1,721,053 research outputs found
A modified LOESS normalization applied to microRNA arrays: a comparative evaluation.
No full textMOTIVATION: Microarray normalization is a fundamental step in removing systematic bias and noise variability caused by technical and experimental artefacts. Several approaches, suitable for large-scale genome arrays, have been proposed and shown to be effective in the reduction of systematic errors. Most of these methodologies are based on specific assumptions that are reasonable for whole-genome arrays, but possibly unsuitable for small microRNA (miRNA) platforms. In this work, we propose a novel normalization (loessM), and we investigate, through simulated and real datasets, the influence that normalizations for two-colour miRNA arrays have on the identification of differentially expressed genes. RESULTS: We show that normalizations usually applied to large-scale arrays, in several cases, modify the actual structure of miRNA data, leading to large portions of false positives and false negatives. Nevertheless, loessM is able to outperform other techniques in most experimental scenarios. Moreover, when usual assumptions on differential expression distribution are missed, channel effect has a strikingly negative influence on small arrays, bias that cannot be removed by normalizations but rather by an appropriate experimental design. We find that the combination of loessM with eCADS, an experimental design based on biological replicates dye-swap recently proposed for channel-effect reduction, gives better results in most of the experimental conditions in terms of specificity/sensitivity both on simulated and real data. AVAILABILITY: LoessM R function is freely available at http://gefu.cribi.unipd.it/papers/miRNA-simulation
Alteration, reduction and taste loss: Main causes and potential implications on dietary habits
Full text linkOur sense of taste arises from the sensory information generated after compounds in the oral cavity and oropharynx activate taste receptor cells situated on taste buds. This produces the perception of sweet, bitter, salty, sour, or umami stimuli, depending on the chemical nature of the tastant. Taste impairments (dysgeusia) are alterations of this normal gustatory functioning that may result in complete taste losses (ageusia), partial reductions (hypogeusia), or over-acuteness of the sense of taste (hypergeusia). Taste impairments are not life-threatening conditions, but they can cause su_cient discomfort and lead to appetite loss and changes in eating habits, with possible e_ects on health. Determinants of such alterations are multiple and consist of both genetic and environmental factors, including aging, exposure to chemicals, drugs, trauma, high alcohol consumption, cigarette smoking, poor oral health, malnutrition, and viral upper respiratory infections including influenza. Disturbances or loss of smell, taste, and chemesthesis have also emerged as predominant neurological symptoms of infection by the recent Coronavirus disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus strain 2 (SARS-CoV-2), as well as by previous both endemic and pandemic coronaviruses such as Middle East Respiratory Syndrome Coronavirus (MERS-CoV) and SARS-CoV. This review is focused on the main causes of alteration, reduction, and loss of taste and their potential repercussion on dietary habits and health, with a special focus on the recently developed hypotheses regarding the mechanisms through which SARS-CoV-2 might alter taste perception
A modified LOESS normalisation applied to microRNA arrays: a comparative evaluation
No full textMotivation: Microarray normalization is a fundamental step in removing systematic bias and noise variability caused by technical and experimental artefacts. Several approaches, suitable for large- scale genome arrays, have been proposed and shown to be effective in the reduction of systematic errors. Most of these methodologies are based on specific assumptions that are reasonable for whole- genome arrays, but possibly unsuitable for small microRNA (miRNA) platforms. In this work, we propose a novel normalization (loessM), and we investigate, through simulated and real datasets, the influence that normalizations for two-colour miRNA arrays have on the identification of differentially expressed genes.
