Digital elevation models of the sea-ice surface from airborne laser scanning during MOSAiC

Airborne laser scanners (ALS) are used to map the sea-ice surface at sub-meter resolution. We conducted 64 flights over the Arctic sea ice between September 2019 and September 2020 during the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition to measure sea-ice surface elevation. The flights ranged from repeated, local-scale 5 × 5 km2 floe grid surveys to regional-scale transects more than 100 km long. We provide data at different processing levels: geolocated elevation point clouds and gridded segments of elevation and freeboard with a spatial resolution of 0.5 m. The latter product is corrected for atmospheric backscatter, sea-ice drift, and offset in elevation due to degraded INS/GNSS solutions > 85° N. For floe grid surveys, all data are combined to merged two-dimensional elevation maps. Other provided parameters include laser reflectance and echo width. The presented data offer a unique possibility to study the temporal evolution, spatial distribution, and variability of the snow and sea-ice surface and their properties in addition to validating satellite products.

Helicopter-borne RGB orthomosaics and photogrammetric digital elevation models from the MOSAiC Expedition

The Multidisciplinary Drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition took place between October 2019 and September 2020 giving the rare opportunity to monitor sea-ice properties over a full annual cycle. Here we present 24 high-resolution orthomosaics and 14 photogrammetric digital elevation models of the sea-ice surface around the icebreaker RV Polarstern between March and September 2020. The dataset is based on >34.000 images acquired by a helicopter-borne optical camera system with survey flights covering areas between 1.8 and 96.5 km² around the vessel. Depending on the flight pattern and altitude of the helicopter, ground resolutions of the orthomosaics range between 0.03 and 0.5 m. By combining the photogrammetric products with contemporaneously acquired airborne laser scanner reflectance measurements selected orthomosaics could be corrected for cloud shadows which facilitates their usage for sea-ice and melt pond classification algorithms. The presented dataset is a valuable data source for the interdisciplinary MOSAiC community building a temporal and spatially resolved baseline to accompany various remote sensing and in situ research projects.

[Why is the histomorphological diagnosis of small salivary gland tumours so much more difficult?]

There is a widespread impression among clinicians and pathologists that the histomorphological diagnosis of minor salivary gland tumours is more difficult and more frequently misdiagnosed than that of major glands. This is based on subjective clinical impression; scientific proof of and potential reasons for this difference are lacking. We identified 14 putative clinical, histopathological and combined clinical-histological reasons and four consequences, which together could explain the perceived greater difficulty of diagnosing minor gland tumours. We performed a thorough literature search and a statistical comparison of data from a personal large consultation series (biased for "difficult" cases) with cumulated data from a routine, unselected (non-consultation) series from the literature. Through this comparison, we could prove with statistical significance a series of reasons and consequences for this greater diagnostic difficulty in minor glands. Frequent incisional biopsies, almost obligatory low-grade bland cytology in malignant tumours and insufficient clinical-pathological communication emerged as the most important reasons. The special anatomic location of the hard palate contributes to further diagnostic difficulties, such as tumour necrosis, mucosal ulceration, pseudoinvasion and the "tumoural-mucosal fusion" phenomenon. Knowledge of these pitfalls in clinic and pathology can help overcome these difficulties and reduce the misdiagnosis rate in minor gland tumours. Our findings result in a series of recommendations both for the clinic and pathology.

[New information about tumours of the salivary glands : WHO classification 2022]

The WHO 2022 classification of head and neck tumours contains another slight increase in the number of listed benign and malignant tumour entities of the salivary glands. This includes conceptual changes and alterations in the terminology of some entities. While some new features are regarded as preliminary or provisional, others are strongly disputed (for example the terminology of intraductal carcinoma). The impact of molecular findings, mainly recurrent gene fusions, continues to increase rapidly and some have been included in the definition of certain tumour entities. The significance of molecular findings is, however, still largely restricted to diagnostic aspects. Newly included entities include microsecretory carcinoma (defined by an SS18::MEF2C fusion), sclerosing microcystic adenocarcinoma (similar to skin adnexal tumours of the same name) and mucinous adenocarcinoma (characterized by AKT1 mutations with heterogeneous morphology).

Identification of Multimorbidity Patterns in Rheumatoid Arthritis Through Machine Learning

OBJECTIVE

Recognizing that the interrelationships between chronic conditions that complicate rheumatoid arthritis (RA) are poorly understood, we aimed to identify patterns of multimorbidity and to define their prevalence in RA through machine learning.

