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1.
Pharmacoepidemiol Drug Saf ; 31(9): 944-952, 2022 09.
Artigo em Inglês | MEDLINE | ID: mdl-35689299

RESUMO

With availability of voluminous sets of observational data, an empirical paradigm to screen for drug repurposing opportunities (i.e., beneficial effects of drugs on nonindicated outcomes) is feasible. In this article, we use a linked claims and electronic health record database to comprehensively explore repurposing effects of antihypertensive drugs. We follow a target trial emulation framework for causal inference to emulate randomized controlled trials estimating confounding adjusted effects of antihypertensives on each of 262 outcomes of interest. We then fit hierarchical models to the results as a form of postprocessing to account for multiple comparisons and to sift through the results in a principled way. Our motivation is twofold. We seek both to surface genuinely intriguing drug repurposing opportunities and to elucidate through a real application some study design decisions and potential biases that arise in this context.


Assuntos
Anti-Hipertensivos , Reposicionamento de Medicamentos , Anti-Hipertensivos/farmacologia , Anti-Hipertensivos/uso terapêutico , Causalidade , Bases de Dados Factuais , Registros Eletrônicos de Saúde , Humanos , Ensaios Clínicos Controlados Aleatórios como Assunto
2.
Nano Lett ; 21(19): 8160-8165, 2021 10 13.
Artigo em Inglês | MEDLINE | ID: mdl-34543039

RESUMO

Airborne particular matter (PM) pollution is an increasing global issue and alternative sources of filter fibers are now an area of significant focus. Compared with relatively mature hazardous gas treatments, state of the art high-efficiency PM filters still lack thermal decomposition ability for organic PM pollutants, such as soot from coal-fired power plants and waste-combustion incinerators, resulting in frequent replacement, high cost, and second-hand pollution. In this manuscript, we propose a bottom-up synthesis method to make the first all-thermal-catalyst air filter (ATCAF). Self-assembled from ∼50 nm diameter TiO2 fibers, ATCAF could not only capture the combustion-generated PM pollutants with >99.999% efficiency but also catalyze the complete decomposition of the as-captured hydrocarbon pollutants at high temperature. It has the potential of in situ eliminating the PM pollutants from burning of hydrocarbon materials leveraging the burning heat.


Assuntos
Poluentes Atmosféricos , Poluentes Atmosféricos/análise , Catálise , Temperatura Alta , Centrais Elétricas
3.
Bioinformatics ; 36(9): 2813-2820, 2020 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-31971581

RESUMO

MOTIVATION: Gradual population-level changes in tissues can be driven by stochastic plasticity, meaning rare stochastic transitions of single-cell phenotype. Quantifying the rates of these stochastic transitions requires time-intensive experiments, and analysis is generally confounded by simultaneous bidirectional transitions and asymmetric proliferation kinetics. To quantify cellular plasticity, we developed Transcompp (Transition Rate ANalysis of Single Cells to Observe and Measure Phenotypic Plasticity), a Markov modeling algorithm that uses optimization and resampling to compute best-fit rates and statistical intervals for stochastic cell-state transitions. RESULTS: We applied Transcompp to time-series datasets in which purified subpopulations of stem-like or non-stem cancer cells were exposed to various cell culture environments, and allowed to re-equilibrate spontaneously over time. Results revealed that commonly used cell culture reagents hydrocortisone and cholera toxin shifted the cell population equilibrium toward stem-like or non-stem states, respectively, in the basal-like breast cancer cell line MCF10CA1a. In addition, applying Transcompp to patient-derived cells showed that transition rates computed from short-term experiments could predict long-term trajectories and equilibrium convergence of the cultured cell population. AVAILABILITY AND IMPLEMENTATION: Freely available for download at http://github.com/nsuhasj/Transcompp. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Algoritmos , Neoplasias da Mama , Adaptação Fisiológica , Células Cultivadas , Humanos
4.
Sensors (Basel) ; 21(23)2021 Nov 25.
Artigo em Inglês | MEDLINE | ID: mdl-34883854

