Spind: a package for computing spatially corrected accuracy measures

Using an appropriate accuracy measure is essential for assessing prediction accuracy in species distribution modelling. Therefore, model evaluation as an analytical uncertainty is a challenging problem. Although a variety of accuracy measures for the assessment of prediction errors in presence/absence models is available, there is a lack of spatial accuracy measures, i.e. measures that are sensitive to the spatial arrangement of the predictions. We present ‘spind’, a new software package (based on the R software program) that provides spatial performance measures for grid‐based models. These accuracy measures are generalized, spatially corrected versions of the classical ones, thus enabling comparisons between them. Our method for evaluation consists of the following steps: 1) incorporate additional autocorrelation until spatial autocorrelation in predictions and actuals is balanced, 2) cross‐classify predictions and adjusted actuals in a 4 × 4 contingency table, 3) use a refined weighting pattern for errors, and 4) calculate weighted Kappa, sensitivity, specificity and subsequently ROC, AUC, TSS to get spatially corrected indices. To illustrate the impact of our spatial method we present an example of simulated data as well as an example of presence/absence data of the plant species Dianthus carthusianorum across Germany. Our analysis includes a statistic for the comparison of spatial and classical (non‐spatial) indices. We find that our spatial indices tend to result in higher values than classical ones. These differences are statistically significant at medium and high autocorrelation levels. We conclude that these spatial accuracy measures may contribute to evaluate prediction errors in presence/absence models, especially in case of medium or high degree of similarity of adjacent data, i.e. aggregated (clumped) or continuous species distributions.     

Genes,social transmission,but not maternal effects influence responses of wild Japanese macaques (<Emphasis Type="Italic">Macaca fuscata</Emphasis>) to novel-object and novel-food tests

Using long-term maternal pedigree data, microsatellite analysis, and behavioral tests, we examined whether personality differences in wild Japanese macaques (Macaca fuscata) are associated with additive genetic effects, maternal influences, or belonging to a particular social group. Behaviors elicited by novel-object tests were defined by a component related to caution around novel-objects (Ob-PC1) and behaviors elicited by novel food-tests were defined by correlated components related to consummatory responses (Fo-PC1) and caution around novel foods (Fo-PC2). The repeatability of Ob-PC1 was modest and not significant; the repeatabilities of Fo-PC1 and Fo-PC2 were moderate and significant. Linear mixed effects models found that sex, age, sex × age, provisioning, trial number, date, time of day, season, and distance to the closest monkey were not related to personality. Linear mixed effects models of females older than 2 years found that high rank was associated with greater caution around novel objects. Linear models were used to determine whether sex, age, group membership, maternal kinship, or relatedness had independent effects on the personality similarity of dyads. These analyses found that pairs of macaques that lived in the same group were less similar in their caution around novel objects, more closely related pairs of macaques were more similar in their tendency to eat novel food, and that pairs of macaques in the same group were more similar in how cautious they were around novel foods. Together, these findings suggest that personality in this population of wild monkeys was driven by rank, genetic effects, and group effects, the latter possibly including the need to exploit different niches in the environment.     

β<Subscript>2</Subscript>-adrenergic receptor maladaptations to high power resistance exercise overreaching

The effects of a recovery drink on overreaching induced by high frequency, high power resistance exercise was assessed. Resistance trained men were assigned to a supplemented (SUP, n = 8), placebo (PL, n = 3) or control (CON, n = 6) groups. All groups completed two weeks of familiarization training using the barbell squat. In week three, SUP and PL performed ten sets of five repetitions of speed squats twice daily, for a total of 15 training sessions. CON maintained their prior training schedule. Data were collected before week three (T1), after week three (T2) and after a week of recovery by training cessation (T3). During week three, SUP consumed an amino acid, carbohydrate and creatine monohydrate containing recovery drink immediately after each training bout. PL was provided a drink of similar appearance and taste but containing minimal nutritional value. At T2, both SUP and PL decreased mean squat velocity and power at 70% 1RM. Additionally, SUP and PL decreased muscle β₂-adrenergic receptor (β₂-AR) expression by 61 and 83%, respectively. Increases in the ratio of nocturnal urinary epinephrine/β₂-AR ratio (EPI: β₂AR) for SUP and PL suggested impaired sympathetic nervous system sensitivity. SUP demonstrated a smaller decrease in β₂-AR expression and a lower EPI: β₂AR, suggesting the recovery drink attenuated the detrimental effects of overreaching on the sympathetic activity. In conclusion, high power resistance exercise overreaching can induce performance decrements and impair sympathetic activity, but these effects may be attenuated by supplementation.     

High-Precision (MC-ICPMS) Isotope Ratio Analysis Reveals Contrasting Sources of Elevated Blood Lead Levels of an Adult with Retained Bullet Fragments,and of His Child,in Milwaukee,Wisconsin

This study aimed at evaluation of a relationship between blood selenium concentration (Se-B) and blood cystatin C concentration (CST) in a randomly selected population of healthy children, environmentally exposed to lead and cadmium. The studies were conducted on 172 randomly selected children (7.98 ± 0.97 years). Among participants, the subgroups were distinguished, manifesting marginally low blood selenium concentration (Se-B 40–59 μg/l), suboptimal blood selenium concentration (Se-B: 60–79 μg/l) or optimal blood selenium concentration (Se-B ≥ 80 μg/l). At the subsequent stage, analogous subgroups of participants were selected separately in groups of children with BMI below median value (BMI <16.48 kg/m²) and in children with BMI ≥ median value (BMI ≥16.48 kg/m²). In all participants, values of Se-B and CST were estimated. In the entire group of examined children no significant differences in mean CST values were detected between groups distinguished on the base of normative Se-B values. Among children with BMI below 16.48 kg/m², children with marginally low Se-B manifested significantly higher mean CST values, as compared to children with optimum Se-B (0.95 ± 0.07 vs. 0.82 ± 0.15 mg/l, p < 0.05). In summary, in a randomly selected population of healthy children no relationships could be detected between blood selenium concentration and blood cystatin C concentration. On the other hand, in children with low body mass index, a negative non-linear relationship was present between blood selenium concentration and blood cystatin C concentration.     

