Implementing Monte Carlo tests with P-value buckets

Software packages usually report the results of statistical tests using p-values. Users often interpret these by comparing them to standard thresholds, e.g. 0.1%, 1% and 5%, which is sometimes reinforced by a star rating (***, **, *). We consider an arbitrary statistical test whose p-value p is not available explicitly, but can be approximated by Monte Carlo samples, e.g. by bootstrap or permutation tests. The standard implementation of such tests usually draws a fixed number of samples to approximate p. However, the probability that the exact and the approximated p-value lie on different sides of a threshold (the resampling risk) can be high, particularly for p-values close to a threshold. We present a method to overcome this. We consider a finite set of user-specified intervals which cover [0,1] and which can be overlapping. We call these p-value buckets. We present algorithms that, with arbitrarily high probability, return a p-value bucket containing p. We prove that for both a bounded resampling risk and a finite runtime, overlapping buckets need to be employed, and that our methods both bound the resampling risk and guarantee a finite runtime for such overlapping buckets. To interpret decisions with overlapping buckets, we propose an extension of the star rating system. We demonstrate that our methods are suitable for use in standard software, including for low p-value thresholds occurring in multiple testing settings, and that they can be computationally more efficient than standard implementations

Genetic parameters for Photobacterium damselae subsp. piscicida resistance, immunological markers and body weight in gilthead seabream (Sparus aurata)

A challenge test for Photobacterium damselae subsp. piscicida (Phdp) resistance was carried out in two juvenile populations of gilthead seabream (Sparus aurata L.): F2_ATL and F0_MED. At 250 days post-hatching (dph), a fish plasma sample was collected to measure humoral immune markers (peroxidase activity, bactericidal activity, and IgM immunoglobulin levels), and at 272 dph fish were weighed and inoculated with bacteria Phdp. From that time onwards, surviving fish were recorded for nine days, and days to death was registered. Heritabilities for body weight and Phdp survival were moderate, although for days to death the heritability was low. Regarding humoral immune markers, for peroxidase activity it was moderate, and for IgM levels and for bactericidal activity it was low. Genetic correlations for body weight with Phdp survival and days to death were high and positive, while with peroxidase activity and IgM levels they tended to be positive, although these estimates were not accurate. Regarding genetic correlations between Phdp survival and humoral immune markers, they were very high, positive with peroxidase activity, and negative with IgM levels and bactericidal activity. Some humoral immune markers, particularly peroxidase activity, along with performance traits such as body weight and absence of deformities, are proposed to be included in a selective breeding program to raise fish that are capable of coping with diseasesVersión del editor2,04

A systematic conservation strategy for crop wild relatives in the Czech Republic

Aim: To create a crop wild relative (CWR) conservation strategy for the Czech Republic: the first national CWR conservation strategy for Central and Eastern Europe. Location: Czech Republic. Methods: We generated a CWR checklist for the Czech Republic and then prioritized taxa, using widely adopted criteria modified with input from local experts, to create a national CWR inventory. For 204 priority CWR species, we collated 206,760 presence records. We carried out spatial analyses to identify patterns in species richness, gaps in existing conservation actions, complementary conservation networks and collecting strategies to increase representativeness of gene bank accessions. We considered both specific and genetic conservation, using geographic and ecogeographic proxies for the latter. Results: Passive in situ conservation of CWR in the Czech Republic is comprehensive at present, with all but one priority CWR species being contained in protected areas. Active in situ CWR conservation could be focussed within 11 ca. 10-km-by-10-km grid cells containing 94% of priority species, or their overlapping protected areas. To augment the genetic coverage of the in situ conservation network, active CWR conservation is encouraged within 11 supplementary areas. Meanwhile, there are huge gaps in ex situ collections, with no known conserved material for 134 of the 204 priority species. Furthermore, existing accessions are generally unrepresentative of genetic diversity. Main conclusions: In the Czech Republic, active in situ conservation of priority CWR should be instigated within the 22 recommended grid cell areas or their 14 overlapping protected areas. For ex situ conservation, strategic and targeted collection of germplasm would markedly increase the value of gene bank collections. Diversity of priority Czech CWR is concentrated in South Moravia, making this a particularly important CWR area for the country and for Europe

The mediating role of shared flow and perceived emotional synchrony on compassion for others in a mindful-dancing program

