Extinction risk in cloud forest fragments under climate change and habitat loss

Aim: To quantify the consequences of major threats to biodiversity, such as climate and land-use change, it is important to use explicit measures of species persistence, such as extinction risk. The extinction risk of metapopulations can be approximated through simple models, providing a regional snapshot of the extinction probability of a species. We evaluated the extinction risk of three species under different climate change scenarios in three different regions of the Mexican cloud forest, a highly fragmented habitat that is particularly vulnerable to climate change. Location: Cloud forests in Mexico. Methods: Using Maxent, we estimated the potential distribution of cloud forest for three different time horizons (2030, 2050 and 2080) and their overlap with protected areas. Then, we calculated the extinction risk of three contrasting vertebrate species for two scenarios: (1) climate change only (all suitable areas of cloud forest through time) and (2) climate and land-use change (only suitable areas within a currently protected area), using an explicit patch-occupancy approximation model and calculating the joint probability of all populations becoming extinct when the number of remaining patches was less than five. Results: Our results show that the extent of environmentally suitable areas for cloud forest in Mexico will sharply decline in the next 70 years. We discovered that if all habitat outside protected areas is transformed, then only species with small area requirements are likely to persist. With habitat loss through climate change only, high dispersal rates are sufficient for persistence, but this requires protection of all remaining cloud forest areas. Main conclusions: Even if high dispersal rates mitigate the extinction risk of species due to climate change, the synergistic impacts of changing climate and land use further threaten the persistence of species with higher area requirements. Our approach for assessing the impacts of threats on biodiversity is particularly useful when there is little time or data for detailed population viability analyses. © 2013 John Wiley & Sons Ltd.

Low probability differentials and the cryptanalysis of full-round CLEFIA-128

So far, low probability differentials for the key schedule of block ciphers have been used as a straightforward proof of security against related-key differential analysis. To achieve resistance, it is believed that for cipher with k-bit key it suffices the upper bound on the probability to be 2− k . Surprisingly, we show that this reasonable assumption is incorrect, and the probability should be (much) lower than 2− k . Our counter example is a related-key differential analysis of the well established block cipher CLEFIA-128. We show that although the key schedule of CLEFIA-128 prevents differentials with a probability higher than 2− 128, the linear part of the key schedule that produces the round keys, and the Feistel structure of the cipher, allow to exploit particularly chosen differentials with a probability as low as 2− 128. CLEFIA-128 has 214 such differentials, which translate to 214 pairs of weak keys. The probability of each differential is too low, but the weak keys have a special structure which allows with a divide-and-conquer approach to gain an advantage of 27 over generic analysis. We exploit the advantage and give a membership test for the weak-key class and provide analysis of the hashing modes. The proposed analysis has been tested with computer experiments on small-scale variants of CLEFIA-128. Our results do not threaten the practical use of CLEFIA.

Feature overlap slows lexical selection: Evidence from the picture–word interference paradigm

How does the presence of a categorically related word influence picture naming latencies? In order to test competitive and noncompetitive accounts of lexical selection in spoken word production, we employed the picture–word interference (PWI) paradigm to investigate how conceptual feature overlap influences naming latencies when distractors are category coordinates of the target picture. Mahon et al. (2007. Lexical selection is not by competition: A reinterpretation of semantic interference and facilitation effects in the picture-word interference paradigm. Journal of Experimental Psychology. Learning, Memory, and Cognition, 33(3), 503–535. doi:10.1037/0278-7393.33.3.503) reported that semantically close distractors (e.g., zebra) facilitated target picture naming latencies (e.g., HORSE) compared to far distractors (e.g., whale). We failed to replicate a facilitation effect for within-category close versus far target–distractor pairings using near-identical materials based on feature production norms, instead obtaining reliably larger interference effects (Experiments 1 and 2). The interference effect did not show a monotonic increase across multiple levels of within-category semantic distance, although there was evidence of a linear trend when unrelated distractors were included in analyses (Experiment 2). Our results show that semantic interference in PWI is greater for semantically close than for far category coordinate relations, reflecting the extent of conceptual feature overlap between target and distractor. These findings are consistent with the assumptions of prominent competitive lexical selection models of speech production.

