Sensitivity of predictive species distribution models to change in grain size

Predictive species distribution modelling (SDM) has become an essential tool in biodiversity conservation and management. The choice of grain size (resolution) of environmental layers used in modelling is one important factor that may affect predictions. We applied 10 distinct modelling techniques to presence-only data for 50 species in five different regions, to test whether: (1) a 10-fold coarsening of resolution affects predictive performance of SDMs, and (2) any observed effects are dependent on the type of region, modelling technique, or species considered. Results show that a 10 times change in grain size does not severely affect predictions from species distribution models. The overall trend is towards degradation of model performance, but improvement can also be observed. Changing grain size does not equally affect models across regions, techniques, and species types. The strongest effect is on regions and species types, with tree species in the data sets (regions) with highest locational accuracy being most affected. Changing grain size had little influence on the ranking of techniques: boosted regression trees remain best at both resolutions. The number of occurrences used for model training had an important effect, with larger sample sizes resulting in better models, which tended to be more sensitive to grain. Effect of grain change was only noticeable for models reaching sufficient performance and/or with initial data that have an intrinsic error smaller than the coarser grain size.

The genetic consequences of hatchery-induced sperm competition in a salmonid

Supportive breeding is an important tool in conservation management, but its long-term genetic consequences are not well understood. Among the factors that could affect the genetics of the offspring is sperm competition as a consequence of mixed-milt fertilizations - which is still a common practice in many hatcheries. Here, we measured and combined the relevant factors to predict the genetic consequences of various kinds of hatchery-induced sperm competition. We drew a random sample of male Coregonus zugensis (an Alpine whitefish) from a hatchery program and quantified their in vitro sperm potency by integrating sperm velocity during the first minute after activation, and their in vitro milt potency by multiplying sperm potency with milt volume and sperm cell density. We found that not controlling for sperm density and/or milt volume would, at a constant population size, decrease the variance effective number of male breeders N-em by around 40-50%. This loss would decrease with increasing population growth rates. Partial multifactorial breeding and the separate rearing of in total 799 batches of eggs revealed that neither sperm nor milt potency was significantly linked to egg survival. Sperm and milt potency was also not significantly correlated to other potential quality measures such as breeding tubercles or condition factor. However, sperm potency was correlated to male age and milt potency to male growth rate. Our findings suggest that hatchery-induced sperm competition not only increases the loss of genetic variation but may also induce artificial selection, depending on the fertilization protocol. By not equalizing milt volume in multi-male fertilization hatchery managers lose relatively more genetic variation and give fast-growing males a reproductive advantage, while equalizing milt volume reduces the loss of genetic variation and favors younger males who may have fast sperm to compensate for their subdominance at the spawning place. (c) 2007 Elsevier Ltd. All rights reserved.

Swain: Stata module to correct the SEM chi-square overidentification test in small sample sizes or complex models. Statistical Software Components S457617, Boston College Department of Economics.

Swain corrects the chi-square overidentification test (i.e., likelihood ratio test of fit) for structural equation models whethr with or without latent variables. The chi-square statistic is asymptotically correct; however, it does not behave as expected in small samples and/or when the model is complex (cf. Herzog, Boomsma, & Reinecke, 2007). Thus, particularly in situations where the ratio of sample size (n) to the number of parameters estimated (p) is relatively small (i.e., the p to n ratio is large), the chi-square test will tend to overreject correctly specified models. To obtain a closer approximation to the distribution of the chi-square statistic, Swain (1975) developed a correction; this scaling factor, which converges to 1 asymptotically, is multiplied with the chi-square statistic. The correction better approximates the chi-square distribution resulting in more appropriate Type 1 reject error rates (see Herzog & Boomsma, 2009; Herzog, et al., 2007).

Health indicators associated with poor sleep quality among university students

Objective To associate the sleep quality of Brazilian undergraduate students with health indicators. Method A cross-sectional study was developed with a random sample of 662 undergraduate students from Fortaleza, Brazil. The demographic data, Pittsburgh Sleep Quality Index and health data indicators (smoking, alcoholism, sedentary lifestyle, nutritional condition and serum cholesterol) were collected through a self-administered questionnaire. Blood was collected at a clinical laboratory. In order to estimate the size of the associations, a Poisson Regression was used. Results For students who are daily smokers, the occurrence of poor sleep was higher than in non-smokers (p<0.001). Prevalence rate values were nevertheless close to 1. Conclusion The likelihood of poor sleep is almost the same in smokers and in alcoholics.


