Efficiencies in multivariate paired experiments

Lower and upper bounds are given for the asymptotic efficiency of the paired T² test relative to the two-sample T² test in comparative multivariate experiments. Consistent estimates for these bounds are illustrated numerically and their relevance to small samples is discussed. Conditions are given such that each procedure dominates the other globally; when these fail the sets of alternatives are characterized at which each procedure dominates the other locally.     

Stomatal and photosynthetic responses of olive (Olea europaea L.) leaves to water deficits

The leaf gas exchange of mature olive trees (Olea europaea L.) was characterized over a wide range of water deficits in the field during 1998, in Cordoba, Spain. Leaf photosynthesis (A) and stomatal conductance (g_l) responded diurnally and seasonally to variations in tree water status and evaporative demand. In the absence of water stress, A and g_l were generally high during autumn and low in days of high vapour pressure deficits (VPD). Leaf A varied between 0 and 2 µmol m^?2 s^?1 under severe water deficits that lowered the stem water potential (Ψ_x) to ?8·0 MPa, but recovered rapidly following rehydration. Transpiration efficiency (TE) was curvilinearly related to VPD and not influenced by water deficits except in cases of severe water stress, where low TE values were observed at Ψ_x below ?4 MPa. Three models of leaf conductance were calibrated and validated with the experimental data; two were based on the model proposed by Leuning (L) and the other was derived from the widely used Jarvis (J) model. The L models performed better than the J model in two validation tests. The scatter of the predictions and the limited accuracy of all three models suggest that, in addition to the physiological and environmental variables considered, there are additional endogenous factors influencing the g_l of olive leaves.     

Generation of knock‐in mice that express nuclear enhanced green fluorescent protein and tamoxifen‐inducible Cre recombinase in the notochord from Foxa2 and T loci

The node and the notochord are important embryonic signaling centers that control embryonic pattern formation. Notochord progenitor cells present in the node and later in the posterior end of the notochord move anteriorly to generate the notochord. To understand the dynamics of cell movement during notochord development and the molecular mechanisms controlling this event, analyses of cell movements using time‐lapse imaging and conditional manipulation of gene activities are required. To achieve this goal, we generated two knock‐in mouse lines that simultaneously express nuclear enhanced green fluorescent protein (EGFP) and tamoxifen‐inducible Cre, CreER^T2, from two notochord gene loci, Foxa2 and T (Brachury). In Foxa2^{nEGFP‐CreERT2/+} and T^{nEGFP‐CreERT2/+} embryos, nuclei of the Foxa2 or T‐expressing cells, which include the node, notochord, and endoderm (Foxa2) or wide range of posterior mesoderm (T), were labeled with EGFP at intensities that can be used for live imaging. Cre activity was also induced in cells expressing Foxa2 and T 1 day after tamoxifen administration. These mice are expected to be useful tools for analyzing the mechanisms of notochord development. genesis 51:210–218, 2013. © 2013 Wiley Periodicals, Inc.     

Temperature dependences of carbon assimilation processes in four dominant species from mountain grassland ecosystem

Temperature responses of carbon assimilation processes were studied in four dominant species from mountain grassland ecosystem, i.e. Holcus mollis (L.), Hypericum maculatum (Cr.), Festuca rubra (L.), and Nardus stricta (L.), using the gas exchange technique. Leaf temperature (T _L) of all species was adjusted within the range 13–30 °C using the Peltier thermoelectric cooler. The temperature responses of metabolic processes were subsequently modelled using the Arrhenius exponential function involving the temperature coefficient Q ₁₀. The expected increase of global temperature led to a significant increase of dark respiration rate (R _D; Q ₁₀ = 2.0±0.5), maximum carboxylation rate (V _Cmax; Q ₁₀ = 2.2±0.6), and maximum electron transport rate (J _max; Q ₁₀ = 1.6±0.4) in dominant species of mountain grassland ecosystems. Contrariwise, the ratio between J _max and V _Cmax linearly decreased with T _L [y = −0.884 T _L + 5.24; r ² = 0.78]. Hence temperature did not control the ratio between intercellular and ambient CO₂ concentration, apparent quantum efficiency, and photon-saturated CO₂ assimilation rate (P _max). P _max primarily correlated with maximum stomatal conductance irrespective of T _L. Water use efficiency tended to decrease with T _L [y = −0.21 T _L + 8.1; r ² = 0.87].     

