Adjacent Sequences Research Articles

Learning Spatio-temporal features to detect manipulated facial videos created by the Deepfake techniques

In the last years, the face synthetic video generation has been rapid, and hyper-realistic forged videos are based on Deepfake techniques. It leads to a loss of trust in videos' content and makes it malicious by spreading forged videos on the internet. Until now, there are a few algorithms that have been suggested for detecting forged videos created by Deepfake techniques, but most of them based on analyzing or learning features on frames separately in a video. Those algorithms often pay less attention to Spatio-temporal features, so these algorithms' accuracy is usually not good. This paper proposes a 3-dimensional (3-D) convolutional neural network model that can learn Spatio-temporal features from an adjacent frame sequence in a video. Our proposed network's binary detection accuracy reached over 99% on the two largest benchmark datasets as Deepfake of FaceForensics++ and VidTIMIT datasets. The experimental results of the proposed method outperform state-of-the-art methods.

Origin of Subsequent Malignant Neoplasms in Patients with History of Testicular Germ Cell Tumor.

Simple SummaryAlthough testicular germ cell tumor (TGCT) carries a high cure rate, some patients still die from it. We investigated the genetic landscape and cellular origins of cancers that develop later in life after treatment for TGCT and found evidence that a common progenitor cell might be responsible for both. This study shows the possible importance of stem-like cells in the development of cancer.Although genetic changes may be pivotal in the origin of cancer, cellular context is paramount. This is particularly relevant in a progenitor germ cell tumor and its differentiated mature teratoma counterpart when it concerns tumor heterogeneity and cancer dormancy in subsequent second malignancies (subsequent malignant neoplasms (SMNs)). From our tumor registry database, we identified 655 testicular germ cell tumor (TGCT) patients who developed SMNs between January 1990 and September 2018. Of the 113 solid organ SMNs, 42 had sufficient tumor tissue available for fluorescence in situ hybridization (FISH) analysis of isochromosome 12p [i(12p)]. We identified seven additional patients for targeted DNA and RNA sequencing of teratomas and adjacent somatic transformation. Finally, we established cell lines from freshly resected post-chemotherapy teratomas and evaluated the cells for stemness expression by flow cytometry and by the formation of teratomas in a xenograft model. In our cohort, SMNs comprising non-germ cell tumors occurred about 18 years after a diagnosis of TGCT. Of the 42 SMNs examined, 5 (12%) contained i(12p) and 16 (38%) had 12p gain. When comparing a teratoma and adjacent somatic transformation, targeted DNA and RNA sequencing demonstrated high concordance. Studies of post-chemotherapy teratoma-derived cell lines revealed cancer-initiating cells expressing multipotency as well as early differentiation markers. For the first time, we demonstrated the prevalence of i(12p) in SMNs and the presence of progenitor cells embedded within mature teratomas after chemotherapy. Our findings suggest a progenitor stem-like cell of origin in SMN and TGCT and highlight the importance of cellular context in this disease.

Targeted Long-Read Sequencing Identifies a Retrotransposon Insertion as a Cause of Altered GNAS Exon A/B Methylation in a Family With Autosomal Dominant Pseudohypoparathyroidism Type 1b (PHP1B).

