19,382 results match your criteria inference methods

BACON: A tool for reverse inference in brain activation and alteration.

Hum Brain Mapp 2021 May 15. Epub 2021 May 15.

GCS-fMRI, Koelliker Hospital and Department of Psychology, University of Turin, Turin, Italy.

Over the past decades, powerful MRI-based methods have been developed, which yield both voxel-based maps of the brain activity and anatomical variation related to different conditions. With regard to functional or structural MRI data, forward inferences try to determine which areas are involved given a mental function or a brain disorder. A major drawback of forward inference is its lack of specificity, as it suggests the involvement of brain areas that are not specific for the process/condition under investigation. Read More

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Changes in Job Control and Perceptions of General Health: A Longitudinal Analysis of Australian Workers, 2005-2017.

J Occup Environ Med 2021 May 14. Epub 2021 May 14.

Department of Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia (Taouk, Spittal, Disney, LaMontagne); School of Health & Social Development, Determinants of Health Research Domain, Institute for Health Transformation, Deakin University, Geelong, Victoria, Australia (LaMontagne).

Objective: This longitudinal study of Australian workers explores a possible causal relationship between job control and general health.

Methods: Our sample included 105,017 observations (18,574 persons) over 13 annual waves from working age participants with information on job control, general health, and other sociodemographic and health factors. Three complementary longitudinal modelling approaches were used to explore the causal relationship. Read More

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Do educational reforms increase or decrease health inequalities: A matter of methods?

Soc Sci Med 2021 May 7;279:114003. Epub 2021 May 7.

Department of Public Health, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands. Electronic address:

Evaluating whether social policies reduce health inequalities is complicated by the fact that these upstream determinants may also change the socioeconomic distribution. Failure to account for these compositional changes may severely bias the effect estimation procedure. In this article, we illustrate how a health inequality impact assessment of a policy that (also) changes the socioeconomic distribution may produce biased results. Read More

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Pharmacotherapy for Attention-Deficit/Hyperactivity Disorder and Retention in Outpatient Substance Use Disorder Treatment: A Retrospective Cohort Study.

J Clin Psychiatry 2021 Feb 23;82(2). Epub 2021 Feb 23.

Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts.

Objective: To assess the relationship between short- and longer-term retention in outpatient substance use disorder (SUD) treatment and pharmacotherapy for comorbid attention-deficit/hyperactivity disorder (ADHD).

Methods: In this retrospective cohort study conducted in a single addiction psychiatry clinic, electronic health record data from July 14, 2014, through January 15, 2020, were queried for clinical ADHD diagnosis (DSM-5 criteria), ADHD pharmacotherapy, treatment duration, demographic variables, comorbid psychiatric and SUD diagnoses, and buprenorphine therapy. Individuals with ADHD (n = 203) were grouped by ADHD pharmacotherapy status (171 receiving medication compared to 32 receiving none). Read More

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February 2021

EXPRESS: Combined Spectroscopic Analysis of Terrestrial Analogs from a Simulated Astronaut Mission Using the Laser-Induced Breakdown Spectroscopy (LIBS) Raman Sensor: Implications for Mars.

Appl Spectrosc 2021 May 14:37028211016892. Epub 2021 May 14.

York University Faculty of Science and Engineering, Centre for Research in Earth and Space Science , 4700 Keele St, Toronto, Ontario, Canada.

One of the primary objectives of planetary exploration is the search for signs of life (past, present, or future). Formulating an understanding of the geochemical processes on planetary bodies may allow us to define the precursors for biological processes, thus providing insight into the evolution of past life on Earth and other planets, and perhaps a projection into future biological processes. Several techniques have emerged for detecting biomarker signals on an atomic or molecular level, including laser-induced breakdown spectroscopy (LIBS), Raman spectroscopy, laser-induced fluorescence spectroscopy (LIF), and attenuated total reflectance Fourier-transform infrared (ATR-FTIR) spectroscopy, each of which addresses complementary aspects of the elemental composition, mineralogy, and organic characterization of a sample. Read More

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Mitogenomics of five leafhoppers (Hemiptera: Cicadellidae: Coelidiinae) and their phylogenetic implications.

