Quantifying uncertainty of taxonomic placement in DNA barcoding and metabarcoding

A crucial step in the use of DNA markers for biodiversity surveys is the assignment of Linnaean taxonomies (species, genus, etc.) to sequence reads. This allows the use of all the information known based on the taxonomic names. Taxonomic placement of DNA barcoding sequences is inherently probabilistic because DNA sequences contain errors, because there is natural variation among sequences within a species, and because reference data bases are incomplete and can have false annotations. However, most existing bioinformatics methods for taxonomic placement either exclude uncertainty, or quantify it using metrics other than probability. In this paper we evaluate the performance of the recently proposed probabilistic taxonomic placement method PROTAX by applying it to both annotated reference sequence data as well as to unknown environmental data. Our four case studies include contrasting taxonomic groups (fungi, bacteria, mammals and insects), variation in the length and quality of the barcoding sequences (from individually Sanger-sequenced sequences to short Illumina reads), variation in the structures and sizes of the taxonomies (800–130 000 species) and variation in the completeness of the reference data bases (representing 15–100% of known species). Our results demonstrate that PROTAX yields essentially unbiased probabilities of taxonomic placement, which means its quantification of species identification uncertainty is reliable. As expected, the accuracy of taxonomic placement increases with increasing coverage of taxonomic and reference sequence data bases, and with increasing ratio of genetic variation among taxonomic levels over within taxonomic levels. We conclude that reliable species-level identification from environmental samples is still challenging and that neglecting identification uncertainty can lead to spurious inference. A key aim for future research is the completion of taxonomic and reference sequence data bases and making these two types of data compatible

New insights into the genetic etiology of Alzheimer's disease and related dementias

Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele

Helium identification with LHCb

The identification of helium nuclei at LHCb is achieved using a method based on measurements of ionisation losses in the silicon sensors and timing measurements in the Outer Tracker drift tubes. The background from photon conversions is reduced using the RICH detectors and an isolation requirement. The method is developed using pp collision data at √(s) = 13 TeV recorded by the LHCb experiment in the years 2016 to 2018, corresponding to an integrated luminosity of 5.5 fb-1. A total of around 105 helium and antihelium candidates are identified with negligible background contamination. The helium identification efficiency is estimated to be approximately 50% with a corresponding background rejection rate of up to O(10^12). These results demonstrate the feasibility of a rich programme of measurements of QCD and astrophysics interest involving light nuclei

Momentum scale calibration of the LHCb spectrometer

For accurate determination of particle masses accurate knowledge of the momentum scale of the detectors is crucial. The procedure used to calibrate the momentum scale of the LHCb spectrometer is described and illustrated using the performance obtained with an integrated luminosity of 1.6 fb-1 collected during 2016 in pp running. The procedure uses large samples of J/ψ → μ + μ - and B+ → J/ψ K + decays and leads to a relative accuracy of 3 × 10-4 on the momentum scale

Curvature-bias corrections using a pseudomass method

Momentum measurements for very high momentum charged particles, such as muons from electroweak vector boson decays, are particularly susceptible to charge-dependent curvature biases that arise from misalignments of tracking detectors. Low momentum charged particles used in alignment procedures have limited sensitivity to coherent displacements of such detectors, and therefore are unable to fully constrain these misalignments to the precision necessary for studies of electroweak physics. Additional approaches are therefore required to understand and correct for these effects. In this paper the curvature biases present at the LHCb detector are studied using the pseudomass method in proton-proton collision data recorded at centre of mass energy √(s)=13 TeV during 2016, 2017 and 2018. The biases are determined using Z→μ + μ - decays in intervals defined by the data-taking period, magnet polarity and muon direction. Correcting for these biases, which are typically at the 10-4 GeV-1 level, improves the Z→μ + μ - mass resolution by roughly 18% and eliminates several pathological trends in the kinematic-dependence of the mean dimuon invariant mass

