A modified gambler's ruin model of polyethylene chains in the amorphous region.

Polyethylene chains in the amorphous region between two crystalline lamellae M unit apart are modeled as random walks with one-step memory on a cubic lattice between two absorbing boundaries. These walks avoid the two preceding steps, though they are not true self-avoiding walks. Systems of difference equations are introduced to calculate the statistics of the restricted random walks. They yield that the fraction of loops is (2M - 2)/(2M + 1), the fraction of ties 3/(2M + 1), the average length of loops 2M - 0.5, the average length of ties 2/3M2 + 2/3M - 4/3, the average length of walks equals 3M - 3, the variance of the loop length 16/15M3 + O(M2), the variance of the tie length 28/45M4 + O(M3), and the variance of the walk length 2M3 + O(M2).

Ras-catalyzed hydrolysis of GTP: a new perspective from model studies.

Despite the biological and medical importance of signal transduction via Ras proteins and despite considerable kinetic and structural studies of wild-type and mutant Ras proteins, the mechanism of Ras-catalyzed GTP hydrolysis remains controversial. We take a different approach to this problem: the uncatalyzed hydrolysis of GTP is analyzed, and the understanding derived is applied to the Ras-catalyzed reaction. Evaluation of previous mechanistic proposals from this chemical perspective suggests that proton abstraction from the attacking water by a general base and stabilization of charge development on the gamma-phosphoryl oxygen atoms would not be catalytic. Rather, this analysis focuses attention on the GDP leaving group, including the beta-gamma bridge oxygen of GTP, the atom that undergoes the largest change in charge in going from the ground state to the transition state. This leads to a new catalytic proposal in which a hydrogen bond from the backbone amide of Gly-13 to this bridge oxygen is strengthened in the transition state relative to the ground state, within an active site that provides a template complementary to the transition state. Strengthened transition state interactions of the active site lysine, Lys-16, with the beta-nonbridging phosphoryl oxygens and a network of interactions that positions the nucleophilic water molecule and gamma-phosphoryl group with respect to one another may also contribute to catalysis. It is speculated that a significant fraction of the GAP-activated GTPase activity of Ras arises from an additional interaction of the beta-gamma bridge oxygen with an Arg side chain that is provided in trans by GAP. The conclusions for Ras and related G proteins are expected to apply more widely to other enzymes that catalyze phosphoryl (-PO(3)2-) transfer, including kinases and phosphatases.

Elevated interleukin 6 is induced by prostaglandin E2 in a murine model of inflammation: possible role of cyclooxygenase-2.

Injection of mineral oils such as pristane into the peritoneal cavities of BALB/c mice results in a chronic peritonitis associated with high tissue levels of interleukin 6 (IL-6). Here we show that increased prostaglandin E2 (PGE2) synthesis causes induction of IL-6 and that expression of an inducible cyclooxygenase, Cox-2, may mediate this process. Levels of both PGE2 and IL-6 are elevated in inflammatory exudates from pristane-treated mice compared with lavage samples from untreated mice. The Cox-2 gene is induced in the peritoneal macrophage fraction isolated from the mice. A cause and effect relationship between increased macrophage PGE2 and IL-6 production is shown in vitro. When peritoneal macrophages are activated with an inflammatory stimulus (polymerized albumin), the Cox-2 gene is induced and secretion of PGE2 and IL-6 increases, with elevated PGE2 appearing before IL-6. Cotreatment with 1 microM indomethacin inhibits PGE2 production by the cells and reduces the induction of IL-6 mRNA but has no effect on Cox-2 mRNA, consistent with the fact that the drug inhibits catalytic activity of the cyclooxygenase but does not affect expression of the gene. Addition of exogenous PGE2 to macrophages induces IL-6 protein and mRNA synthesis, indicating that the eicosanoid stimulates IL-6 production at the level of gene expression. PGE2-stimulated IL-6 production is unaffected by addition of indomethacin. Taken together with the earlier finding that indomethacin diminishes the elevation of IL-6 in pristane-treated mice, the results show that PGE2 can induce IL-6 production in vivo and implicate expression of the Cox-2 gene in the regulation of this cytokine.

Switch from a type 2 to a type 1 T helper cell response and cure of established Leishmania major infection in mice is induced by combined therapy with interleukin 12 and Pentostam.

