Improved modelling of liquid GeSe2_2: the impact of the exchange-correlation functional

The structural properties of liquid GeSe$_2$ are studied by using first-principles molecular dynamics in conjuncton with the Becke, Lee, Yang and Parr (BLYP) generalized gradient approximation for the exchange and correlation energy. The results on partial pair correlation functions, coordination numbers, bond angle distributions and partial structure factors are compared with available experimental data and with previous first-principle molecular dynamics results obtained within the Perdew and Wang (PW) generalized gradient approximation for the exchange and correlation energy. We found that the BLYP approach substantially improves upon the PW one in the case of the short-range properties. In particular, the Ge$-$Ge pair correlation function takes a more structured profile that includes a marked first peak due to homopolar bonds, a first maximum exhibiting a clear shoulder and a deep minimum, all these features being absent in the previous PW results. Overall, the amount of tetrahedral order is significantly increased, in spite of a larger number of Ge$-$Ge homopolar connections. Due to the smaller number of miscoordinations, diffusion coefficients obtained by the present BLYP calculation are smaller by at least one order of magnitude than in the PW case.Comment: 6 figure

Design and validation of a partial-genome microarray for transcriptional profiling of the Bradyrhizobium japonicum symbiotic gene region

The design and use of a pilot microarray for transcriptome analysis of the symbiotic, nitrogen-fixing Bradyrhizobium japonicum is reported here. The custom-synthesized chip (Affymetrix GeneChip®) features 738 genes, more than half of which belong to a 400-kb chromosomal segment strongly associated with symbiosis-related functions. RNA was isolated following an optimized protocol from wild-type cells grown aerobically and microaerobically, and from cells of aerobically grown regR mutant and microaerobically grown nifA mutant. Comparative microarray analyses thus revealed genes that are transcribed in either a RegR- or a NifA-dependent manner plus genes whose expression depends on the cellular oxygen status. Several genes were newly identified as members of the RegR and NifA regulons, beyond genes, which had been known from previous work. A comprehensive transcription analysis was performed with one of the new RegR-controlled genes (id880). Expression levels determined by microarray analysis of selected NifA- and RegR-controlled genes corresponded well with quantitative real-time PCR data, demonstrating the high complementarity of microarray analysis to classical methods of gene expression analysis in B. japonicum. Nevertheless, several previously established members of the NifA regulon were not detected as transcribed genes by microarray analysis, confirming the potential pitfalls of this approach also observed by other authors. By and large, this pilot study has paved the way towards the genome-wide transcriptome analysis of the 9.1-Mb B. japonicum genom

The role of spatial frequency information for ERP components sensitive to faces and emotional facial expression

To investigate the impact of spatial frequency on emotional facial expression analysis, ERPs were recorded in response to low spatial frequency (LSF), high spatial frequency (HSF), and unfiltered broad spatial frequency (BSF) faces with fearful or neutral expressions, houses, and chairs. In line with previous findings, BSF fearful facial expressions elicited a greater frontal positivity than BSF neutral facial expressions, starting at about 150 ms after stimulus onset. In contrast, this emotional expression effect was absent for HSF and LSF faces. Given that some brain regions involved in emotion processing, such as amygdala and connected structures, are selectively tuned to LSF visual inputs, these data suggest that ERP effects of emotional facial expression do not directly reflect activity in these regions. It is argued that higher order neocortical brain systems are involved in the generation of emotion-specific waveform modulations. The face-sensitive N170 component was neither affected by emotional facial expression nor by spatial frequency information

Straightforward quantification of endogenous steroids with liquid chromatography-tandem mass spectrometry: Comparing calibration approaches.

