Comparison of breeding value prediction for two traits in a Nellore-Angus crossbred population using different Bayesian modeling methodologies

The objectives of this study were to 1) compare four models for breeding value prediction using genomic or pedigree information and 2) evaluate the impact of fixed effects that account for family structure. Comparisons were made in a Nellore-Angus population comprising F₂, F₃ and half-siblings to embryo transfer F₂ calves with records for overall temperament at weaning (TEMP; n = 769) and Warner-Bratzler shear force (WBSF; n = 387). After quality control, there were 34,913 whole genome SNP markers remaining. Bayesian methods employed were BayesB ($\tilde{\pi }$ = 0.995 or 0.997 for WBSF or TEMP, respectively) and BayesC (π = 0 and $\tilde{\pi }$), where $\tilde{\pi }$ is the ideal proportion of markers not included. Direct genomic values (DGV) from single trait Bayesian analyses were compared to conventional pedigree-based animal model breeding values. Numerically, BayesC procedures (using $\tilde{\pi }$) had the highest accuracy of all models for WBSF and TEMP ($\widehat{\rho }$_gĝ = 0.843 and 0.923, respectively), but BayesB had the least bias (regression of performance on prediction closest to 1, $\widehat{\beta }$_y,x = 2.886 and 1.755, respectively). Accounting for family structure decreased accuracy and increased bias in prediction of DGV indicating a detrimental impact when used in these prediction methods that simultaneously fit many markers.     

Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities

Great Boiling Spring is a large, circumneutral, geothermal spring in the US Great Basin. Twelve samples were collected from water and four different sediment sites on four different dates. Microbial community composition and diversity were assessed by PCR amplification of a portion of the small subunit rRNA gene using a universal primer set followed by pyrosequencing of the V8 region. Analysis of 164 178 quality-filtered pyrotags clearly distinguished sediment and water microbial communities. Water communities were extremely uneven and dominated by the bacterium Thermocrinis. Sediment microbial communities grouped according to temperature and sampling location, with a strong, negative, linear relationship between temperature and richness at all taxonomic levels. Two sediment locations, Site A (87–80 °C) and Site B (79 °C), were predominantly composed of single phylotypes of the bacterial lineage GAL35 ($\widehat{p}$=36.1%), Aeropyrum ($\widehat{p}$=16.6%), the archaeal lineage pSL4 ($\widehat{p}$=15.9%), the archaeal lineage NAG1 ($\widehat{p}$=10.6%) and Thermocrinis ($\widehat{p}$=7.6%). The ammonia-oxidizing archaeon ‘Candidatus Nitrosocaldus'' was relatively abundant in all sediment samples <82 °C ($\widehat{p}$=9.51%), delineating the upper temperature limit for chemolithotrophic ammonia oxidation in this spring. This study underscores the distinctness of water and sediment communities in GBS and the importance of temperature in driving microbial diversity, composition and, ultimately, the functioning of biogeochemical cycles.     

Mixed Venous and Arterial Pco2

The rebreathing method of measuring oxygenated mixed venous Pco₂ (P$\bar{v}$co₂) was originally introduced as a bloodless way to estimate arterial Pco₂ (Paco₂). It has become common practice to subtract 6 mm Hg from the P$\bar{v}$co₂ to obtain the Paco₂ but there are many circumstances in which this leads to an overestimate of the Paco₂. Measurements of P$\bar{v}$co₂ and Paco₂ in 19 patients have shown that a better approximation to Paco₂ under normal conditions of cardiac output and arterial O₂ saturation is Paco₂ = 0·8 P$\bar{v}$co₂. These studies also showed that the P$\bar{v}$co₂ — Paco₂ difference may be much wider, particularly in the presence of arterial unsaturation and a low cardiac output.The factors governing the venoarterial Pco₂ difference are reviewed and their magnitude is calculated to emphasize the complementary roles of measurements of P$\bar{v}$co₂ and Paco₂ in the assessment of patients with cardiorespiratory disease.     

