Assessment of age-related features of the condition of heavy-duty truck drivers based on spectral analysis of EEG-ECG and stress tests during mass occupational examinations

The authors studied the physiological characteristics of drivers of heavy-duty coal mine vehicles based on spectral analysis of EEG-ECG and stress tests, which have prognostic value in professional activity. The study aims to assess the functional condition of heavy-duty truck drivers of different age groups based on a comprehensive spectral analysis of EEG-ECG under occupational examinations. During the survey, the authors have studied the spectral parameters of the EEG‒ECG in 300 male drivers aged 25 to 66 years. Specialists have performed EEG registration when placing electrodes in the 10–20 system. The EEG analysis was performed with a preliminary visual analysis followed by the removal of artifacts. The scientists assessed the level of representation of the main alpha rhythm and its spatial distribution. The ECG registration was in the first lead. The duration of EEG-ECG registration is about 15 minutes in a typical sequence of stress tests: baseline, rhythmic photostimulation, hyperventilation with recovery periods. The spectral analysis of the EEG‒ECG was performed automatically on a Neurotravel device (Italy). The authors found lower alpha and delta activity in the initial EEG spectra in older drivers aged 45–66 years, which contributed to the cumulative effect of stress load. Light stress stimulation significantly reduced alpha and delta activity and increased beta EEG activity in both groups, while in the older group the high-frequency range significantly exceeded the low-frequency range. Simultaneously with the changes in the EEG, stress photostimulation increased the energy of the ECG spectra in all frequency ranges. The authors established the appearance of additional stress indicators during light stimulation in older drivers based on the correlation of EEG‒ECG spectra (alpha/delta) and the absence of such changes in the group of young drivers aged 25–35 years. Moreover, the EEG–ECG correlation coefficients and their critical values increased in groups in increments of 6 years — from 35 to 65 years. Elderly drivers, based on neuro-cardiodynamic indicators, were in a state of chronic stress and the resulting risks to health and professional activity, and the identified physiological mechanisms of stress may be at the heart of ways to prevent it. Limitations. The study is limited to the assessment of EEG and ECG indicators in 300 heavy truck drivers. Ethics. The study was performed using non-invasive methods and approved by the Bioethical Committee of the Research Institute of Complex Problems of Hygiene and Occupational Diseases, Protocol No. 5, § 1 dated 12/26/2018, in accordance with the Helsinki Declaration of the World Medical Association "Ethical Principles of conducting medical research with human participation as a subject" as amended in 2013 and the "Rules of Good Clinical Practice" approved by by Order of the Ministry of Health of the Russian Federation No. 200n dated April 1, 2016. All the examined patients signed a voluntary informed consent to participate in the study.

Some Convergence Types of Function Sequences and Their Relations

Some Convergence Types of Function Sequences and Their Relations

THE DETECTION OF DISTOMOLAR TEETH ON PANORAMIC RADIOGRAPHS USING DIFFERENT ARTIFICIAL INTELLIGENCE MODELS.

One notable anomaly, presence of distomolars, arises beyond the typical sequence of the human dental system. In this study, convolutional neural networks (CNNs) based machine learning methods were employed to classify distomolar tooth existence using panoramic radiography (PR). PRs dataset, composed of 117 subjects with distomolar teeth and 146 subjects without distomolar teeth, was constructed. These images were assessed using AlexNet, DarkNet, DenseNet, EfficientNet, GoogLeNet, ResNet, MobileNet, NasNet-Mobile, VGG, and XceptionNet frameworks for distomolar teeth existence. Considering the moderate number dataset samples, transfer learning was also utilized to improve the performance of these CNN based networks along with 5-fold cross-validation. The final classification was obtained through the fusion of the classifiers results. Performance of the experimental studies was assessed utilizing accuracy (Acc), sensitivity (sen), specificity (spe) and precision (pre) metrics. Best accuracy value of 96.2% was obtained for the fusion of DarkNet, DenseNet, and ResNet, three best individual performing architectures, in distomolar teeth classification problem. In summary, this study has demonstrated the significant potential of CNNs in accurately detecting distomolar teeth in dental radiographs, a critical task for clinical diagnosis and treatment planning. The fusion of CNN architectures, particularly ResNet, Darknet, and DenseNet, has shown exceptional performance, pointing towards the future of artificial intelligence (AI) driven dental diagnostics. Our findings showed that these systems can help clinicians during radiologic examinations.

