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1.
J Clin Neurosci ; 123: 23-29, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38518385

RESUMO

Three dimensional (3D) virtual models for neurosurgery have demonstrated substantial clinical utility, especially for neuro-oncological cases. Computer-aided design (CAD) modelling of radiological images can provide realistic and high-quality 3D models which neurosurgeons may use pre-operatively for surgical planning. 3D virtual models are useful as they are the basis for other models that build off this design. 3D virtual models are quick to segment but can also be easily added to normal neurosurgical and radiological workflow without disruption. Three anatomically complex neuro-oncology cases that were referred from a single institution by three different neurosurgeons were segmented and 3D virtual models were created for pre-operative surgical planning. A face-to-face interview was performed with the surgeons after the models were delivered to gauge the usefulness of the model in pre-surgical planning. All three neurosurgeons found that the 3D virtual model was useful for presurgical planning. Specifically, the virtual model helped in planning operative positioning, understanding spatial relationship between lesion and surrounding critical anatomy and identifying anatomy that will be encountered intra-operatively in a sequential manner. It provided benefit in Multidisciplinary team (MDT) meetings and patient education for shared decision making.3D virtual models are beneficial for pre-surgical planning and patient education for shared decision making for neurosurgical neuro-oncology cases. We believe this could be further expanded to other surgical specialties. The integration of 3D virtual models into normal workflow as the initial step will provide an easier transition into modalities that build off the virtual models such as printed, virtual, augmented and mixed reality models.


Assuntos
Imageamento Tridimensional , Procedimentos Neurocirúrgicos , Humanos , Imageamento Tridimensional/métodos , Procedimentos Neurocirúrgicos/métodos , Neoplasias Encefálicas/cirurgia , Neoplasias Encefálicas/diagnóstico por imagem , Modelos Anatômicos , Masculino , Feminino , Desenho Assistido por Computador , Planejamento de Assistência ao Paciente , Pessoa de Meia-Idade
2.
Genes (Basel) ; 15(2)2024 Jan 23.
Artigo em Inglês | MEDLINE | ID: mdl-38397134

RESUMO

Characterization of gene regulatory mechanisms in cancer is a key task in cancer genomics. CCCTC-binding factor (CTCF), a DNA binding protein, exhibits specific binding patterns in the genome of cancer cells and has a non-canonical function to facilitate oncogenic transcription programs by cooperating with transcription factors bound at flanking distal regions. Identification of DNA sequence features from a broad genomic region that distinguish cancer-specific CTCF binding sites from regular CTCF binding sites can help find oncogenic transcription factors in a cancer type. However, the presence of long DNA sequences without localization information makes it difficult to perform conventional motif analysis. Here, we present DNAResDualNet (DARDN), a computational method that utilizes convolutional neural networks (CNNs) for predicting cancer-specific CTCF binding sites from long DNA sequences and employs DeepLIFT, a method for interpretability of deep learning models that explains the model's output in terms of the contributions of its input features. The method is used for identifying DNA sequence features associated with cancer-specific CTCF binding. Evaluation on DNA sequences associated with CTCF binding sites in T-cell acute lymphoblastic leukemia (T-ALL) and other cancer types demonstrates DARDN's ability in classifying DNA sequences surrounding cancer-specific CTCF binding from control constitutive CTCF binding and identifying sequence motifs for transcription factors potentially active in each specific cancer type. We identify potential oncogenic transcription factors in T-ALL, acute myeloid leukemia (AML), breast cancer (BRCA), colorectal cancer (CRC), lung adenocarcinoma (LUAD), and prostate cancer (PRAD). Our work demonstrates the power of advanced machine learning and feature discovery approach in finding biologically meaningful information from complex high-throughput sequencing data.


