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1.
Front Psychol ; 15: 1332098, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38371709

RESUMO

With the popularity of learning vocabulary online among English as a Foreign Language (EFL) learners today, educators and researchers have been considering ways to enhance the effectiveness of this approach. Prior research has underscored the significance of contextual clues in vocabulary acquisition. However, few studies have compared the context provided by instructional materials and that generated by learners themselves. Hence, this present study sought to explore the impact of internal-generated contextual clues in comparison to those provided by instructional materials on EFL learners' online vocabulary acquisition. A total of 26 university students were enrolled and underwent electroencephalography (EEG). Based on a within-subjects design, all participants learned two groups of vocabulary words through a series of video clips under two conditions: one where the contexts were externally provided and the other where participants themselves generated the contexts. In this regard, participants were tasked with either viewing contextual clues presented on the screen or creating their own contextual clues for word comprehension. EEG signals were recorded during the learning process to explore neural activities, and post-tests were conducted to assess learning performance after each vocabulary learning session. Our behavioral results indicated that comprehending words with internal-generated contextual clues resulted in superior learning performance compared to using context provided by instructional materials. Furthermore, EEG data revealed that learners expended greater cognitive resources and mental effort in semantically integrating the meaning of words when they self-created contextual clues, as evidenced by stronger alpha and beta-band oscillations. Moreover, the stronger alpha-band oscillations and lower inter-subject correlation (ISC) among learners suggested that the generative task of creating context enhanced their top-down attentional control mechanisms and selective visual processing when learning vocabulary from videos. These findings underscored the positive effects of internal-generated contextual clues, indicating that instructors should encourage learners to construct their own contexts in online EFL vocabulary instruction rather than providing pre-defined contexts. Future research should aim to explore the limits and conditions of employing these two types of contextual clues in online EFL vocabulary learning. This could be achieved by manipulating the quality and understandability of contexts and considering learners' language proficiency levels.

2.
Nature ; 621(7978): 355-364, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-37612510

RESUMO

The prevalence of highly repetitive sequences within the human Y chromosome has prevented its complete assembly to date1 and led to its systematic omission from genomic analyses. Here we present de novo assemblies of 43 Y chromosomes spanning 182,900 years of human evolution and report considerable diversity in size and structure. Half of the male-specific euchromatic region is subject to large inversions with a greater than twofold higher recurrence rate compared with all other chromosomes2. Ampliconic sequences associated with these inversions show differing mutation rates that are sequence context dependent, and some ampliconic genes exhibit evidence for concerted evolution with the acquisition and purging of lineage-specific pseudogenes. The largest heterochromatic region in the human genome, Yq12, is composed of alternating repeat arrays that show extensive variation in the number, size and distribution, but retain a 1:1 copy-number ratio. Finally, our data suggest that the boundary between the recombining pseudoautosomal region 1 and the non-recombining portions of the X and Y chromosomes lies 500 kb away from the currently established1 boundary. The availability of fully sequence-resolved Y chromosomes from multiple individuals provides a unique opportunity for identifying new associations of traits with specific Y-chromosomal variants and garnering insights into the evolution and function of complex regions of the human genome.


Assuntos
Cromossomos Humanos Y , Evolução Molecular , Humanos , Masculino , Cromossomos Humanos Y/genética , Genoma Humano/genética , Genômica , Taxa de Mutação , Fenótipo , Eucromatina/genética , Pseudogenes , Variação Genética/genética , Cromossomos Humanos X/genética , Regiões Pseudoautossômicas/genética
3.
bioRxiv ; 2023 Apr 21.
Artigo em Inglês | MEDLINE | ID: mdl-36778249

