Penalized Binary Regression for Gene Expression Profiling

2004 ◽  
Vol 43 (05) ◽  
pp. 439-444 ◽  
Author(s):  
Michae Schimek
Keyword(s):  
Microarray Analysis ◽  
Predictive Performance ◽  
Small Sample ◽  
Probit Regression ◽  
Binary Regression ◽  
Data Set ◽  
Small Sample Sizes ◽  
Bayesian Probit Regression

Summary Objectives: A typical bioinformatics task in microarray analysis is the classification of biological samples into two alternative categories. A procedure is needed which, based on the expression levels measured, allows us to compute the probability that a new sample belongs to a certain class. Methods: For the purpose of classification the statistical approach of binary regression is considered. High-dimensionality and at the same time small sample sizes make it a challenging task. Standard logit or probit regression fails because of condition problems and poor predictive performance. The concepts of frequentist and of Bayesian penalization for binary regression are introduced. A Bayesian interpretation of the penalized log-likelihood is given. Finally the role of cross-validation for regularization and feature selection is discussed. Results: Penalization makes classical binary regression a suitable tool for microarray analysis. We illustrate penalized logit and Bayesian probit regression on a well-known data set and compare the obtained results, also with respect to published results from decision trees. Conclusions: The frequentist and the Bayesian penalization concept work equally well on the example data, however some method-specific differences can be made out. Moreover the Bayesian approach yields a quantification (posterior probabilities) of the bias due to the constraining assumptions.

scholarly journals Mapping influenza transmission in the ferret model to transmission in humans

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Michael G Buhnerkempe ◽  
Katelyn Gostic ◽  
Miran Park ◽  
Prianna Ahsan ◽  
Jessica A Belser ◽  
...  
Keyword(s):  
Avian Influenza ◽  
Small Sample ◽  
Influenza Viruses ◽  
Epidemic Spread ◽  
Avian Influenza Viruses ◽  
Transmission Potential ◽  
Influenza Transmission ◽  
Small Sample Sizes

The controversy surrounding 'gain-of-function' experiments on high-consequence avian influenza viruses has highlighted the role of ferret transmission experiments in studying the transmission potential of novel influenza strains. However, the mapping between influenza transmission in ferrets and in humans is unsubstantiated. We address this gap by compiling and analyzing 240 estimates of influenza transmission in ferrets and humans. We demonstrate that estimates of ferret secondary attack rate (SAR) explain 66% of the variation in human SAR estimates at the subtype level. Further analysis shows that ferret transmission experiments have potential to identify influenza viruses of concern for epidemic spread in humans, though small sample sizes and biological uncertainties prevent definitive classification of human transmissibility. Thus, ferret transmission experiments provide valid predictions of pandemic potential of novel influenza strains, though results should continue to be corroborated by targeted virological and epidemiological research.

scholarly journals Radiomics for the Diagnosis and Differentiation of Pancreatic Cystic Lesions

Diagnostics ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 505
Author(s):  
Jorge D. Machicado ◽  
Eugene J. Koay ◽  
Somashekar G. Krishna
Keyword(s):  
Predictive Accuracy ◽  
Quantitative Imaging ◽  
Standard Of Care ◽  
Small Sample ◽  
Cystic Lesions ◽  
Current Standard ◽  
Cross Sectional ◽  
Small Sample Sizes ◽  
Insight Into

Radiomics, also known as quantitative imaging or texture analysis, involves extracting a large number of features traditionally unmeasured in conventional radiological cross-sectional images and converting them into mathematical models. This review describes this approach and its use in the evaluation of pancreatic cystic lesions (PCLs). This discipline has the potential of more accurately assessing, classifying, risk stratifying, and guiding the management of PCLs. Existing studies have provided important insight into the role of radiomics in managing PCLs. Although these studies are limited by the use of retrospective design, single center data, and small sample sizes, radiomic features in combination with clinical data appear to be superior to the current standard of care in differentiating cyst type and in identifying mucinous PCLs with high-grade dysplasia. Combining radiomic features with other novel endoscopic diagnostics, including cyst fluid molecular analysis and confocal endomicroscopy, can potentially optimize the predictive accuracy of these models. There is a need for multicenter prospective studies to elucidate the role of radiomics in the management of PCLs.

scholarly journals What Role Does the Prefrontal Cortex Play in the Processing of Negative and Positive Stimuli in Adolescent Depression?

