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.     

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.     

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.     

Correlation of a Decline in Aerobic Capacity with Development of Emphysema in Patients with Chronic Obstructive Pulmonary Disease: A Prospective Observational Study

In patients with COPD, CT assessment of emphysema and airway disease is known to be associated with lung function and 6-minute walk distance. However, it remains to be determined whether low attenuation area (LAA) on CT is associated with aerobic capacity assessed using cardiopulmonary exercise testing (CPET). In this prospective observational study, we repeatedly conducted high-resolution CT and CPET using a treadmill in 81 COPD patients over a median interval of 3.5 years. Two investigators independently scored LAA on images obtained at the aortic arch level, tracheal bifurcation level, and supradiaphragmatic level. Grades for the images of each lung were added to yield the total LAA score. Total LAA score was negatively correlated with peak aerobic capacity (V˙O2) (p<0.001, r = -0.485). LAA scores of the upper (aortic arch level) and the lower (supradiaphragmatic level) lungs were both significantly associated with peak V˙O2. There was a significant correlation between total LAA score and peak CO₂ output (V˙CO2) (p<0.001, r = -0.433). Total LAA score was correlated with oxygen saturation at peak exercise (p<0.001, r = -0.634) and the estimated dead space fraction (p<0.001, r = 0.416). The mean annual change in total LAA score was significantly correlated with those in peak V˙O2 (p<0.001, r = -0.546) and peak V˙CO2 (p<0.001, r = -0.488). The extent of emphysema measured by CT was associated with the results of CPET. The time-dependent changes in CPET data were also correlated with that in total LAA score. CT assessment could be a non-invasive tool to predict aerobic capacity in patients with COPD.     

A Novel Method for Quantifying the Inhaled Dose of Air Pollutants Based on Heart Rate,Breathing Rate and Forced Vital Capacity

To better understand the interaction of physical activity and air pollution exposure, it is important to quantify the change in ventilation rate incurred by activity. In this paper, we describe a method for estimating ventilation using easily-measured variables such as heart rate (HR), breathing rate (f_B), and forced vital capacity (FVC). We recruited healthy adolescents to use a treadmill while we continuously measured HR, f_B, and the tidal volume (V_T) of each breath. Participants began at rest then walked and ran at increasing speed until HR was 160–180 beats per minute followed by a cool down period. The novel feature of this method is that minute ventilation (V˙E) was normalized by FVC. We used general linear mixed models with a random effect for subject and identified nine potential predictor variables that influence either V˙E or FVC. We assessed predictive performance with a five-fold cross-validation procedure. We used a brute force selection process to identify the best performing models based on cross-validation percent error, the Akaike Information Criterion and the p-value of parameter estimates. We found a two-predictor model including HR and f_B to have the best predictive performance (V˙E/FVC = -4.247+0.0595HR+0.226f_B, mean percent error = 8.1±29%); however, given the ubiquity of HR measurements, a one-predictor model including HR may also be useful (V˙E/FVC = -3.859+0.101HR, mean percent error = 11.3±36%).     

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.     

Influence of Adjuvant Therapy in Cancer Survivors on Endothelial Function and Skeletal Muscle Deoxygenation