RESUMO

The transfer of mitochondrial DNA into the nuclear genomes of eukaryotes (Numts) has been linked to lifespan in non-human species 1-3 and recently demonstrated to occur in rare instances from one human generation to the next 4. Here we investigated numtogenesis dynamics in humans in two ways. First, we quantified Numts in 1,187 post-mortem brain and blood samples from different individuals. Compared to circulating immune cells (n=389), post-mitotic brain tissue (n=798) contained more Numts, consistent with their potential somatic accumulation. Within brain samples we observed a 5.5-fold enrichment of somatic Numt insertions in the dorsolateral prefrontal cortex compared to cerebellum samples, suggesting that brain Numts arose spontaneously during development or across the lifespan. Moreover, more brain Numts was linked to earlier mortality. The brains of individuals with no cognitive impairment who died at younger ages carried approximately 2 more Numts per decade of life lost than those who lived longer. Second, we tested the dynamic transfer of Numts using a repeated-measures WGS design in a human fibroblast model that recapitulates several molecular hallmarks of aging 5. These longitudinal experiments revealed a gradual accumulation of one Numt every ~13 days. Numtogenesis was independent of large-scale genomic instability and unlikely driven cell clonality. Targeted pharmacological perturbations including chronic glucocorticoid signaling or impairing mitochondrial oxidative phosphorylation (OxPhos) only modestly increased the rate of numtogenesis, whereas patient-derived SURF1-mutant cells exhibiting mtDNA instability accumulated Numts 4.7-fold faster than healthy donors. Combined, our data document spontaneous numtogenesis in human cells and demonstrate an association between brain cortical somatic Numts and human lifespan. These findings open the possibility that mito-nuclear horizontal gene transfer among human post-mitotic tissues produce functionally-relevant human Numts over timescales shorter than previously assumed.

4.
Fetal Diagn Ther ; 50(1): 22-28, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36626876

RESUMO

INTRODUCTION: The current retrospective case-control study evaluates the diagnostic value of screening for a fetal cleft palate by using the ultra-sound-based observation of the "superimposed-line" sign appearing at the junction of the vomer and maxilla in the first trimester of pregnancy. METHODS: Retrospective analyses were performed of ultrasonographic images of nuchal translucency obtained during the first trimester of pregnancy (11-13+6 weeks) from 45 fetuses with a cleft palate later confirmed following parturition or induced labor (cases) and 4,500 normal fetuses confirmed after parturition (controls). Ultrasonographic features of the "superimposed-line" sign were observed and recorded, and between-group comparisons were performed. RESULTS: The "superimposed-line" sign was absent in 39 cases (86.67%), including 4 (8.89%) with simple secondary hard palate cleft and 35 (77.78%) with secondary hard palate cleft complicated by a primary cleft palate. The "superimposed-line" sign was shown in 6 cases (13.33%), including 2 (4.44%) with a simple secondary soft palate cleft, 1 (2.22%) with a simple secondary bifid uvula, and 3 (6.67%) with a simple primary cleft palate. Among the 4,500 controls, 31 fetuses showed an absence of the "superimposed-line" sign (0.69%) and 4,469 showed the "superimposed-line" sign (99.31%). The between-group difference was significant (p < 0.05). The sensitivity, specificity, positive predictive value, and negative predictive values of the "superimposed-line" sign in the first trimester of pregnancy for predicting fetal cleft palate were 86.67% (39/45), 99.31% (4,469/4,500), 55.71% (39/70), and 99.86% (4,469/4,475), respectively. CONCLUSION: The "superimposed-line" sign did not appear in fetuses with secondary hard palate cleft and primary cleft palate only when a secondary hard palate cleft is present. The sign appeared in normal fetuses and those with a simple primary cleft palate, simple secondary soft palate cleft, or a simple secondary bifid uvula. Based on these results, we propose that the "superimposed-line" sign in the mid-sagittal plane of the fetal face in the first trimester of pregnancy (11-13+6 weeks) is an important tool in screening for fetal cleft palate, especially secondary hard palate cleft.


