Automatic generation of active coordinates for quantum dynamics calculations: application to the dynamics of benzene photochemistry

A new practical method to generate a subspace of active coordinates for quantum dynamics calculations is presented. These reduced coordinates are obtained as the normal modes of an analytical quadratic representation of the energy difference between excited and ground states within the complete active space self-consistent field method. At the Franck-Condon point, the largest negative eigenvalues of this Hessian correspond to the photoactive modes: those that reduce the energy difference and lead to the conical intersection; eigenvalues close to 0 correspond to bath modes, while modes with large positive eigenvalues are photoinactive vibrations, which increase the energy difference. The efficacy of quantum dynamics run in the subspace of the photoactive modes is illustrated with the photochemistry of benzene, where theoretical simulations are designed to assist optimal control experiments

Sib mating without inbreeding in the longhorn crazy ant.

Sib matings increase homozygosity and, hence, the frequency of detrimental phenotypes caused by recessive deleterious alleles. However, many species have evolved adaptations that prevent the genetic costs associated with inbreeding. We discovered that the highly invasive longhorn crazy ant, Paratrechina longicornis, has evolved an unusual mode of reproduction whereby sib mating does not result in inbreeding. A population genetic study of P. longicornis revealed dramatic differences in allele frequencies between queens, males and workers. Mother-offspring analyses demonstrated that these allele frequency differences resulted from the fact that the three castes were all produced through different means. Workers developed through normal sexual reproduction between queens and males. However, queens were produced clonally and, thus, were genetically identical to their mothers. In contrast, males never inherited maternal alleles and were genetically identical to their fathers. The outcome of this system is that genetic inbreeding is impossible because queen and male genomes remain completely separate. Moreover, the sexually produced worker offspring retain the same genotype, combining alleles from both the maternal and paternal lineage over generations. Thus, queens may mate with their brothers in the parental nest, yet their offspring are no more homozygous than if the queen mated with a male randomly chosen from the population. The complete segregation of the male and female gene pools allows the queens to circumvent the costs associated with inbreeding and therefore may act as an important pre-adaptation for the crazy ant's tremendous invasive success.

No evidence that within-group male relatedness reduces harm to females in Drosophila.

Conflict between males and females over whether, when, and how often to mate often leads to the evolution of sexually antagonistic interactions that reduce female reproductive success. Because the offspring of relatives contribute to inclusive fitness, high relatedness between rival males might be expected to reduce competition and result in the evolution of reduced harm to females. A recent study investigated this possibility in Drosophila melanogaster and concluded that groups of brothers cause less harm to females than groups of unrelated males, attributing the effect to kin selection. That study did not control for the rearing environment of males, rendering the results impossible to interpret in the context of kin selection. Here, we conducted a similar experiment while manipulating whether males developed with kin prior to being placed with females. We found no difference between related and unrelated males in the harm caused to females when males were reared separately. In contrast, when related males developed and emerged together before the experiment, female reproductive output was higher. Our results show that relatedness among males is insufficient to reduce harm to females, while a shared rearing environment - resulting in males similar to or familiar with one another - is necessary to generate this pattern.

Measuring ecological niche overlap from occurrence and spatial environmental data

1. Aim - Concerns over how global change will influence species distributions, in conjunction with increased emphasis on understanding niche dynamics in evolutionary and community contexts, highlight the growing need for robust methods to quantify niche differences between or within taxa. We propose a statistical framework to describe and compare environmental niches from occurrence and spatial environmental data.¦2. Location - Europe, North America, South America¦3. Methods - The framework applies kernel smoothers to densities of species occurrence in gridded environmental space to calculate metrics of niche overlap and test hypotheses regarding niche conservatism. We use this framework and simulated species with predefined distributions and amounts of niche overlap to evaluate several ordination and species distribution modeling techniques for quantifying niche overlap. We illustrate the approach with data on two well-studied invasive species.¦4. Results - We show that niche overlap can be accurately detected with the framework when variables driving the distributions are known. The method is robust to known and previously undocumented biases related to the dependence of species occurrences on the frequency of environmental conditions that occur across geographic space. The use of a kernel smoother makes the process of moving from geographical space to multivariate environmental space independent of both sampling effort and arbitrary choice of resolution in environmental space. However, the use of ordination and species distribution model techniques for selecting, combining and weighting variables on which niche overlap is calculated provide contrasting results.¦5. Main conclusions - The framework meets the increasing need for robust methods to quantify niche differences. It is appropriate to study niche differences between species, subspecies or intraspecific lineages that differ in their geographical distributions. Alternatively, it can be used to measure the degree to which the environmental niche of a species or intraspecific lineage has changed over time.

