Spinor-Vector Duality in Heterotic String Orbifolds

The three generation heterotic-string models in the free fermionic formulation are among the most realistic string vacua constructed to date, which motivated their detailed investigation. The classification of free fermion heterotic string vacua has revealed a duality under the exchange of spinor and vector representations of the SO(10) GUT symmetry over the space of models. We demonstrate the existence of the spinor-vector duality using orbifold techniques, and elaborate on the relation of these vacua to free fermionic models.Comment: 20 pages. v2 minor corrections. Version to appear on JHEP. v3 misprints correcte

Powerful and interpretable behavioural features for quantitative phenotyping of C. elegans

Behaviour is a sensitive and integrative readout of nervous system function and therefore an attractive measure for assessing the effects of mutation or drug treatment on animals. Video data provide a rich but high-dimensional representation of behaviour, and so the first step of analysis is often some form of tracking and feature extraction to reduce dimensionality while maintaining relevant information. Modern machine-learning methods are powerful but notoriously difficult to interpret, while handcrafted features are interpretable but do not always perform as well. Here, we report a new set of handcrafted features to compactly quantify Caenorhabditis elegans behaviour. The features are designed to be interpretable but to capture as much of the phenotypic differences between worms as possible. We show that the full feature set is more powerful than a previously defined feature set in classifying mutant strains. We then use a combination of automated and manual feature selection to define a core set of interpretable features that still provides sufficient power to detect behavioural differences between mutant strains and the wild-type. Finally, we apply the new features to detect time-resolved behavioural differences in a series of optogenetic experiments targeting different neural subsets

Participatory Geographic Information Systems as an Organizational Platform for the Integration of Traditional and Scientific Knowledge in Contemporary Fire and Fuels Management

Traditional knowledge about fire and its effects held by indigenous people, who are connected to specific landscapes, holds promise for informing contemporary fire and fuels management strategies and augmenting knowledge and information derived from western science. In practice, however, inadequate means to organize and communicate this traditional knowledge with scientists and managers can limit its consideration in decisions, requiring novel approaches to interdisciplinary and cross-cultural communication and collaboration. We propose that Participatory Geographic Information Systems (PGIS) is one platform for the assemblage and communication of traditional knowledge vital to fire and fuels management, while preserving linkages to broader cultural contexts. We provide summaries of four preliminary case studies in the Intermountain West of North America to illustrate different potential applications of a PGIS tool in this context and describe some remaining challenges. Management and Policy Implications: Participatory Geographic Information Systems (PGIS) can offer a powerful approach for enhancing current decisionmaking by allowing for the integration of traditional and scientific knowledge systems with spatial environmental data in an interactive participatory process. Integrated data sets can allow traditional and scientific knowledge experts to share, explore, manage, analyze, and interpret multidimensional data in a common spatial context to develop more informed management decisions. Such combined data sets could provide a more comprehensive assessment of fire-related ecological change than is currently used in decisionmaking and enhance inclusion of effects on local resource utility values and areas of cultural significance. The use of a PGIS interface creates opportunities for traditional knowledge holders to share information and potential prescriptions while maintaining confidentiality. Knowledge integration efforts using PGIS as an organizational tool would help to bridge the communication gap that commonly exists between scientists, managers, and traditional knowledge holders as ecosystems continue to be altered through processes of land management and climate change

Impressões sobre o teste rápido para o HIV entre usuários de drogas injetáveis no Brasil

OBJECTIVE: To describe perceptions, experiences, knowledge, beliefs and the willingness of injecting drug users to be HIV tested by using rapid tests. METHODS: A qualitative exploratory study was carried out among injecting drug users from December 2003 to February 2004 in five Brazilian cities, located in four regions of Brazil. A semi-structured interview guide containing both closed and open-ended questions was used to address perceptions about non-conventional testing procedures, and non-traditional ways to provide testing access to injecting drug users. A total of 106 interviews, about 26 per region, were conducted. RESULTS: Characteristics of the population studied, common thoughts about HIV rapid testing, preference for using blood or saliva specimens, and other testing preferences, were presented together with reported advantages and disadvantages of each option. The study findings showed that the use of rapid tests among these users is feasible and that they are willing to be tested using rapid HIV tests, especially if some issues related to privacy and reliability of the test could be addressed. CONCLUSIONS: The study findings showed that rapid tests may be well accepted for this population. These tests can be considered a valuable tool, allowing a more injecting drug users to learn their HIV status and possibly be referred to treatment and should support more effective testing strategies for them.OBJETIVO: Descrever as impressões, experiências, conhecimentos, crenças e a receptividade de usuários de drogas injetáveis para participar das estratégias de testagem rápida para HIV. MÉTODOS: Estudo qualitativo exploratório foi conduzido entre usuários de drogas injetáveis, de dezembro de 2003 a fevereiro de 2004, em cinco cidades brasileiras, localizadas em quatro regiões do País. Um roteiro de entrevista semi-estruturado contendo questões fechadas e abertas foi usado para avaliar percepções desses usuários sobre procedimentos e formas alternativas de acesso e testagem. Foram realizadas 106 entrevistas, aproximadamente 26 por região. RESULTADOS: Características da população estudada, opiniões sobre o teste rápido e preferências por usar amostras de sangue ou saliva foram apresentadas junto com as vantagens e desvantagens associadas a cada opção. Os resultados mostraram a viabilidade do uso de testes rápidos entre usuários de drogas injetáveis e o interesse deles quanto à utilização destes métodos, especialmente se puderem ser equacionadas questões relacionadas à confidencialidade e confiabilidade dos testes. CONCLUSÕES: Os resultados indicam que os testes rápidos para HIV seriam bem recebidos por essa população. Esses testes podem ser considerados uma ferramenta valiosa, ao permitir que mais usuários de drogas injetáveis conheçam sua sorologia para o HIV e possam ser referidos para tratamento, como subsidiar a melhoria das estratégias de testagem entre usuários de drogas injetáveis

