Fuzzy p-values in latent variable problems

We consider the problem of testing a statistical hypothesiswhere the scientifically meaningful test statistic is a functionof latent variables. In particular, we consider detection ofgenetic linkage, where the latent variables are patterns ofinheritance at specific genome locations. Introduced by Geyer& Meeden (2005), fuzzy p-values are random variables, describedby their probability distributions, that are interpreted asp-values. For latent variable problems, we introduce the notionof a fuzzy p-value as having the conditional distribution ofthe latent p-value given the observed data, where the latentp-value is the random variable that would be the p-value ifthe latent variables were observed. The fuzzy p-value provides an exact test using two sets of simulationsof the latent variables under the null hypothesis, one unconditionaland the other conditional on the observed data. It providesnot only an expression of the strength of the evidence againstthe null hypothesis but also an expression of the uncertaintyin that expression owing to lack of knowledge of the latentvariables. We illustrate these features with an example of simulateddata mimicking a real example of the detection of genetic linkage.     

Cell Cycle Duration in the Root Meristem of Sonoran Desert Cactaceae as Estimated by Cell-flow and Rate-of-cell-production Methods

Slow rates of cactus growth in the Sonoran Desert and high productivityof some Cactaceae under cultivation suggest that relativelylow growth rates are not the consequence of a long cell divisioncycle but of short optimal periods for growth and adverse environmentalfactors. To verify this hypothesis, the duration of the celldivision cycle (T)in the root apical meristem of seedlings ofthree sympatric species from the Sonoran Desert [Ferocactuspeninsulae(F. A. C. Weber) Britton & Rose ‘Townsendianus’(Britton & Rose) N. P. Taylor, stat. nov.,Stenocereus gummosus(Engelm.)Gibson & Horak andPachycereus pringlei(S. Watson) Britton& Rose] was estimated with the rate-of-cell-production (RCP)and the cell-flow (colchicine) methods. Both methods were appliedduring the steady-state growth phase, which was relatively shortin the first two species because of the determinate patternof root growth. The RCP method permitted estimation ofTin eachroot individually. Durations of the cell division cycle wereinversely proportional to the rate of root growth (r²rangedfrom 0.42 to 0.88,P<0.05).T,determined by the cell-flow method,ranged from 14.4 to 19.3 h in these species and was within thesame range asTdetermined by the RCP method. The averageTdeterminedby the RCP method was 67 to 75% of that determined by the cell-flowmethod. Results obtained with both methods are compared andanalysed. The proposed hypothesis appears to be correct, indicatingthat these species can be more productive under cultivationthan in the wild due to the relatively short duration of thecell division cycle. Adaptive features of these findings arealso considered.Copyright 1998 Annals of Botany Company Cactaceae, cell division cycle, root growth, root meristem, Sonoran Desert     

Vertical distribution, life cycle and body allometry of two oceanic calanoid copepods (Pleuromamma scutullata and Heterorhabdus tanneri) in the Oyashio region, western North Pacific Ocean

 Diel and seasonal vertical distribution, life cycle andbody allometry of Pleuromamma scutullata and Heterorhabdus tanneriwere investigated in the Oyashio region during September 1996through October 1997. Monthly samples were collected with 0.1mm mesh closing nets towed through five discrete depths betweenthe surface and     