The cardiotoxic effects of adjuvant cancer treatments (i.e., chemotherapy and radiation treatment) have been well documented, but the effects on peripheral cardiovascular function are still unclear. We hypothesized that cancer survivors i) would have decreased resting endothelial function; and ii) altered muscle deoxygenation response during moderate intensity cycling exercise compared to cancer-free controls. A total of 8 cancer survivors (~70 months post-treatment) and 9 healthy controls completed a brachial artery FMD test, an index of endothelial-dependent dilation, followed by an incremental exercise test up to the ventilatory threshold (VT) on a cycle ergometer during which pulmonary V˙O2 and changes in near-infrared spectroscopy (NIRS)-derived microvascular tissue oxygenation (TOI), total hemoglobin concentration ([Hb]_total), and muscle deoxygenation ([HHb] ≈ fractional O₂ extraction) were measured. There were no significant differences in age, height, weight, and resting blood pressure between cancer survivors and control participants. Brachial artery FMD was similar between groups (P = 0.98). During exercise at the VT, TOI was similar between groups, but [Hb]_total and [HHb] were significantly decreased in cancer survivors compared to controls (P < 0.01) The rate of change for TOI (ΔTOIΔ/V˙O2) and [HHb] (Δ[HHb]/ΔV˙O2) relative to ΔV˙O2 were decreased in cancer survivors compared to controls (P = 0.02 and P = 0.03 respectively). In cancer survivors, a decreased skeletal muscle microvascular function was observed during moderate intensity cycling exercise. These data suggest that adjuvant cancer therapies have an effect on the integrated relationship between O₂ extraction, V˙O2 and O₂ delivery during exercise.     

An Improved Fst Estimator

The fixation index F _st plays a central role in ecological and evolutionary genetic studies. The estimators of Wright (F^st1), Weir and Cockerham (F^st2), and Hudson et al. (F^st3) are widely used to measure genetic differences among different populations, but all have limitations. We propose a minimum variance estimator F^stm using F^st1 and F^st2. We tested F^stm in simulations and applied it to 120 unrelated East African individuals from Ethiopia and 11 subpopulations in HapMap 3 with 464,642 SNPs. Our simulation study showed that F^stm has smaller bias than F^st2 for small sample sizes and smaller bias than F^st1 for large sample sizes. Also, F^stm has smaller variance than F^st2 for small F _st values and smaller variance than F^st1 for large F _st values. We demonstrated that approximately 30 subpopulations and 30 individuals per subpopulation are required in order to accurately estimate F _st.     

Effect of Ocean Acidification and pH Fluctuations on the Growth and Development of Coralline Algal Recruits,and an Associated Benthic Algal Assemblage

Coralline algae are susceptible to the changes in the seawater carbonate system associated with ocean acidification (OA). However, the coastal environments in which corallines grow are subject to large daily pH fluctuations which may affect their responses to OA. Here, we followed the growth and development of the juvenile coralline alga Arthrocardia corymbosa, which had recruited into experimental conditions during a prior experiment, using a novel OA laboratory culture system to simulate the pH fluctuations observed within a kelp forest. Microscopic life history stages are considered more susceptible to environmental stress than adult stages; we compared the responses of newly recruited A. corymbosa to static and fluctuating seawater pH with those of their field-collected parents. Recruits were cultivated for 16 weeks under static pH 8.05 and 7.65, representing ambient and 4× preindustrial pCO₂ concentrations, respectively, and two fluctuating pH treatments of daily x~ = 8.05 (daytime pH = 8.45, night-time pH = 7.65) and daily x~ = 7.65 (daytime pH = 8.05, night-time pH = 7.25). Positive growth rates of new recruits were recorded in all treatments, and were highest under static pH 8.05 and lowest under fluctuating pH 7.65. This pattern was similar to the adults’ response, except that adults had zero growth under fluctuating pH 7.65. The % dry weight of MgCO₃ in calcite of the juveniles was reduced from 10% at pH 8.05 to 8% at pH 7.65, but there was no effect of pH fluctuation. A wide range of fleshy macroalgae and at least 6 species of benthic diatoms recruited across all experimental treatments, from cryptic spores associated with the adult A. corymbosa. There was no effect of experimental treatment on the growth of the benthic diatoms. On the community level, pH-sensitive species may survive lower pH in the presence of diatoms and fleshy macroalgae, whose high metabolic activity may raise the pH of the local microhabitat.     