Assuntos
Fenda Labial , Fissura Palatina , Feminino , Gravidez , Humanos , Fissura Palatina/diagnóstico por imagem , Primeiro Trimestre da Gravidez , Maxila/diagnóstico por imagem , Estudos de Casos e Controles , Estudos Retrospectivos , Vômer , Ultrassonografia Pré-Natal/métodos , Feto
5.
Genome Biol ; 22(1): 298, 2021 10 27.
Artigo em Inglês | MEDLINE | ID: mdl-34706748

RESUMO

We present SquiggleNet, the first deep-learning model that can classify nanopore reads directly from their electrical signals. SquiggleNet operates faster than DNA passes through the pore, allowing real-time classification and read ejection. Using 1 s of sequencing data, the classifier achieves significantly higher accuracy than base calling followed by sequence alignment. Our approach is also faster and requires an order of magnitude less memory than alignment-based approaches. SquiggleNet distinguished human from bacterial DNA with over 90% accuracy, generalized to unseen bacterial species in a human respiratory meta genome sample, and accurately classified sequences containing human long interspersed repeat elements.


Assuntos
Aprendizado Profundo , Sequenciamento por Nanoporos/métodos , DNA Bacteriano/análise , Humanos , Elementos Nucleotídeos Longos e Dispersos , Metagenoma , Sistema Respiratório/microbiologia
7.
Nat Commun ; 12(1): 3586, 2021 06 11.
Artigo em Inglês | MEDLINE | ID: mdl-34117247

RESUMO

Mobile element insertions (MEIs) are repetitive genomic sequences that contribute to genetic variation and can lead to genetic disorders. Targeted and whole-genome approaches using short-read sequencing have been developed to identify reference and non-reference MEIs; however, the read length hampers detection of these elements in complex genomic regions. Here, we pair Cas9-targeted nanopore sequencing with computational methodologies to capture active MEIs in human genomes. We demonstrate parallel enrichment for distinct classes of MEIs, averaging 44% of reads on-targeted signals and exhibiting a 13.4-54x enrichment over whole-genome approaches. We show an individual flow cell can recover most MEIs (97% L1Hs, 93% AluYb, 51% AluYa, 99% SVA_F, and 65% SVA_E). We identify seventeen non-reference MEIs in GM12878 overlooked by modern, long-read analysis pipelines, primarily in repetitive genomic regions. This work introduces the utility of nanopore sequencing for MEI enrichment and lays the foundation for rapid discovery of elusive, repetitive genetic elements.


Assuntos
Sistemas CRISPR-Cas , Genômica , Sequências Repetitivas Dispersas , Sequenciamento por Nanoporos/métodos , Linhagem Celular , Proteínas de Ligação a DNA , Genoma Humano , Humanos , Sequências Repetitivas de Ácido Nucleico , Ribonucleoproteínas/metabolismo , Análise de Sequência de DNA
8.
Biomaterials ; 274: 120856, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-33984634

RESUMO

T-cell based immune response can attack cancer cells formidably when certain immune checkpoint (e.g., PD-1/PD-L1) is blocked. Unfortunately, PD-1/PD-L1 blockade only provoke limited immune response because the differentiation of tumor-reactive T lymphocytes is often suppressed by TGF-ß pathway. Namely, the combating cancer weapon is weakened. In this study, other than employing photothermal therapy (PTT) to eliminate the primary tumor, we also aimed to expose in situ tumor-associated antigens and exert immune response for metastases inhibition. This enhanced immunotherapeutic strategy is achieved by IR780/SB-505124 based nanoliposomes (Nano-IR-SB@Lip). Upon administration, TGF-ß pathway is inhibited by SB to drive effector T cells into a responsive state and reduce the infiltration of Treg cells, eventually greatly enhancing the weapon against cancer. In the meantime, the immunosuppressive "protection" of tumor cells is also neutralized by blocking PD-1/PD-L1 immune checkpoint. By virtue of inherent characteristics of IR780, Nano-IR-SB@Lip can selectively accumulate, penetrate deeply in tumor tissues, and preferentially retain in mitochondria. The above features are of critical importance to tumor therapy. Thus, highly effective cancer immunotherapy is implemented via selective accumulation/deep penetration of Nano-IR-SB@Lip in tumor, achieving PTT induced immunogenic cell death and dual mitigation of immunosuppression strategy (TGF-ß inhibition/PD-1/PD-L1 blockade), which is a promising therapeutic modality for cancer.