Different calibration strategies are used in liquid chromatography hyphenated to mass spectrometry (LC-MS) bioanalysis. Currently, the surrogate matrix and surrogate analyte represent the most widely used approaches to compensate for the lack of analyte-free matrices in endogenous compounds quantification. In this context, there is a growing interest in rationalizing and simplifying quantitative analysis using a one-point concentration level of stable isotope-labeled (SIL) standards as surrogate calibrants. Accordingly, an internal calibration (IC) can be applied when the instrument response is translated into analyte concentration via the analyte-to-SIL ratio performed directly in the study sample. Since SILs are generally used as internal standards to normalize variability between authentic study sample matrix and surrogate matrix used for the calibration, IC can be calculated even if the calibration protocol was achieved for an external calibration (EC). In this study, a complete dataset of a published and fully validated method to quantify an extended steroid profile in serum was recomputed by adapting the role of SIL internal standards as surrogate calibrants. Using the validation samples, the quantitative performances for IC were comparable with the original method, showing acceptable trueness (79%-115%) and precision (0.8%-11.8%) for the 21 detected steroids. The IC methodology was then applied to human serum samples (n = 51) from healthy women and women diagnosed with mild hyperandrogenism, showing high agreement (R <sup>2</sup> > 0.98) with the concentrations obtained using the conventional quantification based on EC. For IC, Passing-Bablok regression showed proportional biases between -15.0% and 11.3% for all quantified steroids, with an average difference of -5.8% compared to EC. These results highlight the reliability and the advantages of implementing IC in clinical laboratories routine to simplify quantification in LC-MS bioanalysis, especially when a large panel of analytes is monitored

The STARTWAVE atmospheric water database

International audienceThe STARTWAVE (STudies in Atmospheric Radiative Transfer and Water Vapour Effects) project aims to investigate the role which water vapour plays in the climate system, and in particular its interaction with radiation. Within this framework, an ongoing water vapour database project was set up which comprises integrated water vapour (IWV) measurements made over the last ten years by ground-based microwave radiometers, Global Positioning System (GPS) receivers and sun photometers located throughout Switzerland at altitudes between 330 and 3584 m. At Bern (46.95° N, 7.44° E) tropospheric and stratospheric water vapour profiles are obtained on a regular basis and integrated liquid water, which is important for cloud characterisation, is also measured. Additional stratospheric water vapour profiles are obtained by an airborne microwave radiometer which observes large parts of the northern hemisphere during yearly flight campaigns. The database allows us to validate the various water vapour measurement techniques. Comparisons between IWV measured by the Payerne radiosonde with that measured at Bern by two microwave radiometers, GPS and sun photometer showed instrument biases within ±0.5 mm. The bias in GPS relative to sun photometer over the 2001 to 2004 period was ?0.8 mm at Payerne (46.81° N, 6.94° E, 490 m), which lies in the Swiss plains north of the Alps, and +0.6 mm at Davos (46.81° N, 9.84° E, 1598 m), which is located within the Alps in the eastern part of Switzerland. At Locarno (46.18° N, 8.78° E, 366 m), which is located on the south side of the Alps, the bias is +1.9 mm. The sun photometer at Locarno was found to have a bias of ?2.2 mm (13% of the mean annual IWV) relative to the data from the closest radiosonde station at Milano. This result led to a yearly rotation of the sun photometer instruments between low and high altitude stations to improve the calibrations. In order to demonstrate the capabilites of the database for studying water vapour variations, we investigated a front which crossed Switzerland between 18 November 2004 and 19 November 2004. During the frontal passage, the GPS and microwave radiometers at Bern and Payerne showed an increase in IWV of between 7 and 9 mm. The GPS IWV measurements were corrected to a standard height of 500 m, using an empirically derived exponential relationship between IWV and altitude. A qualitative comparison was made between plots of the IWV distribution measured by the GPS and the 6.2 µm water vapour channel on the Meteosat Second Generation (MSG) satellite. Both showed that the moist air moved in from a northerly direction, although the MSG showed an increase in water vapour several hours before increases in IWV were detected by GPS or microwave radiometer. This is probably due to the fact that the satellite instrument is sensitive to an atmospheric layer at around 320 hPa, which makes a contribution of one percent or less to the IWV