Effect of tryptophan and of glucose on exercise capacity of horses

We hypothesized that central fatigue may have a role in limitingthe endurance capacity of horses. Therefore, we tested the effect ofinfusing tryptophan and/or glucose on endurance time and plasmaconcentrations of free tryptophan and other substrates thought toaffect tryptophan uptake into the brain of seven mares (3-4 yr ofage, 353-435 kg) that ran on a treadmill at 50% of maximalO₂ consumption to fatigue. Withuse of a counterbalanced crossover design, the horses were infused withtryptophan (100 mg/kg in saline solution) or a similar volume of salinesolution (placebo) before exercise. During exercise, horses receivedinfusions of glucose (2 g/min, 50% wt/vol) or a similar volume ofsaline. Thus the treatments were 1)tryptophan and glucose (T & G), 2) tryptophan and placebo (T & P), 3)placebo and glucose (P & G), and 4)placebo and placebo (P & P). Mean heart rate, hematocrit, andconcentration of plasma total solids before and during exercise weresimilar for all trials. Mean time to exhaustion was reduced (P < 0.05) for T & P and T & Gcompared with P & P [86.1 ± 6.9 and 87.1 ± 6.8 vs. 102.3 ± 10.3 (SE) min], whereas endurance for P & G(122.4 ± 11.9 min) was greater than for all other trials (P < 0.05). Compared withnontryptophan trials, during the tryptophan trials plasma prolactinincreased (P < 0.05) nearlythreefold before exercise and almost twofold early in exercise. Muscleglycogen concentrations were reduced(P < 0.05) below preexercise values in the P & G and P & P trials only. However, glucose infusions (P & G)did not affect (P > 0.05)concentrations of plasma free fatty acids or ratios of branched-chainamino acids to free tryptophan. In conclusion, tryptophan infusionreduced endurance time, which was consistent with the central fatiguehypothesis. The failure of glucose infusion to alleviate the effects oftryptophan and the absence of significant muscle glycogen reduction inthe tryptophan trials suggest that the early onset of fatigue in thetryptophan trials is not due to a lack of readily available substrate.

     

Mesh selection and filtration efficiency of the Continuous Plankton Recorder

The filtration efficiency [volume filtered/(inlet aperture areax distance travelled through the water)] and retention of copepodsby the Continuous Plankton Recorder (CPR) were measured in seatrials. Filtration efficiency was independent of tow speed (n= 14 trials, range of speeds 5–13 knots, F_1.12 = 0.1,P = 0.73), but was influenced by the extent to which the bodyof the CPR was sealed. The retention of copepods on the silkfiltering mesh routinely used in CPRs did not differ significantlyfrom that predicted for a 270 µm nylon mesh and did notvary with tow speed.     

Grazing of echinoderm larvae (Paracentrotus lividus and Arbacia lixula) on naturally occurring particulate matter

Larvae (72 hr old) of P. lividus and A. lixula grazed on varioussuspensions of natural particulate matter with a size rangeof 2 to 30 microns, and on two species of algae (Phaeodactylumtricor-nutum and Nitzschia sp.) — Larvae graze most in the size range where the particleconcentration is highest. — If larvae deplete certain size categories of particlesthey then graze other size ranges in which the concentrationis still high. — The grazing rate of the two species varied between 988and 91.949 µm³ per pluteus per hour. — For A. lixula larvae the grazing rate increases withincreasing temperature to a maximum at 22°C.     

Apple Fruit Bud Development and Growth; Analysis and an Empirical Model

Analysis of the information available on apple bud developmentand growth after dormancy leads to an empirical model of growthto full bloom. The analysis and model are set in the frameworkof the physiological mechanisms considered to be responsiblefor dormancy and subsequent bud growth. It is necessary to introducean arbitrary ‘growth unit’ scale to describe theseprocesses quantitatively, which is done by the equation G = A/(I+be^–k(I).P) where G and A are in growth units, the value of k is controlledby a dormancy index I and P is a temperature summation. Themodel fulfils the main requirements laid down for it and thevalues of P at full bloom, derived from controlled environmentwork and field observations, are very similar.     

Uptake and Distribution of Copper in Chrysanthemum morifolium

The effects of various levels of copper on the uptake and distributionof copper in Chrysanthemum morifolium grown in solution cultureand peat-sand have been examined. Whole plants growing in shortdays were sampled at regular intervals, divided into roots,stem, leaves and lateral shoots, and analysed for copper. Thepartitioning of copper between these tissues showed that a relativelylarge proportion (30–40 per cent) of the total plant copperwas accumulated in the roots of normal plants during the harvestingperiod, compared with approximately 10 per cent in the rootsof copper deficient plants. Whilst the copper content (ug g^–1) of leaves and stemfrom normal plants was negatively correlated with the amountof dry matter produced (P < 0·001), the correspondingcopper deficient tissues showed little variation in copper contentwith increases in tissue dry weight. A more detailed investigationof the copper content of leaves from normal plants showed thatgradients existed within the plant with respect to both leafposition and time of harvest which could be described by a singlecubic surface equation (P < 0·001).     

