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1.
Chemosphere ; 2632021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-33184521

RESUMO

The interfacial tracer test (ITT) conducted via aqueous miscible-displacement column experiments is one of a few methods available to measure air-water interfacial areas for porous media. The primary objective of this study was to examine the robustness of air-water interfacial area measurements obtained with interfacial tracer tests, and to examine the overall validity of the method. The potential occurrence and impact of surfactant-induced flow was investigated, as was measurement replication. The column and the effluent samples were weighed during the tests to monitor for potential changes in water saturation and flux. Minimal changes in water saturation and flux were observed for experiments wherein steady flow conditions were maintained using a vacuum-chamber system. The air-water interfacial areas measured with the miscible-displacement method completely matched interfacial areas measured with methods that are not influenced by surfactant-induced flow. This successful benchmarking was observed for all three media tested, and over a range of saturations. A mathematical model explicitly accounting for nonlinear and rate-limited adsorption of surfactant at the solid-water and air-water interfaces as well as the influence of changes in surface tension on matric potentials and flow was used to simulate the tracer tests. The independently-predicted simulations provided excellent matches to the measured data, and revealed that the use of the vacuum system minimized the occurrence of surfactant-induced flow and its associated effects. These results in total unequivocally demonstrate that the miscible-displacement ITT method produced accurate and robust measurements of air-water interfacial area under the extant conditions.


Assuntos
Ar/análise , Água/química , Adsorção , Benchmarking , Modelos Teóricos , Fenômenos Físicos , Porosidade , Tensão Superficial , Tensoativos/química
2.
Int J Biometeorol ; 64(12): 1985-1994, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33155128

RESUMO

While the associations of heat with health outcomes is well researched, there is less consensus on the measures used to define heat exposure and the short-term and delayed impacts of different temperature metrics on health outcomes. We investigate the nonlinear and short-term relationship of three temperature metrics and reported incidence of three gastrointestinal illnesses: salmonellosis, campylobacteriosis and cryptosporidiosis in the Australian Capital Territory (ACT). We also examine the nonlinear association of these illnesses with extreme heat (5th, 75th, 90th percentile of all heat measures). Generalized linear models with Poisson regression accounting for overdispersion, seasonal and long-term trend, weekly number of outbreaks and rainfall were developed for mean and maximum weekly temperature and the heat stress index (EHIaccl). Bacterial illnesses (salmonellosis and campylobacteriosis) showed an overall positive association with extreme heat (75th and 90th percentile of all three heat measures) and an inverse association with low temperature (5th percentile). The shape of the exposure-response curve across a range of temperatures and the lagged effects varied for each disease. Modelling the short-term and delayed effects of heat using different metrics across a range of illnesses can help identify the most appropriate measure to inform local public health intervention planning for heat-related emergencies.


Assuntos
Benchmarking , Calor Extremo , Austrália/epidemiologia , Território da Capital Australiana/epidemiologia , Temperatura Alta , Temperatura
3.
N C Med J ; 81(6): 355-362, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33139463