METHODS

We constructed RA and age- and sex-matched (1:1) non-RA cohorts within a large commercial insurance database (MarketScan) and the Veterans Health Administration (VHA). Chronic conditions (n = 44) were identified from diagnosis codes from outpatient and inpatient encounters. Exploratory factor analysis was performed separately in both databases, stratified by RA diagnosis and sex, to identify multimorbidity patterns. The association of RA with different multimorbidity patterns was determined using conditional logistic regression.

RESULTS

We studied 226,850 patients in MarketScan (76% female) and 120,780 patients in the VHA (89% male). The primary multimorbidity patterns identified were characterized by the presence of cardiopulmonary, cardiometabolic, and mental health and chronic pain disorders. Multimorbidity patterns were similar between RA and non-RA patients, female and male patients, and patients in MarketScan and the VHA. RA patients had higher odds of each multimorbidity pattern (odds ratios [ORs] 1.17-2.96), with mental health and chronic pain disorders being the multimorbidity pattern most strongly associated with RA (ORs 2.07-2.96).

CONCLUSION

Cardiopulmonary, cardiometabolic, and mental health and chronic pain disorders represent predominant multimorbidity patterns, each of which is overrepresented in RA. The identification of multimorbidity patterns occurring more frequently in RA is an important first step in progressing toward a holistic approach to RA management and warrants assessment of their clinical and predictive utility.

Impact of Imputation Strategies on Fairness in Machine Learning

Research on Fairness and Bias Mitigation in Machine Learning often uses a set of reference datasets for the design and evaluation of novel approaches or definitions. While these datasets are well structured and useful for the comparison of various approaches, they do not reflect that datasets commonly used in real-world applications can have missing values. When such missing values are encountered, the use of imputation strategies is commonplace. However, as imputation strategies potentially alter the distribution of data they can also affect the performance, and potentially the fairness, of the resulting predictions, a topic not yet well understood in the fairness literature. In this article, we investigate the impact of different imputation strategies on classical performance and fairness in classification settings. We find that the selected imputation strategy, along with other factors including the type of classification algorithm, can significantly affect performance and fairness outcomes. The results of our experiments indicate that the choice of imputation strategy is an important factor when considering fairness in Machine Learning. We also provide some insights and guidance for researchers to help navigate imputation approaches for fairness.

Monitoring a changing Arctic: Recent advancements in the study of sea ice microbial communities

Sea ice continues to decline across many regions of the Arctic, with remaining ice becoming increasingly younger and more dynamic. These changes alter the habitats of microbial life that live within the sea ice, which support healthy functioning of the marine ecosystem and provision of resources for human-consumption, in addition to influencing biogeochemical cycles (e.g. air-sea CO₂ exchange). With the susceptibility of sea ice ecosystems to climate change, there is a pressing need to fill knowledge gaps surrounding sea ice habitats and their microbial communities. Of fundamental importance to this goal is the development of new methodologies that permit effective study of them. Based on outcomes from the DiatomARCTIC project, this paper integrates existing knowledge with case studies to provide insight on how to best document sea ice microbial communities, which contributes to the sustainable use and protection of Arctic marine and coastal ecosystems in a time of environmental change.

New entity of microsecretory adenocarcinoma of salivary glands: first case with recurrence and metastases - proof of malignancy

Microsecretory adenocarcinoma (MSA) of the salivary glands is a recently described entity. Due to lack of reported metastases, in 30 cases described until now, the designation as low-grade cancer was so far solely based on demonstration of local tumor invasion and in a single case with perineural invasion. We herein describe the first documented case with local recurrence and hematogenous metastases.

Results after spica cast immobilization following hip reconstruction in 95 cases: is there a need for alternative techniques?

INTRODUCTION

Developmental dysplasia of the hip (DDH), neurogenic dysplasia of the hip (NDH), and Perthes disease often require surgical treatment. Spica casting is a common postoperative immobilization. The purpose of this study was to evaluate the complications related to the immobilization.

MATERIALS AND METHODS

In a retrospective analysis, we included 83 patients (95 hips), who underwent hip reconstructive surgery between 2008 and 2018. We had 43 female and 40 male patients. Age reached from 3 months to 19 years. All patients were treated with a spica cast postoperatively for a 6-week protocol. Complications were analyzed using the full medical documentation and classified according to Clavien-Dindo.

RESULTS

We had complications in 23 patients (27.7%). We counted superficial skin lesions in seven, deep skin lesions in three, spasticity of adductors in three, subluxation in two, infection of the plate in one, fracture of the plate in one, compliance problem in one, dislocations of the cast in two, reluxation in one, delayed bone healing in one and spasticity of knee flexors in one case. According to the classification of Clavien-Dindo, we were able to count ten type I, four type II, nine type III, zero type IV and zero type V adverse events.