Directional Tests for the Analysis of Clinical Trials with Multiple Endpoints Allowing for Incomplete Data

Incomplete data are a serious problem in the multivariate analysis of clinical trials. Usually a complete-case analysis is performed: All incomplete observation vectors are excluded from the analysis. Provided that observations are missing randomly, an easy-to-handle available-case analysis is introduced, allowing the analysis of all data without insertion or deletion of observations. This method is applied to parametric and nonparametric test procedures of the O'Brien type, which are more powerful than the conventional Hotelling's T² for detecting alternatives where the (treatment) effect has the same direction for all observed variables. In addition, the applicability of these so-called directional tests, especially in the case of small samples, and their pros and cons are discussed.     

Efficiency Indices for Second-Order Designs

Design efficiencies are studied for inferences regarding the coefficients of second-order models. Subspaces of parameters are identified wherein each of two designs dominates the other locally, or the two designs are equally efficient. Both Fisher efficiency in estimation and Pitman efficiency in hypothesis testing are considered. Eight small second-order designs in k=3 regressor variables are screened using a four-part efficiency index. Of these, the central composite, Box-Behnken, small composite, and hybrid H310 and H311 B designs are found to be generally superior and roughly comparable. Detailed comparisons among these five designs are then undertaken. This work provides further tools for use in design evaluation, requiring only basic matrix operations independently of experimental data.     

Cytolytic T lymphocytes: an overview of their characteristics

Cloned T cells have been useful for assessing the lytic potential of distinct T cell subsets and for determining the relative contribution of different effector mechanism involved in the lytic process. Alloreactive CD8⁺ murine T cell clones and cloned murine CD4⁺ T_H1 and T_H2 T cells reactive with nominal antigen (ovalbumin) lysed nucleated target cells bearing antigen or coated with anti-CD3 monoclonal antibody in a short term⁵¹Cr-release assay. These clones were also evaluated for their ability to lyse efficiently sheep erythrocyte (SRBC) target cells coated with anti-CD3 mAb by a mechanism (presumably involving membrane damage) that does not involve nuclear degradation. Three patterns of lysis were observed: CD8⁺ and some CD4⁺ T_H2 effector cells lysed efficiently nucleated target cells and anucleated SRBC coated with anti-CD3 mAb. However, CD4⁺ T_H1 (and a few T_H2) T cells which lysed nucleated target cells bearing antigen or coated with anti-CD3 mAb didnotlyse efficiently the SRBC coated with anti-CD3 mAb. One CD4 bearing T_H2 cell failed to lyse efficiently either nucleated target cells or anucleated SRBC coated with anti-CD3 mAb. These results indicate that both T_H1 and T_H2 clones have lytic capabilities. Furthermore, they suggest that some but not all T_H2 murine T cell clones have lytic characteristics similar to those of conventional CD8⁺ CTL. However, it is not certain how these patterns of lysis of target cellsin vitro relates to the capacity of CTL to lyse such target cellsin vivo.     

Power of tests for QTL detection using replicated progenies derived from a diallel cross