RESUMO

It is found that nodes in Delay Tolerant Networks (DTN) exhibit stable social attributes similar to those of people. In this paper, an adaptive routing algorithm based on Relation Tree (AR-RT) for DTN is proposed. Each node constructs its own Relation Tree based on the historical encounter frequency, and will adopt different forwarding strategies based on the Relation Tree in the forwarding phase, so as to achieve more targeted forwarding. To further improve the scalability of the algorithm, the source node dynamically controls the initial maximum number of message copies according to its own cache occupancy, which enables the node to make negative feedback to network environment changes. Simulation results show that the AR-RT algorithm proposed in this paper has significant advantages over existing routing algorithms in terms of average delay, average hop count, and message delivery rate.


Assuntos
Algoritmos , Simulação por Computador , Humanos
5.
Gastric Cancer ; 19(2): 453-465, 2016 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-26205786

RESUMO

BACKGROUND: Gastric cancer, a leading cause of cancer death worldwide, has been little studied compared with other cancers that impose similar health burdens. Our goal is to assess genomic copy-number loss and the possible functional consequences and therapeutic implications thereof across a large series of gastric adenocarcinomas. METHODS: We used high-density single-nucleotide polymorphism microarrays to determine patterns of copy-number loss and allelic imbalance in 74 gastric adenocarcinomas. We investigated whether suppressor of tumorigenesis and/or proliferation (STOP) genes are associated with genomic copy-number loss. We also analyzed the extent to which copy-number loss affects Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS (CYCLOPS) genes-genes that may be attractive targets for therapeutic inhibition when partially deleted. RESULTS: The proportion of the genome subject to copy-number loss varies considerably from tumor to tumor, with a median of 5.5 %, and a mean of 12 % (range 0-58.5 %). On average, 91 STOP genes were subject to copy-number loss per tumor (median 35, range 0-452), and STOP genes tended to have lower copy-number compared with the rest of the genes. Furthermore, on average, 1.6 CYCLOPS genes per tumor were both subject to copy-number loss and downregulated, and 51.4 % of the tumors had at least one such gene. CONCLUSIONS: The enrichment of STOP genes in regions of copy-number loss indicates that their deletion may contribute to gastric carcinogenesis. Furthermore, the presence of several deleted and downregulated CYCLOPS genes in some tumors suggests potential therapeutic targets in these tumors.


Assuntos
Adenocarcinoma/genética , Dosagem de Genes , Regulação Neoplásica da Expressão Gênica , Neoplasias Gástricas/genética , Adenocarcinoma/mortalidade , Adenocarcinoma/patologia , Proliferação de Células , Genes Supressores de Tumor , Humanos , Perda de Heterozigosidade , Polimorfismo de Nucleotídeo Único , Neoplasias Gástricas/mortalidade , Neoplasias Gástricas/patologia
6.
J Hepatol ; 61(2): 260-269, 2014 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-24583249

RESUMO

BACKGROUND & AIMS: There is increasing need for accurate assessment of liver fibrosis/cirrhosis. We aimed to develop qFibrosis, a fully-automated assessment method combining quantification of histopathological architectural features, to address unmet needs in core biopsy evaluation of fibrosis in chronic hepatitis B (CHB) patients. METHODS: qFibrosis was established as a combined index based on 87 parameters of architectural features. Images acquired from 25 Thioacetamide-treated rat samples and 162 CHB core biopsies were used to train and test qFibrosis and to demonstrate its reproducibility. qFibrosis scoring was analyzed employing Metavir and Ishak fibrosis staging as standard references, and collagen proportionate area (CPA) measurement for comparison. RESULTS: qFibrosis faithfully and reliably recapitulates Metavir fibrosis scores, as it can identify differences between all stages in both animal samples (p<0.001) and human biopsies (p<0.05). It is robust to sampling size, allowing for discrimination of different stages in samples of different sizes (area under the curve (AUC): 0.93-0.99 for animal samples: 1-16 mm(2); AUC: 0.84-0.97 for biopsies: 10-44 mm in length). qFibrosis can significantly predict staging underestimation in suboptimal biopsies (<15 mm) and under- and over-scoring by different pathologists (p<0.001). qFibrosis can also differentiate between Ishak stages 5 and 6 (AUC: 0.73, p=0.008), suggesting the possibility of monitoring intra-stage cirrhosis changes. Best of all, qFibrosis demonstrates superior performance to CPA on all counts. CONCLUSIONS: qFibrosis can improve fibrosis scoring accuracy and throughput, thus allowing for reproducible and reliable analysis of efficacies of anti-fibrotic therapies in clinical research and practice.