CONCLUSION

The usage of a spica cast after hip reconstructive surgery is still the most popular way of aftertreatment. It has a low complication rate, which may be lowered by well-applied casts and foam padding. Known complications such as spasticity in patients with cerebral palsy, skin lesions, and pressure sores should be observed and avoided. Shorter protocols for immobilization with the usage of foam padding and foam splints lead to less complications.

CLINICAL RELEVANCE

Evidence level level IV, case series.

Identifying Glycemic Variability in Diabetes Patient Cohorts and Evaluating Disease Outcomes

Glycemic variability (GV) is an obstacle to effective blood glucose control and an autonomous risk factor for diabetes complications. We, therefore, explored sample data of patients with diabetes mellitus who maintained better amplitude of glycemic fluctuations and compared their disease outcomes with groups having poor control. A retrospective study was conducted using electronic data of patients having hemoglobin A1C (HbA1c) values with five recent time points from Think Whole Person Healthcare (TWPH). The control variability grid analysis (CVGA) plot and coefficient of variability (CV) were used to identify and cluster glycemic fluctuation. We selected important variables using LASSO. Chi-Square, Fisher’s exact test, Bonferroni chi-Square adjusted residual analysis, and multivariate Kruskal–Wallis tests were used to evaluate eventual disease outcomes. Patients with very high CV were strongly associated (p < 0.05) with disorders of lipoprotein (p = 0.0014), fluid, electrolyte, and acid–base balance (p = 0.0032), while those with low CV were statistically significant for factors influencing health status such as screening for other disorders (p = 0.0137), long-term (current) drug therapy (p = 0.0019), and screening for malignant neoplasms (p = 0.0072). Reducing glycemic variability may balance alterations in electrolytes and reduce differences in lipid profiles, which may assist in strategies for managing patients with diabetes mellitus.

Seed-Fill-Shift-Repair: A redistricting heuristic for civic deliberation

Political redistricting is the redrawing of electoral district boundaries. It is normally undertaken to reflect population changes. The process can be abused, in what is called gerrymandering, to favor one party or interest group over another, resulting thereby in broadly undemocratic outcomes that misrepresent the views of the voters. Gerrymandering is especially vexing in the United States. This paper introduces an algorithm, with an implementation, for creating districting plans (whether for political redistricting or for other districting applications). The algorithm, Seed-Fill-Shift-Repair (SFSR), is demonstrated for Congressional redistricting in American states. SFSR is able to create thousands of valid redistricting plans, which may then be used as points of departure for public deliberation regarding how best to redistrict a given polity. The main objectives of this paper are: (i) to present SFSR in a broadly accessible form, including code that implements it and test data, so that it may be used for both civic deliberations by the public and for research purposes. (ii) to make the case for what SFSR essays to do, which is to approach redistricting, and districting generally, from a constraint satisfaction perspective and from the perspective of producing a plurality of feasible solutions that may then serve in subsequent deliberations. To further these goals, we make the code publicly available. The paper presents, for illustration purposes, a corpus of 11,206 valid redistricting plans for the Commonwealth of Pennsylvania (produced by SFSR), using the 2017 American Community Survey, along with descriptive statistics. Also, the paper presents 1,000 plans for each of the states of Arizona, Michigan, North Carolina, Pennsylvania, and Wisconsin, using the 2018 American Community Survey, along with descriptive statistics on these plans and the computations involved in their creation.

Assigning forensic body fluids to donors in mixed body fluids by targeted RNA/DNA deep sequencing of coding region SNPs

Biological traces found at crime scenes are analysed not only to genetically identify the donor(s) but also to determine the composition of the stain. For some cases, it is essential to associate a body fluid with a donor. Especially in mixed body fluid stains, but also in body fluid stains that appear to be single-source, this may be of importance. Linking a DNA profile (sub-source level) with evidence from a presumptive test or mRNA analysis (source level) is not straightforward. Our results support that associating donors and body fluids by means of comparing mixture ratios in RNA and DNA is not recommended. We introduce a set of 35 coding region SNPs (cSNPs) in body fluid-specific mRNA transcripts that represent a direct link between the body fluids and their donors. The discrimination power of the cSNPs was estimated based on allele frequencies calculated from a population sample (n = 188), and we investigated the practical application of the cSNPs in different scenarios. The results demonstrate that more cSNPs are needed to improve the discrimination power. However, the findings are promising as we were able to associate donors with body fluids in mixtures of different body fluids as well as in stains where both donors have contributed the same body fluid, e.g. a blood-blood mixture. In addition, the cSNP assay can be used for body fluid identification. The results of this proof-of-concept study support the use of cSNPs to assign body fluids to the respective donors.