In crop species, most QTL (quantitative trait loci) mapping strategies use segregating populations derived from an initial cross between two lines. However, schemes including more than two parents could also be used. We propose an approach using a high-density restriction fragment length polymorphism (RFLP) map established on six F ₂ populations derived from diallel crosses among four inbred lines and the phenotypic performances of two types of replicated progenies (F ₃ and topcross). The QTL is supposed to be on the marker locus considered. Three linear model tests for the detection of QTL effects (T ₁, T ₂ and T ₃) are described and their power studied for the two types of progeny. T ₁ tests the global genetic effects of the QTL (additivity and dominance) and T ₂ tests only additive effects assuming dominance is absent when it could exist. The models of these two tests assume that the main effects of QTL alleles are constant in different genetic backgrounds. The additive model of test T ₃ considers the six F ₂ populations independently, and T ₃ is the equivalent of the classical mean comparison test if we neglect dominance; it uses only contrasts between the homozygote marker classes. The results show that T ₂ is much more powerful than T ₃. The power of T ₁ and T ₂ depends on the relative sizes of the additive and dominance effects, and their comparison is not easy to establish. Nevertheless, T ₂ seems to be the more powerful in most situations, indicating that it is often more interesting to ignore dominance when testing for a QTL effect. For a given size of genetic effects, the power is affected by the total number of individuals genotyped in F ₂ and the recombination rate between the marker locus and the putative QTL. The approach presented in this paper has some drawbacks but could be easily generalized to other sizes of diallels and different progeny types.     

Asymptotic Efficiency of the Chi-Square Test for Heterogeneity of Proportions in Some Sparse-Data Cases

We consider the problem of testing for heterogeneity of K proportions when K is not small and the binomial sample sizes may not be large. We assume that the binomial proportions are normally distributed with variance σ². The asymptotic relative efficiency (ARE) of the usual chi-square test is found relative to the likelihood-based tests for σ²=0. The chi-square test is found to have ARE = 1 when the binomial sample sizes are all equal and high relative efficiency for other cases. The efficiency is low only in cases where there is insufficient data to use the chi-square test.     

Response of wheat growth,grain yield and water use to elevated CO2 under a Free‐Air CO2 Enrichment (FACE) experiment and modelling in a semi‐arid environment

The response of wheat crops to elevated CO₂ (eCO₂) was measured and modelled with the Australian Grains Free‐Air CO₂ Enrichment experiment, located at Horsham, Australia. Treatments included CO₂ by water, N and temperature. The location represents a semi‐arid environment with a seasonal VPD of around 0.5 kPa. Over 3 years, the observed mean biomass at anthesis and grain yield ranged from 4200 to 10 200 kg ha^?1 and 1600 to 3900 kg ha^?1, respectively, over various sowing times and irrigation regimes. The mean observed response to daytime eCO₂ (from 365 to 550 μmol mol^?1 CO₂) was relatively consistent for biomass at stem elongation and at anthesis and LAI at anthesis and grain yield with 21%, 23%, 21% and 26%, respectively. Seasonal water use was decreased from 320 to 301 mm (P = 0.10) by eCO₂, increasing water use efficiency for biomass and yield, 36% and 31%, respectively. The performance of six models (APSIM‐Wheat, APSIM‐Nwheat, CAT‐Wheat, CROPSYST, OLEARY‐CONNOR and SALUS) in simulating crop responses to eCO₂ was similar and within or close to the experimental error for accumulated biomass, yield and water use response, despite some variations in early growth and LAI. The primary mechanism of biomass accumulation via radiation use efficiency (RUE) or transpiration efficiency (TE) was not critical to define the overall response to eCO₂. However, under irrigation, the effect of late sowing on response to eCO₂ to biomass accumulation at DC65 was substantial in the observed data (~40%), but the simulated response was smaller, ranging from 17% to 28%. Simulated response from all six models under no water or nitrogen stress showed similar response to eCO₂ under irrigation, but the differences compared to the dryland treatment were small. Further experimental work on the interactive effects of eCO₂, water and temperature is required to resolve these model discrepancies.     