Relationship between the Absorption and Emission Spectra and the "Red Drop" in the Action Spectra of Fluorescence In Vivo

The Stepanov equation, relating the intensity of emission, f_e($\bar{v}$), at a given frequency, and that of absorption, k($\bar{v}$), at the same frequency, is applied, in its modified form (see equation 3 in text) to suspensions of Chlorella, Porphyridium, and Anacystis and to chlorophyll solutions. This application can reveal whether the yield of fluorescence, Φ($\bar{v}$), is constant, or changes with frequency. In Chlorella (green alga) a sharp drop of Φ($\bar{v}$) is indicated towards the lower frequencies (longer waves), beginning around $\bar{v}$ = 1.48 × 10⁴cm^-1 (680 mμ); the Φ($\bar{v}$) function calculated from the Stepanov equation is in fair agreement with the directly determined action spectrum for the excitation of chlorophyll fluorescence in this organism. In Porphyridium (red alga) and Anacystis (blue-green alga) application of the Stepanov equation supports the conclusions, derived from direct measurements, of a much earlier “red drop” of the fluorescence excitation spectra. Direct measurements suggest that the drop in Porphyridium may begin at about 1.53 × 10⁴cm^-1 (654 mμ); in Anacystis, it may begin already above 1.57 × 10⁴cm^-1 (<637mμ). These results confirm the relation, postulated earlier by Duysens and others, between the action spectra of photosynthesis and of chlorophyll a fluorescence in algal cells. The relation of these findings to spectroscopic evidence, suggesting the existence of two main chlorophyll a components in vivo, in green as well as in red and blue-green algae, is discussed.     

A Variable Sampling Interval Synthetic Xbar Chart for the Process Mean

The usual practice of using a control chart to monitor a process is to take samples from the process with fixed sampling interval (FSI). In this paper, a synthetic X¯ control chart with the variable sampling interval (VSI) feature is proposed for monitoring changes in the process mean. The VSI synthetic X¯ chart integrates the VSI X¯ chart and the VSI conforming run length (CRL) chart. The proposed VSI synthetic X¯ chart is evaluated using the average time to signal (ATS) criterion. The optimal charting parameters of the proposed chart are obtained by minimizing the out-of-control ATS for a desired shift. Comparisons between the VSI synthetic X¯ chart and the existing X¯, synthetic X¯, VSI X¯ and EWMA X¯ charts, in terms of ATS, are made. The ATS results show that the VSI synthetic X¯ chart outperforms the other X¯ type charts for detecting moderate and large shifts. An illustrative example is also presented to explain the application of the VSI synthetic X¯ chart.     

Angle of Inclination of Tank-Treading Red Cells: Dependence on Shear Rate and Suspending Medium

Red cells suspended in solutions much more viscous than blood plasma assume an almost steady-state orientation when sheared above a threshold value of shear rate. This orientation is a consequence of the motion of the membrane around the red cell called tank-treading. Observed along the undisturbed vorticity of the shear flow, tank-treading red cells appear as slender bodies. Their orientation can be quantified as an angle of inclination (θ) of the major axis with respect to the undisturbed flow direction. We measured θ using solution viscosities (η₀) and shear rates (γ˙) covering one and three orders of magnitude, respectively. At the lower values of η₀, θ was almost independent of γ˙. At the higher values of η₀, θ displayed a maximum at intermediate shear rates. The respective maximal values of θ increased by ∼10° from 10.7 to 104 mPas. After accounting for the absent membrane viscosity in models by using an increased cytoplasmic viscosity, their predictions of θ agree qualitatively with our data. Comparison of the observed variation of θ at constant γ˙ with model results suggests a change in the reference configuration of the shear stiffness of the membrane.     

