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Abstract: In this work we studied oxygen diffusion in polycrystalline PrBaCo2O5+δ by isotope exchange-depth profiling (IEDP). Diffusion profiles of 18O are produced from Secondary Ion Mass Spectrometry (SIMS) depth profiles. We obtained high values of diffusivity; D ∗ =1.57×10−10 cm2/s and k ∗ =4.9×10−8 cm/s; at temperature as low as 350°C. We also observed that at temperatures higher than 500°C, the diffusion length exceeds 10μm even for very short exchange times, thus the extrapolation of diffusivity values became uncertain since the physical limit of depth profiling is approached. Our results are compared with existing literature and the discrepancies among the different values are discussed in terms of analysis technique, isotope exchange procedure and micro-structural effects. [Copyright &y& Elsevier]

Abstract: A UO2 single crystal implanted with 83Kr was analysed with a shielded Cameca IMS 6f SIMS. The main objective was to develop measurement and quantification procedures for krypton in irradiated nuclear fuel. It was found that good quality 83Kr+ depth profiles could be obtained with a 16O2 + primary ion beam, a positive offset voltage of around 20V and an oxygen leak. To convert erosion time to depth the craters produced during depth profiling were measured using an interferometer microscope. The measured depth profiles were in good agreement with the Gaussian implantation profiles. The 83Kr+ signal intensity, I, increased with current density, J, in accordance with the relationship I = A′J 2 + B′J which indicates that ionisation occurred above the sample surface by inelastic collisions with oxygen atoms. [Copyright &y& Elsevier]

Abstract: The results of a wide-ranging post-irradiation study of a PWR nuclear fuel by secondary ion mass spectrometry are presented. The average cross-section burn-up and the radial burn-up profile were determined from the radial distributions of one or more of the stable isotopes of fission product Nd. The fission gas Kr was analysed in-situ in a nuclear fuel for the first time and an investigation of the total fission gas content of the high burn-up structure using depth profiling was performed. It was confirmed that Kr is together with Xe in the pores of the high burn-up structure, and that almost all the fission gas lost from the fuel matrix is contained in the pores. In addition to Xe and Kr, the volatile fission products Te, Cs, I and Rb were also detected in the pores. The radial distributions of the minor actinides in the fuel are also reported. It was found that 237Np, unlike the isotopes of Pu, Am, and Cm, does not increase in concentration at the fuel rim. [Copyright &y& Elsevier]

The identification of transcriptomic and protein biomarkers prognosticating recurrence risk after chemoradiation of localized squamous cell carcinoma of the anus (SCCA) has been limited by a lack of available fresh tissue at initial presentation. We analyzed archival FFPE SCCA specimens from pretreatment biopsies prior to chemoradiation for protein and RNA biomarkers from patients with localized SCCA who recurred (N = 23) and who did not recur (N = 25). Tumor cells and the tumor microenvironment (TME) were analyzed separately to identify biomarkers with significantly different expression between the recurrent and non-recurrent groups. Recurrent patients had higher mean protein expression of FoxP3, MAPK-activation markers (BRAF, p38-MAPK) and PI3K/Akt activation (phospho-Akt) within the tumor regions. The TME was characterized by the higher protein expression of immune checkpoint biomarkers such as PD-1, OX40L and LAG3. For patients with recurrent SCCA, the higher mean protein expression of fibronectin was observed in the tumor and TME compartments. No significant differences in RNA expression were observed. The higher baseline expression of immune checkpoint biomarkers, together with markers of MAPK and PI3K/Akt signaling, are associated with recurrence following chemoradiation for patients with localized SCCA. These data provide a rationale towards the application of immune-based therapeutic strategies to improve curative-intent outcomes beyond conventional therapies for patients with SCCA.

