Where will conflicts between alien and rare species occur after climate and land-use change? A test with a novel combined modelling approach

Protecting native biodiversity against alien invasive species requires powerful methods to anticipate these invasions and to protect native species assumed to be at risk. Here, we describe how species distribution models (SDMs) can be used to identify areas predicted as suitable for rare native species and also predicted as highly susceptible to invasion by alien species, at present and under future climate and land-use scenarios. To assess the condition and dynamics of such conflicts, we developed a combined predictive modelling (CPM) approach, which predicts species distributions by combining two SDMs fitted using subsets of predictors classified as acting at either regional or local scales. We illustrate the CPM approach for an alien invader and a rare species associated to similar habitats in northwest Portugal. Combined models predict a wider variety of potential species responses, providing more informative projections of species distributions and future dynamics than traditional, non-combined models. They also provide more informative insight regarding current and future rare-invasive conflict areas. For our studied species, conflict areas of highest conservation relevance are predicted to decrease over the next decade, supporting previous reports that some invasive species may contract their geographic range and impact due to climate change. More generally, our results highlight the more informative character of the combined approach to address practical issues in conservation and management programs, especially those aimed at mitigating the impact of invasive plants, land-use and climate changes in sensitive regions

Comparison of the clientele of an anonymous HIV test centre and persons tested in the general population.

This study compares the clientele of a Swiss anonymous test centre with the general population tested. Information was obtained through similar questionnaires submitted to two samples of HIV-tested people aged from 17 to 45 years: the first administered in the context of a general population telephone survey (n = 245) and the second completed during face-to-face interviews of the clientele of an anonymous test centre (n = 250). The test centre sample has higher proportions of younger and single people. Attenders for anonymous testing were more likely to have acquired a new regular partner during the year preceding the interview (48.0% versus 14.4%). These differences remain when controlling for age and gender. Decision to test comes mostly from the respondent's own initiative, but suggestion from a doctor is more frequent in the general population (23.8% versus 0.8%), whereas suggestion from partner or friends is more frequent in the anonymous centre (44.4% versus 3.0%). The anonymous test centre clientele is not different from the general population tested except for the relational situation and origin of decision for testing. The test centre has become a place where the general population finds a response to a situation-specific need for HIV testing.

Multivariate QST-FST comparisons: a neutrality test for the evolution of the g matrix in structured populations.

Neutrality tests in quantitative genetics provide a statistical framework for the detection of selection on polygenic traits in wild populations. However, the existing method based on comparisons of divergence at neutral markers and quantitative traits (Q(st)-F(st)) suffers from several limitations that hinder a clear interpretation of the results with typical empirical designs. In this article, we propose a multivariate extension of this neutrality test based on empirical estimates of the among-populations (D) and within-populations (G) covariance matrices by MANOVA. A simple pattern is expected under neutrality: D = 2F(st)/(1 - F(st))G, so that neutrality implies both proportionality of the two matrices and a specific value of the proportionality coefficient. This pattern is tested using Flury's framework for matrix comparison [common principal-component (CPC) analysis], a well-known tool in G matrix evolution studies. We show the importance of using a Bartlett adjustment of the test for the small sample sizes typically found in empirical studies. We propose a dual test: (i) that the proportionality coefficient is not different from its neutral expectation [2F(st)/(1 - F(st))] and (ii) that the MANOVA estimates of mean square matrices between and among populations are proportional. These two tests combined provide a more stringent test for neutrality than the classic Q(st)-F(st) comparison and avoid several statistical problems. Extensive simulations of realistic empirical designs suggest that these tests correctly detect the expected pattern under neutrality and have enough power to efficiently detect mild to strong selection (homogeneous, heterogeneous, or mixed) when it is occurring on a set of traits. This method also provides a rigorous and quantitative framework for disentangling the effects of different selection regimes and of drift on the evolution of the G matrix. We discuss practical requirements for the proper application of our test in empirical studies and potential extensions.

Reliability and validity of the Alcohol Use Disorders Identification Test (AUDIT) imbedded within a general health risk screening questionnaire: results of a survey in 332 primary care patients.

