A low-cost hyperspectral scanner for natural imaging and the study of animal colour vision above and under water

Hyperspectral imaging is a widely used technology for industrial and scientific purposes, but the high cost and large size of commercial setups have made them impractical for most basic research. Here, we designed and implemented a fully open source and low-cost hyperspectral scanner based on a commercial spectrometer coupled to custom optical, mechanical and electronic components. We demonstrate our scanner's utility for natural imaging in both terrestrial and underwater environments. Our design provides sub-nm spectral resolution between 350-950 nm, including the UV part of the light spectrum which has been mostly absent from commercial solutions and previous natural imaging studies. By comparing the full light spectra from natural scenes to the spectral sensitivity of animals, we show how our system can be used to identify subtle variations in chromatic details detectable by different species. In addition, we have created an open access database for hyperspectral datasets collected from natural scenes in the UK and India. Together with comprehensive online build- and use-instructions, our setup provides an inexpensive and customisable solution to gather and share hyperspectral imaging data

Sequencing of Lynch syndrome tumors reveals the importance of epigenetic alterations

Genomic instability and epigenetic aberrations are important classifiers of human tumors, yet, their interrelations are poorly understood. We used Lynch syndrome (LS) to address such relationships. Forty-five tumors (11 colorectal adenomas, 18 colorectal carcinomas, and 16 ovarian carcinomas) were profiled for CpG Island Methylator Phenotype (CIMP) and somatic mutations. All tumors showed high-degree microsatellite instability. Panel sequencing of 578 cancer-relevant genes revealed the average number of 1433, 1124, and 657 non-synonymous somatic mutations per colorectal adenoma, colorectal carcinoma, and ovarian carcinoma, respectively. Genes harboring mutations with allele frequency 25 % or higher in at least 31 % of tumors were regarded to be possible drivers. Among 72 and 10 such genes identified in colorectal and ovarian tumors, respectively, the most frequently mutated genes BRD4 and MLL2 (62 % of colorectal tumors) and ARID1A (50 % of ovarian carcinomas) are involved in epigenetic regulation. The total number of somatic mutations or mutant genes per tumor were significantly associated with CIMP. Our results suggest that even in an inherited disease, tumor type-specific epigenetic changes are significant and may result from regulatory changes (CIMP) or structural events (mutations of epigenetic regulatory genes). The findings are clinically relevant since many of the affected pathways can be therapeutically targeted.Peer reviewe

Reliability of prehospital patient classification in helicopter emergency medical service missions

Background Several scores and codes are used in prehospital clinical quality registries but little is known of their reliability. The aim of this study is to evaluate the inter-rater reliability of the American Society of Anesthesiologists physical status (ASA-PS) classification system, HEMS benefit score (HBS), International Classification of Primary Care, second edition (ICPC-2) and Eastern Cooperative Oncology Group (ECOG) performance status in a helicopter emergency medical service (HEMS) clinical quality registry (CQR). Methods All physicians and paramedics working in HEMS in Finland and responsible for patient registration were asked to participate in this study. The participants entered data of six written fictional missions in the national CQR. The inter-rater reliability of the ASA-PS, HBS, ICPC-2 and ECOG were evaluated using an overall agreement and free-marginal multi-rater kappa (Kappa(free)). Results All 59 Finnish HEMS physicians and paramedics were invited to participate in this study, of which 43 responded and 16 did not answer. One participant was excluded due to unfinished data entering. ASA-PS had an overall agreement of 40.2% and Kappa(free) of 0.28 in this study. HBS had an overall agreement of 44.7% and Kappa(free) of 0.39. ICPC-2 coding had an overall agreement of 51.5% and Kappa(free) of 0.47. ECOG had an overall agreement of 49.6% and Kappa(free) of 0.40. Conclusion This study suggests a marked inter-rater unreliability in prehospital patient scoring and coding even in a relatively uniform group of practitioners working in a highly focused environment. This indicates that the scores and codes should be specifically designed or adapted for prehospital use, and the users should be provided with clear and thorough instructions on how to use them.Peer reviewe

Reentrant stability of superconducting films and the vanishing of dendritic flux instability

We propose a mechanism responsible for the abrupt vanishing of the dendritic flux instability found in many superconducting films when an increasing magnetic field is applied. The onset of flux avalanches and the subsequent reentrance of stability in NbN films were investigated using magneto-optical imaging, and the threshold fields were measured as functions of critical current density jc. The results are explained with excellent quantitative agreement by a thermomagnetic model published recently [D. V. Denisov et al., Phys. Rev. B 73, 014512 (2006)], showing that the reentrant stability is a direct consequence of a monotonously decreasing jc versus fiel

