Nevin Manimala

Efficient and Accurate Extracting of Unstructured EHRs on Cancer Therapy Responses for the Development of RECIST Natural Language Processing Tools: Part I, the Corpus.

JCO Clin Cancer Inform. 2020 May;4:383-391

Authors: Li Y, Luo YH, Wampfler JA, Rubinstein SM, Tiryaki F, Ashok K, Warner JL, Xu H, Yang P

Abstract
PURPOSE: Electronic health records (EHRs) are created primarily for nonresearch purposes; thus, the amounts of data are enormous, and the data are crude, heterogeneous, incomplete, and largely unstructured, presenting challenges to effective analyses for timely, reliable results. Particularly, research dealing with clinical notes relevant to patient care and outcome is seldom conducted, due to the complexity of data extraction and accurate annotation in the past. RECIST is a set of widely accepted research criteria to evaluate tumor response in patients undergoing antineoplastic therapy. The aim for this study was to identify textual sources for RECIST information in EHRs and to develop a corpus of pharmacotherapy and response entities for development of natural language processing tools.
METHODS: We focused on pharmacotherapies and patient responses, using 55,120 medical notes (n = 72 types) in Mayo Clinic’s EHRs from 622 randomly selected patients who signed authorization for research. Using the Multidocument Annotation Environment tool, we applied and evaluated predefined keywords, and time interval and note-type filters for identifying RECIST information and established a gold standard data set for patient outcome research.
RESULTS: Key words reduced clinical notes to 37,406, and using four note types within 12 months postdiagnosis further reduced the number of notes to 5,005 that were manually annotated, which covered 97.9% of all cases (n = 609 of 622). The resulting data set of 609 cases (n = 503 for training and n = 106 for validation purpose), contains 736 fully annotated, deidentified clinical notes, with pharmacotherapies and four response end points: complete response, partial response, stable disease, and progressive disease. This resource is readily expandable to specific drugs, regimens, and most solid tumors.
CONCLUSION: We have established a gold standard data set to accommodate development of biomedical informatics tools in accelerating research into antineoplastic therapeutic response.

PMID: 32364754 [PubMed – in process]

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Toward a “treadmill test” for cognition: Improved prediction of general cognitive ability from the task activated brain.

Hum Brain Mapp. 2020 May 04;:

Authors: Sripada C, Angstadt M, Rutherford S, Taxali A, Shedden K

Abstract
General cognitive ability (GCA) refers to a trait-like ability that contributes to performance across diverse cognitive tasks. Identifying brain-based markers of GCA has been a longstanding goal of cognitive and clinical neuroscience. Recently, predictive modeling methods have emerged that build whole-brain, distributed neural signatures for phenotypes of interest. In this study, we employ a predictive modeling approach to predict GCA based on fMRI task activation patterns during the N-back working memory task as well as six other tasks in the Human Connectome Project dataset (n = 967), encompassing 15 task contrasts in total. We found tasks are a highly effective basis for prediction of GCA: The 2-back versus 0-back contrast achieved a 0.50 correlation with GCA scores in 10-fold cross-validation, and 13 out of 15 task contrasts afforded statistically significant prediction of GCA. Additionally, we found that task contrasts that produce greater frontoparietal activation and default mode network deactivation-a brain activation pattern associated with executive processing and higher cognitive demand-are more effective in the prediction of GCA. These results suggest a picture analogous to treadmill testing for cardiac function: Placing the brain in a more cognitively demanding task state significantly improves brain-based prediction of GCA.

PMID: 32364670 [PubMed – as supplied by publisher]

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The home care work environment’s relationships with work engagement and burnout: A cross-sectional multi-centre study in Switzerland.

