In silico evaluation of WHO-endorsed molecular methods to detect drug resistant tuberculosis

Universal drug susceptibility testing (DST) for tuberculosis is a major goal of the END TB strategy. PCR-based molecular diagnostic tests have been instrumental in increasing DST globally and several assays have now been endorsed by the World Health Organization (WHO) for use in the diagnosis of drug resistance. These endorsed assays, however, each interrogate a limited number of mutations associated with resistance, potentially limiting their sensitivity compared to sequencing-based methods. We applied an in silico method to compare the sensitivity and specificity of WHO-endorsed molecular based diagnostics to the mutation set identified by the WHO mutations catalogue using phenotypic DST as the reference. We found that, in silico, the mutation sets used by probe-based molecular diagnostic tests to identify rifampicin, isoniazid, pyrazinamide, levofloxacin, moxifloxacin, amikacin, capreomycin and kanamycin resistance produced similar sensitivities and specificities to the WHO mutation catalogue. PCR-based diagnostic tests were most sensitive for drugs where mechanisms of resistance are well established and localised to small genetic regions or a few prevalent mutations. Approaches using sequencing technologies can provide advantages for drugs where our knowledge of resistance is limited, or where complex resistance signatures exist

Effects of variable magma supply on mid-ocean ridge eruptions : constraints from mapped lava flow fields along the Galápagos Spreading Center

Author Posting. © American Geophysical Union, 2012. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 13 (2012): Q08014, doi:10.1029/2012GC004163.Mapping and sampling of 18 eruptive units in two study areas along the Galápagos Spreading Center (GSC) provide insight into how magma supply affects mid-ocean ridge (MOR) volcanic eruptions. The two study areas have similar spreading rates (53 versus 55 mm/yr), but differ by 30% in the time-averaged rate of magma supply (0.3 × 106 versus 0.4 × 106 m3/yr/km). Detailed geologic maps of each study area incorporate observations of flow contacts and sediment thickness, in addition to sample petrology, geomagnetic paleointensity, and inferences from high-resolution bathymetry data. At the lower-magma-supply study area, eruptions typically produce irregularly shaped clusters of pillow mounds with total eruptive volumes ranging from 0.09 to 1.3 km3. At the higher-magma-supply study area, lava morphologies characteristic of higher effusion rates are more common, eruptions typically occur along elongated fissures, and eruptive volumes are an order of magnitude smaller (0.002–0.13 km3). At this site, glass MgO contents (2.7–8.4 wt. %) and corresponding liquidus temperatures are lower on average, and more variable, than those at the lower-magma-supply study area (6.2–9.1 wt. % MgO). The differences in eruptive volume, lava temperature, morphology, and inferred eruption rates observed between the two areas along the GSC are similar to those that have previously been related to variable spreading rates on the global MOR system. Importantly, the documentation of multiple sequences of eruptions at each study area, representing hundreds to thousands of years, provides constraints on the variability in eruptive style at a given magma supply and spreading rate.This work was supported by the National Science Foundation grants OCE08–49813, OCE08–50052, and OCE08– 49711.2013-02-2

Happiness around the world: A combined etic-emic approach across 63 countries.

What does it mean to be happy? The vast majority of cross-cultural studies on happiness have employed a Western-origin, or "WEIRD" measure of happiness that conceptualizes it as a self-centered (or "independent"), high-arousal emotion. However, research from Eastern cultures, particularly Japan, conceptualizes happiness as including an interpersonal aspect emphasizing harmony and connectedness to others. Following a combined emic-etic approach (Cheung, van de Vijver & Leong, 2011), we assessed the cross-cultural applicability of a measure of independent happiness developed in the US (Subjective Happiness Scale; Lyubomirsky & Lepper, 1999) and a measure of interdependent happiness developed in Japan (Interdependent Happiness Scale; Hitokoto & Uchida, 2015), with data from 63 countries representing 7 sociocultural regions. Results indicate that the schema of independent happiness was more coherent in more WEIRD countries. In contrast, the coherence of interdependent happiness was unrelated to a country's "WEIRD-ness." Reliabilities of both happiness measures were lowest in African and Middle Eastern countries, suggesting these two conceptualizations of happiness may not be globally comprehensive. Overall, while the two measures had many similar correlates and properties, the self-focused concept of independent happiness is "WEIRD-er" than interdependent happiness, suggesting cross-cultural researchers should attend to both conceptualizations

The development and validation of a scoring tool to predict the operative duration of elective laparoscopic cholecystectomy