Many clinical studies have evaluated the effect of probiotics, but only a few have assessed their dose effects on gut microbiota and host. We conducted a randomized, double-blind, controlled intervention clinical trial to assess the safety (primary endpoint) of and gut microbiota response (secondary endpoint) to the daily ingestion for 4 weeks of two doses (1 or 3 bottles/day) of a fermented milk product (Test) in 96 healthy adults. The Test product is a multi-strain fermented milk product, combining yogurt strains and probiotic candidate strains Lactobacillus paracasei subsp. paracasei CNCM I-1518 and CNCM I-3689 and Lactobacillus rhamnosus CNCM I-3690. We assessed the safety of the Test product on the following parameters: adverse events, vital signs, hematological and metabolic profile, hepatic, kidney or thyroid function, inflammatory markers, bowel habits and digestive symptoms. We explored the longitudinal gut microbiota response to product consumption and dose, by 16S rRNA gene sequencing and functional contribution by shotgun metagenomics. Safety results did not show any significant difference between the Test and Control products whatever the parameters assessed, at the two doses ingested daily over a 4-week-period. Probiotic candidate strains were detected only during consumption period, and at a significantly higher level for the three strains in subjects who consumed 3 products bottles/day. The global structure of the gut microbiota as assessed by alpha and beta-diversity, was not altered by consumption of the product for four weeks. A zero-inflated beta regression model with random effects (ZIBR) identified a few bacterial genera with differential responses to test product consumption dose compared to control. Shotgun metagenomics analysis revealed a functional contribution to the gut microbiome of probiotic candidates.

Objectives: Aim of this study was to assess the effect of a fermented milk product containing Bifidobacterium lactis CNCM I-2494 (FMP) on gastrointestinal (GI) symptoms and exhaled H2 and CH4 during a nutrient and lactulose challenge in patients with irritable bowel syndrome (IBS)., Methods: We included 125 patients with IBS (Rome III). Fasted subjects were served a 400ml liquid test meal containing 25g lactulose. The intensity of eight GI symptoms and the amount of exhaled H2 and CH4 were assessed before and during 4h after meal intake. The challenge was repeated after 14 days consumption of FMP or a control product in a double-blind, randomized, parallel design. The metabolic potential of fecal microbiota was profiled using 16S MiSeq analysis of samples obtained before and after the intervention., Results: 106 patients with IBS were randomized. No difference between FMP or control groups was found on GI symptoms or breath H2 and CH4 in the whole cohort. A post-hoc analysis in patients stratified according to their fasting H2 levels showed that in high H2 producers (fasting H2 level≥10ppm, n = 35), FMP consumption reduced fasting H2 levels (p = 0.003) and H2 production during the challenge (p = 0.002) and tended to decrease GI discomfort (p = 0.05) vs. control product. The Prevotella/Bacteroides metabolic potential at baseline was higher in high H2 producers (p<0.05) vs. low H2 producers and FMP consumption reduced this ratio (p<0.05) vs. control product., Conclusions: The response to a fermented milk product containing Bifidobacterium lactis CNCM I-2494 (FMP) in patients with IBS seems to be associated with the metabolic potential of the gut microbiota., Trial Registration: ClinicalTrial.gov NCT01252550. These results were presented as congress posters at Digestive Disease Week 2016 in San Diego, USA and United European Gastroenterology Week 2016 in Vienna, Austria., Competing Interests: Funding by Danone Nutricia Research. This does not alter our adherence to PLOS ONE policies on sharing data and materials. B Le Nevé, J Tap, M Derrien, R Brazeilles and S Cools- Portier are employees of Danone Nutricia Research. D Guyonnet is employee of Diana Nova and was employee of Danone Nutricia Research when this work was performed. H Törnblom has received an unrestricted research grant from Tillotts Pharma and served as a consultant/advisory board member for Allergan, Almirall Nordic and Shire. M Simrén has received unrestricted research grants from Danone and Ferring and served as a Consultant/Advisory Board member for AstraZeneca, Danone, Novartis, Almirall, Allergan, Glycom, Nestlé and Shire/Movetis. L Ohman and S Störsrud have nothing to disclose.

The adequate storage of fecal samples from clinical trials is crucial if analyses are to be performed later and in long-term studies. However, it is unknown whether the composition of the microbiota is preserved during long-term stool storage (>1 year). We therefore evaluated the influence of long-term storage on the microbiota composition of human stool samples collected in RNAlater and stored for approximately five years at -80 °C. We compared storage effects on stool samples from 24 subjects with the effects of technical variation due to different sequencing runs and biological variation (intra- and inter-subject), in another 101 subjects, based on alpha-diversity, beta-diversity and taxonomic composition. We also evaluated the impact of initial alpha-diversity and fecal microbiota composition on beta-diversity instability upon storage. Overall, long-term stool storage at -80 °C had only limited effects on the microbiota composition of human feces. The magnitude of changes in alpha- and beta- diversity and taxonomic composition after long-term storage was similar to inter-sequencing variation and smaller than biological variation (both intra- and inter-subject). The likelihood of fecal samples being affected by long-term storage correlated with the initial relative abundance of some genera and tend to be affected by initial taxonomic richness.