The genome of the fire ant Solenopsis invicta.

Ants have evolved very complex societies and are key ecosystem members. Some ants, such as the fire ant Solenopsis invicta, are also major pests. Here, we present a draft genome of S. invicta, assembled from Roche 454 and Illumina sequencing reads obtained from a focal haploid male and his brothers. We used comparative genomic methods to obtain insight into the unique features of the S. invicta genome. For example, we found that this genome harbors four adjacent copies of vitellogenin. A phylogenetic analysis revealed that an ancestral vitellogenin gene first underwent a duplication that was followed by possibly independent duplications of each of the daughter vitellogenins. The vitellogenin genes have undergone subfunctionalization with queen- and worker-specific expression, possibly reflecting differential selection acting on the queen and worker castes. Additionally, we identified more than 400 putative olfactory receptors of which at least 297 are intact. This represents the largest repertoire reported so far in insects. S. invicta also harbors an expansion of a specific family of lipid-processing genes, two putative orthologs to the transformer/feminizer sex differentiation gene, a functional DNA methylation system, and a single putative telomerase ortholog. EST data indicate that this S. invicta telomerase ortholog has at least four spliceforms that differ in their use of two sets of mutually exclusive exons. Some of these and other unique aspects of the fire ant genome are likely linked to the complex social behavior of this species.

The major genetic determinants of HIV-1 control affect HLA class I peptide presentation.

Infectious and inflammatory diseases have repeatedly shown strong genetic associations within the major histocompatibility complex (MHC); however, the basis for these associations remains elusive. To define host genetic effects on the outcome of a chronic viral infection, we performed genome-wide association analysis in a multiethnic cohort of HIV-1 controllers and progressors, and we analyzed the effects of individual amino acids within the classical human leukocyte antigen (HLA) proteins. We identified >300 genome-wide significant single-nucleotide polymorphisms (SNPs) within the MHC and none elsewhere. Specific amino acids in the HLA-B peptide binding groove, as well as an independent HLA-C effect, explain the SNP associations and reconcile both protective and risk HLA alleles. These results implicate the nature of the HLA-viral peptide interaction as the major factor modulating durable control of HIV infection.

Comparação dos métodos de pesquisa de parasitas intestinais utilizados nos laboratórios clínicos em Cabo Verde com o método de Ritchie modificado – O caso de Rincão

Os parasitas intestinais constituem um problema médico-sanitário de grande importância, tanto pela frequência que ocorrem como causarem muitas vezes, distúrbios orgânicos capazes de incapacitarem os indivíduos infectados, reduzindo a resistência do organismo, predispondo-o inclusive a outras infecções ( MARCONDES et al., 2003 ) . Devido a estas incapacitações e maleficência que estes podem causar ao homem, tornase necessário que seja feito um diagnóstico fidedigno, através de técnicas sensíveis e específicas, pois o diagnóstico laboratorial constitui um processo importante e essencial no mecanismo de controlo e combate aos parasitas intestinais. Várias técnicas são usadas na identificação destes microrganismos, entre os quais o exame direto ou a fresco e vários métodos de concentração, como o método de Willis, Faust e Cols,Ritchie modificado, técnicas de sedimentação como Hoffmam, Pons e Janer, método de Baermann, método de Graham ( fita adesiva ) , métodos de coloração com a hematoxilina férrica, coloração tricrómica, assim como o uso de técnicas moleculares e testes rápidos ( DOLDMAN, 2009 ) . Utilizado na pesquisa sobretudo de ovos de helmintos, o método de concentração de Willis fundamenta-se na propriedade que determinados ovos têm em flutuarem na superfície de uma solução saturada com cloreto de sódio e ficarem na superfície, aderindo assim a uma lamela colocada a superfície e observada ao microscópio ( NEVES, 2005) . O método de concentração difásico de Ritchie modificado constitui uma das técnicas mais utilizadas na pesquisa de quistos de protozoários e helmintos. Esta baseia-se na sedimentação por centrifugação e lavagem do material com éter, um solvente orgânico que forma uma fase apolar, retendo os artefactos vegetais e lípidos contida na amostra, durante a centrifugação da suspensão de fezes ( REY, 2001) . Para um melhor diagnóstico, é importante associar aos métodos de pesquisa de parasitas intestinais, métodos indirectos, como a avaliação da eosinofilia sanguínea, esteatoreia e a pesquisa de cristais de Charcot-Leyden nas fezes, ou seja, métodos auxiliares na pesquisa e identificação de parasitas intestinais ( ENGELKIRK et ENGELKIRK, 2008 ) . O estudo teve como objetivo avaliar a sensibilidade e especificidades das técnicas utilizadas no diagnóstico de parasitas intestinais, comparando com as técnicas utilizadas nos laboratórios públicos de análises clínicas em Cabo Verde com o método de Ritchie modificado.

