James Hutton’s geological tours of Scotland : romanticism, literary strategies, and the scientific quest

This article explores a somewhat neglected part of the story of the emergence of geology as a science and discourse in the late eighteenth century – James Hutton’s posthumously published accounts of the geological tours of Scotland that he undertook in the years 1785 to 1788 in search of empirical evidence in support of his theory of the Earth and that he intended to include in the projected third volume of his Theory of the Earth of 1795. The article brings some of the assumptions and techniques of literary criticism to bear on Hutton’s scientific travel writing in order to open up new connections between geology, Romantic aesthetics and eighteenth-century travel writing about Scotland. Close analysis of Hutton’s accounts of his field trips to Glen Tilt, Galloway and Arran, supplemented by later accounts of the discoveries at Jedburgh and Siccar Point, reveals the interplay between desire, travel and the scientific quest and foregrounds the textual strategies that Hutton uses to persuade his readers that they share in the experience of geological discovery and interpretation as ‘virtual witnesses’. As well as allowing us to revisit the interrelation between scientific theory and discovery, this article concludes that Hutton was a much better writer than he has been given credit for and suggests that if these geological tours had been published in 1795 they would have made it impossible for critics to dismiss him as an armchair geologist

Initial evidence of reduction of malaria cases and deaths in Rwanda and Ethiopia due to rapid scale-up of malaria prevention and treatment

<p>Abstract</p> <p>Background</p> <p>An increasing number of malaria-endemic African countries are rapidly scaling up malaria prevention and treatment. To have an initial estimate of the impact of these efforts, time trends in health facility records were evaluated in selected districts in Ethiopia and Rwanda, where long-lasting insecticidal nets (LLIN) and artemisinin-based combination therapy (ACT) had been distributed nationwide by 2007.</p> <p>Methods</p> <p>In Ethiopia, a stratified convenience sample covered four major regions where (moderately) endemic malaria occurs. In Rwanda, two districts were sampled in all five provinces, with one rural health centre and one rural hospital selected in each district. The main impact indicator was percentage change in number of in-patient malaria cases and deaths in children < 5 years old prior to (2001–2005/6) and after (2007) nationwide implementation of LLIN and ACT.</p> <p>Results</p> <p>In-patient malaria cases and deaths in children < 5 years old in Rwanda fell by 55% and 67%, respectively, and in Ethiopia by 73% and 62%. Over this same time period, non-malaria cases and deaths generally remained stable or increased.</p> <p>Conclusion</p> <p>Initial evidence indicated that the combination of mass distribution of LLIN to all children < 5 years or all households and nationwide distribution of ACT in the public sector was associated with substantial declines of in-patient malaria cases and deaths in Rwanda and Ethiopia. Clinic-based data was a useful tool for local monitoring of the impact of malaria programmes.</p

Low oxygen affects photophysiology and the level of expression of two-carbon metabolism genes in the seagrass <i>Zostera muelleri</i>

© 2017, Springer Science+Business Media B.V. Seagrasses are a diverse group of angiosperms that evolved to live in shallow coastal waters, an environment regularly subjected to changes in oxygen, carbon dioxide and irradiance. Zostera muelleri is the dominant species in south-eastern Australia, and is critical for healthy coastal ecosystems. Despite its ecological importance, little is known about the pathways of carbon fixation in Z. muelleri and their regulation in response to environmental changes. In this study, the response of Z. muelleri exposed to control and very low oxygen conditions was investigated by using (i) oxygen microsensors combined with a custom-made flow chamber to measure changes in photosynthesis and respiration, and (ii) reverse transcription quantitative real-time PCR to measure changes in expression levels of key genes involved in C4 metabolism. We found that very low levels of oxygen (i) altered the photophysiology of Z. muelleri, a characteristic of C3 mechanism of carbon assimilation, and (ii) decreased the expression levels of phosphoenolpyruvate carboxylase and carbonic anhydrase. These molecular-physiological results suggest that regulation of the photophysiology of Z. muelleri might involve a close integration between the C3 and C4, or other CO2 concentrating mechanisms metabolic pathways. Overall, this study highlights that the photophysiological response of Z. muelleri to changing oxygen in water is capable of rapid acclimation and the dynamic modulation of pathways should be considered when assessing seagrass primary production

Analysis of gene mutations associated with isoniazid, rifampicin and ethambutol resistance among Mycobacterium tuberculosis isolates from Ethiopia