Enhancement of Chemotactic Cell Aggregation by Haptotactic Cell-To-Cell Interaction

The crawling of biological cell is a complex phenomenon involving various biochemical and mechanical processes. Some of these processes are intrinsic to individual cells, while others pertain to cell-to-cell interactions and to their responses to extrinsically imposed cues. Here, we report an interesting aggregation dynamics of mathematical model cells, when they perform chemotaxis in response to an externally imposed global chemical gradient while they influence each other through a haptotaxis-mediated social interaction, which confers intriguing trail patterns. In the absence of the cell-to-cell interaction, the equilibrium population density profile fits well to that of a simple Keller-Segal population dynamic model, in which a chemotactic current density J→chemo∼∇p competes with a normal diffusive current density J→diff∼∇ρ, where p and ρ refer to the concentration of chemoattractant and population density, respectively. We find that the cell-to-cell interaction confers a far more compact aggregation resulting in a much higher peak equilibrium cell density. The mathematical model system is applicable to many biological systems such as swarming microglia and neutrophils or accumulating ants towards a localized food source.     

Hunting,Exotic Carnivores,and Habitat Loss: Anthropogenic Effects on a Native Carnivore Community,Madagascar

The wide-ranging, cumulative, negative effects of anthropogenic disturbance, including habitat degradation, exotic species, and hunting, on native wildlife has been well documented across a range of habitats worldwide with carnivores potentially being the most vulnerable due to their more extinction prone characteristics. Investigating the effects of anthropogenic pressures on sympatric carnivores is needed to improve our ability to develop targeted, effective management plans for carnivore conservation worldwide. Utilizing photographic, line-transect, and habitat sampling, as well as landscape analyses and village-based bushmeat hunting surveys, we provide the first investigation of how multiple forms of habitat degradation (fragmentation, exotic carnivores, human encroachment, and hunting) affect carnivore occupancy across Madagascar’s largest protected area: the Masoala-Makira landscape. We found that as degradation increased, native carnivore occupancy and encounter rates decreased while exotic carnivore occupancy and encounter rates increased. Feral cats (Felis species) and domestic dogs (Canis familiaris) had higher occupancy than half of the native carnivore species across Madagascar’s largest protected landscape. Bird and small mammal encounter rates were negatively associated with exotic carnivore occupancy, but positively associated with the occupancy of four native carnivore species. Spotted fanaloka (Fossa fossana) occupancy was constrained by the presence of exotic feral cats and exotic small Indian civet (Viverricula indica). Hunting was intense across the four study sites where hunting was studied, with the highest rates for the small Indian civet (x¯ = 90 individuals consumed/year), the ring-tailed vontsira (Galidia elegans) (x¯ = 58 consumed/year), and the fosa (Cryptoprocta ferox) (x¯ = 31 consumed/year). Our modeling results suggest hunters target intact forest where carnivore occupancy, abundance, and species richness, are highest. These various anthropogenic pressures and their effects on carnivore populations, especially increases in exotic carnivores and hunting, have wide-ranging, global implications and demand effective management plans to target the influx of exotic carnivores and unsustainable hunting that is affecting carnivore populations across Madagascar and worldwide.     

Endurance Training-Induced Increase in Circulating Irisin Levels Is Associated with Reduction of Abdominal Visceral Fat in Middle-Aged and Older Adults

To elucidate the effects of endurance training on circulating irisin levels in young and middle-aged/older adults, and to determine the association between endurance training-induced alteration of irisin and reduction in body fat. Twenty-five healthy young (age 21 ± 1 years; 16 men, 9 women) and 28 healthy middle-aged/older adults (age 67 ± 8 years; 12 men, 16 women) participated in the study. Each age cohort was divided into two groups: the endurance-training group (14 young, 14 middle-aged/older) and the control group. Subjects in the training groups completed an 8-week endurance-training program (cycling at 60-70% peak oxygen uptake [V˙O_2peak] for 45 min, 3 days/week). Before and after the intervention, we evaluated serum irisin level, V˙O_2peak, and body composition. The increase in V˙O_2peak in the young and middle-aged/older training groups after the intervention period was significantly greater than those in the young and middle-aged/older control groups (P < 0.05). Serum irisin level was significantly increased in the middle-aged/older training group after the intervention period (P < 0.01), but not in the young training group. Furthermore, in the middle-aged/older training group, the endurance training-induced reduction in visceral adipose tissue area was negatively correlated with the change in serum irisin level (r = −0.54, P < 0.05). These results suggest a possible role for secreted irisin in the exercise-induced alteration of abdominal visceral fat in middle-aged and older adults.     