In search of good probability assessors: An experimental comparison of elicitation rules for confidence judgments

In this paper, we use an experimental design to compare the performance of elicitation rules for subjective beliefs. Contrary to previous works in which elicited beliefs are compared to an objective benchmark, we consider a purely subjective belief framework (confidence in one’s own performance in a cognitive task and a perceptual task). The performance of different elicitation rules is assessed according to the accuracy of stated beliefs in predicting success. We measure this accuracy using two main factors: calibration and discrimination. For each of them, we propose two statistical indexes and we compare the rules’ performances for each measurement. The matching probability method provides more accurate beliefs in terms of discrimination, while the quadratic scoring rule reduces overconfidence and the free rule, a simple rule with no incentives, which succeeds in eliciting accurate beliefs. Nevertheless, the matching probability appears to be the best mechanism for eliciting beliefs due to its performances in terms of calibration and discrimination, but also its ability to elicit consistent beliefs across measures and across tasks, as well as its empirical and theoretical properties.

Association of variants at 1q32 and STAT3 with ankylosing spondylitis suggests genetic overlap with Crohn's disease

Ankylosing spondylitis (AS) is a common inflammatory arthritic condition. Overt inflammatory bowel disease (IBD) occurs in about 10% of AS patients, and in addition 70% of AS cases may have subclinical terminal ileitis. Spondyloarthritis is also common in IBD patients. We therefore tested Crohn's disease susceptibility genes for association with AS, aiming to identify pleiotropic genetic associations with both diseases. Genotyping was carried out using Sequenom and Applied Biosystems TaqMan and OpenArray technologies on 53 markers selected from 30 Crohn's disease associated genomic regions. We tested genotypes in a population of unrelated individual cases (n = 2,773) and controls (n = 2,215) of white European ancestry for association with AS. Statistical analysis was carried out using a Cochran-Armitage test for trend in PLINK. Strong association was detected at chr1q32 near KIF21B (rs11584383, P = 1.66 x 10-10, odds ratio (OR) = 0.74, 95% CI:0.68-0.82). Association with disease was also detected for 2 variants within STAT3 (rs6503695, P = 4.6×10-4. OR = 0.86 (95% CI:0.79-0.93); rs744166, P = 2.6×10-5, OR = 0.84 (95% CI:0.77-0.91)). Association was confirmed for IL23R (rs11465804, P = 1.2×10-5, OR = 0.65 (95% CI:0.54-0.79)), and further associations were detected for IL12B (rs10045431, P = 5.261025, OR = 0.83 (95% CI:0.76-0.91)), CDKAL1 (rs6908425, P = 1.1×10-4, OR = 0.82 (95% CI:0.74-0.91)), LRRK2/MUC19 (rs11175593, P = 9.9×10-5, OR = 1.92 (95% CI: 1.38-2.67)), and chr13q14 (rs3764147, P = 5.9×10-4, OR = 1.19 (95% CI: 1.08-1.31)). Excluding cases with clinical IBD did not significantly affect these findings. This study identifies chr1q32 and STAT3 as ankylosing spondylitis susceptibility loci. It also further confirms association for IL23R and detects suggestive association with another 4 loci. STAT3 is a key signaling molecule within the Th17 lymphocyte differentiation pathway and further enhances the case for a major role of this T-lymphocyte subset in ankylosing spondylitis. Finally these findings suggest common aetiopathogenic pathways for AS and Crohn's disease and further highlight the involvement of common risk variants across multiple diseases.

On the probability that the determinant of an nxn matrix over a finite field vanishe

An expression is derived for the probability that the determinant of an n x n matrix over a finite field vanishes; from this it is deduced that for a fixed field this probability tends to 1 as n tends to.

Assessment of prey overlap between a native (Polistes humilis) and an introduced (Vespula germanica) social wasp using morphology and phylogenetic analyses of 16S rDNA

In newly invaded communities, interspecific competition is thought to play an important role in determining the success of the invader and its impact on the native community. In southern Australia, the native Polistes humilis was the predominant social wasp prior to the arrival of the exotic Vespula germanica (Hymenoptera: Vespidae). Both species forage for similar resources (water, pulp, carbohydrate and protein prey), and concerns have arisen about potential competition between them. The aim of this study was to identify the protein foods that these wasps feed on. As many prey items are masticated by these wasps to the degree that they cannot be identified using conventional means, morphological identification was complemented by sequencing fragments of the mitochondrial 16S rRNA gene. GenBank searches using blast and phylogenetic analyses were used to identify prey items to at least order level. The results were used to construct complete prey inventories for the two species. These indicate that while P. humilis is restricted to feeding on lepidopteran larvae, V. germanica collects a variety of prey of invertebrate and vertebrate origin. Calculated values of prey overlap between the two species are used to discuss the implications of V. germanica impacting on P. humilis. Results obtained are compared to those gained by solely 'conventional' methods, and the advantages of using DNA-based taxonomy in ecological studies are emphasized.