Assuntos
Hepatite B Crônica/complicações , Cirrose Hepática Experimental/diagnóstico , Animais , Biópsia , Colágeno/análise , Modelos Animais de Doenças , Humanos , Fígado/patologia , Cirrose Hepática Experimental/patologia , Ratos
7.
Genomics ; 101(2): 101-12, 2013 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-23195410

RESUMO

We developed a model of influenza virus infection of neutrophils by inducing differentiation of the MPRO promyelocytic cell line. After 5 days of differentiation, about 20-30% of mature neutrophils could be detected. Only a fraction of neutrophils were infected by highly virulent influenza (HVI) virus, but were unable to support active viral replication compared with MDCK cells. HVI infection of neutrophils augmented early and late apoptosis as indicated by annexin V and TUNEL assays. Comparison between the global transcriptomic responses of neutrophils to HVI and low virulent influenza (LVI) revealed that the IFN regulatory factor and IFN signaling pathways were the most significantly overrepresented pathways, with activation of related genes in HVI as early as 3 h. Relatively consistent results were obtained by real-time RT-PCR of selected genes associated with the type I IFN pathway. Early after HVI infection, comparatively enhanced expression of apoptosis-related genes was also elicited.


Assuntos
Apoptose , Influenza Humana/imunologia , Interferon Tipo I/imunologia , Neutrófilos/virologia , Transdução de Sinais , Animais , Linhagem Celular , Cães , Humanos , Vírus da Influenza A Subtipo H3N2/fisiologia , Células Madin Darby de Rim Canino , Neutrófilos/citologia , Transcriptoma , Replicação Viral
8.
J Big Data ; 10(1): 92, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37303479

RESUMO

Nitrogen Dioxide (NO2) is a common air pollutant associated with several adverse health problems such as pediatric asthma, cardiovascular mortality,and respiratory mortality. Due to the urgent society's need to reduce pollutant concentration, several scientific efforts have been allocated to understand pollutant patterns and predict pollutants' future concentrations using machine learning and deep learning techniques. The latter techniques have recently gained much attention due it's capability to tackle complex and challenging problems in computer vision, natural language processing, etc. In the NO2 context, there is still a research gap in adopting those advanced methods to predict the concentration of pollutants. This study fills in the gap by comparing the performance of several state-of-the-art artificial intelligence models that haven't been adopted in this context yet. The models were trained using time series cross-validation on a rolling base and tested across different periods using NO2 data from 20 monitoring ground-based stations collected by Environment Agency- Abu Dhabi, United Arab Emirates. Using the seasonal Mann-Kendall trend test and Sen's slope estimator, we further explored and investigated the pollutants trends across the different stations. This study is the first comprehensive study that reported the temporal characteristic of NO2 across seven environmental assessment points and compared the performance of the state-of-the-art deep learning models for predicting the pollutants' future concentration. Our results reveal a difference in the pollutants concentrations level due to the geographic location of the different stations, with a statistically significant decrease in the NO2 annual trend for the majority of the stations. Overall, NO2 concentrations exhibit a similar daily and weekly pattern across the different stations, with an increase in the pollutants level during the early morning and the first working day. Comparing the state-of-the-art model performance transformer model demonstrate the superiority of ( MAE:0.04 (± 0.04),MSE:0.06 (± 0.04), RMSE:0.001 (± 0.01), R2: 0.98 (± 0.05)), compared with LSTM (MAE:0.26 (± 0.19), MSE:0.31 (± 0.21), RMSE:0.14 (± 0.17), R2: 0.56 (± 0.33)), InceptionTime (MAE: 0.19 (± 0.18), MSE: 0.22 (± 0.18), RMSE:0.08 (± 0.13), R2:0.38 (± 1.35) ), ResNet (MAE:0.24 (± 0.16), MSE:0.28 (± 0.16), RMSE:0.11 (± 0.12), R2:0.35 (± 1.19) ), XceptionTime (MAE:0.7 (± 0.55), MSE:0.79 (± 0.54), RMSE:0.91 (± 1.06), R2: -4.83 (± 9.38) ), and MiniRocket (MAE:0.21 (± 0.07), MSE:0.26 (± 0.08), RMSE:0.07 (± 0.04), R2: 0.65 (± 0.28) ) to tackle this challenge. The transformer model is a powerful model for improving the accurate forecast of the NO2 levels and could strengthen the current monitoring system to control and manage the air quality in the region. Supplementary Information: The online version contains supplementary material available at 10.1186/s40537-023-00754-z.