RESUMO

BACKGROUND Deaths from unintentional opioid overdose have increased markedly over the last decade in North Carolina. In 2017 the state created a North Carolina Opioid Action Plan, which laid out a multisectoral response to the crisis that included the medical community, law enforcement, emergency medical services, and treatment professionals. It also created a website providing county-level data associated with the crisis. Using this publicly available data, we examine trends and associations between opioid-related mortality and strategies to reduce opioid prescriptions, reduce fatality of overdose, and improve treatment and recovery.METHOD We examine yearly trends from 2010-2017 for statewide unintentional opioid-related death rates, prescription of opioid pills, buprenorphine prescription rates, naloxone administrations, and number of Certified Peer Support Specialists. We compare recent opioid-related death rates for 2015-2017 with an earlier period (2010-2012) at the county level, and examine the association between death rates and rates of the supply, treatment, and recovery metrics.RESULTS Trends for all metrics increased from 2010-2017, although the number of opioid pills per capita has declined since 2015. Between 2010 and 2017, 84 of the state's 100 counties experienced an increase in opioid-related mortality. County-level mortality was positively associated with opioid prescription rate (r = +0.12, P = 0.24) and with naloxone administrations (r = +0.20, P = 0.05). Prescription of buprenorphine was associated with a reduction in opioid mortality (r = -0.27, P = 0.01). The effect of Certified Peer Support Specialists was not discernable.LIMITATIONS Data are available for only eight years and aggregated at the county level. Mortality data are based on death certificates using ICD-10 codes from the North Carolina State Center for Health Statistics, Vital Statistics, which may not capture all opioid-related fatalities. Drug-related deaths may involve multiple non-opioid substances; in addition, determining the intent of the deceased individual may be difficult (suicide versus unintentional). Naloxone administration data only includes data from emergency medical services, not community-administered naloxone, because that data was only available for 2013 and later and is based only on self-reports.CONCLUSIONS The potential efficacy of buprenorphine is promising and should be further explored. All interventions should be monitored.


Assuntos
Epidemia de Opioides , Analgésicos Opioides/envenenamento , Benchmarking , Overdose de Drogas/tratamento farmacológico , Overdose de Drogas/mortalidade , Humanos , North Carolina/epidemiologia , Epidemia de Opioides/prevenção & controle , Epidemia de Opioides/tendências
4.
Biomedica ; 40(Supl. 2): 131-138, 2020 10 30.
Artigo em Inglês, Espanhol | MEDLINE | ID: mdl-33152196

RESUMO

Introduction: Public health surveillance together with good sanitary decisions is essential for the proper management of the SARS-CoV-2 pandemic. Objective: To compare the performance of Colombian departments based on the quality of the data and to build the national ranking. Materials and methods: We analyzed the accumulated cases published between March 6 and September 1, 2020, by the Instituto Nacional de Salud. To achieve comparability, the analyses considered the day the first case was diagnosed as the first analysis date for each department. The fulfillment of Benford's law was assessed with p-values in the log-likelihood ratio or chi-square tests. The analysis was completed with the lethality observed in each department and then the performance ranking was established. Results: Bogotá and Valle del Cauca had optimal public health surveillance performance all along. The data suggest that Antioquia, Nariño, and Tolima had good containment and adequate public health surveillance after the economic opening beginning on June 1, 2020. Conclusion: We obtained the ranking of the departments regarding the quality of public health surveillance data. The best five departments can be case studies to identify the elements associated with good performance.


Assuntos
Betacoronavirus , Infecções por Coronavirus/epidemiologia , Pandemias , Pneumonia Viral/epidemiologia , Vigilância da População , Benchmarking , Colômbia/epidemiologia , Notificação de Doenças , Geografia Médica , Humanos , População Rural/estatística & dados numéricos , Distribuições Estatísticas , Análise de Sobrevida , População Urbana/estatística & dados numéricos
5.
Artigo em Inglês | MEDLINE | ID: mdl-33143327

RESUMO

The prolonged lockdown imposed to contain the COrona VIrus Disease 19 COVID-19 pandemic prevented many people from direct contact with nature and greenspaces, raising alarms for a possible worsening of mental health. This study investigated the effectiveness of a simple and affordable remedy for improving psychological well-being, based on audio-visual stimuli brought by a short computer video showing forest environments, with an urban video as a control. Randomly selected participants were assigned the forest or urban video, to look at and listen to early in the morning, and questionnaires to fill out. In particular, the State-Trait Anxiety Inventory (STAI) Form Y collected in baseline condition and at the end of the study and the Part II of the Sheehan Patient Rated Anxiety Scale (SPRAS) collected every day immediately before and after watching the video. The virtual exposure to forest environments showed effective to reduce perceived anxiety levels in people forced by lockdown in limited spaces and environmental deprivation. Although significant, the effects were observed only in the short term, highlighting the limitation of the virtual experiences. The reported effects might also represent a benchmark to disentangle the determinants of health effects due to real forest experiences, for example, the inhalation of biogenic volatile organic compounds (BVOC).