BACKGROUND: Self-administered, general health risk screening questionnaires that are administered while patients wait in the doctor's office may be a reasonable and timesaving approach to address the requirements of preventive medicine in a typical 10-min medical visit. The psychometric characteristics of the Alcohol Use Disorders Identification Test (AUDIT) incorporated within a health questionnaire (H-AUDIT) have not been examined. METHODS: The reliability and validity of the self-administered AUDIT were compared between the H-AUDIT and the AUDIT used as a single scale (S-AUDIT) in 332 primary care patients. RESULTS: No major demographic or alcohol use characteristics were found between the 166 subjects who completed the H-AUDIT and the 166 individuals who completed the S-AUDIT. The test-retest reliability of the 166 subjects who completed the H-AUDIT [estimated by Spearman correlation coefficient at a 6-week interval (0.88), internal consistency (total correlation coefficients for all items ranged from 0.38 to 0.69; Cronbach alpha index 0.85), and the sensitivity and specificity of the H-AUDIT were used to identify at-risk drinkers' areas under receiver operating characteristic (0.77) and alcohol-dependent subjects' areas under receiver operating characteristic (0.89)] was similar to the same measurements obtained with the 166 individuals who completed the S-AUDIT. CONCLUSIONS: The AUDIT incorporated in a health risk screening questionnaire is a reliable and valid self-administered instrument to identify at-risk drinkers and alcohol-dependent individuals in primary care settings.

Rapid Diagnostic Test-Based Management of Malaria: An Effectiveness Study in Papua New Guinean Infants With Plasmodium falciparum and Plasmodium vivax Malaria.

Background. In malaria-endemic areas it is recommended that febrile children be tested for malaria by rapid diagnostic test (RDT) or blood slide (BS) and receive effective malaria treatment only if results are positive. However, RDTs are known to perform less well for Plasmodium vivax. We evaluated the safety of withholding antimalarial drugs from young Papua New Guinean children with negative RDT results in areas with high levels of both Plasmodium falciparum and P. vivax infections. Methods. longitudinal prospective study of children aged 3-27 months visiting outpatient clinics for fever. RDT was administered at first visit. RDT and microscopy were performed if children returned because of persistent symptoms. Outcomes were rates of reattendance and occurrence of severe illnesses. Results. Of 5670 febrile episodes, 3942 (70%) involved a negative RDT result. In 133 cases (3.4%), the children reattended the clinic within 7 days for fever, of whom 29 (0.7%) were parasitemic by RDT or microscopy. Of children who reattended, 24 (0.7%) presented with a severe illness: 2 had lower respiratory tract infections (LRTIs) with low-density P. vivax on BS; 2 received a diagnosis of P. vivax malaria on the basis of RDT but BSs were negative; 16 had LRTIs; 3 had alternative diagnoses. Of these 24, 22 were cured at day 28. Two children died of illnesses other than malaria and were RDT and BS negative at the initial and subsequent visits. Conclusion. Treatment for malaria based on RDT results is safe and feasible even in infants living in areas with moderate to high endemicity for both P. falciparum and P. vivax infections.

Testing advances in molecular discrimination among Chinook salmon life histories: evidence from a blind test.

The application of DNA-based markers toward the task of discriminating among alternate salmon runs has evolved in accordance with ongoing genomic developments and increasingly has enabled resolution of which genetic markers associate with important life-history differences. Accurate and efficient identification of the most likely origin for salmon encountered during ocean fisheries, or at salvage from fresh water diversion and monitoring facilities, has far-reaching consequences for improving measures for management, restoration and conservation. Near-real-time provision of high-resolution identity information enables prompt response to changes in encounter rates. We thus continue to develop new tools to provide the greatest statistical power for run identification. As a proof of concept for genetic identification improvements, we conducted simulation and blind tests for 623 known-origin Chinook salmon (Oncorhynchus tshawytscha) to compare and contrast the accuracy of different population sampling baselines and microsatellite loci panels. This test included 35 microsatellite loci (1266 alleles), some known to be associated with specific coding regions of functional significance, such as the circadian rhythm cryptochrome genes, and others not known to be associated with any functional importance. The identification of fall run with unprecedented accuracy was demonstrated. Overall, the top performing panel and baseline (HMSC21) were predicted to have a success rate of 98%, but the blind-test success rate was 84%. Findings for bias or non-bias are discussed to target primary areas for further research and resolution.