Technical variation in metagenomic analysis must be minimized to confidently assess the contributions of microbiota to human health. Here we tested 21 representative DNA extraction protocols on the same fecal samples and quantified differences in observed microbial community composition. We compared them with differences due to library preparation and sample storage, which we contrasted with observed biological variation within the same specimen or within an individual over time. We found that DNA extraction had the largest effect on the outcome of metagenomic analysis. To rank DNA extraction protocols, we considered resulting DNA quantity and quality, and we ascertained biases in estimates of community diversity and the ratio between Gram-positive and Gram-negative bacteria. We recommend a standardized DNA extraction method for human fecal samples, for which transferability across labs was established and which was further benchmarked using a mock community of known composition. Its adoption will improve comparability of human gut microbiome studies and facilitate meta-analyses.

Background & Aims: We have limited knowledge about the association between the composition of the intestinal microbiota and clinical features of irritable bowel syndrome (IBS). We collected information on the fecal and mucosa-associated microbiota of patients with IBS and evaluated whether these were associated with symptoms., Methods: We collected fecal and mucosal samples from adult patients who met the Rome III criteria for IBS at a secondary/tertiary care outpatient clinics in Sweden, as well as from healthy subjects. The exploratory set comprised 149 subjects (110 with IBS and 39 healthy subjects); 232 fecal samples and 59 mucosal biopsy samples were collected and analyzed by 16S ribosomal RNA targeted pyrosequencing. The validation set comprised 46 subjects (29 with IBS and 17 healthy subjects); 46 fecal samples, but no mucosal samples, were collected and analyzed. For each subject, we measured exhaled H 2 and CH 4 , oro-anal transit time, and the severity of psychological and gastrointestinal symptoms. Fecal methanogens were measured by quantitative polymerase chain reaction. Numerical ecology analyses and a machine learning procedure were used to analyze the data., Results: Fecal microbiota showed covariation with mucosal adherent microbiota. By using classic approaches, we found no differences in fecal microbiota abundance or composition between patients with IBS vs healthy patients. A machine learning procedure, a computational statistical technique, allowed us to reduce the 16S ribosomal RNA data complexity into a microbial signature for severe IBS, consisting of 90 bacterial operational taxonomic units. We confirmed the robustness of the intestinal microbial signature for severe IBS in the validation set. The signature was able to discriminate between patients with severe symptoms, patients with mild/moderate symptoms, and healthy subjects. By using this intestinal microbiota signature, we found IBS symptom severity to be associated negatively with microbial richness, exhaled CH 4 , presence of methanogens, and enterotypes enriched with Clostridiales or Prevotella species. This microbiota signature could not be explained by differences in diet or use of medications., Conclusions: In analyzing fecal and mucosal microbiota from patients with IBS and healthy individuals, we identified an intestinal microbiota profile that is associated with the severity of IBS symptoms., Trial Registration Number: NCT01252550., (Copyright © 2017 AGA Institute. Published by Elsevier Inc. All rights reserved.)

Patients with recessive dystrophic epidermolysis bullosa (RDEB) lack type VII collagen and therefore have severely impaired dermal-epidermal stability causing recurrent skin and mucosal blistering. There is currently no specific approved treatment for RDEB. We present preclinical data showing that intradermal injections of genetically corrected patient-derived RDEB fibroblasts using a Good Manufacturing Practices grade self-inactivating COL7A1 retroviral vector reverse the disease phenotype in a xenograft model in nude mice. We obtained 50% transduction efficiency in primary human RDEB fibroblasts with an average low copy number (range = 1-2) of integrated provirus. Transduced fibroblasts showed strong type VII collagen re-expression, improved adhesion properties, normal proliferative capabilities, and viability in vitro. We show that a single intradermal injection of 3 × 10(6) genetically corrected RDEB fibroblasts beneath RDEB skin equivalents grafted onto mice allows type VII collagen deposition, anchoring fibril formation at the dermal-epidermal junction, and improved dermal-epidermal adherence 2 months after treatment, supporting functional correction in vivo. Gene-corrected fibroblasts previously showed no tumorigenicity. These data show the efficacy and safety of gene-corrected fibroblast therapy using a self-inactivating vector that has now been good manufacturing grade-certified and pave the way for clinical translation to treat nonhealing wounds in RDEB patients., (Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.)