Spatial heterogeneity and genetic variation in the copepod Neocalanus cristatus along two transects in the North Pacific sampled by the Continuous Plankton Recorder

We present a macrogeographic study of spatial heterogeneityin an important subarctic Pacific copepod and describe the firstgenetic analysis of population structure using Continuous PlanktonRecorder (CPR) samples. Samples of Neocalanus cristatus werecollected at a constant depth of 7 m from two CPR tow-routes,(i) an east–west 6500-km transect from Vancouver Island,Canada to Hokkaido Island, Japan, and (ii) a north–southtransect of 2250 km from Anchorage, Alaska to Tacoma, Washington.Analysis of these samples revealed three features of the biologyof N. cristatus. First, N. cristatus undergoes small-scale dielvertical migration that is larger among stages CV–adult(3–6 times more abundant at 7 m at night), than stagesCI–CIV (only 2–4 times higher at night). Secondly,while there were no regions where N. cristatus did not appear,each transect sampled a few large-scale macrogeographic patches.Thirdly, an analysis of molecular variation, using a partialsequence of the N. cristatus cytochrome oxidase I gene, revealedthat 7.3% (P < 0.0001) of the total genetic variation amongN. cristatus sampled from macrogeographic patches by the CPRcould be explained by spatial heterogeneity. We suggest thatspatial heterogeneity at macrogeographic scales may be importantin plankton evolution.     

Mechanical strain regulates syndecan-4 expression and shedding in smooth muscle cells through differential activation of MAP kinase signaling pathways

Syndecan-4 (S4) belongs to a family of transmembrane proteoglycans, acts as a coreceptor for growth factor binding as well as cell-matrix and cell-cell interactions, and is induced in neointimal smooth muscle cells (SMCs) after balloon catheter injury. We investigated S4 expression in SMCs in response to several force profiles and the role of MAP kinase signaling pathways in regulating these responses. S4 mRNA expression increased in response to 5% and 10% cyclic strain (4 h: 200 ± 34% and 182 ± 17%, respectively; P < 0.05) before returning to basal levels by 24 h. Notably, the SMC mechanosensor mechanism was reset after an initial 24-h "preconditioning" period, as evident by an increase in S4 gene expression following a change in cyclic stress from 10% to 20% (28 h: 181 ± 1%; P < 0.05). Mechanical stress induced a late decrease in cell-associated S4 protein levels (24 h: 70 ± 6%; P < 0.05), with an associated increase in S4 shedding (24 h: 537 ± 109%; P < 0.05). To examine the role of MAP kinases, cells were treated with U-0126 (ERK1/2 inhibitor), SB-203580 (p38 inhibitor), or JNKI I (JNK/SAPK inhibitor). Late reduction in cell-associated S4 levels was attributed to ERK1/2 and p38 signaling. In contrast, accelerated S4 shedding required both ERK1/2 (5-fold reduction in accelerated shedding; P < 0.05) and JNK/SAPK (4-fold reduction; P < 0.05) signaling. Given the varied functions of S4, stress-induced effects on SMC S4 expression and shedding may represent an additional component of the proinflammatory, growth-stimulating pathways that are activated in response to changes in the mechanical microenvironment of the vascular wall. heparan sulfate proteoglycan     

Mesh selection of copepodite and nauplius stages of four calanoid copepod species

High-speed plankton nets, using mesh sizes of 61, 90, 124,190and 270 µn, were deployed in the North Sea to catch Calanusspp., Pseudocalanus minutus, Paracalanus parvus and Temora longicomis.These species were identified to their nauplii, copepodite andadult stages, and the numbers caught in each stage were convertedto numbers m^–3 seawater filtered. The width and lengthof a representative sample of each stage was measured, and theproportion caught by the different mesh sizes is presented.The selection pattern was described by a mathematical model,which showed that a mesh size of 75% of the copepod carapacewidth catches 95% of the individuals of that size present inthe seawater. Some recommendations for mesh sizes required tosample copepods are given.     