An inexact restoration direct multisearch filter approach to multiobjective constrained derivative-free optimization

Direct Multisearch (DMS) is a well-established class of methods for multiobjective derivative-free optimization, where constraints are addressed by an extreme barrier approach, only evaluating feasible points. In this work, we propose the replacement of this extreme barrier approach by a filter strategy, combined with an inexact feasibility restoration step, to address constraints in the DMS framework. The filter approach treats feasibility as an additional component of the objective function that needs to be minimized. The inexact restoration step attempts to generate new feasible points, contributing to prioritize this feasibility, a requirement for the good performance of any filter approach. Theoretical results are provided, analysing the different types of sequences of points generated by the new algorithm, and numerical experiments on a set of nonlinearly constrained biobjective problems are reported, stating the good algorithmic performance of the proposed approach.

Molecular characterization of a novel thioredoxin-related transmembrane protein gene AcTMX3 that plays important roles in antioxidant defence in Arma chinensis diapause.

Protein disulphide isomerase (PDI) possesses disulphide isomerase, oxidoreductase and molecular chaperone activities, and is involved in regulating various physiological processes. However, there are few studies on the function in insect diapause. In this study, we cloned one novel member PDI family (TMX3, thioredoxin-related transmembrane protein 3) in Arma chinensis. The AcTMX3 encodes 426 amino acids that contains a predicted N-terminal signal sequence, a thioredoxin-like domain with the CXXC active site and a potential transmembrane region, which are typical sequence features of TMX3. RT-qPCR results showed that AcTMX3 was mainly expressed in the head under non-diapause conditions, while AcTMX3 was highly expressed in the fat body (central metabolic organ) under diapause conditions. Moreover, temporal expression profile showed that compared with non-diapause conditions, diapause conditions significantly induced AcTMX3 expression, and the expression of AcTMX3 was enhanced at 15°C. Silencing AcTMX3 in A. chinensis significantly inhibited the expression of antioxidant genes (AcTrx2 and AcTrx-like), increased the content of H2O2 and ascorbate and reduced the survival rate of A. chinensis under diapause conditions. Our results suggested that AcTMX3 played an important role in the resistance of A. chinensis to oxidative stress under diapause conditions.

Change and Inequality in German Teenagers’ Typical Time-Use Sequences Between 1991 and 2013

How children spend their time is widely regarded as a key factor shaping their development and wellbeing, as well as the intergenerational transmission of socio-economic and gender inequalities. While there is much evidence on the aggregate amount of time teenagers spent on different activities, we know little about how teenagers’ activities unfold during a typical day. We use social sequence analysis and data collected in 1991/92, 2001/02 and 2012/13 via high-frequency time-use diaries of teenagers aged 12-16 in Germany to provide a fine-grained description of teenagers’ everyday time-use sequences. We identify and visualize a typology of teenagers’ time-use during weekdays and weekend days, respectively, which groups teenagers into clusters of typical time-use sequences. These typical time-use sequences change in prevalence over time, and are stratified by teenagers’ socio-economic background, gender, and age. Our findings reveal the sequential structure of teenagers’ time use, provide new evidence corroborating theories of the social stratification of teenagers’ time use, and complement existing evidence on teenagers’ aggregate time-use. Our identification of teenagers’ typical time-use sequences forms the basis for future research to examine their causes and consequences, as well as their role in the reproduction of social inequalities.

Change and Inequality in German Teenagers’ Typical Time-Use Sequences Between 1991 and 2013. Online Appendix

How children spend their time is widely regarded as a key factor shaping their development and wellbeing, as well as the intergenerational transmission of socio-economic and gender inequalities. While there is much evidence on the aggregate amount of time teenagers spent on different activities, we know little about how teenagers’ activities unfold during a typical day. We use social sequence analysis and data collected in 1991/92, 2001/02 and 2012/13 via high-frequency time-use diaries of teenagers aged 12-16 in Germany to provide a fine-grained description of teenagers’ everyday time-use sequences. We identify and visualize a typology of teenagers’ time-use during weekdays and weekend days, respectively, which groups teenagers into clusters of typical time-use sequences. These typical time-use sequences change in prevalence over time, and are stratified by teenagers’ socio-economic background, gender, and age. Our findings reveal the sequential structure of teenagers’ time use, provide new evidence corroborating theories of the social stratification of teenagers’ time use, and complement existing evidence on teenagers’ aggregate time-use. Our identification of teenagers’ typical time-use sequences forms the basis for future research to examine their causes and consequences, as well as their role in the reproduction of social inequalities.

