Spatial regularity of InAs-GaAs quantum dots: quantifying the dependence of lateral ordering on growth rate.

The lateral ordering of arrays of self-assembled InAs-GaAs quantum dots (QDs) has been quantified as a function of growth rate, using the Hopkins-Skellam index (HSI). Coherent QD arrays have a spatial distribution which is neither random nor ordered, but intermediate. The lateral ordering improves as the growth rate is increased and can be explained by more spatially regular nucleation as the QD density increases. By contrast, large and irregular 3D islands are distributed randomly on the surface. This is consistent with a random selection of the mature QDs relaxing by dislocation nucleation at a later stage in the growth, independently of each QD's surroundings. In addition we explore the statistical variability of the HSI as a function of the number N of spatial points analysed, and we recommend N > 10(3) to reliably distinguish random from ordered arrays

Macro deformation and micro structure of 3D granular assemblies subjected to rotation of principal stress axes

This paper presents a numerical investigation on the behavior of three dimensional granular materials during continuous rotation of principal stress axes using the discrete element method. A dense specimen has been prepared as a representative element using the deposition method and subjected to stress rotation at different deviatoric stress levels. Significant plastic deformation has been observed despite that the principal stresses are kept constant. This contradicts the classical plasticity theory, but is in agreement with previous laboratory observations on sand and glass beads. Typical deformation characteristics, including volume contraction, deformation non-coaxiality, have been successfully reproduced. After a larger number of rotational cycles, the sample approaches the ultimate state with constant void ratio and follows a periodic strain path. The internal structure anisotropy has been quantified in terms of the contact-based fabric tensor. Rotation of principal stress axes densifies the packing, and leads to the increase in coordination numbers. A cyclic rotation in material anisotropy has been observed. The larger the stress ratio, the structure becomes more anisotropic. A larger fabric trajectory suggests more significant structure re-organization when rotating and explains the occurrence of more significant strain rate. The trajectory of the contact-normal based fabric is not centered in the origin, due to the anisotropy in particle orientation generated during sample generation which is persistent throughout the shearing process. The sample sheared at a lower intermediate principal stress ratio (b=0.0) (b=0.0) has been observed to approach a smaller strain trajectory as compared to the case b=0.5 b=0.5 , consistent with a smaller fabric trajectory and less significant structural re-organisation. It also experiences less volume contraction with the out-of plane strain component being dilative

Prevalence of enteropathogenic viruses and molecular characterization of group A rotavirus among children with diarrhea in Dar es Salaam Tanzania

Different groups of viruses have been shown to be responsible for acute diarrhea among children during their first few years of life. Epidemiological knowledge of viral agents is critical for the development of effective preventive measures, including vaccines. In this study we determined the prevalence of the four major enteropathogenic viruses - rotavirus, norovirus, adenovirus and astrovirus - was determined in 270 stool samples collected from children aged 0 - 60 months who were admitted with diarrhea in four hospitals in Dar es Salaam, Tanzania, using commercially available ELISA kits. In addition, the molecular epidemiology of group A rotavirus was investigated using reverse transcriptase multiplex polymerase chain reaction (RT-PCR). At least one viral agent was detected in 87/270 (32.2%) of the children. The prevalence of rotavirus, norovirus, adenovirus and astrovirus was 18.1%, 13.7%, 2.6% and 0.4%, respectively. In most cases (62.1%) of viruses were detected in children aged 7-12 months. The G and P types (VP7 and VP4 genotypes respectively) were further investigated in 49 rotavirus ELISA positive samples. G9 was the predominant G type (81.6%), followed by G1 (10.2%) and G3 (0.2%). P[8] was the predominant P type (83.7%), followed by P[6] (0.4%) and P[4] (0.2%). The following G and P types were not detected in this study population; G2, G4, G8 G10, P[9], P[10] and P[11]. The dominating G/P combination was G9P[8], accounting for 39 (90.7%) of the 43 fully characterized strains. Three (6.1%) of the 49 rotavirus strains could not be typed. Nearly one third of children with diarrhea admitted to hospitals in Dar es Salaam had one of the four viral agents. The predominance of rotavirus serotype G9 may have implication for rotavirus vaccination in Tanzania