Assuntos
Tolerância Imunológica , Imunoterapia , Linhagem Celular Tumoral , Terapia de Imunossupressão , Fototerapia
9.
J Nanobiotechnology ; 19(1): 87, 2021 Mar 26.
Artigo em Inglês | MEDLINE | ID: mdl-33771168

RESUMO

BACKGROUND: Sonodynamic therapy (SDT) is an emerging non-invasive therapeutic technique. SDT-based cancer therapy strategies are presently underway, and it may be perceived as a promising approach to improve the efficiency of anti-cancer treatment. In this work, multifunctional theranostic nanoparticles (NPs) were synthesized for synergistic starvation therapy and SDT by loading glucose oxidase (GOx, termed G) and 5,10,15,20-tetrakis (4-chlorophenyl) porphyrin) Cl (T (p-Cl) PPMnCl, termed PMnC) in Poly (lactic-co-glycolic) acid (PLGA) NPs (designated as MG@P NPs). RESULTS: On account of the peroxidase-like activity of PMnC, MG@P NPs can catalyze hydrogen peroxide (H2O2) in tumor regions to produce oxygen (O2), thus enhancing synergistic therapeutic effects by accelerating the decomposition of glucose and promoting the production of cytotoxic singlet oxygen (1O2) induced by ultrasound (US) irradiation. Furthermore, the NPs can also serve as excellent photoacoustic (PA)/magnetic resonance (MR) imaging contrast agents, effectuating imaging-guided cancer treatment. CONCLUSION: Multifunctional MG@P NPs can effectuate the synergistic amplification effect of cancer starvation therapy and SDT by hypoxia modulation, and act as contrast agents to enhance MR/PA dual-modal imaging. Consequently, MG@P NPs might be a promising nano-platform for highly efficient cancer theranostics.


Assuntos
Hipóxia/tratamento farmacológico , Nanomedicina/métodos , Nanopartículas/uso terapêutico , Inanição , Animais , Antineoplásicos/uso terapêutico , Glicemia , Linhagem Celular Tumoral , Contenção de Riscos Biológicos , Feminino , Humanos , Peróxido de Hidrogênio , Imageamento por Ressonância Magnética , Camundongos Endogâmicos BALB C , Nanopartículas/química , Oxigênio , Preparações Farmacêuticas
10.
Genome Biol ; 22(1): 92, 2021 03 29.
Artigo em Inglês | MEDLINE | ID: mdl-33781308

RESUMO

BACKGROUND: Post-zygotic mutations incurred during DNA replication, DNA repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. However, detecting mosaic variants in DNA from non-cancerous somatic tissues poses significant challenges, particularly if the variants only are present in a small fraction of cells. RESULTS: Here, the Brain Somatic Mosaicism Network conducts a coordinated, multi-institutional study to examine the ability of existing methods to detect simulated somatic single-nucleotide variants (SNVs) in DNA mixing experiments, generate multiple replicates of whole-genome sequencing data from the dorsolateral prefrontal cortex, other brain regions, dura mater, and dural fibroblasts of a single neurotypical individual, devise strategies to discover somatic SNVs, and apply various approaches to validate somatic SNVs. These efforts lead to the identification of 43 bona fide somatic SNVs that range in variant allele fractions from ~ 0.005 to ~ 0.28. Guided by these results, we devise best practices for calling mosaic SNVs from 250× whole-genome sequencing data in the accessible portion of the human genome that achieve 90% specificity and sensitivity. Finally, we demonstrate that analysis of multiple bulk DNA samples from a single individual allows the reconstruction of early developmental cell lineage trees. CONCLUSIONS: This study provides a unified set of best practices to detect somatic SNVs in non-cancerous tissues. The data and methods are freely available to the scientific community and should serve as a guide to assess the contributions of somatic SNVs to neuropsychiatric diseases.


