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Machine-learned metrics for predicting the likelihood of success in materials discovery

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npj Computational Materials 2020年第1期6卷 539-547页

作者： Yoolhee Kim Edward Kim erin Antono Bryce Meredig Julia Ling Citrine Informatics Redwood CityCA 94063USA

Materials discovery is often compared to the challenge of finding a needle in a *** much work has focused on accurately predicting the properties of candidate materials with machine learning(ML),which amounts to evaluating whether a given candidate is a piece of straw or a needle,less attention has been paid to a critical question:are we searching in the right haystack?We refer to the haystack as the design space for a particular materials discovery problem(i.e.,the set of possible candidate materials to synthesize),and thus frame this question as one of design space *** this paper,we introduce two metrics,the predicted fraction of improved candidates(PFIC),and the cumulative maximum likelihood of improvement(CMLI),which we demonstrate can identify discovery-rich and discovery-poor design spaces,respectively.A combined classification system,composed of the CMLI and PFIC metrics,is then used to identify optimal design spaces with high precision,and thus show the potential to significantly accelerate ML-driven materials discovery.

关键词： likelihood predicting searching

Effect and feasibility of wearable physical activity trackers and pedometers for increasing physical activity and improving health outcomes in cancer survivors:A systematic review and meta-analysis

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Journal of Sport and Health Science 2022年第2期11卷 184-193页

作者： Benjamin Singh Eva M.Zopf erin J Howden Gallipoli Medical Research Foundation Greenslopes Private HospitalGreenslopesQLD 4120Australia Mary MacKillop Institute for Health Research Australian Catholic UniversityMelbourneVIC 3000Australia Baker Heart and Diabetes Institute MelbourneVIC 3004Australia

Purpose:This systematic review and meta-analysis aimed to evaluate the effect of wearable devices for improving physical activity and healthrelated outcomes in cancer ***:CINAHL,Cochrane,Ebscohost,MEDLINE,Pubmed,ProQuest Health and Medical Complete,ProQuest Nursing and Allied Health Source,ScienceDirect,and SPORTDiscus databases were searched for randomized controlled trials published before September 1,2020,that evaluated interventions involving wearable devices in cancer *** mean differences(SMDs)were calculated to assess effects on physical activity and health-related *** analyses were conducted to assess whether the effects differed by interventions and cancer *** of bias was assessed using the Cochrane risk of bias ***:Thirty-five trials were included(breast cancer,n=15,43%).Intervention durations ranged between 4 weeks and 1 *** trials(n=25,71%)involved pedometer-based physical activity ***(20%)involved Fitbit-based interventions,and 3(9%)involved other wearable physical activity trackers(e.g.,Polar,Garmin).Compared to usual care,wearable devices had moderate-to-large effects(SMD range 0.54-0.87,p<0.001)on moderate-intensity physical activity,moderate-to-vigorous-intensity physical activity,total physical activity,and daily *** to usual care,those in the intervention had higher quality of life,aerobic fitness,physical function,and reduced fatigue(SMD range=0.18-0.66,all p<0.05).Conclusion:Wearable physical activity trackers and pedometers are effective tools that increase physical activity and improve health-related outcomes in individuals with *** how these devices can be implemented for longer-term use with other intervention components remains an area for future research.

关键词： Activity tracker Cancer Exercise Physical activity Wearable

Presenting patterns of dermatology conditions to an Australian emergency department

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World Journal of Emergency Medicine 2020年第2期11卷 74-78页

作者： Emily Shao Chantelle Judge erin McMeniman Tina Bazianas Rob Eley Emergency Department Princess Alexandra HospitalBrisbaneAustralia Faculty of Medicine University of QueenslandBrisbaneAustralia Dermatology Department Princess Alexandra HospitalBrisbaneAustralia

BACKGROUND: Approximately 5%–8% of emergency department(ED) presentations are due to a dermatological *** study aimed to identify and characterise patients with skin conditions presenting to a busy ***: A 5-year retrospective study on patients with dermatological conditions presenting to the Princess Alexandra Hospital ED in Brisbane, Australia was *** medical records were used to compare demographics and admission status of the dermatology group and the total ED group presentations.A prospective survey was conducted on low priority triage(triage 4 and 5) patients identifying reasons presenting to the ***: Of a total 281,718 ED presentations, 11,748 dermatology presentations were identified between January 2012 to December *** the dermatology presentations, 41.5% were female and had an average age of *** most common dermatology presentations were cellulitis, abscess, rash unspecified, and *** those admitted, 36% were female, average age was 53, mean length of stay of 294 minutes and 83.1% had an infectious *** triage 4 and 5 presentations, 66% patients we approached had been seen by a health practitioner prior to coming to the ***: Within the population presenting with a skin related condition to the Princess Alexandra Hospital ED, characteristics associated with admission include male sex, older age, and an infectious *** data may help ED clinicians decide on the discharge disposition of these *** may be a role for streamlined admissions for skin related infections, or improved hospital in the home services to support this group.