Understanding how the human gut microbiota and host are affected by probiotic bacterial strains requires carefully controlled studies in humans and in mouse models of the gut ecosystem where potentially confounding variables that are difficult to control in humans can be constrained. Therefore, we characterized the fecal microbiomes and metatranscriptomes of adult female monozygotic twin pairs through repeated sampling 4 weeks before, 7 weeks during, and 4 weeks after consumption of a commercially available fermented milk product (FMP) containing a consortium of Bifidobacterium animalis subsp. lactis, two strains of Lactobacillus delbrueckii subsp. bulgaricus, Lactococcus lactis subsp. cremoris, and Streptococcus thermophilus. In addition, gnotobiotic mice harboring a 15-species model human gut microbiota whose genomes contain 58,399 known or predicted protein-coding genes were studied before and after gavage with all five sequenced FMP strains. No significant changes in bacterial species composition or in the proportional representation of genes encoding known enzymes were observed in the feces of humans consuming the FMP. Only minimal changes in microbiota configuration were noted in mice after single or repeated gavage with the FMP consortium. However, RNA-Seq analysis of fecal samples and follow-up mass spectrometry of urinary metabolites disclosed that introducing the FMP strains into mice results in significant changes in expression of microbiome-encoded enzymes involved in numerous metabolic pathways, most prominently those related to carbohydrate metabolism. B. animalis subsp. lactis, the dominant persistent member of the FMP consortium in gnotobiotic mice, up-regulates a locus in vivo that is involved in the catabolism of xylooligosaccharides, a class of glycans widely distributed in fruits, vegetables, and other foods, underscoring the importance of these sugars to this bacterial species. The human fecal metatranscriptome exhibited significant changes, confined to the period of FMP consumption, that mirror changes in gnotobiotic mice, including those related to plant polysaccharide metabolism. These experiments illustrate a translational research pipeline for characterizing the effects of FMPs on the human gut microbiome.

We applied two methods of broth microdilution and Etest for measuring minimal inhibition concentration (MIC) of lactic acid bacteria and bifidobacteria for 15 antimicrobial agents to compare the feasibility, reproducibility, and equivalence of the two methods. Both methods were originally described by the European projects PROSAFE and ACE-ART. In 84% combinations of strains and antimicrobial agents MIC differences between the two methods were within one Log(2) dilution. In the case of rifampicin the difference between the two methods was more than ten-fold. We further determined MICs of 70 strains (14 strains of Lactobacillus delbrueckii ssp. bulgaricus, 16 strains of Lactococcus lactis, 30 strains of Streptococcus thermophilus, and 10 strains of Bifidobacterium longum) by the broth microdilution method. In most cases, MIC distributions were uni-modal and within 5 Log(2) dilutions except for the MIC distribution of L. lactis to the aminoglycoside group which was broader. These data are a good basis for improving knowledge of antimicrobial susceptibility of lactic acid bacteria and bifidobacteria, and can be used to revise tentative epidemiological cut-off values.

Background: The best method for titration of continuous positive airway pressure (CPAP) therapy in obstructive sleep apnea (OSA) syndrome has not yet been established. The 90th or 95th percentiles of the pressure titrated over time by automatic CPAP (A-CPAP) have been recommended as reference for prescribing therapeutic fixed CPAP (F-CPAP). We compared A-CPAP to F-CPAP, which was determined by a common prediction formula., Methods: Forty-five patients who were habituated to F-CPAP underwent titration polysomnography. In a double-blind, randomized order, each patient used an A-CPAP device in the autotitration and in the fixed pressure mode during one half of the night. Apnea-hypopnea index (AHI) and pressure profiles were primary outcomes. Bias and precision were additionally assessed for both CPAP modes., Results: No significant differences in various sleep parameters or in subjective sleep quality evaluation were found. The AHI was effectively lowered in both CPAP modes (A-CPAP 7.7 [10.8]events/h versus F-CPAP 5.4 [9.0]events/h, p=0.061). Comparison of group means showed that F-CPAP closely paralleled mean (Pmean) and median (P50), but not the 95th percentile (P95) pressure, of A-CPAP. While bias was lowest for Pmean and P50, there was a lack of precision in all A-CPAP pressure categories., Conclusions: We confirm that F-CPAP set by prediction formula is not worse in terms of AHI control than A-CPAP. On average, F-CPAP parallels Pmean and P50 but not P95. However, due to imprecise matching, individual F-CPAP values cannot be derived from Pmean or P50.