Assuntos
Aprendizado Profundo , Leucemia-Linfoma Linfoblástico de Células T Precursoras , Humanos , Fator de Ligação a CCCTC/genética , Fator de Ligação a CCCTC/metabolismo , DNA/genética , Fatores de Transcrição/metabolismo
3.
Epidemiol Health ; 45: e2023063, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37448125

RESUMO

OBJECTIVES: Numerous studies have investigated the efficacy of whole grains; however, research on multigrain remains limited. Grains exhibit combined positive effects against various diseases. The purpose of this study was to examine the impact of multigrain and white rice consumption on periodontitis. METHODS: We analyzed data from the Korea National Health and Nutrition Examination Survey V-3 and VI, collected between 2012 and 2015, which included 12,450 patients (4,859 male and 7,591 female) aged 19-64 years. The World Health Organization's Community Periodontal Index (CPI) was utilized to assess the presence of periodontitis, with periodontitis defined as a CPI index score of ≥3. Multivariable logistic regression analysis was performed after adjusting for potential confounding variables. RESULTS: The group that consumed only multigrain rice was less likely to have periodontitis than the group that consumed only white rice (odds ratio [OR], 0.80; 95% confidence interval [CI], 0.69 to 0.93). When stratified by sex, the risk of periodontitis demonstrated a 24% decrease in female who consumed only multigrain rice (OR, 0.76; 95% CI, 0.62 to 0.93). A similar result was observed in the age group of 40-64 years (OR, 0.84; 95% CI, 0.71 to 0.99). In the diabetes stratification model, the normal group that consumed only multigrain rice exhibited a 25% decrease in the odds of periodontitis (OR, 0.75; 95% CI, 0.62 to 0.91). CONCLUSIONS: Our findings suggest that the prevalence of periodontitis may vary depending on the type of rice consumed.


Assuntos
Oryza , Periodontite , Humanos , Masculino , Feminino , Adulto , Pessoa de Meia-Idade , Inquéritos Nutricionais , Periodontite/epidemiologia , Prevalência , República da Coreia/epidemiologia
4.
BMC Oral Health ; 23(1): 496, 2023 07 17.
Artigo em Inglês | MEDLINE | ID: mdl-37461022

RESUMO

OBJECTIVES: The effect of breastfeeding on periodontal disease in women remains unclear. This cross-sectional study used data from the Korean National Health and Nutrition Examination Survey to explore the association between breastfeeding and periodontitis in Korean women using data from the Korean National Health and Nutrition Examination Survey (KNHANES VII). MATERIALS AND METHODS: Cross-sectional data was analyzed from the KNHANES 2016-2018. The study population included 5,587 parous women aged ≥ 30 years. The outcome variable was the presence or absence of periodontitis. The explanatory variable, period of breastfeeding, was defined as "none", "1-11 months", and "more than 12 months". Confounder variables (socio-educational, personal healthcare practice, and systemic medical characteristics) were adjusted for in the logistic regression analysis. RESULTS: Approximately 60% of the participants breastfed for ≥ 12 months. In all statistical models, the prevalence of periodontitis was approximately 60% greater in women that did not breastfeed compared to women that had breastfed for 12 months or longer. When adjusted for age, statistical significance was only present in the 50-59 years age group (adjusted odds ratio [aOR], 1.678; 95% confidence interval [CIs], 1.046-2.691). CONCLUSION: Our study shows that women that breastfed for a relatively long duration had a lower risk of periodontitis. Therefore, breastfeeding may be beneficial for women's periodontal health. These results are expected to be helpful in oral health education for pregnant women.


Assuntos
Aleitamento Materno , Periodontite , Gravidez , Humanos , Feminino , Pessoa de Meia-Idade , Masculino , Estudos Transversais , Inquéritos Nutricionais , Periodontite/epidemiologia , República da Coreia/epidemiologia
5.
Front Public Health ; 11: 1090911, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37006560