Assuntos
Infecções por Coronavirus/psicologia , Florestas , Saúde Mental/estatística & dados numéricos , Pandemias , Quarentena/psicologia , Estresse Psicológico/psicologia , Adulto , Idoso , Ansiedade/epidemiologia , Benchmarking , Betacoronavirus , Infecções por Coronavirus/epidemiologia , Feminino , Humanos , Pessoa de Meia-Idade , Pneumonia Viral/epidemiologia , Pneumonia Viral/psicologia , Estresse Fisiológico , Estresse Psicológico/epidemiologia , Gravação em Vídeo
6.
BMC Health Serv Res ; 20(1): 998, 2020 Oct 31.
Artigo em Inglês | MEDLINE | ID: mdl-33129362

RESUMO

BACKGROUND: Between-center variation in outcome may offer opportunities to identify variation in quality of care. By intervening on these quality differences, patient outcomes may be improved. However, whether observed differences in outcome reflect the true quality improvement potential is not known for many diseases. Therefore, we aimed to analyze the effect of differences in performance on structure and processes of care, and case-mix on between-center differences in outcome after endovascular treatment (EVT) for ischemic stroke. METHODS: In this observational cohort study, ischemic stroke patients who received EVT between 2014 and 2017 in all 17 Dutch EVT-centers were included. Primary outcome was the modified Rankin Scale, ranging from 0 (no symptoms) to 6 (death), at 90 days. We used random effect proportional odds regression modelling, to analyze the effect of differences in structure indicators (center volume and year of admission), process indicators (time to treatment and use of general anesthesia) and case-mix, by tracking changes in tau2, which represents the amount of between-center variation in outcome. RESULTS: Three thousand two hundred seventy-nine patients were included. Performance on structure and process indicators varied significantly between EVT-centers (P < 0.001). Predicted probability of good functional outcome (modified Rankin Scale 0-2 at 90 days), which can be interpreted as an overall measure of a center's case-mix, varied significantly between 17 and 50% across centers. The amount of between-center variation (tau2) was estimated at 0.040 in a model only accounting for random variation. This estimate more than doubled after adding case-mix variables (tau2: 0.086) to the model, while a small amount of between-center variation was explained by variation in performance on structure and process indicators (tau2: 0.081 and 0.089, respectively). This indicates that variation in case-mix affects the differences in outcome to a much larger extent. CONCLUSIONS: Between-center variation in outcome of ischemic stroke patients mostly reflects differences in case-mix, rather than differences in structure or process of care. Since the latter two capture the real quality improvement potential, these should be used as indicators for comparing center performance. Especially when a strong association exists between those indicators and outcome, as is the case for time to treatment in ischemic stroke.


Assuntos
Benchmarking , Melhoria de Qualidade , Acidente Vascular Cerebral/terapia , Idoso , Idoso de 80 Anos ou mais , Estudos de Coortes , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Resultado do Tratamento
7.
J Rehabil Med ; 52(10): jrm00113, 2020 Oct 16.
Artigo em Inglês | MEDLINE | ID: mdl-33000174

