Expert-Augmented Machine Learning

Machine Learning is proving invaluable across disciplines. However, its success is often limited by the quality and quantity of available data, while its adoption by the level of trust that models afford users. Human vs. machine performance is commonly compared empirically to decide whether a certain task should be performed by a computer or an expert. In reality, the optimal learning strategy may involve combining the complementary strengths of man and machine. Here we present Expert-Augmented Machine Learning (EAML), an automated method that guides the extraction of expert knowledge and its integration into machine-learned models. We use a large dataset of intensive care patient data to predict mortality and show that we can extract expert knowledge using an online platform, help reveal hidden confounders, improve generalizability on a different population and learn using less data. EAML presents a novel framework for high performance and dependable machine learning in critical applications

Photometric Variability in the Ultracool Dwarf BRI 0021-0214: Possible Evidence for Dust Clouds

We report CCD photometric monitoring of the nonemission ultracool dwarf BRI 0021-0214 (M9.5) obtained during 10 nights in 1995 November and 4 nights in 1996 August, with CCD cameras at 1 m class telescopes on the observatories of the Canary Islands. We present differential photometry of BRI 0021-0214, and we report significant variability in the I-band light curve obtained in 1995. A periodogram analysis finds a strong peak at a period of 0.84 day. This modulation appears to be transient because it is present in the 1995 data but not in the 1996 data. We also find a possible period of 0.20 day, which appears to be present in both the 1995 and 1996 datasets. However, we do not find any periodicity close to the rotation period expected from the spectroscopic rotational broadening (< 0.14 day). BRI 0021-0214 is a very inactive object, with extremely low levels of Halpha and X-ray emission. Thus, it is unlikely that magnetically induced cool spots can account for the photometric variability. The photometric variability of BRI 0021-0214 could be explained by the presence of an active meteorology that leads to inhomogeneous clouds on the surface. The lack of photometric modulation at the expected rotational period suggests that the pattern of surface features may be more complicated than previously anticipated.Comment: Accepted for publication in ApJ. 26 pages, 13 figures include

Patient-Centered Outcomes Measurement: Does It Require Information From Patients?

Purpose: Since collecting outcome measure data from patients can be expensive, time-consuming, and subject to memory and nonresponse bias, we sought to learn whether outcomes important to patients can be obtained from data in the electronic health record (EHR) or health insurance claims. Methods: We previously identified 21 outcomes rated important by patients who had advanced imaging tests for back or abdominal pain. Telephone surveys about experiencing those outcomes 1 year after their test from 321 people consenting to use of their medical record and claims data were compared with audits of the participants’ EHR progress notes over the time period between the imaging test and survey completion. We also compared survey data with algorithmically extracted data from claims files for outcomes for which data might be available from that source. Results: Of the 16 outcomes for which patients’ survey responses were considered to be the best information source, only 2 outcomes for back pain and 3 for abdominal pain had kappa scores above a very modest level of ≥ 0.2 for chart audit of EHR data and none for algorithmically obtained EHR/claims data. Of the other 5 outcomes for which claims data were considered to be the best information source, only 2 outcomes from patient surveys and 3 outcomes from chart audits had kappa scores ≥ 0.2. Conclusions: For the types of outcomes studied here, medical record or claims data do not provide an adequate source of information except for a few outcomes where patient reports may be less accurate

Clinician perceptions of factors influencing referrals to a smoking cessation program

<p>Abstract</p> <p>Background</p> <p>Referral of patients to smoking cessation telephone counseling (i.e., quitline) is an underutilized resource by primary care physicians. Previously, we conducted a randomized trial to determine the effectiveness of benchmarked feedback on clinician referrals to a quitline. Subsequently, we sought to understand the successful practices used by the high-referring clinicians, and the perceptions of the barriers of referring patients to a quitline among both high and non-referring clinicians in the trial.</p> <p>Methods</p> <p>We conducted a qualitative sub-study with subjects from the randomized trial, comparing high- and non-referring clinicians. Structured interviews were conducted and two investigators employed a thematic analysis of the transcribed data. Themes and included categories were organized into a thematic framework to represent the main response sets.</p> <p>Results</p> <p>As compared to non-referring clinicians, high-referring clinicians more often reported use of the quitline as a primary source of referral, an appreciation of the quitline as an additional resource, reduced barriers to use of the quitline referral process, and a greater personal motivation related to tobacco cessation. Time and competing demands were critical barriers to initiating smoking cessation treatment with patients for all clinicians. Clinicians reported that having one referral source, a referral coordinator, and reimbursement for tobacco counseling (as a billable code) would aid referral.</p> <p>Conclusion</p> <p>Further research is needed to test the effectiveness of new approaches in improving the connection of patients with smoking cessation resources.</p> <p>Trial Registration Number</p> <p>Clinicaltrials.gov NCT00529256</p