Negative density-dependent dispersal in tsetse (Glossina spp): An artefact of inappropriate analysis

Published analysis of genetic material from field-collected tsetse (Glossina spp, primarily from the Palpalis group) has been used to predict that the distance (δ) dispersed per generation increases as effective population densities (D_e) decrease, displaying negative density-dependent dispersal (NDDD). Using the published data we show this result is an artefact arising primarily from errors in estimates of S, the area occupied by a subpopulation, and thereby in D_e. The errors arise from the assumption that S can be estimated as the area (S^) regarded as being covered by traps. We use modelling to show that such errors result in anomalously high correlations between δ^ and S^ and the appearance of NDDD, with a slope of -0.5 for the regressions of log(δ^) on log(D^e), even in simulations where we specifically assume density-independent dispersal (DID). A complementary mathematical analysis confirms our findings. Modelling of field results shows, similarly, that the false signal of NDDD can be produced by varying trap deployment patterns. Errors in the estimates of δ in the published analysis were magnified because variation in estimates of S were greater than for all other variables measured, and accounted for the greatest proportion of variation in δ^. Errors in census population estimates result from an erroneous understanding of the relationship between trap placement and expected tsetse catch, exacerbated through failure to adjust for variations in trapping intensity, trap performance, and in capture probabilities between geographical situations and between tsetse species. Claims of support in the literature for NDDD are spurious. There is no suggested explanation for how NDDD might have evolved. We reject the NDDD hypothesis and caution that the idea should not be allowed to influence policy on tsetse and trypanosomiasis control.     

The effects of fasting on swimming performance in juvenile qingbo (Spinibarbus sinensis) at two temperatures

We measured the following variables to investigate the effects of fasting and temperature on swimming performance in juvenile qingbo (Spinibarbus sinensis): the critical swimming speed (U_crit), resting metabolic rate ${(\dot{\mathrm{M}}O}_{\mathrm{2rest}})$ and active metabolic rate ${(\dot{\mathrm{M}}O}_{2active})$ of fish fasting for 0 (control), 1, 2 and 4 weeks at low and high acclimation temperatures (15 and 25 °C). Both fasting treatment and temperature acclimation had significant effects on all parameters measured (P<0.05). Fasting at the higher temperature had a negative effect on all measured parameters after 1 week (P<0.05). However, when acclimated to the lower temperature, fasting had a negative effect on U_crit until week 2 and on ${(\dot{\mathrm{M}}O}_{\mathrm{2rest}})$, ${(\dot{\mathrm{M}}O}_{\mathrm{2active}})$ and metabolic scope (MS, ${(\dot{\mathrm{M}}O}_{\mathrm{2active}})$–${(\dot{\mathrm{M}}O}_{\mathrm{2rest}})$) until week 4 (P<0.05). The values of all parameters at the lower temperature were significantly lower than those at the higher temperature in the identical fasting period groups except for ${(\dot{\mathrm{M}}O}_{\mathrm{2rest}})$ of the fish that fasted for 2 weeks. The relationship between fasting time (T) and U_crit was described as U_crit(15)=−0.302T²−0.800T+35.877 (r=0.781, n=32, P<0.001) and U_crit(25)=0.471T²−3.781T+50.097 (r=0.766, n=32, P<0.001₎ at 15 and 25 °C, respectively. The swimming performance showed less decrease in the early stage of fasting but more decrease in the later stage at the low temperature compared to the high temperature, which might be related to thermal acclimation time, resting metabolism, respiratory capacity, energy stores, enzyme activity in muscle tissue and energy substrate utilization changes with fasting between low and high temperatures. The divergent response of the swimming performance to fasting in qingbo at different temperatures might be an adaptive strategy to seasonal temperature and food resource variation in their habitat.     