Pseudohypoparathyroidism type Ib (PHP1B) is characterized predominantly by resistance to parathyroid hormone (PTH) leading to hypocalcemia and hyperphosphatemia. These laboratory abnormalities are caused by maternal loss-of-methylation (LOM) at GNAS exon A/B, which reduces in cis expression of the stimulatory G protein α-subunit (Gsα). Paternal Gsα expression in proximal renal tubules is silenced through unknown mechanisms, hence LOM at exon A/B reduces further Gsα protein in this kidney portion, leading to PTH resistance. In a previously reported PHP1B family, affected members showed variable LOM at exon A/B, yet no genetic defect was found by whole-genome sequencing despite linkage to GNAS. Using targeted long-read sequencing (T-LRS), we discovered an approximately 2800-bp maternally inherited retrotransposon insertion nearly 1200 bp downstream of exon XL not found in public databases or in 13,675 DNA samples analyzed by short-read whole-genome sequencing. T-LRS data furthermore confirmed normal methylation at exons XL, AS, and NESP and showed that LOM comprising exon A/B is broader than previously thought. The retrotransposon most likely causes the observed epigenetic defect by impairing function of a maternally derived NESP transcript, consistent with findings in mice lacking full-length NESP mRNA and in PHP1B patients with deletion of exon NESP and adjacent intronic sequences. In addition to demonstrating that T-LRS is an effective strategy for identifying a small disease-causing variant that abolishes or severely reduces exon A/B methylation, our data demonstrate that this sequencing technology has major advantages for simultaneously identifying structural defects and altered methylation. © 2022 American Society for Bone and Mineral Research (ASBMR).

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: Triggering a Lethal Fight to Keep Control of the Ten-Eleven Translocase (TET)-Associated DNA Demethylation?

The extended and diverse interference of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in multiple host functions and the diverse associated symptoms implicate its involvement in fundamental cellular regulatory processes. The activity of ten-eleven translocase 2 (TET2) responsible for selective DNA demethylation, has been recently identified as a regulator of endogenous virus inactivation and viral invasion, possibly by proteasomal deregulation of the TET2/TET3 activities. In a recent report, we presented a detailed list of factors that can be affected by TET activity, including recognition of zinc finger protein binding sites and bimodal promoters, by enhancing the flexibility of adjacent sequences. In this review, we summarize the TET-associated processes and factors that could account for SARS-CoV-2 diverse symptoms. Moreover, we provide a correlation for the observed virus-induced symptoms that have been previously associated with TET activities by in vitro and in vitro studies. These include early hypoxia, neuronal regulation, smell and taste development, liver, intestinal, and cardiomyocyte differentiation. Finally, we propose that the high mortality of SARS-CoV-2 among adult patients, the different clinical symptoms of adults compared to children, the higher risk of patients with metabolic deregulation, and the low mortality rates among women can all be accounted for by the complex balance of the three enzymes with TET activity, which is developmentally regulated. This activity is age-dependent, related to telomere homeostasis and integrity, and associated with X chromosome inactivation via (de)regulation of the responsible XIST gene expression.

Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots.

Plant cells undergo two types of cell cycles–the mitotic cycle in which DNA replication is coupled to mitosis, and the endocycle in which DNA replication occurs in the absence of cell division. To investigate DNA replication programs in these two types of cell cycles, we pulse labeled intact root tips of maize (Zea mays) with 5-ethynyl-2’-deoxyuridine (EdU) and used flow sorting of nuclei to examine DNA replication timing (RT) during the transition from a mitotic cycle to an endocycle. Comparison of the sequence-based RT profiles showed that most regions of the maize genome replicate at the same time during S phase in mitotic and endocycling cells, despite the need to replicate twice as much DNA in the endocycle and the fact that endocycling is typically associated with cell differentiation. However, regions collectively corresponding to 2% of the genome displayed significant changes in timing between the two types of cell cycles. The majority of these regions are small with a median size of 135 kb, shift to a later RT in the endocycle, and are enriched for genes expressed in the root tip. We found larger regions that shifted RT in centromeres of seven of the ten maize chromosomes. These regions covered the majority of the previously defined functional centromere, which ranged between 1 and 2 Mb in size in the reference genome. They replicate mainly during mid S phase in mitotic cells but primarily in late S phase of the endocycle. In contrast, the immediately adjacent pericentromere sequences are primarily late replicating in both cell cycles. Analysis of CENH3 enrichment levels in 8C vs 2C nuclei suggested that there is only a partial replacement of CENH3 nucleosomes after endocycle replication is complete. The shift to later replication of centromeres and possible reduction in CENH3 enrichment after endocycle replication is consistent with a hypothesis that centromeres are inactivated when their function is no longer needed.