Results: We show that normalizations usually applied to large-scale arrays, in several cases, modify the actual structure of miRNA data, leading to large portions of false positives and false negatives. Nevertheless, loessM is able to outperform other techniques in most experimental scenarios. Moreover, when usual assumptions on differential expression distribution are missed, channel effect has a strikingly negative influence on small arrays, bias that cannot be removed by normalizations but rather by an appropriate experimental design. We find that the combination of loessM with eCADS, an experimental design based on biological replicates dye-swap recently proposed for channel-effect reduction, gives better results in most of the experimental conditions in terms of specificity/sensitivity both on simulated and real data
A Bartlett-type correction for likelihood ratio tests with application to testing equality of Gaussian graphical models
Full text linkThis work defines a new correction for the likelihood ratio test for a two-sample problem within the multivariate normal context. This correction applies to decomposable graphical models, where testing equality of distributions can be decomposed into lower dimensional problems
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Adaptive control for improved efficiency of hydraulic systems for high-speed tilting trains
No full textTilting trains are a mature technology using either hydraulic or electrical actuation to perform carbody tilting to reduce centrifugal force in curves at passengers level, thereby maintaining a good passenger comfort at enhanced service speed. The hydraulic actuation systems used in tilting trains operate at constant pressure, which is established to allow operation against the maximum loads at minimum ambient temperatures. However, these conditions occur seldom and unnecessary power is dissipated as heat under normal operating conditions that normally occur for more than 95% of the service time. A research activity was performed to define a variable pressure system adapting the discharge pressure as a function of the outside temperature and of the force to be developed by the actuators. In this system, the variable pressure is established as a function of an appropriate control strategy in order to minimize the power losses while keeping the required dynamic performance. This system architecture provides a large power saving; a reduction between 25 and 50% power is obtained depending on the severity of the track and on the operating conditions. Moreover, lower average heat dissipation and lower average system pressure lead to a reduction of the size of the heat exchanger and to lower stresses in the system components. The paper presents a description of the system and of the control strategy providing the adaptivity of the pump discharge pressure, the thermal and performance analyses, the simulations of the system behaviour at different environmental conditions. This is done for a train in service along tracks for which the time histories of train speed, acceleration and tilt angles were know
The effect of polydextrose on fecal bulk and bowel function in mildly constipated healthy adults: a double-blind, placebo controlled study
Full text linkBackground: Polydextrose (PDX) (8-30g/day) increases fecal bulk and consistency, helping to ease stool passage. However, the results of its effect on defecation frequency and colonic transit have been discordant, and most focused on either healthy or highly constipated adults, leaving the question on if and how PDX could also aid mildly constipated individuals partially unanswered. Material and Methods: We investigated the effects of PDX consumption by healthy subjects experiencing one or more symptoms of mild constipation on fecal bulk, defecation frequency, stool consistency, ease of stool passage, and total colonic transit time to further characterize and generate additional evidence regarding the potential beneficial effects of this fibre. 51 subjects participated in a 4-week, two-center, randomized, double-blind, placebo-controlled, parallel study testing a control (CON) and a PDX treatment (18 g/d included in biscuits and drink mixtures) (registered on clinicaltrials.gov with the identifier" NCT05309837"). Results: Consumption of PDX resulted in 120.7 g and 25.7 g higher fecal wet and dry weight, respectively (p < 0.05). Colonic transit time was ~4 h shorter in the PDX group: although this difference did not reach significance (p > 0.05) as it was underpowered to detect a significant difference for this secondary outcome, this result still carries a physiological importance. Consumption of PDX was well-tolerated, with some PDX volunteers reporting more mild flatulence (p < 0.05). Conclusion: All in all, our study adds new evidence on how a moderate (18g) daily intake of PDX could increase fecal bulking and potentially shorten colonic transit time, making this ingredient a good candidate to be used to reformulate packaged goods by replacing caloric carbohydrates with lower caloric content, enriching food items easily consumed to enhance fibre intake and support bowel function
Adaptive Control for Improved Efficiency of Hydraulic Systems for High Speed Tilting Trains
No full textAdvanced Diagnostics of Position Sensors for the Actuation Systems of High-Speed Tilting Trains
Full text linkTrains tilting permits a train to travel at a high speed while maintaining an acceptable passenger ride quality with respect to the lateral acceleration, and the consequent lateral force, received by the passengers when the train travels on a curved track at a speed in excess of the balance speed built into the curve geometry. The tilting of a train carbody is performed by a control and actuation system which operates as a closed servoloop accepting the commands from the train control system, generating the torque necessary to tilt the carbody with respect to the bogie and measuring the tilt angle to close the control loop. Measurement of the tilt angle of each train vehicle is performed by two sensors located in the front and rear part of the vehicle. Since a correct tilt angle measurement is vital for the system operation and for ensuring a safe ride, in case of discrepancy between the signals of the two tilt angle sensors of any vehicle, the tilting operation is disabled and the train speed is reduced. An innovative tilt angle sensors health management system is herein presented that makes intelligent use of all available information to allow detection of malfunctioning of an individual tilt angle sensor, thereby enabling a continued operation of the tilting system and a high speed travel after a sensor failure occurs
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