Report on the activity of the GILDA-CRG beamline 2009-2013

Index Technical description of the beamline..................................................................................................3 Introduction ....................................................................................................................................3 Optics..............................................................................................................................................3 The XAS end station........................................................................................................................6 Standard data collection setup.....................................................................................................6 Surface XAS apparata.................................................................................................................8 Recent sample environment and Instrumentation developments................................................9 The x-ray diffraction (XRD) end-station.......................................................................................13 Beamline control...........................................................................................................................14 Administrative aspects........................................................................................................................16 Organisation..................................................................................................................................16 Beamline Staff Situation................................................................................................................17 Statistical data on Users and scientific production.............................................................................21 Future perspectives and plans for upgrade.........................................................................................25 Aim of the project.........................................................................................................................25 Design...........................................................................................................................................26 Timetable......................................................................................................................................31 Overview of the overall scientific activity.........................................................................................33 Selection of five publications........................................................................................................33 Highlights of the scientific activity................................................................................................34 Local order in semiconductors..................................................................................................34 Nanotechnology.......................................................................................................................44 Cements and porous systems....................................................................................................48 Chemistry.................................................................................................................................56 Earth Science............................................................................................................................61 Environment.............................................................................................................................67 Cultural Heritage.......................................................................................................................72 Health, medicine and life science .............................................................................................77 Acknowledgements...........................................................................................................................84 References.........................................................................................................................................85 Generic References.......................................................................................................................85 GILDA 2009-2013 Publications....................................................................................................8

Unveiling the atomic position of C in Mn5Ge3 Cx thin films

Heavily carbon-doped Mn5Ge3 is a unique compound for spintronics applications as it meets all the requirements for spin injection and detection in group-IV semiconductors. Despite the great improvement of the magnetic properties induced by C incorporation into Mn5Ge3 compounds, very little information is available on its structural properties and the genuine role played by C atoms. In this paper, we have used a combination of advanced techniques to extensively characterize the structural and magnetic properties of Mn5Ge3Cx films grown on Ge(111) by solid phase epitaxy as a function of C concentration. The increase of the Curie temperature induced by C doping up to 435 K is accompanied by a decrease of the out-of-plane c-lattice parameter. The Mn and C chemical environments and positions in the Mn5Ge3 lattice have been thoroughly investigated using x-ray absorption spectroscopy techniques (x-ray absorption near-edge structures and extended x-ray absorption fine structures) and scanning transmission electronic microscopy (STEM) combined to electron energy loss spectroscopy for the chemical analysis. The results have been systematically compared to a variety of structures that were identified as favorable in terms of formation energy by ab initio calculations. For x≤0.5, the C atoms are mainly located in the octahedral voids formed by Mn atoms, which is confirmed by simulations and seen for the first time in real space by STEM. However, the latter reveals an inhomogeneous C incorporation, which is qualitatively correlated to the broad magnetic transition temperature. A higher C concentration leads to the formation of manganese carbide clusters that we identified as Mn23C6. Interestingly, other types of defects, such as interstitial Ge atoms, vacancies of Mn, and their association into line defects have been detected. They take part in the strain relaxation process and are likely to be intimately related to the growth process. This paper provides a complete picture of the structure of Mn5Ge3Cx in thin films grown by solid phase epitaxy, which is essential for optimizing their magnetic properties

Relationship between programmed cell death and the cell cycle in the tobacco BY-2 cell line

Ethylene is an established plant growth regulator linked with programmed cell death (PCD). To investigate the relationship between the cell cycle and PCD, ethylene was used to see if it induced mortality in a cell cycle specific manner. Tobacco BY-2 cultures synchronized with aphidicolin were treated with ethylene. Cell cycle progression and mortality, measured at hourly intervals, showed distinct peaks of mortality at the G2/M boundary and S-phase. In conjunction with this, DNA fragmentation increased at G2/M. Furthermore, ethylene caused a significant reduction in cell size of the cycling population. Simultaneous addition of silver nitrate with ethylene ameliorated ethylene-induced G2/M mortality, although a toxic effect of silver alone was evident. Due to the toxicity of silver, 1-MCP, an alternative chemical for blocking ethylene receptors was used. 1-MCP neither affected the BY-2 cell cycle nor mortality levels. In addition, 1-MCP ameliorated ethylene-induced G2/M mortality. To balance the chemical approaches to blocking ethylene receptors, tobacco BY-2 cells were transformed with Atetrl that encodes a dominant insensitive form of the Arabidopsis ETR1 ethylene receptor. Atetrl expression caused a massive perturbation to the tobacco BY-2 cell cycle, especially in S-phase, and resulted in high levels of mortality throughout the cell cycle. Ethylene treatment caused a doubling of G2 duration but did not affect temporal distribution of mortality. However, ethylene treatment generated a peak of mortality in S-phase. These results suggest that ethylene induces PCD at G2/M through the known ethylene signaling pathway. Furthermore, it confirms that 1-MCP and Atetrl result in ethylene insensitivity. To examine the G2/M transition, Spcdc25, a positive regulator of G2/M in fission yeast was transformed into the tobacco BY-2 cell line. This resulted in premature entry into mitosis, a shortened cell cycle, and reduced cell size. This was similar to Spcdc25 over-expression in fission yeast and suggests the presence of a CDC25-like phosphatase in plants.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Prognostic value of specific KRAS mutations in patients with colorectal peritoneal metastases