Comparação dos métodos de pesquisa de parasitas intestinais utilizados nos laboratórios clínicos em Cabo Verde com o método de Ritchie modificado.

As parasitoses intestinais constituem um grave problema de saúde pública, sendo o diagnóstico laboratorial essencial na sua identificação e controlo, tornando- se importante a escolha do método de eleição no processo, para que seja feito um diagnóstico fidedigno, através de técnicas sensíveis e específicas. Várias técnicas são usadas na identificação e pesquisas destes microrganismos, entre os quais o exame directo/ a fresco, métodos de concentração, como método de Willis, método de Faust e Cols, método bifásico de Ritchie modificado, técnicas de sedimentação como Hoffmam, Pons e Janer, método de Baermann, método de Graham (fita adesiva), métodos de coloração como hematoxilina férrica, coloração tricrômica, assim como uso de técnicas moleculares e testes rápidos (DOLDMAN, 2009). O presente estudo teve como objectivo avaliar a sensibilidade e especificidades das técnicas utilizadas no diagnóstico de parasitas intestinais nos laboratórios públicos de análises clínicas em Cabo Verde comparativamente ao método de Ritchie modificado. O estudo envolveu a análise de 251 amostras recolhidas em crianças dos 2 a 12 anos da comunidade de Rincão de Santa Catarina. Os métodos de diagnóstico laboratoriais utilizados foram os métodos de concentração de Willis, Ritchie modificado por Sales de Cunha e exame a fresco/directo. As amostras foram analisadas na Unidade Sanitária Base de Rincão e no Laboratório análises Clínica do Hospital Regional Santiago Norte. Para análise estatística, foram utilizadas Excel (2007), SPSS (versão 17). O método de Ritchie modificado mostrou ser mais sensível que o método de concentração de Willis. Também verificou-se a necessidade da realização de técnicas cada vez mais sensíveis no diagnóstico laboratorial dos parasitas intestinais nos laboratórios de análises clínicas estatais no Pais.

Relationship and transaction lending in a crisis

We study how relationship lending and transaction lending varyover the business cycle. We develop a model in which relationshipbanks gather information on their borrowers, which allows them toprovide loans for profitable firms during a crisis. Due to the servicesthey provide, operating costs of relationship-banks are higher thanthose of transaction-banks. In our model, where relationship-bankscompete with transaction-banks, a key result is that relationship-banks charge a higher intermediation spread in normal times, butoffer continuation-lending at more favorable terms than transactionbanks to profitable firms in a crisis. Using detailed credit registerinformation for Italian banks before and after the Lehman Brothers'default, we are able to study how relationship and transaction-banksresponded to the crisis and we test existing theories of relationshipbanking. Our empirical analysis confirms the basic prediction of themodel that relationship banks charged a higher spread before the crisis, offered more favorable continuation-lending terms in response tothe crisis, and suffered fewer defaults, thus confirming the informational advantage of relationship banking.

Genome-wide association study of blood pressure extremes identifies variant near UMOD associated with hypertension.

Hypertension is a heritable and major contributor to the global burden of disease. The sum of rare and common genetic variants robustly identified so far explain only 1%-2% of the population variation in BP and hypertension. This suggests the existence of more undiscovered common variants. We conducted a genome-wide association study in 1,621 hypertensive cases and 1,699 controls and follow-up validation analyses in 19,845 cases and 16,541 controls using an extreme case-control design. We identified a locus on chromosome 16 in the 5' region of Uromodulin (UMOD; rs13333226, combined P value of 3.6×10(-11)). The minor G allele is associated with a lower risk of hypertension (OR [95%CI]: 0.87 [0.84-0.91]), reduced urinary uromodulin excretion, better renal function; and each copy of the G allele is associated with a 7.7% reduction in risk of CVD events after adjusting for age, sex, BMI, and smoking status (H.R. = 0.923, 95% CI 0.860-0.991; p = 0.027). In a subset of 13,446 individuals with estimated glomerular filtration rate (eGFR) measurements, we show that rs13333226 is independently associated with hypertension (unadjusted for eGFR: 0.89 [0.83-0.96], p = 0.004; after eGFR adjustment: 0.89 [0.83-0.96], p = 0.003). In clinical functional studies, we also consistently show the minor G allele is associated with lower urinary uromodulin excretion. The exclusive expression of uromodulin in the thick portion of the ascending limb of Henle suggests a putative role of this variant in hypertension through an effect on sodium homeostasis. The newly discovered UMOD locus for hypertension has the potential to give new insights into the role of uromodulin in BP regulation and to identify novel drugable targets for reducing cardiovascular risk.