9.
Funct Integr Genomics ; 12(1): 105-17, 2012 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-21874528

RESUMO

Investigating the relationships between critical influenza viral mutations contributing to increased virulence and host expression factors will shed light on the process of severe pathogenesis from the systems biology perspective. We previously generated a mouse-adapted, highly virulent influenza (HVI) virus through serial lung-to-lung passaging of a human influenza H3N2 virus strain that causes low virulent influenza (LVI) in murine lungs. This HVI virus is characterized by enhanced replication kinetics, severe lung injury, and systemic spread to major organs. Our gene microarray investigations compared the host transcriptomic responses of murine lungs to LVI virus and its HVI descendant at 12, 48, and 96 h following infection. More intense expression of genes associated with cytokine activity, type 1 interferon response, and apoptosis was evident in HVI at all time-points. We highlighted dysregulation of the TREM1 signaling pathway (an amplifier of cytokine production) that is likely to be upregulated in infiltrating neutrophils in HVI-infected lungs. The cytokine gene expression changes were corroborated by elevated levels of multiple cytokine and chemokine proteins in the bronchoalveolar lavage fluid of infected mice, especially at 12 h post-infection. Concomitantly, the downregulation of genes that mediate proliferative, developmental, and metabolic processes likely contributed to the lethality of HVI as well as lack of lung repair. Overall, our comparative transcriptomic study provided insights into key host factors that influence the dynamics, pathogenesis, and outcome of severe influenza.


Assuntos
Citocinas/metabolismo , Vírus da Influenza A Subtipo H3N2/patogenicidade , Pulmão/metabolismo , Glicoproteínas de Membrana/metabolismo , Infecções por Orthomyxoviridae/metabolismo , Receptores Imunológicos/metabolismo , Transcriptoma , Animais , Proteínas Reguladoras de Apoptose/genética , Proteínas Reguladoras de Apoptose/metabolismo , Líquido da Lavagem Broncoalveolar , Quimiocinas/genética , Quimiocinas/metabolismo , Citocinas/genética , Feminino , Perfilação da Expressão Gênica , Redes Reguladoras de Genes , Interações Hospedeiro-Patógeno , Vírus da Influenza A Subtipo H3N2/genética , Vírus da Influenza A Subtipo H3N2/fisiologia , Pulmão/imunologia , Pulmão/patologia , Pulmão/virologia , Glicoproteínas de Membrana/genética , Camundongos , Camundongos Endogâmicos BALB C , Infecções por Orthomyxoviridae/genética , Infecções por Orthomyxoviridae/imunologia , Infecções por Orthomyxoviridae/virologia , Receptores Imunológicos/genética , Transdução de Sinais , Biologia de Sistemas , Receptor Gatilho 1 Expresso em Células Mieloides , Virulência/genética
10.
PLoS Comput Biol ; 7(7): e1002119, 2011 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-21799663

