Contamination Bias Research Articles

Peeling off foregrounds with the constrained moment ILC method to unveil primordial CMB B modes

ABSTRACT Galactic foregrounds are the main obstacle to observations of the cosmic microwave background (CMB) B-mode polarization. In addition to obscuring the inflationary B-mode signal by several orders of magnitude, Galactic foregrounds have non-trivial spectral signatures that are partially unknown and distorted by averaging effects along the line of sight, within the pixel/beam window, and by various analysis choices (e.g. spherical harmonic transforms and filters). Statistical moment expansion methods provide a powerful tool for modelling the effective Galactic foreground emission resulting from these averaging effects in CMB observations, while blind component separation treatments can handle unknown foregrounds. In this work, we combine these two approaches to develop a new semiblind component separation method at the intersection of parametric and blind methods, called constrained moment ILC (cMILC). This method adds several constraints to the standard ILC method to deproject the main statistical moments of the Galactic foreground emission. Applications to maps are performed in needlet space and when compared to the NILC method, this helps in significantly reducing residual foreground contamination (bias, variance, and skewness) in the reconstructed CMB B-mode map, power spectrum, and tensor-to-scalar ratio. We consider sky simulations for experimental settings similar to those of LiteBIRD and PICO, illustrating which trade-offs between residual foreground biases and degradation of the constraint on r can be expected within the new cMILC framework. We also outline several directions that require more work in preparation for the coming analysis challenges.

Comparing metatranscriptomics, PCR-based methods, and morphology in estimating diversity and composition of zooplankton mock communities

Studying complex metazoan communities requires taxonomic expertise and laborious work if done using the traditional morphological approach. Nowadays, the popular use of molecular25 based methods accompanied by massively parallel sequencing (MPS) provides rapid and higher resolution diversity analyses. However, diversity estimates derived from the molecular-based approach can be biased by the co-detection of environmental DNA (eDNA), pseudogene contamination, and PCR amplification biases. Here, we constructed microcrustacean zooplankton mock communities to compare species diversity and composition estimates from PCR-based methods using genomic (gDNA) and complementary DNA (cDNA), metatranscriptomic transcripts, and morphology data. Mock community analyses show that gDNA mitochondrial cytochrome c oxidase I (mtCOI) amplicons inflate species richness due to environmental and nontarget species sequence contamination. Significantly higher amplicon sequence variant (ASV) and nucleotide diversity in gDNA amplicons than cDNA indicated the presence of putative pseudogenes. Last, PCR-based methods failed to detect the most abundant species in mock communities due to priming site mismatch. Overall, metatranscriptomic transcripts provided estimates of species richness and composition that closely resembled morphological data. The use of metatranscriptomic transcripts was further tested in field samples. The results showed that it could provide consistent species diversity estimates among biological and technical replicates while allowing monitoring of the zooplankton temporal species composition changes using different mitochondrial markers. These findings show that community characterization based on metatranscriptomic transcripts reflects the actual community more than PCR-based approaches.

A Quality Improvement Intervention to Enhance Access to Kidney Transplantation and Living Kidney Donation (EnAKT LKD) in Patients With Chronic Kidney Disease: Clinical Research Protocol of a Cluster-Randomized Clinical Trial.