PeerJ 2021 27;9:e11086. Epub 2021 Apr 27.

Institute of Entomology, Guizhou University, Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang, Guizhou Provincial, China.

Similar morphological characteristics and limited molecular data of resulted in their unknown phylogenetic statuses and equivocal relationships. To further understand the genus , we sequenced and annotated five complete mitochondrial genomes (mitogenomes). Our results show that mitogenomes range from 15,205 bp to 15,993 bp in length and include 37 typical genes (13 protein-coding genes, 22 tRNAs, and 2 rRNAs) and a control region. Read More

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Causal Isotonic Regression.

J R Stat Soc Series B Stat Methodol 2020 Jul 13;82(3):719-747. Epub 2020 May 13.

Department of Biostatistics, University of Washington.

In observational studies, potential confounders may distort the causal relationship between an exposure and an outcome. However, under some conditions, a causal dose-response curve can be recovered using the -computation formula. Most classical methods for estimating such curves when the exposure is continuous rely on restrictive parametric assumptions, which carry significant risk of model misspecification. Read More

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Alcohol outlets, drug paraphernalia sales, and neighborhood drug overdose.

Int J Drug Policy 2021 May 10;95:103289. Epub 2021 May 10.

Columbia University Mailman School of Public Health, Department of Epidemiology, 722 W168th St, 5th floor, New York, NY, 10032, USA.

Background: Alcohol outlets have been associated with various forms of injury and may contribute to neighborhood disparities in drug overdose. Few studies have examined the associations between alcohol outlets and drug overdose. This study investigated whether alcohol outlets were associated with the neighborhood drug overdose rate and whether the sale of drug paraphernalia contributes to this association. Read More

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Simulating longitudinal data from marginal structural models using the additive hazard model.

Biom J 2021 May 13. Epub 2021 May 13.

Department of Medical Statistics, London School of Hygiene & Tropical Medicine, London, UK.

Observational longitudinal data on treatments and covariates are increasingly used to investigate treatment effects, but are often subject to time-dependent confounding. Marginal structural models (MSMs), estimated using inverse probability of treatment weighting or the g-formula, are popular for handling this problem. With increasing development of advanced causal inference methods, it is important to be able to assess their performance in different scenarios to guide their application. Read More

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pSONIC: Ploidy-aware Syntenic Orthologous Networks Identified via Collinearity.

G3 (Bethesda) 2021 May 13. Epub 2021 May 13.

Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA.

With the rapid rise in availability of high-quality genomes for closely related species, methods for orthology inference that incorporate synteny are increasingly useful. Polyploidy perturbs the 1:1 expected frequencies of orthologs between two species, complicating the identification of orthologs. Here we present a method of ortholog inference, Ploidy-aware Syntenic Orthologous Networks Identified via Collinearity (pSONIC). Read More

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Phylogenomic subsampling and the search for phylogenetically reliable loci.

Mol Biol Evol 2021 May 13. Epub 2021 May 13.

Department of Earth & Planetary Sciences, Yale University. 210 Whitney Avenue, New Haven, CT 06511, USA.

Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale datasets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods, or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing their behavior across different datasets. Read More

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Soil sample pooling generates no consistent inference bias: a meta-analysis of 71 plant-soil feedback experiments.

New Phytol 2021 May 13. Epub 2021 May 13.

Bio-Protection Research Centre, School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand.

There is current debate on how soil sample pooling affects the measurement of plant-soil feedbacks. Several studies have suggested that pooling soil samples among experimental units reduces variance and can bias estimates of plant-soil feedbacks. However, it is unclear whether pooling has resulted in systematic mismeasurement of plant-soil feedbacks in the literature. Read More

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Propensity score weighting for causal subgroup analysis.