RESUMO

OBJECTIVE: To evaluate the effects of introducing the practice of targeting a discharge date for patients admitted to an inpatient stroke rehabilitation unit on process and patient outcomes. DESIGN: Comparison of retrospective (control group n = 69) and prospective (experimental group n = 60) patients. METHODS: Rehabilitation professionals assessed both groups at admission and discharge using a standard-ized assessment toolkit. Benchmarks for length of rehabilitation stay (LoRS) were introduced based on median severity-specific LoRSs in the control group. The multidisciplinary team documented facilitators and obstacles affecting the prediction of patient benchmark attainment. Categorical variables were compared using a χ2 test with exact probabilities. Ordinal and continuous variables were analysed using rank-based non-parametric analysis of variance. Effect sizes were estimated using a relative treatment effect statistic. RESULTS: The mean combined length of stay in acute care and rehabilitation beds for the experimental group (82 days) was shorter (p = 0.0084) than that of the control group (103 days). This 21-day reduction in combined length of stay included a 10-day reduction in the mean time between stroke onset and admission to the stroke rehabilitation unit (p = 0.000014). Improvements in 6 func-tional and sensorimotor outcomes with rehabilitation were of similar magnitude in both groups, while Functional Independence Measure (FIMTM) efficiency improved (p = 0.022). The team was 87% successful in predicting which patients were discharged on the LoRS benchmark. CONCLUSION: Benchmarking the length of stay in rehabilitation resulted in reduced bed occupation and system costs without adversely affecting functional and sensorimotor patient outcomes.


Assuntos
Benchmarking/métodos , Tempo de Internação/estatística & dados numéricos , Reabilitação do Acidente Vascular Cerebral/métodos , Feminino , Humanos , Pacientes Internados , Masculino , Estudos Prospectivos , Estudos Retrospectivos
8.
PLoS One ; 15(10): e0236384, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33108404

RESUMO

Neurofilaments are structural components of neurons and are particularly abundant in highly myelinated axons. The levels of neurofilament light chain (NfL) in both cerebrospinal fluid (CSF) and plasma have been related to degeneration in several neurodegenerative conditions including frontotemporal dementia (FTD) and NfL is currently considered as the most promising diagnostic and prognostic fluid biomarker in FTD. Although the location and function of filaments in the healthy nervous system suggests a link between increased NfL and white matter degeneration, such a claim has not been fully elucidated in vivo, especially in the context of FTD. The present study provides evidence of an association between the plasma levels of NfL and white matter involvement in behavioral variant FTD (bvFTD) by relating plasma concentration of NfL to diffusion tensor imaging (DTI) metrics in a group of 20 bvFTD patients. The results of both voxel-wise and tract specific analysis showed that increased plasma NfL concentration is associated with a reduction in fractional anisotropy (FA) in a widespread set of white matter tracts including the superior longitudinal fasciculus, the fronto-occipital fasciculus the anterior thalamic radiation and the dorsal cingulum bundle. Plasma NfL concentration also correlated with cortical thinning in a portion of the right medial prefrontal cortex and of the right lateral orbitofrontal cortex. These results support the hypothesis that blood NfL levels reflect the global level of neurodegeneration in bvFTD and help to advance our understanding of the association between this blood biomarker for FTD and the disease process.


Assuntos
Benchmarking , Biomarcadores/sangue , Imagem de Tensor de Difusão/métodos , Demência Frontotemporal/patologia , Proteínas de Neurofilamentos/sangue , Idoso , Feminino , Demência Frontotemporal/sangue , Demência Frontotemporal/diagnóstico por imagem , Humanos , Estudos Longitudinais , Masculino
9.
Surg Clin North Am ; 100(6): 1021-1047, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33128878

RESUMO

Quality improvement is a dynamic process that requires continuously monitoring quality indicators and benchmarking these with national and professional standards. Endoscopists have formed societal task forces to propose quality indicators and performance goals. Institutions are now incentivized by payers and value-based reimbursement agreements to have processes in place to measure, report, and act on these quality metrics. Nationwide registries, such as the Gastrointestinal Quality Improvement Consortium, are used to report quality data to these merit-based incentive payment systems. Quality improvement processes such as these are instrumental to improve patient safety, health, and satisfaction while decreasing costs and medical errors.