On the convergence rates of pairs of adjacent sequences

In this paper we give a suitable definition for the pairs of adjacent (convergent) sequences of real numbers, we present some two-sided estimations which caracterize the order of convergence to its limits of some of these sequences and we give certain general explanations for its similar orders of convergence.

Features of the Influence of a DNA Sequence on Its Adjacent Sequence.

To explore the features of the influence of a DNA sequence (here called sequence A) on its adjacent sequence (here called sequence B), we linked some DNA repeated sequences to the 5′-end of the T7 promoter in the plasmid pET-42a (+) or the 5′- and/or 3′-end(s) of the EcoRI site in some DNA fragments using PCR and other molecular cloning methods. As a result, we found that the efficiency of the T7 promoter and EcoRI could be impacted by some flanking sequences, indicating that sequence B could be impacted by sequence A. The features of such influence include the following: (i) sequence A can directly impact sequence B without changing/modifying the base composition of sequence B or destroying the inherent connection between sequence B and its function-related sequences; (ii) such influence does not need the participation of trans-acting factors or products of sequence A (if any); (iii) such an influence might be undetectable when the activities of trans-acting factors of sequence B are normal but might become detectable when those are lower than the normal one; (iv) such an influence might be enhancive, inhibitory, or unobvious; (v) the influence of sequence A linked to the 5′-end of sequence B might be the same as or opposite to that of sequence A linked to the 3′-end; and (vi) the influences of sequence A linked to different ends of sequence B could enhance or partially offset each other when sequence A is linked to both 5′- and 3′-ends of sequence B. These findings might give us a further understanding of the interaction of two adjacent DNA sequences.

Genome of Tetraploid Fish Schizothorax o'connori Provides Insights into Early Re-diploidization and High-Altitude Adaptation.

SummaryWhole-genome duplications (WGDs) of Schizothoracinae are believed to have played a significant role in speciation and environmental adaptation on the Qinghai-Tibet Plateau (QTP). Here, we present a genome for Schizothorax o'connori, a QTP endemic fish and showed the species as a young tetraploid with a recent WGD later than ∼1.23 mya. We exhibited that massive insertions between duplicated genomes caused by transposon bursts could induce mutagenesis in adjacent sequences and alter the expression of neighboring genes, representing an early re-diploidization process in a polyploid genome after WGD. Meanwhile, we found that many genes involved in DNA repair and folate transport/metabolism experienced natural selection and might contribute to the environmental adaptation of this species. Therefore, the S. o'connori genome could serve as a young tetraploid model for investigations of early re-diploidization in polyploid genomes and offers an invaluable genetic resource for environmental adaptation studies of the endemic fish of the QTP.

Hyper-Parameter Optimization by Using the Genetic Algorithm for Upper Limb Activities Recognition Based on Neural Networks

A method of Upper Limb Activities Recognition (UPLA) based on Neural Networks is presented. The accuracy of activity recognition will be influenced by the size of sliding window, the overlapping of adjacent sequences and the number of neurons for neural networks. Whereas, there is less work in hyper parameters optimization of neural networks automatically. It is very time-consuming to optimize hyper parameters by experts through an experience and error approach. In the paper, Genetic algorithm is used to find the best hyper parameters automatically: the size of sliding window, the overlapping of adjacent sequences and the number of neurons for neural networks. The basic genetic algorithm has a slow convergence problem and it is very easy to fall into a local optimum. To solve the problem, the population selection mechanism is improved. A comparison is made for the improving method with seven traditional classification algorithms and convolutional neural network, an accuracy of 97.9% is reached by using the new method. Finally, an App is developed that can collect and recognize upper limb activity in real time.

A Forward Genetic Approach to Mapping a P-Element Second Site Mutation Identifies DCP2 as a Novel Tumor Suppressor in Drosophila melanogaster.