RESUMO

Objective: The study aimed to examine the association between patient-reported oral health outcomes and the dental service sector and trust in dentists. The possible interaction effect of trust on this association was also explored. Methods: Randomly selected adults aged over 18 years living in South Australia were surveyed using self-administered questionnaires. The outcome variables were self-rated dental health and the evaluation outcome of the Oral Health Impact Profile. The dental service sector and the Dentist Trust Scale were included in bivariate and adjusted analyses with sociodemographic covariates. Results: Data from 4,027 respondents were analyzed. Unadjusted analysis showed that poor dental health and oral health impact were associated with sociodemographic characteristics, including lower income/education, public dental service, and lower trust in dentists (p < 0.01). Adjusted associations were similarly maintained (p < 0.05) but attenuated with the loss of statistical significance, mainly in the trust tertiles. Lower trust in dentists in the private sector had an interaction effect, with a higher prevalence ratio of oral health impact (prevalence ratio = 1.51; 95% confidence interval, 1.06-2.14; p < 0.05). Conclusion: Patient-reported oral health outcomes were associated with sociodemographic characteristics, the dental service sector, and trust in dentists. Implications for public health: The inequality of oral health outcomes between dental service sectors needs to be addressed both independently and in association with covariates including socioeconomic disadvantage.


Assuntos
Saúde Bucal , Confiança , Adulto , Humanos , Pessoa de Meia-Idade , Inquéritos e Questionários , Odontólogos , Assistência Odontológica
6.
Bioinformatics ; 39(4)2023 04 03.
Artigo em Inglês | MEDLINE | ID: mdl-36864611

RESUMO

MOTIVATION: Despite the success of recent machine learning algorithms' applications to survival analysis, their black-box nature hinders interpretability, which is arguably the most important aspect. Similarly, multi-omics data integration for survival analysis is often constrained by the underlying relationships and correlations that are rarely well understood. The goal of this work is to alleviate the interpretability problem in machine learning approaches for survival analysis and also demonstrate how multi-omics data integration improves survival analysis and pathway enrichment. We use meta-learning, a machine-learning algorithm that is trained on a variety of related datasets and allows quick adaptations to new tasks, to perform survival analysis and pathway enrichment on pan-cancer datasets. In recent machine learning research, meta-learning has been effectively used for knowledge transfer among multiple related datasets. RESULTS: We use meta-learning with Cox hazard loss to show that the integration of TCGA pan-cancer data increases the performance of survival analysis. We also apply advanced model interpretability method called DeepLIFT (Deep Learning Important FeaTures) to show different sets of enriched pathways for multi-omics and transcriptomics data. Our results show that multi-omics cancer survival analysis enhances performance compared with using transcriptomics or clinical data alone. Additionally, we show a correlation between variable importance assignment from DeepLIFT and gene coenrichment, suggesting that genes with higher and similar contribution scores are more likely to be enriched together in the same enrichment sets. AVAILABILITY AND IMPLEMENTATION: https://github.com/berkuva/TCGA-omics-integration.


Assuntos
Multiômica , Neoplasias , Humanos , Algoritmos , Neoplasias/genética , Perfilação da Expressão Gênica , Aprendizado de Máquina
8.
PLoS One ; 17(8): e0273220, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35980951

RESUMO

BACKGROUND: Headache, a highly prevalent neurological disorder, has consistently been linked with an elevated risk of dementia. However, most studies are focused on the relationship with migraine in limited age groups. Therefore, the objective of this research was to look at the link between various type of headaches and dementias based on longitudinal population-based data. METHODS AND RESULTS: Participants diagnosed with headache from 2002 to 2005 were selected and major covariates were collected. The diagnoses of Alzheimer's disease, vascular dementia, and other dementias were observed from 2006 until 2013. The adjusted hazard ratios (aHRs) and 95% confidence intervals (CIs) of dementias according to headache type were calculated by Cox proportional hazards regression. A number of 470,652 participants were observed for a mean of 7.6 years (standard deviation: 1.2), for approximately 3.6 million person-years. Both tension type headache (TTH) and migraine elevated the risk of all-cause dementias (TTH, aHR 1.18, 95% CI 1.13-2.24; migraine, aHR 1.18, 95% CI 1.13-2.24). Headaches had a greater influence in females and non-smokers as a risk factor of dementias. Patients with migraine who consumed alcohol had a higher risk of dementia, however this was not true with TTH patients. Among participants without comorbidities, TTH patients were more susceptible to dementia than migraine patients. Headache patients had a higher proportion of females regardless of headache type and approximately 1.5 times more individuals had three or more comorbidities compared to those without headache. CONCLUSIONS: Headache could be an independent predictor for subsequent dementia risk. Future studies should focus on clarifying pathogenic pathways and possible dementia-related preventive measures in headache populations.


