Teaching computers to fold proteins

A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The iterative update rule contains two thermodynamic averages which are estimated by (generalized ensemble) Monte Carlo. We test the learning algorithm on a Lennard-Jones (LJ) force field with a torsional angle degrees-of-freedom and a single-atom side-chain. In a test with 24 peptides of known structure, none folded correctly with the initial potential functions, but two-thirds came within 3{\AA} to their native fold after optimizing the potential functions.Comment: 4 pages, 3 figure

High precision U-PB geochronology and implications for the tectonic evolution of the Superior Province

The underlying mechanisms of Archean tectonics and the degree to which modern plate tectonic models are applicable early in Earth's history continue to be a subject of considerable debate. A precise knowledge of the timing of geological events is of the utmost importance in studying this problem. The high precision U-Pb method has been applied in recent years to rock units in many areas of the Superior Province. Most of these data have precisions of about + or - 2-3 Ma. The resulting detailed chronologies of local igneous development and the regional age relationships furnish tight constraints on any Archean tectonic model. Superior province terrains can be classified into 3 types: (1) low grade areas dominated by meta-volcanic rocks (greenstone belts); (2) high grade, largely metaplutonic areas with abundant orthogneiss and foliated to massive I-type granitoid bodies; and (3) high grade areas with abundant metasediments, paragneiss and S-type plutons. Most of the U-Pb age determinations have been done on type 1 terrains with very few having been done in type 3 terrains. A compilation of over 120 ages indicates that the major part of igneous activity took place in the period 2760-2670 Ma, known as the Kenoran event. This event was ubiquitous throughout the Superior Province

Visiting a Farm: An Exploratory Study of the Social Construction of Animal Farming in Norway and the Netherlands based on Sensory Perception

Most citizens in modern societies have little personal knowledge or experience of animal farming. This study explores the social construction of animal farming by studying how citizens perceive and evaluate modern farming after visiting a farm in real life. We wanted to understand how (non-farming) citizens develop an opinion of modern dairy farming when experiencing dairy farming in real life and practice, and how they translate what they see, smell and feel into an evaluative perception and mental image. We therefore conducted dairy farm visits with citizen panels in Norway and the Netherlands and asked the panel members to register what they saw, heard, smelled and felt and what they appreciated (or not) on the farm. The aspects that respondents registered could be grouped into four themes: the animals and their products, the rural landscape, farm practices and the farmer. When respondents described their experiences of these aspects on a specific farm, they appeared to look at them from three angles: modernity, tradition and naturality. Most respondents wanted farms to be modern, traditional as well as natural, but they were ready to negotiate and to accept compromises. Many respondents considered the farmer to be responsible for reconciling modernity, tradition and naturality. By taking different topics and issues into account and looking at animal farms from multiple angles, the respondents’ developed a balanced and nuanced opinion of animal farming. The image that they constructed was not dualistic (arcadia versus factory) but pluralistic, thus at the same time more complex but also more flexible than expected. We expect that the development of a pluralistic image and balanced opinion was facilitated through the direct experience of dairy farming and farm life. The article starts with a theoretical analysis and aims to contribute to recent debates in rural sociology in two ways: 1) it studies how material experience and mental perception interact in the construction of an evaluative image of animal farming; and 2) it explores the social construction of animal farming as embedded into to the construction of nature, rurality and human-animal relationships. It concludes by discussing the contribution of the findings to the ongoing theoretical debate in this fiel

U-Pb isotopic results for single shocked and polycrystalline zircons record 550-65.5-Ma ages for a K-T target site and 2700-1850-Ma ages for the Sudbury impact event

The refractory mineral zircon develops distinct morphological features during shock metamorphism and retains these features under conditions that would anneal them in other minerals. In addition, weakly shocked zircon grains give primary ages for the impact site, while highly reconstituted (polycrystalline) single grains give ages that approach the age of the impact event. Data for a series of originally coeval grains will define a mixing line that gives both of these ages providing that no subsequent geological disturbances have overprinted the isotopic systematics. In this study, we have shown that the three zircon grain types described by Bohor, from both K-T distal ejecta (Fireball layer, Raton Basin, Colorado) and the Onaping Formation, represent a progressive increase in impact-related morphological change that coincides with a progressive increase in isotopic resetting in zircons from the ejecta and basement rocks. Unshocked grains are least affected by isotopic resetting while polycrystalline grains are most affected. U-Pb isotopic results for 12 of 14 single zircon grains from the Fireball layer plot on or close to a line recording a primary age of 550 +/- 10 Ma and a secondary age of 65.5 +/- 3 Ma. Data for the least and most shocked grains plot closest to the primary and secondary ages respectively. The two other grains each give ages between 300 and 350 Ma. This implies that the target ejecta was dominated by 550-Ma rocks and that the recrystallization features of the zircon were superimposed during the impact event at 65.5 Ma. A predominant age of 550 Ma for zircons from the Fireball layer provides an excellent opportunity to identify the impact site and to test the hypothesis that multiple impacts occurred at this time. A volcanic origin for the Fireball layer is ruled out by shock-related morphological changes in zircon and the fact that the least shocked grains are old. Basement Levack gneisses north of the Sudbury structure have a primary age of 2711 Ma. Data for three single zircons from this rock, which record a progressive increase in shock features, are displaced 24, 36, and 45 percent along a Pb-loss line toward the 1850 +/- 1 Ma minimum age for the impact as defined by the age of the norite. Southeast of the structure three shocked grains from the Murray granite record a primary age of 2468 Ma and are displaced 24, 41, and 56 percent toward the 1853 +/- 4 Ma even as defined by coexisting titanite