Research on Multi-Objective Optimization Methods of Urban Rail Train Automatic Driving Based on NSGA-II

In order to improve the control performance of automatic train operation (ATO) in urban rail trains, five typical operating sequences of urban rail trains were studied. Under the condition of meeting the safety and comfort principles of train operation, a train dynamics model was established to achieve the goals of low energy consumption, short running time, and high stopping accuracy in urban rail transit trains. In the process of finding a multi-objective solution to this problem, the Non-dominated Sorting Genetic Algorithm II (NSGA-II) was used with an elite retention strategy, and the optimal Pareto multi-objective solution set was sought. In the process of optimal solution weight assignment, the hierarchical analysis Mahalanobis distance method, which combines subjective and objective analysis, was used. Finally, taking the Beijing Yizhuang subway line as the background design example, the simulation verified the effectiveness and feasibility of the algorithm and obtained high-quality automatic train driving curves under various working conditions. This research has important reference significance for the actual operation of automatic driving in urban rail trains.

Hygrothermal aging and durability prediction of 3D-printed hybrid fiber composites with continuous carbon/Kevlar-fiber and short carbon-fiber

Hybrid Fiber Reinforced Polymers (HFRP) have excellent mechanical properties. However, preparation with 3D-printing technology is prone to hydrothermal aging compared to conventional method. Currently, complex hygrothermal aging and degradation mechanisms of 3D-printed HFRP are still unclear. Thus, hygrothermal aging and durability prediction of 3D-printed HFRP with continuous carbon/Kevlar-fiber and short carbon-fiber are studied, which considers four typical stacking sequences. All experimental samples are manufactured by Fused Deposition Modeling (FDM) 3D-printing. The artificial accelerate aging testing is conducted on samples at different times, and then flexural testing is adopted to evaluate the residual mechanical properties and failure modes. The results show that the stacking sequence significantly influences the moisture absorption behaviors, and [OC4O2K4]S absorbed more moisture than [OK4O2C4]S. During the aging process, the flexural properties of the 3D-printed HFRP first decrease rapidly and then keep stable. Among them, [OK4O2C4]S have the fastest degradation but possessed the highest residual strength. OC8O4K8O possess the slowest degradation but have a lower residual strength. The morphologies and micro failure modes/mechanisms are analyzed to explain the significant mechanical degradation. Finally, the Arrhenius relationship is adopted to accurately predict and analyze the degradation evolution process of specimens. This work offers a novel perspective on the hygrothermal aging and durability of 3D-printed HFRP.

A novel deep eutectic solvent-based green extraction and purification of DPP-IV inhibitory peptides from tilapia (Oreochromis niloticus) viscera hydrolysate

The use of green and low-cost techniques to produce bioactive peptides with anti-diabetic properties from protein-rich fish waste is a sustainable way to manage agro-fishery and food industrial waste. This study investigated a novel ultrasound (UL) assisted deep eutectic solvent (DES) based extraction approach to recover bioactive protein-rich extracts from tilapia fish viscera waste under optimized conditions (52.52% ultrasound amplitude, 1:4 DES molar ratio, 25 min extraction time). The aqueous two-phase system (ATPS) method successfully concentrated the crude proteins in the top phase and back-extracted proteins to the bottom phase with a high recovery yield. Hydrolysis by Alcalase produced tilapia viscera protein hydrolysate (TVPH) with low molecular weight (MW) peptides and low dipeptidyl peptidase (DPP)-IV half-maximal inhibitory concentration (IC50) value of 1.57 ±0.16 mg/mL. Notably, TVPH-3 fraction and TVPH-3-2 sub-fraction exhibited appreciable DPP-IV IC50 values of 1.36 ±0.08 mg/mL and 0.42 ±0.01 mg/mL, respectively. Ultrafiltration combined with RP-HPLC enriched the DPP-IV inhibitory concentration of the individual protein fractions. TVPH-3-2 sub-fraction contained hydrophobic amino acids and peptide sequences with typical DPP-IV inhibitory peptide sequence motifs. The results presented in this study indicate that tilapia viscera biomass is a potential source for protein recovery aided with a green extraction approach, and tilapia viscera protein-derived hydrolysates have potential applications as a potent functional food ingredient for the management of metabolic diseases like type-2 diabetes.