Assuntos
Demência , Transtornos de Enxaqueca , Cefaleia do Tipo Tensional , Estudos de Coortes , Demência/epidemiologia , Feminino , Cefaleia/complicações , Cefaleia/epidemiologia , Humanos , Transtornos de Enxaqueca/complicações , Transtornos de Enxaqueca/epidemiologia , Cefaleia do Tipo Tensional/diagnóstico
9.
Sci Rep ; 12(1): 13853, 2022 08 16.
Artigo em Inglês | MEDLINE | ID: mdl-35974036

RESUMO

This study aimed to investigate the effect of interdental brushes and dental floss on the prevention of periodontitis in participants with ≥ 20 or < 20 remaining teeth by using the Korea National Health and Nutrition Examination Survey 2016-2018. Data from 11,614 participants were analysed using multivariate logistic regression after adjusting for sociodemographic factors (age and sex), socioeconomic factors (level of education and individual income), oral health-related variables (daily toothbrushing), and systemic health-related variables (smoking, diabetes, and obesity). The adjusted odds ratio (AOR) showed statistically significant results for both floss (AOR, 1.41; 95% confidence interval (CI) 1.22-1.64) and interdental brushes (AOR, 1.16; 95% CI 1.01-1.34). However, no significant difference was found in the subjects with fewer than 20 teeth. The subgroup analysis showed that interdental brushes had a significant preventive effect on women who had more than 20 teeth. Among participants with fewer than 20 teeth, interdental brush users had more periodontitis in men. Regarding those with more than 20 teeth, health inequality was alleviated when floss and interdental brushes were used. The bottom line is that the effect of preventing periodontitis in interdental brushes and dental floss was more evident in participants with ≥ 20 remaining teeth rather than in participants with < 20 remaining teeth.


Assuntos
Doenças Periodontais , Periodontite , Adulto , Feminino , Disparidades nos Níveis de Saúde , Humanos , Masculino , Inquéritos Nutricionais , Doenças Periodontais/epidemiologia , Doenças Periodontais/prevenção & controle , Periodontite/epidemiologia , Periodontite/prevenção & controle , República da Coreia/epidemiologia , Escovação Dentária/métodos
10.
J Clin Neurosci ; 103: 112-118, 2022 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-35868227

RESUMO

Prophylactic antiepileptic drug (pAED) use for craniotomy surgery is currently not supported in literature [1-5] except possibly in traumatic brain injury (TBI) [6]. Post craniotomy driving restrictions using the Austroad guidelines are based upon literature on TBI and not specifically craniotomy [16-18]. This study was to review Australian and New Zealand neurosurgeons on their use of pAED and advice on driving restrictions post craniotomy surgery. A voluntary and anonymous survey link was distributed to the members of the Neurosurgical Society of Australasia (NSA) through the NSA newsletter. The survey was available on the SurveyMonkey platform in the year 2021 August to December. Questions regarding the use of pAED and duration of driving restrictions were presented to survey participants. Sixty-one (26 %) out of 231 neurosurgeons responded to the survey. Thirty-six percent of respondents stated that they prescribed pAEDs regularly whilst thirty-two percent of respondents did not routinely prescribe pAEDs for craniotomy surgery. Driving restrictions varied but the most common driving restriction post craniotomy surgery was 6 months. There were divided opinions among NSA members in regards to pAED use and driving restrictions. The rationale for pAED use and prolonged driving restrictions for craniotomy surgery needs to be re-evaluated with current literature. The significant effect this may have on the well-being and quality life of patients need to be considered before prescribing pAEDs or long driving restrictions.