Assuntos
Encéfalo/metabolismo , Estudos de Associação Genética , Variação Genética , Alelos , Mapeamento Cromossômico , Biologia Computacional/métodos , Estudos de Associação Genética/métodos , Genômica/métodos , Células Germinativas/metabolismo , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Especificidade de Órgãos/genética , Polimorfismo de Nucleotídeo Único
11.
Science ; 372(6537)2021 04 02.
Artigo em Inglês | MEDLINE | ID: mdl-33632895

RESUMO

Long-read and strand-specific sequencing technologies together facilitate the de novo assembly of high-quality haplotype-resolved human genomes without parent-child trio data. We present 64 assembled haplotypes from 32 diverse human genomes. These highly contiguous haplotype assemblies (average minimum contig length needed to cover 50% of the genome: 26 million base pairs) integrate all forms of genetic variation, even across complex loci. We identified 107,590 structural variants (SVs), of which 68% were not discovered with short-read sequencing, and 278 SV hotspots (spanning megabases of gene-rich sequence). We characterized 130 of the most active mobile element source elements and found that 63% of all SVs arise through homology-mediated mechanisms. This resource enables reliable graph-based genotyping from short reads of up to 50,340 SVs, resulting in the identification of 1526 expression quantitative trait loci as well as SV candidates for adaptive selection within the human population.


Assuntos
Variação Genética , Genoma Humano , Haplótipos , Feminino , Genótipo , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Mutação INDEL , Sequências Repetitivas Dispersas , Masculino , Grupos Populacionais/genética , Locos de Características Quantitativas , Retroelementos , Análise de Sequência de DNA , Inversão de Sequência , Sequenciamento Completo do Genoma
12.
Gigascience ; 10(1)2021 01 13.
Artigo em Inglês | MEDLINE | ID: mdl-33438729

RESUMO

BACKGROUND: The main goal of this collaborative effort is to provide genome-wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals representing major regions of Ukraine that were consented for public data release. BGISEQ-500 sequence data and genotypes by an Illumina GWAS chip were cross-validated on multiple samples and additionally referenced to 1 sample that has been resequenced by Illumina NovaSeq6000 S4 at high coverage. RESULTS: The genome data have been searched for genomic variation represented in this population, and a number of variants have been reported: large structural variants, indels, copy number variations, single-nucletide polymorphisms, and microsatellites. To our knowledge, this study provides the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for medical research in a large understudied population. CONCLUSIONS: Our results indicate that the genetic diversity of the Ukrainian population is uniquely shaped by evolutionary and demographic forces and cannot be ignored in future genetic and biomedical studies. These data will contribute a wealth of new information bringing forth a wealth of novel, endemic and medically related alleles.


Assuntos
Variações do Número de Cópias de DNA , Polimorfismo de Nucleotídeo Único , Genoma , Genômica , Humanos , Ucrânia
13.
Ann Palliat Med ; 9(5): 3402-3409, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-33065790