Background: There is little evidence on KRAS mutational profiles in colorectal cancer (CRC) peritoneal metastases (PM). This study aims to determine the prevalence of specific KRAS mutations and their prognostic value in a homogeneous cohort of patients with isolated CRC PM treated with cytoreductive surgery and hyperthermic intraperitoneal chemotherapy. Materials and methods: Data were collected from 13 Italian centers, gathered in a collaborative group of the Italian Society of Surgical Oncology. KRAS mutation subtypes have been correlated with clinical and pathological characteristics and survival [overall survival (OS), local (peritoneal) disease-free survival (LDFS) and disease-free survival (DFS)]. Results: KRAS mutations occurred in 172 patients (47.5%) out of the 362 analyzed. Two different prognostic groups of KRAS mutation subtypes were identified: KRASMUT1 (G12R, G13A, G13C, G13V, Q61H, K117N, A146V), median OS > 120 months and KRASMUT2 (G12A, G12C, G12D, G12S, G12V, G13D, A59E, A59V, A146T), OS: 31.2 months. KRASMUT2 mutations mainly occurred in the P-loop region (P < 0.001) with decreased guanosine triphosphate (GTP) hydrolysis activity (P < 0.001) and were more frequently related to size (P < 0.001) and polarity change (P < 0.001) of the substituted amino acid (AA). When KRASMUT1 and KRASMUT2 were combined with other known prognostic factors (peritoneal cancer index, completeness of cytoreduction score, grading, signet ring cell, N status) in multivariate analysis, KRASMUT1 showed a similar survival rate to KRASWT patients, whereas KRASMUT2 was independently associated with poorer prognosis (hazard ratios: OS 2.1, P < 0.001; DFS 1.9, P < 0.001; LDFS 2.5, P < 0.0001). Conclusions: In patients with CRC PM, different KRAS mutation subgroups can be determined according to specific codon substitution, with some mutations (KRASMUT1) that could have a similar prognosis to wild-type patients. These findings should be further investigated in larger series

Ideal cardiovascular health and inflammation in European adolescents: The HELENA study

Background and aims Inflammation plays a key role in atherosclerosis and this process seems to appear in childhood. The ideal cardiovascular health index (ICHI) has been inversely related to atherosclerotic plaque in adults. However, evidence regarding inflammation and ICHI in adolescents is scarce. The aim is to assess the association between ICHI and inflammation in European adolescents. Methods and results As many as 543 adolescents (251 boys and 292 girls) from the Healthy Lifestyle in Europe by Nutrition in Adolescence (HELENA) study, a cross-sectional multi-center study including 9 European countries, were measured. C-reactive protein (CRP), complement factors C3 and C4, leptin and white blood cell counts were used to compute an inflammatory score. Multilevel linear models and multilevel logistic regression were used to assess the association between ICHI and inflammation controlling by covariates. Higher ICHI was associated with a lower inflammatory score, as well as with several individual components, both in boys and girls (p < 0.01). In addition, adolescents with at least 4 ideal components of the ICHI had significantly lower inflammatory score and lower levels of the study biomarkers, except CRP. Finally, the multilevel logistic regression showed that for every unit increase in the ICHI, the probability of having an inflammatory profile decreased by 28.1% in girls. Conclusion Results from this study suggest that a better ICHI is associated with a lower inflammatory profile already in adolescence. Improving these health behaviors, and health factors included in the ICHI, could play an important role in CVD prevention

Evaluation of iron status in European adolescents through biochemical iron indicators: the HELENA Study