Which is the optimal sampling strategy for habitat suitability modelling

Designing an efficient sampling strategy is of crucial importance for habitat suitability modelling. This paper compares four such strategies, namely, 'random', 'regular', 'proportional-stratified' and 'equal -stratified'- to investigate (1) how they affect prediction accuracy and (2) how sensitive they are to sample size. In order to compare them, a virtual species approach (Ecol. Model. 145 (2001) 111) in a real landscape, based on reliable data, was chosen. The distribution of the virtual species was sampled 300 times using each of the four strategies in four sample sizes. The sampled data were then fed into a GLM to make two types of prediction: (1) habitat suitability and (2) presence/ absence. Comparing the predictions to the known distribution of the virtual species allows model accuracy to be assessed. Habitat suitability predictions were assessed by Pearson's correlation coefficient and presence/absence predictions by Cohen's K agreement coefficient. The results show the 'regular' and 'equal-stratified' sampling strategies to be the most accurate and most robust. We propose the following characteristics to improve sample design: (1) increase sample size, (2) prefer systematic to random sampling and (3) include environmental information in the design'

Batch effect confounding leads to strong bias in performance estimates obtained by cross-validation.

BACKGROUND: With the large amount of biological data that is currently publicly available, many investigators combine multiple data sets to increase the sample size and potentially also the power of their analyses. However, technical differences ("batch effects") as well as differences in sample composition between the data sets may significantly affect the ability to draw generalizable conclusions from such studies. FOCUS: The current study focuses on the construction of classifiers, and the use of cross-validation to estimate their performance. In particular, we investigate the impact of batch effects and differences in sample composition between batches on the accuracy of the classification performance estimate obtained via cross-validation. The focus on estimation bias is a main difference compared to previous studies, which have mostly focused on the predictive performance and how it relates to the presence of batch effects. DATA: We work on simulated data sets. To have realistic intensity distributions, we use real gene expression data as the basis for our simulation. Random samples from this expression matrix are selected and assigned to group 1 (e.g., 'control') or group 2 (e.g., 'treated'). We introduce batch effects and select some features to be differentially expressed between the two groups. We consider several scenarios for our study, most importantly different levels of confounding between groups and batch effects. METHODS: We focus on well-known classifiers: logistic regression, Support Vector Machines (SVM), k-nearest neighbors (kNN) and Random Forests (RF). Feature selection is performed with the Wilcoxon test or the lasso. Parameter tuning and feature selection, as well as the estimation of the prediction performance of each classifier, is performed within a nested cross-validation scheme. The estimated classification performance is then compared to what is obtained when applying the classifier to independent data.

Uso de la estadística en la oncología y la hematología

En este artículo abordamos el uso y la importancia de las herramientas estadísticas que se utilizan principalmente en los estudios médicos del ámbito de la oncología y la hematología, pero aplicables a muchos otros campos tanto médicos como experimentales o industriales. El objetivo del presente trabajo es presentar de una manera clara y precisa la metodología estadística necesaria para analizar los datos obtenidos en los estudios rigurosa y concisamente en cuanto a las hipótesis de trabajo planteadas por los investigadores. La medida de la respuesta al tratamiento elegidas en al tipo de estudio elegido determinarán los métodos estadísticos que se utilizarán durante el análisis de los datos del estudio y también el tamaño de muestra. Mediante la correcta aplicación del análisis estadístico y de una adecuada planificación se puede determinar si la relación encontrada entre la exposición a un tratamiento y un resultado es casual o por el contrario, está sujeto a una relación no aleatoria que podría establecer una relación de causalidad. Hemos estudiado los principales tipos de diseño de los estudios médicos más utilizados, tales como ensayos clínicos y estudios observacionales (cohortes, casos y controles, estudios de prevalencia y estudios ecológicos). También se presenta una sección sobre el cálculo del tamaño muestral de los estudios y cómo calcularlo, ¿Qué prueba estadística debe utilizarse?, los aspectos sobre fuerza del efecto ¿odds ratio¿ (OR) y riesgo relativo (RR), el análisis de supervivencia. Se presentan ejemplos en la mayoría de secciones del artículo y bibliografía más relevante.

