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Nevin Manimala Statistics

Agent-based and continuous models of hopper bands for the Australian plague locust: How resource consumption mediates pulse formation and geometry.

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Agent-based and continuous models of hopper bands for the Australian plague locust: How resource consumption mediates pulse formation and geometry.

PLoS Comput Biol. 2020 May 04;16(5):e1007820

Authors: Bernoff AJ, Culshaw-Maurer M, Everett RA, Hohn ME, Strickland WC, Weinburd J

Abstract
Locusts are significant agricultural pests. Under favorable environmental conditions flightless juveniles may aggregate into coherent, aligned swarms referred to as hopper bands. These bands are often observed as a propagating wave having a dense front with rapidly decreasing density in the wake. A tantalizing and common observation is that these fronts slow and steepen in the presence of green vegetation. This suggests the collective motion of the band is mediated by resource consumption. Our goal is to model and quantify this effect. We focus on the Australian plague locust, for which excellent field and experimental data is available. Exploiting the alignment of locusts in hopper bands, we concentrate solely on the density variation perpendicular to the front. We develop two models in tandem; an agent-based model that tracks the position of individuals and a partial differential equation model that describes locust density. In both these models, locust are either stationary (and feeding) or moving. Resources decrease with feeding. The rate at which locusts transition between moving and stationary (and vice versa) is enhanced (diminished) by resource abundance. This effect proves essential to the formation, shape, and speed of locust hopper bands in our models. From the biological literature we estimate ranges for the ten input parameters of our models. Sobol sensitivity analysis yields insight into how the band’s collective characteristics vary with changes in the input parameters. By examining 4.4 million parameter combinations, we identify biologically consistent parameters that reproduce field observations. We thus demonstrate that resource-dependent behavior can explain the density distribution observed in locust hopper bands. This work suggests that feeding behaviors should be an intrinsic part of future modeling efforts.

PMID: 32365072 [PubMed – as supplied by publisher]

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Nevin Manimala Statistics

Integration of cortical thickness data in a statistical shape model of the scapula.

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Integration of cortical thickness data in a statistical shape model of the scapula.

Comput Methods Biomech Biomed Engin. 2020 May 04;:1-7

Authors: Pitocchi J, Wirix-Speetjens R, van Lenthe GH, Pérez MÁ

Abstract
Knowledge about bone morphology and bone quality of the scapula throughout the population is fundamental in the design of shoulder implants. In particular, regions with the best bone stock (cortical bone) are taken into account when planning the supporting screws, aiming for an optimal fixation. As an alternative to manual measurements, statistical shape models (SSMs) have been commonly used to describe shape variability within a population. However, explicitly including cortical thickness information in an SSM of the scapula still remains a challenge. Therefore, the goal of this study is to combine scapular bone shape and cortex morphology in an SSM. First, a method to estimate cortical thickness, based on HU (Hounsfield Unit) profile analysis, was developed and validated. Then, based on the manual segmentations of 32 healthy scapulae, a statistical shape model including cortical information was created and evaluated. Generalization, specificity and compactness were calculated in order to assess the quality of the SSM. The average cortical thickness of the SSM was 2.0 ± 0.63 mm. Generalization, specificity and compactness performances confirmed that the combined SSM was able to capture the bone quality changes in the population. In this work we integrated information on the cortical thickness in an SSM for the scapula. From the results we conclude that this methodology is a valuable tool for automatically generating a large population of scapulae and deducing statistics on the cortex. Hence, this SSM can be useful to automate implant design and screw placement in shoulder arthroplasty.

PMID: 32364819 [PubMed – as supplied by publisher]

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Nevin Manimala Statistics

Effect of acclimated temperature on thermal tolerance, immune response and expression of HSP genes in Labeo rohita, Catla catla and their intergeneric hybrids.

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Effect of acclimated temperature on thermal tolerance, immune response and expression of HSP genes in Labeo rohita, Catla catla and their intergeneric hybrids.

J Therm Biol. 2020 Apr;89:102570

Authors: Ahmad M, Zuberi A, Ali M, Syed A, Murtaza MUH, Khan A, Kamran M

Abstract
The ability of a species and population to respond to a decrease or an increase in temperature depends on their adaptive potential. Here, the critical thermal tolerance (CTmax and CTmin) of four populations: Labeo rohita, Catla catla, and their reciprocal hybrids L. rohita♀× C. catla♂ (RC) and C. catla♀ × L. rohita♂ (CR) being acclimatized at four acclimation temperatures (22, 26, 30 and 34 °C) were determined. All populations indicated substantial variations (P < 0.05) in CTmax and CTmin values. L. rohita displayed, comparatively the highest CTmax with largest total and intrinsic polygon zones as well as the upper and lower acquired thermal tolerance zones followed by RC and CR hybrids, while C. catla showed significantly the highest CTmin value and the smallest intrinsic and acquired thermal tolerance zones. Both hybrids illustrated low parent heterosis (≤11%). Additionally, the highest expression of Hsp70 and Hsp90 (heat shock proteins) genes, serum lysozyme level, respiratory burst activity and lowest lipid peroxidation level under lower and higher temperature shock further illustrated strong physiological mechanism of L. rohita in contrast to C. catla, to deal with acute temperature, while hybrids, especially F1 RC hybrid appeared as a good option to replace C. catla in relatively higher and lower temperature areas.

PMID: 32364999 [PubMed – in process]

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Nevin Manimala Statistics

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

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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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Nevin Manimala Statistics

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

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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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Nevin Manimala Statistics

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

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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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Nevin Manimala Statistics

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

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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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Nevin Manimala Statistics

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

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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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Nevin Manimala Statistics

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

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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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Nevin Manimala Statistics

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

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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]