Immunoprofiles and DNA Methylation of Inflammatory Marker Genes in Ulcerative Colitis-Associated Colorectal Tumorigenesis

Immunological and epigenetic changes are interconnected and contribute to tumorigenesis. We determined the immunoprofiles and promoter methylation of inflammation-related genes for colitis-associated colorectal carcinomas (CA-CRC). The results were compared with Lynch syndrome (LS)-associated colorectal tumors, which are characterized by an active immune environment through inherited mismatch repair defects. CA-CRCs (n = 31) were immunohistochemically evaluated for immune cell scores (ICSs) and PDCD1 and CD274 expression. Seven inflammation-associated genes (CD274, NTSR1, PPARG, PTGS2, PYCARD, SOCS1, and SOCS2), the repair gene MGMT, and eight standard marker genes for the CpG Island Methylator Phenotype (CIMP) were investigated for promoter methylation in CA-CRCs, LS tumors (n = 29), and paired normal mucosae by multiplex ligation-dependent probe amplification. All but one CA-CRCs were microsatellite-stable and all LS tumors were microsatellite-unstable. Most CA-CRCs had a high ICS (55%) and a positive CD274 expression in immune cells (52%). NTSR1 revealed frequent tumor-specific hypermethylation in CA-CRC and LS. When compared to LS mucosae, normal mucosae from patients with CA-CRC showed significantly higher methylation of NTSR1 and most CIMP markers. In conclusion, CA-CRCs share a frequent ICShigh/CD274pos expression pattern with LS tumors. Elevated methylation in normal mucosa may indicate field cancerization as a feature of CA-CRC-associated tumorigenesis

Immunoprofiles and DNA Methylation of Inflammatory Marker Genes in Ulcerative Colitis-Associated Colorectal Tumorigenesis

Immunological and epigenetic changes are interconnected and contribute to tumorigenesis. We determined the immunoprofiles and promoter methylation of inflammation-related genes for colitis-associated colorectal carcinomas (CA-CRC). The results were compared with Lynch syndrome (LS)-associated colorectal tumors, which are characterized by an active immune environment through inherited mismatch repair defects. CA-CRCs (n = 31) were immunohistochemically evaluated for immune cell scores (ICSs) and PDCD1 and CD274 expression. Seven inflammation-associated genes (CD274, NTSR1, PPARG, PTGS2, PYCARD, SOCS1, and SOCS2), the repair gene MGMT, and eight standard marker genes for the CpG Island Methylator Phenotype (CIMP) were investigated for promoter methylation in CA-CRCs, LS tumors (n = 29), and paired normal mucosae by multiplex ligation-dependent probe amplification. All but one CA-CRCs were microsatellite-stable and all LS tumors were microsatellite-unstable. Most CA-CRCs had a high ICS (55%) and a positive CD274 expression in immune cells (52%). NTSR1 revealed frequent tumor-specific hypermethylation in CA-CRC and LS. When compared to LS mucosae, normal mucosae from patients with CA-CRC showed significantly higher methylation of NTSR1 and most CIMP markers. In conclusion, CA-CRCs share a frequent ICShigh/CD274pos expression pattern with LS tumors. Elevated methylation in normal mucosa may indicate field cancerization as a feature of CA-CRC-associated tumorigenesis

'Return to Work' Coordinator Model and Work Participation of Employees: A Natural Intervention Study in Finland

Purpose Employers increasingly use 'return to work' (RTW) coordinators to support work ability and extend working careers, particularly among employees with reduced work ability. We examined whether applying this model was associated with changes in employee sickness absence and disability retirements. Methods We used data from the Finnish Public Sector study from 2009 until 2015. Employees where the model was introduced in 2012 constituted the cases (n = 4120, one municipality) and employees where the model was not in use during the follow-up, represented the controls (n = 5600, two municipalities). We analysed risk of disability retirement in 2013-2015 and risk of sickness absence after (2013-2015) vs. before (2009-2011) intervention by case-control status. Results The incidence of disability retirement after the intervention was lower in cases compared to controls both in the total population (hazard ratio HR = 0.49, 95% CI 0.30-0.79) and in the subgroup of participants with reduced work ability (HR = 0.34, 95% CI 0.12-0.99). The risk of sickness absence increased from pre-intervention to post-intervention period both among cases and controls although the relative increase was greater among cases (RRpost- vs. pre-intervention = 1.26, 95% CI 1.14-1.40) than controls (RRpost- vs. pre-intervention = 1.03, 95% CI 0.97-1.08). In the group of employees with reduced work ability, no difference in sickness absence trends between cases and controls was observed. Conclusions These findings suggest that RTW-coordinator model may increase employee sickness absence, but decrease the risk of disability retirement, i.e., permanent exclusion from the labour market