Mechanisms of hydration effects on the structural-dynamic and functional characteristics of photosynthetic membranes in various purple bacteria

NMR spectra and T₁, T₂ relaxation times for ¹H, ¹³C and ³¹P nuclei in membranes of R. rubrum and Rb. sphaeroides recorded at different relative humidity, as well as hydration curves and electron transfer efficiency of these membranes and membranes of E. shaposhnikovii, reveal complicated relations between structural-dynamic and functional characteristics. A number of sites of the electron transfer chain are shown to be under the control of structural-dynamic mechanisms. Different parameters characterizing these membranes at low humidity and during hydration have been established. These findings and analysis of the data from model systems reveal four different stages of hydration. Each of them is associated with specific changes in structure, dynamics, and function of photosynthetic membranes and their components. In the first stage the hydration of some polar groups leads to local changes in the dynamics of the protein component and this influences the recombination between photoactive pigment P and intermediate acceptor Q_A. The second stage is induced by incorporation of water molecules into the hydrogen bonds between the polar head groups of the lipids and within macromolecules. This results in changes of the dynamics of the membranes, the efficiency of the electron transfer between the quinones and the efficiency of photooxidation of cytochrome c. In the third stage all polar groups are hydrated owing to the appearance of free water with a high dielectric constant. This makes possible lateral mobility of membrane components and changes in distances between the interacting macromolecular components. Therefore, the regulation of photosynthetic processes can be mediated with the participation of mobile carriers. Finally, in the fourth stage, complete humidification provides conditions for regulation of photosynthesis at the cell level. The mechanisms influencing these processes and the efficiency and regulation of electron transfer in various parts of the photosynthetic chain are discussed. Received: 1 August 1996 / Accepted: 4 July 1997     

Acquired TET2 mutation in one patient with familial platelet disorder with predisposition to AML led to the development of pre‐leukaemic clone resulting in T2‐ALL and AML‐M0

Familial platelet disorder with predisposition to acute myeloid leukaemia (FPD/AML) is characterized by germline RUNX1 mutations, thrombocytopaenia, platelet dysfunction and a risk of developing acute myeloid and in rare cases lymphoid T leukaemia. Here, we focus on a case of a man with a familial history of RUNX1^R174Q mutation who developed at the age of 42 years a T2‐ALL and, 2 years after remission, an AML‐M0. Both AML‐M0 and T2‐ALL blast populations demonstrated a loss of 1p36.32‐23 and 17q11.2 regions as well as other small deletions, clonal rearrangements of both TCRγ and TCRδ and a presence of 18 variants at a frequency of more than 40%. Additional variants were identified only in T2‐ALL or in AML‐M0 evoking the existence of a common original clone, which gave rise to subclonal populations. Next generation sequencing (NGS) performed on peripheral blood‐derived CD34⁺ cells 5 years prior to T2‐ALL development revealed only the missense TET2^P1962T mutation at a frequency of 1%, which increases to more than 40% in fully transformed leukaemic T2‐ALL and AML‐M0 clones. This result suggests that TET2^P1962T mutation in association with germline RUNX1^R174Q mutation leads to amplification of a haematopoietic clone susceptible to acquire other transforming alterations.     

Variation in phosphorus efficiency among 73 bread and durum wheat genotypes grown in a phosphorus-deficient calcareous soil