Tumor markers in breast cancer - European Group on Tumor Markers recommendations

Recommendations are presented for the routine clinical use of serum and tissue-based markers in the diagnosis and management of patients with breast cancer. Their low sensitivity and specificity preclude the use of serum markers such as the MUC-1 mucin glycoproteins ( CA 15.3, BR 27.29) and carcinoembryonic antigen in the diagnosis of early breast cancer. However, serial measurement of these markers can result in the early detection of recurrent disease as well as indicate the efficacy of therapy. Of the tissue-based markers, measurement of estrogen and progesterone receptors is mandatory in the selection of patients for treatment with hormone therapy, while HER-2 is essential in selecting patients with advanced breast cancer for treatment with Herceptin ( trastuzumab). Urokinase plasminogen activator and plasminogen activator inhibitor 1 are recently validated prognostic markers for lymph node-negative breast cancer patients and thus may be of value in selecting node-negative patients that do not require adjuvant chemotherapy. Copyright (C) 2005 S. Karger AG, Basel

Moving carbon between spheres, the potential oxalate-carbonate pathway of Brosimum alicastrum Sw.; Moraceae.

Aims The Oxalate-Carbonate Pathway (OCP) is a biogeochemical process that transfers atmospheric CO2 into the geologic reservoir as CaCO3; however, until now all investigations on this process have focused on species with limited food benefits. This study evaluates a potential OCP associated with Brosimum alicastrum, a Neotropical species with agroforestry potential (ca. 70–200 kg-nuts yr−1), in the calcareous soils of Haiti and Mexico. Methods / results Enzymatic analysis demonstrated significant concentrations of calcium oxalate (5.97 % D.W.) were associated with B. alicastrum tissue in all sample sites. The presence of oxalotrophism was also confirmed with microbiological analyses in both countries. High concentrations of total calcium (>7 g kg−1) and lithogenic carbonate obscured the localised alkalinisation and identification of secondary carbonate associated with the OCP at most sample sites, except Ma Rouge, Haiti. Soils adjacent to subjects in Ma Rouge demonstrated an increase in pH (0.63) and CaCO3 concentration (5.9 %) that, when coupled with root-like secondary carbonate deposits in Mexico, implies that the OCP does also occur in calcareous soils. Conclusions Therefore this study confirms that the OCP also occurs in calcareous soils, adjacent to B. alicastrum, and could play a fundamental and un-accounted role in the global calcium-carbon coupled cycle

Investigation of the Interaction between the Large and Small Subunits of Potato ADP-Glucose Pyrophosphorylase

ADP-glucose pyrophosphorylase (AGPase), a key allosteric enzyme involved in higher plant starch biosynthesis, is composed of pairs of large (LS) and small subunits (SS). Current evidence indicates that the two subunit types play distinct roles in enzyme function. Recently the heterotetrameric structure of potato AGPase has been modeled. In the current study, we have applied the molecular mechanics generalized born surface area (MM-GBSA) method and identified critical amino acids of the potato AGPase LS and SS subunits that interact with each other during the native heterotetrameric structure formation. We have further shown the role of the LS amino acids in subunit-subunit interaction by yeast two-hybrid, bacterial complementation assay and native gel. Comparison of the computational results with the experiments has indicated that the backbone energy contribution (rather than the side chain energies) of the interface residues is more important in identifying critical residues. We have found that lateral interaction of the LS-SS is much stronger than the longitudinal one, and it is mainly mediated by hydrophobic interactions. This study will not only enhance our understanding of the interaction between the SS and the LS of AGPase, but will also enable us to engineer proteins to obtain better assembled variants of AGPase which can be used for the improvement of plant yield

Kilonova from post-merger ejecta as an optical and near-Infrared counterpart of GW170817

Recent detection of gravitational waves from a neutron star (NS) merger event GW170817 and identification of an electromagnetic counterpart provide a unique opportunity to study the physical processes in NS mergers. To derive properties of ejected material from the NS merger, we perform radiative transfer simulations of kilonova, optical and near-infrared emissions powered by radioactive decays of r-process nuclei synthesized in the merger. We find that the observed near-infrared emission lasting for >10 d is explained by 0.03 M⊙ of ejecta containing lanthanide elements. However, the blue optical component observed at the initial phases requires an ejecta component with a relatively high electron fraction (Ye). We show that both optical and near-infrared emissions are simultaneously reproduced by the ejecta with a medium Ye of ∼0.25. We suggest that a dominant component powering the emission is post-merger ejecta, which exhibits that the mass ejection after the first dynamical ejection is quite efficient. Our results indicate that NS mergers synthesize a wide range of r-process elements and strengthen the hypothesis that NS mergers are the origin of r-process elements in the Universe

A laboratory study of anisotropic geomaterials incorporating recent micromechanical understanding