The reliability and accuracy of operational system data in a nationwide helicopter emergency medical services mission database

Aim The aim of this study was to evaluate the reliability and accuracy of documentation in FinnHEMS database, which is a nationwide helicopter emergency service (HEMS) clinical quality registry. Methods This is a nationwide study based on written fictional clinical scenarios. Study subjects were HEMS physicians and paramedics, who filled in the clinical quality registry based on the clinical scenarios. The inter-rater -reliability of the collected data was analyzed with percent agreement and free-marginal multi-rater kappa. Results Dispatch coding had a percent agreement of 91% and free-marginal multi-rater kappa value of 0.83. Coding for transportation or mission cancellation resulted in an agreement of 84% and free-marginal kappa value of 0.68. An agreement of 82% and a kappa value of 0.73 for dispatcher coding was found. Mission end, arrival at hospital and HEMS unit dispatch -times had agreements from 80 to 85% and kappa values from 0.61 to 0.73. The emergency call to dispatch centre time had an agreement of 71% and kappa value of 0.56. The documentation of pain had an agreement of 73% on both the first and second measurements. All other vital parameters had less than 70% agreement and 0.40 kappa value in the first measurement. The documentation of secondary vital parameter measurements resulted in agreements from 72 to 91% and kappa values from 0.43 to 0.64. Conclusion Data from HEMS operations can be gathered reliably in a national clinical quality registry. This study revealed some inaccuracies in data registration and data quality, which are important to detect to improve the overall reliability and validity of the HEMS clinical quality register

Reliability of prehospital patient classification in helicopter emergency medical service missions

BackgroundSeveral scores and codes are used in prehospital clinical quality registries but little is known of their reliability. The aim of this study is to evaluate the inter-rater reliability of the American Society of Anesthesiologists physical status (ASA-PS) classification system, HEMS benefit score (HBS), International Classification of Primary Care, second edition (ICPC-2) and Eastern Cooperative Oncology Group (ECOG) performance status in a helicopter emergency medical service (HEMS) clinical quality registry (CQR).MethodsAll physicians and paramedics working in HEMS in Finland and responsible for patient registration were asked to participate in this study. The participants entered data of six written fictional missions in the national CQR. The inter-rater reliability of the ASA-PS, HBS, ICPC-2 and ECOG were evaluated using an overall agreement and free-marginal multi-rater kappa (Kappa(free)). ResultsAll 59 Finnish HEMS physicians and paramedics were invited to participate in this study, of which 43 responded and 16 did not answer. One participant was excluded due to unfinished data entering. ASA-PS had an overall agreement of 40.2% and Kappa(free) of 0.28 in this study. HBS had an overall agreement of 44.7% and Kappa(free) of 0.39. ICPC-2 coding had an overall agreement of 51.5% and Kappa(free) of 0.47. ECOG had an overall agreement of 49.6% and Kappa(free) of 0.40.ConclusionThis study suggests a marked inter-rater unreliability in prehospital patient scoring and coding even in a relatively uniform group of practitioners working in a highly focused environment. This indicates that the scores and codes should be specifically designed or adapted for prehospital use, and the users should be provided with clear and thorough instructions on how to use them.</div

The reliability and accuracy of operational system data in a nationwide helicopter emergency medical services mission database

Aim The aim of this study was to evaluate the reliability and accuracy of documentation in FinnHEMS database, which is a nationwide helicopter emergency service (HEMS) clinical quality registry. Methods This is a nationwide study based on written fictional clinical scenarios. Study subjects were HEMS physicians and paramedics, who filled in the clinical quality registry based on the clinical scenarios. The inter-rater -reliability of the collected data was analyzed with percent agreement and free-marginal multi-rater kappa. Results Dispatch coding had a percent agreement of 91% and free-marginal multi-rater kappa value of 0.83. Coding for transportation or mission cancellation resulted in an agreement of 84% and free-marginal kappa value of 0.68. An agreement of 82% and a kappa value of 0.73 for dispatcher coding was found. Mission end, arrival at hospital and HEMS unit dispatch -times had agreements from 80 to 85% and kappa values from 0.61 to 0.73. The emergency call to dispatch centre time had an agreement of 71% and kappa value of 0.56. The documentation of pain had an agreement of 73% on both the first and second measurements. All other vital parameters had less than 70% agreement and 0.40 kappa value in the first measurement. The documentation of secondary vital parameter measurements resulted in agreements from 72 to 91% and kappa values from 0.43 to 0.64. Conclusion Data from HEMS operations can be gathered reliably in a national clinical quality registry. This study revealed some inaccuracies in data registration and data quality, which are important to detect to improve the overall reliability and validity of the HEMS clinical quality register.Peer reviewe