A greenhouse experiment was carried out to study the severity of phosphorus (P) deficiency symptoms on leaves, shoot dry matter production, and shoot concentration and content (the total amount per shoot) of P in 39 bread wheat (Triticum aestivum L.) and 34 durum wheat (Triticum durum L.) genotypes grown in a severely P-deficient calcareous soil with low (20mgPkg⁻¹ soil) and adequate (80mgPkg⁻¹ soil) P supply for 39 days. As the seed P concentration or content can affect plant performance under P-deficient conditions, the seeds of the genotypes used in the present study were also analyzed for P concentration. Phosphorus efficiency (relative shoot growth) of genotypes, calculated by the ratio of shoot dry matter production under low P to that under adequate P supply, significantly differed among the genotypes, and varied between 46.7% and 78.6%. Phosphorus efficiency ranged from 51% to 71% with an average of 61% for bread and from 47% to 79% with an average of 66% for durum wheat genotypes. There was no correlation between P efficiency ratio and P concentration of plants (R ²=0.0001), but P efficiency of all bread and durum wheat genotypes showed a very significant correlation with the P content (the total amount of P per shoot) (R ²=0.333^***). The relationship between the P efficiency and total amount of P per shoot was much more significant in bread (R ²=0.341^***) than in durum wheat (R ²=0.135^*). Like shoot P concentrations, also severity of visible leaf symptoms of P deficiency on older leaves, including leaf chlorosis and necrosis, did not correlate with P efficiency. In most cases, genotypes showing higher P efficiency had higher absolute shoot dry weight under P deficient conditions. Under P deficient conditions, the absolute shoot dry weight very significantly correlated with shoot P content (R ²=0.665^***), but the correlation between the absolute shoot dry weight and shoot P concentration tended to be negative. There was also variation in native seed P reserve of the genotypes, but this variation had no influence on the P efficiency. The results indicate that the total amount of P per shoot and shoot dry matter production at low P supply are most reliable parameters in ranking genotypes for P efficiency at early growth stage. In wheat germplasm tested in the present study, several wheat genotypes are available showing both very high P efficiency and very high shoot content and concentration of P suggesting that P acquisition ability should be most important mechanism for high P efficiency in such genotypes. On the other hand, there are also genotypes in the germplasm having more or less same P concentration or P content in shoot but differing substantially in P efficiency, indicating importance of P utilization at cellular level in P efficiency. All these results suggest that P efficiency mechanisms can be different from one genotype to other within a given plant species.     

Net ecosystem productivity of boreal jack pine stands regenerating from clearcutting under current and future climates

Life cycle analysis of climate and disturbance effects on forest net ecosystem productivity (NEP) is necessary to assess changes in forest carbon (C) stocks under current or future climates. Ecosystem models used in such assessments need to undergo well-constrained tests of their hypotheses for climate and disturbance effects on the processes that determine CO₂ exchange between forests and the atmosphere. We tested the ability of the model ecosys to simulate diurnal changes in CO₂ fluxes under changing air temperatures (T_a) and soil water contents during forest regeneration with eddy covariance measurements over boreal jack pine (Pinus banksiana) stands along a postclearcut chronosequence. Model hypotheses for hydraulic and nutrient constraints on CO₂ fixation allowed ecosys to simulate the recovery of C cycling during the transition of boreal jack pine stands from C sources following clearcutting (NEP from −150 to −200 g C m⁻² yr⁻¹) to C sinks at maturity (NEP from 20 to 80 g C m⁻² yr⁻¹) with large interannual variability. Over a 126-year logging cycle, annualized NEP, C harvest, and net biome productivity (NBP=NEP–harvest removals) of boreal jack pine averaged 47, 33 and 14 g C m⁻² yr⁻¹. Under an IPCC SRES climate change scenario, rising T_a exacerbated hydraulic constraints that adversely affected NEP of boreal jack pine after 75 years. These adverse effects were avoided in the model by replacing the boreal jack pine ecotype with one adapted to warmer T_a. This replacement raised annualized NEP, C harvest, and NBP to 81, 56 and 25 g C m⁻² yr⁻¹ during a 126-year logging cycle under the same climate change scenario.     

High‐Performance Electrocatalytic Conversion of N2 to NH3 Using Oxygen‐Vacancy‐Rich TiO2 In Situ Grown on Ti3C2Tx MXene

To achieve the energy‐effective ammonia (NH₃) production via the ambient‐condition electrochemical N₂ reduction reaction (NRR), it is vital to ingeniously design an efficient electrocatalyst assembling the features of abundant surface deficiency, good dispersibility, high conductivity, and large surface specific area (SSA) via a simple way. Inspired by the fact that the MXene contains thermodynamically metastable marginal transition metal atoms, the oxygen‐vacancy‐rich TiO₂ nanoparticles (NPs) in situ grown on the Ti₃C₂T_x nanosheets (TiO₂/Ti₃C₂T_x) are prepared via a one‐step ethanol‐thermal treatment of the Ti₃C₂T_x MXene. The oxygen vacancies act as the main active sites for the NH₃ synthesis. The highly conductive interior untreated Ti₃C₂T_x nanosheets could not only facilitate the electron transport but also avoid the self‐aggregation of the TiO₂ NPs. Meanwhile, the TiO₂ NPs generation could enhance the SSA of the Ti₃C₂T_x in return. Accordingly, the as‐prepared electrocatalyst exhibits an NH₃ yield of 32.17 µg h^?1 mg^?1_cat. at ?0.55 V versus reversible hydrogen electrode (RHE) and a remarkable Faradaic efficiency of 16.07% at ?0.45 V versus RHE in 0.1 m HCl, placing it as one of the most promising NRR electrocatalysts. Moreover, the density functional theory calculations confirm the lowest NRR energy barrier (0.40 eV) of TiO₂ (101)/Ti₃C₂T_x compared with Ti₃C₂T_x or TiO₂ (101) alone.     