People of the British Isles: preliminary analysis of genotypes and surnames in a UK control population

There is a great deal of interest in fine scale population structure in the UK, both as a signature of historical immigration events and because of the effect population structure may have on disease association studies. Although population structure appears to have a minor impact on the current generation of genome-wide association studies, it is likely to play a significant part in the next generation of studies designed to search for rare variants. A powerful way of detecting such structure is to control and document carefully the provenance of the samples involved. Here we describe the collection of a cohort of rural UK samples (The People of the British Isles), aimed at providing a well-characterised UK control population that can be used as a resource by the research community as well as providing fine scale genetic information on the British population. So far, some 4,000 samples have been collected, the majority of which fit the criteria of coming from a rural area and having all four grandparents from approximately the same area. Analysis of the first 3,865 samples that have been geocoded indicates that 75% have a mean distance between grandparental places of birth of 37.3km, and that about 70% of grandparental places of birth can be classed as rural. Preliminary genotyping of 1,057 samples demonstrates the value of these samples for investigating fine scale population structure within the UK, and shows how this can be enhanced by the use of surnames

Resuscitation of Newborn Piglets. Short-Term Influence of FiO2 on Matrix Metalloproteinases, Caspase-3 and BDNF

Perinatal hypoxia-ischemia is a major cause of mortality and cerebral morbidity, and using oxygen during newborn resuscitation may further harm the brain. The aim was to examine how supplementary oxygen used for newborn resuscitation would influence early brain tissue injury, cell death and repair processes and the regulation of genes related to apoptosis, neurodegeneration and neuroprotection.Anesthetized newborn piglets were subjected to global hypoxia and then randomly assigned to resuscitation with 21%, 40% or 100% O(2) for 30 min and followed for 9 h. An additional group received 100% O(2) for 30 min without preceding hypoxia. The left hemisphere was used for histopathology and immunohistochemistry and the right hemisphere was used for in situ zymography in the corpus striatum; gene expression and the activity of various relevant biofactors were measured in the frontal cortex. There was an increase in the net matrix metalloproteinase gelatinolytic activity in the corpus striatum from piglets resuscitated with 100% oxygen vs. 21%. Hematoxylin-eosin (HE) staining revealed no significant changes. Nine hours after oxygen-assisted resuscitation, caspase-3 expression and activity was increased by 30-40% in the 100% O(2) group (n = 9/10) vs. the 21% O(2) group (n = 10; p<0.04), whereas brain-derived neurotrophic factor (BDNF) activity was decreased by 65% p<0.03.The use of 100% oxygen for resuscitation resulted in increased potentially harmful proteolytic activities and attenuated BDNF activity when compared with 21%. Although there were no significant changes in short term cell loss, hyperoxia seems to cause an early imbalance between neuroprotective and neurotoxic mechanisms that might compromise the final pathological outcome

Polymeric Branched Flocculant Effect on the Flocculation Process of Pulp Suspensions in the Papermaking Industry

This paper presents the effect of the structure of cationic polyacrylamides (CPAMs) on flocculation of pulp suspensions and floc properties. A focused beam reflectance measurement (FBRM) probe was used to monitor flocculation, deflocculation, and reflocculation processes in real time. To carry out the study, 1% elemental chlorine free (ECF) eucalyptus kraft pulp containing 20% ground calcium carbonate (GCC) was used. Results show that the effect of the CPAM structure depends on charge density and polymer dose. Floc size does not always decrease with branching degree, whereas floc stability and reflocculation ability increased when highly charged and branched CPAM was used. These findings indicate that the use of highly branched CPAMs with very high molecular weight is very promising as a retention aid method to improve the papermaking process