Effects of the fungal endophyte, Neotyphodium lolii, on net photosynthesis and growth rates of perennial ryegrass (Lolium perenne) are independent of In Planta endophyte concentration

• Background and Aims Neotyphodium lolii is a fungal endophyteof perennial ryegrass (Lolium perenne), improving grass fitnessthrough production of bioactive alkaloids. Neotyphodium speciescan also affect growth and physiology of their host grasses(family Poaceae, sub-family Pooideae), but little is known aboutthe mechanisms. This study examined the effect of N. lolii onnet photosynthesis (P_n) and growth rates in ryegrass genotypesdiffering in endophyte concentration in all leaf tissues. • Methods Plants from two ryegrass genotypes, Nui D andNui UIV, infected with N. lolii (E+) differing approx. 2-foldin endophyte concentration or uninfected clones thereof (E–)were grown in a controlled environment. For each genotype xendophyte treatment, plant growth rates were assessed as tilleringand leaf extension rates, and the light response of P_n, darkrespiration and transpiration measured in leaves of young (30–45d old) and old (>90 d old) plants with a single-chamber openinfrared gas-exchange system. • Key Results Neotyphodium lolii affected CO₂-limited ratesof P_n, which were approx. 17 % lower in E+ than E– plants(P < 0·05) in the young plants. Apparent photon yieldand dark respiration were unaffected by the endophyte (P >0·05). Neotyphodium lolii also decreased transpiration(P < 0·05), but only in complete darkness. There wereno endophyte effects on P_n in the old plants (P > 0·05).E+ plants grew faster immediately after replanting (P < 0·05),but had approx. 10 % lower growth rates during mid-log growth(P < 0·05) than E– plants, but there was noeffect on final plant biomass (P > 0·05). The endophyteeffects on P_n and growth tended to be more pronounced in NuiUIV, despite having a lower endophyte concentration than NuiD. • Conclusions Neotyphodium lolii affects CO₂ fixation,but not light interception and photochemistry of P_n. The impactof N. lolii on plant growth and photosynthesis is independentof endophyte concentration in the plant, suggesting that theendophyte mycelium is not simply an energy drain to the plant.However, the endophyte effects on P_n and plant growth are stronglydependent on the plant growth phase.     

A method for isolating adult and neonatal airway smooth muscle cells and measuring shortening velocity

Methods are described for isolating smooth muscle cells from thetracheae of adult and neonatal sheep and measuring the single-cell shortening velocity. Isolated cells were elongated,Ca²⁺ tolerant, and contractedrapidly and substantially when exposed to cholinergic agonists, KCl,serotonin, or caffeine. Adult cells were longer and widerthan preterm cells. Mean cell length in 1.6 mMCaCl₂ was 194 ± 57 (SD) µm(n = 66) for adult cells and 93 ± 32 µm (n = 20) for preterm cells(P < 0.05). Mean cell width at thewidest point of the adult cells was 8.2 ± 1.8 µm(n = 66) and 5.2 ± 1.5 µm(n = 20) for preterm cells(P < 0.05). Cells were loaded into aperfusion dish maintained at 35°C and exposed to agonists, andcontractions were videotaped. Cell lengths were measured from 30 videoframes and plotted as a function of time. Nonlinear fitting of celllength to an exponential model gave shortening velocities faster thanmost of those reported for airway smooth muscle tissues. For a sampleof 10 adult and 10 preterm cells stimulated with 100 µM carbachol,mean (± SD) shortening velocity of the preterm cells was notdifferent from that of the adult cells (0.64 ± 0.30 vs. 0.54 ± 0.27 s¹, respectively), butpreterm cells shortened more than adult cells (68 ± 12 vs. 55 ± 11% of starting length, respectively;P < 0.05). The preparative andanalytic methods described here are widely applicable to other smoothmuscles and will allow contraction to be studied quantitatively at thesingle-cell level.

     

Chlorophyll Fluorescence during Drying and Rehydration in the Mosses Rhytidiadelphus loreus (Hedw.) Warnst.,Anomodon viticulosus (Hedw.) Hook. & Tayl. and Grimmia pulvinata (Hedw.) Sm.

