Evaluation of colon cancer histomorphology: a comparison between formalin and PAXgene tissue fixation by an international ring trial.

The aim of our study was to evaluate the quality of histo- and cytomorphological features of PAXgene-fixed specimens and their suitability for histomorphological classification in comparison to standard formalin fixation. Fifteen colon cancer tissues were collected, divided into two mirrored samples and either formalin fixed (FFPE) or PAXgene fixed (PFPE) before paraffin embedding. HE- and PAS-stained sections were scanned and evaluated in a blinded, randomised ring trial by 20 pathologists from Europe and the USA using virtual microscopy. The pathologists evaluated histological grading, histological subtype, presence of adenoma, presence of lymphovascular invasion, quality of histomorphology and quality of nuclear features. Statistical analysis revealed that the reproducibility with regard to grading between both fixation methods was rather satisfactory (weighted kappa statistic (k w) = 0.73 (95 % confidence interval (CI), 0.41-0.94)), with a higher agreement between the reference evaluation and the PFPE samples (k w = 0.86 (95 % CI, 0.67-1.00)). Independent from preservation method, inter-observer reproducibility was not completely satisfactory (k w = 0.60). Histomorphological quality parameters were scored equal or better for PFPE than for FFPE samples. For example, overall quality and nuclear features, especially the detection of mitosis, were judged significantly better for PFPE cases. By contrast, significant retraction artefacts were observed more frequently in PFPE samples. In conclusion, our findings suggest that the PAXgene Tissue System leads to excellent preservation of histomorphology and nuclear features of colon cancer tissue and allows routine morphological diagnosis.

The interplay between host genetic variation, viral replication and microbial translocation in untreated HIV-infected individuals.

Systemic immune activation, a major determinant of HIV disease progression, is the result of a complex interplay between viral replication, dysregulation of the immune system, and microbial translocation due to gut mucosal damage. While human genetic variants influencing HIV viral load have been identified, it is unknown to what extent the host genetic background contributes to inter-individual differences in other determinants of HIV pathogenesis like gut damage and microbial translocation. Using samples and data from 717 untreated participants in the Swiss HIV Cohort Study and a genome-wide association study design, we searched for human genetic determinants of plasma levels of intestinal fatty-acid binding protein (I-FABP/FABP2), a marker of gut damage, and of soluble sCD14 (sCD14), a marker of LPS bioactivity and microbial translocation. We also assessed the correlations between HIV viral load, sCD14 and I-FABP. While we found no genome-wide significant determinant of the tested plasma markers, we observed strong associations between sCD14 and both HIV viral load and I-FABP, shedding new light on the relationships between processes that drive progression of untreated HIV infection.

Crop Yield Responses to Temperature Fluctuations in 19th Century Finland: Provincial Variation in Relation to Climate and Tree Rings

Past agricultural responses to climate variability can helps us to better understand the current and future impacts of climate change on agricultural production. We studied rye (Secale cereale) and barley (Hordeum vulgare) yield responses to temperature fluctuations in Finland during the period 1861–1913. Our analyses demonstrate the high sensitivity of non-industrialised northern agriculture to temperature anomalies. We found evidence of a strong relationship between monthly and seasonal mean temperatures and crop yields. In particular, high spring temperatures were associated with higher yields. Additionally, we tested temperature-sensitive tree-ring series for their value in indicating previous agricultural outputs. The results imply that tree-ring proxies (in particular, maximum latewood density) can provide novel material for studies of historical periods and locations where instrumentally measured climate and harvest data are not available.

The ring vaccination trial: a novel cluster randomised controlled trial design to evaluate vaccine efficacy and effectiveness during outbreaks, with special reference to Ebola

A World Health Organization expert meeting on Ebola vaccines proposed urgent safety and efficacy studies in response to the outbreak in West Africa. One approach to communicable disease control is ring vaccination of individuals at high risk of infection due to their social or geographical connection to a known case. This paper describes the protocol for a novel cluster randomised controlled trial design which uses ring vaccination.In the Ebola ça suffit ring vaccination trial, rings are randomised 1:1 to (a) immediate vaccination of eligible adults with single dose vaccination or (b) vaccination delayed by 21 days. Vaccine efficacy against disease is assessed in participants over equivalent periods from the day of randomisation. Secondary objectives include vaccine effectiveness at the level of the ring, and incidence of serious adverse events.Ring vaccination trials are adaptive, can be run until disease elimination, allow interim analysis, and can go dormant during inter-epidemic periods.