Rhinos in the Parks: An Island-Wide Survey of the Last Wild Population of the Sumatran Rhinoceros

In the 200 years since the Sumatran rhinoceros was first scientifically described (Fisher 1814), the range of the species has contracted from a broad region in Southeast Asia to three areas on the island of Sumatra and one in Kalimantan, Indonesia. Assessing population and spatial distribution of this very rare species is challenging because of their elusiveness and very low population number. Using an occupancy model with spatial dependency, we assessed the fraction of the total landscape occupied by Sumatran rhinos over a 30,345-km² survey area and the effects of covariates in the areas where they are known to occur. In the Leuser Landscape (surveyed in 2007), the model averaging result of conditional occupancy estimate was ψ^(SE[ψ^])=0.151(0.109) or 2,371.47 km², and the model averaging result of replicated level detection probability p^(SE[p^])=0.252(0.267); in Way Kambas National Park—2008: ψ^(SE[ψ^])=0.468(0.165) or 634.18 km², and p^(SE[p^])=0.138(0.571); and in Bukit Barisan Selatan National Park—2010: ψ^(SE[ψ^])=0.322(0.049) or 819.67 km², and p^(SE[p^])=0.365(0.42). In the Leuser Landscape, rhino occurrence was positively associated with primary dry land forest and rivers, and negatively associated with the presence of a road. In Way Kambas, occurrence was negatively associated with the presence of a road. In Bukit Barisan Selatan, occurrence was negatively associated with presence of primary dryland forest and rivers. Using the probabilities of site occupancy, we developed spatially explicit maps that can be used to outline intensive protection zones for in-situ conservation efforts, and provide a detailed assessment of conserving Sumatran rhinos in the wild. We summarize our core recommendation in four points: consolidate small population, strong protection, determine the percentage of breeding females, and recognize the cost of doing nothing. To reduce the probability of poaching, here we present only the randomized location of site level occupancy in our result while retaining the overall estimation of occupancy for a given area.     

Cardiorespiratory Adaptations during Concurrent Aerobic and Strength Training in Men and Women

This study investigated the effects of endurance followed by strength training (ES, men n = 16; women n = 15), the reverse exercise order (SE, men n = 18, women n = 13) and concurrent endurance and strength training performed on alternating days (AD, men n = 21, women n = 18) on cardiorespiratory parameters. Peak oxygen consumption (V˙O_2peak) and oxygen consumption at sub-maximal power outputs (V˙O_2submax) of 50 to 175 Watts in men and 50 to 125 Watts in women were assessed during an incremental cycling test both before and after 24 weeks of training. Increases in V˙O_2peak in both men and women were statistically larger in AD (18±9% and 25±11%) compared to ES (7±9% and 12±12%, p = 0.002 and 0.009, respectively) and SE (7±9% and 10±8%, p = 0.005 and 0.008, respectively). No statistical group interaction was observed for V˙O_2submax in men, but in women V˙O_2submax was statistically lower at week 24 in ES compared to AD at 75 W (-2±6% vs. +3±6%, p = 0.027) and 125 W (-4±5% vs. +2±5%, p = 0.010). These findings indicate that endurance and strength training performed on alternating days may optimize the adaptations in V˙O_2peak in both sexes, while performing ES training in women may optimize cardiorespiratory fitness at sub-maximal power outputs.     

A Global Analysis of Deforestation in Moist Tropical Forest Protected Areas

Protected areas (PAs) have been established to conserve tropical forests, but their effectiveness at reducing deforestation is uncertain. To explore this issue, we combined high resolution data of global forest loss over the period 2000–2012 with data on PAs. For each PA we quantified forest loss within the PA, in buffer zones 1, 5, 10 and 15 km outside the PA boundary as well as a 1 km buffer within the PA boundary. We analysed 3376 tropical and subtropical moist forest PAs in 56 countries over 4 continents. We found that 73% of PAs experienced substantial deforestation pressure, with >0.1% a⁻¹ forest loss in the outer 1 km buffer. Forest loss within PAs was greatest in Asia (0.25% a⁻¹) compared to Africa (0.1% a⁻¹), the Neotropics (0.1% a⁻¹) and Australasia (Australia and Papua New Guinea; 0.03% a⁻¹). We defined performance (P) of a PA as the ratio of forest loss in the inner 1 km buffer compared to the loss that would have occurred in the absence of the PA, calculated as the loss in the outer 1 km buffer corrected for any difference in deforestation pressure between the two buffers. To remove the potential bias due to terrain, we analysed a subset of PAs (n = 1804) where slope and elevation in inner and outer 1 km buffers were similar (within 1° and 100 m, respectively). We found 41% of PAs in this subset reduced forest loss in the inner buffer by at least 25% compared to the expected inner buffer forest loss (P<0.75). Median performance (P˜) of subset reserves was 0.87, meaning a reduction in forest loss within the PA of 13%. We found PAs were most effective in Australasia (P˜=0.16), moderately successful in the Neotropics (P˜=0.72) and Africa (P˜=0.83), but ineffective in Asia (P˜=1). We found many countries have PAs that give little or no protection to forest loss, particularly in parts of Asia, west Africa and central America. Across the tropics, the median effectiveness of PAs at the national level improved with gross domestic product per capita. Whilst tropical and subtropical moist forest PAs do reduce forest loss, widely varying performance suggests substantial opportunities for improved protection, particularly in Asia.     