Characterization of Ksg1 protein kinase-dependent phosphoproteome in the fission yeast S. pombe

Ksg1 is an essential protein kinase of the fission yeast S. pombe that belongs to the AGC kinase family and is homologous to the mammalian PDPK1 kinase. Previous studies have shown that Ksg1 functions in the nutrient-sensing TOR signaling pathway and is involved in the phosphorylation and activation of other AGC kinases, thereby affecting various downstream targets related to metabolism, cell division, stress response, and gene expression. To date, the molecular function of Ksg1 has been analyzed using its temperature sensitive mutants or mutants expressing its truncated isoforms, which are not always suitable for functional studies of Ksg1 and the identification of its targets. To overcome these limitations, we employed a chemical genetic strategy and used a conditional ksg1as mutant sensitive to an ATP analog. Combining this mutant with quantitative phosphoproteomics analysis, we identified 1986 phosphosites that were differentially phosphorylated when Ksg1as kinase was inhibited by an ATP analog. We found that proteins whose phosphorylation was dysregulated after inhibition of Ksg1as kinase were mainly represented by those involved in the regulation of cytokinesis, contractile ring contraction, cell division, septation initiation signaling cascade, intracellular protein kinase cascade, barrier septum formation, protein phosphorylation, intracellular signal transduction, cytoskeleton organization, cellular response to stimulus, or in RNA, ncRNA and rRNA processing. Importantly, proteins with significantly down-regulated phosphorylation were specifically enriched for R-X-X-S and R-X-R-X-X-S motifs, which are typical consensus substrate sequences for phosphorylation by the AGC family of kinases. The results of this study provide a basis for further analysis of the role of the Ksg1 kinase and its targets in S. pombe and may also be useful for studying Ksg1 orthologs in other organisms.

A Survey of New York State Physical Educators’ Use of Game-Based Approaches in K–12 Physical Education

Background/Purpose: The purpose of this study was to investigate physical educators’ self-reported use, understanding, and confidence with game-based approaches (GBAs) in their K–12 physical education programs. Method: A survey of New York State physical education professionals was conducted that yielded quantitative data on how they used game-based approaches. Data were analyzed using Observation Oriented Modeling (version 5.4.2022), a tool well suited for survey data, especially teachers’ reports of game-based lesson sequences. Results: Physical educators reported both awareness and confidence with various GBAs spending most physical education game-based lessons teaching invasion games with emphasis on the psychomotor domain. Respondents’ typical game lesson sequences did not match model GBA lesson sequences. Conclusions: Findings from this study indicate respondents do not use GBAs for their game-based lessons. Beyond teacher preparation, intentional professional development should address conceptual, pedagogical, cultural, and political obstacles, and may help practitioners become more pedagogically fluent with GBAs.

Peripheral Non-Contrast MR Angiography Using FBI: Scan Time and T2 Blurring Reduction with 2D Parallel Imaging.

