Introduction to protein folding for physicists

The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the conformational behaviour of flexible molecules is nothing more than a complex physical problem, increasingly more physicists are moving into the study of protein systems, bringing with them powerful mathematical and computational tools, as well as the sharp intuition and deep images inherent to the physics discipline. This work attempts to facilitate the first steps of such a transition. In order to achieve this goal, we provide an exhaustive account of the reasons underlying the protein folding problem enormous relevance and summarize the present-day status of the methods aimed to solving it. We also provide an introduction to the particular structure of these biological heteropolymers, and we physically define the problem stating the assumptions behind this (commonly implicit) definition. Finally, we review the 'special flavor' of statistical mechanics that is typically used to study the astronomically large phase spaces of macromolecules. Throughout the whole work, much material that is found scattered in the literature has been put together here to improve comprehension and to serve as a handy reference.Comment: 53 pages, 18 figures, the figures are at a low resolution due to arXiv restrictions, for high-res figures, go to http://www.pabloechenique.co

Nightly treatment of primary insomnia with prolonged release melatonin for 6 months: a randomized placebo controlled trial on age and endogenous melatonin as predictors of efficacy and safety

<p>Background: Melatonin is extensively used in the USA in a non-regulated manner for sleep disorders. Prolonged release melatonin (PRM) is licensed in Europe and other countries for the short term treatment of primary insomnia in patients aged 55 years and over. However, a clear definition of the target patient population and well-controlled studies of long-term efficacy and safety are lacking. It is known that melatonin production declines with age. Some young insomnia patients also may have low melatonin levels. The study investigated whether older age or low melatonin excretion is a better predictor of response to PRM, whether the efficacy observed in short-term studies is sustained during continued treatment and the long term safety of such treatment.</p> <p>Methods: Adult outpatients (791, aged 18-80 years) with primary insomnia, were treated with placebo (2 weeks) and then randomized, double-blind to 3 weeks with PRM or placebo nightly. PRM patients continued whereas placebo completers were re-randomized 1:1 to PRM or placebo for 26 weeks with 2 weeks of single-blind placebo run-out. Main outcome measures were sleep latency derived from a sleep diary, Pittsburgh Sleep Quality Index (PSQI), Quality of Life (World Health Organzaton-5) Clinical Global Impression of Improvement (CGI-I) and adverse effects and vital signs recorded at each visit.</p> <p>Results: On the primary efficacy variable, sleep latency, the effects of PRM (3 weeks) in patients with low endogenous melatonin (6-sulphatoxymelatonin [6-SMT] ≤8 μg/night) regardless of age did not differ from the placebo, whereas PRM significantly reduced sleep latency compared to the placebo in elderly patients regardless of melatonin levels (-19.1 versus -1.7 min; P = 0.002). The effects on sleep latency and additional sleep and daytime parameters that improved with PRM were maintained or enhanced over the 6-month period with no signs of tolerance. Most adverse events were mild in severity with no clinically relevant differences between PRM and placebo for any safety outcome.</p> <p>Conclusions: The results demonstrate short- and long-term efficacy and safety of PRM in elderly insomnia patients. Low melatonin production regardless of age is not useful in predicting responses to melatonin therapy in insomnia. The age cut-off for response warrants further investigation.</p&gt

SPARTAN: a global network to evaluate and enhance satellite-based estimates of ground-level particulate matter for global health applications