Health Soc Care Community. 2020 May 04;:

Authors: Möckli N, Denhaerynck K, De Geest S, Leppla L, Beckmann S, Hediger H, Zúñiga F

Abstract
This study aimed to investigate the levels of burnout and work engagement among home care workers in Switzerland and to test their association with job demands and job resources. We conducted a multi-centre, cross-sectional survey in the German-speaking part of Switzerland with a convenience sample of seven home care agencies. Data were collected between September 2017 and January 2018. We assessed burnout with the Maslach Burnout Inventory (MBI) and work engagement with the Utrecht Work Engagement Scale (UWES) as well as job demands (overtime, work-family conflicts, experienced aggression and work stressors) and job resources (predictability, staffing, teamwork, leadership, collaboration, social support, sense of community, feedback). To investigate the levels of burnout and work engagement, we applied descriptive statistics. Based on Bakker and colleagues’ Job Demands-Resources model, we used a path analysis to test the associations of job demands and job resources with burnout and work engagement. We analysed data from 448 home care workers (response rate 61.8%, mean age 44 years (SD 13.2), 96% female). The frequency of burnout in our sample was low, while that of work engagement was high. Job demands correlated positively with emotional exhaustion (β = .54, p < .001) and negatively with work engagement (β = -.25, p < .001). Job resources correlated negatively with emotional exhaustion (β = -.28, p < .001) and positively with work engagement (β = .41, p < .001). Work-family conflicts and work stressors correlated strongest with emotional exhaustion, whereas social support and feedback were found to correlate strongest with work engagement. Improvements to the home care work environment might enhance work engagement and reduce burnout. Corrective interventions could focus on reducing specific aspects of job demands, such as work-family conflicts and work stressors, as well as on increasing aspects of job resources, especially social support and feedback.

PMID: 32364334 [PubMed – as supplied by publisher]

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Fatal anaphylaxis in Italy: Analysis of cause-of-death national data, 2004-2016.

Allergy. 2020 May 04;:

Authors: Bilò MB, Corsi A, Martini M, Penza E, Grippo F, Bignardi D

Abstract
BACKGROUND: Epidemiological data on fatal anaphylaxis are underestimated worldwide. Few Italian data do exist. The aims of the study are to determine the anaphylaxis mortality rate in Italy and its associations with demographic characteristics (gender, age, and geographical distribution), and to investigate which are the most common triggers of fatal anaphylaxis.
MATERIAL AND METHODS: This is a descriptive study analyzing data reported to the National Register of Causes of Death database and managed by the Italian National Institute of Statistics for the years 2004-2016. An analytical method was developed to identify all the ICD-10 codes related to anaphylaxis deaths, which were divided into two classes: “Definite anaphylaxis deaths” and “Possible anaphylaxis deaths”.
RESULTS: From 2004 through 2016, 392 definite anaphylaxis deaths and 220 possible anaphylaxis deaths were recorded. The average mortality rate for definite anaphylaxis, from 2004 to 2016, was 0.51 per million population per year. Definite fatal anaphylaxis was mostly due to the use of medications (73.7%), followed by unspecified causes (20.7%) and hymenoptera stings (5.6%). Concerning possible anaphylaxis deaths, the most common cause was venom-stinging insect (51.4%). We did not find any data on food fatal anaphylaxis. Unspecified anaphylaxis accounted for 21-28% of all cases, underlining the difficulty in accurately ascertaining the causes of fatal anaphylaxis and therefore in assigning the proper ICD-10 code.
CONCLUSION: This is the first study of anaphylaxis-related mortality coming from an official database of the whole Italian population. However, the actual number of deaths by anaphylaxis, and their related triggers, are probably underreported, mostly due to limitations of the current recording system, and to a poor allergy education. Corrective actions should be undertaken for the benefit of the Health System.

PMID: 32364284 [PubMed – as supplied by publisher]

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Analysis of related factors and disease costs of respiratory infection and environmental pollution in children.

Technol Health Care. 2020 Apr 24;:

Authors: Hu F, Jing L, Shi R

Abstract
BACKGROUND: In recent years, air pollution and the number of children with respiratory tract infections increased. This also increased the burden related to the treatment of disease, so the government and relevant departments need to strengthen their management.
OBJECTIVE: The aim of the present study was to quantitatively analyze the relationship between respiratory infection and air quality in children and gain insight into the burden of related diseases.
METHODS: Data regarding outpatient and emergency department visits in children of 14 years or younger in 16 public and private medical institutions were collected for four months. Routine air quality monitoring data in Shanghai from the same period were correlated with these medical data by descriptive statistics, Pearson’s correlation analysis and multivariate linear regression analysis.
RESULTS: There was a positive correlation between respiratory tract infections in 73376 children and AQI, PM2.5, SO2 and NO2 levels. The total medical expense per patient was 80.22 yuan, and the average compensation ratio of medical insurance per patient was 18.95%. The increase in AQI and the concentration of major air pollutants will lead to increased medical treatment for children with respiratory diseases.
CONCLUSION: It is suggested that the intensity of air pollution control should be increased, so that the special period of childhood respiratory protection is strengthened. Moreover, child medical insurance coverage should also be moderately increased to safeguard the rights and interests of children’s health.