Multiple osteochondromas (MO) is an autosomal-dominant inherited disorder. The two genes responsible (EXT1 and EXT2) have been identified. We investigated 12 MO families for phenotype details and the genetic basis by cosegregation and mutation analysis (seven novel pathogenic mutations [five frameshift, one splice site, and one gross deletion] and one novel missense polymorphism). We found EXT1 to be responsible in seven families (19 affected members) and EXT2 in four families (17 affected members). One family remains undetermined. We found a tendency to a more severe phenotype in EXT1 families. As a novel finding, we could identify a single parameter (ulna/height ratio) that separates EXT1 family from EXT2 family in our series.

Hereditary multiple exostoses (HME) is an autosomal dominant skeletal disorder with a wide spectrum of clinical manifestations. In 52 out of 60 individuals from HME+ families, exostoses became clinically apparent. In this study, the clinical and radiological outcome of these 52 HME patients (19 families) was investigated by medical history, clinical examination, and radiographs. In addition to correlating phenotype with genotype, a linkage/exclusion analysis was performed in 35 HME patients. We found several correlations between HME genes (EXT1, EXT2) and phenotype. Compared to EXT2-linkage, female individuals with EXT1-linkage were smaller in stature. Patients with EXT1-linkage and patients with undetermined linkage (EXT?) were more severely affected, underwent more surgeries, and showed a higher number of exostoses at follow-up. Moreover, we found an increased phenotype risk for limb shortening for EXT1- and EXT?-linkage. This study corresponds to data of other investigators who showed that EXT1 mutations are associated with a more severe phenotype than other EXT forms. (c) 2007 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 25:1541-1551, 2007.

In this article Power Spectral Density Analysis of the velocity profile of handwriting tasks is applied to estimate movement noise in poor and proficient writers. It is hypothesized that poor writers are less effective in the inhibition of neuromotor noise. Evidence for this theory is found in an analysis of electronically sampled handwriting movements of 48 children from grade 2, 3 and 4 (mean ages 8, 9 and 10, resp.). Twenty-four were poor and 24 were good writers, as judged by their teachers. Subjects were matched on age, sex, handedness and educational level. They performed handwriting tasks consisting of simple garlands and arcades, or meaningless words built from the letters 'e', 'n' and 'm'. In the tasks stroke accuracy, size and rotational direction were systematically varied. The results reveal that movement times were not different between the two groups, but poor writers and good writers used different movement strategies. Movements of the less proficient children were larger and were produced with higher movement velocities. Power Spectral Density Analysis disclosed that handwriting movements of poor writers were substantially more noisy than those of proficient writers, with a consistent peaking of the noise energy in that region of the spectrum which is representative for neuromotor tremor. Also, poor writers were less successful in adapting the level of noise to increased accuracy demands of the tasks. The results support the view that deviant biomechanical strategies might be responsible for deficient motor performance.

Sixteen adult subjects were served in an experiment in which the writing of six unfamiliar graphemes was practiced. To investigate the learning process, we analyzed the absolute and relative changes of movement time of the first three consecutive segments as a function of practice. The results showed that movement time of all three segments decreased. This decrease was significantly less in the first segment that it was in the second and third segment, however. We interpret these effects of practice, from an information-processing viewpoint, as follows: (a) Initially separate response segments become integrated in more comprehensive response chunks, and (b) the preparation of later segments of the grapheme is realized more and more during the real-time execution of the initial segment. The results further revealed that these learning effects were more pronounced in graphemes composed of familiar segments than in graphemes that contained unfamiliar segments. Finally, it turned out that similarity between initial and final segments hindered the writing speed of the first segment; the effect of similarity was independent of the above-mentioned effects of practice. The latter effect is interpreted as confirming evidence for the view that the preparation of later segments of a grapheme is reflected by changes of movement time of the first segments of a grapheme.