While there is a growing understanding of the relationship between mindfulness and compassion, this largely relates to the form of mindfulness employed in first-generation mindfulness-based interventions such as Mindfulness-Based Stress Reduction. Consequently, there is limited knowledge of the relationship between mindfulness and compassion in respect of the type of mindfulness employed in second-generation mindfulness-based interventions (SG-MBIs), including those that employ the principle of working harmoniously as a “secular sangha.” Understanding this relationship is important because research indicates that perceived emotional synchrony (PES) and shared flow—that often arise during participation in harmonized group contemplative activities—can enhance outcomes relating to compassion, subjective well-being, and group identity fusion. This pilot study analyzed the effects of participation in a mindful-dancing SG-MBI on compassion and investigated the mediating role of shared flow and PES. A total of 130 participants were enrolled into the study that followed a quasi-experimental design with an intervention and control group. Results confirmed the salutary effect of participating in a collective mindful-dancing program, and demonstrated that shared flow and PES fully meditated the effects of collective mindfulness on the kindness and common humanity dimensions of compassion. Further research is warranted to explore whether collective mindfulness approaches, such as mindful dancing, may be a means of enhancing compassion and subjective well-being outcomes due to the mediating role of PES and shared flow.N/

HIGH AND LOW THRESHOLD FOR STARTLE REACTIVITY ASSOCIATED WITH PTSD SYMPTOMS BUT NOT PTSD RISK: EVIDENCE FROM A PROSPECTIVE STUDY OF ACTIVE DUTY MARINES

BackgroundHeightened startle response is a symptom of PTSD, but evidence for exaggerated startle in PTSD is inconsistent. This prospective study aimed to clarify whether altered startle reactivity represents a trait risk-factor for developing PTSD or a marker of current PTSD symptoms.MethodsMarines and Navy Corpsmen were assessed before (n = 2,571) and after (n = 1,632) deployments to Iraq or Afghanistan with the Clinician-Administered PTSD Scale (CAPS). A predeployment startle-threshold task was completed with startle probes presented over 80-114 dB[A] levels. Latent class mixture modeling identified three growth classes of startle performance: "high," "low," and "moderate" threshold classes. Zero-inflated negative binomial regression was used to assess relationships between predeployment startle threshold and pre- and postdeployment psychiatric symptoms.ResultsAt predeployment, the low-threshold class had higher PTSD symptom scores. Relative to the moderate-threshold class, low-threshold class membership was associated with decreased likelihood of being symptom-free at predeployment, based on CAPS, with particular associations with numbing and hyperarousal subscales, whereas high-threshold class membership was associated with more severe predeployment PTSD symptoms, in particular avoidance. Associations between low-threshold membership and CAPS symptoms were independent from measures of trauma burden, whereas associations between high-threshold membership and CAPS were not. Predeployment startle threshold did not predict postdeployment symptoms.ConclusionsThis study found that both low startle threshold (heightened reactivity) and high startle threshold (blunted reactivity) were associated with greater current PTSD symptomatology, suggesting that startle reactivity is associated with current PTSD rather than a risk marker for developing PTSD

Effects of repeated pup exposure on behavioral, neural, and adrenocortical responses to pups in male California mice (Peromyscus californicus)

In biparental mammals, the factors facilitating the onset of male parental behavior are not well understood. While hormonal changes in fathers may play a role, prior experience with pups has also been implicated. We evaluated effects of prior exposure to pups on paternal responsiveness in the biparental California mouse (Peromyscus californicus). We analyzed behavioral, neural, and corticosterone responses to pups in adult virgin males that were interacting with a pup for the first time, adult virgin males that had been exposed to pups 3 times for 20min each in the previous week, and new fathers. Control groups of virgins were similarly tested with a novel object (marble). Previous exposure to pups decreased virgins' latency to approach pups and initiate paternal care, and increased time spent in paternal care. Responses to pups did not differ between virgins with repeated exposure to pups and new fathers. In contrast, repeated exposure to a marble had no effects. Neither basal corticosterone levels nor corticosterone levels following acute pup or marble exposure differed among groups. Finally, Fos expression in the medial preoptic area, ventral and dorsal bed nucleus of the stria terminalis was higher following exposure to a pup than to a marble. Fos expression was not, however, affected by previous exposure to these stimuli. These results suggest that previous experience with pups can facilitate the onset of parental behavior in male California mice, similar to findings in female rodents, and that this effect is not associated with a general reduction in neophobia