<p>Abstract</p> <p>Background</p> <p>The emergence of drug resistance is one of the most important threats to tuberculosis control programs. This study was aimed to analyze the frequency of gene mutations associated with resistance to isoniazid (INH), rifampicin (RMP) and ethambutol (EMB) among <it>Mycobacterium tuberculosis </it>isolates from Northwest Ethiopia, and to assess the performance of the GenoType^®MTBDRplus and GenoType^®MTBDRsl assays as compared to the BacT/ALERT 3D system.</p> <p>Methods</p> <p>Two hundred sixty <it>Mycobacterium tuberculosis </it>isolates from smear positive tuberculosis patients diagnosed between March 2009 and July 2009 were included in this study. Drug susceptibility tests were performed in the Institute of Medical Microbiology and Epidemiology of Infectious Diseases, University Hospital of Leipzig, Germany.</p> <p>Results</p> <p>Of 260 isolates, mutations conferring resistance to INH, RMP, or EMB were detected in 35, 15, and 8 isolates, respectively, while multidrug resistance (MDR) was present in 13 of the isolates. Of 35 INH resistant strains, 33 had mutations in the <it>katG </it>gene at Ser315Thr 1 and two strains had mutation in the <it>inhA </it>gene at C15T. Among 15 RMP resistant isolates, 11 had <it>rpoB </it>gene mutation at Ser531Leu, one at His526Asp, and three strains had mutations only at the wild type probes. Of 8 EMB resistant strains, two had mutations in the <it>embB </it>gene at Met306Ile, one at Met306Val, and five strains had mutations only at the wild type probes. The GenoType^®MTBDRplus assay had a sensitivity of 92% and specificity of 99% for INH resistance, and 100% sensitivity and specificity to detect RMP resistance and MDR. The GenoType^®MTBDRsl assay had a sensitivity of 42% and specificity of 100% for EMB resistance.</p> <p>Conclusion</p> <p>The dominance of single gene mutations associated with the resistance to INH and RMP was observed in the codon 315 of the <it>katG </it>gene and codon 531 of the <it>rpoB </it>gene, respectively. The GenoType^®MTBDRplus assay is a sensitive and specific tool for diagnosis of resistance to INH, RMP and MDR. However, the GenoType^®MTBDRsl assay shows limitations in detecting resistance to EMB.</p

Top scoring pairs for feature selection in machine learning and applications to cancer outcome prediction

&lt;b&gt;Background&lt;/b&gt; The widely used k top scoring pair (k-TSP) algorithm is a simple yet powerful parameter-free classifier. It owes its success in many cancer microarray datasets to an effective feature selection algorithm that is based on relative expression ordering of gene pairs. However, its general robustness does not extend to some difficult datasets, such as those involving cancer outcome prediction, which may be due to the relatively simple voting scheme used by the classifier. We believe that the performance can be enhanced by separating its effective feature selection component and combining it with a powerful classifier such as the support vector machine (SVM). More generally the top scoring pairs generated by the k-TSP ranking algorithm can be used as a dimensionally reduced subspace for other machine learning classifiers.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Results&lt;/b&gt; We developed an approach integrating the k-TSP ranking algorithm (TSP) with other machine learning methods, allowing combination of the computationally efficient, multivariate feature ranking of k-TSP with multivariate classifiers such as SVM. We evaluated this hybrid scheme (k-TSP+SVM) in a range of simulated datasets with known data structures. As compared with other feature selection methods, such as a univariate method similar to Fisher's discriminant criterion (Fisher), or a recursive feature elimination embedded in SVM (RFE), TSP is increasingly more effective than the other two methods as the informative genes become progressively more correlated, which is demonstrated both in terms of the classification performance and the ability to recover true informative genes. We also applied this hybrid scheme to four cancer prognosis datasets, in which k-TSP+SVM outperforms k-TSP classifier in all datasets, and achieves either comparable or superior performance to that using SVM alone. In concurrence with what is observed in simulation, TSP appears to be a better feature selector than Fisher and RFE in some of the cancer datasets.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Conclusions&lt;/b&gt; The k-TSP ranking algorithm can be used as a computationally efficient, multivariate filter method for feature selection in machine learning. SVM in combination with k-TSP ranking algorithm outperforms k-TSP and SVM alone in simulated datasets and in some cancer prognosis datasets. Simulation studies suggest that as a feature selector, it is better tuned to certain data characteristics, i.e. correlations among informative genes, which is potentially interesting as an alternative feature ranking method in pathway analysis

Recovery in Stroke Rehabilitation through the Rotation of Preferred Directions Induced by Bimanual Movements: A Computational Study