Background:Many patients with kidney failure will live longer and healthier lives if they receive a kidney transplant rather than dialysis. However, multiple barriers prevent patients from accessing this treatment option.Objective:To determine if a quality improvement intervention provided in chronic kidney disease (CKD) programs (vs. usual care) enables more patients with no recorded contraindications to kidney transplant to complete more steps toward receiving a kidney transplant.Design:This protocol describes a pragmatic 2-arm, parallel-group, open-label, registry-based, cluster-randomized clinical trial—the Enhance Access to Kidney Transplantation and Living Kidney Donation (EnAKT LKD) trial.Setting:All 26 CKD programs in Ontario, Canada, with a trial start date of November 1, 2017. The original end date of March 31, 2021 (3.4 years) has been extended to December 31, 2021 (4.1 years) due to the COVID-19 pandemic.Participants:During the trial, the 26 CKD programs are expected to care for more than 10 000 adult patients with CKD (including patients approaching the need for dialysis and patients receiving dialysis) with no recorded contraindications to a kidney transplant.Intervention:Programs were randomly allocated to provide a quality improvement intervention or usual care. The intervention has 4 main components: (1) local quality improvement teams and administrative support; (2) tailored education and resources for staff, patients, and living kidney donor candidates; (3) support from kidney transplant recipients and living kidney donors; and (4) program-level performance reports and oversight by program leaders.Primary Outcome:The primary outcome is the number of key steps completed toward receiving a kidney transplant analyzed at the cluster level (CKD program). The following 4 unique steps per patient will be counted: (1) patient referred to a transplant center for evaluation, (2) at least one living kidney donor candidate contacts a transplant center for an intended recipient and completes a health history questionnaire to begin their evaluation, (3) patient added to the deceased donor transplant wait list, and (4) patient receives a kidney transplant from a living or deceased donor.Planned Primary Analysis:Study data will be obtained from Ontario’s linked administrative healthcare databases. An intent-to-treat analysis will be conducted comparing the primary outcome between randomized groups using a 2-stage approach. First stage: residuals are obtained from fitting a regression model to individual-level variables ignoring intervention and clustering effects. Second stage: residuals from the first stage are aggregated at the cluster level as the outcome.Limitations:It may not be possible to isolate independent effects of each intervention component, the usual care group could adopt intervention components leading to contamination bias, and the relatively small number of clusters could mean the 2 arms are not balanced on all baseline prognostic factors.Conclusions:The EnAKT LKD trial will provide high-quality evidence on whether a multi-component quality improvement intervention helps patients complete more steps toward receiving a kidney transplant.Trial registration:Clinicaltrials.gov; identifier: NCT03329521.

Assessing the effect of hyperbaric oxygen therapy in breast cancer patients with late radiation toxicity (HONEY trial): a trial protocol using a trial within a cohort design

BackgroundBreast cancer treatment with radiotherapy can induce late radiation toxicity, characterized by pain, fibrosis, edema, impaired arm mobility, and poor cosmetic outcome. Hyperbaric oxygen therapy (HBOT) has been proposed as treatment for late radiation toxicity; however, high-level evidence of effectiveness is lacking. As HBOT is standard treatment and reimbursed by insurers, performing classic randomized controlled trials is difficult. The “Hyperbaric OxygeN therapy on brEast cancer patients with late radiation toxicity” (HONEY) trial aims to evaluate the effectiveness of HBOT on late radiation toxicity in breast cancer patients using the trial within cohorts (TwiCs) design.MethodsThe HONEY trial will be conducted within the Utrecht cohort for Multiple BREast cancer intervention studies and Long-term evaluation (UMBRELLA). Within UMBRELLA, breast cancer patients referred for radiotherapy to the University Medical Centre Utrecht are eligible for inclusion. Patients consent to collection of clinical data and patient-reported outcomes and provide broad consent for randomization into future intervention studies. Patients who meet the HONEY in- and exclusion criteria (participation ≥ 12 months in UMBRELLA, moderate/severe breast or chest wall pain, completed primary breast cancer treatment except hormonal treatment, no prior treatment with HBOT, no contraindications for HBOT, no clinical signs of metastatic or recurrent disease) will be randomized to HBOT or control group on a 2:1 ratio (n = 120). Patients in the control group will not be informed about participation in the trial. Patients in the intervention arm will undergo 30–40 HBOT treatment sessions in a high pressure chamber (2.4 atmospheres absolute) where they inhale 100% oxygen through a mask. Cohort outcome measures (i.e., physical outcomes, quality of life, fatigue, and cosmetic satisfaction) of the HBOT group will be compared to the control group at 3 months follow-up.DiscussionThis pragmatic trial within the UMBELLA cohort was designed to evaluate the effectiveness of HBOT on late radiation toxicity in breast cancer patients using the TwiCs design. Use of the TwiCs design is expected to address issues encountered in classic randomized controlled trials, such as contamination (i.e., HBOT in the control group) and disappointment bias, and generate information about acceptability of HBOT.Trial registrationClinicalTrials.gov. NCT04193722. Registered on 10 December 2019.