Role of hepatitis C virus genotype 3 in liver fibrosis progression: a systematic review and meta-analysis.

The progression of liver fibrosis in chronic hepatitis C has long been considered to be independent from viral genotypes. However, recent studies suggest an association between Hepatitis C virus (HCV) genotype 3 and accelerated liver disease progression. We completed a systematic review and meta-analysis of studies evaluating the association between HCV genotypes and fibrosis progression. PubMed, Embase and ISI Web of Knowledge databases were searched for cohort, cross-sectional and case-control studies on treatment-naïve HCV-infected adults in which liver fibrosis progression rate (FPR) was assessed by the ratio of fibrosis stage in one single biopsy to the duration of infection (single-biopsy studies) or from the change in fibrosis stage between two biopsies (paired biopsies studies). A random effect model was used to derive FPR among different HCV genotypes. Eight single-biopsy studies (3182 patients, mean/median duration of infection ranging from 9 to 21 years) and eight paired biopsies studies (mean interval between biopsies 2-12 years) met the selection criteria. The odds ratio for the association of genotype 3 with accelerated fibrosis progression was 1.52 (95% CI 1.12-2.07, P = 0.007) in single-biopsy studies and 1.37 (95% CI 0.87-2.17, P = 0.17) in paired biopsy studies. In conclusion, viral genotype 3 was associated with faster fibrosis progression in single-biopsy studies. This observation may have important consequences on the clinical management of genotype 3-infected patients. The association was not significant in paired biopsies studies, although the latter may be limited by important indication bias, short observation time and small sample size.

Test result-based sampling: an efficient design for estimating the accuracy of patient safety indicators.

OBJECTIVE: Accuracy studies of Patient Safety Indicators (PSIs) are critical but limited by the large samples required due to low occurrence of most events. We tested a sampling design based on test results (verification-biased sampling [VBS]) that minimizes the number of subjects to be verified. METHODS: We considered 3 real PSIs, whose rates were calculated using 3 years of discharge data from a university hospital and a hypothetical screen of very rare events. Sample size estimates, based on the expected sensitivity and precision, were compared across 4 study designs: random and VBS, with and without constraints on the size of the population to be screened. RESULTS: Over sensitivities ranging from 0.3 to 0.7 and PSI prevalence levels ranging from 0.02 to 0.2, the optimal VBS strategy makes it possible to reduce sample size by up to 60% in comparison with simple random sampling. For PSI prevalence levels below 1%, the minimal sample size required was still over 5000. CONCLUSIONS: Verification-biased sampling permits substantial savings in the required sample size for PSI validation studies. However, sample sizes still need to be very large for many of the rarer PSIs.

Gait and foot clearance parameters obtained using shoe-worn inertial sensors in a large-population sample of older adults

In order to distinguish dysfunctional gait; clinicians require a measure of reference gait parameters for each population. This study provided normative values for widely used parameters in more than 1400 able-bodied adults over the age of 65. We also measured the foot clearance parameters (i.e., height of the foot above ground during swing phase) that are crucial to understand the complex relationship between gait and falls as well as obstacle negotiation strategies. We used a shoe-worn inertial sensor on each foot and previously validated algorithms to extract the gait parameters during 20 m walking trials in a corridor at a self-selected pace. We investigated the difference of the gait parameters between male and female participants by considering the effect of age and height factors. Besides; we examined the inter-relation of the clearance parameters with the gait speed. The sample size and breadth of gait parameters provided in this study offer a unique reference resource for the researchers.

Effect of an ectoparasite on reproduction in great tits.