A Comparison between Conductive and Infrared Devices for Measuring Mean Skin Temperature at Rest,during Exercise in the Heat,and Recovery

PurposeSkin temperature assessment has historically been undertaken with conductive devices affixed to the skin. With the development of technology, infrared devices are increasingly utilised in the measurement of skin temperature. Therefore, our purpose was to evaluate the agreement between four skin temperature devices at rest, during exercise in the heat, and recovery.MethodsMean skin temperature (T-sk) was assessed in thirty healthy males during 30 min rest (24.0 ± 1.2°C, 56 ± 8%), 30 min cycle in the heat (38.0 ± 0.5°C, 41 ± 2%), and 45 min recovery (24.0 ± 1.3°C, 56 ± 9%). T-sk was assessed at four sites using two conductive devices (thermistors, iButtons) and two infrared devices (infrared thermometer, infrared camera).ResultsBland–Altman plots demonstrated mean bias ± limits of agreement between the thermistors and iButtons as follows (rest, exercise, recovery): -0.01 ± 0.04, 0.26 ± 0.85, -0.37 ± 0.98°C; thermistors and infrared thermometer: 0.34 ± 0.44, -0.44 ± 1.23, -1.04 ± 1.75°C; thermistors and infrared camera (rest, recovery): 0.83 ± 0.77, 1.88 ± 1.87°C. Pairwise comparisons of T-sk found significant differences (p < 0.05) between thermistors and both infrared devices during resting conditions, and significant differences between the thermistors and all other devices tested during exercise in the heat and recovery.ConclusionsThese results indicate poor agreement between conductive and infrared devices at rest, during exercise in the heat, and subsequent recovery. Infrared devices may not be suitable for monitoring T-sk in the presence of, or following, metabolic and environmental induced heat stress.     

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.     

The Effects of Exercise Intensity vs. Metabolic State on the Variability and Magnitude of Left Ventricular Twist Mechanics during Exercise

Increased left ventricular (LV) twist and untwisting rate (LV twist mechanics) are essential responses of the heart to exercise. However, previously a large variability in LV twist mechanics during exercise has been observed, which complicates the interpretation of results. This study aimed to determine some of the physiological sources of variability in LV twist mechanics during exercise. Sixteen healthy males (age: 22 ± 4 years, V˙O_2peak: 45.5 ± 6.9 ml∙kg^-1∙min^-1, range of individual anaerobic threshold (IAT): 32–69% of V˙O_2peak) were assessed at rest and during exercise at: i) the same relative exercise intensity, 40%_peak, ii) at 2% above IAT, and, iii) at 40%_peak with hypoxia (40%_peak+HYP). LV volumes were not significantly different between exercise conditions (P > 0.05). However, the mean margin of error of LV twist was significantly lower (F_2,47 = 2.08, P < 0.05) during 40%peak compared with IAT (3.0 vs. 4.1 degrees). Despite the same workload and similar LV volumes, hypoxia increased LV twist and untwisting rate (P < 0.05), but the mean margin of error remained similar to that during 40%peak (3.2 degrees, P > 0.05). Overall, LV twist mechanics were linearly related to rate pressure product. During exercise, the intra-individual variability of LV twist mechanics is smaller at the same relative exercise intensity compared with IAT. However, the absolute magnitude (degrees) of LV twist mechanics appears to be associated with the prevailing rate pressure product. Exercise tests that evaluate LV twist mechanics should be standardised by relative exercise intensity and rate pressure product be taken into account when interpreting results.     

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.     

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.