Physician Practice Patterns and Variation in the Delivery of Preventive Services

BACKGROUND: Strategies to improve preventive services delivery (PSD) have yielded modest effects. A multidimensional approach that examines distinctive configurations of physician attributes, practice processes, and contextual factors may be informative in understanding delivery of this important form of care. OBJECTIVE: We identified naturally occurring configurations of physician practice characteristics (PPCs) and assessed their association with PSD, including variation within configurations. DESIGN: Cross-sectional study. PARTICIPANTS: One hundred thirty-eight family physicians in 84 community practices and 4,046 outpatient visits. MEASUREMENTS: Physician knowledge, attitudes, use of tools and staff, and practice patterns were assessed by ethnographic and survey methods. PSD was assessed using direct observation of the visit and medical record review. Cluster analysis identified unique configurations of PPCs. A priori hypotheses of the configurations likely to perform the best on PSD were tested using a multilevel random effects model. RESULTS: Six distinct PPC configurations were identified. Although PSD significantly differed across configurations, mean differences between configurations with the lowest and highest PSD were small (i.e., 3.4, 7.7, and 10.8 points for health behavior counseling, screening, and immunizations, respectively, on a 100-point scale). Hypotheses were not confirmed. Considerable variation of PSD rates within configurations was observed. CONCLUSIONS: Similar rates of PSD can be attained through diverse physician practice configurations. Significant within-configuration variation may reflect dynamic interactions between PPCs as well as between these characteristics and the contexts in which physicians function. Striving for a single ideal configuration may be less valuable for improving PSD than understanding and leveraging existing characteristics within primary care practices

Characteristics of tropospheric ozone depletion events in the Arctic spring: analysis of the ARCTAS, ARCPAC, and ARCIONS measurements and satellite BrO observations

Arctic ozone depletion events (ODEs) are caused by halogen catalyzed ozone loss. In situ chemistry, advection of ozone-poor air mass, and vertical mixing in the lower troposphere are important factors affecting ODEs. To better characterize the ODEs, we analyze the combined set of surface, ozonesonde, and aircraft in situ measurements of ozone and bromine compounds during the Arctic Research of the Composition of the Troposphere from Aircraft and Satellites (ARCTAS), the Aerosol, Radiation, and Cloud Processes affecting Arctic Climate (ARCPAC), and the Arctic Intensive Ozonesonde Network Study (ARCIONS) experiments (April 2008). Tropospheric BrO columns retrieved from satellite measurements and back trajectory calculations are also used to investigate the characteristics of observed ODEs. In situ observations from these field experiments are inadequate to validate tropospheric BrO columns derived from satellite measurements. In view of this difficulty, we construct an ensemble of tropospheric column BrO estimates from two satellite (OMI and GOME-2) measurements and with three independent methods of calculating stratospheric BrO columns. Furthermore, we select analysis methods that do not depend on the absolute magnitude of column BrO, such as time-lagged correlation analysis of ozone and tropospheric column BrO, to understand characteristics of ODEs. Time-lagged correlation analysis between in situ (surface and ozonesonde) measurements of ozone and satellite derived tropospheric BrO columns indicates that the ODEs are due to either local halogen-driven ozone loss or short-range (&amp;sim;1 day) transport from nearby regions with ozone depletion. The effect of in situ ozone loss is also evident in the diurnal variation difference between low (10th and 25th percentiles) and higher percentiles of surface ozone concentrations at Alert, Canada. Aircraft observations indicate low-ozone air mass transported from adjacent high-BrO regions. Correlation analyses of ozone with potential temperature and time-lagged tropospheric BrO column show that the vertical extent of local ozone loss is surprisingly deep (1–2 km) at Resolute and Churchill, Canada. The unstable boundary layer during ODEs at Churchill could potentially provide a source of free-tropospheric BrO through convective transport and explain the significant negative correlation between free-tropospheric ozone and tropospheric BrO column at this site

Genetic variations in VEGF and VEGFR2 and glioblastoma outcome

Vascular endothelial growth factor (VEGF) and its receptors (VEGFR) are central components in the development and progression of glioblastoma. To investigate if genetic variation in VEGF and VEGFR2 is associated with glioblastoma prognosis, we examined blood samples from 154 glioblastoma cases collected in Sweden and Denmark between 2000 and 2004. Seventeen tagging single nucleotide polymorphisms (SNPs) in VEGF and 27 in VEGFR2 were genotyped and analysed, covering 90% of the genetic variability within the genes. In VEGF, we found no SNPs associated with survival. In VEGFR2, we found two SNPs significantly associated to survival, namely rs2071559 and rs12502008. However, these results are likely to be false positives due to multiple testing and could not be confirmed in a separate dataset. Overall, this study provides little evidence that VEGF and VEGFR2 polymorphisms are important for glioblastoma survival