Multiplatform biomarker identification using a data-driven approach enables single-sample classification

BACKGROUND

High-throughput gene expression profiles have allowed discovery of potential biomarkers enabling early diagnosis, prognosis and developing individualized treatment. However, it remains a challenge to identify a set of reliable and reproducible biomarkers across various gene expression platforms and laboratories for single sample diagnosis and prognosis. We address this need with our Data-Driven Reference (DDR) approach, which employs stably expressed housekeeping genes as references to eliminate platform-specific biases and non-biological variabilities.

RESULTS

Our method identifies biomarkers with "built-in" features, and these features can be interpreted consistently regardless of profiling technology, which enable classification of single-sample independent of platforms. Validation with RNA-seq data of blood platelets shows that DDR achieves the superior performance in classification of six different tumor types as well as molecular target statuses (such as MET or HER2-positive, and mutant KRAS, EGFR or PIK3CA) with smaller sets of biomarkers. We demonstrate on the three microarray datasets that our method is capable of identifying robust biomarkers for subgrouping medulloblastoma samples with data perturbation due to different microarray platforms. In addition to identifying the majority of subgroup-specific biomarkers in CodeSet of nanoString, some potential new biomarkers for subgrouping medulloblastoma were detected by our method.

CONCLUSIONS

In this study, we present a simple, yet powerful data-driven method which contributes significantly to identification of robust cross-platform gene signature for disease classification of single-patient to facilitate precision medicine. In addition, our method provides a new strategy for transcriptome analysis.

Two-Sided Matching for mentor-mentee allocations-Algorithms and manipulation strategies

In scenarios where allocations are determined by participant’s preferences, Two-Sided Matching is a well-established approach with applications in College Admissions, School Choice, and Mentor-Mentee matching problems. In such a context, participants in the matching have preferences with whom they want to be matched with. This article studies two important concepts in Two-Sided Matching: multiple objectives when finding a solution, and manipulation of preferences by participants. We use real data sets from a Mentor-Mentee program for the evaluation to provide insight on realistic effects and implications of the two concepts. In the first part of the article, we consider the quality of solutions found by different algorithms using a variety of solution criteria. Most current algorithms focus on one criterion (number of participants matched), while not directly taking into account additional objectives. Hence, we evaluate different algorithms, including multi-objective heuristics, and the resulting trade-offs. The evaluation shows that existing algorithms for the considered problem sizes perform similarly well and close to the optimal solution, yet multi-objective heuristics provide the additional benefit of yielding solutions with better quality on multiple criteria. In the second part, we consider the effects of different types of preference manipulation on the participants and the overall solution. Preference manipulation is a concept that is well established in theory, yet its practical effects on the participants and the solution quality are less clear. Hence, we evaluate the effects of three manipulation strategies on the participants and the overall solution quality, and investigate if the effects depend on the used solution algorithm as well.

GHB614 × T304-40 × GHB119 × COT102 Cotton: Protein Expression Analyses of Field-Grown Samples

Food and feed safety assessment is not enhanced by performing protein expression analysis on stacked trait products. The expression levels of six proteins in cotton matrices from four single cotton events and three conventionally stacked trait cotton products are reported. Three proteins were for insect control; two proteins confer herbicide tolerance; and one protein was a transformation-selectable marker. The cotton matrices were produced at three U.S., five Brazil, and two Argentina field trials. Similar protein expression was observed for all six proteins in the stacked trait products and the single events. However, when two copies of the bar gene were present in the stacked trait products, the expression level of phosphinothricin acetyl transferase herbicide tolerance was additive. Conventional breeding of genetically engineered traits does not alter the level or pattern of expression of the newly introduced proteins, except when multiple copies of the same transgene are present.