AMPKα1‐LDH pathway regulates muscle stem cell self‐renewal by controlling metabolic homeostasis

Control of stem cell fate to either enter terminal differentiation versus returning to quiescence (self‐renewal) is crucial for tissue repair. Here, we showed that AMP‐activated protein kinase (AMPK), the master metabolic regulator of the cell, controls muscle stem cell (MuSC) self‐renewal. AMPKα1^?/? MuSCs displayed a high self‐renewal rate, which impairs muscle regeneration. AMPKα1^?/? MuSCs showed a Warburg‐like switch of their metabolism to higher glycolysis. We identified lactate dehydrogenase (LDH) as a new functional target of AMPKα1. LDH, which is a non‐limiting enzyme of glycolysis in differentiated cells, was tightly regulated in stem cells. In functional experiments, LDH overexpression phenocopied AMPKα1^?/? phenotype, that is shifted MuSC metabolism toward glycolysis triggering their return to quiescence, while inhibition of LDH activity rescued AMPKα1^?/? MuSC self‐renewal. Finally, providing specific nutrients (galactose/glucose) to MuSCs directly controlled their fate through the AMPKα1/LDH pathway, emphasizing the importance of metabolism in stem cell fate.     

Genetic diversity and population structure of food-borne Staphylococcus carnosus strains

The species Staphylococcus carnosus is a non-pathogenic representative of the coagulase negative staphylococci. Specific strains are applied as meat starter cultures. The species consists of two subspecies, S. carnosus ssp. carnosus and S. carnosus ssp. utilis. In order to place S. carnosus strains, characterized in former studies, in a genetic background that allows a typing of candidates for starter cultures, a Multilocus Sequence Typing (MLST) scheme was developed. Internal fragments of the genes tpiA, xprT, dat, gmk, glpK, narG, cstA, encoding triosephosphate isomerase, xanthine phosphoribosyltransferase, d-amino acid aminotransferase, guanylate kinase, glycerol kinase, the α-chain of the respiratory nitrate reductase, and a carbon starvation protein where chosen. Genes were selected based on their equal distribution in the genome, taxonomic value in subspecies differentiation and metabolic function. This MLST was applied to 44 S. carnosus strains, most of them previously analyzed for their suitability as starter cultures.The number of alleles varied between zero (tpiA) and five (cstA) and allowed the definition of nine sequence types (ST). ST1 was most abundant (18 strains), followed by ST2 (8) and ST4 (6). The nine STs confirmed a close relationship of all strains despite their isolation source and year, but lacked correlation with physiological activities relevant for starter cultures. The low amount of STs in the strain set lets us suggest that recombination between strains is rare. Thus, it is hypothesized that evolutionary events seem to be due to single point mutations rather than intrachromosomal recombination, and that the species possesses a clonal population structure.     

Automated quantification of steatosis: agreement with stereological point counting

Background

Steatosis is routinely assessed histologically in clinical practice and research. Automated image analysis can reduce the effort of quantifying steatosis. Since reproducibility is essential for practical use, we have evaluated different analysis methods in terms of their agreement with stereological point counting (SPC) performed by a hepatologist.

Methods

The evaluation was based on a large and representative data set of 970 histological images from human patients with different liver diseases. Three of the evaluated methods were built on previously published approaches. One method incorporated a new approach to improve the robustness to image variability.

Results

The new method showed the strongest agreement with the expert. At 20× resolution, it reproduced steatosis area fractions with a mean absolute error of 0.011 for absent or mild steatosis and 0.036 for moderate or severe steatosis. At 10× resolution, it was more accurate than and twice as fast as all other methods at 20× resolution. When compared with SPC performed by two additional human observers, its error was substantially lower than one and only slightly above the other observer.

Conclusions

The results suggest that the new method can be a suitable automated replacement for SPC. Before further improvements can be verified, it is necessary to thoroughly assess the variability of SPC between human observers.

     

Cognition in aged rhesus monkeys: effect of DHEA and correlation with steroidogenic gene expression

Estradiol supplementation has been shown to enhance cognitive performance in old ovariectomized rhesus macaques (Macaca mulatta). To determine if similar benefits could be achieved in perimenopausal animals using alternative hormonal supplements, we administered dehydroepiandrosterone (DHEA) to old ovary‐intact female rhesus macaques for ～2.5 months. Using computerized touch screen memory tasks, including delayed response (DR) and delayed matching‐to‐sample (DMS), we observed improved performance with time in all of the animals but failed to detect a significant effect of DHEA. On the other hand, gene expression profiling disclosed a significant correlation between cognitive performance and the expression of several steroidogenic and steroid‐responsive genes. The DR performance was positively correlated with hippocampal expression of AKR1C3 and STAR and negatively correlated with the expression of SDRD5A1. A positive correlation was also found between DMS performance and prefrontal cortical expression of AKR1C3 and a negative correlation with STAR, as well as a negative correlation with the hippocampal expression of HSD11B1 and NR3C1. Taken together, the results suggest that steroidogenic gene regulation within the brain may help to maintain cognitive function during the perimenopausal transition period, despite a decline in sex‐steroid levels in the circulation.