Successful treatment in allergic, autoimmune, and infectious diseases often requires altering the nature of a detrimental immune response mediated by a particular CD4+ T helper (Th) cell subset. While several factors contribute to the development of CD4+ Th1 and Th2 cells, the requirements for switching an established response are not understood. Here we use infection with Leishmania major as a model to investigate those requirements. We report that treatment with interleukin 12 (IL-12), in combination with the antimony-based leishmanicidal drug Pentostam, induces healing in L. major-infected mice and that healing is associated with a switch from a Th2 to a Th1 response. The data suggest that decreasing antigen levels may be required for IL-12 to inhibit a Th2 response and enhance a Th1 response. These observations are important for treatment of nonhealing forms of human leishmaniasis and also demonstrate that in a chronic infectious disease an inappropriate Th2 response can be switched to an effective Th1 response.

Constraining the GRB-Magnetar Model by Means of the Galactic Pulsar Population

A large fraction of Gamma-ray bursts (GRBs) displays an X-ray plateau phase within <105 s from the prompt emission, proposed to be powered by the spin-down energy of a rapidly spinning newly born magnetar. In this work we use the properties of the Galactic neutron star population to constrain the GRB-magnetar scenario. We re-analyze the X-ray plateaus of all Swift GRBs with known redshift, between 2005 January and 2014 August. From the derived initial magnetic field distribution for the possible magnetars left behind by the GRBs, we study the evolution and properties of a simulated GRB-magnetar population using numerical simulations of magnetic field evolution, coupled with Monte Carlo simulations of Pulsar Population Synthesis in our Galaxy. We find that if the GRB X-ray plateaus are powered by the rotational energy of a newly formed magnetar, the current observational properties of the Galactic magnetar population are not compatible with being formed within the GRB scenario (regardless of the GRB type or rate at z = 0). Direct consequences would be that we should allow the existence of magnetars and "super-magnetars" having different progenitors, and that Type Ib/c SNe related to Long GRBs form systematically neutron stars with higher initial magnetic fields. We put an upper limit of ≤16 "super-magnetars" formed by a GRB in our Galaxy in the past Myr (at 99% c.l.). This limit is somewhat smaller than what is roughly expected from Long GRB rates, although the very large uncertainties do not allow us to draw strong conclusion in this respect.

Geochemistry and age model of sediment core BDP96-1

Within the framework of the Baikal Drilling Project (BDP), a 192 m long sediment core (BDP-96-1) was recovered from the Academician Ridge, a submerged topographic high between the North and Central Basins of Lake Baikal. Sedimentological, clay mineralogical and geochemical investigations were carried out on the core interval between 90 and 124 m depth, corresponding to ca. 2.4-3.4 Ma. The aim was to reconstruct the climatic and tectonic history of the continental region during the intensification of Northern Hemisphere glaciation in Late Pliocene time. A major climate change occurred in the Lake Baikal area at about 2.65 Ma. Enhanced physical weathering in the catchment, mirrored in the illite to smectite ratio, and temporarily reduced bioproduction in the lake, reflected by the diatom abundance, evidence a change towards a colder and more arid climate, probably associated with an intensification of the Siberian High. In addition, the coincident onset of distinct fluctuations in these parameters and in the Zr/Al ratio suggests the beginning of the Late Cenozoic high amplitude climate cycles at about 2.65 Ma. Fluctuations in the Zr/Al ratio are traced back to changes in the aeolian input, with high values in warmer, more humid phases due to a weaker Siberian High. Assuming that the sand content in the sediment reflects tectonic pulses, the Lake Baikal area was tectonically active during the entire investigated period, but in particular around 2.65 Ma. Tectonic movements have likely led to a gradual catchment change since about 3.15 Ma from the western towards the eastern lake surroundings, as indicated in the geochemistry and clay mineralogy of the sediments. The strong coincidence between tectonic and climatic changes in the Baikal area hints at the Himalayan uplift being one of the triggers for the Northern Hemisphere Glaciation.