Assuntos
Anticonvulsivantes , Lesões Encefálicas Traumáticas , Austrália , Craniotomia , Humanos , Neurocirurgiões , Nova Zelândia , Convulsões
11.
Community Dent Oral Epidemiol ; 50(5): 414-420, 2022 10.
Artigo em Inglês | MEDLINE | ID: mdl-34369614

RESUMO

OBJECTIVES: To estimate the association between the use of interdental cleaning devices and proximal caries experience. METHODS: This study used a cross-sectional data from the Sixth Korea National Health and Nutrition Examination Survey (2013-2015). A total of 13 525 adults aged 19-64 years who participated in both the nutrition survey and the health examination survey were included. Data on sociodemographic factors (age and sex), socioeconomic factors (level of education and household income) and personal health practices (frequency of toothbrushing, visits to dental clinic, frequency of snacking and self-rated oral health status), and number of proximal caries were collected. Prevalence ratios (PRs) and 95% confidence intervals (95% CI) were calculated using the multivariable Poisson generalized linear model according to use of dental floss or an interdental brush. The risk of proximal caries for dental floss following the stratification of participants into various subgroups related to oral health was assessed. RESULTS: While nonflossers had 1.46 times (PR 1.46, 95% CI: 1.16-1.84) higher risk for proximal caries than flossers, the use of an interdental brush was not associated with proximal caries. In the nonflossers, the association for proximal caries was the strongest in those in their 40s (PR 2.28, 95% CI: 1.29-4.03), followed by those in their 30s (PR 1.85, 95% CI: 1.18-2.90). Although nonflossers with middle-low household income had a 59% higher risk (PR 1.59, 95% CI: 1.24-2.03) for proximal caries than those with high household income, there were no significant differences in household income in flossers. CONCLUSIONS: The findings of the study suggest that flossing at home along with toothbrushing is one of the easiest ways to prevent proximal caries. Therefore, dental floss should not be excluded from oral healthcare products.


Assuntos
Cárie Dentária , Dispositivos para o Cuidado Bucal Domiciliar , Adulto , Estudos Transversais , Cárie Dentária/epidemiologia , Cárie Dentária/prevenção & controle , Suscetibilidade à Cárie Dentária , Humanos , Inquéritos Nutricionais , Escovação Dentária
12.
Int J Gen Med ; 14: 7121-7131, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34729021

RESUMO

BACKGROUND: While evidence is accumulating to propose a specific contribution of sleep disorders and low quality sleep in the pathogenesis of temporomandibular disorders (TMD), management of primary sleep disorders in the process of preventing and treating TMD still remains scientifically unsupported. OBJECTIVE: To investigate the association of primary sleep disorders with TMD risk in South Korea. PATIENTS AND METHODS: This study was based on the National Health Insurance Service-National Health Screening Cohort (NHIS-HEALS) of South Korea with 468,882 participants. After excluding participants diagnosed in 2002, those with a diagnosis of a primary sleep disorder in 2003-2005 were recruited. All participants diagnosed with TMD between January 1, 2006 and December 31, 2013 received follow-up. Cox proportional hazards regression was performed to determine the adjusted hazard ratios (aHR) and 95% confidence interval (CI) for TMD according to the presence or absence of a primary sleep disorder diagnosis. RESULTS: After adjusting for all covariates, primary sleep disorder patients had a 44% higher risk for TMD compared with non-sleep disorder participants (aHR 1.44, 95% CI 1.02-2.04). The incidence rate of TMD was nearly twice as high in participants with sleep disorders compared with those without (6.08 vs 3.27, per 104 person-years). In subgroup analysis, an association was observed with those over 60 years old or who frequently exercised physically. CONCLUSION: Primary sleep disorders could be an important independent risk factor for the initiation and maintenance of TMD. Patients with sleep disorders should be monitored for possible co-occurrence of TMD-related symptoms that could aggravate sleep disorders in turn.