Airborne Observations of Summer Thinning of Multiyear Sea Ice Originating From the Lincoln Sea

To better understand recent changes of Arctic sea ice thickness and extent, it is important to distinguish between the contributions of winter growth and summer melt to the sea ice mass balance. In this study we present a Lagrangian approach to quantify summer sea ice melt in which multiyear ice (MYI) floes that were surveyed by airborne electromagnetic thickness sounding within Nares Strait during summer were backtracked, using satellite imagery, to a region in close proximity (3-20 km) to spring ice thickness surveys carried out in the Lincoln Sea. Typical modal total MYI thicknesses, including ~0.4-m snow, ranged between 3.9 and 4.7 m in the Lincoln Sea during April. Ice-only modal thicknesses were between 2.2 and 3.0 m in Nares Strait during August. Total thinning including snow and ice was 1.3 ± 0.1 m including 0.4 ± 0.09 m of snow melt and 0.9 ± 0.2 m of ice melt. This translates to a seasonal net heat input of 305 ± 69 MJ/m2 (262 ± 60 MJ/m2 for ice only) and seasonal net heat flux of 57 ± 13 W/m2 (45 ± 10 W/m2 for ice only), which is unlikely to be explained by solar radiation fluxes alone. Furthermore, our approach provides an improvement on traditional ice mass balance buoy estimates because it integrates melt over larger spatial scales, where melt can be highly variable due to differential melt experienced between melt ponds, bare ice, hummocks, and ridges.

Finding optimal mentor-mentee matches: A case study in applied two-sided matching

Two-Sided Matching is a well-established approach to find allocations and matchings based on the participants' preferences. While its most prominent applications are College Admissions and School Choice problems, this paper applies the concept to the matching of mentors to mentees in a higher education context. Both mentors and mentees have preferences with whom they ideally want to be matched, as well as who they want to avoid. As the general formulation for these types of preferences is NP-hard, several existing approximation algorithms and heuristics are compared with respect to their ability to find a matching with desirable properties. The results show that a combination of evolutionary heuristics and local search approaches works best in finding high-quality solutions, allowing us to find mentor-mentee pairs which are close to the respective ideal match.

Improved method for MR microscopy of brain tissue cultured with the interface method combined with Lenz lenses

MR in microscopy can non-invasively image the morphology of living tissue, which is of particular interest in studying the mammalian brain. Many studies use live animals for basic research on brain functions, disease pathogenesis, and drug development. However, in vitro systems are on the rise, due to advantages such as the absence of a blood-brain barrier, predictable pharmacokinetics, and reduced ethical restrictions. Hence, they present an inexpensive and adequate technique to answer scientific questions and to perform drug screenings. Some publications report the use of acute brain slices for MR microscopy studies, but these only permit single measurements over several hours. Repetitive MR measurements in longitudinal studies demand an MR-compatible setup which allows cultivation for several days or weeks, and hence properly functioning in vitro systems. Organotypic hippocampal slice cultures (OHSC) are a well-established and robust in vitro system which still exhibits most histological hallmarks of the hippocampal network in vivo. An MR compatible incubation platform is introduced in which OHSC are cultivated according to the interface method following Stoppini et al. In this cultivation method a tissue slice is placed onto a membrane with nutrition medium underneath and a gas atmosphere above, where the air-tissue interface perpendicular to the B₀ field induces strong artefacts. We introduce a handling protocol that suppresses these artefacts and increases signal quality significantly to acquire high resolution images of tissue slices. An additional challenge is the lack of available of MR microscopy equipment suitable for small animal scanners. A Lenz lens with an attached capacitor can dramatically increase the SNR in these cases, and wirelessly bring the detection system in close proximity to the sample without compromising the OHSC system through the introduction of wired detectors. The resultant signal gain is demonstrated by imaging a PFA-fixed brain slice with a 72 mm diameter volume coil without a Lenz lens, and with a broadband and a self-resonant Lenz lens. In our setting, the self-resonant Lenz lens increases the SNR 10-fold over using the volume coil only.

Detection of painted-over traces of blood and seminal fluid

Dealing with a refurbished crime scene is a special challenge for forensic investigators. In such cases, a crime scene may not have only been cleaned in order to erase all traces but the walls of an indoor crime scene could also be painted over in order to mask traces of the crime. So far, very few publications have shown that painted-over traces of blood and seminal fluid can be detected using a forensic light source or infrared photography. To date, there have been no systematically executed research studies including guidelines on which settings to use depending on the color of the wall. Moreover, no comparative study has addressed the question of whether it is better to use infrared photography or a forensic light source to visualize painted-over bloodstains. The present study covers the aforementioned gaps and shows that painted-over bloodstains are most easily visualized by infrared photography, while traces of seminal fluid are most easily visualized at 440 nm in combination with a yellow filter-both independent of the color of the wall paint.