Sedimentological investigations and age model on sediment core PS2561-2

Benthic d13C values (F. wuellerstorfi), kaolinite/chlorite ratios and sortable silt median grain sizes in sediments of a core from the abyssal Agulhas Basin record the varying impact of North Atlantic Deep Water (NADW) and Antarctic Bottom Water (AABW) during the last 200 ka. The data indicate that NADW influence decreased during glacials and increased during interglacials, in concert with the global climatic changes of the late Quaternary. In contrast, AABW displays a much more complex behaviour. Two independent modes of deep-water formation contributed to the AABW production in the Weddell Sea: 1) brine rejection during sea ice formation in polynyas and in the sea ice zone (Polynya Mode) and 2) super-cooling of Ice Shelf Water (ISW) beneath the Antarctic ice shelves (Ice Shelf Mode). Varying contributions of the two modes lead to a high millennial-scale variability of AABW production and export to the Agulhas Basin. Highest rates of AABW production occur during early glacials when increased sea ice formation and an active ISW production formed substantial amounts of deep water. Once full glacial conditions were reached and the Antarctic ice sheet grounded on the shelf, ISW production shut down and only brine rejection generated moderate amounts of deep water. AABW production rates dropped to an absolute minimum during Terminations I and II and the Marine Isotope Transition (MIS) 4/3 transition. Reduced sea ice formation concurrent with an enhanced fresh water influx from melting ice lowered the density of the surface water in the Weddell Sea, thus further reducing deep water formation via brine rejection, while the ISW formation was not yet operating again. During interglacials and the moderate interglacial MIS 3 both brine formation and ISW production were operating, contributing various amounts to AABW formation in the Weddell Sea.

Chemical composition of the soluble fraction of oxidate portions of Lakes Shebadnowan ferromanganese concretions

Shebandowan Lakes, Ontario, are the site of at least 49 shallow (2-12 m) ferromanganese concretion deposits, widely distributed throughout the 48 km of the watercourse. X-ray diffraction and Mossbauer methods have revealed the presence of goethite in some of the concretions. Chemical analyses of the acid soluble portions of 72 samples gave an average composition of 43.1% Fe and 5.65% Mn with a low content of trace elements. The Shebandowan concretions are among the richest in iron of lake concretions reported, possibly because only the acid soluble portion was analysed. Their low content of trace elements suggests rapid growth rates and a relatively young age. A positive correlation was found between Mn and K, Ca, Mg, Cu, Ni, and Co and the relationship between the last three and Mn was deemed significant. Zn was independent of association with either Mn and Fe, probably due to the presence locally of zinc sulphide deposits. Analyses of lake bottom and influent waters suggested that frequent resampling of the sites would be required throughout the year to permit meaningful interpretation of the effect of water composition of concretions. Analyses of sediment cores from 20 concretion sites indicated an upward increase in Fe and Mn and in the Mn/Fe ratio, consistent with the model of upward migration of the elements, where Mn is more mobile than Fe. This study concludes that a considerable proportion of the elements have been supplied to the Shebandowan concretions via the diagenetic process; generally a minor fraction of the elements has been abstracted directly from the superjacent water.

Age model and ostracod countings from IODP Site 306-U1314

We present a detailed study of glacial/interglacial deep sea benthic ostracod assemblage variability at IODP Site U1314 (subpolar North Atlantic) in relation to the history of ice-rafting events and changes in deep ocean circulation over the past 170 ky. Our records of ostracod diversity, abundance and dissolution and sediment properties (IRD and CaCO3) show an excellent correspondence to high amplitude orbital and millennial variability observed in the climate records (d13C and d18O) from neighboring deep water sites, suggesting that the benthic meiofauna fluctuates synchronously with the prevailing oceanographic conditions (surface ocean conditions, deep ocean circulation and water temperature and food flux). Krithe (dominant), Argilloecia and Cytheropteron are the most abundant and diverse genera in association with Rockallia enigmatica. Three ostracod assemblages are recognized. The genera Pennyella, Argilloecia, Pelecocythere, Ambocythere, Pseudobosquetina, Bradleya and Nannocythere are associated with interglacials and interstadials, and possibly reflect increased flux of food to the sediments and more vigorous NADW formation. A transitional assemblage composed of species of Cytheropteron, Xestoleberis and Eucythere is restricted to climatic transitions and indicate moderate environmental conditions and seasonal productivity. A glacial/stadial assemblage is characterized by a temporal predominance of either intermediate-depth and shallow water Arctic/subarctic species (belonging to Cytheropteron, Polycope, Pedicythere, Swainocythere, Cluthia, Heterocyprideis, Elofsonella and Finmarchinella) or abyssal North Atlantic ostracods (Bythocythere, Dutoitella, Bathycythere and Bythocypris). The influx of high latitude taxa can be partially explained by ice-rafting, but may also represent a shift of the location of intermediate and deep water convection to the area south of Iceland. Therefore the combination of species characteristic of different watermasses during glacials may reflect shifts in the influence of high nutrient southern source water (e.g. AABW) vs. low nutrient GNAIW during glacials.