Stroke patients recover more effectively when they are rehabilitated with bimanual movement rather than with unimanual movement; however, it remains unclear why bimanual movement is more effective for stroke recovery. Using a computational model of stroke recovery, this study suggests that bimanual movement facilitates the reorganization of a damaged motor cortex because this movement induces rotations in the preferred directions (PDs) of motor cortex neurons. Although the tuning curves of these neurons differ during unimanual and bimanual movement, changes in PD, but not changes in modulation depth, facilitate such reorganization. In addition, this reorganization was facilitated only when encoding PDs are rotated, but decoding PDs are not rotated. Bimanual movement facilitates reorganization because this movement changes neural activities through inter-hemispheric inhibition without changing cortical-spinal-muscle connections. Furthermore, stronger inter-hemispheric inhibition between motor cortices results in more effective reorganization. Thus, this study suggests that bimanual movement is effective for stroke rehabilitation because this movement rotates the encoding PDs of motor cortex neurons

Current challenges in software solutions for mass spectrometry-based quantitative proteomics

This work was in part supported by the PRIME-XS project, grant agreement number 262067, funded by the European Union seventh Framework Programme; The Netherlands Proteomics Centre, embedded in The Netherlands Genomics Initiative; The Netherlands Bioinformatics Centre; and the Centre for Biomedical Genetics (to S.C., B.B. and A.J.R.H); by NIH grants NCRR RR001614 and RR019934 (to the UCSF Mass Spectrometry Facility, director: A.L. Burlingame, P.B.); and by grants from the MRC, CR-UK, BBSRC and Barts and the London Charity (to P.C.

Geodiversity assessment of Paraná state (Brazil): an innovative approach

Geodiversity is considered as the natural range of geological, geomorphological, and soil features, including their assemblages, relationships, properties, interpretations, and systems. A method developed for the quantitative assessment of geodiversity was applied to Parana ́ , a Brazilian state with an area of about 200,000 km2. The method is based on the overlay of a grid over different maps at scales ranging from 1/500,000 to 1/650,000, with the final Geodiversity Index the sum of five partial indexes calculated on a 25 9 25 km grid. The partial indexes represent the main components of geodi- versity, including geology (stratigraphy and lithology), geomorphology, paleontology, and soils. The fifth partial index covers mineral occurrences of geodiversity, such precious stones and metals, energy and industrial minerals, mineral waters, and springs. The Geodiversity Index takes the form of an isoline map that can be used as a tool in land-use planning, particularly in identifying priority areas for conservation, management, and use of natural resources at the state level.The Portuguese authors express their gratitude for the financial support given by the Fundacao para a Ciencia e a Tecnologia to the Centro de Geologia da Universidade do Porto, which partially supports this research. The Brazilian author expresses his gratitude for the financial support given by the CNPq (Conselho Nacional de Desenvolvimento Cientifico e Tecnologico) (Process Number 200074/2011-3)

Lives saved by Global Fund-supported HIV/AIDS, tuberculosis and malaria programs: estimation approach and results between 2003 and end-2007

<p>Abstract</p> <p>Background</p> <p>Since 2003, the Global Fund has supported the scale-up of HIV/AIDS, tuberculosis and malaria control in low- and middle-income countries. This paper presents and discusses a methodology for estimating the lives saved through selected service deliveries reported to the Global Fund.</p> <p>Methods</p> <p>Global Fund-supported programs reported, by end-2007, 1.4 million HIV-infected persons on antiretroviral treatment (ARV), 3.3 million new smear-positive tuberculosis cases detected in DOTS (directly observed TB treatment, short course) programs, and 46 million insecticide-treated mosquito nets (ITNs) delivered. We estimated the corresponding lives saved using adaptations of existing epidemiological estimation models.</p> <p>Results</p> <p>By end-2007, an estimated 681,000 lives (95% uncertainty range 619,000-774,000) were saved and 1,097,000 (993,000-1,249,000) life-years gained by ARV. DOTS treatment would have saved 1.63 million lives (1.09 - 2.17 million) when compared against no treatment, or 408,000 lives (265,000-551,000) when compared against non-DOTS treatment. ITN distributions in countries with stable endemic <it>falciparum </it>malaria were estimated to have achieved protection from malaria for 26 million of child-years at risk cumulatively, resulting in 130,000 (27,000-232,000) under-5 deaths prevented.</p> <p>Conclusions</p> <p>These results illustrate the scale of mortality effects that supported programs may have achieved in recent years, despite margins of uncertainty and covering only selected intervention components. Evidence-based evaluation of disease impact of the programs supported by the Global Fund with international and in-country partners must be strengthened using population-level data on intervention coverage and demographic outcomes, information on quality of services, and trends in disease burdens recorded in national health information systems.</p