Pan-Arctic sea ice-algal chl a biomass and suitable habitat are largely underestimated for multiyear ice

There is mounting evidence that multiyear ice (MYI) is a unique component of the Arctic Ocean and may play a more important ecological role than previously assumed. This study improves our understanding of the potential of MYI as a suitable habitat for sea ice algae on a pan-Arctic scale. We sampled sea ice cores from MYI and first-year sea ice (FYI) within the Lincoln Sea during four consecutive spring seasons. This included four MYI hummocks with a mean chl a biomass of 2.0 mg/m² , a value significantly higher than FYI and MYI refrozen ponds. Our results support the hypothesis that MYI hummocks can host substantial ice-algal biomass and represent a reliable ice-algal habitat due to the (quasi-) permanent low-snow surface of these features. We identified an ice-algal habitat threshold value for calculated light transmittance of 0.014%. Ice classes and coverage of suitable ice-algal habitat were determined from snow and ice surveys. These ice classes and associated coverage of suitable habitat were applied to pan-Arctic CryoSat-2 snow and ice thickness data products. This habitat classification accounted for the variability of the snow and ice properties and showed an areal coverage of suitable ice-algal habitat within the MYI-covered region of 0.54 million km² (8.5% of total ice area). This is 27 times greater than the areal coverage of 0.02 million km² (0.3% of total ice area) determined using the conventional block-model classification, which assigns single-parameter values to each grid cell and does not account for subgrid cell variability. This emphasizes the importance of accounting for variable snow and ice conditions in all sea ice studies. Furthermore, our results indicate the loss of MYI will also mean the loss of reliable ice-algal habitat during spring when food is sparse and many organisms depend on ice-algae.

Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 15-18 March 2016

[This corrects the article DOI: 10.1186/s13054-016-1208-6.].

Multi-Center Evaluation of the Fully Automated PCR-Based Idylla™ KRAS Mutation Assay for Rapid KRAS Mutation Status Determination on Formalin-Fixed Paraffin-Embedded Tissue of Human Colorectal Cancer

Since the advent of monoclonal antibodies against epidermal growth factor receptor (EGFR) in colorectal cancer therapy, the determination of RAS mutational status is needed for therapeutic decision-making. Most prevalent in colorectal cancer are KRAS exon 2 mutations (40% prevalence); lower prevalence is observed for KRAS exon 3 and 4 mutations (6%) and NRAS exon 2, 3, and 4 mutations (5%). The Idylla™ KRAS Mutation Test on the molecular diagnostics Idylla™ platform is a simple (<2 minutes hands-on time), highly reliable, and rapid (approximately 2 hours turnaround time) in vitro diagnostic sample-to-result solution. This test enables qualitative detection of 21 mutations in codons 12, 13, 59, 61, 117, and 146 of the KRAS oncogene being clinically relevant according to the latest clinical guidelines. Here, the performance of the Idylla™ KRAS Mutation Assay, for Research Use Only, was assessed on archived formalin-fixed paraffin-embedded (FFPE) tissue sections by comparing its results with the results previously obtained by routine reference approaches for KRAS genotyping. In case of discordance, samples were assessed further by additional methods. Among the 374 colorectal cancer FFPE samples tested, the overall concordance between the Idylla™ KRAS Mutation Assay and the confirmed reference routine test results was found to be 98.9%. The Idylla™ KRAS Mutation Assay enabled detection of 5 additional KRAS-mutated samples not detected previously with reference methods. As conclusion the Idylla™ KRAS Mutation Test can be applied as routine tool in any clinical setting, without needing molecular infrastructure or expertise, to guide the personalized treatment of colorectal cancer patients.

First detection of sarcoptic mange in free-ranging wild boar (Sus scrofa) in Switzerland

In Switzerland sarcoptic mange is frequent in free-ranging wild carnivores but until recent years no cases had been recorded in wild ungulates. Since 2010, cases have been observed in wild boar in the cantons of Solothurn, Tessin and Thurgau. Here, we report the detection of mange-like skin lesions in wild boars by photo-trapping and the post-mortem findings in 6 culled animals presenting different stages of the disease. Potential sources of infection include mangy red foxes, outdoor domestic pigs and wild boars from surrounding countries. Disease spread in the wild boar population may become relevant not only for wildlife but also for domestic pig health in the future if piggeries' biosecurity is insufficient to prevent interactions with wild boar.