Ground-based observations have insufficient spatial coverage to assess long-term human exposure to fine particulate matter (PM2.5) at the global scale. Satellite remote sensing offers a promising approach to provide information on both short-and long-term exposure to PM2.5 at local-to-global scales, but there are limitations and outstanding questions about the accuracy and precision with which ground-level aerosol mass concentrations can be inferred from satellite remote sensing alone. A key source of uncertainty is the global distribution of the relationship between annual average PM2.5 and discontinuous satellite observations of columnar aerosol optical depth (AOD). We have initiated a global network of ground-level monitoring stations designed to evaluate and enhance satellite remote sensing estimates for application in health-effects research and risk assessment. This Surface PARTiculate mAtter Network (SPARTAN) includes a global federation of ground-level monitors of hourly PM2.5 situated primarily in highly populated regions and collocated with existing ground-based sun photometers that measure AOD. The instruments, a three-wavelength nephelometer and impaction filter sampler for both PM2.5 and PM10, are highly autonomous. Hourly PM2.5 concentrations are inferred from the combination of weighed filters and nephelometer data. Data from existing networks were used to develop and evaluate network sampling characteristics. SPARTAN filters are analyzed for mass, black carbon, water-soluble ions, and metals. These measurements provide, in a variety of regions around the world, the key data required to evaluate and enhance satellite-based PM2.5 estimates used for assessing the health effects of aerosols. Mean PM2.5 concentrations across sites vary by more than 1 order of magnitude. Our initial measurements indicate that the ratio of AOD to ground-level PM2.5 is driven temporally and spatially by the vertical profile in aerosol scattering. Spatially this ratio is also strongly influenced by the mass scattering efficiency.Fil: Snider, G.. Dalhousie University Halifax; CanadáFil: Weagle, C. L.. Dalhousie University Halifax; CanadáFil: Martin, R. V.. Dalhousie University Halifax; Canadá. University of Cambridge; Reino UnidoFil: van Donkelaar, A.. Dalhousie University Halifax; CanadáFil: Conrad, K.. Dalhousie University Halifax; CanadáFil: Cunningham, D.. Dalhousie University Halifax; CanadáFil: Gordon, C.. Dalhousie University Halifax; CanadáFil: Zwicker, M.. Dalhousie University Halifax; CanadáFil: Akoshile, C.. University of Ilorin; NigeriaFil: Artaxo, P.. Governo Do Estado de Sao Paulo; BrasilFil: Anh, N. X.. Vietnam Academy of Science and Technology. Institute of Geophysics; VietnamFil: Brook, J.. University of Toronto; CanadáFil: Dong, J.. Tsinghua University; ChinaFil: Garland, R. M.. North-West University; SudáfricaFil: Greenwald, R.. Rollins School of Public Health; Estados UnidosFil: Griffith, D.. Council for Scientific and Industrial Research; SudáfricaFil: He, K.. Tsinghua University; ChinaFil: Holben, B. N.. NASA Goddard Space Flight Center; Estados UnidosFil: Kahn, R.. NASA Goddard Space Flight Center; Estados UnidosFil: Koren, I.. Weizmann Institute Of Science Israel; IsraelFil: Lagrosas, N.. Manila Observatory, Ateneo de Manila University campus; FilipinasFil: Lestari, P.. Institut Teknologi Bandung; IndonesiaFil: Ma, Z.. Rollins School of Public Health; Estados UnidosFil: Vanderlei Martins, J.. University of Maryland; Estados UnidosFil: Quel, Eduardo Jaime. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Rudich, Y.. Weizmann Institute Of Science Israel; IsraelFil: Salam, A.. University Of Dhaka; BangladeshFil: Tripathi, S. N.. Indian Institute Of Technology, Kanpur; IndiaFil: Yu, C.. Rollins School of Public Health; Estados UnidosFil: Zhang, Q.. Tsinghua University; ChinaFil: Zhang, Y.. Tsinghua University; ChinaFil: Brauer, M.. University of British Columbia; CanadáFil: Cohen, A.. Health Effects Institute; Estados UnidosFil: Gibson, M. D.. Dalhousie University Halifax; CanadáFil: Liu, Y.. Rollins School of Public Health; Estados Unido

Education for sustainable development: A study in adolescent perception changes towards sustainability following a strategic planning-based intervention-the young persons' plan for the planet program