Stat Med 2021 May 12. Epub 2021 May 12.

Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina, USA.

A common goal in comparative effectiveness research is to estimate treatment effects on prespecified subpopulations of patients. Though widely used in medical research, causal inference methods for such subgroup analysis (SGA) remain underdeveloped, particularly in observational studies. In this article, we develop a suite of analytical methods and visualization tools for causal SGA. Read More

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A review of dynamical systems approaches for the detection of chaotic attractors in cancer networks.

Patterns (N Y) 2021 Apr 9;2(4):100226. Epub 2021 Apr 9.

Concordia University, Montreal, QC, Canada.

Cancers are complex dynamical systems. They remain the leading cause of disease-related pediatric mortality in North America. To overcome this burden, we must decipher the state-space attractor dynamics of gene expression patterns and protein oscillations orchestrated by cancer stemness networks. Read More

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Ordinal losses for classification of cervical cancer risk.

PeerJ Comput Sci 2021 23;7:e457. Epub 2021 Apr 23.

Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal.

Cervical cancer is the fourth leading cause of cancer-related deaths in women, especially in low to middle-income countries. Despite the outburst of recent scientific advances, there is no totally effective treatment, especially when diagnosed in an advanced stage. Screening tests, such as cytology or colposcopy, have been responsible for a substantial decrease in cervical cancer deaths. Read More

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Capecitabine as Maintenance Therapy for High-Risk, Resected Colorectal Cancer.

Gastrointest Tumors 2021 Apr 10;8(2):81-86. Epub 2021 Mar 10.

Department of Medicine, West Virginia University, Morgantown, West Virginia, USA.

Introduction: In 2020, colorectal cancer will be the fourth most frequently diagnosed malignant neoplasm and the second leading cause of site-specific, cancer-related deaths in the USA. Notably, 80% of the new cases are, by staging criteria, potentially curable even those with completely resected stage 4 disease. If slightly more than half the losses can be attributed to metastatic disease at presentation, then the remaining portion of deaths may be linked to disease relapse after surgery and, if applicable, adjuvant chemotherapy. Read More

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A discovery about the positional distribution pattern among candidate homologous pixels and its potential application in aerial multi-view image matching.

Sci Rep 2021 May 12;11(1):10161. Epub 2021 May 12.

Key Laboratory of Virtual Geographic Environment (Nanjing Normal University), Ministry of Education, 1# WenYuan Road, Nanjing, 210023, People's Republic of China.

In aerial multi-view photogrammetry, whether there is a special positional distribution pattern among candidate homologous pixels of a matching pixel in the multi-view images? If so, can this positional pattern be used to precisely confirm the real homologous pixels? These problems have not been studied at present. Therefore, the study of the positional distribution pattern among candidate homologous pixels based on the adjustment theory in surveying is investigated in this paper. Firstly, the definition and computing method of pixel's pseudo object-space coordinates are given, which can transform the problem of multi-view matching for confirming real homologous pixels into the problem of surveying adjustment for computing the pseudo object-space coordinates of the matching pixel. Read More

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How combining different caries lesions characteristics may be helpful in short-term caries progression prediction: model development on occlusal surfaces of primary teeth.

BMC Oral Health 2021 May 12;21(1):255. Epub 2021 May 12.

Department of Orthodontics and Paediatric Dentistry, School of Dentistry, University of Sao Paulo, Avenida Professor Lineu Prestes, 2227, Cidade Universitária, São Paulo, SP, Brazil.

Background: Few studies have addressed the clinical parameters' predictive power related to caries lesion associated with their progression. This study assessed the predictive validity and proposed simplified models to predict short-term caries progression using clinical parameters related to caries lesion activity status.

