A multiple source model for 6 MV photon beam dose calculations using Monte Carlo

A multiple source model (MSM) for the 6 MV beam of a Varian Clinac 2300 C/D was developed by simulating radiation transport through the accelerator head for a set of square fields using the GEANT Monte Carlo (MC) code. The corresponding phase space (PS) data enabled the characterization of 12 sources representing the main components of the beam defining system. By parametrizing the source characteristics and by evaluating the dependence of the parameters on field size, it was possible to extend the validity of the model to arbitrary rectangular fields which include the central 3 x 3 cm2 field without additional precalculated PS data. Finally, a sampling procedure was developed in order to reproduce the PS data. To validate the MSM, the fluence, energy fluence and mean energy distributions determined from the original and the reproduced PS data were compared and showed very good agreement. In addition, the MC calculated primary energy spectrum was verified by an energy spectrum derived from transmission measurements. Comparisons of MC calculated depth dose curves and profiles, using original and PS data reproduced by the MSM, agree within 1% and 1 mm. Deviations from measured dose distributions are within 1.5% and 1 mm. However, the real beam leads to some larger deviations outside the geometrical beam area for large fields. Calculated output factors in 10 cm water depth agree within 1.5% with experimentally determined data. In conclusion, the MSM produces accurate PS data for MC photon dose calculations for the rectangular fields specified.

DISSECTION OF STRESS RESPONSE NETWORKS REGULATING MULTIPLE STRESSES IN RICE

Important food crops like rice are constantly exposed to various stresses that can have devastating effect on their survival and productivity. Being sessile, these highly evolved organisms have developed elaborate molecular machineries to sense a mixture of stress signals and elicit a precise response to minimize the damage. However, recent discoveries revealed that the interplay of these stress regulatory and signaling molecules is highly complex and remains largely unknown. In this work, we conducted large scale analysis of differential gene expression using advanced computational methods to dissect regulation of stress response which is at the heart of all molecular changes leading to the observed phenotypic susceptibility. One of the most important stress conditions in terms of loss of productivity is drought. We performed genomic and proteomic analysis of epigenetic and miRNA mechanisms in regulation of drought responsive genes in rice and found subsets of genes with striking properties. Overexpressed genesets included higher number of epigenetic marks, miRNA targets and transcription factors which regulate drought tolerance. On the other hand, underexpressed genesets were poor in above features but were rich in number of metabolic genes with multiple co-expression partners contributing majorly towards drought resistance. Identification and characterization of the patterns exhibited by differentially expressed genes hold key to uncover the synergistic and antagonistic components of the cross talk between stress response mechanisms. We performed meta-analysis on drought and bacterial stresses in rice and Arabidopsis, and identified hundreds of shared genes. We found high level of conservation of gene expression between these stresses. Weighted co-expression network analysis detected two tight clusters of genes made up of master transcription factors and signaling genes showing strikingly opposite expression status. To comprehensively identify the shared stress responsive genes between multiple abiotic and biotic stresses in rice, we performed meta-analyses of microarray studies from seven different abiotic and six biotic stresses separately and found more than thirteen hundred shared stress responsive genes. Various machine learning techniques utilizing these genes classified the stresses into two major classes' namely abiotic and biotic stresses and multiple classes of individual stresses with high accuracy and identified the top genes showing distinct patterns of expression. Functional enrichment and co-expression network analysis revealed the different roles of plant hormones, transcription factors in conserved and non-conserved genesets in regulation of stress response.

Hierarchical modeling gave plausible estimates of associations between metabolic syndrome and components of antiretroviral therapy

OBJECTIVE: Hierarchical modeling has been proposed as a solution to the multiple exposure problem. We estimate associations between metabolic syndrome and different components of antiretroviral therapy using both conventional and hierarchical models. STUDY DESIGN AND SETTING: We use discrete time survival analysis to estimate the association between metabolic syndrome and cumulative exposure to 16 antiretrovirals from four drug classes. We fit a hierarchical model where the drug class provides a prior model of the association between metabolic syndrome and exposure to each antiretroviral. RESULTS: One thousand two hundred and eighteen patients were followed for a median of 27 months, with 242 cases of metabolic syndrome (20%) at a rate of 7.5 cases per 100 patient years. Metabolic syndrome was more likely to develop in patients exposed to stavudine, but was less likely to develop in those exposed to atazanavir. The estimate for exposure to atazanavir increased from hazard ratio of 0.06 per 6 months' use in the conventional model to 0.37 in the hierarchical model (or from 0.57 to 0.81 when using spline-based covariate adjustment). CONCLUSION: These results are consistent with trials that show the disadvantage of stavudine and advantage of atazanavir relative to other drugs in their respective classes. The hierarchical model gave more plausible results than the equivalent conventional model.