Proposed vehicle impact speed: Severe injury probability relationships for selected crash types

Speed is recognised as a key contributor to crash likelihood and severity, and to road safety performance in general. Its fundamental role has been recognised by making Safe Speeds one of the four pillars of the Safe System. In this context, impact speeds above which humans are likely to sustain fatal injuries have been accepted as a reference in many Safe System infrastructure policy and planning discussions. To date, there have been no proposed relationships for impact speeds above which humans are likely to sustain fatal or serious (severe) injury, a more relevant Safe System measure. A research project on Safe System intersection design required a critical review of published literature on the relationship between impact speed and probability of injury. This has led to a number of questions being raised about the origins, accuracy and appropriateness of the currently accepted impact speed–fatality probability relationships (Wramborg 2005) in many policy documents. The literature review identified alternative, more recent and more precise relationships derived from the US crash reconstruction databases (NASS/CDS). The paper proposes for discussion a set of alternative relationships between vehicle impact speed and probability of MAIS3+ (fatal and serious) injury for selected common crash types. Proposed Safe System critical impact speed values are also proposed for use in road infrastructure assessment. The paper presents the methodology and assumptions used in developing these relationships. It identifies further research needed to confirm and refine these relationships. Such relationships would form valuable inputs into future road safety policies in Australia and New Zealand.

An Adaptive Scheme for Learning the Probability Threshold in Pattern Recognition

The statistical minimum risk pattern recognition problem, when the classification costs are random variables of unknown statistics, is considered. Using medical diagnosis as a possible application, the problem of learning the optimal decision scheme is studied for a two-class twoaction case, as a first step. This reduces to the problem of learning the optimum threshold (for taking appropriate action) on the a posteriori probability of one class. A recursive procedure for updating an estimate of the threshold is proposed. The estimation procedure does not require the knowledge of actual class labels of the sample patterns in the design set. The adaptive scheme of using the present threshold estimate for taking action on the next sample is shown to converge, in probability, to the optimum. The results of a computer simulation study of three learning schemes demonstrate the theoretically predictable salient features of the adaptive scheme.

The impact of inter-fraction set-up errors on the probability of pulmonary and cardiac complication in left-sided breast cancer patients

Purpose This study evaluated the impact of patient set-up errors on the probability of pulmonary and cardiac complications in the irradiation of left-sided breast cancer. Methods and Materials Using the CMS XiO Version 4.6 (CMS Inc., St Louis, MO) radiotherapy planning system's NTCP algorithm and the Lyman -Kutcher-Burman (LKB) model, we calculated the DVH indices for the ipsilateral lung and heart and the resultant normal tissue complication probabilities (NTCP) for radiation-induced pneumonitis and excess cardiac mortality in 12 left-sided breast cancer patients. Results Isocenter shifts in the posterior direction had the greatest effect on the lung V20, heart V25, mean and maximum doses to the lung and the heart. Dose volume histograms (DVH) results show that the ipsilateral lung V20 tolerance was exceeded in 58% of the patients after 1cm posterior shifts. Similarly, the heart V25 tolerance was exceeded after 1cm antero-posterior and left-right isocentric shifts in 70% of the patients. The baseline NTCPs for radiation-induced pneumonitis ranged from 0.73% - 3.4% with a mean value of 1.7%. The maximum reported NTCP for radiation-induced pneumonitis was 5.8% (mean 2.6%) after 1cm posterior isocentric shift. The NTCP for excess cardiac mortality were 0 % in 100% of the patients (n=12) before and after setup error simulations. Conclusions Set-up errors in left sided breast cancer patients have a statistically significant impact on the Lung NTCPs and DVH indices. However, with a central lung distance of 3cm or less (CLD <3cm), and a maximum heart distance of 1.5cm or less (MHD<1.5cm), the treatment plans could tolerate set-up errors of up to 1cm without any change in the NTCP to the heart.