Using DEM to model ore breakage within a pilot scale SAG mill

The best accepted method for design of autogenous and semi-autogenous (AG/SAG) mills is to carry out pilot scale test work using a 1.8 m diameter by 0.6 m long pilot scale test mill. The load in such a mill typically contains 250,000-450,000 particles larger than 6 mm, allowing correct representation of more than 90% of the charge in Discrete Element Method (DEM) simulations. Most AG/SAG mills use discharge grate slots which are 15 mm or more in width. The mass in each size fraction usually decreases rapidly below grate size. This scale of DEM model is now within the possible range of standard workstations running an efficient DEM code. This paper describes various ways of extracting collision data front the DEM model and translating it into breakage estimates. Account is taken of the different breakage mechanisms (impact and abrasion) and of the specific impact histories of the particles in order to assess the breakage rates for various size fractions in the mills. At some future time, the integration of smoothed particle hydrodynamics with DEM will allow for the inclusion of slurry within the pilot mill simulation. (C) 2004 Elsevier Ltd. All rights reserved.

A simulation model of cereal-legume intercropping systems for semi-arid regions I. Model development

Cereal-legume intercropping plays an important role in subsistence food production in developing countries, especially in situations of limited water resources. Crop simulation can be used to assess risk for intercrop productivity over time and space. In this study, a simple model for intercropping was developed for cereal and legume growth and yield, under semi-arid conditions. The model is based on radiation interception and use, and incorporates a water stress factor. Total dry matter and yield are functions of photosynthetically active radiation (PAR), the fraction of radiation intercepted and radiation use efficiency (RUE). One of two PAR sub-models was used to estimate PAR from solar radiation; either PAR is 50% of solar radiation or the ratio of PAR to solar radiation (PAR/SR) is a function of the clearness index (K-T). The fraction of radiation intercepted was calculated either based on Beer's Law with crop extinction coefficients (K) from field experiments or from previous reports. RUE was calculated as a function of available soil water to a depth of 900 mm (ASW). Either the soil water balance method or the decay curve approach was used to determine ASW. Thus, two alternatives for each of three factors, i.e., PAR/SR, K and ASW, were considered, giving eight possible models (2 methods x 3 factors). The model calibration and validation were carried out with maize-bean intercropping systems using data collected in a semi-arid region (Bloemfontein, Free State, South Africa) during seven growing seasons (1996/1997-2002/2003). The combination of PAR estimated from the clearness index, a crop extinction coefficient from the field experiment and the decay curve model gave the most reasonable and acceptable result. The intercrop model developed in this study is simple, so this modelling approach can be employed to develop other cereal-legume intercrop models for semi-arid regions. (c) 2004 Elsevier B.V. All rights reserved.

Iron (Fe) bioavailability and the distribution of anti-Fe nutrition biochemicals in the unpolished, and bran fraction of five rice gei polished grain riotypes

Iron (Fe) bioavailability in unpolished, polished grain and bran fraction of five rice genotypes with a range of Fe contents was measured by in vitro digestion and cultured Caco-2 cells of cooked grain. There was a significant difference in Fe bioavailability among the five rice genotypes tested, in both the unpolished and polished grain. The range of Fe bioavailability variation in polished rice was much wider than that of unpolished, suggesting the importance of using Fe levels and bioavailability in polished rice grain as the basis for selecting high-Fe rice cultivars for both agronomic and breeding purposes. Milling and polishing the grain to produce polished (or white) rice increased Fe bioavailability in all genotypes. Iron bioavailability in polished rice was high in the UBON2 and Nishiki, intermediate in both IR68144 and KDML105, and low in CMU122. All genotypes had low bioavailability of Fe in bran fraction compared to unpolished and polished grain, except in CMU122. CMU122 contained the lowest level of bioavailable Fe in unpolished and polished grain and bran, because of the dark purple pericarp colored grain and associated tannin content. The level of bioavailable Fe was not significantly correlated with grain Fe concentration or grain phytate levels among these five genotypes tested. The negative relationship between Fe bioavailability and the levels of total extractable phenol was only observed in unpolished (r = -0.83**) and bran fraction (r = -0.50*). The present results suggested that total extractable phenol and tannin contents could also contribute to lowering bioavailability of Fe in rice grain, in addition to phytate. (c) 2006 Society of Chemical Industry