Non-contrast magnetic resonance angiography (NC-MRA), including fresh blood imaging (FBI), is a suitable choice for evaluating patients with peripheral artery disease (PAD). We evaluated standard FBI (sFBI) and centric ky-kz FBI (cFBI) acquisitions, using 1D and 2D parallel imaging factors (PIFs) to assess the trade-off between scan time and image quality due to blurring. The bilateral legs of four volunteers (mean age 33 years, two females) were imaged in the coronal plane using a body array coil with a posterior spine coil. Two types of sFBI and cFBI sequences with 1D PIF factor 5 in the phase encode (PE) direction (in-plane) and 2D PIF 3 (PE) × 2 (slice encode (SE)) (in-plane, through-slice) were studied. Image quality was evaluated by a radiologist, the vessel's signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) were measured, and major vessel width was measured on the coronal maximum intensity projection (MIP) and 80-degree MIP. Results showed significant time reductions from 184 to 206 s on average when using sFBI down to 98 to 162 s when using cFBI (p = 0.003). Similar SNRs (averaging 200 to 370 across all sequences and PIF) and CNRs (averaging 190 to 360) for all techniques (p > 0.08) were found. There was no significant difference in the image quality (averaging 4.0 to 4.5; p > 0.2) or vessel width (averaging 4.1 to 4.9 mm; p > 0.1) on coronal MIP due to sequence or PIF. However, vessel width measured using 80-degree MIP demonstrated a significantly wider vessel in cFBI (5.6 to 6.8 mm) compared to sFBI (4.5 to 4.7 mm) (p = 0.022), and in 1D (4.7 to 6.8 mm) compared to 2D (4.5 to 5.6 mm) (p < 0.05) PIF. This demonstrated a trade-off in T2 blurring between 1D and 2D PIF: 1D using a PIF of 5 shortened the acquisition window, resulting in sharper arterial blood vessels in coronal images but significant blur in the 80-degree MIP. Two-dimensional PIF for cFBI provided a good balance between shorter scan time (relative to sFBI) and good sharpness in both in- and through-plane, while no benefit of 2D PIF was seen for sFBI. In conclusion, this study demonstrated the usefulness of FBI-based techniques for peripheral artery imaging and underscored the need to strike a balance between scan time and image quality in different planes through the use of 2D parallel imaging.

Virulence gene polymorphisms in Shandong Helicobacter pylori strains and their relevance to gastric cancer.

Helicobacter pylori (H. pylori) virulence factors, particularly the cagA and vacA genotypes, play important roles in the pathogenic process of gastrointestinal disease. The cagA and vacA genotypes of 87 H. pylori strains were determined by PCR and sequencing. The EPIYA and CM motif patterns were analyzed and related to clinical outcomes. We examined the associations between the virulence genes of H. pylori and gastrointestinal diseases in Shandong, and the results were analyzed via the chi-square test and logistic regression model. Overall, 76 (87.36%) of the strains carried the East Asian-type CagA, with the ABD types being the most prevalent (90.79%). However, no significant differences were observed among the different clinical outcomes. The analysis of CagA sequence types revealed 8 distinct types, encompassing 250 EPIYA motifs, including 4 types of EPIYA or EPIYA-like sequences. Additionally, 28 CM motifs were identified, with the most prevalent patterns being E (66.67%), D (16.09%), and W-W (5.75%). Notably, a significant association was discovered between strains with GC and the CM motif pattern D (P < 0.01). With respect to the vacA genotypes, the strains were identified as s1, s2, m1, m2, i1, i2, d1, d2, c1, and c2 in 87 (100%), 0 (0), 26 (29.89%), 61 (70.11%), 73 (83.91%), 14 (16.09%), 76 (87.36%), 11 (12.64%), 18 (20.69%), and 69 (79.31%), respectively. Specifically, the vacA m1 and c1 genotypes presented a significantly greater prevalence in strains from GC compared to CG (P < 0.05). Following adjustment for age and sex, the vacA c1 genotype demonstrated a notable association with GC (OR = 5.174; 95% CI, 1.402-20.810; P = 0.012). This association was both independent of and more pronounced than the correlations between vacA m1 and GC. CagA proteins possessing CM motif pattern D were more frequently observed in patients with GC (P < 0.01), implying a potentially higher virulence of CM motif pattern D than the other CM motif patterns. Moreover, a strong positive association was identified between the vacA c1 genotype and GC, indicating that the vacA c1 genotype is a robust risk indicator for GC among male patients aged ≥55 years in Shandong.

Influence Analysis of Material Parameter Uncertainties on the Stability Safety Factor of Concrete Gravity Dams: A Probabilistic Method

Anti-sliding stability safety is a critical issue that must be given sufficient and widespread attention during the entire lifecycle of gravity dams. The calculated anti-sliding stability safety factor (ASS-SF) is usually compared with the allowable value required by the standards in the traditional method, which ignores the influence of material parameter uncertainties and leads to unreasonable safety evaluation results. Therefore, the nonlinear functional relationship between the stability safety factor (SF) and the random variable parameters is constructed based on the response surface equations, and the distribution types of SF sequences calculated by the Monte Carlo sampling are determined, then a probabilistic stability evaluation method for concrete gravity dams is proposed. Engineering application shows that the calculated SF obeys the normal distribution; the minimum guaranteed rate of different sliding paths in a gravity dam is 86.66%, and the guaranteed rate for the overload safety factor (OSF) is 36.00%. The results imply that a guaranteed rate for the allowable value of the ASS-SF should be provided when making the stability safety evaluation of the dams, especially the OSF. The outcome of this research will advance the understanding of stability evaluation of concrete dams, and reduce the potential risk of sliding instability of concrete dams.