2019 ◽  
Vol 9 (5) ◽  
pp. 104 ◽  
Author(s):  
Siyabend Kaya ◽  
Ciara McCabe
Keyword(s):  
Prefrontal Cortex ◽  
Adolescent Depression ◽  
Region Of Interest ◽  
Small Sample ◽  
Symptoms Of Depression ◽  
Small Sample Sizes ◽  
Positive Stimuli ◽  
Larger Sample ◽  
Negative Stimuli

This perspective describes the contribution of the prefrontal cortex to the symptoms of depression in adolescents and specifically the processing of positive and negative information. We also discuss how the prefrontal cortex (PFC) activity and connectivity during tasks and at rest might be a biomarker for risk for depression onset in adolescents. We include some of our recent work examining not only the anticipation and consummation of positive and negative stimuli, but also effort to gain positive and avoid negative stimuli in adolescents with depression. We find, using region of interest analyses, that the PFC is blunted in those with depression compared to controls across the different phases but in a larger sample the PFC is blunted in the anticipatory phase of the study only. Taken together, in adolescents with depression there is evidence for dysfunctional PFC activity across different studies and tasks. However, the data are limited with small sample sizes and inconsistent findings. Larger longitudinal studies with more detailed assessments of symptoms across the spectrum are needed to further evaluate the role of the PFC in adolescent depression.

scholarly journals MECHANISMS IN ENDOCRINOLOGY: Epigenetic modifications and gestational diabetes: a systematic review of published literature

2017 ◽  
Vol 176 (5) ◽  
pp. R247-R267 ◽  
Author(s):  
Gunn-Helen Moen ◽  
Christine Sommer ◽  
Rashmi B Prasad ◽  
Line Sletner ◽  
Leif Groop ◽  
...  
Keyword(s):  
Systematic Review ◽  
Gestational Diabetes ◽  
Current Knowledge ◽  
Epigenetic Modifications ◽  
Research Literature ◽  
Small Sample ◽  
Epigenetic Alterations ◽  
Search Terms ◽  
Small Sample Sizes

ObjectiveTo summarize the current knowledge on epigenetic alterations in mother and offspring subjected to gestational diabetes (GDM) and indicate future topics for research.DesignSystematic review.MethodsWe performed extensive searches in PubMed, EMBASE and Google scholar, using a combination of the search terms: GDM, gestational diabetes, epigenetic(s), methylation, histone modification, histone methylation, histone acetylation, microRNA and miRNA. Studies that compared women diagnosed with GDM and healthy controls were included. Two authors independently scanned the abstracts, and all included papers were read by at least two authors. The searches were completed on October 31st, 2016.ResultsWe identified 236 articles, of which 43 were considered relevant for this systematic review. Studies published showed that epigenetic alterations could be found in both mothers with GDM and their offspring. However, differences in methodology, diagnostic criteria for GDM and populations studied, together with a limited number of published studies and small sample sizes, preclude clear conclusions about the role of epigenetic modifications in transmitting risk from GDM mothers to their offspring.ConclusionThe current research literature suggests that GDM may have impact on epigenetic modifications in the mother and offspring. However, larger studies that include multiple cohorts of GDM patients and their offspring are needed.

scholarly journals Minimum Relevant features to Obtain Explainable Systems for Predicting Cardiovascular Disease Using the Statlog Dataset

2020 ◽  
Author(s):  
Roberto Porto ◽  
Jose M. Molina ◽  
Antonio Berlanga ◽  
Miguel A. Patricio
Keyword(s):  
Cardiovascular Disease ◽  
Performance Metrics ◽  
Predictive Performance ◽  
Large Set ◽  
Data Set ◽  
Error Metrics ◽  
Automated Learning ◽  
And Performance ◽  
The Cost

Learning systems have been very focused on creating models that are capable of obtaining the best results in error metrics. Recently, the focus has shifted to improvement in order to interpret and explain their results. The need for interpretation is greater when these models are used to support decision making. In some areas this becomes an indispensable requirement, such as in medicine. This paper focuses on the prediction of cardiovascular disease by analyzing the well-known Statlog (Heart) Data Set from the UCI’s Automated Learning Repository. This study will analyze the cost of making predictions easier to interpret by reducing the number of features that explain the classification of health status versus the cost in accuracy. It will be analyzed on a large set of classification techniques and performance metrics. Demonstrating that it is possible to make explainable and reliable models that have a good commitment to predictive performance.

