The Multivariate Nonparametric Methods for Identifying Gene Sets with Differential Expression

Background

Gene Set Analysis (GSA) identifies differential expression gene sets amid the different phenotypes. The results of published papers in this filed are inconsistent and there is no consensus on the best method. In this paper two new methods, in comparison to the previous ones, are introduced for GSA.

Methods

The MMGSA and MRGSA methods based on multivariate nonparametric techniques were presented. The implementation of five GSA methods (Hotelling's T², Globaltest, Abs_Cat, Med_Cat and Rs_Cat) and the novel methods to detect differential gene expression between phenotypes were compared using simulated and real microarray data sets.

Results

In a real dataset, the results showed that the powers of MMGSA and MRGSA were as well as Globaltest and Tsai. The MRGSA method has not a good performance in the simulation dataset.

Conclusions

The Globaltest method is the best method in the real or simulation datasets. The performance of MMGSA in simulation dataset is good in small-size gene sets. The GLS methods are not good in the simulated data, except the Med_Cat method in large-size gene sets.     

Phenological models of development in Pandemis heparana and Adoxophyes orana for timing the application of Insect Growth Regulators with juvenile-hormone activity

Control of leafrollers using Insect Growth Regulators with juvenile-hormone acitivity (IGR) is a major issue in research on Integrated Pest Management in apple orchards. The IGR is applied at the time of emergence of the last-larval instar of leafrollers, thus causing a disturbance of metamorphosis.Simulation models on the development of Pandemis heparana (Denn. et Schiff.) and Adoxophyes orana (F.v.R.) were developed, partly on the basis of experiments, partly on data from literature, to predict the time of emergence of the various stages, particularly of the last-larval instar and the pupa. The models use the state-variable approach, and include only temperature as a driving variable.Simulated curves of emergence of last-instar larvae, pupae and moths corresponded well with observations on field-collected larvae, reared to adult stage in an outdoor insectary. The curves of pheromone trap catches showed a delay relative to the calculated and observed curves for the eclosion of pupae.To investigate whether the time of IGR application could be related to a temperature sum, the relation between emergence curves of last-instar larvae and temperature sums was studied for several years. For this purpose simulated curves were used, because observations on emergence of last-instar covered only a few years.

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Résumé Le contrôle des Tordeuses par les régulateurs de croissance d'Insectes (IGR), à activité d'hormone juvénile, est un progrès majeur dans la recherche pour la lutte intégrée contre les ennemis des vergers de pommiers.L'IGR appliqué lors de l'apparition du dernier stade larvaire des Tordeuses, perturbe ainsi la métamorphose ultérieure. Afin de prévoir le moment d'apparition des différents stades, et plus particulièrement du dernier stade larvaire, des modèles de simulation du développement de Pandemis heparana (Denn. et Schiff.) et Adoxophyes orana (F.v.R.) ont été élaborés à partir d'expériences et en se basant sur des résultats de la littérature.Le modèle est basé sur l'examen de la variable d'état, la température étant la variable discriminante suivie.Les courbes simulées d'apparition des larves de dernier stade, des nymphes et des papillons correspondent aux observations faites sur les larves récoltées dans la nature et élevées jusqu'au stade adulte dans un insectarium en plein air.Le taux de capture dans les pièges à phéromone présente un retard par rapport aux courbes calculées et observées pour l'éclosion des nymphes. Différentes causes peuvent être attribuées à cette différence, mais l'influence d'aucune d'elles n'a été étudiée.Afin de déterminer si le moment de l'application d'IGR peut être lié à une somme de températures, les courbes d'apparition des larves de dernier stade ont été étudiées en relation avec les sommes de températures portant sur plusieurs années. Les observations concernant l'apparition des larves de dernier stade ne couvrant que 2 années, des courbes simulées ont été utilisées à cet effet. L'emploid de la relation liant le moment de l'apparition à la somme des températures permet de n'avoir à calculer que les sommes de températures pour déterminer le moment opportun de l'application des IGR.

     

Diurnal courses of net photosynthesis and photosystem II quantum efficiency of submerged Lagarosiphon major under natural light conditions

An optode device for net-photosynthesis measurements, based on oxygen-depending quenching of fluorescence from O₂-specific sensors, and PAM fluorometry have been used to study diurnal courses of net-photosynthesis and the F_v/F_m ratio of the submerged plant Lagarosiphon major. Plants were pre-cultivated and studied in large mesocosm flow-through outdoor tanks under 50% and 80% shade cloth, respectively. Growth under the different shade cloths resulted in similar light compensation points (∼20 μmol photons m⁻² s⁻¹), but strongly different light saturation levels, with about 150 μmol m⁻² s⁻¹ for plants grown under 80% shade cloth and about 350 μmol m⁻² s⁻¹ for plants grown under 50% shade cloth. Plants under both growth conditions showed a transient reduction of the maximum F_v/F_m value in the afternoon (down to 70% of the morning control values under 80% shade cloth and down to 85% under 50% shade cloth), which was not accompanied by a reduction of the net photosynthetic rate. This indicated that the fluorescence parameter F_v/F_m must not be a reliable indicator of the rate of photosynthesis under all conditions. The new photo-optical device became evidenced as a valuable tool not only for laboratory experiments, but also for field studies of gas exchange of submerged plants.     