Outcomes of TB Treatment by HIV Status in National Recording Systems in Brazil, 2003–2008

BACKGROUND: Although the Brazilian national reporting system for tuberculosis cases (SINAN) has enormous potential to generate data for policy makers, formal assessments of treatment outcomes and other aspects of TB morbidity and mortality are not produced with enough depth and rigor. In particular, the effect of HIV status on these outcomes has not been fully explored, partly due to incomplete recording in the national database. METHODOLOGY/PRINCIPAL FINDINGS: In a retrospective cohort study, we assessed TB treatment outcomes, including rates of cure, default, mortality, transfer and multidrug resistant TB (MDR-TB) among a purposively chosen sample of 161,481 new cases reported in SINAN between 2003 and 2008. The study population included all new cases reported in the six States with the highest level of completeness of the HIV status field in the system. These cases were mostly male (67%), white (62%), had pulmonary TB (79%) and a suspect chest X ray (83%). Treatment outcomes were best for those HIV negative cases and worst for those known HIV positive patients (cure rate of 85.7% and 55.7% respectively). In multivariate modeling, the risk of having an unfavorable outcome (all outcomes except cure) was 3.09 times higher for those HIV positive compared with those HIV negative (95% CI 3.02-3.16). The risk of death and default also increased with HIV positivity. The group without a known HIV status showed intermediate outcomes between the groups above, suggesting that this group includes some with HIV infection. CONCLUSIONS: HIV status played an important role in TB treatment outcomes in the study period. The outcomes observed in those with known HIV were poor and need to be improved. Those in the group with unknown HIV status indicate the need for wider HIV testing among new TB cases

Characterisation of the bacterial and fungal communities associated with different lesion sizes of Dark Spot Syndrome occurring in the Coral Stephanocoenia intersepta

The number and prevalence of coral diseases/syndromes are increasing worldwide. Dark Spot Syndrome (DSS) afflicts numerous coral species and is widespread throughout the Caribbean, yet there are no known causal agents. In this study we aimed to characterise the microbial communities (bacteria and fungi) associated with DSS lesions affecting the coral Stephanocoenia intersepta using nonculture molecular techniques. Bacterial diversity of healthy tissues (H), those in advance of the lesion interface (apparently healthy AH), and three sizes of disease lesions (small, medium, and large) varied significantly (ANOSIM R = 0.052 p,0.001), apart from the medium and large lesions, which were similar in their community profile. Four bacteria fitted into the pattern expected from potential pathogens; namely absent from H, increasing in abundance within AH, and dominant in the lesions themselves. These included ribotypes related to Corynebacterium (KC190237), Acinetobacter (KC190251), Parvularculaceae (KC19027), and Oscillatoria (KC190271). Furthermore, two Vibrio species, a genus including many proposed coral pathogens, dominated the disease lesion and were absent from H and AH tissues, making them candidates as potential pathogens for DSS. In contrast, other members of bacteria from the same genus, such as V. harveyii were present throughout all sample types, supporting previous studies where potential coral pathogens exist in healthy tissues. Fungal diversity varied significantly as well, however the main difference between diseased and healthy tissues was the dominance of one ribotype, closely related to the plant pathogen, Rhytisma acerinum, a known causal agent of tar spot on tree leaves. As the corals’ symbiotic algae have been shown to turn to a darker pigmented state in DSS (giving rise to the syndromes name), the two most likely pathogens are R. acerinum and the bacterium Oscillatoria, which has been identified as the causal agent of the colouration in Black Band Disease, another widespread coral disease

Trabecular bone volume and osteoprotegerin expression in uremic rats given high calcium