This paper presents an experimental investigation revisiting the anisotropic stress–strain–strength behaviour of geomaterials in drained monotonic shear using hollow cylinder apparatus. The test programme has been designed to cover the effect of material anisotropy, preshearing, material density and intermediate principal stress on the behaviour of Leighton Buzzard sand. Experiments have also been performed on glass beads to understand the effect of particle shape. This paper explains phenomenological observations based on recently acquired understanding in micromechanics, with attention focused on strength anisotropy and deformation non-coaxiality, i.e. non-coincidence between the principal stress direction and the principal strain rate direction. The test results demonstrate that the effects of initial anisotropy produced during sample preparation are significant. The stress–strain–strength behaviour of the specimen shows strong dependence on the principal stress direction. Preloading history, material density and particle shape are also found to be influential. In particular, it was found that non-coaxiality is more significant in presheared specimens. The observations on the strength anisotropy and deformation non-coaxiality were explained based on the stress–force–fabric relationship. It was observed that intermediate principal stress parameter b(b = (σ2 − σ3)/(σ1 − σ3)) has a significant effect on the non-coaxiality of sand. The lower the b-value, the higher the degree of non-coaxiality is induced. Visual inspection of shear band formed at the end of HCA testing has also been presented. The inclinations of the shear bands at different loading directions can be predicted well by taking account of the relative direction of the mobilized planes to the bedding plane

Genome wide SNP comparative analysis between EGFR and KRAS mutated NSCLC and characterization of two models of oncogenic cooperation in non-small cell lung carcinoma

<p>Abstract</p> <p>Background</p> <p>Lung cancer with EGFR mutation was shown to be a specific clinical entity. In order to better understand the biology behind this disease we used a genome wide characterization of loss of heterozygosity and amplification by Single Nucleotide Polymorphism (SNP) Array analysis to point out chromosome segments linked to <it>EGFR </it>mutations. To do so, we compared genetic profiles between <it>EGFR </it>mutated adenocarcinomas (ADC) and <it>KRAS </it>mutated ADC from 24 women with localized lung cancer.</p> <p>Results</p> <p>Patterns of alterations were different between <it>EGFR </it>and <it>KRAS </it>mutated tumors and specific chromosomes alterations were linked to the <it>EGFR </it>mutated group. Indeed chromosome regions 14q21.3 (p = 0.027), 7p21.3-p21.2 (p = 0.032), 7p21.3 (p = 0.042) and 7p21.2-7p15.3 (p = 0.043) were found significantly amplified in EGFR mutated tumors. Within those regions 3 genes are of special interest <it>ITGB8</it>, <it>HDAC9 </it>and <it>TWIST1</it>. Moreover, homozygous deletions at <it>CDKN2A </it>and LOH at <it>RB1 </it>were identified in <it>EGFR </it>mutated tumors. We therefore tested the existence of a link between EGFR mutation, CDKN2A homozygous deletion and cyclin amplification in a larger series of tumors. Indeed, in a series of non-small-cell lung carcinoma (n = 98) we showed that homozygous deletions at <it>CDKN2A </it>were linked to <it>EGFR </it>mutations and absence of smoking whereas cyclin amplifications (<it>CCNE1 </it>and <it>CCND1</it>) were associated to <it>TP53 </it>mutations and smoking habit.</p> <p>Conclusion</p> <p>All together, our results show that genome wide patterns of alteration differ between <it>EGFR </it>and <it>KRAS </it>mutated lung ADC, describe two models of oncogenic cooperation involving either <it>EGFR </it>mutation and <it>CDKN2A </it>deletion or cyclin amplification and <it>TP53 </it>inactivating mutations and identified new chromosome regions at 7p and 14q associated to EGFR mutations in lung cancer.</p

Meta-analysis indicates that common variants at the DISC1 locus are not associated with schizophrenia

Several polymorphisms in the Disrupted-in-Schizophrenia-1 (DISC1) gene are reported to be associated with schizophrenia. However, to date, there has been little effort to evaluate the evidence for association systematically. We carried out an imputation-driven meta-analysis, the most comprehensive to date, using data collected from 10 candidate gene studies and three genome-wide association studies containing a total of 11 626 cases and 15 237 controls. We tested 1241 single-nucleotide polymorphisms in total, and estimated that our power to detect an effect from a variant with minor allele frequency >5% was 99% for an odds ratio of 1.5 and 51% for an odds ratio of 1.1. We find no evidence that common variants at the DISC1 locus are associated with schizophrenia