For better or for worse? Visualizing previous intensity levels improves emotion (dynamic) measurement in experience sampling

It is a long known reality that humans have difficulty to accurately rate the absolute intensity of internal experiences, yet the predominant way experience sampling (ESM) researchers assess participants’ momentary emotion levels is by means of absolute measurement scales. In a daily-life experiment (n = 178), we evaluate the efficacy of two alternative assessment methods that should solicit a simpler, relative emotional evaluation: (a) visualizing a relative anchor point on the absolute rating scale that depicts people’s previous emotion rating and (b) phrasing emotion items in a relative way by asking for a comparison with earlier emotion levels, using a relative rating scale. Determining five quality criteria relevant for ESM, we conclude that a visual “Last” anchor significantly improves emotion measurement in daily life: (a) Theoretically, this method has the best perceived user experience, as people, for example, find it the easiest and most accurate way to rate their momentary emotions. Methodologically, this type of measurement generates ESM time series that (b) exhibit less measurement error, produce person-level emotion dynamic measures that are (c) often more stable, and in a few cases show stronger (d) univariate and (e) incremental relations with external criteria like neuroticism and borderline personality (e.g., emotional variability). In sum, we see value in the addition of a relative “Last” anchor to absolute measurement scales of future ESM studies on emotions, as it structures the ambiguous rating space and introduces more standardization within and between individuals. In contrast, using relatively phrased emotion items is not recommended. (PsycInfo Database Record (c) 2023 APA, all rights reserved

Femtosecond Dynamics of Isolated Phenylcarbenes

International audienceUnderstanding the primary photophysical processes in molecules is essential for interpreting their photochemistry, because molecules rarely react from the initially excited electronic state. In this study the ultrafast excited-state dynamics of chlorophenylcarbene (CPC) and trifluoromethylphenylcarbene (TFPC), two species that are considered as models for carbene dynamics, were investigated by femtosecond time-resolved pump probe spectroscopy in the gas phase. Their dynamics was followed in real time by time-resolved photoionization and photoelectron imaging. CPC was excited at 265 nm into the 3 1A′ state, corresponding to excitation from a π-orbital of the aromatic ring into the LUMO. The LUMO contains a contribution of the p-orbital at the carbene center. Three time constants are apparent in the photoelectron images: A fast decay process with τ1 ≈ 40 fs, a second time constant of τ2 ≈ 350 fs, and an additional time constant of τ3 ≈ 1 ps. The third time constant is only visible in the time-dependence of low kinetic energy electrons. Due to the dense manifold of excited states between 3.9 and 5 eV, known from ab initio calculations, the recorded time-resolved electron images show broad and unstructured bands. A clear population transfer between the states thus can not directly be observed. The fast deactivation process is linked to either a population transfer between the strongly coupled excited states between 3.9 and 5.0 eV or the movement of the produced wave packet out of the Franck−Condon region. Since the third long time constant is only visible for photoelectrons at low kinetic energy, evidence is given that this time constant corresponds to the lifetime of the lowest excited A 1A′ state. The remaining time constant reflects a deactivation of the manifold of states in the range 3.9−5.0 eV down to the A 1A′ state

Gas Phase dynamics of spiropyrans and spirooxazines molecules

The gas-phase dynamics of two classes of photochromic molecules, three spiropyrans and one spirooxazine, have been investigated here using both time-resolved mass spectrometry and photoelectron spectroscopy approaches. It is, to our knowledge, the first gas-phase experiment done of these kinds of molecules. The molecules are excited at 266 nm and probed at 800 nm. The comparison of the dynamics of these four molecules has been used to propose a sequential photoisomerization mechanism involving four steps occurring in the first 100 ps. Each of these steps is discussed and related to the observed condensed-phase dynamics and to theoretical calculations

Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival

MiRNAs regulate gene expression at a post-transcriptional level and their dysregulation can play major roles in the pathogenesis of many different forms of cancer, including neuroblastoma, an often fatal paediatric cancer originating from precursor cells of the sympathetic nervous system. We have analyzed a set of neuroblastoma (n = 145) that is broadly representative of the genetic subtypes of this disease for miRNA expression (430 loci by stem-loop RT qPCR) and for DNA copy number alterations (array CGH) to assess miRNA involvement in disease pathogenesis. The tumors were stratified and then randomly split into a training set (n = 96) and a validation set (n = 49) for data analysis. Thirty-seven miRNAs were significantly over-or under-expressed in MYCN amplified tumors relative to MYCN single copy tumors, indicating a potential role for the MYCN transcription factor in either the direct or indirect dysregulation of these loci. In addition, we also determined that there was a highly significant correlation between miRNA expression levels and DNA copy number, indicating a role for large-scale genomic imbalances in the dysregulation of miRNA expression. In order to directly assess whether miRNA expression was predictive of clinical outcome, we used the Random Forest classifier to identify miRNAs that were most significantly associated with poor overall patient survival and developed a 15 miRNA signature that was predictive of overall survival with 72.7% sensitivity and 86.5% specificity in the validation set of tumors. We conclude that there is widespread dysregulation of miRNA expression in neuroblastoma tumors caused by both over-expression of the MYCN transcription factor and by large-scale chromosomal imbalances. MiRNA expression patterns are also predicative of clinical outcome, highlighting the potential for miRNA mediated diagnostics and therapeutics

Time resolved observation of multiple electronic configurations in the electronic relaxation of isolated molecules by photoelectron imaging

Contains fulltext : 60272.pdf (preprint version ) (Open Access

Conservation implications of <i>Sabellaria spinulosa</i> reef patches in a dynamic sandy-bottom environment

Biogenic reefs form biodiversity hotspots and are key components of marine ecosystems, making them priority habitats for nature conservation. However, the conservation status of biogenic reefs generally depends on their size and stability. Dynamic, patchy reefs may therefore be excluded from protection. Here, we studied epibenthos and epifauna density, richness, and community composition of patchy, dynamic Sabellaria spinulosa (ross worm) reefs in the North Sea. This study was conducted by comparing boxcore (endobenthos) and video transect (epifauna) data from two research campaigns in 2017 and 2019 to the Brown Bank area on the Dutch Continental Shelf, where S. spinulosa reefs were first discovered in 2017. The Brown Bank area is characterized by dynamic, migratory bedforms at multiple scales which potentially affect biogenic reef stability. We showed that S. spinulosa habitats had a patchy distribution and alternated with habitats comprised of plain sand. Average S. spinulosa habitat patch size was 5.57 ± 0.99 m and 3.94 ± 0.22 m in 2017 and 2019 respectively (mean ± SE), which especially in 2019 closely resembled the small-scale megaripple bedforms. Contrary to the endobenthos communities that were unaffected by S. spinulosa, epifauna density and species richness were at least two times higher in S. spinulosa habitats compared to sandy habitats, resulting in different community compositions between the two habitat types. We showed that S. spinulosa persisted in the area for almost 2 years. Although the stability of individual patches remained unclear, we demonstrated that even patchy biogenic reefs may promote density and local biodiversity of mobile, epibenthic species, very likely as a result of increased habitat heterogeneity provided by reef habitat patches. This indicates that patchy biogenic reefs that occur in dynamic environments may also have high ecological value and their conservation status should be (re)considered to ensure their protection

San Francisco Bay Area corporate history : a selected annotated bibliography

Human activities, among which dredging and land use change in river basins, are altering estuarine ecosystems. These activities may result in changes in sedimentary processes, affecting biodiversity of sediment macrofauna. As macrofauna controls sediment chemistry and fluxes of energy and matter between water column and sediment, changes in the structure of macrobenthic communities could affect the functioning of an entire ecosystem. We assessed the impact of sediment deposition on intertidal macrobenthic communities and on rates of an important ecosystem function, i.e. sediment community oxygen consumption (SCOC). An experiment was performed with undisturbed sediment samples from the Scheldt river estuary (SW Netherlands). The samples were subjected to four sedimentation regimes: one control and three with a deposited sediment layer of 1, 2 or 5 cm. Oxygen consumption was measured during incubation at ambient temperature. Luminophores applied at the surface, and a seawater–bromide mixture, served as tracers for bioturbation and bio-irrigation, respectively. After incubation, the macrofauna was extracted, identified, and counted and then classified into functional groups based on motility and sediment reworking capacity. Total macrofaunal densities dropped already under the thinnest deposits. The most affected fauna were surficial and low-motility animals, occurring at high densities in the control. Their mortality resulted in a drop in SCOC, which decreased steadily with increasing deposit thickness, while bio-irrigation and bioturbation activity showed increases in the lower sediment deposition regimes but decreases in the more extreme treatments. The initial increased activity likely counteracted the effects of the drop in low-motility, surficial fauna densities, resulting in a steady rather than sudden fall in oxygen consumption. We conclude that the functional identity in terms of motility and sediment reworking can be crucial in our understanding of the regulation of ecosystem functioning and the impact of habitat alterations such as sediment deposition

Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay.