Observation of single collisionally cooled trapped ions in a buffer gas

Individual Ba ions are trapped in a gas-filled linear ion trap and observed with a high signal-to-noise ratio by resonance fluorescence. Single-ion storage times of ~5 min (~1 min) are achieved using He (Ar) as a buffer gas at pressures in the range 8e-5 - 4e-3 torr. Trap dynamics in buffer gases are experimentally studied in the simple case of single ions. In particular, the cooling effects of light gases such as He and Ar and the destabilizing properties of heavier gases such as Xe are studied. A simple model is offered to explain the observed phenomenology.Comment: 5 pages, 4 figures, accepted for publication in Phys. Rev. A. Minor text and figure change

A deficit of spatial remapping in constructional apraxia after right-hemisphere stroke

This Article is provided by the Brunel Open Access Publising Fund - Copyright @ 2010 Oxford University PressConstructional apraxia refers to the inability of patients to copy accurately drawings or three-dimensional constructions. It is a common disorder after right parietal stroke, often persisting after initial problems such as visuospatial neglect have resolved. However, there has been very little experimental investigation regarding mechanisms that might contribute to the syndrome. Here, we examined whether a key deficit might be failure to integrate visual information correctly from one fixation to the next. Specifically, we tested whether this deficit might concern remapping of spatial locations across saccades. Right-hemisphere stroke patients with constructional apraxia were compared to patients without constructional problems and neurologically healthy controls. Participants judged whether a pattern shifted position (spatial task) or changed in pattern (non-spatial task) across two saccades, compared to a control condition with an equivalent delay but without intervening eye movements. Patients with constructional apraxia were found to be significantly impaired in position judgements with intervening saccades, particularly when the first saccade of the sequence was to the right. The importance of these remapping deficits in constructional apraxia was confirmed through a highly significant correlation between saccade task performance and constructional impairment on standard neuropsychological tasks. A second study revealed that even single saccades to the right can impair constructional apraxia patients’ perception of location shifts. These data are consistent with the view that rightward eye movements result in loss of remembered spatial information from previous fixations, presumably due to constructional apraxia patients’ damage to the right-hemisphere regions involved in remapping locations across saccades. These findings provide the first evidence for a deficit in remapping visual information across saccades underlying right-hemisphere constructional apraxia.European Commission Marie Curie Intra-European Fellowship (011457 to C.R.) and a Wellcome Trust Senior Fellowship (to M.H.)

Association of Trace Element Levels with Outcomes in Critically Ill COVID-19 Patients.

The primary objective of this study was to compare the plasma levels of copper, selenium, and zinc between critically ill COVID-19 patients and less severe COVID-19 patients. The secondary objective was to investigate the association of these trace element levels with adverse outcomes, including the duration of mechanical ventilation, occurrence of septic shock, and mortality in critically ill COVID-19 patients. All COVID-19 patients admitted to the ICU of the Geneva University Hospitals between 9 March 2020 and 19 May 2020 were included in the study. Plasma levels of copper, selenium and zinc were measured on admission to the ICU and compared with levels measured in COVID-19 patients hospitalized on the ward and in non-hospitalized COVID-19 patients. To analyze the association of trace elements with clinical outcomes, multivariate linear and logistic regressions were performed. Patients in the ICU had significantly lower levels of selenium and zinc and higher levels of copper compared to COVID-19 patients hospitalized on the ward and in non-hospitalized COVID-19 patients. In ICU patients, lower zinc levels tended to be associated with more septic shock and increased mortality compared to those with higher zinc levels (p = 0.07 for both). Having lower copper or selenium levels was associated with a longer time under mechanical ventilation (p = 0.01 and 0.04, respectively). These associations remained significant in multivariate analyses (p = 0.03 for copper and p = 0.04 for selenium). These data support the need for interventional studies to assess the potential benefit of zinc, copper and selenium supplementation in severe COVID-19 patients