640 research outputs found
Deriving information from missing data: implications for mood prediction
The availability of mobile technologies has enabled the efficient collection prospective longitudinal, ecologically valid self-reported mood data from psychiatric patients. These data streams have potential for improving the efficiency and accuracy of psychiatric diagnosis as well predicting future mood states enabling earlier intervention. However, missing responses are common in such datasets and there is little consensus as to how this should be dealt with in practice. A signature-based method was used to capture different elements of self-reported mood alongside missing data to both classify diagnostic group and predict future mood in patients with bipolar disorder, borderline personality disorder and healthy controls. The missing-response-incorporated signature-based method achieves roughly 66\% correct diagnosis, with f1 scores for three different clinic groups 59\% (bipolar disorder), 75\% (healthy control) and 61\% (borderline personality disorder) respectively. This was significantly more efficient than the naive model which excluded missing data. Accuracies of predicting subsequent mood states and scores were also improved by inclusion of missing responses. The signature method provided an effective approach to the analysis of prospectively collected mood data where missing data was common and should be considered as an approach in other similar datasets
Identifying psychiatric diagnosis from missing mood data through the use of log-signature features
The availability of mobile technologies has enabled the efficient collection of prospective longitudinal, ecologically valid self-reported clinical questionnaires from people with psychiatric diagnoses. These data streams have potential for improving the efficiency and accuracy of psychiatric diagnosis as well predicting future mood states enabling earlier intervention. However, missing responses are common in such datasets and there is little consensus as to how these should be dealt with in practice. In this study, the missing-response-incorporated log-signature method achieves roughly 74.8% correct diagnosis, with f1 scores for three diagnostic groups 66% (bipolar disorder), 83% (healthy control) and 75% (borderline personality disorder) respectively. This was superior to the naive model which excluded missing data and advanced models which implemented different imputation approaches, namely, k-nearest neighbours (KNN), probabilistic principal components analysis (PPCA) and random forest-based multiple imputation by chained equations (rfMICE). The log-signature method provided an effective approach to the analysis of prospectively collected mood data where missing data was common and should be considered as an approach in other similar datasets. Because of treating missing responses as a signal, its superiority also highlights that missing data conveys valuable clinical information
QTL associated with resistance to cassava brown streak and cassava mosaic diseases in a bi-parental cross of two Tanzanian farmer varieties, Namikonga and Albert
Article purchasedCassava production in Africa is compromised by cassava brown streak disease (CBSD) and cassava mosaic disease (CMD). To reduce costs and increase the precision of resistance breeding, a QTL study was conducted to identify molecular markers linked to resistance against these diseases. A bi-parental F1 mapping population was developed from a cross between the Tanzanian farmer varieties, Namikonga and Albert. A one-step genetic linkage map comprising 943 SNP markers and 18 linkage groups spanning 1776.2 cM was generated. Phenotypic data from 240 F1 progeny were obtained from two disease hotspots in Tanzania, over two successive seasons, 2013 and 2014. Two consistent QTLs linked to resistance to CBSD-induced root necrosis were identified in Namikonga on chromosomes II (qCBSDRNFc2Nm) and XI (qCBSDRNc11Nm) and a putative QTL on chromosome XVIII (qCBSDRNc18Nm). qCBSDRNFc2Nm was identified at Naliendele in both seasons. The same QTL was also associated with CBSD foliar resistance. qCBSDRNc11Nm was identified at Chambezi in both seasons, and was characterized by three peaks, spanning a distance of 253 kb. Twenty-seven genes were identified within this region including two LRR proteins and a signal recognition particle. In addition, two highly significant CMD resistance QTL (qCMDc12.1A and qCMDc12.2A) were detected in Albert, on chromosome 12. Both qCMDc12.1A and qCMDc12.2A lay within the range of markers reported earlier, defining the CMD2 locus. This is the first time that two loci have been identified within the CMD2 QTL, and in germplasm of apparent East African origin. Additional QTLs with minor effects on CBSD and CMD resistance were also identified