Cretaceous cyclic peritidal carbonates of the Apulia Carbonate Platform (Apulia, southern Italy) in a hierarchical sequence‐stratigraphic perspective: A case study from the Murge area (the Giovinazzo sea‐cliff section)

AbstractCretaceous cyclic peritidal carbonates form the bulk of the Apulia Region in Italy and represent the vestiges of the Apulia Carbonate Platform. To show from a sequence stratigraphic perspective the architecture of peritidal carbonates, the 17 m thick Albian Giovinazzo sea‐cliff section was studied at a centimetre detail, aiming to: (i) describe cyclic facies organisation in beds and bedsets; (ii) reconstruct the relative sea‐level curve and its evolution over time; (iii) interpret the long‐term evolution of the accommodation space in terms of sequence stratigraphy. The hierarchical stacking pattern of facies in beds and bedsets reveals Milankovitch cyclicity. As a working hypothesis, elementary sequences are assumed to represent the precession cycle (ca 20 kyr) and small‐scale and medium‐scale sequences the short (ca 100 kyr) and long (ca 400 kyr) eccentricity cycles, respectively. Four different types of elementary sequences (condensed, catch‐down, catch‐up and give‐up) are recognised and interpreted in terms of relative sea‐level changes to reconstruct the relative sea‐level curve of the entire succession. The envelope of the reconstructed relative sea‐level curve is used to represent the long‐term accommodation change on the platform, which covers a time span of approximately 1.8 Myr. Most of this time was spent in subaerial exposure, as approximately 1.2 Myr was predicted to be condensed in a stratigraphic interval encompassing both the sequence‐boundary zone/falling stage deposits and the lowstand deposits. Moreover, it was interpreted that about two‐third of the total thickness of the succession was formed in only 280 kyr and consisted of both transgressive and maximum‐flooding deposits. The main implication of this study is that unconformities do not necessarily correspond to single surfaces but, rather, to very amalgamated intervals or unconformity zones. Moreover, based on biostratigraphic constraints, there is a correlation between the unconformity zone of the studied succession and the third‐order KAl4 sequence boundary of the Cretaceous eustatic cycle chart.

Transposable elements contribute to tissue-specific gene regulation in humans.

Transposable elements (TEs) contribute to approximately half of the human genome, and along with many other functions, they have been known to play a role in gene regulation in the genome. With TEs' active/repressed states varying across tissue and cell types, they have the potential to regulate gene expression in a tissue-specific manner. To provide a systematic analysis of TEs' contribution in tissue-specific gene regulation, we examined the regulatory elements and genes in association with TE-derived regulatory sequences in 14 human cell lines belonging to 10 different tissue types using the functional genomics data from the ENCODE project. Specifically, we separately analyzed regulatory regions identified by three different approaches (DNase hypersensitive sites (DHS), histone active sites (HA), and histone repressive sites (HR)). These regulatory regions showed to be distinct from each other by sharing less than 2.5% among all three types and more than 95% showed to be cell line-specific. Despite a lower total TE content overall than the genome average, each regulatory sequence type showed enrichment for one or two specific TE type(s): DHS for long terminal repeats (LTRs) and DNA transposons, HA for short interspersed nucleotide elements (SINEs), and HR for LTRs. In contrast, SINE was shown to be overrepresented in all three types of regulatory sequences located in gene-neighboring regions. TE-regulated genes were mostly shown to have cell line specific pattern, and tissue-specific genes (TSGs) showed higher usage of TE regulatory sequences in the tissue of their expression. While TEs in the regulatory sequences showed to be older than their genome-wide counterparts, younger TEs were shown to be more likely used in cell line specific regulatory sequences. Collectively, our study provided further evidence enforcing an important contribution of TEs to tissue-specific gene regulation in humans.