Body-worn cameras' effects on police officers and citizen behavior: A systematic review.

Body-worn cameras' effects on police officers and citizen behavior: A systematic review.

Family group decision-making for children at risk of abuse or neglect: A systematic review.

Family group decision-making for children at risk of abuse or neglect: A systematic review.

Contamination in complex healthcare trials: the falls in care homes (FinCH) study experience

BackgroundTrials are at risk of contamination bias which can occur when participants in the control group are inadvertently exposed to the intervention. This is a particular risk in rehabilitation studies where it is easy for trial interventions to be either intentionally or inadvertently adopted in control settings. The Falls in Care Homes (FinCH) trial is used in this paper as an example of a large randomised controlled trial of a complex intervention to explore the potential risks of contamination bias. We outline the FinCH trial design, present the potential risks from contamination bias, and the strategies used in the design of the trial to minimise or mitigate against this. The FinCH trial was a multi-centre randomised controlled trial, with embedded process evaluation, which evaluated whether systematic training in the use of the Guide to Action Tool for Care Homes reduced falls in care home residents.Data were collected from a number of sources to explore contamination in the FinCH trial. Where specific procedures were adopted to reduce risk of, or mitigate against, contamination, this was recorded. Data were collected from study e-mails, meetings with clinicians, research assistant and clinician network communications, and an embedded process evaluation in six intervention care homes.During the FinCH trial, there were six new falls prevention initiatives implemented outside the study which could have contaminated our intervention and findings. Methods used to minimise contamination were: cluster randomisation at the level of care home; engagement with the clinical community to highlight the risks of early adoption; establishing local collaborators in each site familiar with the local context; signing agreements with NHS falls specialists that they would maintain confidentiality regarding details of the intervention; opening additional research sites; and by raising awareness about the importance of contamination in research among participants.ConclusionComplex rehabilitation trials are at risk of contamination bias. The potential for contamination bias in studies can be minimized by strengthening collaboration and dialogue with the clinical community. Researchers should recognise that clinicians may contaminate a study through lack of research expertise.

Methodological Quality of Economic Evaluations in Integrated Care: Evidence from a Systematic Review.

Introduction:The aim of this review is to systematically assess the methodological quality of economic evaluations in integrated care and to identify challenges with conducting such studies.Theory and methods:Searches of grey-literature and scientific papers were performed, from January 2000 to December 2018. A checklist was developed to assess the quality of economic evaluations. Authors’ statements of challenges encountered during their evaluations were qualitatively coded.Results:Forty-four articles were eligible for inclusion. The review found that study design, measurement of cost and outcomes, statistical analysis and presentation of data were the areas with most quality variation. Authors identified challenges mostly related to time horizon of the evaluation, inadequate or lack of comparator group, contamination bias, and a post-hoc evaluation culture.Discussion:Our review found significant differences in quality, with some studies showing poor methodological rigor; challenging conclusions on the cost-effectiveness of integrated care.Conclusion:It is essential for evaluators to use best-practice standards when planning and conducting economic evaluations, in order to build a reliable evidence base for decision-making in integrated care.