The use of transposons to create mutations has been the cornerstone of Drosophila genetics in the past few decades. Second-site mutations caused by transpositions are often devoid of transposons and thereby affect subsequent analyses. In a P-element mutagenesis screen, a second site mutation was identified on chromosome 3, wherein the homozygous mutants exhibit classic hallmarks of tumor suppressor mutants, including brain tumor and lethality; hence the mutant line was initially named as lethal (3) tumorous brain [l(3)tb]. Classical genetic approaches relying on meiotic recombination and subsequent complementation with chromosomal deletions and gene mutations mapped the mutation to CG6169, the mRNA decapping protein 2 (DCP2), on the left arm of the third chromosome (3L). Thus the mutation was renamed as DCP2l(3)tb. Fine mapping of the mutation further identified the presence of a Gypsy-LTR like sequence in the 5′UTR coding region of DCP2, along with the expansion of the adjacent upstream intergenic AT-rich sequence. The mutant phenotypes are rescued by the introduction of a functional copy of DCP2 in the mutant background, thereby establishing the causal role of the mutation and providing a genetic validation of the allelism. With the increasing repertoire of genes being associated with tumor biology, this is the first instance of mRNA decapping protein being implicated in Drosophila tumorigenesis. Our findings, therefore, imply a plausible role for the mRNA degradation pathway in tumorigenesis and identify DCP2 as a potential candidate for future explorations of cell cycle regulatory mechanisms.

Deorphanizing FAM19A proteins as pan-neurexin ligands with an unusual biosynthetic binding mechanism.

Neurexins are presynaptic adhesion molecules that organize synapses by binding to diverse trans-synaptic ligands, but how neurexins are regulated is incompletely understood. Here we identify FAM19A/TAFA proteins, "orphan" cytokines, as neurexin regulators that interact with all neurexins, except for neurexin-1γ, via an unusual mechanism. Specifically, we show that FAM19A1-A4 bind to the cysteine-loop domain of neurexins by forming intermolecular disulfide bonds during transport through the secretory pathway. FAM19A-binding required both the cysteines of the cysteine-loop domain and an adjacent sequence of neurexins. Genetic deletion of neurexins suppressed FAM19A1 expression, demonstrating that FAM19As physiologically interact with neurexins. In hippocampal cultures, expression of exogenous FAM19A1 decreased neurexin O-glycosylation and suppressed its heparan sulfate modification, suggesting that FAM19As regulate the post-translational modification of neurexins. Given the selective expression of FAM19As in specific subtypes of neurons and their activity-dependent regulation, these results suggest that FAM19As serve as cell type-specific regulators of neurexin modifications.

The novel insight into the outcomes of CRISPR/Cas9 editing intra- and inter-species

The CRISPR/Cas (clustered regularly interspaced short palindromic repeat technology/CRISPR-associated protein) is a widely used and powerful research tool in biosciences and a promising therapeutic agent for treating genetic diseases. Mutations induced by Cas9 are generally considered stochastic and unpredictable, thus hindering its applications where precise genetic alternations are required. Here, through deep sequencing and analysis of genome editing outcomes of multiple sites in four distinct species, we found that Cas9-induced mutations are coincident in mutation types but are significantly different in indel patterns among species. In human and mouse cells, indels were almost evenly distributed at both ends of the cleavage sites. However, the indels mainly appeared at the upstream of cleavage sites in Bombyx mori, while they predominantly occurred downstream of the cleavage sites in the zebrafish Danio rerio. We also found that within a species, indel patterns are sequence dependent, wherein deletions between two adjacent micro-homology sequences were the most frequently observed mutations in the repair spectrum. These results suggested the species differences in DNA repair processes during Cas9-induced gene editing, and the important role of sequence structure at the target site in predicting the gene editing outcome.