Methods: The occlusal surfaces of primary molars, presenting no frank cavitation, were examined according to the following clinical predictors: colour, luster, cavitation, texture, and clinical depth. Read More

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Spatial prediction of human brucellosis (HB) using a GIS-based adaptive neuro-fuzzy inference system (ANFIS).

Acta Trop 2021 May 9:105951. Epub 2021 May 9.

Department of GIS, Faculty of Geodesy and Geomatics Engineering, K. N. Toosi University of Technology, Tehran, Iran. Electronic address:

Objective: This study pursues three main objectives: 1) exploring the spatial distribution patterns of human brucellosis (HB); 2) identifying parameters affecting the disease spread; and 3) modeling and predicting the spatial distribution of HB cases in 2012-2016 and 2017-2018, respectively, in rural districts of Mazandaran province, Iran.

Methods: We collected data on the disease incidence, demography, ecology, climate, topography, and vegetation. Using the Global Moran's I statistic, we measured spatial autocorrelation between log (number of HB cases). Read More

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Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events in Alchemilla s.l. (Rosaceae).

Syst Biol 2021 May 12. Epub 2021 May 12.

Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, MN 55108, USA.

Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci, especially in groups experiencing whole-genome duplication (WGD) events. Common approaches for processing paralogs in target enrichment data sets include random selection, manual pruning, and mainly, the removal of entire genes that show any evidence of paralogy. Read More

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Inferring the experimental design for accurate gene regulatory network inference.

Bioinformatics 2021 May 12. Epub 2021 May 12.

Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, Solna, 17121, Sweden.

Motivation: Accurate inference of gene regulatory interactions is of importance for understanding the mechanisms of underlying biological processes. For gene expression data gathered from targeted perturbations, gene regulatory network (GRN) inference methods that use the perturbation design are the top performing methods. However, the connection between the perturbation design and gene expression can be obfuscated due to problems such as experimental noise or off-target effects, limiting the methods' ability to reconstruct the true GRN. Read More

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Bayesian neural network with pretrained protein embedding enhances prediction accuracy of drug-protein interaction.

Bioinformatics 2021 May 12. Epub 2021 May 12.

Department of Physics and Astronomy, Institute of Applied Physics, Seoul National University, Gwanak-gu, Seoul 08826, Republic of Korea.

Motivation: Characterizing drug-protein interactions is crucial to the high-throughput screening for drug discovery. The deep learning-based approaches have attracted attention because they can predict drug-protein interactions without human trial and error. However, because data labeling requires significant resources, the available protein data size is relatively small, which consequently decreases model performance. Read More

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Limits and Convergence properties of the Sequentially Markovian Coalescent.

Mol Ecol Resour 2021 May 12. Epub 2021 May 12.

Department of Life Science Systems, Technical University of Munich.

Several methods based on the SequentiallyMarkovian Coalescent (SMC) make use of full genome sequence data from samples to infer population demographic history including past changes in population size, admixture, migration events and population structure. More recently, the original theoretical framework has been extended to allow the simultaneous estimation of population size changes along with other life-history traits such as selfing or seed banking. The latter developments enhance the applicability of SMC methods to non-model species. Read More

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Phylogeography and genetic diversity of the widespread katydid (Thunberg, 1815) across China.

Ecol Evol 2021 May 8;11(9):4276-4294. Epub 2021 Mar 8.

College of Life Science Institute of Life Science and Green Development Hebei University Baoding China.

Habitat fragmentation can lower migration rates and genetic connectivity among remaining populations of native species. is one of the most widespread katydids in China, but little is known about its genetic structure and phylogeographic distribution. We combined the five-prime region of cytochrome c oxidase subunit I (COI-5P), 11 newly developed microsatellite loci coupled with an ecological niche model (ENM) to examine the genetic diversity and population structure of in China and beyond to Laos and Singapore. Read More

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Non-native rats detected on uninhabited southern Grenadine islands with seabird colonies.

Ecol Evol 2021 May 9;11(9):4172-4181. Epub 2021 Mar 9.