Influence of CYP3A5 genetic variation on everolimus maintenance dosing after cardiac transplantation

BACKGROUND Everolimus (ERL) has become an alternative to calcineurin inhibitors (CNIs) due to its renal-sparing properties, especially in heart transplant (HTx) recipients with kidney dysfunction. However, ERL dosing is challenging due to its narrow therapeutic window combined with high inter-individual pharmacokinetic variability. Our aim was to evaluate the effect of clinical and genetic factors on ERL dosing in a pilot cohort of 37 HTx recipients. METHODS Variants in CYP3A5, CYP3A4, CYP2C8, POR, NR1I2, and ABCB1 were genotyped and clinical data were retrieved from patient charts. RESULTS While ERL trough concentration (C0 ) was within the targeted range for most patients, over 30-fold variability in the dose-adjusted ERL C0 was observed. Regression analysis revealed a significant effect of the non-functional CYP3A5*3 variant on the dose-adjusted ERL C0 (P = 0.031). ERL dose requirement was 0.02 mg/kg/day higher in patients with CYP3A5*1/*3 genotype compared to patients with CYP3A5*3/*3 to reach the targeted C0 (P = 0.041). ERL therapy substantially improved estimated glomerular filtration rate (28.6 ± 6.6 ml/min/1.73m(2) ) in patients with baseline kidney dysfunction. CONCLUSION ERL pharmacokinetics in HTx recipients is highly variable. Our preliminary data on patients on a CNI-free therapy regimen suggest that CYP3A5 genetic variation may contribute to this variability. This article is protected by copyright. All rights reserved.

Striking sequence similarity in inter- and intra-specific comparisons of class I SLG alleles from Brassica oleracea and Brassica campestris: Implications for the evolution and recognition mechanism

Self-incompatibility in Brassica is controlled by a single multi-allelic locus (S locus), which contains at least two highly polymorphic genes expressed in the stigma: an S glycoprotein gene (SLG) and an S receptor kinase gene (SRK). The putative ligand-binding domain of SRK exhibits high homology to the secretory protein SLG, and it is believed that SLG and SRK form an active receptor kinase complex with a self-pollen ligand, which leads to the rejection of self-pollen. Here, we report 31 novel SLG sequences of Brassica oleracea and Brassica campestris. Sequence comparisons of a large number of SLG alleles and SLG-related genes revealed the following points. (i) The striking sequence similarity observed in an inter-specific comparison (95.6% identity between SLG14 of B. oleracea and SLG25 of B. campestris in deduced amino acid sequence) suggests that SLG diversification predates speciation. (ii) A perfect match of the sequences in hypervariable regions, which are thought to determine S specificity in an intra-specific comparison (SLG8 and SLG46 of B. campestris) and the observation that the hypervariable regions of SLG and SRK of the same S haplotype were not necessarily highly similar suggests that SLG and SRK bind different sites of the pollen ligand and that they together determine S specificity. (iii) Comparison of the hypervariable regions of SLG alleles suggests that intragenic recombination, together with point mutations, has contributed to the generation of the high level of sequence variation in SLG alleles. Models for the evolution of SLG/SRK are presented.

Inter-strand C-H...O hydrogen bonds stabilizing four-stranded intercalated molecules: stereoelectronic effects of O4' in cytosine-rich DNA.

DNA fragments with stretches of cytosine residues can fold into four-stranded structures in which two parallel duplexes, held together by hemiprotonated cytosine.cytosine+ (C.C+) base pairs, intercalate into each other with opposite polarity. The structural details of this intercalated DNA quadruplex have been assessed by solution NMR and single crystal x-ray diffraction studies of cytosine-rich sequences, including those present in metazoan telomeres. A conserved feature of these structures is the absence of stabilizing stacking interactions between the aromatic ring systems of adjacent C.C+ base pairs from intercalated duplexes. Effective stacking involves only the exocyclic keto groups and amino groups of the cytidine bases. The apparent absence of stability provided by stacking interactions between the bases in this intercalated DNA has prompted us to examine the available structures in detail, in particular with regard to unusual features that could compensate for the lack of base stacking. In addition to base-on-deoxyribose stacking and intra-cytidine C-H...O hydrogen bonds, this analysis reveals the presence of a hitherto unobserved, systematic intermolecular C-H...O hydrogen bonding network between the deoxyribose sugar moieties of antiparallel backbones in the four-stranded molecule.

