Latent physiological factors of complex human diseases revealed by independent component analysis of clinarrays

<p>Abstract</p> <p>Background</p> <p>Diagnosis and treatment of patients in the clinical setting is often driven by known symptomatic factors that distinguish one particular condition from another. Treatment based on noticeable symptoms, however, is limited to the types of clinical biomarkers collected, and is prone to overlooking dysfunctions in physiological factors not easily evident to medical practitioners. We used a vector-based representation of patient clinical biomarkers, or clinarrays, to search for latent physiological factors that underlie human diseases directly from clinical laboratory data. Knowledge of these factors could be used to improve assessment of disease severity and help to refine strategies for diagnosis and monitoring disease progression.</p> <p>Results</p> <p>Applying Independent Component Analysis on clinarrays built from patient laboratory measurements revealed both known and novel concomitant physiological factors for asthma, types 1 and 2 diabetes, cystic fibrosis, and Duchenne muscular dystrophy. Serum sodium was found to be the most significant factor for both type 1 and type 2 diabetes, and was also significant in asthma. TSH3, a measure of thyroid function, and blood urea nitrogen, indicative of kidney function, were factors unique to type 1 diabetes respective to type 2 diabetes. Platelet count was significant across all the diseases analyzed.</p> <p>Conclusions</p> <p>The results demonstrate that large-scale analyses of clinical biomarkers using unsupervised methods can offer novel insights into the pathophysiological basis of human disease, and suggest novel clinical utility of established laboratory measurements.</p

Relative validity of a semiquantitative food frequency questionnaire designed for schoolchildren in western Greece

<p>Abstract</p> <p>Background</p> <p>The use of food frequency questionnaires (FFQs) has become increasingly important in epidemiologic studies. During the past few decades, a wide variety of nutritional studies have used the semiquantitative FFQ as a tool for assessing and evaluating dietary intake. One of the main concerns in a dietary analysis is the validity of the collected dietary data.</p> <p>Methods</p> <p>This paper discusses several methodological and statistical issues related to the validation of a semiquantitative FFQ. This questionnaire was used to assess the nutritional habits of schoolchildren in western Greece. For validation purposes, we selected 200 schoolchildren and contacted their respective parents. We evaluated the relative validity of 400 FFQs (200 children's FFQs and 200 parents' FFQs).</p> <p>Results</p> <p>The correlations between the children's and the parents' questionnaire responses showed that the questionnaire we designed was appropriate for fulfilling the purposes of our study and in ranking subjects according to food group intake.</p> <p>Conclusion</p> <p>Our study shows that the semiquantitative FFQ provides a reasonably reliable measure of dietary intake and corroborates the relative validity of our questionnaire.</p

Beverage patterns and trends among school-aged children in the US, 1989-2008

<p>Abstract</p> <p>Background</p> <p>High intake of sugar-sweetened beverages in childhood is linked to increased risk of obesity and type II diabetes later in life. Using three nationally representative surveys of dietary intake, we investigated beverage patterns and trends among US school-aged children from 1989/91 to 2007/08.</p> <p>Methods</p> <p>3, 583 participants ages 6-11 y old were included. We reported per capita trends in beverage consumption, percent consuming, and amount per consumer for the following categories of beverages: sugar-sweetened beverages (SSB), caloric nutritional beverages (CNB) and low calorie beverages (LCB). Statistically significant differences were tested using the Student's t test in Stata 11.</p> <p>Results</p> <p>While per capita kcal contribution from total beverages remained constant over the study period, per capita consumption of SSBs increased and CNBs decreased in similar magnitude. The substantial increase in consumption of certain SSBs, such as fruit drinks and soda, high fat high sugar milk, and sports drinks, coupled with the decrease in consumption of high fat low sugar milk was responsible for this shift. The percent consuming SSBs as well as the amount per consumer increased significantly over time. Per capita intake of total milk declined, but the caloric contribution from high fat high sugar milk increased substantially. Among ethnicities, important differences in consumption trends of certain SSBs and 100% juice indicate the complexity in determining strategies for children's beverage calorie reduction.</p> <p>Conclusions</p> <p>As upward trends of SSB consumption parallel increases in childhood obesity, educational and policy interventions should be considered.</p

Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV

The performance of muon reconstruction, identification, and triggering in CMS has been studied using 40 inverse picobarns of data collected in pp collisions at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection criteria covering a wide range of physics analysis needs have been examined. For all considered selections, the efficiency to reconstruct and identify a muon with a transverse momentum pT larger than a few GeV is above 95% over the whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4, while the probability to misidentify a hadron as a muon is well below 1%. The efficiency to trigger on single muons with pT above a few GeV is higher than 90% over the full eta range, and typically substantially better. The overall momentum scale is measured to a precision of 0.2% with muons from Z decays. The transverse momentum resolution varies from 1% to 6% depending on pseudorapidity for muons with pT below 100 GeV and, using cosmic rays, it is shown to be better than 10% in the central region up to pT = 1 TeV. Observed distributions of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO

Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV

The performance of muon reconstruction, identification, and triggering in CMS has been studied using 40 inverse picobarns of data collected in pp collisions at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection criteria covering a wide range of physics analysis needs have been examined. For all considered selections, the efficiency to reconstruct and identify a muon with a transverse momentum pT larger than a few GeV is above 95% over the whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4, while the probability to misidentify a hadron as a muon is well below 1%. The efficiency to trigger on single muons with pT above a few GeV is higher than 90% over the full eta range, and typically substantially better. The overall momentum scale is measured to a precision of 0.2% with muons from Z decays. The transverse momentum resolution varies from 1% to 6% depending on pseudorapidity for muons with pT below 100 GeV and, using cosmic rays, it is shown to be better than 10% in the central region up to pT = 1 TeV. Observed distributions of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO

Azimuthal anisotropy of charged particles at high transverse momenta in PbPb collisions at sqrt(s[NN]) = 2.76 TeV

The azimuthal anisotropy of charged particles in PbPb collisions at nucleon-nucleon center-of-mass energy of 2.76 TeV is measured with the CMS detector at the LHC over an extended transverse momentum (pt) range up to approximately 60 GeV. The data cover both the low-pt region associated with hydrodynamic flow phenomena and the high-pt region where the anisotropies may reflect the path-length dependence of parton energy loss in the created medium. The anisotropy parameter (v2) of the particles is extracted by correlating charged tracks with respect to the event-plane reconstructed by using the energy deposited in forward-angle calorimeters. For the six bins of collision centrality studied, spanning the range of 0-60% most-central events, the observed v2 values are found to first increase with pt, reaching a maximum around pt = 3 GeV, and then to gradually decrease to almost zero, with the decline persisting up to at least pt = 40 GeV over the full centrality range measured.Comment: Replaced with published version. Added journal reference and DO

Compressed representation of a partially defined integer function over multiple arguments

In OLAP (OnLine Analitical Processing) data are analysed in an n-dimensional cube. The cube may be represented as a partially defined function over n arguments. Considering that often the function is not defined everywhere, we ask: is there a known way of representing the function or the points in which it is defined, in a more compact manner than the trivial one

Search for new physics with same-sign isolated dilepton events with jets and missing transverse energy

A search for new physics is performed in events with two same-sign isolated leptons, hadronic jets, and missing transverse energy in the final state. The analysis is based on a data sample corresponding to an integrated luminosity of 4.98 inverse femtobarns produced in pp collisions at a center-of-mass energy of 7 TeV collected by the CMS experiment at the LHC. This constitutes a factor of 140 increase in integrated luminosity over previously published results. The observed yields agree with the standard model predictions and thus no evidence for new physics is found. The observations are used to set upper limits on possible new physics contributions and to constrain supersymmetric models. To facilitate the interpretation of the data in a broader range of new physics scenarios, information on the event selection, detector response, and efficiencies is provided.Comment: Published in Physical Review Letter

Measurement of jet fragmentation into charged particles in pp and PbPb collisions at sqrt(s[NN]) = 2.76 TeV

Jet fragmentation in pp and PbPb collisions at a centre-of-mass energy of 2.76 TeV per nucleon pair was studied using data collected with the CMS detector at the LHC. Fragmentation functions are constructed using charged-particle tracks with transverse momenta pt > 4 GeV for dijet events with a leading jet of pt > 100 GeV. The fragmentation functions in PbPb events are compared to those in pp data as a function of collision centrality, as well as dijet-pt imbalance. Special emphasis is placed on the most central PbPb events including dijets with unbalanced momentum, indicative of energy loss of the hard scattered parent partons. The fragmentation patterns for both the leading and subleading jets in PbPb collisions agree with those seen in pp data at 2.76 TeV. The results provide evidence that, despite the large parton energy loss observed in PbPb collisions, the partition of the remaining momentum within the jet cone into high-pt particles is not strongly modified in comparison to that observed for jets in vacuum.Comment: Submitted to the Journal of High Energy Physic

Measurement of prompt J/ψ pair production in pp collisions at √s = 7 Tev

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