The Impact of Prior Information on Estimates of Disease Transmissibility Using Bayesian Tools

The basic reproductive number (R₀) and the distribution of the serial interval (SI) are often used to quantify transmission during an infectious disease outbreak. In this paper, we present estimates of R₀ and SI from the 2003 SARS outbreak in Hong Kong and Singapore, and the 2009 pandemic influenza A(H1N1) outbreak in South Africa using methods that expand upon an existing Bayesian framework. This expanded framework allows for the incorporation of additional information, such as contact tracing or household data, through prior distributions. The results for the R₀ and the SI from the influenza outbreak in South Africa were similar regardless of the prior information (R^0 = 1.36–1.46, μ^ = 2.0–2.7, μ^ = mean of the SI). The estimates of R₀ and μ for the SARS outbreak ranged from 2.0–4.4 and 7.4–11.3, respectively, and were shown to vary depending on the use of contact tracing data. The impact of the contact tracing data was likely due to the small number of SARS cases relative to the size of the contact tracing sample.     

Determination of sedimentation coefficients of subcellular particles of rat liver homogenates. A theoretical and experimental approach

A simple and convenient method is described for the determination of the average sedimentation coefficients ($\overline{S}?values$) of subcellular particles in a homogenous solution by velocity sedimentation in the preparative ultracentrifuge (swinging-bucket rotor). Theoretically the method is based on the distribution of intact organelles between sediment and supernatant and the convergence of their sedimentation at high centrifugal effects. The data have been treated according to the rate equation of parallel sedimentation in horizontal cylindrical tubes which has been converted to a linear function. By measuring activities of marker enzymes in the sediments, the theory has been confirmed experimentally in the determination of $\overline{S}?values$ and the distribution between supernatant and sediment of intact mitochondria, lysosomes and peroxisomes of rat liver homogenates. The effect of particle concentration on the $\overline{S}?values$ of mitochondria has been determined.     

Reproductive biology of the horned viper,Cerastes cerastes gasperettii in the central region of Saudi Arabia

The reproductive biology of the horned viper, Cerastes cerastes gasperettii, in Riyadh region of Saudi Arabia was investigated over a period of one year. Study of reproductive cycle of male and female C. c. gasperettii revealed that the breeding season is relatively short (April and May). Thereafter females laid eggs by mid of July and hatching probably had taken place by the end of September. No activity was observed during winter, this may indicate just a single clutch per year. Relative testis weight to body weight was drastically increased (X¯ = 0.88%) during the peak of reproductive activity (May) where maximal expansion of seminiferous tubules was also attained during April and May (X¯ = 209 μm and 191 μm, respectively). Likewise, the ovarian activity was the highest during May where ovarian parameters were greater in terms of relative ovarian weight to body weight and ova diameter being 0.46% and 2.29 mm, respectively. Fat body weight was increased drastically just before the peak of reproductive activity then started to decline during June. It could be concluded that the harsh desert conditions and similar environments certainly affect reproductive activity of Saudi Arabian reptiles including snakes.