1. The effect of a haematophageous ectoparasite, the hen flea, on quality an number of offspring was experimentally investigated in the great tit. The experiment consisted of a controlled infestation of a random sample of nests with the parasitic flea and of a regular treatment of control nests with Microwaves in order to eliminate the naturally occurring fleas. 2. To assess the effects of fleas on variables related to offspring number, we considered the number of hatchlings and fledglings, the mortality between hatching and fledging, and the hatching and fledging success. For assessment of offspring quality, we measured body mass, tarsus and wing length, and calculated the nutritional condition of, nestlings as the ratio of body mass to tarsus length. A physiological variable, the haematocrit level, was also measured. 3. Hatching success and hatchling numbers did not differ between the two experimental groups. Offspring mortality between hatching and fledging was significantly higher in the infested broods (xBAR = 0.22 chicks dead per day) than in the parasite-free broods (xBAR = 0.07 dead per day). Fledging success was 83% in the parasite-free broods, but only 53% in the infested ones. The number of fledglings in infested broods (xBAR = 3.7 fledglings +/-2.1 SD) was significantly lower than in the parasite-free (xBAR = 4.9 +/- 1.1 SD) broods. 4. Body mass of chicks in the infested broods was significantly smaller than in the parasite-free broods both 14 days and 17 days after hatching. The chicks in the infested broods reached a significantly smaller tarsus length than the ones in the parasite-free broods. Close to fledging, the nutritional condition of chicks was significantly lower in infested broods. Haematocrit levels were significantly lower in the infested broods. 5. Brood size correlated differently with body mass and condition of chicks in infested and parasite-free nests. In parasite-free broods both body mass and condition of chicks at age 17 days, i.e. close to fledging, were significantly higher in small broods than in large ones. However, in the infested broods chicks were of the same body mass and condition in large as in small broods. Therefore, in parasite-free broods fitness can potentially be gained through offspring quality or number or both, whereas in infested broods it can be gained through offspring quantity only. In other words, a trade-off between quality and number of offspring is feasible only in the absence of the parasitic hen flea. 6. These results emphasize the need to study the effects of ectoparasites on ecological, behavioural and evolutionary traits of their bird hosts. A knowledge of these effects is essential for the understanding of population dynamics, behaviour and life-history traits of the hosts.

Cambios en los cuidadores informales en cuanto a estilos de vida, relaciones y alteraciones de salud mental

Changes in the informal caregiver life styles, relations and alterations of mental health. Justification.The increase of the population aged 65 years and older in developed countries is generating a proportional increasing of the dependency caused by chronic pathologies. The care of these persons is being carried out by relatives, informal carers, leading to some alterations in diverse areas, among them mental alterations, as a consequence of taking care. Objectives. To develop a profile of the informal carers and to correlate the caregiver burden with the carers disorders. To detect risk factors to allow carrying out premature nursing interventions to diminish the disorders in the informal carers. Design. An observational and cross-sectional study is made in primary care health services area of the city of Girona. Methodology. Random sample of carer of dependent people at their home , assigned to the program of domiciliary attention (ATDOM) of the educational basic areas of health (ABS). A sample size of 269 persons, with a level of precision of 9% was needed. Questionnaire ICUB 97, the test of Barthel, the Philadelphia Geriatric Center scale, and a questionnaire are used as instruments that includes demographic and social variables, and mental and physical carers disorders.Results. A total of 80 participants were interviewed. The most common problems as consequence of taking care were the backache, to feel more tired, to feel impotent and to have less free time. Correlation between the level of dependence of the patient with the number of problems perceived by the caretaker does not exist. Since they are informal carers they eat frequently outside the habitual schedule, took place an increase or loss of weight, experienced more disorders in sexual life and an increasing lack of interest in surroundings. A 33% of the informal carers are being treated for problems related to the mental health.Conclusion. The fact of being informal carer carries important consequences in their health, the lifestyles and the social relations. These can be attenuated if the nursing interventions are able to consider to the well-taken care of subject, and its surroundings in an holistic way. The professionals of infirmary of mental health must contribute to their knowledge and abilities contributing to make an assessment, a diagnosis and an intervention paying special attention to psycho-social aspects mentioned

Cambios en los cuidadores informales en cuanto a estilos de vida, relaciones y alteraciones de salud mental

Changes in the informal caregiver life styles, relations and alterations of mental health. Justification.The increase of the population aged 65 years and older in developed countries is generating a proportional increasing of the dependency caused by chronic pathologies. The care of these persons is being carried out by relatives, informal carers, leading to some alterations in diverse areas, among them mental alterations, as a consequence of taking care. Objectives. To develop a profile of the informal carers and to correlate the caregiver burden with the carers disorders. To detect risk factors to allow carrying out premature nursing interventions to diminish the disorders in the informal carers. Design. An observational and cross-sectional study is made in primary care health services area of the city of Girona. Methodology. Random sample of carer of dependent people at their home , assigned to the program of domiciliary attention (ATDOM) of the educational basic areas of health (ABS). A sample size of 269 persons, with a level of precision of 9% was needed. Questionnaire ICUB 97, the test of Barthel, the Philadelphia Geriatric Center scale, and a questionnaire are used as instruments that includes demographic and social variables, and mental and physical carers disorders.Results. A total of 80 participants were interviewed. The most common problems as consequence of taking care were the backache, to feel more tired, to feel impotent and to have less free time. Correlation between the level of dependence of the patient with the number of problems perceived by the caretaker does not exist. Since they are informal carers they eat frequently outside the habitual schedule, took place an increase or loss of weight, experienced more disorders in sexual life and an increasing lack of interest in surroundings. A 33% of the informal carers are being treated for problems related to the mental health.Conclusion. The fact of being informal carer carries important consequences in their health, the lifestyles and the social relations. These can be attenuated if the nursing interventions are able to consider to the well-taken care of subject, and its surroundings in an holistic way. The professionals of infirmary of mental health must contribute to their knowledge and abilities contributing to make an assessment, a diagnosis and an intervention paying special attention to psycho-social aspects mentioned