Contact tracing investigation after professional exposure to tuberculosis in a Swiss hospital using both tuberculin skin test and IGRA.

SETTING: A 950 bed teaching hospital in Switzerland. AIM: To describe the result of a contact investigation among health care workers (HCW) and patients after exposure to a physician with smear-positive pulmonary tuberculosis in a hospital setting using standard tuberculin skin tests (TST) and Interferon-gamma release assay (IGRA). METHOD: HCW with a negative or unknown TST at hiring had a TST two weeks after the last contact with the index case (T0), repeated six weeks later if negative (T6). All exposed HCW had a T-SPOT.TB at T0 and T6. Exposed patients had a TST six weeks after the last contact, and a T-SPOT.TB if the TST was positive. RESULTS: Among 101 HCW, 17/73 (22%) had a positive TST at T0. TST was repeated in 50 at T6 and converted from negative to positive in eight (16%). Twelve HCW had a positive T-SPOT.TB at T0 and ten converted from negative to positive at T6. Seven HCW with a positive T-SPOT.TB reverted to negative at T6 or at later controls, most of them with test values close to the cut-off. Among 27 exposed patients tested at six weeks, ten had a positive TST, five of them confirmed by a positive T-SPOT.TB. CONCLUSIONS: HCW tested twice after exposure to a case of smear-positive pulmonary TB demonstrated a possible conversion in 10% with T-SPOT and 16% with TST. Some T-SPOT.TB reverted from positive to negative during the follow-up, mostly tests with a value close to the cut-off. Due to the variability of the test results, it seems advisable to repeat the test with values close to the cut-off before diagnosing the presence of a tuberculous infection.

Cardiorespiratory responses to the 30-15 intermittent ice test

PURPOSE: In this study, the authors compared the cardiorespiratory responses between the 30-15 Intermittent Ice Test (30-15(IIT)) and the 30-15 Intermittent Fitness Test (30-15(IFT)) in semiprofessional hockey players. METHODS: Ten players (age 24 ± 6 y) from a Swiss League B team performed the 30-15(IIT) and 30-15(IFT) in random order (13 ± 4 d between trials). Cardiorespiratory variables were measured with a portable gas analyzer. Ventilatory threshold (VT), respiratory-compensation point (RCP), and maximal speeds were measured for both tests. Peak blood lactate ([La(peak)]) was measured at 1 min postexercise. RESULTS: Compared with 30-15(IFT), 30-15(IIT) peak heart rate (HR(peak); mean ± SD 185 ± 7 vs 189 ± 10 beats/min, P = .02) and peak oxygen consumption (VO(2peak)); 60 ± 7 vs 62.7 ± 4 mL/min/kg, P = .02) were lower, whereas [La(peak)] was higher (10.9 ± 1 vs 8.6 ± 2 mmol/L, P < .01) for the 30-15(IIT). VT and RCP values during the 30-15(IIT) and 30-15(IFT) were similar for %HR(peak) (76.3% ± 5% vs 75.5% ± 3%, P = .53, and 90.6% ± 3% vs. 89.8% ± 3%, P = .45) and % VO(2peak) (62.3% ± 5% vs 64.2% ± 6%, P = .46, and 85.9% ± 5% vs 84.0% ± 7%, P = .33). VO(2peak ))(r = .93, P < .001), HR(peak) (r = .86, P = .001), and final velocities (r = .69, P = .029) were all largely to almost perfectly correlated. CONCLUSIONS: Despite slightly lower maximal cardiorespiratory responses than in the field-running version of the test, the on-ice 30-15(IIT) is of practical interest since it is a specific maximal test with a higher anaerobic component.

A flow cytometry based oligotrophic pollutant exposure test to detect bacterial growth inhibition and cell injury.