© 2019 by the authors. In 2016, the United Nations (UN) launched the 17 Sustainable Development Goals (SDGs) as a framework for sustainable development and a sustainable future. However, the global challenge has been to engage, connect, and empower communities, particularly young people, to both understand and deliver the 17 SDGs. In this study, we show the benefit of a strategic planning-based experiential learning tool, the Young Persons' Plan for the Planet (YPPP) Program, to improve the underlying competencies of Australian and Mauritian adolescents in increasing understanding and delivering the SDGs. The study was conducted with 300 middle to senior high school students, in 25 schools throughout Australia and Mauritius, over an 18-month period. The intervention included the development of research, strategic planning, management, STEM (Science Technology, Engineering, Maths) and global competency skills in the students, to enable them to build and deliver regional and national SDG plans. Research methods included pre- and post-intervention testing of the attitudes of these students to sustainable development outcomes and compared these attitudes to subsets of scientists and the Australian national population. Our results, from both qualitative and quantitative evidence, demonstrate significant improvements in these adolescents' appreciation of, and attitudes towards, the SDGs and sustainable outcomes, across a range of key parameters. The results from the 76 students who attended the International Conference in Mauritius in December 2018 demonstrate significant improvements in mean levels of understanding, and attitudes of the students towards the SDGs awareness (+85%), understanding/engagement (+75%), motivation (+57%), and action orientation/empowerment (+66%). These changes were tested across a range of socio-demographic, geographic, and cultural parameters, with consistent results. These findings have significant implications for the challenge of sustainable education and achieving community engagement and action towards the SDGs in Australia and Mauritius, particularly for young people. As the intervention can be replicated and scaled, the findings also highlight the opportunity to extend both the research and this type of experiential learning intervention across both broader geographies and other generation and community segments

The Sloan Digital Sky Survey Quasar Catalog V. Seventh Data Release

We present the fifth edition of the Sloan Digital Sky Survey (SDSS) Quasar Catalog, which is based upon the SDSS Seventh Data Release. The catalog, which contains 105,783 spectroscopically confirmed quasars, represents the conclusion of the SDSS-I and SDSS-II quasar survey. The catalog consists of the SDSS objects that have luminosities larger than M_i = -22.0 (in a cosmology with H_0 = 70 km/s/Mpc Omega_M = 0.3, and Omega_Lambda = 0.7) have at least one emission line with FWHM larger than 1000 km/s or have interesting/complex absorption features, are fainter than i > 15.0 and have highly reliable redshifts. The catalog covers an area of 9380 deg^2. The quasar redshifts range from 0.065 to 5.46, with a median value of 1.49; the catalog includes 1248 quasars at redshifts greater than four, of which 56 are at redshifts greater than five. The catalog contains 9210 quasars with i < 18; slightly over half of the entries have i< 19. For each object the catalog presents positions accurate to better than 0.1" rms per coordinate, five-band (ugriz) CCD-based photometry with typical accuracy of 0.03 mag, and information on the morphology and selection method. The catalog also contains radio, near-infrared, and X-ray emission properties of the quasars, when available, from other large-area surveys. The calibrated digital spectra cover the wavelength region 3800-9200 Ang. at a spectral resolution R = 2000 the spectra can be retrieved from the SDSS public database using the information provided in the catalog. Over 96% of the objects in the catalog were discovered by the SDSS. We also include a supplemental list of an additional 207 quasars with SDSS spectra whose archive photometric information is incomplete.Comment: Accepted, to appear in AJ, 7 figures, electronic version of Table 2 is available, see http://www.sdss.org/dr7/products/value_added/qsocat_dr7.htm

Leftovers:The presence of manufacture-derived aquatic lipids in Alaskan Pottery

Lipids preserved within the walls of ancient pottery vessels are routinely analysed to reveal their original contents. The provenience of aquatic lipids in pottery is generally connected to vessel function (e.g., for cooking or storing fish, shellfish and aquatic mammals). However, ethnographic reports from early historic Alaska mention the use of aquatic oils for waterproofing low-fired pottery. Results of lipid residue studies on Alaskan pottery reflect an exclusive function of pottery to process aquatic resources. However, can one be sure these residues are the product of vessel function and not a remnant of the manufacturing process? The study presents the results of an experiment where the preservation of aquatic lipids during the firing process at different temperatures was measured. It was found that nearly all lipids were removed at firing temperatures of ≥ 400°C. Petrographic analysis of Alaskan pottery samples indicates that firing temperatures were generally &gt; 550°C but &lt; 800°C. The contribution of pre-firing manufacture-derived lipids to samples fired at these temperatures may be regarded as negligible. While the possible presence of aquatic lipids from post-firing surface treatments cannot be excluded, such treatments appear unnecessary for well-fired pottery.</p