Noncommutative Geometry from D0-branes in a Background B-field

We study D0-branes in type IIA on $T^2$ with a background B-field turned on. We calculate explicitly how the background B-field modifies the D0-brane action. The effect of the B-field is to replace ordinary multiplication with a noncommutative product. This enables us to find the matrix model for M-theory on $T^2$ with a background 3-form potential along the torus and the lightlike circle. This matrix model is exactly the non-local 2+1 dim SYM theory on a dual $T^2$ proposed by Connes, Douglas and Schwarz. We calculate the radii and the gauge coupling for the SYM on the dual $T^2$ for all choices of longitudinal momentum and membrane wrapping number on the $T^2$.Comment: 13pp, harvmac with five eps figures; final version in Nuclear Physics

Archived U-Pb (zircon) dates from southern New Brunswick

U-Pb (zircon) ages for eight samples from southern New Brunswick were determined during the early 1990's as part of a regional mapping and correlation program. Although most of the dates have been subsequently quoted in the literature through personal communications, and some preliminary isochron diagrams have been incorporated in papers, the results have not been published in their entirety. The units sampled and best estimates for their ages are the Lobster Brook Formation (554 ± 6 Ma), Leavitts Head Formation (554 ± 3 Ma), Ragged Falls Suite (553 ± 2 Ma), Mosquito Lake Road Formation (514 ± 2 Ma, maximum age), Bayswater Formation (436 ± 3 Ma), Centreton Granite (437 ± 3 Ma), felsic dyke of North Head, Grand Manan Island (396+3/-2 Ma), and Lake George Cupola, Lake George Mine (414 ± 2 Ma). RÉSUMÉ Des datations au U-Pb (à partir de zircon) de huit échantillons du Sud du Nouveau-Brunswick avaient été réalisées au début des années 90 dans le cadre d'un programme régional de cartographie et de corrélation. Même si la majorité des dates ont subséquemment été citées dans de la documentation par le biais de communications personnelles et que certains schémas isochrones préliminaires ont été incorporés dans des communications, les résultats n'ont pas été publiés dans leur intégralité. Les unités échantillonnées et leur meilleurs âges estimatifs comprennent la Formation de Lobster Brook (554 ± 6 Ma), la Formation de Leavitts Head (554 ± 3 Ma), le cortège de Ragged Falls (553 ± 2 Ma), la Formation de Mosquito Lake Road (514 ± 2 Ma, âge maximal), la Formation de Bayswater (436 ± 3 Ma), le granite de Centreton (437 ± 3 Ma), le dyke felsique de North Head, dans l'île Grand Manan (396+3/-2 Ma), et la coupole du lac George, à la mine du lac George (414 ± 2 Ma). [Traduit par la rédaction

Mixed Electron Emission from Lead Zirconate-Titanate Ceramics

Simultaneous ferroelectric and plasma emission from Pb(Zr,Ti)O3 was observed with only a negative driving pulse applied to the sample, and without an extraction potential on the electron collector. Plasma emission was a strong, inconsistent, and self-destructive process. In addition, a positive ion current was detected. Comparatively, ferroelectric emission was a relatively stable self-emission process, exhibiting no apparent delay time, and no positive ion current. The relationship between the switching and emission current of ferroelectric samples measured simultaneously cannot only be used to determine the existence of ferroelectric emission, but can also give direction to choosing suitable ferroelectric materials for emitter applications

Medical ovariectomy in menopausal breast cancer patients with high testosterone levels : a further step toward tailored therapy

Five years of adjuvant therapy with anti-estrogens reduce the incidence of disease progression by about 50% in estrogen receptor-positive breast cancer patients, but late relapse can still occur after anti-estrogens have been discontinued. In these patients, excessive androgen production may account for renewed excessive estrogen formation and increased risks of late relapse. In the 50% of patients who do not benefit with anti-estrogens, the effect of therapy is limited by de novo or acquired resistance to treatment. Androgen receptor and epidermal growth factor receptor overexpression are recognized mechanisms of endocrine resistance suggesting the involvement of androgens as activators of the androgen receptor pathway and as stimulators of epidermal growth factor synthesis and function. Data from a series of prospective studies on operable breast cancer patients, showing high serum testosterone levels are associated to increased risk of recurrence, provide further support to a role for androgens in breast cancer progression. According to the above reported evidence, we proposed to counteract excessive androgen production in the adjuvant setting of estrogen receptor-positive patients and suggested selecting postmenopausal patients with elevated levels of serum testosterone, marker of ovarian hyperandrogenemia, for adjuvant treatment with a gonadotropins-releasing hormone analogue (medical oophorectomy) in addition to standard therapy with anti-estrogens. The proposed approach provides an attempt of personalized medicine that needs to be further investigated in clinical trials