Advances in vaccination against Helicobacter pylori.

A vaccination against Helicobacter pylori may represent both prophylactic and therapeutic approaches to the control of H. pylori infection. Different protective H. pylori-derived antigens, such as urease, vacuolating cytotoxin A, cytotoxin-associated antigen, neutrophil-activating protein and others can be produced at low cost in prokaryote expression systems and most of these antigens have already been administered to humans and shown to be safe. The recent development by Graham et al. of the model of H. pylori challenge in humans, the recent published clinical trials and the last insight generated in animal models of H. pylori infection regarding the immune mechanisms leading to vaccine-induced Helicobacter clearance will facilitate the evaluation of immunogenicity and efficacy of H. pylori vaccine candidates in Phase II and III clinical trials.

Novel methods improve prediction of species' distributions from occurrence data

Prediction of species' distributions is central to diverse applications in ecology, evolution and conservation science. There is increasing electronic access to vast sets of occurrence records in museums and herbaria, yet little effective guidance on how best to use this information in the context of numerous approaches for modelling distributions. To meet this need, we compared 16 modelling methods over 226 species from 6 regions of the world, creating the most comprehensive set of model comparisons to date. We used presence-only data to fit models, and independent presence-absence data to evaluate the predictions. Along with well-established modelling methods such as generalised additive models and GARP and BIOCLIM, we explored methods that either have been developed recently or have rarely been applied to modelling species' distributions. These include machine-learning methods and community models, both of which have features that may make them particularly well suited to noisy or sparse information, as is typical of species' occurrence data. Presence-only data were effective for modelling species' distributions for many species and regions. The novel methods consistently outperformed more established methods. The results of our analysis are promising for the use of data from museums and herbaria, especially as methods suited to the noise inherent in such data improve.

Meadow Saffron Used as a Spice

Introduction: Intoxications with colchicine usually occur by ingestion of meadow saffron leaves (Colchicum autumnale) which are mistakenly collected for alimentary purposes instead of the leaves of crow garlic (Allium ursinum). Colchicine, the main alkaloid of Colchicum autumnale, is present in all parts of the plant. We report a rarer source of mistake, i.e. between the flowers of Colchicum autumnale and Crocus sativus. The similarity in this case is limited to the appearance of the flowers, but Colchicum autumnale, which is also flowering in autumn, lacks the crimson stigma from which the saffron spice is derived from Crocus sativus. Case report: A 47-year-old woman collected the stamens of a flower resembling Crocus sativus for use as saffron. Her knowledge about Crocus sativus was limited to having seen this plant previously at a museum of saffron (Mund, Switzerland). She prepared a meal with rice using three pinches of ''saffron'' for ten tablespoons of rice. She and her 8-year-old child, both ate the usual amount of rice (6 and 2 tablespoons, respectively). The 2 brothers (4- and 9-years-old) only ate 3 teaspoons of rice each. A slightly bitter taste and the absence of a yellow colouration were peculiar. Three to four hours after the meal, the mother developed nausea and contacted the Swiss Toxicological Information Centre, suspecting a plant misidentification. All family members were referred to the regional university hospital for administration of oral activated charcoal. No other symptoms were reported, notably no symptoms in the 8-year-old boy and his brothers. Colchicine serum concentration (blood sample obtained 15 hours after ingestion) measured by HPLC-mass spectrometry was 0.36 mg/L for the mother, and 0.13 mg/L for the 8-year-old child, respectively (therapeutic levels: 0.30-2.5 mg/L). Conclusion: This report demonstrates that a significant amount of colchicine may be absorbed even after ingestion of very small quantities of Colchicum autumnale, which in this case was confused with Crocus sativus. Serum colchicine concentrations in the sub-/therapeutic range can be quantified by HPLC-mass spectrometry, which allows a very sensitive and specific detection of this alkaloid in blood and urine.