A setwise EWMA scheme for monitoring high-dimensional datastreams

The monitoring of high-dimensional data streams has become increasingly important for real-time detection of abnormal activities in many statistical process control (SPC) applications. Although the multivariate SPC has been extensively studied in the literature, the challenges associated with designing a practical monitoring scheme for high-dimensional processes when between-streams correlation exists are yet to be addressed well. Classical [Formula: see text]-test-based schemes do not work well because the contamination bias in estimating the covariance matrix grows rapidly with the increase of dimension. We propose a test statistic which is based on the “divide-and-conquer” strategy, and integrate this statistic into the multivariate exponentially weighted moving average charting scheme for Phase II process monitoring. The key idea is to calculate the [Formula: see text] statistics on low-dimensional sub-vectors and to combine them together. The proposed procedure is essentially distribution-free and computation efficient. The control limit is obtained through the asymptotic distribution of the test statistic under some mild conditions on the dependence structure of stream observations. Our asymptotic results also shed light on quantifying the size of a reference sample required. Both theoretical analysis and numerical results show that the proposed method is able to control the false alarm rate and deliver robust change detection.

A multimodal and multidisciplinary program to prevent loss of mobility in patients aged over 70\u2009years: study protocol of a multicenter cluster randomized study in primary care (the PRISME-3P study)

BackgroundReduced mobility is the first sign of functional decline and can lead to dependency in elderly people. Screening for the risk of mobility limitation in this population is an important public health issue to prevent further disabilities. Despite the current lack of guidelines, primary care healthcare providers may have a central role to play in this type of screening. Multi-domain physical exercise interventions in older persons have shown some efficacy/effectiveness on frailty status, yet, to the best of our knowledge, no published study has focused on patients screened in primary care.MethodThe PRISME-3P study is a national, interventional, multicenter, cluster randomized trial. Patients over 70 years of age will be systematically screened by their general practitioner (GP) on the basis of clinical criteria of mobility limitation. To avoid contamination bias, the unit of randomization will be the GP practice. In the intervention group, patients will consult a geriatrician and a dietician, and will receive a physical training program from a personal trainer who will demonstrate the exercises and provide follow-up coaching. The control group will receive standard care. The primary outcome will be the change in Short Physical Performance Battery (SPPB) scores between inclusion and 6-months follow-up.DiscussionWe expect an improvement of the SPPB between inclusion and 6 months of follow-up.Trial registrationThis study is registered in ClinicalTrials.gov (NCT02847871, 27 July 2016).

Assessing Coastal SMAP Surface Salinity Accuracy and Its Application to Monitoring Gulf of Maine Circulation Dynamics

Monitoring the cold and productive waters of the Gulf of Maine and their interactions with the nearby northwestern (NW) Atlantic shelf is important but challenging. Although remotely sensed sea surface temperature (SST), ocean color, and sea level have become routine, much of the water exchange physics is reflected in salinity fields. The recent invention of satellite salinity sensors, including the Soil Moisture Active Passive (SMAP) radiometer, opens new prospects in regional shelf studies. However, local sea surface salinity (SSS) retrieval is challenging due to both cold SST limiting salinity sensor sensitivity and proximity to land. For the NW Atlantic, our analysis shows that SMAP SSS is subject to an SST-dependent bias that is negative and amplifies in winter and early spring due to the SST-related drop in SMAP sensor sensitivity. On top of that, SMAP SSS is subject to a land contamination bias. The latter bias becomes noticeable and negative when the antenna land contamination factor (LC) exceeds 0.2%, and attains maximum negative values at LC = 0.4%. Coastward of LC = 0.5%, a significant positive land contamination bias in absolute SMAP SSS is evident. SST and land contamination bias components are seasonally dependent due to seasonal changes in SST/winds and terrestrial microwave properties. Fortunately, it is shown that SSS anomalies computed relative to a satellite SSS climatology can effectively remove such seasonal biases along with the real seasonal cycle. SMAP monthly SSS anomalies have sufficient accuracy and applicability to extend nearer to the coasts. They are used to examine the Gulf of Maine water inflow, which displayed important water intrusions in between Georges Banks and Nova Scotia in the winters of 2016/17 and 2017/18. Water intrusion patterns observed by SMAP are generally consistent with independent measurements from the European Soil Moisture Ocean Salinity (SMOS) mission. Circulation dynamics related to the 2016/2017 period and enhanced wind-driven Scotian Shelf transport into the Gulf of Maine are discussed.