Background: The ability to accurately predict operative duration has the potential to optimise theatre efficiency and utilisation, thus reducing costs and increasing staff and patient satisfaction. With laparoscopic cholecystectomy being one of the most commonly performed procedures worldwide, a tool to predict operative duration could be extremely beneficial to healthcare organisations. Methods: Data collected from the CholeS study on patients undergoing cholecystectomy in UK and Irish hospitals between 04/2014 and 05/2014 were used to study operative duration. A multivariable binary logistic regression model was produced in order to identify significant independent predictors of long (> 90 min) operations. The resulting model was converted to a risk score, which was subsequently validated on second cohort of patients using ROC curves. Results: After exclusions, data were available for 7227 patients in the derivation (CholeS) cohort. The median operative duration was 60 min (interquartile range 45–85), with 17.7% of operations lasting longer than 90 min. Ten factors were found to be significant independent predictors of operative durations > 90 min, including ASA, age, previous surgical admissions, BMI, gallbladder wall thickness and CBD diameter. A risk score was then produced from these factors, and applied to a cohort of 2405 patients from a tertiary centre for external validation. This returned an area under the ROC curve of 0.708 (SE = 0.013, p  90 min increasing more than eightfold from 5.1 to 41.8% in the extremes of the score. Conclusion: The scoring tool produced in this study was found to be significantly predictive of long operative durations on validation in an external cohort. As such, the tool may have the potential to enable organisations to better organise theatre lists and deliver greater efficiencies in care

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis.

Background: Molecular diagnostics are considered the most promising route to achievement of rapid, universal drug susceptibility testing for Mycobacterium tuberculosis complex (MTBC). We aimed to generate a WHO-endorsed catalogue of mutations to serve as a global standard for interpreting molecular information for drug resistance prediction. Methods: In this systematic analysis, we used a candidate gene approach to identify mutations associated with resistance or consistent with susceptibility for 13 WHO-endorsed antituberculosis drugs. We collected existing worldwide MTBC whole-genome sequencing data and phenotypic data from academic groups and consortia, reference laboratories, public health organisations, and published literature. We categorised phenotypes as follows: methods and critical concentrations currently endorsed by WHO (category 1); critical concentrations previously endorsed by WHO for those methods (category 2); methods or critical concentrations not currently endorsed by WHO (category 3). For each mutation, we used a contingency table of binary phenotypes and presence or absence of the mutation to compute positive predictive value, and we used Fisher's exact tests to generate odds ratios and Benjamini-Hochberg corrected p values. Mutations were graded as associated with resistance if present in at least five isolates, if the odds ratio was more than 1 with a statistically significant corrected p value, and if the lower bound of the 95% CI on the positive predictive value for phenotypic resistance was greater than 25%. A series of expert rules were applied for final confidence grading of each mutation. Findings: We analysed 41 137 MTBC isolates with phenotypic and whole-genome sequencing data from 45 countries. 38 215 MTBC isolates passed quality control steps and were included in the final analysis. 15 667 associations were computed for 13 211 unique mutations linked to one or more drugs. 1149 (7·3%) of 15 667 mutations were classified as associated with phenotypic resistance and 107 (0·7%) were deemed consistent with susceptibility. For rifampicin, isoniazid, ethambutol, fluoroquinolones, and streptomycin, the mutations' pooled sensitivity was more than 80%. Specificity was over 95% for all drugs except ethionamide (91·4%), moxifloxacin (91·6%) and ethambutol (93·3%). Only two resistance mutations were identified for bedaquiline, delamanid, clofazimine, and linezolid as prevalence of phenotypic resistance was low for these drugs. Interpretation: We present the first WHO-endorsed catalogue of molecular targets for MTBC drug susceptibility testing, which is intended to provide a global standard for resistance interpretation. The existence of this catalogue should encourage the implementation of molecular diagnostics by national tuberculosis programmes. Funding: Unitaid, Wellcome Trust, UK Medical Research Council, and Bill and Melinda Gates Foundation

Effects of variable magma supply on magma reservoirs and eruption characteristics along the Galápagos spreading center

Ph.D. University of Hawaii at Manoa 2014.Includes bibliographical references.This dissertation examines the effects of magma supply on mid-ocean ridge magma reservoirs and eruption characteristics, using mapped lava flow fields erupted at two locations along the Galápagos Spreading Center. Low-and high-magma-supply study areas at 95° and 92°W have similar spreading rates, but differ by 30% in the rate of magma supply due to varying proximity to the Galápagos hotspot. Detailed geologic maps of each study area incorporate observations of flow contacts and sediment thickness, in addition to sample petrology, geomagnetic paleointensity, and bathymetry data. Mapped lava flow fields are used to compare characteristics of eruptions at the two locations. At the 92°W study area, lava morphologies characteristic of higher effusion rates are more common, and eruptions typically occur along elongated fissures with total eruptive volumes ranging from 0.002--0.13 km3. In contrast, at the 95°W study area, eruptions typically produce axial seamounts or more irregular clusters of pillow mounds, and eruptive volumes are an order of magnitude larger (0.09 to 1.3 km3). Whereas a seismically imaged melt lens exists ~1.7 km below the seafloor at the 92°W study area, no melt lens has been detected at the 95°W study area. Measurements of CO2 and H2O in olivine-hosted melt inclusions are used to constrain depths of magma residence at the low-magma-supply study area. Results indicate that prior to three recent eruptions, magma resided at depths of 3.0-3.4 km below the seafloor. Compositional data were used to compare the characteristics of magmatic systems at the two locations. At 92°W, the rate of magma supply is sufficient to sustain a shallow melt lens (Blacic et al., 2004), within which the competing effects of fractional crystallization and frequent magmatic recharge result in eruption of lavas with low crystal contents and highly variable MgO. In contrast, melt-rich bodies at 95°W are likely only present intermittently; magmatic evolution at this location appears to be dominated by processes involving crystal-rich mush, which is mixed in varying proportions with hotter, more melt-rich magma during recharge events that closely precede eruptions. Limited residence within melt-rich lenses allows mixing trends to be preserved in erupted lavas