Assuntos
Endoscopia do Sistema Digestório/normas , Guias de Prática Clínica como Assunto/normas , Melhoria de Qualidade , Benchmarking/normas , Competência Clínica , Endoscopia/normas , Endossonografia/normas , Humanos , Segurança do Paciente/normas , Melhoria de Qualidade/normas , Indicadores de Qualidade em Assistência à Saúde/normas
11.
BMC Bioinformatics ; 21(1): 459, 2020 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-33059593

RESUMO

BACKGROUND: High-throughput sequencing can establish the functional capacity of a microbial community by cataloging the protein-coding sequences (CDS) present in the metagenome of the community. The relative performance of different computational methods for identifying CDS from whole-genome shotgun sequencing is not fully established. RESULTS: Here we present an automated benchmarking workflow, using synthetic shotgun sequencing reads for which we know the true CDS content of the underlying communities, to determine the relative performance (sensitivity, positive predictive value or PPV, and computational efficiency) of different metagenome analysis tools for extracting the CDS content of a microbial community. Assembly-based methods are limited by coverage depth, with poor sensitivity for CDS at < 5X depth of sequencing, but have excellent PPV. Mapping-based techniques are more sensitive at low coverage depths, but can struggle with PPV. We additionally describe an expectation maximization based iterative algorithmic approach which we show to successfully improve the PPV of a mapping based technique while retaining improved sensitivity and computational efficiency. CONCLUSION: Our benchmarking approach reveals the trade-offs of assembly versus alignment-based approaches and the relative performance of specific implementations when one wishes to extract the protein coding capacity of microbial communities.


Assuntos
Benchmarking , Simulação por Computador , Metagenoma , Fases de Leitura Aberta/genética , Algoritmos , Humanos , Metagenômica , Microbiota/genética , Valor Preditivo dos Testes
12.
Can J Surg ; 63(5): E435-E441, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33009902

RESUMO

BACKGROUND: Most of the literature on emergency general surgery (EGS) has investigated appendiceal and biliary disease; however, EGS surgeons manage many other complex conditions. This study aimed to describe the operative burden of these conditions throughout Canada. METHODS: This multicentre retrospective cohort study evaluated EGS patients at 7 centres across Canada in 2014. Adult patients (aged ≥ 18 yr) undergoing nonelective operative interventions for nonbiliary, nonappendiceal diseases were included. Data collected included information on patients' demographic characteristics, diagnosis, procedure details, complications and hospital length of stay. Logistic regression was used to identify predictors of morbidity and mortality. RESULTS: A total of 2595 patients were included, with a median age of 60 years (interquartile range 46-73 yr). The most common principal diagnoses were small bowel obstruction (16%), hernia (15%), malignancy (11%) and perianal disease (9%). The most commonly performed procedures were bowel resection (30%), hernia repair (15%), adhesiolysis (11%) and débridement of skin and soft tissue infections (10%). A total of 47% of cases were completed overnight (between 5 pm and 8 am). The overall inhospital mortality rate was 8%. Thirty-three percent of patients had a complication, with independent predictors including increasing age (p = 0.001), increasing American Society of Anesthesiologists score (p = 0.02) and transfer from another centre (p = 0.001). CONCLUSION: This study characterizes the epidemiology of nonbiliary, nonappendiceal EGS operative interventions across Canada. Canadian surgeons are performing a large volume of EGS, and conditions treated by EGS services are associated with a substantial risk of morbidity and mortality. Results of this study will be used to guide future research efforts and set benchmarks for quality improvement.