Increasing return-to-work among people on sick leave due to common mental disorders: design of a cluster-randomized controlled trial of a problem-solving intervention versus care-as-usual conducted in the Swedish primary health care system (PROSA)

BackgroundCommon mental disorders affect about one-third of the European working-age population and are one of the leading causes of sick leave in Sweden and other OECD countries. Besides the individual suffering, the costs for society are high. This paper describes the design of a study to evaluate a work-related, problem-solving intervention provided at primary health care centers for employees on sick leave due to common mental disorders.MethodsThe study has a two-armed cluster randomized design in which the participating rehabilitation coordinators are randomized into delivering the intervention or providing care-as-usual. Employees on sick leave due to common mental disorders will be recruited by an independent research assistant. The intervention aims to improve the employee’s return-to-work process by identifying problems perceived as hindering return-to-work and finding solutions. The rehabilitation coordinator facilitates a participatory approach, in which the employee and the employer together identify obstacles and solutions in relation to the work situation. The primary outcome is total number of sick leave days during the 18-month follow-up after inclusion. A long-term follow-up at 36 months is planned. Secondary outcomes are short-term sick leave (min. 2 weeks and max. 12 weeks), psychological symptoms, work ability, presenteeism and health related quality of life assessed at baseline, 6 and 12-month follow-up. Intervention fidelity, reach, dose delivered and dose received will be examined in a process evaluation. An economic evaluation will put health-related quality of life and sick leave in relation to costs from the perspectives of society and health care services. A parallel ethical evaluation will focus on the interventions consequences for patient autonomy, privacy, equality, fairness and professional ethos and integrity.DiscussionThe study is a pragmatic trial which will include analyses of the intervention’s effectiveness, and a process evaluation in primary health care settings. Methodological strengths and challenges are discussed, such as the risk of selection bias, contamination and detection bias. If the intervention shows promising results for return-to-work, the prospects are good for implementing the intervention in routine primary health care.Trial registrationClinicalTrials.gov Identifier: NCT03346395 Registered January, 12 2018.

An efficient method to isolate Kupffer cells eliminating endothelial cell contamination and selective bias.

Multicolor flow cytometry and cell sorting are powerful immunologic tools for the study of hepatic mϕ, yet there is no consensus on the optimal method to prepare liver homogenates for these analyses. Using a combination of mϕ and endothelial cell reporter mice, flow cytometry, and confocal imaging, we have shown that conventional flow‐cytometric strategies for identification of Kupffer cells (KCs) leads to inclusion of a significant proportion of CD31hi endothelial cells. These cells were present regardless of the method used to prepare cells for flow cytometry and represented endothelium tightly adhered to remnants of KC membrane. Antibodies to endothelial markers, such as CD31, were vital for their exclusion. This result brings into focus recently published microarray datasets that identify high expression of endothelial cell‐associated genes by KCs compared with other tissue‐resident mϕ. Our studies also revealed significant and specific loss of KCs among leukocytes with commonly used isolation methods that led to enrichment of proliferating and monocyte‐derived mϕ. Hence, we present an optimal method to generate high yields of liver myeloid cells without bias for cell type or contamination with endothelial cells.