RESUMO

Advances in proteomic technologies continue to substantially accelerate capability for generating experimental data on protein levels, states, and activities in biological samples. For example, studies on receptor tyrosine kinase signaling networks can now capture the phosphorylation state of hundreds to thousands of proteins across multiple conditions. However, little is known about the function of many of these protein modifications, or the enzymes responsible for modifying them. To address this challenge, we have developed an approach that enhances the power of clustering techniques to infer functional and regulatory meaning of protein states in cell signaling networks. We have created a new computational framework for applying clustering to biological data in order to overcome the typical dependence on specific a priori assumptions and expert knowledge concerning the technical aspects of clustering. Multiple clustering analysis methodology ('MCAM') employs an array of diverse data transformations, distance metrics, set sizes, and clustering algorithms, in a combinatorial fashion, to create a suite of clustering sets. These sets are then evaluated based on their ability to produce biological insights through statistical enrichment of metadata relating to knowledge concerning protein functions, kinase substrates, and sequence motifs. We applied MCAM to a set of dynamic phosphorylation measurements of the ERRB network to explore the relationships between algorithmic parameters and the biological meaning that could be inferred and report on interesting biological predictions. Further, we applied MCAM to multiple phosphoproteomic datasets for the ERBB network, which allowed us to compare independent and incomplete overlapping measurements of phosphorylation sites in the network. We report specific and global differences of the ERBB network stimulated with different ligands and with changes in HER2 expression. Overall, we offer MCAM as a broadly-applicable approach for analysis of proteomic data which may help increase the current understanding of molecular networks in a variety of biological problems.


Assuntos
Análise por Conglomerados , Bases de Dados de Proteínas , Proteômica/métodos , Algoritmos , Humanos , Modelos Biológicos
11.
Mol Cell Proteomics ; 9(11): 2558-70, 2010 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-20631208

RESUMO

The rate of discovery of post-translational modification (PTM) sites is increasing rapidly and is significantly outpacing our biological understanding of the function and regulation of those modifications. To help meet this challenge, we have created PTMScout, a web-based interface for viewing, manipulating, and analyzing high throughput experimental measurements of PTMs in an effort to facilitate biological understanding of protein modifications in signaling networks. PTMScout is constructed around a custom database of PTM experiments and contains information from external protein and post-translational resources, including gene ontology annotations, Pfam domains, and Scansite predictions of kinase and phosphopeptide binding domain interactions. PTMScout functionality comprises data set comparison tools, data set summary views, and tools for protein assignments of peptides identified by mass spectrometry. Analysis tools in PTMScout focus on informed subset selection via common criteria and on automated hypothesis generation through subset labeling derived from identification of statistically significant enrichment of other annotations in the experiment. Subset selection can be applied through the PTMScout flexible query interface available for quantitative data measurements and data annotations as well as an interface for importing data set groupings by external means, such as unsupervised learning. We exemplify the various functions of PTMScout in application to data sets that contain relative quantitative measurements as well as data sets lacking quantitative measurements, producing a set of interesting biological hypotheses. PTMScout is designed to be a widely accessible tool, enabling generation of multiple types of biological hypotheses from high throughput PTM experiments and advancing functional assignment of novel PTM sites. PTMScout is available at http://ptmscout.mit.edu.


Assuntos
Ensaios de Triagem em Larga Escala , Internet , Processamento de Proteína Pós-Traducional , Proteômica/métodos , Software , Sequência de Aminoácidos , Bases de Dados de Proteínas , Dados de Sequência Molecular , Proteínas/química , Proteínas/genética
12.
Artigo em Inglês | MEDLINE | ID: mdl-35270766

RESUMO

The first wave of COVID-19 in China began in December 2019. The outbreak was quickly and effectively controlled through strict infection prevention and control with multipronged measures. By the end of March 2020, the outbreak had basically ended. Therefore, there are relatively complete and effective infection prevention and control (IPC) processes in China to curb virus transmission. Furthermore, there were two large-scale updates for the daily reports by the National Health Commission of the People's Republic of China in the early stage of the pandemic. We retrospectively studied the transmission characteristics and IPC of COVID-19 in China. Additionally, we analyzed and modeled the data in the two revisions. We found that most cases were limited to Hubei Province, especially in Wuhan, and the mortality rate was lower in non-Wuhan areas. We studied the two revisions and utilized the proposed transmission model to revise the daily confirmed cases at the beginning of the pandemic in Wuhan. Moreover, we estimated the cases and deaths for the same stage and analyzed the effect of IPC in China. The results show that strong and effective IPC with strict implementation was able to effectively and quickly control the pandemic.