Assuntos
Tratamento de Emergência/estatística & dados numéricos , Cirurgia Geral/estatística & dados numéricos , Complicações Pós-Operatórias/epidemiologia , Padrões de Prática Médica/estatística & dados numéricos , Procedimentos Cirúrgicos Operatórios/estatística & dados numéricos , Idoso , Benchmarking , Canadá , Serviço Hospitalar de Emergência/organização & administração , Serviço Hospitalar de Emergência/estatística & dados numéricos , Tratamento de Emergência/efeitos adversos , Feminino , Cirurgia Geral/organização & administração , Mortalidade Hospitalar , Humanos , Masculino , Pessoa de Meia-Idade , Complicações Pós-Operatórias/etiologia , Padrões de Prática Médica/organização & administração , Melhoria de Qualidade , Estudos Retrospectivos , Procedimentos Cirúrgicos Operatórios/efeitos adversos , Resultado do Tratamento
13.
Annu Int Conf IEEE Eng Med Biol Soc ; 2020: 5939-5942, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-33019326

RESUMO

Respiratory rate (RR) can be estimated from the photoplethysmogram (PPG) recorded by optical sensors in wearable devices. The fusion of estimates from different PPG features has lead to an increase in accuracy, but also reduced the numbers of available final estimates due to discarding of unreliable data. We propose a novel, tunable fusion algorithm using covariance intersection to estimate the RR from PPG (CIF). The algorithm is adaptive to the number of available feature estimates and takes each estimates' trustworthiness into account. In a benchmarking experiment using the CapnoBase dataset with reference RR from capnography, we compared the CIF against the state-of-the-art Smart Fusion (SF) algorithm. The median root mean square error was 1.4 breaths/min for the CIF and 1.8 breaths/min for the SF. The CIF significantly increased the retention rate distribution of all recordings from 0.46 to 0.90 (p < 0.001). The agreement with the reference RR was high with a Pearson's correlation coefficient of 0.94, a bias of 0.3 breaths/min, and limits of agreement of -4.6 and 5.2 breaths/min. In addition, the algorithm was computationally efficient. Therefore, CIF could contribute to a more robust RR estimation from wearable PPG recordings.


Assuntos
Fotopletismografia , Taxa Respiratória , Algoritmos , Benchmarking , Capnografia
14.
BMJ Glob Health ; 5(10)2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-33033053

RESUMO

Infectious disease outbreaks pose major threats to human health and security. Countries with robust capacities for preventing, detecting and responding to outbreaks can avert many of the social, political, economic and health system costs of such crises. The Global Health Security Index (GHS Index)-the first comprehensive assessment and benchmarking of health security and related capabilities across 195 countries-recently found that no country is sufficiently prepared for epidemics or pandemics. The GHS Index can help health security stakeholders identify areas of weakness, as well as opportunities to collaborate across sectors, collectively strengthen health systems and achieve shared public health goals. Some scholars have recently offered constructive critiques of the GHS Index's approach to scoring and ranking countries; its weighting of select indicators; its emphasis on transparency; its focus on biosecurity and biosafety capacities; and divergence between select country scores and corresponding COVID-19-associated caseloads, morbidity, and mortality. Here, we (1) describe the practical value of the GHS Index; (2) present potential use cases to help policymakers and practitioners maximise the utility of the tool; (3) discuss the importance of scoring and ranking; (4) describe the robust methodology underpinning country scores and ranks; (5) highlight the GHS Index's emphasis on transparency and (6) articulate caveats for users wishing to use GHS Index data in health security research, policymaking and practice.


Assuntos
Saúde Global , Medidas de Segurança/organização & administração , Benchmarking/organização & administração , Betacoronavirus , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/mortalidade , Infecções por Coronavirus/prevenção & controle , Humanos , Liderança , Pandemias/prevenção & controle , Pneumonia Viral/epidemiologia , Pneumonia Viral/mortalidade , Pneumonia Viral/prevenção & controle
15.
BMC Bioinformatics ; 21(1): 445, 2020 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-33028187