Crop growth,water-use efficiency and carbon isotope discrimination in groundnut (Arachis hypogaea L.) genotypes under end-of season drought conditions*

Ten groundnut genotypes were grown under adequately irrigated conditions or subjected to drought during the pod filling phase (83–113 days after sowing) in a medium deep Alfisol at the ICRISAT Centre during the 1986–1987 post-rainy season. Crop growth was measured in both treatments, but transpiration (7) and water-use efficiency (W) were quantified only in the drought treatment. Leaf samples from both treatments were assayed for discrimination against ¹³CO₂ fixed in leaves (Δ) to examine the relationships between Δ, crop growth, and W under field conditions. The shoot dry matter accumulated during the period of drought (Y) ranged from 72–150 g m^-2 and was closely related to transpiration. This indicates scope for selection of traits and practices to increase T. Water-use efficiencies ranged from 1.38–2.50 g kg^-1 and were inversely related to Δ in eight out of the 10 genotypes. For the other two genotypes, there was evidence that T was underestimated by field measurements. Water-use efficiency and transpiration were not correlated suggesting that these two traits might be combined through breeding. Variation between genotypes was greatest for the partitioning of total dry matter to pods (73%), followed by water-use efficiency (31%) and transpiration (29%). Crop growth rates were negatively related to Δ under irrigated conditions but not under drought.     

Diagnosing and assessing uncertainties of terrestrial ecosystem models in a multimodel ensemble experiment: 1. Primary production

We conducted an ensemble modeling exercise using the Terrestrial Observation and Prediction System (TOPS) to evaluate sources of uncertainty in carbon flux estimates resulting from structural differences among ecosystem models. The experiment ran public‐domain versions of biome‐bgc, lpj, casa , and tops‐bgc over North America at 8 km resolution and for the period of 1982–2006. We developed the Hierarchical Framework for Diagnosing Ecosystem Models (HFDEM) to separate the simulated biogeochemistry into a cascade of three functional tiers and sequentially examine their characteristics in climate (temperature–precipitation) and other spaces. Analysis of the simulated annual gross primary production (GPP) in the climate domain indicates a general agreement among the models, all showing optimal GPP in regions where the relationship between annual average temperature (T, °C) and annual total precipitation (P, mm) is defined by P=50T+500. However, differences in simulated GPP are identified in magnitudes and distribution patterns. For forests, the GPP gradient along P=50T+500 ranges from ～50 g C yr^?1 m^?2 °C^?1 (casa ) to ～125 g C yr^?1 m^?2 °C^?1 (biome‐bgc ) in cold/temperate regions; for nonforests, the diversity among GPP distributions is even larger. Positive linear relationships are found between annual GPP and annual mean leaf area index (LAI) in all models. For biome‐bgc and lpj , such relationships lead to a positive feedback from LAI growth to GPP enhancement. Different approaches to constrain this feedback lead to different sensitivity of the models to disturbances such as fire, which contribute significantly to the diversity in GPP stated above. The ratios between independently simulated NPP and GPP are close to 50% on average; however, their distribution patterns vary significantly between models, reflecting the difficulties in estimating autotrophic respiration across various climate regimes. Although these results are drawn from our experiments with the tested model versions, the developed methodology has potential for other model exercises.