Consensus for experimental design in electromyography (CEDE) project: Single motor unit matrix

The analysis of single motor unit (SMU) activity provides the foundation from which information about the neural strategies underlying the control of muscle force can be identified, due to the one-to-one association between the action potentials generated by an alpha motor neuron and those received by the innervated muscle fibers. Such a powerful assessment has been conventionally performed with invasive electrodes (i.e., intramuscular electromyography (EMG)), however, recent advances in signal processing techniques have enabled the identification of single motor unit (SMU) activity in high-density surface electromyography (HDsEMG) recordings. This matrix, developed by the Consensus for Experimental Design in Electromyography (CEDE) project, provides recommendations for the recording and analysis of SMU activity with both invasive (needle and fine-wire EMG) and non-invasive (HDsEMG) SMU identification methods, summarizing their advantages and disadvantages when used during different testing conditions. Recommendations for the analysis and reporting of discharge rate and peripheral (i.e., muscle fiber conduction velocity) SMU properties are also provided. The results of the Delphi process to reach consensus are contained in an appendix. This matrix is intended to help researchers to collect, report, and interpret SMU data in the context of both research and clinical applications.     

Fluorinated End‐Groups in Electrolytes Induce Ordered Electrolyte/Anode Interface Even at Open‐Circuit Potential as Revealed by Sum Frequency Generation Vibrational Spectroscopy

Fluorine‐based additives have a tremendously beneficial effect on the performance of lithium‐ion batteries, yet the origin of this phenomenon is unclear. This paper shows that the formation of a solid‐electrolyte interphase (SEI) on the anode surface in the first five charge/discharge cycles is affected by the stereochemistry of the electrolyte molecules on the anode surface starting at open‐circuit potential (OCP). This study shows an anode‐specific model system, the reduction of 1,2‐diethoxy ethane with lithium bis(trifluoromethane)sulfonimide, as a salt on an amorphous silicon anode, and compares the electrochemical response and SEI formation to its fluorinated version, bis(2,2,2‐trifluoroethoxy) ethane (BTFEOE), by sum frequency generation (SFG) vibrational spectroscopy under reaction conditions. The SFG results suggest that the ? CF₃ end‐groups of the linear ether BTFEOE change their adsorption orientation on the a‐Si surface at OCP, leading to a better protective layer. Supporting evidence from ex situ scanning electron microscopy and X‐ray photoelectron spectroscopy depth profiling measurements shows that the fluorinated ether, BTFEOE, yields a smooth SEI on the a‐Si surface and enables lithium ions to intercalate deeper into the a‐Si bulk.     

Confidence intervals for directly standardized rates using mid‐p gamma intervals

Directly standardized rates continue to be an integral tool for presenting rates for diseases that are highly dependent on age, such as cancer. Statistically, these rates are modeled as a weighted sum of Poisson random variables. This is a difficult statistical problem, because there are k observed Poisson variables and k unknown means. The gamma confidence interval has been shown through simulations to have at least nominal coverage in all simulated scenarios, but it can be overly conservative. Previous modifications to that method have closer to nominal coverage on average, but they do not achieve the nominal coverage bound in all situations. Further, those modifications are not central intervals, and the upper coverage error rate can be substantially more than half the nominal error. Here we apply a mid‐p modification to the gamma confidence interval. Typical mid‐p methods forsake guaranteed coverage to get coverage that is sometimes higher and sometimes lower than the nominal coverage rate, depending on the values of the parameters. The mid‐p gamma interval does not have guaranteed coverage in all situations; however, in the (not rare) situations where the gamma method is overly conservative, the mid‐p gamma interval often has at least nominal coverage. The mid‐p gamma interval is especially appropriate when one wants a central interval, since simulations show that in many situations both the upper and lower coverage error rates are on average less than or equal to half the nominal error rate.     

Monitoring surgical performance using risk-adjusted cumulative sum charts

The cumulative sum (CUSUM) procedure is a graphical method that is widely used for quality monitoring in industrial settings. More recently it has been used to monitor surgical outcomes whereby it 'signals' if sufficient evidence has accumulated that there has been a change in the surgical failure rate. A limitation of the standard CUSUM procedure in this context is that since it is simply based on the observed surgical outcomes, it may signal as a result of changes in the referral pattern, such as an increased proportion of high-risk patients, rather than due to a change in the actual surgical performance. We describe a new CUSUM procedure that adjusts for each patient's pre-operative risk of surgical failure through the use of a likelihood-based scoring method. The procedure is therefore ideally suited for settings where there is a variable mix of patients over time.     

Latitudinal comparison of altitudinal changes in forest structure,leaf-type,and species richness in humid monsoon Asia

A new template for mountain vegetation zonation along latitudinal gradients is proposed for examining geographical pattern of various forest attributes in humid monsoon Asia. The contrasting temperature regime in tropical and temperate mountains, i.e., the former is a non-seasonal, temperature-sum controlled environment, and the latter is a seasonal, low temperature limiting environment, leads to different altitudinal patterns of tree height distribution and species richness. In the tropical mountains, both tree height and species richness decrease steeply, and the tree height often stepwise. The decline of tree height and species diversity in the temperate mountains is far less pronounced except near the forest limit. Both trends are explained by their temperature regime.     

Prediction of flight of apple sawfly, Hoplocampa testudinea, using temperature sums

A method to predict the beginning of the flight of apple sawfly, Hoplocampa testudinea (Klug) (Hymenoptera, Tenthredinidae) is presented. Adults were monitored during 8 years at the experimental orchard De Schuilenburg, Kesteren, The Netherlands, with visual sticky traps. Temperature sums, accumulated until the day of the first capture of sawfly, were calculated for different starting dates of the summations. Beginning on 1 January, variation of the temperature sums, calculated in each of 8 years, decreased when later starting dates for temperature summation were chosen, reaching a minimum on 1 April for soil temperatures (–5 cm). The soil temperature sum, accumulated from 1 April until the first capture, was on average 134 day-degrees above a threshold of 4 °C. So this was the most suitable starting date to predict the beginning of sawfly flight activity. As use of the summation method based on air temperatures is in practice more appropriate for timing of trap installation by extension services and apple growers, trap deployment is recommended at an adapted value of 157 day-degrees from 15 March.