RESUMO

BACKGROUND: As a machine learning method with high performance and excellent generalization ability, extreme learning machine (ELM) is gaining popularity in various studies. Various ELM-based methods for different fields have been proposed. However, the robustness to noise and outliers is always the main problem affecting the performance of ELM. RESULTS: In this paper, an integrated method named correntropy induced loss based sparse robust graph regularized extreme learning machine (CSRGELM) is proposed. The introduction of correntropy induced loss improves the robustness of ELM and weakens the negative effects of noise and outliers. By using the L2,1-norm to constrain the output weight matrix, we tend to obtain a sparse output weight matrix to construct a simpler single hidden layer feedforward neural network model. By introducing the graph regularization to preserve the local structural information of the data, the classification performance of the new method is further improved. Besides, we design an iterative optimization method based on the idea of half quadratic optimization to solve the non-convex problem of CSRGELM. CONCLUSIONS: The classification results on the benchmark dataset show that CSRGELM can obtain better classification results compared with other methods. More importantly, we also apply the new method to the classification problems of cancer samples and get a good classification effect.


Assuntos
Aprendizado de Máquina , Neoplasias/classificação , Benchmarking , Biologia Computacional/métodos , Bases de Dados Factuais , Humanos , Neoplasias/patologia
16.
BMC Bioinformatics ; 21(1): 429, 2020 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-33004007

RESUMO

BACKGROUND: PacBio sequencing is an incredibly valuable third-generation DNA sequencing method due to very long read lengths, ability to detect methylated bases, and its real-time sequencing methodology. Yet, hitherto no tool was available for analyzing the quality of, subsampling, and filtering PacBio data. RESULTS: Here we present SequelTools, a command-line program containing three tools: Quality Control, Read Subsampling, and Read Filtering. The Quality Control tool quickly processes PacBio Sequel raw sequence data from multiple SMRTcells producing multiple statistics and publication-quality plots describing the quality of the data including N50, read length and count statistics, PSR, and ZOR. The Read Subsampling tool allows the user to subsample reads by one or more of the following criteria: longest subreads per CLR or random CLR selection. The Read Filtering tool provides options for normalizing data by filtering out certain low-quality scraps reads and/or by minimum CLR length. SequelTools is implemented in bash, R, and Python using only standard libraries and packages and is platform independent. CONCLUSIONS: SequelTools is a program that provides the only free, fast, and easy-to-use quality control tool, and the only program providing this kind of read subsampling and read filtering for PacBio Sequel raw sequence data, and is available at https://github.com/ISUgenomics/SequelTools .


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala/métodos , Software , Arabidopsis/genética , Benchmarking , Sequenciamento de Nucleotídeos em Larga Escala/normas , Controle de Qualidade
17.
Artigo em Inglês | MEDLINE | ID: mdl-33017923

RESUMO

This study had two main objectives: (i) to study the effects of volume conduction on different connectivity metrics (Amplitude Envelope Correlation AEC, Phase Lag Index PLI, and Magnitude Squared Coherence MSCOH), comparing the coupling patterns at electrode- and sensor-level; and (ii) to characterize spontaneous EEG activity during different stages of Alzheimer's disease (AD) continuum by means of three complementary network parameters: node degree (k), characteristic path length (L), and clustering coefficient (C). Our results revealed that PLI and AEC are weakly influenced by volume conduction compared to MSCOH, but they are not immune to it. Furthermore, network parameters obtained from PLI showed that AD continuum is characterized by an increase in L and C in low frequency bands, suggesting lower integration and higher segregation as the disease progresses. These network changes reflect the abnormalities during AD continuum and are mainly due to neuronal alterations, because PLI is slightly affected by volume conduction effects.


Assuntos
Doença de Alzheimer , Benchmarking , Encéfalo , Eletroencefalografia , Humanos , Rede Nervosa
18.
Annu Int Conf IEEE Eng Med Biol Soc ; 2020: 1132-1135, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-33018186