Development of a model based on Bayesian networks to estimate the probability of sheep lice presence at shearing

This paper describes the development of a model, based on Bayesian networks, to estimate the likelihood that sheep flocks are infested with lice at shearing and to assist farm managers or advisers to assess whether or not to apply a lousicide treatment. The risk of lice comes from three main sources: (i) lice may have been present at the previous shearing and not eradicated; (ii) lice may have been introduced with purchased sheep; and (iii) lice may have entered with strays. A Bayesian network is used to assess the probability of each of these events independently and combine them for an overall assessment. Rubbing is a common indicator of lice but there are other causes too. If rubbing has been observed, an additional Bayesian network is used to assess the probability that lice are the cause. The presence or absence of rubbing and its possible cause are combined with these networks to improve the overall risk assessment.

Exact calculations of survival probability for diffusion on growing lines, disks, and spheres: The role of dimension

Unlike standard applications of transport theory, the transport of molecules and cells during embryonic development often takes place within growing multidimensional tissues. In this work, we consider a model of diffusion on uniformly growing lines, disks, and spheres. An exact solution of the partial differential equation governing the diffusion of a population of individuals on the growing domain is derived. Using this solution, we study the survival probability, S(t). For the standard nongrowing case with an absorbing boundary, we observe that S(t) decays to zero in the long time limit. In contrast, when the domain grows linearly or exponentially with time, we show that S(t) decays to a constant, positive value, indicating that a proportion of the diffusing substance remains on the growing domain indefinitely. Comparing S(t) for diffusion on lines, disks, and spheres indicates that there are minimal differences in S(t) in the limit of zero growth and minimal differences in S(t) in the limit of fast growth. In contrast, for intermediate growth rates, we observe modest differences in S(t) between different geometries. These differences can be quantified by evaluating the exact expressions derived and presented here.

Survival probability for a diffusive process on a growing domain

We consider the motion of a diffusive population on a growing domain, 0 < x < L(t ), which is motivated by various applications in developmental biology. Individuals in the diffusing population, which could represent molecules or cells in a developmental scenario, undergo two different kinds of motion: (i) undirected movement, characterized by a diffusion coefficient, D, and (ii) directed movement, associated with the underlying domain growth. For a general class of problems with a reflecting boundary at x = 0, and an absorbing boundary at x = L(t ), we provide an exact solution to the partial differential equation describing the evolution of the population density function, C(x,t ). Using this solution, we derive an exact expression for the survival probability, S(t ), and an accurate approximation for the long-time limit, S = limt→∞ S(t ). Unlike traditional analyses on a nongrowing domain, where S ≡ 0, we show that domain growth leads to a very different situation where S can be positive. The theoretical tools developed and validated in this study allow us to distinguish between situations where the diffusive population reaches the moving boundary at x = L(t ) from other situations where the diffusive population never reaches the moving boundary at x = L(t ). Making this distinction is relevant to certain applications in developmental biology, such as the development of the enteric nervous system (ENS). All theoretical predictions are verified by implementing a discrete stochastic model.

Improving the estimation of probability of bidder participation in procurement auctions

Anticipating the number and identity of bidders has significant influence in many theoretical results of the auction itself and bidders’ bidding behaviour. This is because when a bidder knows in advance which specific bidders are likely competitors, this knowledge gives a company a head start when setting the bid price. However, despite these competitive implications, most previous studies have focused almost entirely on forecasting the number of bidders and only a few authors have dealt with the identity dimension qualitatively. Using a case study with immediate real-life applications, this paper develops a method for estimating every potential bidder’s probability of participating in a future auction as a function of the tender economic size removing the bias caused by the contract size opportunities distribution. This way, a bidder or auctioner will be able to estimate the likelihood of a specific group of key, previously identified bidders in a future tender.

On the probability of dizygotic twins being concordant for two alleles at multiple polymorphic loci

Accurate determination of same-sex twin zygosity is important for medical, scientific and personal reasons. Determination may be based upon questionnaire data, blood group, enzyme isoforms and fetal membrane examination, but assignment of zygosity must ultimately be confirmed by genotypic data. Here methods are reviewed for calculating average probabilities of correctly concluding a twin pair is monozygotic, given they share the same genotypes across all loci for commonly utilized multiplex short tandem repeat (STR) kits.