scholarly journals The Current Role of Induced Endometrial Trauma (Endometrial Scratch) in Women Undergoing Infertility Treatment

2021 ◽  
Author(s):  
Mostafa Metwally ◽  
Stephen Walters ◽  
Robin Chatters
Keyword(s):  
Low Cost ◽  
Small Sample ◽  
Pregnancy Rates ◽  
Mechanical Trauma ◽  
Fertility Treatments ◽  
Current State ◽  
Randomized Controlled Studies ◽  
Endometrial Scratch ◽  
Small Sample Sizes

AbstractInduced endometrial trauma, otherwise known as endometrial scratch is a simple technique that has been rapidly adopted into clinical practice, mainly for women having IVF treatment, in an attempt to increase pregnancy rates. The introduction of endometrial scratch followed early reports of improved clinical pregnancy rates in women with repetitive implantation failure after having the procedure and follows on from evidence from animal models in the early 20th century suggesting that mechanical trauma to the endometrium can induce decidual changes. Due to the ease and low cost of the procedure, it has been rapidly adopted as an add-on to fertility treatments, in many cases where evidence is still lacking. Despite the initial publication of a large number of studies that demonstrated encouraging improvements in pregnancy rates in women who underwent this procedure, these studies were mainly limited by the small sample sizes and heterogeneity of their study populations, leading to limited validity of the evidence provided by these studies. More recently, three large randomized controlled studies have been published that paint a different picture regarding the value of this procedure. This article explores the evolution of the evidence and the current state of endometrial scratch as an adjuvant therapy for women undergoing IVF treatment.

scholarly journals Exercise and Nutrition Impact on Osteoporosis and Sarcopenia—The Incidence of Osteosarcopenia: A Narrative Review

Nutrients ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 4499
Author(s):  
Sousana K. Papadopoulou ◽  
Konstantinos Papadimitriou ◽  
Gavriela Voulgaridou ◽  
Evridiki Georgaki ◽  
Eudoxia Tsotidou ◽  
...  
Keyword(s):  
Older Adults ◽  
Protective Role ◽  
Scientific Data ◽  
Bone Diseases ◽  
Small Sample ◽  
Narrative Review ◽  
Prevention Of Osteoporosis ◽  
Small Sample Sizes ◽  
Meta Analyses

Osteoporosis and sarcopenia are diseases which affect the myoskeletal system and often occur in older adults. They are characterized by low bone density and loss of muscle mass and strength, factors which reduce the quality of life and mobility. Recently, apart from pharmaceutical interventions, many studies have focused on non-pharmaceutical approaches for the prevention of osteoporosis and sarcopenia with exercise and nutrition to being the most important and well studied of those. The purpose of the current narrative review is to describe the role of exercise and nutrition on prevention of osteoporosis and sarcopenia in older adults and to define the incidence of osteosarcopenia. Most of the publications which were included in this review show that resistance and endurance exercises prevent the development of osteoporosis and sarcopenia. Furthermore, protein and vitamin D intake, as well as a healthy diet, present a protective role against the development of the above bone diseases. However, current scientific data are not sufficient for reaching solid conclusions. Although the roles of exercise and nutrition on osteoporosis and sarcopenia seem to have been largely evaluated in literature over the recent years, most of the studies which have been conducted present high heterogeneity and small sample sizes. Therefore, they cannot reach final conclusions. In addition, osteosarcopenia seems to be caused by the effects of osteoporosis and sarcopenia on elderly. Larger meta-analyses and randomized controlled trials are needed designed based on strict inclusion criteria, in order to describe the exact role of exercise and nutrition on osteoporosis and sarcopenia.

scholarly journals A Critical Review of Multimodal Interventions for Cachexia

2020 ◽  
Author(s):  
Clare McKeaveney ◽  
Peter Maxwell ◽  
Helen Noble ◽  
Joanne Reid
Keyword(s):  
Body Composition ◽  
Sample Size ◽  
Small Sample ◽  
Cochrane Library ◽  
Chronic Obstructive ◽  
Obstructive Pulmonary Disease ◽  
Treatment Groups ◽  
Small Sample Sizes