13.
Healthcare (Basel) ; 9(9)2021 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-34575013

RESUMO

This study assessed the effect of triweekly interdental brushing for a period of 6 months using the bleeding on full-mouth interdental brushing (BOFIB) index. All participants answered questionnaires and were instructed to clean all interdental areas using an interdental brush at least every second day. A dentist assessed the BOFIB index of 28 participants at baseline and at 3- and 6-month follow-up visits. We stratified the participants into three groups: IB-NN, those who used the interdental brush less than three times per week both before and after this program; IB-NY, those who used the interdental brush less than three times per week before the program but at least three times per week after the program; and IB-YY, those who used it at least three times per week both before and after the program. Owing to the weekly number of interdental brushings, the IB-YY and the other two groups showed a significant difference at baseline. At the 6-month follow-up, the weekly number of interdental brushings led to a significant difference between the IB-NN and the other two groups. The BOFIB index was lower among the compliant participants than among the noncompliant participants after 3 and 6 months of triweekly interdental brushing.

14.
BMC Oral Health ; 21(1): 388, 2021 08 09.
Artigo em Inglês | MEDLINE | ID: mdl-34372836

RESUMO

BACKGROUND: Periodontitis is one of major oral diseases, which has no consensus on early screening tool. This study aimed to compare the association and screening ability of S100A8 and S100A9 in saliva, blood and gingival crevicular fluid (GCF) for periodontitis status. METHODS: We recruited 149 community Korean adults, 50 no or initial periodontitis (NIPERIO) and 99 established periodontitis (PERIO). Using clinical attachment loss and a panoramic radiograph, stage II-IV of new classification of periodontitis proposed at 2018 was considered cases as PERIO. Enzyme linked immunosorbent assay kit was used to quantify S100A8 and S100A9. T-test, analysis of covariance, Mann-Whitney test and correlation analysis were applied to compare the relationship of S100A8 and S100A9 in saliva, blood, and GCF for periodontitis. Receiver operating characteristic curve was applied for screening ability. RESULTS: Among S100A8 and S100A9 in saliva, blood and GCF, S100A8 in saliva was significantly higher in PERIO than in NIPERIO (p < 0.05). However, S100A8 and S100A9 in GCF were higher in NIPERIO (p < 0.05). The screening ability of salivary S100A8 was 75% for PERIO, while that of GCF S100A8 was 74% for NIPERIO. Salivary S100A8 was positively correlated to blood S100A8 (p < 0.05). CONCLUSION: Salivary S100A8 could be a potential diagnostic marker for established periodontitis and be useful for screening established periodontitis.


Assuntos
Líquido do Sulco Gengival , Periodontite , Calgranulina A , Estudos Transversais , Humanos , Periodontite/diagnóstico , Saliva
15.
Genome Biol ; 22(1): 238, 2021 08 20.
Artigo em Inglês | MEDLINE | ID: mdl-34416909

RESUMO

Functional genomics experiments, like ChIP-Seq or ATAC-Seq, produce results that are summarized as a region set. There is no way to objectively evaluate the effectiveness of region set similarity metrics. We present Bedshift, a tool for perturbing BED files by randomly shifting, adding, and dropping regions from a reference file. The perturbed files can be used to benchmark similarity metrics, as well as for other applications. We highlight differences in behavior between metrics, such as that the Jaccard score is most sensitive to added or dropped regions, while coverage score is most sensitive to shifted regions.


Assuntos
Genoma , Genômica/métodos , Software , Sequenciamento de Cromatina por Imunoprecipitação , Células HCT116 , Humanos
16.
Artigo em Inglês | MEDLINE | ID: mdl-34199343

RESUMO

Although the presence of prosthetic restorations has been associated with plaque accumulation, gingivitis, and periodontitis, there is a lack of large epidemiological investigations providing evidence on the association of prosthetic crowns with periodontitis. This study aimed to analyze the association between the number of prosthetic crowns and the presence of periodontitis. This study was based on the Seventh Korea National Health and Nutrition Examination Survey (2016-2018). A total of 12,689 participants over the age of 19 years were surveyed. Multivariate logistic regression analyses were used to identify the association between the number of prosthetic crowns and periodontitis after adjusting for potential confounders, including demographic variables, socio-economic characteristics, oral health-related variables, and oral and systemic clinical variables. The odds ratio of periodontitis showed statistically significant differences in the anterior and posterior regions, and the prevalence of periodontal disease increased as the number of crown prostheses increased. Participants with 6-10 and 11 prosthetic crowns had 1.24 and 1.28 times higher prevalence of periodontitis, respectively, than patients with no prosthetic crown. The results of this study show that the number of prosthetic crowns present in adults is related to the prevalence of periodontitis.