Northern Hemisphere temperature reconstruction during the last millennium using multiple annual proxies

Previous studies have either exclusively used annual tree-ring data or have combined tree-ring series with other, lower temporal resolution proxy series. Both approaches can lead to significant uncertainties, as tree-rings may underestimate the amplitude of past temperature variations, and the validity of non-annual records cannot be clearly assessed. In this study, we assembled 45 published Northern Hemisphere (NH) temperature proxy records covering the past millennium, each of which satisfied 3 essential criteria: the series must be of annual resolution, span at least a thousand years, and represent an explicit temperature signal. Suitable climate archives included ice cores, varved lake sediments, tree-rings and speleothems. We reconstructed the average annual land temperature series for the NH over the last millennium by applying 3 different reconstruction techniques: (1) principal components (PC) plus second-order autoregressive model (AR2), (2) composite plus scale (CPS) and (3) regularized errors-in-variables approach (EIV). Our reconstruction is in excellent agreement with 6 climate model simulations (including the first 5 models derived from the fifth phase of the Coupled Model Intercomparison Project (CMIP5) and an earth system model of intermediate complexity (LOVECLIM), showing similar temperatures at multi-decadal timescales; however, all simulations appear to underestimate the temperature during the Medieval Warm Period (MWP). A comparison with other NH reconstructions shows that our results are consistent with earlier studies. These results indicate that well-validated annual proxy series should be used to minimize proxy-based artifacts, and that these proxy series contain sufficient information to reconstruct the low-frequency climate variability over the past millennium.

Clathrin heavy chain plays multiple roles in polarizing the Drosophila oocyte downstream of Bic-D

Bicaudal-D (Bic-D), Egalitarian (Egl), microtubules and their motors form a transport machinery that localizes a remarkable diversity of mRNAs to specific cellular regions during oogenesis and embryogenesis. Bic-D family proteins also promote dynein-dependent transport of Golgi vesicles, lipid droplets, synaptic vesicles and nuclei. However, the transport of these different cargoes is still poorly understood. We searched for novel proteins that either mediate Bic-Ddependent transport processes or are transported by them. Clathrin heavy chain (Chc) co-immunopurifies with Bic-D in embryos and ovaries, and a fraction of Chc colocalizes with Bic-D. Both proteins control posterior patterning of the Drosophila oocyte and endocytosis. Although the role of Chc in endocytosis is well established, our results show that Bic-D is also needed for the elevated endocytic activity at the posterior of the oocyte. Apart fromaffecting endocytosis indirectly by its role in osk mRNA localization, Bic-D is also required to transport Chc mRNA into the oocyte and for transport and proper localization of Chc protein to the oocyte cortex, pointing to an additional,more direct role of Bic-D in the endocytic pathway. Furthermore, similar to Bic-D, Chc also contributes to proper localization of osk mRNA and to oocyte growth. However, in contrast to other endocytic components and factors of the endocytic recycling pathway, such as Rabenosyn-5 (Rbsn-5) and Rab11, Chc is needed during early stages of oogenesis (from stage 6 onwards) to localize oskmRNA correctly.Moreover,we also uncovered a novel, presumably endocytosis-independent, role of Chc in the establishment of microtubule polarity in stage 6 oocytes.

Investigation of young water inflow in karst aquifers using SF6–CFC–3H/He–85Kr–39Ar and stable isotope components

Karst aquifers are known for their wide distribution of water transfer velocities. From this observation, a multiple geochemical tracer approach seems to be particularly well suited to provide a significant assessment of groundwater flows, but the choice of adapted tracers is essential. In this study, several common tracers in karst aquifers such as physicochemical parameters, major ions, stable isotopes, and d13C to more specific tracers such as dating tracers – 14C, 3H, 3H–3He, CFC-12, SF6 and 85Kr, and 39Ar – were used, in a fractured karstic carbonated aquifer located in Burgundy (France). The information carried by each tracer and the best sampling strategy are compared on the basis of geochemical monitoring done during several recharge events and over longer time periods (months to years). This study’s results demonstrate that at the seasonal and recharge event time scale, the variability of concentrations is low for most tracers due to the broad spectrum of groundwater mixings. The tracers used traditionally for the study of karst aquifers, i.e., physicochemical parameters and major ions, efficiently describe hydrological processes such as the direct and differed recharge, but require being monitored at short time steps during recharge events to be maximized. From stable isotopes, tritium, and Cl� contents, the proportion of the fast direct recharge by the largest porosity was estimated using a binary mixing model. The use of tracers such as CFC-12, SF6, and 85Kr in karst aquifers provides additional information, notably an estimation of apparent age, but they require good preliminary knowledge of the karst system to interpret the results suitably. The CFC-12 and SF6 methods efficiently determine the apparent age of baseflow, but it is preferable to sample the groundwater during the recharge event. Furthermore, these methods are based on different assumptions such as regional enrichment in atmospheric SF6, excess air, and flow models among others. 85Kr and 39Ar concentrations can potentially provide a more direct estimation of groundwater residence time. Conversely, the 3H–3He method is inefficient in the karst aquifer for dating due to 3He degassing.