PMID: 32364168 [PubMed – as supplied by publisher]

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How accurately can multiparametric magnetic resonance imaging measure the tumour volume of a prostate cancer? Results of a systematic review.

J Med Imaging Radiat Oncol. 2020 May 04;:

Authors: Christie DRH, Sharpley CF

Abstract
The tumour volume of a cancer within the prostate gland is commonly measured with multiparametric MRI. The measurement has a role in many clinical scenarios including focal therapy, but the accuracy of it has never been systematically reviewed. We included articles if they compared tumour volume measurements obtained by mpMRI with a reference volume measurement obtained after radical prostatectomy. Correlation and concordance statistics were summarised. A simple accuracy score was derived by dividing the given mean or median mpMRI volume by the histopathological reference volume. Factors affecting the accuracy were noted. Scores for potential bias and quality were calculated for each article. A total of 18 articles describing 1438 patients were identified. Nine articles gave Pearson’s correlation scores, with a median value of 0.75 but the range was wide (0.42-0.97). A total of 11 articles reported mean values for volume while 9 reported median values. For all 18 articles, the mean or median values for MRI volumes were lower than the corresponding reference values suggesting consistent underestimation. For articles reporting mean and median values for volume, the median accuracy scores were 0.83 and 0.80, respectively. The accuracy was higher for tumours of greater volume, higher grade and when an endorectal coil was used. Accuracy did not seem to improve over time, with a 3 Tesla magnet or by applying a shrinkage factor to the reference measurement. Most studies showed evidence of at least moderate bias, and their quality was highly variable, but neither of these appeared to affect accuracy.

PMID: 32363735 [PubMed – as supplied by publisher]

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The Brownian and Flow-Driven Rotational Dynamics of a Multicomponent DNA Origami-Based Rotor.

Small. 2020 May 03;:e2001855

Authors: Ahmadi Y, Nord AL, Wilson AJ, Hütter C, Schroeder F, Beeby M, Barišić I

Abstract
Nanomechanical devices are becoming increasingly popular due to the very diverse field of potential applications, including nanocomputing, robotics, and drug delivery. DNA is one of the most promising building materials to realize complex 3D structures at the nanoscale level. Several mechanical DNA origami structures have already been designed capable of simple operations such as a DNA box with a controllable lid, bipedal walkers, and cargo sorting robots. However, the nanomechanical properties of mechanically interlinked DNA nanostructures that are in general highly deformable have yet to be extensively experimentally evaluated. In this work, a multicomponent DNA origami-based rotor is created and fully characterized by electron microscopy under negative stain and cryo preparations. The nanodevice is further immobilized on a microfluidic chamber and its Brownian and flow-driven rotational behaviors are analyzed in real time by single-molecule fluorescence microscopy. The rotation in previous DNA rotors based either on strand displacement, electric field or Brownian motion. This study is the first to attempt to manipulate the dynamics of an artificial nanodevice with fluidic flow as a natural force.

PMID: 32363713 [PubMed – as supplied by publisher]

Prevalence and Immunophenotypic Characteristics of Monoclonal B-Cell Lymphocytosis in Healthy Korean Individuals With Lymphocytosis.