Assuntos
Gengivite , Doenças Periodontais , Periodontite , Adulto , Estudos Transversais , Humanos , Inquéritos Nutricionais , Periodontite/epidemiologia , República da Coreia/epidemiologia , Adulto Jovem
17.
Bioinformatics ; 37(23): 4299-4306, 2021 12 07.
Artigo em Inglês | MEDLINE | ID: mdl-34156475

RESUMO

MOTIVATION: Genomic region sets summarize functional genomics data and define locations of interest in the genome such as regulatory regions or transcription factor binding sites. The number of publicly available region sets has increased dramatically, leading to challenges in data analysis. RESULTS: We propose a new method to represent genomic region sets as vectors, or embeddings, using an adapted word2vec approach. We compared our approach to two simpler methods based on interval unions or term frequency-inverse document frequency and evaluated the methods in three ways: First, by classifying the cell line, antibody or tissue type of the region set; second, by assessing whether similarity among embeddings can reflect simulated random perturbations of genomic regions; and third, by testing robustness of the proposed representations to different signal thresholds for calling peaks. Our word2vec-based region set embeddings reduce dimensionality from more than a hundred thousand to 100 without significant loss in classification performance. The vector representation could identify cell line, antibody and tissue type with over 90% accuracy. We also found that the vectors could quantitatively summarize simulated random perturbations to region sets and are more robust to subsampling the data derived from different peak calling thresholds. Our evaluations demonstrate that the vectors retain useful biological information in relatively lower-dimensional spaces. We propose that vector representation of region sets is a promising approach for efficient analysis of genomic region data. AVAILABILITY AND IMPLEMENTATION: https://github.com/databio/regionset-embedding. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Genômica , Ligação Proteica
18.
J Periodontal Implant Sci ; 51(2): 88-99, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-33913632

RESUMO

PURPOSE: Direct intraoral scanning and superimposing methods have recently been applied to measure the dimensions of periodontal tissues. The aim of this study was to analyze various correlations between labial gingival thickness and underlying alveolar bone thickness, as well as clinical parameters among 3 tooth types (central incisors, lateral incisors, and canines) using a digital method. METHODS: In 20 periodontally healthy subjects, cone-beam computed tomography images and intraoral scanned files were obtained. Measurements of labial alveolar bone and gingival thickness at the central incisors, lateral incisors, and canines were performed at points 0-5 mm from the alveolar crest on the superimposed images. Clinical parameters including the crown width/crown length ratio, keratinized gingival width, gingival scallop, and transparency of the periodontal probe through the gingival sulcus were examined. RESULTS: Gingival thickness at the alveolar crest level was positively correlated with the thickness of the alveolar bone plate (P<0.05). The central incisors revealed a strong correlation between labial alveolar bone thickness at 1 and 2 mm, respectively, inferior to the alveolar crest and the thickness of the gingiva at the alveolar crest line (G0), whereas G0 and labial bone thickness at every level were positively correlated in the lateral incisors and canines. No significant correlations were found between clinical parameters and hard or soft tissue thickness. CONCLUSIONS: Gingival thickness at the alveolar crest level revealed a positive correlation with labial alveolar bone thickness, although this correlation at identical depth levels was not significant. Gingival thickness, at or under the alveolar crest level, was not associated with the clinical parameters of the gingival features, such as the crown form, gingival scallop, or keratinized gingival width.