Radiocarbon Measurements of Small-Size Foraminiferal Samples with the Mini Carbon Dating System (MICADAS) at the University of Bern: Implications for Paleoclimate Reconstructions

ABSTRACTRadiocarbon (14C) measurements of foraminifera often provide the only absolute age constraints in marine sediments. However, they are often challenging as their reliability and accuracy can be compromised by reduced availability of adequate sample material. New analytical advances using the MIni CArbon DAting System (MICADAS) allow 14C dating of very small samples, circumventing size limitations inherent to conventional 14C measurements with accelerator mass spectrometry (AMS). Here we use foraminiferal samples and carbonate standard material to assess the reproducibility and precision of MICADAS 14C analyses, quantify contamination biases, and determine foraminiferal 14C blank levels. The reproducibility of conventional 14C ages for our planktic (benthic) foraminiferal samples from gas measurements is 200 (130) yr, and has good precision as illustrated by the agreement between both standards and their reference values as well as between small gas- and larger graphitized foraminiferal samples (within 100±60 yr). We observe a constant contamination bias and slightly higher 14C blanks for foraminifera than for carbonate reference materials, limiting gas (graphite) 14C age determinations for foraminifera from our study sites to ~38 (~42) kyr. Our findings underline the significance of MICADAS gas analyses for 14C on smaller-than-conventional sized foraminiferal samples for paleoclimate reconstructions and dating.

Can Building Design Impact Physical Activity? A Natural Experiment.

Workplace design can impact workday physical activity (PA) and sedentary time. The purpose of this study was to evaluate PA behavior among university employees before and after moving into a new building. A pre-post, experimental versus control group study design was used. PA data were collected using surveys and accelerometers from university faculty and staff. Accelerometry was used to compare those moving into the new building (MOVERS) and those remaining in existing buildings (NONMOVERS) and from a control group (CONTROLS). Survey results showed increased self-reported PA for MOVERS and NONMOVERS. All 3 groups significantly increased in objectively collected daily energy expenditure and steps per day. The greatest steps per day increase was in CONTROLS (29.8%) compared with MOVERS (27.5%) and NONMOVERS (15.9%), but there were no significant differences between groups at pretest or posttest. Self-reported and objectively measured PA increased from pretest to posttest in all groups; thus, the increase cannot be attributed to the new building. Confounding factors may include contamination bias due to proximity of control site to experimental site and introduction of a university PA tracking contest during postdata collection. Methodology and results can inform future studies on best design practices for increasing PA.

Medication Reviews Bridging Healthcare (MedBridge): Study protocol for a pragmatic cluster-randomised crossover trial

Introduction: Mismanaged prescribing and use of medication among elderly puts major pressure on current healthcare systems. Performing a medication review, a structured critical examination of a patient’s medications, by a multidisciplinary team during hospital stay with active follow-up into primary care could optimise treatment benefit and minimise harm. However, a lack of high quality evidence inhibits widespread implementation. This poster will describe the rationale and design of a pragmatic cluster-randomised, crossover trial to fulfil this need for evidence. The aim is to study the effects of hospital-initiated multidisciplinary medication reviews, including active follow-up, on elderly patients’ healthcare utilisation compared to 1) usual care and 2) solely hospital based reviews. Methods: Design: Multicentre, three-treatment, replicated, cluster-randomised, crossover trial. Setting: 8 wards with a multidisciplinary team including clinical pharmacists within 4 hospitals in 3 Swedish counties. Participants: Patients aged 65 years or older, admitted to one of the study wards. Exclusion criteria: Palliative stage; residing in other than the hospital’s county; medication review within the last 30 days; one-day admission. Interventions: 1, comprehensive medication review during hospital stay; 2, same as 1 with the addition of active follow-up into primary care; 3, usual care. Primary outcome measure: Incidence of unplanned hospital visits during a 12-month follow-up period. Data collection and analyses: Extraction from the counties’ medical record system into an electronic data capture system. Intention-treat-analyses using general estimating equation techniques and frailty models. Results: The study starts with patient inclusion in January 2017. In May 2017 we will present the preliminary results from the first inclusion period in terms of included patients, identified medication-related problems and treatment changes made by the multidisciplinary team. Discussion: As healthcare resources are limited, it is important to ensure the resources available are used in an optimal way. We aim to contribute to this by performing this trial with two different interventions compared to each other and usual care. We expect to show valid results on a larger scale and a longer follow-up than previous similar studies. Within a first pilot study with three parallel intervention arms, randomisation at patient level within the study wards was found to be very difficult due to practical reasons. This subsequently led to a high risk of contamination bias. To minimise this risk, the most recent Cochrane review within this field advises new clinical trials to randomise at a cluster level. Conclusions and lessons learned: Conclusions will be based on the results from the first study period. This study, which investigates a new model of multidisciplinary medication reviews with clinical pharmacists integrated in hospital ward teams, eventually has a high potential to show a reduction in elderly patients’ morbidity, contributing to more sustainable healthcare in the long run. Limitations and suggestions for future research: Within the study design, there is a risk of within-cluster carryover effects in terms of usual care being affected after an active study period. As this study will only be performed in Sweden, it would be advisable to conduct similar studies in other countries as well.