RESUMO

BACKGROUND: Grip strength is the gold standard for the assessment of muscle strength. The current methods of measuring grip strength can only reflect the overall function of the muscle group, not an actual muscle lesion or the cause of the lesion. Virtual touch tissue imaging and quantification (VTIQ) technology can provide a representation of muscle properties and quantify alterations in muscle mechanics through measurements of the mean shear wave velocities of the muscle group at a designated location. METHODS: A total of 70 healthy middle-aged females were included. The maximum grip strength and thickness of the forearm and hand muscle under relaxed conditions were measured, and the sum of the muscle thicknesses was calculated. VTIQ was used to measure the shear wave velocity (Vs) of the flexor pollicis longus, flexor digitorum profundus and flexor digitorum superficialis. Intra-group correlation coefficient (ICC) was used to evaluate the test-retest reliability of the grip strength and Vs values, and the correlation of the thickness and Vs of each forearm and hand muscle with grip strength was calculated. RESULTS: (I) The hand-held dynamometer and the VTIQ technology have good test-retest reliability in muscle evaluation (all P<0.001). (II) The muscle thickness of the lumbricals did not exhibit a significant correlation with grip strength (P>0.05). The forearm radial MT (muscle thickness), forearm ulna MT, summation of four MTs, and interosseous MT showed positive correlations with grip strength (r=0.445, 0.824, 0.722, and 0.359, all P<0.05). The Vs values of the flexor pollicis longus, flexor digitorum superficialis, and flexor digitorum profundus showed negative correlations with grip strength (r=-0.962, -0.919, and -0.456, all P<0.01). Stepwise linear regression revealed that forearm radial, ulnar muscle thickness, and flexor digitorum superficialis Vs can be utilized concurrently to predict 90.7% of the variability of grip strength (R2=0.907). CONCLUSIONS: The structure and stiffness values of skeletal muscles obtained through conventional ultrasound coupled with VTIQ showed good correlations with the variation in grip strength and can evaluate the changes of muscle strength.


Assuntos
Antebraço , Força Muscular , Feminino , Antebraço/diagnóstico por imagem , Humanos , Pessoa de Meia-Idade , Músculo Esquelético/diagnóstico por imagem , Reprodutibilidade dos Testes , Ultrassonografia
15.
Nat Biotechnol ; 38(11): 1347-1355, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32541955

RESUMO

New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine research and clinical practice, we developed a sequence-resolved benchmark set for identification of both false-negative and false-positive germline large insertions and deletions. To create this benchmark for a broadly consented son in a Personal Genome Project trio with broadly available cells and DNA, the Genome in a Bottle Consortium integrated 19 sequence-resolved variant calling methods from diverse technologies. The final benchmark set contains 12,745 isolated, sequence-resolved insertion (7,281) and deletion (5,464) calls ≥50 base pairs (bp). The Tier 1 benchmark regions, for which any extra calls are putative false positives, cover 2.51 Gbp and 5,262 insertions and 4,095 deletions supported by ≥1 diploid assembly. We demonstrate that the benchmark set reliably identifies false negatives and false positives in high-quality SV callsets from short-, linked- and long-read sequencing and optical mapping.


Assuntos
Mutação em Linhagem Germinativa/genética , Mutação INDEL/genética , Diploide , Variação Estrutural do Genoma , Humanos , Anotação de Sequência Molecular , Análise de Sequência de DNA
16.
NAR Genom Bioinform ; 2(4): lqaa089, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33575633

RESUMO

The transfer and integration of whole and partial mitochondrial genomes into the nuclear genomes of eukaryotes is an ongoing process that has facilitated the transfer of genes and contributed to the evolution of various cellular pathways. Many previous studies have explored the impact of these insertions, referred to as NumtS, but have focused primarily on older events that have become fixed and are therefore present in all individual genomes for a given species. We previously developed an approach to identify novel Numt polymorphisms from next-generation sequence data and applied it to thousands of human genomes. Here, we extend this analysis to 79 individuals of other great ape species including chimpanzee, bonobo, gorilla, orang-utan and also an old world monkey, macaque. We show that recent Numt insertions are prevalent in each species though at different apparent rates, with chimpanzees exhibiting a significant increase in both polymorphic and fixed Numt sequences as compared to other great apes. We further assessed positional effects in each species in terms of evolutionary time and rate of insertion and identified putative hotspots on chromosome 5 for Numt integration, providing insight into both recent polymorphic and older fixed reference NumtS in great apes in comparison to human events.