Growth and development of body fat distribution from skinfold measurements: Longitudinal principal components

Longitudinal principal components analyses on a combination of four subcutaneous skinfolds (biceps, triceps, subscapular and suprailiac) were performed using data from the London Longitudinal Growth Study. The main objectives were to discover at what age during growth sex differences in body fat distribution occur and to see if there is continuity in body fatness and body fat distribution from childhood into the adult status (18 years). The analyses were done for four age sectors (3mon-3yrs, 3yrs-8yrs, 8yrs-18yrs and 3yrs-18yrs). Longitudinal principal component one (LPC1) for each age interval in both sexes represents the population mean fat curve. Component two (LPC2) is a velocity of fatness component. Component three (LPC3) in the 3mon-3yrs age sector represents infant fat wave in both sexes. In the next two age sectors component three in males represents peaks and shifts in fat growth (change in velocity), while in females it represents body fat distribution. Component four (LPC4) in the same two age sectors is a reversal in the sexes of the patterns seen for component three, i.e., in males it is body fat distribution and in females velocity shifts. Components five and above represent more complicated patterns of change (multiple increases and decreases across the age interval). In both sexes there is strong tracking in fatness from middle childhood to adolescence. In males only there is also a low to moderate tracking of infant fat with middle to late childhood fat. These data are strongly supported in the literature. Several factors are known to predict adult fatness among the most important being previous levels of fatness (at earlier ages) and the age at rebound. In addition we found that the velocity of fat change in middle childhood was highly predictive of later fatness (r $\approx -$0.7), even more so than age at rebound (r $\approx -$0.5). In contrast to fatness (LPC1), body fat distribution (LPC3-LPC4) did not track well even though significant components of body fat distribution occur at each age. Tracking of body fat distribution was higher in females than males. Sex differences in body fat distribution are non existent. Some sex differences are evident with the peripheral-to-central ratios after age 14 years. ^

THE EVALUATION OF PUBLIC HEALTH COMPONENTS OF INTERNATIONAL DISASTER RELIEF OPERATIONS: INDOCHINESE REFUGEES IN THAILAND, 1979-1982

Refugee populations suffer poor health status and yet the activities of refugee relief agencies in the public health sector have not been subjected previously to comprehensive evaluation. The purpose of this study was to examine the effectiveness and cost of the major public health service inputs of the international relief operation for Indochinese refugees in Thailand coordinated by the United Nations High Commissioner for Refugees (UNHCR). The investigator collected data from surveillance reports and agency records pertaining to 11 old refugee camps administered by the Government of Thailand Ministry of Interior (MOI) since an earlier refugee influx, and five new Khmer holding centers administered directly by UNHCR, from November, 1979, to March, 1982.^ Generous international funding permitted UNHCR to maintain a higher level of public health service inputs than refugees usually enjoyed in their countries of origin or than Thais around them enjoyed. Annual per capita expenditure for public health inputs averaged approximately US$151. Indochinese refugees in Thailand, for the most part, had access to adequate general food rations, to supplementary feeding programs, and to preventive health measures, and enjoyed high-quality medical services. Old refugee camps administered by MOI consistently received public health inputs of lower quantity and quality compared with new UNHCR-administered holding centers, despite comparable per capita expenditure after both types of camps had stabilized (static phase).^ Mortality and morbidity rates among new Khmer refugees were catastrophic during the emergency and transition phases of camp development. Health status in the refugee population during the static phase, however, was similar to, or better than, health status in the refugees' countries of origin or the Thai communities surrounding the camps. During the static phase, mortality and morbidity generally remained stable at roughly the same low levels in both types of camps.^ Furthermore, the results of multiple regression analyses demonstrated that combined public health inputs accounted for from one to 23 per cent of the variation in refugee mortality and morbidity. The direction of associations between some public health inputs and specific health outcome variables demonstrated no clear pattern. ^

Geochemistry, sediment components, and paleoproductivity reconstruction for the Miocene to early Pliocene sediments

We reconstruct paleoproductivity at three sites in the Atlantic Ocean (Ocean Drilling Program Sites 982, 925, and 1088) to investigate the presence and extent of the late Miocene to early Pliocene 'biogenic bloom' from 9 to 3 Ma. Our approach involves construction of multiple records including benthic foraminiferal and CaCO3 accumulation rates, Uvigerina counts, dissolution proxies, and geochemical tracers for biogenic and detrital fluxes. This time interval also contains the so-called late Miocene carbon isotope shift, a well-known decrease in benthic foraminiferal d13C values. We find that the timing of paleoproductivity maxima differs among the three sites. At Site 982 (North Atlantic), benthic foraminifera and CaCO3 accumulation were both at a maximum at ~5 Ma, with smaller peaks at ~6 Ma. The paleoproductivity maximum was centered earlier (~6.6-6.0 Ma) in the tropical Atlantic (Site 925). In the South Atlantic (Site 1088), paleoproductivity increased even earlier, between 8.2 Ma and 6.2 Ma, and remained relatively high until ~5.4 Ma. We note that there is some overlap between the interval of maximum productivity between Sites 925 and 1088, as well as the minor productivity increase at Site 982. We conclude that the paleoproductivity results support hypotheses aiming to place the biogenic bloom into a global context of enhanced productivity. In addition, we find that at all three sites the d13C shift is accompanied by carbonate dissolution. This observation is consistent with published studies that have sought a relationship between the late Miocene carbon isotope shift and carbonate preservation.