Blur adaptation explained by a norm-based model of contrast adaptation

Adapting to blurred images makes in-focus images look too sharp, and vice-versa (Webster et al, 2002 Nature Neuroscience 5 839 - 840). We asked how such blur adaptation is related to contrast adaptation. Georgeson (1985 Spatial Vision 1 103 - 112) found that grating contrast adaptation followed a subtractive rule: perceived (matched) contrast of a grating was fairly well predicted by subtracting some fraction k(~0.3) of the adapting contrast from the test contrast. Here we apply that rule to the responses of a set of spatial filters at different scales and orientations. Blur is encoded by the pattern of filter response magnitudes over scale. We tested two versions - the 'norm model' and 'fatigue model' - against blur-matching data obtained after adaptation to sharpened, in-focus or blurred images. In the fatigue model, filter responses are simply reduced by exposure to the adapter. In the norm model, (a) the visual system is pre-adapted to a focused world and (b) discrepancy between observed and expected responses to the experimental adapter leads to additional reduction (or enhancement) of filter responses during experimental adaptation. The two models are closely related, but only the norm model gave a satisfactory account of results across the four experiments analysed, with one free parameter k. This model implies that the visual system is pre-adapted to focused images, that adapting to in-focus or blank images produces no change in adaptation, and that adapting to sharpened or blurred images changes the state of adaptation, leading to changes in perceived blur or sharpness.

Methodology for development of a physiological model incorporating CYP3A and P-glycoprotein for the prediction of intestinal drug absorption

The small intestine poses a major barrier to the efficient absorption of orally administered therapeutics. Intestinal epithelial cells are an extremely important site for extrahepatic clearance, primarily due to prominent P-glycoprotein-mediated active efflux and the presence of cytochrome P450s. We describe a physiologically based pharmacokinetic model which incorporates geometric variations, pH alterations and descriptions of the abundance and distribution of cytochrome 3A and P-glycoprotein along the length of the small intestine. Simulations using preclinical in vitro data for model drugs were performed to establish the influence of P-glycoprotein efflux, cytochrome 3A metabolism and passive permeability on drug available for absorption within the enterocytes. The fraction of drug escaping the enterocyte (F(G)) for 10 cytochrome 3A substrates with a range of intrinsic metabolic clearances were simulated. Following incorporation of P-glycoprotein in vitro efflux ratios all predicted F(G) values were within 20% of observed in vivo F(G). The presence of P-glycoprotein increased the level of cytochrome 3A drug metabolism by up to 12-fold in the distal intestine. F(G) was highly sensitive to changes in intrinsic metabolic clearance but less sensitive to changes in intestinal drug permeability. The model will be valuable for quantifying aspects of intestinal drug absorption and distribution.

Development of a physiologically-based pharmacokinetic model of the rat central nervous system

Central nervous system (CNS) drug disposition is dictated by a drug’s physicochemical properties and its ability to permeate physiological barriers. The blood–brain barrier (BBB), blood-cerebrospinal fluid barrier and centrally located drug transporter proteins influence drug disposition within the central nervous system. Attainment of adequate brain-to-plasma and cerebrospinal fluid-to-plasma partitioning is important in determining the efficacy of centrally acting therapeutics. We have developed a physiologically-based pharmacokinetic model of the rat CNS which incorporates brain interstitial fluid (ISF), choroidal epithelial and total cerebrospinal fluid (CSF) compartments and accurately predicts CNS pharmacokinetics. The model yielded reasonable predictions of unbound brain-to-plasma partition ratio (Kpuu,brain) and CSF:plasma ratio (CSF:Plasmau) using a series of in vitro permeability and unbound fraction parameters. When using in vitro permeability data obtained from L-mdr1a cells to estimate rat in vivo permeability, the model successfully predicted, to within 4-fold, Kpuu,brain and CSF:Plasmau for 81.5% of compounds simulated. The model presented allows for simultaneous simulation and analysis of both brain biophase and CSF to accurately predict CNS pharmacokinetics from preclinical drug parameters routinely available during discovery and development pathways.