17.
Nucleic Acids Res ; 48(3): 1146-1163, 2020 02 20.
Artigo em Inglês | MEDLINE | ID: mdl-31853540

RESUMO

Long Interspersed Element-1 (LINE-1) retrotransposition contributes to inter- and intra-individual genetic variation and occasionally can lead to human genetic disorders. Various strategies have been developed to identify human-specific LINE-1 (L1Hs) insertions from short-read whole genome sequencing (WGS) data; however, they have limitations in detecting insertions in complex repetitive genomic regions. Here, we developed a computational tool (PALMER) and used it to identify 203 non-reference L1Hs insertions in the NA12878 benchmark genome. Using PacBio long-read sequencing data, we identified L1Hs insertions that were absent in previous short-read studies (90/203). Approximately 81% (73/90) of the L1Hs insertions reside within endogenous LINE-1 sequences in the reference assembly and the analysis of unique breakpoint junction sequences revealed 63% (57/90) of these L1Hs insertions could be genotyped in 1000 Genomes Project sequences. Moreover, we observed that amplification biases encountered in single-cell WGS experiments led to a wide variation in L1Hs insertion detection rates between four individual NA12878 cells; under-amplification limited detection to 32% (65/203) of insertions, whereas over-amplification increased false positive calls. In sum, these data indicate that L1Hs insertions are often missed using standard short-read sequencing approaches and long-read sequencing approaches can significantly improve the detection of L1Hs insertions present in individual genomes.


Assuntos
Elementos Nucleotídeos Longos e Dispersos , Análise de Sequência de DNA/métodos , Linhagem Celular , Genoma Humano , Humanos , Polimorfismo Genético , Análise de Célula Única , Software , Sequenciamento Completo do Genoma
18.
J Ultrasound Med ; 39(5): 997-1005, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-31785024

RESUMO

OBJECTIVES: Pain caused by soft tissue injury (STI) is always intractable and will eventually result in physical and psychological problems. This experiment aimed to assess the efficacy and mechanisms of low-intensity focused ultrasound (LIFU) for pain-related STI. METHODS: Rabbits (n = 30) with STI were given fixed treatment for 20 seconds and then mobile treatment for 60 seconds daily for 10 consecutive days by an LIFU device with a power output of 5 to 6 W and a frequency of 0.8 MHz. To evaluate the degree of pain, the levels of ß-endorphin in serum were measured by an enzyme-linked immunosorbent assay before and 5 to 10 minutes after the 1st, 3rd, 7th, and 10th treatments. The pain threshold was measured by an electronic analgesy meter on the 1st, 3rd, 7th, 10th, 17th, and 24th days after the start of the treatment. To investigate inflammation, prostaglandin E2 , interleukin-1ß, and 5-hydroxytryptamine levels were detected by an enzyme-linked immunosorbent assay, and nuclear factor κB messenger RNA levels were determined by a real-time quantitative polymerase chain reaction at the same time as the pain threshold was tested. RESULTS: Compared with non-LIFU groups, ß-endorphin levels and pain thresholds were significantly increased (P < .05), whereas nuclear factor- κB messenger RNA, prostaglandin E2 , interleukin- 1ß, and 5-hydroxytryptamine levels were significantly reduced (P < .05) after LIFU treatment in rabbits with STI. CONCLUSIONS: Low-intensity focused ultrasound can alleviate pain induced by STI and could have further clinical applications.


Assuntos
Manejo da Dor/métodos , Dor/etiologia , Lesões dos Tecidos Moles/complicações , Terapia por Ultrassom/métodos , Animais , Modelos Animais de Doenças , Dor/sangue , Medição da Dor/métodos , Coelhos , Lesões dos Tecidos Moles/sangue , Resultado do Tratamento , beta-Endorfina/sangue
19.
Phys Ther ; 99(11): 1443-1452, 2019 11 25.
Artigo em Inglês | MEDLINE | ID: mdl-31087076