Calcium (Ca)-containing phosphate binders have been recommended for the treatment of hyperphosphatemia in children with chronic kidney disease. To study the effects of high Ca levels on trabecular bone volume (BV) and osteoprotegerin (OPG) expression in uremic young rats, a model of marked overcorrection of secondary hyperparathyroidism was created by providing a diet of high Ca to 5/6 nephrectomized young rats (Nx-Ca) for 4 weeks. The results of chondrocyte proliferation and apoptosis, osteoclastic activity, OPG expression and BV were compared among intact rats given the control diet, intact rats given a high Ca diet and 5/6 nephrectomized rats given the control diet (Nx-Control) and the high Ca diet (Nx-Ca). Ionized Ca levels were higher and parathyroid hormone levels were lower in Nx-Ca rats than in the other groups. Final weight, final length and final tibial length of Nx-Ca rats were significantly less than those of the other groups, although the length gain did not differ among the groups. The hypertrophic zone width was markedly enlarged in Nx-Ca rats. Chondrocyte proliferation rates did not differ among the groups, whereas osteoclastic activity was decreased in Nx-Ca rats compared with the Nx-Control animals. The OPG expression and BV were increased in Nx-Ca rats compared with the Nx-Control rats. Increased BV should improve bone strength, whereas disturbance of osteoclastogenesis interferes with bone remodeling. Bone quality has yet to be determined in high Ca-fed uremic young rats

Phenotypic redshifts with self-organizing maps: A novel method to characterize redshift distributions of source galaxies for weak lensing

Wide-field imaging surveys such as the Dark Energy Survey (DES) rely on coarse measurements of spectral energy distributions in a few filters to estimate the redshift distribution of source galaxies. In this regime, sample variance, shot noise, and selection effects limit the attainable accuracy of redshift calibration and thus of cosmological constraints. We present a new method to combine wide-field, few-filter measurements with catalogs from deep fields with additional filters and sufficiently low photometric noise to break degeneracies in photometric redshifts. The multi-band deep field is used as an intermediary between wide-field observations and accurate redshifts, greatly reducing sample variance, shot noise, and selection effects. Our implementation of the method uses self-organizing maps to group galaxies into phenotypes based on their observed fluxes, and is tested using a mock DES catalog created from N-body simulations. It yields a typical uncertainty on the mean redshift in each of five tomographic bins for an idealized simulation of the DES Year 3 weak-lensing tomographic analysis of $\sigma_{\Delta z} = 0.007$, which is a 60% improvement compared to the Year 1 analysis. Although the implementation of the method is tailored to DES, its formalism can be applied to other large photometric surveys with a similar observing strategy.Comment: 24 pages, 11 figures; matches version accepted to MNRA

A new method to quantify and compare the multiple components of fitness-A study case with kelp niche partition by divergent microstage adaptations to Temperature

Point 1 Management of crops, commercialized or protected species, plagues or life-cycle evolution are subjects requiring comparisons among different demographic strategies. The simpler methods fail in relating changes in vital rates with changes in population viability whereas more complex methods lack accuracy by neglecting interactions among vital rates. Point 2 The difference between the fitness (evaluated by the population growth rate.) of two alternative demographies is decomposed into the contributions of the differences between the pair-wised vital rates and their interactions. This is achieved through a full Taylor expansion (i.e. remainder = 0) of the demographic model. The significance of each term is determined by permutation tests under the null hypothesis that all demographies come from the same pool. Point 3 An example is given with periodic demographic matrices of the microscopic haploid phase of two kelp cryptic species observed to partition their niche occupation along the Chilean coast. The method provided clear and synthetic results showing conditional differentiation of reproduction is an important driver for their differences in fitness along the latitudinal temperature gradient. But it also demonstrated that interactions among vital rates cannot be neglected as they compose a significant part of the differences between demographies. Point 4 This method allows researchers to access the effects of multiple effective changes in a life-cycle from only two experiments. Evolutionists can determine with confidence the effective causes for changes in fitness whereas population managers can determine best strategies from simpler experimental designs.CONICYT-FRENCH EMBASSADY Ph.D. gran

On dynamic network entropy in cancer

The cellular phenotype is described by a complex network of molecular interactions. Elucidating network properties that distinguish disease from the healthy cellular state is therefore of critical importance for gaining systems-level insights into disease mechanisms and ultimately for developing improved therapies. By integrating gene expression data with a protein interaction network to induce a stochastic dynamics on the network, we here demonstrate that cancer cells are characterised by an increase in the dynamic network entropy, compared to cells of normal physiology. Using a fundamental relation between the macroscopic resilience of a dynamical system and the uncertainty (entropy) in the underlying microscopic processes, we argue that cancer cells will be more robust to random gene perturbations. In addition, we formally demonstrate that gene expression differences between normal and cancer tissue are anticorrelated with local dynamic entropy changes, thus providing a systemic link between gene expression changes at the nodes and their local network dynamics. In particular, we also find that genes which drive cell-proliferation in cancer cells and which often encode oncogenes are associated with reductions in the dynamic network entropy. In summary, our results support the view that the observed increased robustness of cancer cells to perturbation and therapy may be due to an increase in the dynamic network entropy that allows cells to adapt to the new cellular stresses. Conversely, genes that exhibit local flux entropy decreases in cancer may render cancer cells more susceptible to targeted intervention and may therefore represent promising drug targets.Comment: 10 pages, 3 figures, 4 tables. Submitte