Candidate genes for field resistance to cassava brown streak disease revealed through the analysis of multiple data sources
Open Access JournalCassava (Manihot esculenta Crantz) is a food and industrial storage root crop with substantial potential to contribute to managing risk associated with climate change due to its inherent resilience and in providing a biodegradable option in manufacturing. In Africa, cassava production is challenged by two viral diseases, cassava brown streak disease (CBSD) and cassava mosaic disease. Here we detect quantitative trait loci (QTL) associated with CBSD in a biparental mapping population of a Tanzanian landrace, Nachinyaya and AR37-80, phenotyped in two locations over three years. The purpose was to use the information to ultimately facilitate either marker-assisted selection or adjust weightings in genomic selection to increase the efficiency of breeding. Results from this study were considered in relation to those from four other biparental populations, of similar genetic backgrounds, that were phenotyped and genotyped simultaneously. Further, we investigated the co-localization of QTL for CBSD resistance across populations and the genetic relationships of parents based on whole genome sequence information. Two QTL on chromosome 4 for resistance to CBSD foliar symptoms and one on each of chromosomes 11 and 18 for root necrosis were of interest. Of significance within the candidate genes underlying the QTL on chromosome 4 are Phenylalanine ammonia-lyase (PAL) and Cinnamoyl-CoA reductase (CCR) genes and three PEPR1-related kinases associated with the lignin pathway. In addition, a CCR gene was also underlying the root necrosis-resistant QTL on chromosome 11. Upregulation of key genes in the cassava lignification pathway from an earlier transcriptome study, including PAL and CCR, in a CBSD-resistant landrace compared to a susceptible landrace suggests a higher level of basal lignin deposition in the CBSD-resistant landrace. Earlier RNAscope® in situ hybridisation imaging experiments demonstrate that cassava brown streak virus (CBSV) is restricted to phloem vessels in CBSV-resistant varieties, and phloem unloading for replication in mesophyll cells is prevented. The results provide evidence for the involvement of the lignin pathway. In addition, five eukaryotic initiation factor (eIF) genes associated with plant virus resistance were found within the priority QTL regions
QTL associated with resistance to cassava brown streak and cassava mosaic diseases in a bi-parental cross of two Tanzanian farmer varieties, Namikonga and Albert
Cassava production in Africa is compromised by
cassava brown streak disease (CBSD) and cassava mosaic
disease (CMD). To reduce costs and increase the precision
of resistance breeding, a QTL study was conducted to identify molecular markers linked to resistance against
these diseases. A bi-parental F1
mapping population was
developed from a cross between the Tanzanian farmer varieties,
Namikonga and Albert. A one-step genetic linkage
map comprising 943 SNP markers and 18 linkage groups
spanning 1776.2 cM was generated. Phenotypic data from
240 F1
progeny were obtained from two disease hotspots
in Tanzania, over two successive seasons, 2013 and 2014.
Two consistent QTLs linked to resistance to CBSD-induced
root necrosis were identified in Namikonga on chromosomes
II (qCBSDRNFc2Nm) and XI (qCBSDRNc11Nm)
and a putative QTL on chromosome XVIII (qCBSDRNc18Nm).
qCBSDRNFc2Nm was identified at Naliendele
in both seasons. The same QTL was also associated
with CBSD foliar resistance. qCBSDRNc11Nm was identified
at Chambezi in both seasons, and was characterized by
three peaks, spanning a distance of 253 kb. Twenty-seven
genes were identified within this region including two LRR
proteins and a signal recognition particle. In addition, two
highly significant CMD resistance QTL (qCMDc12.1A
and qCMDc12.2A) were detected in Albert, on chromosome
12. Both qCMDc12.1A and qCMDc12.2A lay within the range of markers reported earlier, defining the CMD2
locus. This is the first time that two loci have been identified
within the CMD2 QTL, and in germplasm of apparent
East African origin. Additional QTLs with minor effects on
CBSD and CMD resistance were also identified.The Bill and Melinda Gates Foundation for funding under Contract ID OPPGD1016.http://www.sherpa.ac.uk/romeo/issn/0040-5752/am2017Forestry and Agricultural Biotechnology Institute (FABI)Genetic
Search for a W' boson decaying to a bottom quark and a top quark in pp collisions at sqrt(s) = 7 TeV
Results are presented from a search for a W' boson using a dataset
corresponding to 5.0 inverse femtobarns of integrated luminosity collected
during 2011 by the CMS experiment at the LHC in pp collisions at sqrt(s)=7 TeV.