Transplantation of neural progenitor cells in chronic spinal cord injury

Previous studies demonstrated that neural progenitor cells (NPCs) transplanted into a subacute contusion injury improve motor, sensory, and bladder function. In this study we tested whether transplanted NPCs can also improve functional recovery after chronic spinal cord injury (SCI) alone or in combination with the reduction of glial scar and neurotrophic support. Adult rats received a T10 moderate contusion. Thirteen weeks after the injury they were divided into four groups and received either: 1. Medium (control), 2. NPC transplants, 3. NPC+lentivirus vector expressing chondroitinase, or 4. NPC+lentivirus vectors expressing chondroitinase and neurotrophic factors. During the 8 weeks post-transplantation the animals were tested for functional recovery and eventually analyzed by anatomical and immunohistochemical assays. The behavioral tests for motor and sensory function were performed before and after injury, and weekly after transplantation, with some animals also tested for bladder function at the end of the experiment. Transplant survival in the chronic injury model was variable and showed NPCs at the injury site in 60% of the animals in all transplantation groups. The NPC transplants comprised less than 40% of the injury site, without significant anatomical or histological differences among the groups. All groups also showed similar patterns of functional deficits and recovery in the 12 weeks after injury and in the 8 weeks after transplantation using the Basso, Beattie, and Bresnahan rating score, the grid test, and the Von Frey test for mechanical allodynia. A notable exception was group 4 (NPC together with chondroitinase and neurotrophins), which showed a significant improvement in bladder function. This study underscores the therapeutic challenges facing transplantation strategies in a chronic SCI in which even the inclusion of treatments designed to reduce scarring and increase neurotrophic support produce only modest functional improvements. Further studies will have to identify the combination of acute and chronic interventions that will augment the survival and efficacy of neural cell transplants.

Synthesis and NMR analysis of 13C and 15N-labeled long-chain polyamines (LCPAs)

Site specific isotope labels in long-chain polyamines (LCPAs) for the NMR analysis of bioinspired silica nanocomposites.

Microstructural effects of a neuro-modulating drug evaluated by diffusion tensor imaging

In a longitudinal mouse study we evaluated whether diffusion tensor imaging (DTI) can monitor microstructural changes after administration of the neuromodulating drug EPO and whether erythropoietin (EPO) has an effect on cognitive performance. Twelve mice (2 groups with 6 mice each) were scanned in a 7T Bruker Biospin animal scanner with a highly resolved DTI sequence before and 16 days after intraperitoneal injections of EPO or saline. All mice underwent behavioral testing (Morris water maze) and histologic evaluation of hippocampal and corpus callosum cell proliferation and oligodendrogenesis. Whole brain DTI analysis showed significant Trace, RD and AD decrease within the dentate gyrus, subiculum, primary motor, somatosensory, and supplementary somatosensory areas and FA increase in the hippocampus, corpus callosum, and fimbria fornix in EPO treated mice only. ROI-based DTI analysis showed significant Trace and RD decrease and FA increase only in the corpus callosum of EPO treated mice, whereas in the dentate gyrus significant Trace, RD, and AD decrease occurred in both, EPO- and control-group. Behavioral tests showed that EPO treated mice performed better and learned faster than controls. Histologically, the number of BrdU-positive nuclei and optical density of DCX-labeled juvenile neurons significantly increased within the dentate gyrus, corpus callosum and fimbria fornix and the number of NG2-positive oligodendrocyte progenitors in corpus callosum and fimbria fornix, respectively. In conclusion we were able to monitor microstructural changes with DTI and showed EPO treatment-related alterations correlating with enhanced dentate gyrus and corpus callosum cell proliferation and better learning capabilities.

Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels: Results of a collaborative EDNAP exercise

There is increasing interest in forensic ancestry tests, which are part of a growing number of DNA analyses that can enhance routine profiling by obtaining additional genetic information about unidentified DNA donors. Nearly all ancestry tests use single nucleotide polymorphisms (SNPs), but these currently rely on SNaPshot single base extension chemistry that can fail to detect mixed DNA. Insertion-deletion polymorphism (Indel) tests have been developed using dye-labeled primers that allow direct capillary electrophoresis detection of PCR products (PCR-to-CE). PCR-to-CE maintains the direct relationship between input DNA and signal strength as each marker is detected with a single dye, so mixed DNA is more reliably detected. We report the results of a collaborative inter-laboratory exercise of 19 participants (15 from the EDNAP European DNA Profiling group) that assessed a 34-plex SNP test using SNaPshot and a 46-plex Indel test using PCR-to-CE. Laboratories were asked to type five samples with different ancestries and detect an additional mixed DNA sample. Statistical inference of ancestry was made by participants using the Snipper online Bayes analysis portal plus an optional PCA module that analyzes the genotype data alongside calculation of Bayes likelihood ratios. Exercise results indicated consistent genotyping performance from both tests, reaching a particularly high level of reliability for the Indel test. SNP genotyping gave 93.5% concordance (compared to the organizing laboratory's data) that rose to 97.3% excluding one laboratory with a large number of miscalled genotypes. Indel genotyping gave a higher concordance rate of 99.8% and a reduced no-call rate compared to SNP analysis. All participants detected the mixture from their Indel peak height data and successfully assigned the correct ancestry to the other samples using Snipper, with the exception of one laboratory with SNP miscalls that incorrectly assigned ancestry of two samples and did not obtain informative likelihood ratios for a third. Therefore, successful ancestry assignments were achieved by participants in 92 of 95 Snipper analyses. This exercise demonstrates that ancestry inference tests based on binary marker sets can be readily adopted by laboratories that already have well-established CE regimes in place. The Indel test proved to be easy to use and allowed all exercise participants to detect the DNA mixture as well as achieving complete and concordant profiles in nearly all cases. Lastly, two participants successfully ran parallel next-generation sequencing analyses (each using different systems) and achieved high levels of genotyping concordance using the exercise PCR primer mixes unmodified.