The origins and developments of sulfation-prone tyrosine-rich and acidic N- and C-terminal extensions of class ll and lll small leucine-rich repeat proteins shed light on connective tissue evolution in vertebrates

BackgroundSmall leucine-rich repeat protein (SLRP) family members contain conserved leucine-rich repeat motifs flanked by highly variable N- and C-terminal regions. Most class II and III SLRPs have tyrosine-rich N-terminal regions and some of these are sulfated. However, the evolutionary origin and conservation of the tyrosine-rich and acidic terminal regions remain undetermined. In this study, we present the most comprehensive multiple sequence alignment (MSA) analyses of all eight class II and III SLRPs to date. Based on the level of conservation of tyrosine residues and adjacent sequences, we predict which tyrosine residues are most likely to be sulfated in the terminal regions of human class II and III SLRPs.ResultsUsing this novel approach, we predict a total of 22 tyrosine sulfation sites in human SLRPs, of which only 8 sites had been experimentally identified in mammals. Our analyses suggest that sulfation-prone, tyrosine-rich and acidic terminal regions of the class II and III SLRPs emerged via convergent evolution at different stages of vertebrate evolution, coinciding with significant evolutionary events including the development of endochondral bones and articular cartilage, the aquatic to terrestrial transition, and the formation of an amnion.ConclusionsOur study suggests that selective pressures due to changes in life conditions led to the formation of sulfotyrosine-rich and acidic terminal regions. We believe the independent emergence and evolution of sulfotyrosine-rich and acidic N- and C-terminal regions have provided each class II and III SLRP member with novel vital functions required to develop new specialized extracellular matrices and tissues in vertebrate species.

Enzymatically inactive OGG1 binds to DNA and steers base excision repair toward gene transcription.

8‐Oxoguanine DNA glycosylase1 (OGG1)‐initiated base excision repair (BER) is the primary pathway to remove the pre‐mutagenic 8‐oxo‐7,8‐dihydroguanine (8‐oxoG) from DNA. Recent studies documented 8‐oxoG serves as an epigenetic‐like mark and OGG1 modulates gene expression in oxidatively stressed cells. For this new role of OGG1, two distinct mechanisms have been proposed: one is coupled to base excision, while the other only requires substrate binding of OGG1––both resulting in conformational adjustment in the adjacent DNA sequences providing access for transcription factors to their cis‐elements. The present study aimed to examine if BER activity of OGG1 is required for pro‐inflammatory gene expression. To this end, Ogg1/OGG1 knockout/depleted cells were transfected with constructs expressing wild‐type (wt) and repair‐deficient mutants of OGG1. OGG1's promoter enrichment, oxidative state, and gene expression were examined. Results showed that TNFα exposure increased levels of oxidatively modified cysteine(s) of wt OGG1 without impairing its association with promoter and facilitated gene expression. The excision deficient K249Q mutant was even a more potent activator of gene expression; whereas, mutant OGG1 with impaired substrate recognition/binding was not. These data suggested the interaction of OGG1 with its substrate at regulatory regions followed by conformational adjustment in the adjacent DNA is the primary mode to modulate inflammatory gene expression.

Evaluation of the effects of aerobic exercise in the aqueous environment on heart rate variability by using Poincare plot nonlinear method

Background and Aim: Heart rate variability used as a non-invasive method to investigate the effect of aerobics exercise on the cardiac autonomic system. The aim of this study was the nonlinear analysis of the effect of aerobic exercise in the water on the cardiac autonomic system in academic young's males. Materials and Methods: A total of 28 young men were randomly assigned to two groups of control and aerobic exercise in water. In the pre-test period and after the training intervention, all parameters of heart rate variability were measured by examining heart rate sequences, In the pre-test period and after the training intervention, all parameters of heart rate variability were measured by examining heart rate sequences, and then the standard deviation of the recorded sequences was interpreted by using the Poincare plot method. Independent t-test and paired t-test were used to compare the differences in the research stages. Results: Regular participation in aerobic exercise in water caused a significant (45.1±9.2 vs. 34.1±12.3) and standard deviation of time intervals of heart rate sequences compared to their adjacent sequence compared to the control group (P=0.03). The longitudinal standard deviation of time intervals of heart rate sequences compared to the pre-test (P=0.04) had a significant increase (79.5±12.5 vs. 56.9±15.8 After transferring the absolute results to normal, the normal state of the standard deviation of time intervals of heart rate sequences compared to its adjacent sequence compared to the control group (P=0.03) had a significant increase (44.7±12.05 vs. 36.5±13.52). Also, the normal state of the longitudinal standard deviation of time intervals of heart rate sequences compared to the pre-test (P=0.02) increased significantly (76.4±15.29 vs. 61.3±9.32). Conclusion: Performing aerobic exercise in an aqueous environment can be used as a useful training method to improve the responsiveness of the cardiac autonomic system.