Toxicity of chemical pollutants in aquatic environments is often addressed by assays that inquire reproductive inhibition of test microorganisms, such as algae or bacteria. Those tests, however, assess growth of populations as a whole via macroscopic methods such as culture turbidity or colony-forming units. Here we use flow cytometry to interrogate the fate of individual cells in low-density populations of the bacterium Pseudomonas fluorescens SV3 exposed or not under oligotrophic conditions to a number of common pollutants, some of which derive from oil contamination. Cells were stained at regular time intervals during the exposure assay with fluorescent dyes that detect membrane injury (i.e., live-dead assay). Reduction of population growth rates was observed upon toxicant insult and depended on the type of toxicant. Modeling and cell staining indicate that population growth rate decrease is a combined effect of an increased number of injured cells that may or may not multiply, and live cells dividing at normal growth rates. The oligotrophic assay concept presented here could be a useful complement for existing biomarker assays in compliance with new regulations on chemical effect studies or, more specifically, for judging recovery after exposure to fluctuating toxicant conditions.

Evolution of life history traits in a natural population of the shrew Crocidura russula

Abstract Life history traits encompass all the decisions concerning fitness an individual is faced with during his life. The study of these traits is crucial to understand the factors shaping the biology of living organisms. Up until now, most of the information on the evolution of life history traits comes from laboratory studies. While these studies are interesting to test the effect of specific parameters, their conclusions are difficult to extrapolate to natural populations. Investigating the evolution of life history traits in natural populations is of great interest. This may be tricky because it requires information on reproduction, survival and morphology of individuals. Mark-recapture methods allow most of this information to be obtained. However, when direct observations of a species are not possible due to its ecology, indirect methods must be used to infer lifetime reproductive success. In this case, molecular markers are particularly helpful in assessing the genetic relationships between individuals and allow the construction of a pedigree. This thesis focuses on a natural population of a small insectivorous mammal, the greater white-toothed shrew, Crocidura russula. Because of its hidden lifestyle, the two complementary techniques mentioned above were combined to gather information on this population. The data were used to explore diverse aspects of evolutionary biology. We demonstrated that the high genetic variance displayed by the species was not maintained by its mating system because this shrew was less monogamous than previously thought. The large genetic diversity was most likely promoted by gene flow from the neighborhood. Dispersal was thus a central topic in this thesis. We showed that dispersal was not driven by inbreeding avoidance. In addition, we did not find any inbreeding depression in the population. Dispersal was promoted by a high number of vacant territories in the population for both sexes, meaning that territory acquisition played an important role in driving dispersal. Moreover, dispersal propensity was shown to have a genetic basis and, once achieved, to have no effect on individual fitness. Body mass was found to be a life history trait strongly influenced by sexual and viability selection in both sexes. Larger individuals had higher access to reproduction through territory acquisition and defense than lighter ones. By contrast, intermediate size individuals were favored by viability selection presumably because of ecological constraints and metabolic costs. Finally, we demonstrated that the majority of the life history traits in our shrew population has the potential to evolve because they maintained substantial amounts of additive genetic variance. Nonetheless, life history traits had no significant heritability due to their high level of nonadditive or environmental variance. Résumé Les traits d'histoire de vie comprennent toutes les décisions auxquelles un individu est confronté au cours de sa vie et qui concernent sa valeur adaptative. L'étude de ces traits est cruciale pour comprendre les facteurs qui façonnent la biologie des êtres vivants. Jusqu'à ce jour, la majorité des informations sur l'évolution des traits d'histoire de vie provient d'études réalisées en laboratoire. Alors que ces études sont intéressantes pour tester l'effet de paramètres spécifiques, leurs conclusions sont difficilement extrapolables aux populations naturelles. Il est particulièrement intéressant d'étudier l'évolution des traits d'histoire de vie dans des populations naturelles. Toutefois, ces études peuvent se révéler difficiles parce qu'elles requièrent des informations sur la reproduction, la survie et la morphologie des individus. Des méthodes de marquage-recapture permettent d'obtenir ces informations. Cependant, lorsque l'écologie de l'espèce rend les obervations directes impossibles, des méthodes indirectes doivent être utilisées pour obtenir le succès reproducteur des individus. Dans ce cas, les marqueurs moléculaires sont particulièrement utiles pour évaluer les relations génétiques entre individus et permettre la construction d'un pedigree. Cette thèse porte sur une population naturelle d'un petit mammifère insectivore, la musaraigne musette, Crocidura russula. Parce que cette espèce présente un mode de vie souterrain, les deux techniques complémentaires mentionnées ci-dessus ont été combinées pour acquérir les informations nécessaires. Les données ont été utilisées pour explorer divers aspects de biologie evolutive. Nous avons montré que la grande quantité de variance génétique trouvée chez cette espèce n'est pas maintenue par son système d'appariement. Celle-ci s'est en effet avérée être moins monogame que ce qui était admis jusqu'ici. Sa grande diversité génétique est plutôt entretenue par le flux de gènes provenant du voisinage. La dispersion a donc été un sujet phare dans cette thèse. Nous avons montré qu'elle n'est pas provoquée par un évitement de la consanguinité et nous n'avons pas trouvé de dépression de consanguité dans notre population. L'acquisition d'un territoire joue par contre un rôle important dans la dispersion. En outre, la dispersion possède une base génétique chez cette espèce. De plus, une fois qu'ils ont dispersé, les individus n'ont pas une valeur adaptative differente d'individus philopatriques. Le poids s'est avéré être un trait d'histoire de vie fortement influencé par la sélection sexuelle et de viabilité chez les deux sexes. Les gros individus ont accès à la reproduction parce qu'ils acquièrent et défendent un territoire plus facilement que les plus légers. Au contraire, les individus de taille intermédiaire sont favorisés par la sélection de viabilité, certainement à cause de contraintes écologiques et de coûts métaboliques. Finalement, nous avons montré que la majorité des traits d'histoire de vie dans notre population a le potentiel d'évoluer parce qu'elle maintient des quantités considérables de variance génétique additive. Néanmoins, l'héritabilité de ces traits d'histoire de vie n'est pas significative à cause de la grande quantité de variance non-additive ou environmentale associée à ces traits.