A methodology to estimate the potential to move inpatient to one day surgery.

BACKGROUND: The proportion of surgery performed as a day case varies greatly between countries. Low rates suggest a large growth potential in many countries. Measuring the potential development of one day surgery should be grounded on a comprehensive list of eligible procedures, based on a priori criteria, independent of local practices. We propose an algorithmic method, using only routinely available hospital data to identify surgical hospitalizations that could have been performed as one day treatment. METHODS: Moving inpatient surgery to one day surgery was considered feasible if at least one surgical intervention was eligible for one day surgery and if none of the following criteria were present: intervention or affection requiring an inpatient stay, patient transferred or died, and length of stay greater than four days. The eligibility of a procedure to be treated as a day case was mainly established on three a priori criteria: surgical access (endoscopic or not), the invasiveness of the procedure and the size of the operated organ. Few overrides of these criteria occurred when procedures were associated with risk of immediate complications, slow physiological recovery or pain treatment requiring hospital infrastructure. The algorithm was applied to a random sample of one million inpatient US stays and more than 600 thousand Swiss inpatient stays, in the year 2002. RESULTS: The validity of our method was demonstrated by the few discrepancies between the a priori criteria based list of eligible procedures, and a state list used for reimbursement purposes, the low proportion of hospitalizations eligible for one day care found in the US sample (4.9 versus 19.4% in the Swiss sample), and the distribution of the elective procedures found eligible in Swiss hospitals, well supported by the literature. There were large variations of the proportion of candidates for one day surgery among elective surgical hospitalizations between Swiss hospitals (3 to 45.3%). CONCLUSION: The proposed approach allows the monitoring of the proportion of inpatient stay candidates for one day surgery. It could be used for infrastructure planning, resources negotiation and the surveillance of appropriate resource utilization.

The Effect of Family Ownership on Firm Performance: Empirical Evidence from Norway

Tutkimuksen tavoitteena on selvittää, onko perheomistajuus, eli yksityisomistus, kannattavampi omistusmuoto kuin institutionaalinen omistajuus ja, onko yrityksen iällä ja koolla vaikutusta perheyritysten menestymiseen. Aikaisempaan tutkimustietoon tukeutuen, tutkimuksen aluksi käydään myös läpi perheomistajuuteen yleisesti liitettyjä ominaispiirteitä sekä perheyritysten menestymistä verrattuna ei-perheyrityksiin. Empiirinen analyysi perheomistajuuden vaikutuksista yrityksen kannattavuuteen sekä yrityksen iän ja koon vaikutuksista perheyritysten menestymiseen toteutetaan kahden otoksen avulla, jotka koostuvat listaamattomista norjalaisista pienistä ja keskisuurista yrityksistä (pk-yrityksistä). Näin ollen satunnaisotos ja päätoimialaotos, johon listaamattomat pk-yritykset on valittu satunnaisesti Norjan tärkeimmiltä toimialoilta, analysoidaan erikseen. Analyysi toteutetaan käyttäen lineaarista regressioanalyysia. Vaikka satunnaisotoksen perusteella perheyritykset eivät näytä olevan ei-perheyrityksiä kannattavampia, päätoimialaotos osoittaa, että listaamattomissa pk-yrityksissä perhe- eli yksityisomistajuus on merkittävästi institutionaalista omistajuutta kannattavampi omistusmuoto. Eritoten nuoret ja pienet yritykset vastaavat perheyritysten paremmasta kannattavuudesta.