İzmir‐Ankara Suture as a Triassic to Cretaceous Plate Boundary—Data From Central Anatolia

AbstractThe İzmir‐Ankara suture represents part of the boundary between Laurasia and Gondwana along which a wide Tethyan ocean was subducted. In northwest Turkey, it is associated with distinct oceanic subduction‐accretion complexes of Late Triassic, Jurassic, and Late Cretaceous ages. The Late Triassic and Jurassic accretion complexes consist predominantly of basalt with lesser amounts of shale, limestone, chert, Permian (274 Ma zircon U‐Pb age) metagabbro, and serpentinite, which have undergone greenschist facies metamorphism. Ar‐Ar muscovite ages from the phyllites range from 210 Ma down to 145 Ma with a broad southward younging. The Late Cretaceous subduction‐accretion complex, the ophiolitic mélange, consists of basalt, radiolarian chert, shale, and minor amounts of recrystallized limestone, serpentinite, and greywacke, showing various degrees of blueschist facies metamorphism and penetrative deformation. Ar‐Ar phengite ages from two blueschist metabasites are ca. 80 Ma (Campanian). The ophiolitic mélange includes large Jurassic peridotite‐gabbro bodies with plagiogranites with ca. 180 Ma U‐Pb zircon ages. Geochronological and geological data show that Permian to Cretaceous oceanic lithosphere was subducted north under the Pontides from the Late Triassic to the Late Cretaceous. This period was characterized generally by subduction‐accretion, except in the Early Cretaceous, when subduction‐erosion took place. In the Sakarya segment all the subduction‐accretion complexes, as well as the adjacent continental sequences, are unconformably overlain by Lower Eocene red beds. This, along with the stratigraphy of the Sakarya Zone, indicates that the hard collision between the Sakarya Zone and the Anatolide‐Tauride Block took place in Paleocene.

Polarizable Molecular Dynamics Simulations of Two c-kit Oncogene Promoter G-Quadruplexes: Effect of Primary and Secondary Structure on Loop and Ion Sampling.

G-quadruplexes (GQs) are highly ordered nucleic acid structures that play fundamental roles in regulating gene expression and maintaining genomic stability. GQs are topologically diverse and enriched in promoter sequences of growth regulatory genes and proto-oncogenes, suggesting that they may serve as attractive targets for drug design at the level of transcription rather than inhibiting the activity of the protein products of these genes. The c-kit promoter contains three adjacent GQ-forming sequences that have proposed antagonistic effects on gene expression and thus are promising drug targets for diseases such as gastrointestinal stromal tumors, mast cell disease, and leukemia. Because GQ stability is influenced by primary structure, secondary structure, and ion interactions, a greater understanding of GQ structure, dynamics, and ion binding properties is needed to develop novel, GQ-targeting therapeutics. Here, we performed molecular dynamics simulations to systematically study the c-kit2 and c-kit* GQs, evaluating nonpolarizable and polarizable force fields (FFs) and examining the effects of base substitutions and cation type (K+, Na+, and Li+) on the dynamics of their isolated and linked structures. We found that the Drude polarizable FF outperformed the additive CHARMM36 FF in two- and three-tetrad GQs and solutions of KCl, NaCl, and LiCl. Drude simulations with different cations agreed with the known GQ stabilization preference (K+ > Na+ > Li+) and illustrated that tetrad core-ion coordination differs as a function of cation type. Finally, we showed that differences in primary and secondary structure influence loop sampling, ion binding, and core-ion energetics of GQs.