Constraints from Melt Inclusions on Depths of Magma Residence at Intermediate Magma Supply Along the Galápagos Spreading Center

Shallow, seismically imaged melt lenses are a ubiquitous feature of mid-ocean ridges with high magma supply; melt lenses deepen and become less continuous along axis as the rate of magma supply decreases. Despite compelling petrologic evidence for evolution of magma within the crust prior to eruption at lower magma supply, melt lenses are rarely detected along ridge segments with rates of magma supply less than 0.3×106 m3/yr/km, and the depths of sub-axial magma reservoirs are therefore poorly known. We use ion microprobe measurements of H2O and CO2 concentrations of olivine-hosted melt inclusions to calculate vapor saturation pressures that constrain crystallization depths at two locations along the Galápagos Spreading Center (94.2°W and 95°W). These sites were chosen to examine crystallization pressures in the presence (94.2°W) and absence (95°W) of a seismically imaged melt lens. At 95°W, where magma supply is too low to sustain a seismically resolvable melt lens, samples were selected from each of the three most recent eruptive units, allowing us to document temporal variations in vapor saturation pressures and the depth of magma residence at this location. Clusters in melt inclusion entrapment depths for these eruptions range from 3.0 to 3.4 km below the seafloor, indicating that magmas at 95°W resided at a narrow range of mid-crustal depths prior to eruption, generally consistent with the global trend of increasing melt lens depth with decreasing rate of magma supply. A discrepancy between seismic data and the peak in melt inclusion entrapment depths at 94.2°W may reflect temporal variability of magmatic systems at this location. This study demonstrates the potential for using measurements of the concentrations of H2O and CO2 in olivine-hosted melt inclusions to determine the depths of crustal magmatic systems that feed mid-ocean ridge eruptions, even in locations where seismic studies have not detected melt lenses

DIÁLOGOS E EXPERIMENTAÇÃO: UMA PERSPECTIVA FREIREANA PARA O ENSINO DE CIÊNCIAS

O ensino de Ciências requer uma metodologia que aproxime o aluno da sua realidade, de modo a possibilitar uma compreensão científica do mundo em que vivemos. Neste trabalho apresentaremos um relato de experiência sobre as particularidades de uma atividade experimental sobre a temática “Ar”, realizada pela equipe de bolsistas do Programa Institucional de Bolsas de Iniciação à Docência (PIBID). A referida atividade contemplou doze alunos do sexto ano de uma Escola Estadual de Ensino Fundamental do município de Dom Pedrito/RS, a qual está inserida no programa. Nesta ação, os estudantes realizaram um experimento que tinha como objetivo evidenciar que o ar é matéria e, portanto, ocupa lugar no espaço. Para tanto, utilizou-se garrafas pet e algumas bexigas vazias. Os estudantes efetuaram a montagem do experimento e após a realização do mesmo, foram questionados acerca do que haviam aprendido com tal atividade. Consideramos que o resultado desta prática foi muito satisfatório, pois identificamos que a maioria dos estudantes evidenciou, através do experimento, a existência do ar e o espaço que ele ocupa. É oportuno ressaltar a receptividade e o entusiasmo dos educandos com a execução da atividade, pois todos participaram com muita motivação, interesse e curiosidade, evidenciando a importância da realização de práticas diferenciadas para o processo de ensino e aprendizagem. A partir deste pressuposto concluímos que a experimentação pode ser uma aliada no ensino de Ciências. Visto que, possibilita a participação ativa dos alunos, permite a expressão de ideias, opiniões, formulação de hipóteses, fomenta a criticidade e a curiosidade destes sujeitos, bem como os faculta a pensar, imaginar e refletir sobre o que está sendo explorado. E desse modo, poderá contribuir, significativamente, com a efetiva construção do conhecimento científico

Benzophenone as a Cheap and Effective Photosensitizer for the Photocatalytic Synthesis of Dimethyl Cubane-1,4-dicarboxylate

The key intramolecular [2+2] photochemical cycloaddition step in the synthesis of dimethyl cubane-1,4-dicarboxylate is performed with substoichiometric amounts of the photosensitizer benzophenone. The reaction proceeds via a Dexter energy transfer process between the triplet excited state benzophenone and a well-known cubane precursor diene. The use of the cheap and widely available benzophenone as the photosensitizer enables lower energy light to be used than the traditional photochemical process