Temporal variation in saproxylic beetle assemblages in a Mediterranean ecosystem

One of the main challenges in biological conservation has been to understand species distribution across space and time. Over the last decades, many diversity and conservation surveys have been conducted that have revealed that habitat heterogeneity acts as a major factor that determines saproxylic assemblages. However, temporal dynamics have been poorly studied, especially in Mediterranean forests. We analyzed saproxylic beetle distribution at inter and intra-annual scales in a “dehesa” ecosystem, which is a traditional Iberian agrosilvopastoral ecosystem that is characterized by the presence of old and scattered trees that dominate the landscape. Significant differences in effective numbers of families/species and species richness were found at the inter-annual scale, but this was not the case for composition. Temperature and relative humidity did not explain these changes which were mainly due to the presence of rare species. At the intra-annual scale, significant differences in the effective numbers of families/species, species richness and composition between seasons were found, and diversity partitioning revealed that season contributed significantly to gamma-diversity. Saproxylic beetle assemblages exhibited a marked seasonality in richness but not in abundance, with two peaks of activity, the highest between May and June, and the second between September and October. This pattern is mainly driven by the seasonality of the climate in the Mediterranean region, which influences ecosystem dynamics and imposes a marked seasonality on insect assemblages. An extended sampling period over different seasons allowed an overview of saproxylic dynamics, and revealed which families/species were restricted to particular seasons. Recognizing that seasons act as a driver in modelling saproxylic beetle assemblages might be a valuable tool in monitoring and for conservation strategies in Mediterranean forests.

Alpha-cellulose δ13C variation in mangrove tree rings correlates well with annual sea level trend between 1982 and 1999

A pilot study of tree rings in a modern mangrove tree (Rhizophora apiculata) from Leizhou Peninsula, northern South China Sea shows that ( 1) the tree-rings are annual; ( 2) the ring widths decrease; and ( 3) their alpha-cellulose delta(13)C values increase from 1982 to 1999 AD, consistent with the trends of annual sea level, salinity and sea surface temperatures in the same period. We propose that such changes were caused by increasingly longer duration of waterlogging in response to sea-level rise. If this is the case, alpha-cellulose delta(13)C in mangrove tree rings can be used as a potential indicator of past sea level fluctuations.

Characterization of 45º-tilted fiber grating and its polarization function in fiber ring laser

We have proposed and demonstrated a fiber ring laser with single-polarization output using an intracavity 45°-tilted fiber grating (45°-TFG). The properties of the 45°-TFG have been investigated both theoretically and experimentally. The fiber ring laser incorporating the 45°-TFG has been systematically characterized, showing a significant improvement in the polarization extinction ratio (PER) and achieving a PER of >30 dB. The slope efficiencies of the ring laser with and without the 45°-TFG have been measured. This laser shows a very stable polarized output with a PER variation of less than 2 dB for 5 hours at laboratory conditions. In addition, we also demonstrated the tunability of the laser.

An inter-laboratory validation of methods of lipid peroxidation measurement in UVA-treated human plasma samples

Lipid peroxidation products like malondialdehyde, 4-hydroxynonenal and F(2)-isoprostanes are widely used as markers of oxidative stress in vitro and in vivo. This study reports the results of a multi-laboratory validation study by COST Action B35 to assess inter-laboratory and intra-laboratory variation in the measurement of lipid peroxidation. Human plasma samples were exposed to UVA irradiation at different doses (0, 15 J, 20 J), encoded and shipped to 15 laboratories, where analyses of malondialdehyde, 4-hydroxynonenal and isoprostanes were conducted. The results demonstrate a low within-day-variation and a good correlation of results observed on two different days. However, high coefficients of variation were observed between the laboratories. Malondialdehyde determined by HPLC was found to be the most sensitive and reproducible lipid peroxidation product in plasma upon UVA treatment. It is concluded that measurement of malondialdehyde by HPLC has good analytical validity for inter-laboratory studies on lipid peroxidation in human EDTA-plasma samples, although it is acknowledged that this may not translate to biological validity.