Chlorophyll-fluorescence parameters of three mosses, Rhytidiadelphusloreus (Hedw.) Warnst.,Anomodon viticulosus (Hedw.) Hook &Tayl. and Grimmia pulvinata (Hedw.) Sm. were measured duringdrying, and following remoistening after a period of desiccation.Most changed little with drying until the full-turgor pointwas approached, when rapid changes accompanied loss of cellwater. In R. loreus all parameters decreased together down toa water content of about 30% d.wt (RWC approx. 0.15). At lowwater contents (5–16% d.wt; RWC approx. 0.02–0.08)saturating pulses tended to suppress rather than stimulate fluorescence.In A. viticulosus F_v/F_m, q_Pand     

Distinct roles of PMCA isoforms in Ca2+ homeostasis of bladder smooth muscle: evidence from PMCA gene-ablated mice

We previously showed that plasma membrane Ca²⁺-ATPase (PMCA) activity accounted for 25–30% of relaxation in bladder smooth muscle (8). Among the four PMCA isoforms only PMCA1 and PMCA4 are expressed in smooth muscle. To address the role of these isoforms, we measured cytosolic Ca²⁺ ([Ca²⁺]_i) using fura-PE3 and simultaneously measured contractility in bladder smooth muscle from wild-type (WT), Pmca1^+/–, Pmca4^+/–, Pmca4^–/–, and Pmca1^+/–Pmca4^–/– mice. There were no differences in basal [Ca²⁺]_i values between bladder preparations. KCl (80 mM) elicited both larger forces (150–190%) and increases in [Ca²⁺]_i (130–180%) in smooth muscle from Pmca1^+/– and Pmca1^+/–Pmca4^–/– bladders than those in WT or Pmca4^–/–. The responses to carbachol (CCh: 10 µM) were also greater in Pmca1^+/– (120–150%) than in WT bladders. In contrast, the responses in Pmca4^–/– and Pmca1^+/–Pmca4^–/– bladders to CCh were significantly smaller (40–50%) than WT. The rise in half-times of force and [Ca²⁺]_i increases in response to KCl and CCh, and the concomitant half-times of their decrease upon washout of agonist were prolonged in Pmca4^–/– (130–190%) and Pmca1^+/–Pmca4^–/– (120–250%) bladders, but not in Pmca1^+/– bladders with respect to WT. Our evidence indicates distinct isoform functions with the PMCA1 isoform involved in overall Ca²⁺ clearance, while PMCA4 is essential for the [Ca²⁺]_i increase and contractile response to the CCh receptor-mediated signal transduction pathway. PMCA; bladder smooth muscle; gene-altered mice     

Grain Size and Seedling Growth of Wheat at Different Ploidy Levels

A study was made of the influence of grain size variation withinand between diploid, tetraploid and hexaploid wheat, on a numberof seedling growth characters. Differences in grain size within the three ploidy levels appearedto be related to total photosynthetic area and dry weight accretionin the seedling. In the diploids there was a positive correlationbetween seed size and total photosynthetic area (r = +0·99,P < 0·01) and total dry weight (r = +0·84,P < 0·05) of the seedling at 10 weeks after emergence.In the tetraploid and hexaploids, seed size was negatively correlatedwith both total photosynthetic area (r = –0·69,P < 0·05 and r = –0·33, P < 0·05for the tetraploids and hexaploids respectively) and total dryweight (r = –0·69, P < 0·05 and r = –0·59,P < 0·05 for the tetraploids and hexaploids respectively),of the seedlings 10 weeks after emergence. The main physiological distinction between the tetraploids andhexaploids appeared to be the superiority of the hexaploidsin rate of leaf appearance and the lower ratio of expanded tounexpanded leaves in the seedling 10 weeks after emergence.The tetraploids, in turn, appeared to be superior to the diploidsin these two characters. Triticum spp., wheat, polyploidy, grain size, photosynthetic area, net assimilation rate, tiller number     

Size-selective grazing of bacteria by Bosmina longirostris--an image-analysis study