Ann Lab Med. 2020 Sep;40(5):409-413

Authors: Yoo IY, Bang SH, Lim DJ, Kim SJ, Kim K, Kim HJ, Kim SH, Cho D

Abstract
Epidemiological studies of monoclonal B-cell lymphocytosis (MBL) have been conducted in limited geographical regions. Little is known about the prevalence of MBL in Asia. We investigated the prevalence and immunophenotypic characteristics of MBL in Koreans who had idiopathic lymphocytosis (lymphocyte count >4.0×109/L) and were ≥40 years of age. A total of 105 leftover peripheral blood samples met these criteria among those from 73,727 healthy individuals who visited the Health Promotion Center, Samsung Medical Center, Korea, from June 2018 to August 2019. The samples were analyzed using eight-color flow cytometry with the following monoclonal antibodies: CD45, CD5, CD10, CD19, CD20, CD23, and kappa and lambda light chains. The overall prevalence of MBL in the study population was 2.9% (3/105); there was one case of chronic lymphocytic leukemia (CLL)-like MBL (CD5+CD23+), one case of atypical CLL-like MBL (CD5+CD23-), and one case of CD5-MBL with a lambda restriction pattern. This is the first study on the MBL prevalence in an East Asian population, and it reveals a relatively low prevalence of MBL in healthy Korean individuals with lymphocytosis.

PMID: 32311854 [PubMed – as supplied by publisher]

Assessing pain in children with autism spectrum disorders: findings from a preliminary validation study.

Scand J Caring Sci. 2020 Apr 20;:

Authors: Palese A, Conforto L, Meloni F, Bordei V, Domenighini A, Bulfone E, Grassetti L, Gonella S

Abstract
AIMS: Assessing pain in children with autism spectrum disorders (ASDs) can be extremely challenging, since many cannot self-report pain. This study aims to test the validity of the Non-Communicating Children’s Pain Checklist – Revised (NCCPC-R) in identifying pain in children and adolescents affected by ASDs.
MATERIALS AND METHODS: A two-phase validation study based on (a) the translation and cultural adaptation of the NCCPC-R to Italian and to ASD-specific needs and context; and (b) the validation of a modified, 32-item version of the NCCPC-R. In all, 141 carers of children aged 6-16 years with ASDs were asked to recall an in-pain episode and a not-in-pain episode of their child and to rate on a 3-point scale (0 = not at all, 3 = very often) each behaviour included in the tool. Internal consistency (Cronbach’s α), explorative and confirmative factorial structure, as well as concurrent and discriminant validity, were all assessed.
RESULTS: Confirmatory factor analysis established the revised version of the NCCPC-R for children with ASDs (named = NCCPC-RASD ), formed from 10 of the original 30 items categorised into three factors (‘Changing in mood’, ‘Increasing in tension’ and ‘Alerting reaction’) to have an acceptable level of reliability. The tool was internally consistent (α = 0.741 during in-pain episodes, α = 0.790 during not-in-pain episodes) and was able to discriminate between in-pain episodes (13.36 out of 40; CI 95% 12.34-14.39) and not-in-pain episodes (7.84 out of 40; CI 95% 6.86-8.82, p < 0.001).
CONCLUSIONS: These results provide preliminary evidence that the 10-item version of the NCCPC-RASD is a reliable and valid tool for assessing pain in children with ASD.

PMID: 32311779 [PubMed – as supplied by publisher]

Early childhood social determinants and family relationships predict parental separation and living arrangements thereafter.

Acta Paediatr. 2020 Apr 20;:

Authors: Hjern A, Bergström M, Kjaer Urhoj S, Andersen AN

Abstract
AIM: Parental separation has been associated with poor mental health in children. with better outcomes in children living in joint physical custody compared to those living with one parent after the separation. In this study we investigated socioeconomic and relational predictors in early childhood of later parental separation and family arrangements thereafter.
METHODS: This study included 34,768 children from the Danish National Birth Cohort, who were living with both parents at the 6 months’ data collection and followed up in 2010-2014 at age 11 years. Questionnaire data from the two data collections were linked with population registers in Statistics Denmark about parental income, education and psychiatric care and analysed in logistic regression models.
RESULTS: Socioeconomic indicators of the family and parental psychiatric disorders before birth of the child and family relationships in infancy predicted parental separation at age 11year. For children with separated parents, a high family income and a high parental educational level were the main predictors of living in joint physical custody at the eleven year follow-up.
CONCLUSION: Socioeconomic living conditions predict parental separation as well as living arrangements thereafter. Studies of consequences of living arrangements after parental separation should account for family factors preceding the separation.

PMID: 32311778 [PubMed – as supplied by publisher]