Studying the effects of HIV infection on the host transcriptome has typically focused on protein-coding genes. However, recent advances in the field of RNA sequencing revealed that long non-coding RNAs (lncRNAs) add an extensive additional layer to the cell's molecular network. Here, we performed transcriptome profiling throughout a primary HIV infection in vitro to investigate lncRNA expression at the different HIV replication cycle processes (reverse transcription, integration and particle production). Subsequently, guilt-by-association, transcription factor and co-expression analysis were performed to infer biological roles for the lncRNAs identified in the HIV-host interplay. Many lncRNAs were suggested to play a role in mechanisms relying on proteasomal and ubiquitination pathways, apoptosis, DNA damage responses and cell cycle regulation. Through transcription factor binding analysis, we found that lncRNAs display a distinct transcriptional regulation profile as compared to protein coding mRNAs, suggesting that mRNAs and lncRNAs are independently modulated. In addition, we identified five differentially expressed lncRNA-mRNA pairs with mRNA involvement in HIV pathogenesis with possible cis regulatory lncRNAs that control nearby mRNA expression and function. Altogether, the present study demonstrates that lncRNAs add a new dimension to the HIV-host interplay and should be further investigated as they may represent targets for controlling HIV replication

Measuring centimeter-scale sand ripples using multibeam echosounder backscatter data from the Brown Bank area of the Dutch continental shelf

Backscatter data from multibeam echosounders are commonly used to classify seafloor sediment composition. Previously, it was found that the survey azimuth affects backscatter when small organized seafloor structures, such as sand ripples, are present. These sand ripples are too small to be detected in the multibeam bathymetry. Here, we show that such azimuth effects are time dependent and are useful to examine the orientation of sand ripples in relation to the flow direction of the tide. To this end, multibeam echosounder data at four different frequencies were gathered from the area of the Brown Bank in the North Sea. The acoustic results were compared to video and tide-flow data for validation. The sand ripples affected the backscatter at all frequencies, but for the lowest frequencies the effect was spread over more beam angles. Using the acoustic data made it possible to deduce the orientations of the sand ripples over areas of multiple square kilometers. We found that the top centimeter(s) of the seafloor undergoes a complete transformation every six hours, as the orientation of the sand ripples changes with the changing tide. Our methodology allows for morphology change detection at larger scales and higher resolutions than previously achieved

Robust selection of cancer survival signatures from high-throughput genomic data using two-fold subsampling

Identifying relevant signatures for clinical patient outcome is a fundamental task in high-throughput studies. Signatures, composed of features such as mRNAs, miRNAs, SNPs or other molecular variables, are often non-overlapping, even though they have been identified from similar experiments considering samples with the same type of disease. The lack of a consensus is mostly due to the fact that sample sizes are far smaller than the numbers of candidate features to be considered, and therefore signature selection suffers from large variation. We propose a robust signature selection method that enhances the selection stability of penalized regression algorithms for predicting survival risk. Our method is based on an aggregation of multiple, possibly unstable, signatures obtained with the preconditioned lasso algorithm applied to random (internal) subsamples of a given cohort data, where the aggregated signature is shrunken by a simple thresholding strategy. The resulting method, RS-PL, is conceptually simple and easy to apply, relying on parameters automatically tuned by cross validation. Robust signature selection using RS-PL operates within an (external) subsampling framework to estimate the selection probabilities of features in multiple trials of RS-PL. These probabilities are used for identifying reliable features to be included in a signature. Our method was evaluated on microarray data sets from neuroblastoma, lung adenocarcinoma, and breast cancer patients, extracting robust and relevant signatures for predicting survival risk. Signatures obtained by our method achieved high prediction performance and robustness, consistently over the three data sets. Genes with high selection probability in our robust signatures have been reported as cancer-relevant. The ordering of predictor coefficients associated with signatures was well-preserved across multiple trials of RS-PL, demonstrating the capability of our method for identifying a transferable consensus signature. The software is available as an R package rsig at CRAN (http://cran.r-project.org)