Assuntos
COVID-19 , Pandemias , COVID-19/epidemiologia , China/epidemiologia , Humanos , Pandemias/prevenção & controle , Estudos Retrospectivos , SARS-CoV-2
13.
Diagnostics (Basel) ; 12(11)2022 Oct 26.
Artigo em Inglês | MEDLINE | ID: mdl-36359435

RESUMO

Cerebral stroke (CS) is a heterogeneous syndrome caused by multiple disease mechanisms. Ischemic stroke (IS) is a subtype of CS that causes a disruption of cerebral blood flow with subsequent tissue damage. Noncontrast computer tomography (NCCT) is one of the most important IS detection methods. It is difficult to select the features of IS CT within computational image analysis. In this paper, we propose AC-YOLOv5, which is an improved detection algorithm for IS. The algorithm amplifies the features of IS via an NCCT image based on adaptive local region contrast enhancement, which then detects the region of interest via YOLOv5, which is one of the best detection algorithms at present. The proposed algorithm was tested on two datasets, and seven control group experiments were added, including popular detection algorithms at present and other detection algorithms based on image enhancement. The experimental results show that the proposed algorithm has a high accuracy (94.1% and 91.7%) and recall (85.3% and 88.6%) rate; the recall result is especially notable. This proves the excellent performance of the accuracy, robustness, and generalizability of the algorithm.

14.
Nat Commun ; 13(1): 7652, 2022 Dec 10.
Artigo em Inglês | MEDLINE | ID: mdl-36496454

RESUMO

Metformin, a diabetes drug with anti-aging cellular responses, has complex actions that may alter dementia onset. Mixed results are emerging from prior observational studies. To address this complexity, we deploy a causal inference approach accounting for the competing risk of death in emulated clinical trials using two distinct electronic health record systems. In intention-to-treat analyses, metformin use associates with lower hazard of all-cause mortality and lower cause-specific hazard of dementia onset, after accounting for prolonged survival, relative to sulfonylureas. In parallel systems pharmacology studies, the expression of two AD-related proteins, APOE and SPP1, was suppressed by pharmacologic concentrations of metformin in differentiated human neural cells, relative to a sulfonylurea. Together, our findings suggest that metformin might reduce the risk of dementia in diabetes patients through mechanisms beyond glycemic control, and that SPP1 is a candidate biomarker for metformin's action in the brain.


Assuntos
Demência , Diabetes Mellitus Tipo 2 , Metformina , Humanos , Metformina/farmacologia , Metformina/uso terapêutico , Reposicionamento de Medicamentos , Farmacologia em Rede , Diabetes Mellitus Tipo 2/tratamento farmacológico , Diabetes Mellitus Tipo 2/complicações , Compostos de Sulfonilureia , Hipoglicemiantes/farmacologia , Hipoglicemiantes/uso terapêutico , Demência/tratamento farmacológico , Demência/etiologia , Prontuários Médicos
15.
BMC Bioinformatics ; 12 Suppl 13: S19, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-22372978

RESUMO

BACKGROUND: Essential events of cell development and homeostasis are revealed by the associated changes of cell morphology and therefore have been widely used as a key indicator of physiological states and molecular pathways affecting various cellular functions via cytoskeleton. Cell motility is a complex phenomenon primarily driven by the actin network, which plays an important role in shaping the morphology of the cells. Most of the morphology based features are approximated from cell periphery but its dynamics have received none to scant attention. We aim to bridge the gap between membrane dynamics and cell states from the perspective of whole cell movement by identifying cell edge patterns and its correlation with cell dynamics. RESULTS: We present a systematic study to extract, classify, and compare cell dynamics in terms of cell motility and edge activity. Cell motility features extracted by fitting a persistent random walk were used to identify the initial set of cell subpopulations. We propose algorithms to extract edge features along the entire cell periphery such as protrusion and retraction velocity. These constitute a unique set of multivariate time-lapse edge features that are then used to profile subclasses of cell dynamics by unsupervised clustering. CONCLUSIONS: By comparing membrane dynamic patterns exhibited by each subclass of cells, correlated trends of edge and cell movements were identified. Our findings are consistent with published literature and we also identified that motility patterns are influenced by edge features from initial time points compared to later sampling intervals.