Image analyses on the filtering apparatus of Bosmina longirostricshowed that the filter mesh is finer on the gnathobasic filterplates of the second and third trunk limbs (ranges from 0.43to 0.97 µm) and coarser for the outer ones of the thirdlimb (ranges from 0.5 to 1.36 µm), and the intersetulardistances increase with body length. Grazing experiments combinedwith image analysis confirmed the efficient grazing of B.longirostrison natural bacteria with cell lengths equal to or larger thanthe intersetular distances of the gnathobasic filter plates.During the experiments, the animals minimized the average celllength of the bacterioplankton assemblages from 0.77–0.96µm to 0.55–0.68 µm, corresponding to the meanof the filter mesh size on the fine gnathobasic filter platesof the experimental populations. The clearance rates for large,elongated or dividing cells with maximal lengths of 0.88–8.40µm were 2.3–17.7 times higher than those for smallsingle coccoids with a diameter of <0.45 µm. The resultsprovide evidence of a significant differential impact of B.longirostrison the bacterial community structure with respect to the shapeand size of the cells, and demonstrate that the species is amore effective bacterial feeder than considered previously.     

Photosynthesis of Stands of Tomato, Cucumber and Sweet Pepper Measured in Greenhouses under Various CO2-concentrations

The rate of net photosynthesis (P) of whole plant stands oftomato (Lycopersicon esculentum Mill.), cucumber (Cucumis sativusL.) and sweet pepper (Capsicum annuum L.) was measured in sixlong-term experiments in large greenhouses under normal operatingconditions and CO₂-concentrations between 200 and 1200 µmolmol^-1. The objective was to quantify the responses to lightand carbon dioxide and to obtain data sets for testing simulationmodels. The method of measuring canopy photosynthesis involvedan accurate estimation of the greenhouse CO₂ balance, usingnitrous oxide (N₂O) as tracer gas to determine, on-line, theexchange rate between greenhouse and outside air. The estimatedrelative error in the observed P was about ± 10%, exceptthat higher relative errors could occur under particular conditions. A regression equation relating P to the photosynthetically activeradiation, the CO₂ concentration and the leaf area index explained83-91% of the variance. The main canopy photosynthesis characteristicscalculated with the fitted regression equations were: canopyP_max 5-9 g m^-2 h^-1 CO₂ uptake; ratio P_max/LAI 1·5-3 gm^-2 h^-1; light compensation point 32-86 µmol s^-1 m^-2;light use efficiency (quantum yield) at low light 0·06-0·10µmol µmol^-1 and CO₂ compensation point 18-54 µmolmol^-1. The results were related to the prevailing conditions.Copyright1994, 1999 Academic Press Canopy photosynthesis, Capsicum annuum L., carbon dioxide, CO₂, CO₂ balance, CO₂ use efficiency, cucumber, _{Cucumis sativus} L., glasshouse, greenhouse, light use efficiency, Lycopersicon esculentum Mill., sweet pepper, tomato, tracer gas     

Species of criconematids (Nematoda: Criconematina) from Haryana,India

Ten known, viz. Criconema (Nothocriconemella) mutabile (Taylor, 1936) Raski & Luc, 1985, Neolobocriconema aberrans (Jairajpuri & Siddiqi, 1963) Andrássy, 1979, Macroposthonia sphaerocephala (Taylor, 1936) De Grisse & Loof, 1965, Nothocriconemoides basili (Jairajpuri, 1963) Loof & De Grisse, 1974, Hemicriconemoides cocophillus Loos, 1949, H. litchi Edward & Misra, 1963, H. mangiferae Siddiqi, 1961, Aulosphora indica (Siddiqi, 1961) Siddiqi, 1980, Paratylenchus obtusicaudatus Raski, 1975, and Tylenchulus semipenetrans Cobb, 1913, plus three new species of criconematids are recorded from Haryana state, India. Larvae of N. aberrans and N. basili are described for the first time. The main distinguishing features of the new species are as follows. M. paronostris n. sp.: R=117–128, R V=7–9, spear=55–62 μm, submedian lobes present, larvae with smooth annules; Criconemoides punicus n. sp.: R=75–85, R V=5–7, spear=73–81 μm, larvae with crenate annules: Hemicycliophora siddiqii n. sp.: R=185–198, R V=33–42, spear=57–59 μm, one incisure plus longitudinal lines on the cuticle. ac]19860702