The "help" question doesn't help when screening for major depression: external validation of the three-question screening test for primary care patients managed for physical complaints.

BACKGROUND: Major depression, although frequent in primary care, is commonly hidden behind multiple physical complaints that are often the first and only reason for patient consultation. Major depression can be screened by two validated questions that are easier to use in primary care than the full DSM-IV criteria. A third question, called the "help" question, improves the specificity without apparently decreasing the sensitivity of this screening procedure. We validated the abbreviated screening procedure for major depression with and without the "help" question in primary care patients managed for a physical complaint. METHODS: This diagnostic accuracy study used data from a cohort study called SODA (for SOmatisation Depression Anxiety ) conducted by 24 general practitioners (GPs) in western Switzerland that included patients over 18 years of age with at least one physical complaint at index consultation. Major depression was identified with the full Patient Health Questionnaire. GPs were asked to screen patients for major depression with the three screening questions one year after inclusion. RESULTS: Out of 937 patients with at least one physical complaint, 751 were eligible one year after index consultation. Major depression was diagnosed in 69/724 (9.5%) patients. The sensitivity and specificity of the two-question method alone were 91.3% (95% confidence interval 81.4-96.4%) and 65.0% (95% confidence interval 61.2-68.6%), respectively. Adding the "help" question decreased the sensitivity (59.4% ; 95% confidence interval 47.0-70.9%) but improved the specificity (88.2% ; 95% confidence interval 85.4-90.5%) of the three-question method. CONCLUSIONS: The use of two screening questions for major depression was associated with high sensitivity and low specificity in primary care patients presenting a physical complaint. Adding the "help" question improved the specificity but clearly decreased the sensitivity; when using the "help" question; four out of ten patients with depression will be missed, compared to only one out of ten with the two-question method. Therefore, the "help" question is not useful as a screening question, but may help discussing management strategies.