BACKGROUND/OBJECTIVES: To assess the iron status among European adolescents through selected biochemical parameters in a cross-sectional study performed in 10 European cities. SUBJECTS/METHODS: Iron status was defined utilising biochemical indicators. Iron depletion was defined as low serum ferritin (SF8.5 mg/l) plus iron depletion. Iron deficiency anaemia (IDA) was defined as ID with haemoglobin (Hb) below the WHO cutoff for age and sex: 12.0 g/dl for girls and for boys aged 12.5-14.99 years and 13.0 g/dl for boys aged ≥15 years. Enzyme linked immunosorbent assay was used as analytical method for SF, sTfR and C-reactive protein (CRP). Subjects with indication of inflammation (CRP >5 mg/l) were excluded from the analyses. A total of 940 adolescents aged 12.5-17.49 years (438 boys and 502 girls) were involved. RESULTS: The percentage of iron depletion was 17.6%, significantly higher in girls (21.0%) compared with boys (13.8%). The overall percentage of ID and IDA was 4.7 and 1.3%, respectively, with no significant differences between boys and girls. A correlation was observed between log (SF) and Hb (r = 0.36, P < 0.01), and between log (sTfR) and mean corpuscular haemoglobin (r = -0.30, P < 0.01). Iron body stores were estimated on the basis of log (sTfR/SF). A higher percentage of negative values of body iron was recorded in girls (16.5%) with respect to boys (8.3%), and body iron values tended to increase with age in boys, whereas the values remained stable in girls. CONCLUSIONS: To ensure adequate iron stores, specific attention should be given to girls at European level to ensure that their dietary intake of iron is adequate.status: publishe

Dietary animal and plant protein intakes and their associations with obesity and cardio-metabolic indicators in European adolescents: The HELENA cross-sectional study

Background: Previous studies suggest that dietary protein might play a beneficial role in combating obesity and its related chronic diseases. Total, animal and plant protein intakes and their associations with anthropometry and serum biomarkers in European adolescents using one standardised methodology across European countries are not well documented. Objectives: To evaluate total, animal and plant protein intakes in European adolescents stratified by gender and age, and to investigate their associations with cardio-metabolic indicators (anthropometry and biomarkers). Methods: The current analysis included 1804 randomly selected adolescents participating in the HELENA study (conducted in 2006-2007) aged 12.5-17.5 y (47% males) who completed two non-consecutive computerised 24-h dietary recalls. Associations between animal and plant protein intakes, and anthropometry and serum biomarkers were examined with General linear Model multivariate analysis. Results: Average total protein intake exceeded the recommendations of World Health Organization and European Food Safety Authority. Mean total protein intake was 96 g/d (59% derived from animal protein). Total, animal and plant protein intakes (g/d) were significantly lower in females than in males and total and plant protein intakes were lower in younger participants (12.5-14.9 y). Protein intake was significantly lower in underweight subjects and higher in obese ones; the direction of the relationship was reversed after adjustments for body weight (g/(kg.d)). The inverse association of plant protein intakes was stronger with BMI z-score and body fat percentage (BF%) compared to animal protein intakes. Additionally, BMI and BF% were positively associated with energy percentage of animal protein. Conclusions: This sample of European adolescents appeared to have adequate total protein intake. Our findings suggest that plant protein intakes may play a role in preventing obesity among European adolescents. Further longitudinal studies are needed to investigate the potential beneficial effects observed in this study in the prevention of obesity and related chronic diseases

Diversity and ethics in trauma and acute care surgery teams: results from an international survey

Background: Investigating the context of trauma and acute care surgery, the article aims at understanding the factors that can enhance some ethical aspects, namely the importance of patient consent, the perceptiveness of the ethical role of the trauma leader, and the perceived importance of ethics as an educational subject. Methods: The article employs an international questionnaire promoted by the World Society of Emergency Surgery. Results: Through the analysis of 402 fully filled questionnaires by surgeons from 72 different countries, the three main ethical topics are investigated through the lens of gender, membership of an academic or non-academic institution, an official trauma team, and a diverse group. In general terms, results highlight greater attention paid by surgeons belonging to academic institutions, official trauma teams, and diverse groups. Conclusions: Our results underline that some organizational factors (e.g., the fact that the team belongs to a university context or is more diverse) might lead to the development of a higher sensibility on ethical matters. Embracing cultural diversity forces trauma teams to deal with different mindsets. Organizations should, therefore, consider those elements in defining their organizational procedures. Level of evidence: Trauma and acute care teams work under tremendous pressure and complex circumstances, with their members needing to make ethical decisions quickly. The international survey allowed to shed light on how team assembly decisions might represent an opportunity to coordinate team member actions and increase performance