Department of Biological Sciences Arkansas State University State University Jonesboro AR USA.

Seabirds are among the most endangered avian groups, with populations declining worldwide because of various threats, including invasive nest predators. Similar decreasing trends are occurring in the Southern Grenadines; however, the causes of decline remain uncertain, although non-native rats have been suspected. Therefore, our objective was to determine whether non-native rats are present on five Southern Grenadine islands that harbor seabird colonies, during May-July 2014-2017, using four methods (chew cards, tunnels, cameras, and questionnaires). Read More

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What are the applications of single-cell RNA sequencing in cancer research: a systematic review.

J Exp Clin Cancer Res 2021 May 11;40(1):163. Epub 2021 May 11.

NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.

Single-cell RNA sequencing (scRNA-seq) is a tool for studying gene expression at the single-cell level that has been widely used due to its unprecedented high resolution. In the present review, we outline the preparation process and sequencing platforms for the scRNA-seq analysis of solid tumor specimens and discuss the main steps and methods used during data analysis, including quality control, batch-effect correction, normalization, cell cycle phase assignment, clustering, cell trajectory and pseudo-time reconstruction, differential expression analysis and gene set enrichment analysis, as well as gene regulatory network inference. Traditional bulk RNA sequencing does not address the heterogeneity within and between tumors, and since the development of the first scRNA-seq technique, this approach has been widely used in cancer research to better understand cancer cell biology and pathogenetic mechanisms. Read More

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Correlation analysis to investigate unconscious mental processes: A critical appraisal and mini-tutorial.

Cognition 2021 May 8;212:104667. Epub 2021 May 8.

University College London, United Kingdom.

As a method to investigate the scope of unconscious mental processes, researchers frequently obtain concurrent measures of task performance and stimulus awareness across participants. Even though both measures might be significantly greater than zero, the correlation between them might not, encouraging the inference that an unconscious process drives task performance. We highlight the pitfalls of this null-correlation approach and provide a mini-tutorial on ways to avoid them. Read More

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Think fast! The implications of emphasizing urgency in decision-making.

Nathan J Evans

Cognition 2021 May 8;214:104704. Epub 2021 May 8.

School of Psychology, University of Queensland, Australia; Department of Psychology, University of Amsterdam, the Netherlands. Electronic address:

Evidence accumulation models (EAMs) have become the dominant explanation of how the decision-making process operates, proposing that decisions are the result of a process of evidence accumulation. The primary use of EAMs has been as "measurement tools" of the underlying decision-making process, where researchers apply EAMs to empirical data to estimate participants' task ability (i.e. Read More

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A review and perspective on the assessment, management and prevention of fragility fractures in patients with osteoporosis and chronic kidney disease.

Endocrine 2021 May 11. Epub 2021 May 11.

Department of Medicine, Holbæk Hospital, Holbæk, Denmark.

This article aims to review the methods used for the assessment of fracture risk and the use of osteoporosis medications for fracture prevention in the population with CKD, and highlights the difficulties faced by clinicians in the management of these patients and the latest recommendations and guidelines. Chronic kidney disease (CKD) and osteoporosis often co-exist in older adults, and they present a major healthcare challenge. CKD mineral and bone disorder (CKD-MBD) occurs as renal function declines and this syndrome affects most patients in CKD stages 4 and 5. Read More

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MANIEA: A Microbial Association Network Inference Method Based on Improved Eclat Association Rule Mining Algorithm.

Bioinformatics 2021 May 10. Epub 2021 May 10.

College of Systems Engineering, National University of Defense Technology, Changsha, 410073, China.

Motivation: Modelling microbiome systems as complex networks is known as the problem of network inference. Microbial association network inference is of great significance in applications on clinical diagnosis, disease treatment, pathological analysis, etc. However, most current network inference methods focus on mining strong pairwise associations between microorganisms, which is defective in reflecting the comprehensive interactive patterns participated by multiple microorganisms. Read More

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