The W' boson is modeled as a heavy W boson, but different scenarios for the
couplings to fermions are considered, involving both left-handed and
right-handed chiral projections of the fermions, as well as an arbitrary
mixture of the two. The search is performed in the decay channel W' to t b,
leading to a final state signature with a single lepton (e, mu), missing
transverse energy, and jets, at least one of which is tagged as a b-jet. A W'
boson that couples to fermions with the same coupling constant as the W, but to
the right-handed rather than left-handed chiral projections, is excluded for
masses below 1.85 TeV at the 95% confidence level. For the first time using LHC
data, constraints on the W' gauge coupling for a set of left- and right-handed
coupling combinations have been placed. These results represent a significant
improvement over previously published limits.Comment: Submitted to Physics Letters B. Replaced with version publishe
Search for the standard model Higgs boson decaying into two photons in pp collisions at sqrt(s)=7 TeV
A search for a Higgs boson decaying into two photons is described. The
analysis is performed using a dataset recorded by the CMS experiment at the LHC
from pp collisions at a centre-of-mass energy of 7 TeV, which corresponds to an
integrated luminosity of 4.8 inverse femtobarns. Limits are set on the cross
section of the standard model Higgs boson decaying to two photons. The expected
exclusion limit at 95% confidence level is between 1.4 and 2.4 times the
standard model cross section in the mass range between 110 and 150 GeV. The
analysis of the data excludes, at 95% confidence level, the standard model
Higgs boson decaying into two photons in the mass range 128 to 132 GeV. The
largest excess of events above the expected standard model background is
observed for a Higgs boson mass hypothesis of 124 GeV with a local significance
of 3.1 sigma. The global significance of observing an excess with a local
significance greater than 3.1 sigma anywhere in the search range 110-150 GeV is
estimated to be 1.8 sigma. More data are required to ascertain the origin of
this excess.Comment: Submitted to Physics Letters
Measurement of the Lambda(b) cross section and the anti-Lambda(b) to Lambda(b) ratio with Lambda(b) to J/Psi Lambda decays in pp collisions at sqrt(s) = 7 TeV
The Lambda(b) differential production cross section and the cross section
ratio anti-Lambda(b)/Lambda(b) are measured as functions of transverse momentum
pt(Lambda(b)) and rapidity abs(y(Lambda(b))) in pp collisions at sqrt(s) = 7
TeV using data collected by the CMS experiment at the LHC. The measurements are
based on Lambda(b) decays reconstructed in the exclusive final state J/Psi
Lambda, with the subsequent decays J/Psi to an opposite-sign muon pair and
Lambda to proton pion, using a data sample corresponding to an integrated
luminosity of 1.9 inverse femtobarns. The product of the cross section times
the branching ratio for Lambda(b) to J/Psi Lambda versus pt(Lambda(b)) falls
faster than that of b mesons. The measured value of the cross section times the
branching ratio for pt(Lambda(b)) > 10 GeV and abs(y(Lambda(b))) < 2.0 is 1.06
+/- 0.06 +/- 0.12 nb, and the integrated cross section ratio for
anti-Lambda(b)/Lambda(b) is 1.02 +/- 0.07 +/- 0.09, where the uncertainties are
statistical and systematic, respectively.Comment: Submitted to Physics Letters
Search for new physics in events with opposite-sign leptons, jets, and missing transverse energy in pp collisions at sqrt(s) = 7 TeV
A search is presented for physics beyond the standard model (BSM) in final
states with a pair of opposite-sign isolated leptons accompanied by jets and
missing transverse energy. The search uses LHC data recorded at a
center-of-mass energy sqrt(s) = 7 TeV with the CMS detector, corresponding to
an integrated luminosity of approximately 5 inverse femtobarns. Two
complementary search strategies are employed. The first probes models with a
specific dilepton production mechanism that leads to a characteristic kinematic
edge in the dilepton mass distribution. The second strategy probes models of
dilepton production with heavy, colored objects that decay to final states
including invisible particles, leading to very large hadronic activity and
missing transverse energy. No evidence for an event yield in excess of the
standard model expectations is found. Upper limits on the BSM contributions to
the signal regions are deduced from the results, which are used to exclude a
region of the parameter space of the constrained minimal supersymmetric
extension of the standard model. Additional information related to detector
efficiencies and response is provided to allow testing specific models of BSM
physics not considered in this paper.Comment: Replaced with published version. Added journal reference and DO
Measurement of isolated photon production in pp and PbPb collisions at sqrt(sNN) = 2.76 TeV
Isolated photon production is measured in proton-proton and lead-lead
collisions at nucleon-nucleon centre-of-mass energies of 2.76 TeV in the
pseudorapidity range |eta|<1.44 and transverse energies ET between 20 and 80
GeV with the CMS detector at the LHC. The measured ET spectra are found to be
in good agreement with next-to-leading-order perturbative QCD predictions. The
ratio of PbPb to pp isolated photon ET-differential yields, scaled by the
number of incoherent nucleon-nucleon collisions, is consistent with unity for
all PbPb reaction centralities.Comment: Submitted to Physics Letters
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