19.
Clin Spine Surg ; 34(7): 260-268, 2021 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-33044274

RESUMO

STUDY DESIGN: A systematic literature review and meta-analysis. OBJECTIVE: The aim of this study is to compare hybrid constructs with traditional fusion-only constructs for the incidence of adjacent segment degeneration (ASDeg) and clinical outcomes in patients with degenerative lumbar diseases. SUMMARY OF BACKGROUND DATA: Spinal fusion is a standard surgery for various pathologies of the lumbar spine, which results in changes to the biomechanics of the spine, potentially leading to ASDeg. Although ASDeg can occur slowly as a natural course, early-onset ASDeg is regarded to be related to fusion surgery. MATERIALS AND METHODS: A systematic search was conducted to identify studies that match the purpose. Included studies were compared using the incidence of ASDeg, Oswestry Disability Index, Visual Analog Score, and perioperative outcomes. We calculated the Peto odds ratio and mean difference (MD) for the continuous variables, respectively. In the hybrid group, subgroup analysis was also performed among devices. RESULTS: Among 10 papers involving 767 patients, 372 patients underwent hybrid fusion and 395 patients underwent fusion-only. ASDeg occurred in 10.2% in the hybrid and 21.5% in the fusion-only group [Peto odds ratio, 0.39; 95% confidence interval (CI), 0.23-0.64]. The MD for Visual Analog Score were 0.45 (95% CI, 0.05-0.85) between 2 groups, which was statistically significant but was too small to have clinical significance. The MD for Oswestry Disability Index was 0.93 (95% CI, -1.016 to 2.872), which was not statistically different between 2 groups. The hybrid is superior for 18 minutes (95% CI, 5.78-30.72) shorter than typical surgery. CONCLUSIONS: Hybrid lumbar surgery decreased the incidence of early-onset ASDeg for about 2 years of follow-up. Among the hybrid constructs, the interspinous devices group accomplished favorable results with a lower risk. Adjacent segment disease was not as statistically significant as ASDeg, but adjacent segment disease may show a substantial difference for >2-year follow-up.


Assuntos
Degeneração do Disco Intervertebral , Fusão Vertebral , Artefatos , Humanos , Degeneração do Disco Intervertebral/cirurgia , Vértebras Lombares/cirurgia , Região Lombossacral , Fusão Vertebral/efeitos adversos , Resultado do Tratamento
20.
J Clin Periodontol ; 47(10): 1191-1200, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32744384

RESUMO

OBJECTIVES: Salivary diagnostic using matrix metalloproteinase (MMP) and S100 for periodontitis is a promising issue. However, its prognostic effect is still unclear. This study aimed to evaluate the prognostic ability of salivary MMP-9 and S100A8 for periodontitis through non-surgical periodontitis treatment clinical trial. MATERIALS AND METHODS: Total 149 participants, 99 periodontitis and 50 healthy, were recruited. Among 99 non-surgical periodontitis treatment participants, 74 participants were revisited after three months. Periodontitis was classified as stage II-IV of new classification of periodontitis proposed at 2018. Enzyme-linked immunosorbent assay kit was used to quantify salivary MMP-9 and S100A8. Receiver operating characteristic curve was applied for diagnostic ability. Paired t test was applied for prognostic ability evaluating changes in salivary markers between pre- and post-treatment. RESULTS: Salivary MMP-9 and S100A8 were associated with periodontitis (p < .05). The screening ability of algorithm using salivary MMP-9 and S100A8 for periodontitis was 0.86 (p < .05). After treatment, reduction rate of salivary S100A8 and MMP-9 was 83.7% and 23.5%, respectively, (p < .05): only salivary S100A8 was superior compared to clinical parameters. CONCLUSION: Algorithm using salivary MMP-9 and S100A8 showed high diagnostic power for periodontitis. Both salivary S100A8 and MMP-9 showed prognostic ability for periodontitis, but S100A8 was better.


Assuntos
Metaloproteinase 9 da Matriz , Periodontite , Biomarcadores , Humanos , Metaloproteinase 8 da Matriz , Periodontite/diagnóstico , Prognóstico , Saliva
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