Assuntos
Membrana Celular/metabolismo , Movimento Celular , Actinas/metabolismo , Actinas/fisiologia , Animais , Linhagem Celular , Citoesqueleto/metabolismo , Macrófagos/citologia , Macrófagos/metabolismo , Camundongos , Microtúbulos/metabolismo
16.
AMIA Annu Symp Proc ; 2021: 334-342, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-35308969

RESUMO

The central task of causal inference is to remove (via statistical adjustment) confounding bias that would be present in naive unadjusted comparisons of outcomes in different treatment groups. Statistical adjustment can roughly be broken down into two steps. In the first step, the researcher selects some set of variables to adjust for. In the second step, the researcher implements a causal inference algorithm to adjust for the selected variables and estimate the average treatment effect. In this paper, we use a simulation study to explore the operating characteristics and robustness of state-of-the-art methods for step two (statistical adjustment for selected variables) when step one (variable selection) is performed in a realistically sub-optimal manner. More specifically, we study the robustness of a cross-fit machine learning based causal effect estimator to the presence of extraneous variables in the adjustment set. The take-away for practitioners is that there is value to, if possible, identifying a small sufficient adjustment set using subject matter knowledge even when using machine learning methods for adjustment.


Assuntos
Modelos Estatísticos , Viés , Causalidade , Simulação por Computador , Humanos
17.
Neuroimage Clin ; 25: 102186, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32000101

RESUMO

Functional modules in the human brain support its drive for specialization whereas brain hubs act as focal points for information integration. Brain hubs are brain regions that have a large number of both within and between module connections. We argue that weak connections in brain functional networks lead to misclassification of brain regions as hubs. In order to resolve this, we propose a new measure called ambivert degree that considers the node's degree as well as connection weights in order to identify nodes with both high degree and high connection weights as hubs. Using resting-state functional MRI scans from the Human Connectome Project, we show that ambivert degree identifies brain hubs that are not only crucial but also invariable across subjects. We hypothesize that nodal measures based on ambivert degree can be effectively used to classify patients from healthy controls for diseases that are known to have widespread hub disruption. Using patient data for Alzheimer's Disease and Autism Spectrum Disorder, we show that the hubs in the patient and healthy groups are very different for both the diseases and deep feedforward neural networks trained on nodal hub features lead to a significantly higher classification accuracy with significantly fewer trainable weights compared to using functional connectivity features. Thus, the ambivert degree improves identification of crucial brain hubs in healthy subjects and can be used as a diagnostic feature to detect neurological diseases characterized by hub disruption.


Assuntos
Doença de Alzheimer/diagnóstico por imagem , Doença de Alzheimer/fisiopatologia , Transtorno do Espectro Autista/diagnóstico por imagem , Transtorno do Espectro Autista/fisiopatologia , Córtex Cerebral/diagnóstico por imagem , Conectoma/métodos , Aprendizado Profundo , Rede Nervosa/diagnóstico por imagem , Adolescente , Adulto , Idoso , Córtex Cerebral/fisiopatologia , Criança , Humanos , Imageamento por Ressonância Magnética , Rede Nervosa/fisiopatologia , Adulto Jovem
18.
BMC Bioinformatics ; 10 Suppl 15: S4, 2009 Dec 03.
Artigo em Inglês | MEDLINE | ID: mdl-19958514

RESUMO

BACKGROUND: High content screening techniques are increasingly used to understand the regulation and progression of cell motility. The demand of new platforms, coupled with availability of terabytes of data has challenged the traditional technique of identifying cell populations by manual methods and resulted in development of high-dimensional analytical methods. RESULTS: In this paper, we present sub-populations analysis of cells at the tissue level by using dynamic features of the cells. We used active contour without edges for segmentation of cells, which preserves the cell morphology, and autoregressive modeling to model cell trajectories. The sub-populations were obtained by clustering static, dynamic and a combination of both features. We were able to identify three unique sub-populations in combined clustering. CONCLUSION: We report a novel method to identify sub-populations using kinetic features and demonstrate that these features improve sub-population analysis at the tissue level. These advances will facilitate the application of high content screening data analysis to new and complex biological problems.