Glucocorticoid replacement therapy in adrenal insufficiency--a challenge to physicians?

Adrenal insufficiency (AI) is a rare disease caused by destruction of the adrenal glands or dysfunction of the pituitary gland or the hypothalamus. Treatment usually requires lifelong replacement therapy with glucocorticoids. Correct use of glucocorticoids and early dose adjustments are essential to cover the increased glucocorticoid demand in stress. Repeated education of patients and their partners is the best strategy to avoid life-threatening emergencies. However, there is a debate whether physicians' knowledge regarding AI is sufficient, in part due to the rareness of this endocrine disorder. To determine the present specific knowledge of physicians in a large University Department of Internal Medicine with a clinically and scientifically active Division of Endocrinology, all interns, residents / fellows, specialists or senior physicians / consultants were asked to complete a questionnaire with various possible answers on the subject of AI (n=69, median age 30 years, range 23-49 years). The present data suggest that in the investigated University Hospital setting current physicians' knowledge of medical replacement strategies in AI may be insufficient depending on the level of education and experience. Even physicians with training in endocrinology in part demonstrated extensive knowledge gaps. There might be a need for additional structured information and training on AI, even in specialized hospitals.

Distinct bacterial assemblages reside at different depths in Arctic multiyear sea ice

Bacterial communities in Arctic sea ice play an important role in the regulation of nutrient and energy dynamics in the Arctic Ocean. Sea ice has vertical gradients in temperature, brine salinity and volume, and light and UV levels. Multiyear ice (MYI) has at least two distinct ice layers: old fresh ice with limited permeability, and new saline ice, and may also include a surface melt pond layer. Here, we determine whether bacterial communities (1) differ with ice depth due to strong physical and chemical gradients, (2) are relatively homogenous within a layer, but differ between layers, or (3) do not vary with ice depth. Cores of MYI off northern Ellesmere Island, NU, Canada, were subsectioned in 30-cm intervals, and the bacterial assemblage structure was characterized using 16S rRNA gene pyrotag sequencing. Assemblages clustered into three distinct groups: top (0-30 cm); middle (30-150 cm); and bottom (150-236 cm). These layers correspond to the occurrence of refrozen melt pond ice, at least 2-year-old ice, and newly grown first-year ice at the bottom of the ice sheet, respectively. Thus, MYI houses multiple distinct bacterial assemblages, and in situ conditions appear to play a less important role in structuring microbial assemblages than the age or conditions of the ice at the time of formation.

Memorandum on the use of information technology to improve medication safety

BACKGROUND

Information technology in health care has a clear potential to improve the quality and efficiency of health care, especially in the area of medication processes. On the other hand, existing studies show possible adverse effects on patient safety when IT for medication-related processes is developed, introduced or used inappropriately.

OBJECTIVES

To summarize definitions and observations on IT usage in pharmacotherapy and to derive recommendations and future research priorities for decision makers and domain experts.

METHODS

This memorandum was developed in a consensus-based iterative process that included workshops and e-mail discussions among 21 experts coordinated by the Drug Information Systems Working Group of the German Society for Medical Informatics, Biometry and Epidemiology (GMDS).

RESULTS

The recommendations address, among other things, a stepwise and comprehensive strategy for IT usage in medication processes, the integration of contextual information for alert generation, the involvement of patients, the semantic integration of information resources, usability and adaptability of IT solutions, and the need for their continuous evaluation.

CONCLUSION

Information technology can help to improve medication safety. However, challenges remain regarding access to information, quality of information, and measurable benefits.