Stable dual-wavelength oscillation of an Er-doped fiber ring laser at room temperature

We propose a simple Er-doped fiber laser configuration for achieving stable dual-wavelength oscillation at room temperature, in which a high birefringence fiber Bragg grating was used as the wavelength-selective component. Stable dual-wavelength oscillation at room temperature with a wavelength spacing of 0.23 nm and mutually orthogonal polarization stages was achieved by utilizing the polarization hole-burning effect. An amplitude variation of less than 0.7 dB over an 80 s period was obtained for both wavelengths.

Stable dual-wavelength oscillation of an erbium-doped fiber ring laser at room temperature

We propose a simple Er-doped fiber laser configuration for achieving stable dual-wavelength oscillation at room temperature, in which a high birefringence fiber Bragg grating was used as the wavelength-selective component. Stable dual-wavelength oscillation at room temperature with a wavelength spacing of 0.23nm and mutually orthogonal polarisation states was achieved by utilising the polarisation hole burning effect. An amplitude variation of less than 0.7dB over 80s period was obtained for both wavelengths.

Inter-Species Microbial Sharing in Rural Madagascar: A Study of Environmental Influences on the Skin Microbiome

The skin is home to trillions of microbes, many of which are recently implicated in immune system regulation and various health conditions (33). The skin is continuously exposed to the outside environment, inviting microbial transfer between human skin and the people, animals, and surfaces with which an individual comes into contact. Thus, the aim of this study is to assess how different environmental exposures influence skin microbe communities, as this can strengthen our understanding of how microbial variation relates to health outcomes. This study investigated the skin microbial communities of humans and domesticated cattle living in rural Madagascar. The V3 region of the 16S rRNA gene was sequenced from samples of zebu (the domesticated cattle of Madagascar), zebu owners, and non-zebu owners. Overall, human armpits were the least diverse sample site, while ankles were the most diverse. The diversity of zebu samples was significantly different from armpits, irrespective of zebu ownership (one-way ANOVA and Tukey’s HSD, p<0.05). However, zebu owner samples (from the armpit, ankle forearm, and hand) were more similar to other zebu owner samples than they were to zebu, yet no more similar to other zebu owner samples than they were to non-zebu owner samples (unweighted UniFrac distances, p<0.05). These data suggest a lack of a microbial signature shared by zebu owners and zebu, though further taxonomic analysis is required to explain the role of additional environmental variables in dictating the microbial communities of various samples sites. Understanding the magnitude and directionality of microbial sharing has implications for a breadth of microbe-related health outcomes, with the potential to explain mosquito host preference and mitigate the threats of vector-borne diseases.

Inter-site and inter-scanner diffusion MRI data harmonization.

We propose a novel method to harmonize diffusion MRI data acquired from multiple sites and scanners, which is imperative for joint analysis of the data to significantly increase sample size and statistical power of neuroimaging studies. Our method incorporates the following main novelties: i) we take into account the scanner-dependent spatial variability of the diffusion signal in different parts of the brain; ii) our method is independent of compartmental modeling of diffusion (e.g., tensor, and intra/extra cellular compartments) and the acquired signal itself is corrected for scanner related differences; and iii) inter-subject variability as measured by the coefficient of variation is maintained at each site. We represent the signal in a basis of spherical harmonics and compute several rotation invariant spherical harmonic features to estimate a region and tissue specific linear mapping between the signal from different sites (and scanners). We validate our method on diffusion data acquired from seven different sites (including two GE, three Philips, and two Siemens scanners) on a group of age-matched healthy subjects. Since the extracted rotation invariant spherical harmonic features depend on the accuracy of the brain parcellation provided by Freesurfer, we propose a feature based refinement of the original parcellation such that it better characterizes the anatomy and provides robust linear mappings to harmonize the dMRI data. We demonstrate the efficacy of our method by statistically comparing diffusion measures such as fractional anisotropy, mean diffusivity and generalized fractional anisotropy across multiple sites before and after data harmonization. We also show results using tract-based spatial statistics before and after harmonization for independent validation of the proposed methodology. Our experimental results demonstrate that, for nearly identical acquisition protocol across sites, scanner-specific differences can be accurately removed using the proposed method.