关键词： Pcellulitis Skin Dermatology Emergency department

Childhood chronic gastritis and duodenitis: Role of altered sensory neuromediators

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World Journal of Gastroenterology 2016年第37期22卷 8349-8360页

作者： Ali Islek Aygen Yilmaz Gulsum Ozlem Elpek Nuray erin Department of Pediatric Gastro-enterology Akdeniz University School of Medicine Department of Pathology Akdeniz University School of Medicine Department of Medical Pharmacology Akdeniz University School of Medicine

AIM To investigate the roles of the neuropeptides vasoactive intestinal peptide(VIP), substance P(SP), and calcitonin gene-related peptide(CGRP) in chronic gastritis and duodenitis in *** Biopsy samples from the gastric and duodenal mucosa of 52 patients and 30 control subjects were obtained. Samples were taken for pathological examination, immunohistochemical staining, enzyme activity measurements and quantitative measurements of tissue peptide *** We observed differential effects of the disease on peptide levels, which were somewhat different from previously reported changes in chronic gastritis in adults. Specifically, SP was increased and CGRP and VIP were decreased in patients with gastritis. The changes were more prominent at sites where gastritis was severe, but significant changes were also observedin neighboring areas where gastritis was less severe. Furthermore, the degree of changes was correlated with the pathological grade of the disease. The expression of CD10, the enzyme primarily involved in SP hydrolysis, was also decreased in patients with *** Based on these findings, we propose that decreased levels of VIP and CGRP and increased levels of SP contribute to pathological changes in gastric mucosa. Hence, new treatments targeting these molecules may have therapeutic and preventive effects.

关键词： Gastritis Neuropeptides Childhood Neutral endopeptidase

Prediction of esophageal and gastric histology by macroscopic diagnosis during upper endoscopy in pediatric celiac disease

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World Journal of Gastroenterology 2017年第4期23卷 646-652页

作者： erin D Boschee Jason YK Yap Justine M Turner Department of Pediatrics University of Alberta Edmonton Clinic Health Academy University of Alberta Hospital Division of Pediatric Gastroenterology Department of PediatricsUniversity of Alberta

AIMTo determine the sensitivity of macroscopic appearance for predicting histological diagnosis at sites other than duodenum in pediatric celiac disease (CD).METHODSEndoscopic and histologic findings in pediatric patients undergoing upper endoscopy for first-time diagnosis of CD at Stollery Children’s Hospital from 2010-2012 were retrospectively *** charts from 140 patients were reviewed. Esophageal and gastric biopsies were taken in 54.3% and 77.9% of patients, respectively. Endoscopic appearance was normal in the esophagus and stomach in 75% and 86.2%. Endoscopic esophageal diagnoses were eosinophilic esophagitis (EE) (11.8%), esophagitis (7.9%), glycogenic acanthosis (1.3%) and non-specific abnormalities (3.9%). Endoscopic gastric diagnoses were gastritis (8.3%), pancreatic rest (0.9%), and non-specific abnormalities (4.6%). Histology was normal in 76.3% of esophageal and 87.2% of gastric specimens. Abnormal esophageal histology was EE (10.5%), esophagitis (10.5%), glycogenic acanthosis (1.3%) and non-specific (1.3%). Gastritis was reported in 12.8% of specimens. Sensitivity and specificity of normal endoscopy for predicting normal esophageal histology was 86.2% and 61.1%, and for normal gastric histology was 87.4% and 21.4%.CONCLUSIONIn the absence of macroscopic abnormalities, routine esophageal and gastric biopsy during endoscopy for pediatric CD does not identify major pathologies. These findings have cost and time saving implications for clinical practice.

关键词： Endoscopy Histology Esophagus Gastric biopsy Celiac disease

Fecal microbial diversity and putative function in captive western lowland gorillas(Gorilla gorilla gorilla),common chimpanzees(Pan troglodytes),Hamadryas baboons(Papio hamadryas)and binturongs(Arctictis binturong)

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Integrative Zoology 2014年第5期9卷 557-569页

作者： erin A.McKENNEY Melissa ASHWELL Joanna E.LAMBERT Vivek FELLNER Department of Animal Sciences North Carolina State UniversityRaleighNorth CarolinaUSA Department of Anthropology The University of Texas at San AntonioTexasUSA