Mammals OTUs

FASTA file. Mammalian mt 16S rRNA derived from blood meals of 20.000 haematophagous leeches, sequenced by Illumina HiSeq 2000. OTU clustering with 98% similarity. Cluster size included in FASTA ID of each OTU

Data from: Quantifying uncertainty of taxonomic placement in DNA barcoding and metabarcoding

A crucial step in the use of DNA markers for biodiversity surveys is the assignment of Linnaean taxonomies (species, genus, etc.) to sequence reads. This allows the use of all the information known based on the taxonomic names. Taxonomic placement of DNA barcoding sequences is inherently probabilistic because DNA sequences contain errors, because there is natural variation among sequences within a species, and because reference data bases are incomplete and can have false annotations. However, most existing bioinformatics methods for taxonomic placement either exclude uncertainty, or quantify it using metrics other than probability. In this paper we evaluate the performance of the recently proposed probabilistic taxonomic placement method PROTAX by applying it to both annotated reference sequence data as well as to unknown environmental data. Our four case studies include contrasting taxonomic groups (fungi, bacteria, mammals and insects), variation in the length and quality of the barcoding sequences (from individually Sanger-sequenced sequences to short Illumina reads), variation in the structures and sizes of the taxonomies (800–130 000 species) and variation in the completeness of the reference data bases (representing 15–100% of known species). Our results demonstrate that PROTAX yields essentially unbiased probabilities of taxonomic placement, which means its quantification of species identification uncertainty is reliable. As expected, the accuracy of taxonomic placement increases with increasing coverage of taxonomic and reference sequence data bases, and with increasing ratio of genetic variation among taxonomic levels over within taxonomic levels. We conclude that reliable species-level identification from environmental samples is still challenging and that neglecting identification uncertainty can lead to spurious inference. A key aim for future research is the completion of taxonomic and reference sequence data bases and making these two types of data compatible

Fungi OTUs

FASTA file. Fungi ITS2 region sequenced with 454 and clustered at 99% similarity threshold. Homopolymers of 454 reads converted into monomers. Cluster size included in FASTA ID of each OTU

Kvalitetssäkring av ASF-EU genom analys och optimering av testrutiner

Detta examensarbete visar hur man har gått till väga för att planera samt tillverka testskåp som underlättar testningen av maskinmoduler i produktionen av en maskin vid företaget LKI Käldman. Företaget tillverkar olika plåthanteringsmaskiner till metallindustrin runtom i världen. Uppgiften har varit att analysera vilka maskinfunktioner som bör testas med testskåp, hur funktionerna bör testas, planering och val av komponenter till testskåpen samt tillverkning av skåpen. Att programmera PLC och manöverpanel har inte ingått i arbetet, men instruktioner har utformats till den som utför programmeringen. Examensarbetets slutresultat blev ett testskåp som är redo att tas i bruk inom produktionen. Med hjälp av detta skåp kan testningen av maskinmodulen LST underlättas och gå snabbare. Därtill har det även planerats och dokumenterats ett gemensamt testskåp för tre andra maskinmoduler. Dokumentationen är klar så långt att en tillverkning är möjlig.This thesis describes how the planning and manufacture of test cabinets have been done. The test cabinets will facilitate the testing of machine modules in the production of a machine at the company LKI Käldman. The company manufactures various sheet metal handling machines for the metal industry worldwide. The task included an analysis of the machine functions that should be tested with the test cabinets and an analysis of how the functions should be tested. Planning and component selection for the test cabinets, and also the manufacture of the cabinets were included. The programming of the PLC and the control panel has not been part of the thesis, only document guidelines for the person that will program have been made. The end result of the thesis is a test cabinet that is ready for use in the production. The test cabinet facilitates and speeds up the testing of the machine module LST. Also, another test cabinet which can be used for three other machine modules has been planned and documented. The documentation has been done so far that the manufacture of the test cabinet is possible