RESUMO

CAD systems have shown good potential for improving breast cancer diagnosis and anomaly detection in mammograms. A basic enabling step for the utilization of CAD systems in mammographic analysis is the correct identification of the breast region. Therefore, several methods to segment the pectoral muscle in the medio-lateral oblique (MLO) mammographic view have been proposed in the literature. However, currently it is difficult to perform and objective comparison between different chest wall (CW) detection methods since they are often evaluated with different evaluation procedures, datasets and the implementations of the methods are not publicly available. For this reason, we propose a methodology to evaluate and compare the performance of CW detection methods using a publicly available dataset (INbreast). We also propose a new intensity-based method for automatic CW detection. We then utilize the proposed evaluation methodology to compare the performance of our CW detection algorithm with a state-of-the-art CW detection method. The performance was measured in terms of the Dice's coefficient similarity, the area error and mean contour distance. The proposed method achieves yielded the best results in all the performance measures.


Assuntos
Parede Torácica , Benchmarking , Humanos , Mamografia , Reconhecimento Automatizado de Padrão , Interpretação de Imagem Radiográfica Assistida por Computador , Parede Torácica/diagnóstico por imagem
19.
Annu Int Conf IEEE Eng Med Biol Soc ; 2020: 3339-3342, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-33018719

RESUMO

In recent years, many electromyography (EMG) benchmark databases have been made publicly available to the myoelectric control research community. Many small laboratories that lack the instrumentation, access, and experience needed to collect quality EMG data have used these benchmark datasets to explore and propose new signal processing and pattern recognition algorithms. It is widely accepted that noise contamination can affect the performance of myoelectric control systems, and so useful datasets should maintain good signal quality to ensure accurate results for proposed EMG-based gesture recognition systems. Despite the availability and adoption of benchmarks datasets, however, the quality of the EMG signals in these benchmarks has not yet been examined. In this study, the signal quality of the Non-Invasive Adaptive Prosthetics (NinaPro) dataset, the most widely known publicly available benchmark database to date, was comprehensively investigated with the goals of: 1) reporting the level of noise contamination in each NinaPro sub-dataset, 2) proposing signal quality criteria for assessing EMG datasets, 3) analyzing the effect of signal quality on classification performance, and 4) examining the quality of the data labels.


Assuntos
Benchmarking , Gestos , Bases de Dados Factuais , Eletromiografia , Processamento de Sinais Assistido por Computador
20.
Environ Monit Assess ; 192(11): 695, 2020 Oct 11.
Artigo em Inglês | MEDLINE | ID: mdl-33040184

RESUMO

In the present paper, land use/land cover (LULC) change was predicted in the Greater Isfahan area (GIA), central Iran. The GIA has been growing rapidly in recent years, and attempts to simulate its spatial expansion would be essential to make appropriate decisions in LULC management plans and achieve sustainable development. Several modeling tools were employed to outline sustainable scenarios for future dynamics of LULCs in the region. Specifically, we explored past LULC changes in the study area from 1996 to 2018 and predicted its future changes for 2030 and 2050. For this purpose, we performed object-oriented and decision tree techniques on Landsat and Sentinel-2 satellite images. The CA-Markov hybrid model was utilized to analyze past trends and predict future LULC changes. LULC changes were quantitatively measured using landscape metrics. According to the results, the majority of changes were related to increasing residential areas and decreasing irrigated lands. The results indicated that residential lands would grow from 27,886.87 ha to 67,093.62 ha over1996-2050 while irrigated lands decrease from 99,799.4 ha to 50,082.16 ha during the same period of time. The confusion matrix of the 2018 LULC map was built using a total of 525 ground truth points and yielded a Kappa coefficient and overall accuracy of 78% and 82%, respectively. Moreover, the confusion matrix constructed base on the Sentinel-2 map, as a reference, to judge the predicted 2018 LULC map with a Kappa coefficient of 88%. The results of this study provide useful insights for sustainable land management. The results of this research also proved the promising capability of remote sensing algorithms, CA-Markov model and landscape metrics future LULC planning in the study area.


Assuntos
Conservação dos Recursos Naturais , Tecnologia de Sensoriamento Remoto , Benchmarking , Monitoramento Ambiental , Irã (Geográfico)
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