Microbial populations in the gastrointestinal tract contribute to host health and *** gut microbial ecology is well studied in livestock and domestic animals,little is known of the endogenous populations inhabiting primates or *** characterized microbial populations in fecal cultures from gorillas(Gorilla gorilla gorilla),common chimpanzees(Pan troglodytes),Hamadryas baboons(Papio hamadryas)and binturongs(Arctictis binturong)to compare the microbiomes associated with different gastrointestinal morphologies and different omnivorous feeding *** species was fed a distinct standardized diet for 2 weeks prior to fecal *** diets were formulated to reflect the species’feeding strategies in *** fecal samples were pooled within species and used to inoculate in vitro batch ***,propionate,butyrate and valerate were measured after 24 h of *** DNA was extracted from individual fecal samples,pooled,and the cpn60 gene region was amplified and then sequenced to identify the major eubacterial constituents associated with each host *** chain fatty acids(P<0.001)and methane(P<0.001)were significantly different across *** profiles were consistent with fermentation data and suggest an increase in diversity with dietary fiber.

关键词： ecology fermentation gastrointestinal microbiota microbial diversity

A simple modification to the classical SIR model to estimate the proportion of under-reported infections using case studies in flu and COVID-19

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作者： erin Hunter.

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Infectious Disease Modelling 2024年第4期9卷 1147-1162页

作者： Leonid Kalachev Jon Graham erin L.Landguth Mathematical Sciences University of MontanaMissoulaUSA Center for Population Health Research School of Public and Community Health SciencesUniversity of MontanaMissoulaUSA

Background:Under-reporting and,thus,uncertainty around the true incidence of health events is common in all public health reporting *** the problem of underreporting is acknowledged in epidemiology,the guidance and methods available for assessing and correcting the resulting bias are ***:We aim to design a simple modification to the Susceptible e Infected e Removed(SIR)model for estimating the fraction or proportion of reported infection ***:The suggested modification involves rescaling of the classical SIR model producing its mathematically equivalent version with explicit dependence on the reporting parameter(true proportion of cases reported).We justify the rescaling using the phase plane analysis of the SIR model system and show how this rescaling parameter can be estimated from the data along with the other model ***:We demonstrate how the proposed method is cross-validated using simulated data with known disease cases and then apply it to two empirical reported data sets to estimate the fraction of reported cases in Missoula County,Montana,USA,using:(1)flu data for 2016e2017 and(2)COVID-19 data for fall of ***:We establish with the simulated and COVID-19 data that when most of the disease cases are presumed reported,the value of the additional reporting parameter in the modified SIR model is close or equal to one,so that the original SIR model is appropriate for data ***,the flu example shows that when the reporting parameter is close to zero,the original SIR model is not accurately estimating the usual rate parameters,and the re-scaled SIR model should be *** research demonstrates the role of under-reporting of disease data and the importance of accounting for underreporting when modeling simulated,endemic,and pandemic disease *** reporting the“true”number of disease cases will have downstream impacts on predictions of disease dynamics.A simple parameter adjustment

关键词： Modeling of epidemics SIR type models flu and COVID-19 Under-reporting parameter Proportion of reported disease cases

Revisiting classical SIR modelling in light of the COVID-19 pandemic

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Infectious Disease Modelling 2023年第1期8卷 72-83页

作者： Leonid Kalachev erin L.Landguth Jon Graham Mathematical Sciences University of MontanaMissoulaUSA Center for Population Health Research School of Public and Community Health SciencesUniversity of MontanaMissoulaUSA

Background:Classical infectious disease models during epidemics have widespread usage,from predicting the probability of new infections to developing vaccination plans for informing policy decisions and public health ***,it is important to correctly classify reported data and understand how this impacts estimation of model *** COVID-19 pandemic has provided an abundant amount of data that allow for thorough testing of disease modelling assumptions,as well as how we think about classical infectious disease modelling ***:We aim to assess the appropriateness of model parameter estimates and preiction results in classical infectious disease compartmental modelling frameworks given available data types(infected,active,quarantined,and recovered cases)for situations where just one data type is available to fit the *** main focus is on how model prediction results are dependent on data being assigned to the right model ***:We first use simulated data to explore parameter reliability and prediction capability with three formulations of the classical Susceptible-Infected-Removed(SIR)modelling *** then explore two applications with reported data to assess which data and models are sufficient for reliable model parameter estimation and prediction accuracy:a classical influenza outbreak in a boarding school in England and COVID-19 data from the fall of 2020 in Missoula County,Montana,***:We demonstrated the magnitude of parameter estimation errors and subsequent prediction errors resulting from data misclassification to model compartments with simulated *** showed that prediction accuracy in each formulation of the classical disease modelling framework was largely determined by correct data classification versus *** a classical example of influenza epidemics in an England boarding school,we argue that the Susceptible-Infected-Quarantined-Recovered(SIQR)model is more appropriat

关键词： Basic disease reproduction number Communicable disease control Coronavirus COVID-19 Disease transmission Epidemics Epidemiology Influenza data Mathematical models Montana SIR models