Assuntos
Movimento Celular/fisiologia , Biologia Computacional/métodos , Macrófagos/citologia , Animais , Células/citologia , Células Cultivadas , Macrófagos/metabolismo , Camundongos , Reconhecimento Automatizado de Padrão
19.
PLoS One ; 14(10): e0223161, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31603902

RESUMO

In many data classification problems, a number of methods will give similar accuracy. However, when working with people who are not experts in data science such as doctors, lawyers, and judges among others, finding interpretable algorithms can be a critical success factor. Practitioners have a deep understanding of the individual input variables but far less insight into how they interact with each other. For example, there may be ranges of an input variable for which the observed outcome is significantly more or less likely. This paper describes an algorithm for automatic detection of such thresholds, called the Univariate Flagging Algorithm (UFA). The algorithm searches for a separation that optimizes the difference between separated areas while obtaining a high level of support. We evaluate its performance using six sample datasets and demonstrate that thresholds identified by the algorithm align well with published results and known physiological boundaries. We also introduce two classification approaches that use UFA and show that the performance attained on unseen test data is comparable to or better than traditional classifiers when confidence intervals are considered. We identify conditions under which UFA performs well, including applications with large amounts of missing or noisy data, applications with a large number of inputs relative to observations, and applications where incidence of the target is low. We argue that ease of explanation of the results, robustness to missing data and noise, and detection of low incidence adverse outcomes are desirable features for clinical applications that can be achieved with relatively simple classifier, like UFA.


Assuntos
Algoritmos , Neoplasias da Mama/diagnóstico , Diabetes Mellitus/diagnóstico , Leucemia Mieloide Aguda/diagnóstico , Leucemia-Linfoma Linfoblástico de Células Precursoras/diagnóstico , Sepse/diagnóstico , Temperatura Corporal , Neoplasias da Mama/mortalidade , Neoplasias da Mama/patologia , Conjuntos de Dados como Assunto , Diabetes Mellitus/mortalidade , Diabetes Mellitus/patologia , Feminino , Humanos , Leucemia Mieloide Aguda/mortalidade , Leucemia Mieloide Aguda/patologia , Masculino , Modelos Estatísticos , Leucemia-Linfoma Linfoblástico de Células Precursoras/mortalidade , Leucemia-Linfoma Linfoblástico de Células Precursoras/patologia , Sepse/mortalidade , Sepse/patologia , Análise de Sobrevida
20.
PLoS One ; 13(5): e0195518, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29734327

RESUMO

Research on temporal characteristics of human dynamics has attracted much attentions for its contribution to various areas such as communication, medical treatment, finance, etc. Existing studies show that the time intervals between two consecutive events present different non-Poisson characteristics, such as power-law, Pareto, bimodal distribution of power-law, exponential distribution, piecewise power-law, et al. With the occurrences of new services, new types of distributions may arise. In this paper, we study the distributions of the time intervals between two consecutive visits to QQ and WeChat service, the top two popular instant messaging services in China, and present a new finding that when the value of statistical unit T is set to 0.001s, the inter-event time distribution follows a piecewise distribution of exponential and power-law, indicating the heterogeneous character of IM services users' online behavior in different time scales. We infer that the heterogeneous character is related to the communication mechanism of IM and the habits of users. Then we develop a combination model of exponential model and interest model to characterize the heterogeneity. Furthermore, we find that the exponent of the inter-event time distribution of the same service is different in two cities, which is correlated with the popularity of the services. Our research is useful for the application of information diffusion, prediction of economic development of cities, and so on.


Assuntos
Internet , Modelos Estatísticos , Comportamento Social , Envio de Mensagens de Texto/estatística & dados numéricos , Humanos , Fatores de Tempo
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