ABSTRACT Currently, there are no standardized treatments for cachexia or severe wasting. There is a growing consensus advocating multimodal interventions to address the complex pathogenesis and metabolic alterations in these conditions. This review examined multimodal treatments intended to alleviate and/or stabilize cachexia and severe wasting. The objectives of this review were to 1) identify multimodal interventions for the treatment of cachexia or associated wasting syndromes in patients with a chronic illness, 2) assess the quality of these studies, and 3) assess the effectiveness of multimodal interventions. Electronic databases including PubMed, MEDLINE, EMBASE, Scopus, Web of Science, Cochrane Library, CINAHL, PEDro, OpenGrey, and clinicaltrials.org were systematically searched using both text words and MeSH (medical subject heading) terms. The literature revealed a dearth of large, well-conducted trials in this area. Fourteen trials (n = 5 cancer, n = 5 chronic obstructive pulmonary disease, n = 4 chronic kidney disease) were included in this review. A total of 1026 patients were included across all studies; sample size ranged between 21 and 138 patients. Baseline and follow-up data were collected between 6 wk and 24 mo. All demonstrated some improvement in favor of the treatment groups, in relevant measures of body composition, nutrition, biomarkers, and functionality; however, caution should be applied due to the heterogenous nature of the interventions and small sample sizes. Overall, the evidence from this review supports the role of multimodal interventions in the treatment of severe wasting. However, randomized controlled trials with a powered sample size and sufficiently lengthy interaction period are necessary to assess if multimodal interventions are effective forms of therapy for improving body composition and nutritional and physical status in patients with cachexia and wasting. The protocol for this review is registered with Prospero (ID: CRD42019124374).

A comparative geochemical study of Mars and Earth basalt petrogenesis

2013 ◽  
Vol 50 (1) ◽  
pp. 78-93 ◽  
Author(s):  
John D. Greenough ◽  
Avee Ya’acoby
Keyword(s):  
Incompatible Element ◽  
A Priori ◽  
Correlation Coefficients ◽  
Small Sample ◽  
Geochemical Data ◽  
Data Set ◽  
Element Ratios ◽  
Highly Correlated ◽  
Small Sample Sizes ◽  
Priori Information

Geochemical data, from the Mars Meteorite Compendium web site, for 13 basaltic meteorites, possibly from only four localities on Mars, are used to study Martian petrogenetic processes. To achieve this goal, an exploratory data analysis technique, multidimensional scaling (MDS), is used to quantitatively assess the relative behavior (measured with correlation coefficients) of 160 incompatible element ratios involving 25 “trace” elements. The ratios behave as in Earth basalts, suggesting that relative element incompatibility is similar in both planets. Because mineralogy controls incompatibility, the mineralogy of Earth and Mars mantles appears similar. In addition, results suggest that ratios involving elements with highly different incompatibility (e.g., La/Yb) are dominantly controlled by % melting. Plots of SiO2 (pressure proxy; decreases with increasing pressure) versus La/Yb and Nb/Y (decrease as melting increases) imply that Mars basalts, like Earth tholeiites, reflect high percentages of melting, but opposite to Earth, % melting appears to increase with increasing pressure. The moderately correlated, positive, SiO2–La/Yb Mars relationship parallels highly correlated Lunar KREEP data and contrasts with Earth’s negative correlation. The positive relationships may reflect restricted mantle convection in some (Mars and the Moon are smaller) planetary bodies. Using similarly incompatible element ratios that are sensitive to source composition, to compare Mars and Earth with MDS, Mars sources most resemble depleted Earth mantle. Additionally, these ratios group Mars sources into enriched, depleted, and intermediate types. The groupings are the same as those suggested by isotopes, and we conclude that trace element data support the hypothesis that chemical variation in Mars may reflect crystallization of a Mars magma ocean. The natural patterns in ratios and samples revealed using MDS, which has no a priori information about relationships, support integrity of the geochemical data set, despite potential shortcomings such as small sample sizes, alteration, and weathering. However, whether the meteorites are representative of Mars as a whole is unknown.

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