Deep Spatial–Temporal Model Based Cross-Scene Action Recognition Using Commodity WiFi

With the popularization of Internet-of-Things (IoT) systems, passive action recognition on channel state information (CSI) has attracted much attention. Most conventional work under the machine-learning framework utilizes handcrafted features (e.g., statistic features) that are unable to sufficiently describe the sequence data and heavily rely on designers’ experiences. Therefore, how to automatically learn abundant spatial–temporal information from CSI data is a topic worthy of study. In this article, we propose a deep learning framework that integrates spatial features learned from the convolutional neural network (CNN) into the temporal model multilayer bidirectional long short-term memory (Bi-LSTM). Specifically, CSI streams are segmented into a series of patches, from which spatial features are extracted by our designed CNN structure. Considering long-term dependencies between adjacent sequences, the fully connected layer of CNN for each patch is taken as the Bi-LSTM sequential input to further capture temporal features. Our model is appealing in that it can simultaneously learn temporal dynamics and convolutional perceptual representations. To the best of our knowledge, this is the first work to explore deep spatial–temporal features for CSI-based action recognition. Furthermore, in order to solve the problem that the trained model fully fails with environmental changes, we use the off-the-shelf model as the pretrained model and fine-tune it in the new scenario. The transfer method is able to realize cross-scene action recognition with low computational consumption and satisfactory accuracy. We carry out experiments on indoor data and the experimental results validate the effectiveness of our algorithm.

Molecular Analysis of New Crimean Isolates of the Plum Pox Virus

Molecular analysis of new isolates of the plum pox virus (PPV) found in the gene pool collections of peach, apricot, and plum from the Nikitsky Botanical Garden (National Science Center, Russian Academy of Sciences), as well as on wild cherry plum trees in the surrounding area, has been carried out. Using the enzyme-linked immunosorbent assay and reverse transcription polymerase chain reaction, 19 new PPV isolates have been detected. Most of them belonged to the strain D; single isolates of the strains Rec and M were also found. The 3'-terminal sequences of genome of the new isolates were sequenced, including the coat protein (CP) gene and adjacent sequences of the NIb gene and the 3'-nontranslated region. Phylogenetic analysis of these sequences revealed the distribution of PPV-D isolates into several clusters or clades. An average divergence rate between sequences of Crimean PPV-D isolates was 2.0%. A relatively high level of genetic variation indicates a long-standing introduction of the ancestors of the current PPV-D isolates to Nikitsky Botanical Garden (NBG). Isolate H23, identified in the apricot collection, belonged to strain M. This is the first detection of PPV-M in Crimea. Isolate AL-Ch (strain Rec) was found on wild cherry plum. In the CP of isolate K87 (strain D), the K59T mutation was detected, which prevents its recognition by PPV-D-specific 4DG5 monoclonal antibodies. In CP of AL-Ch and previously characterized isolates K28 and Kisl-1pl (strain Rec), amino acid substitutions were detected at position 68, which did not affect the recognition of these isolates by AL monoclonal antibodies. Apparently, position 68 is outside the PPV-M/Rec-specific epitope. The results of the work show that PPV most likely entered the NBG with contaminated drupaceous fruit material as a result of several independent introductions from different regions of the world and spread over plantations by aphids.

Machine‐Learning‐Based Analysis of the Guy‐Greenbrier, Arkansas Earthquakes: A Tale of Two Sequences

AbstractWe revisited the June 2010 to October 2011 Guy‐Greenbrier earthquake sequence in central Arkansas using PhaseNet, a deep neural network trained to pick P and S arrival times. We applied PhaseNet to continuous waveform data and used phase association and hypocenter relocation to locate nearly 90,000 events. Our catalog suggests that the sequence consists of two adjacent earthquake sequences on the same fault and that the second sequence may be associated with the wastewater disposal well to the west of the Guy‐Greenbrier Fault, rather than the wells to the north and the east that were previously implicated. We find that each sequence is composed of many small clusters that exhibit diffusion along the fault at shorter timescales. Our study demonstrates that machine‐learning‐based earthquake catalog development is now feasible and will yield new insights into earthquake behavior.