RESUMO

BACKGROUND: Transplantation and immunosuppressive therapies are the available treatments for aplastic anemia; however, each strategy has its advantages and disadvantages. OBJECTIVE: The aim of this study was to find a new strategy for aplastic anemia treatment. DESIGN: This was an experimental and comparative study. METHODS: The aplastic anemia model was established by injecting rabbits with benzene and cyclophosphamide. The rabbits with aplastic anemia were divided into low-intensity pulsed ultrasound (LIPUS) and control groups. The distal femoral metaphysis of rabbits in the LIPUS group was treated with ultrasound for 30 days (20 min/d), whereas the control group received a sham treatment. Diarrhea, mortality, and blood cell count were evaluated. The levels of forkhead box P3, interleukin 17, interleukin 4, and interferon gamma were measured using an enzyme-linked immunosorbent assay. Bone marrow hyperplasia was observed by hematoxylin-eosin staining and scanning electron microscopy. RESULTS: The numbers of red blood cells (RBCs), white blood cells (WBCs), and platelets (PLTs) were lower, the amount of hematopoietic tissue was lower, and the amount of adipose tissue was higher in the rabbit aplastic anemia model than in the normal rabbits. The numbers of RBCs, WBCs, and PLTs increased after LIPUS treatment. The interleukin 17 level decreased, whereas the forkhead box P3 level increased. The amount of hematopoietic tissue increased, whereas the amount of adipose tissue decreased. LIMITATIONS: The number of hematopoietic stem cells could not be evaluated. CONCLUSIONS: LIPUS improved the hematopoietic microenvironment, accelerated the reconstruction of bone marrow cells, and increased the quantity and quality of RBCs, WBCs, and PLTs in the peripheral blood. Hence, it can serve as a novel treatment strategy for aplastic anemia in the future.


Assuntos
Anemia Aplástica/induzido quimicamente , Benzeno/efeitos adversos , Contagem de Células Sanguíneas , Ciclofosfamida/efeitos adversos , Ondas Ultrassônicas , Animais , Medula Óssea/patologia , Modelos Animais de Doenças , Coelhos
20.
Artif Cells Nanomed Biotechnol ; 47(1): 674-684, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-30835554

RESUMO

In terms to investigate the effect of low-intensity pulsed ultrasound (LIPUS) for differentiation of bone marrow mesenchymal stem cells (BMSCs) and the feasibility of simultaneously inducing into osteoblasts and vascular endothelial cells within the cell culture medium in which two inductive agents are added at the same time with or without LIPUS. Cells were divided into a non-induced group, an osteoblast-induced group, a vascular endothelial-induced group, and a bidirectional differentiation-induced group. Each group was further subdivided into LIPUS and non-LIPUS groups. The cell proliferation in each group was measured by MTT assay. Cell morphological and ultrastructural changes were observed by inverted phase contrast microscopy and transmission electron microscopy. The differentiation of BMSCs was detected by confocal microscopy, flow cytometry and quantitative RT-PCR. Results demonstrated that both osteoblast and vascular endothelial cell differentiation markers were expressed in the bidirectional differentiation induction group and early osteogenesis and angiogenesis appeared. The cell proliferation, differentiation rate and expression of osteocalcin and vWF in the LIPUS groups were all significantly higher than those in the corresponding non-LIPUS group (p < .05), suggesting LIPUS treatment can promote the differentiation efficiency and rate of BMSCs, especially in the bidirectional differentiation induction group. This study suggests the combination of LIPUS and dual-inducing agents could induce and accelerate simultaneous differentiation of BMSCs to osteoblasts and vascular endothelial cells. These findings indicate the method could be applied to research on generating vascularized bone tissue with a shape and function that mimics natural bone to accelerate early osteogenesis and angiogenesis.


Assuntos
Células Endoteliais/citologia , Células-Tronco Mesenquimais/citologia , Osteogênese , Ondas Ultrassônicas , Animais , Diferenciação Celular/efeitos dos fármacos , Regulação da Expressão Gênica , Células-Tronco Mesenquimais/metabolismo , Glicoproteínas da Membrana de Plaquetas/metabolismo , Ratos , Ratos Sprague-Dawley
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