Protocol-Directed Sedation Versus Non-Protocol-Directed Sedation to Reduce the Duration of Mechanical Ventilation in Intensive Care Patients.

Protocol-Directed Sedation Versus Non-Protocol-Directed Sedation to Reduce the Duration of Mechanical Ventilation in Intensive Care Patients.

Diet-derived microRNAs: unicorn or silver bullet?

In ancient lore, a bullet cast from silver is the only effective weapon against monsters. The uptake of active diet-derived microRNAs (miRNAs) in consumers may be the silver bullet long sought after in nutrition and oral therapeutics. However, the majority of scientists consider the transfer and regulation of consumer’s gene activity by these diet-derived miRNAs to be a fantasy akin to spotting a unicorn. Nevertheless, groups like Dr. Chen-Yu Zhang’s lab in Nanjing University have stockpiled breathtaking amounts of data to shoot down these naysayers. Meanwhile, Dr. Ken Witwer at John Hopkins has steadfastly cautioned the field to beware of fallacies caused by contamination, technical artifacts, and confirmation bias. Here, Dr. Witwer and Dr. Zhang share their realities of dietary miRNAs by answering five questions related to this controversial field.

Doppler sonar measurements of bedload transport: Evaluations using computer models and lab trials

Studies have demonstrated that bottom velocity measurements from Doppler sonar systems are proportional to bedload transport rates. Given the complexity of acoustic backscatter and sidelobe interactions near the bottom boundary, the exact source of this signal is not obvious. We explore this measurement using a computer simulation and a series of laboratory trials. The system that we have developed for these studies, MFDop, is a multi-frequency (1.2-2.2 MHz), bistatic Doppler sonar that provides 3-component velocity profiles over a ~ 30 cm profile with ~5 mm resolution at a rate of 50 profiles/sec. Model simulations show that side-lobe contamination biases the velocity measurements above the bottom but that effect is reduced in the bedload layer itself. We report on tests of our system in field conditions at the St. Anthony Falls Laboratory (SAFL). The SAFL facility provides a 1.8 m deep, 2.75 m wide flume tank. In our trials, we used a 1 m depth flow of about 1 m/s over a mobile bed of sand with median grain size d50 = 0.4 mm. We find agreement between transport estimates determined using the MFDop, the sediment trap system integrated in the SAFL flume, and estimates based on bedform migrations.

MBV: a method to solve sample mislabeling and detect technical bias in large combined genotype and sequencing assay datasets.

Large genomic datasets combining genotype and sequence data, such as for expression quantitative trait loci (eQTL) detection, require perfect matching between both data types. We described here MBV (Match BAM to VCF); a method to quickly solve sample mislabeling and detect cross-sample contamination and PCR amplification bias. MBV is implemented in C ++ as an independent component of the QTLtools software package, the binary and source codes are freely available at https://qtltools.github.io/qtltools/ . olivier.delaneau@unige.ch or emmanouil.dermitzakis@unige.ch. Supplementary data are available at Bioinformatics online.