Interactive Sonification for Structural Biology and Structure-based Drug Design

The visualisation of structural biology data can be quite challenging as the datasets are complex, in particular the intrinsic dynamics/flexibility. Therefore some researchers have looked into the use of sonification for the display of proteins. Combining sonification and visualisation appears to be well fitted to this problem, but at the time of writing there are no plugins available for any of the major molecular visualisation applications. Therefore we set out to develop a sonification plugin for one of those applications, released as open-source software, in order to facilitate scrutiny and evaluation from as many parties as possible. This paper presents our open source sonification plugin for UCSF Chimera, which we have developed in collaboration with medicinal chemists and structural biologists. We determined two tasks that we deemed were not well represented visually and developed sonifications for them. Furthermore, we extended a general-purpose Chimera tool to map attributes of protein residues to pitch. We evaluated one of the tasks with eight participants and present the results of this evaluation

Association between plasma tau and postoperative delirium incidence and severity: a prospective observational study

BACKGROUND: Postoperative delirium is associated with increases in the neuronal injury biomarker, neurofilament light (NfL). Here we tested whether two other biomarkers, glial fibrillary acidic protein (GFAP) and tau, are associated with postoperative delirium. METHODS: A total of 114 surgical patients were recruited into two prospective biomarker cohort studies with assessment of delirium severity and incidence. Plasma samples were sent for biomarker analysis including tau, NfL, and GFAP, and a panel of 10 cytokines. We determined a priori to adjust for interleukin-8 (IL-8), a marker of inflammation, when assessing associations between biomarkers and delirium incidence and severity. RESULTS: GFAP concentrations showed no relationship to delirium. The change in tau from preoperative concentrations to postoperative Day 1 was greater in patients with postoperative delirium (P<0.001) and correlated with delirium severity (ρ=0.39, P<0.001). The change in tau correlated with increases in IL-8 (P<0.001) and IL-10 (P=0.0029). Linear regression showed that the relevant clinical predictors of tau changes were age (P=0.037), prior stroke/transient ischaemic attack (P=0.001), and surgical blood loss (P<0.001). After adjusting for age, sex, preoperative cognition, and change in IL-8, tau remained significantly associated with delirium severity (P=0.026). Using linear mixed effect models, only tau (not NfL or IL-8) predicted recovery from delirium (P<0.001). CONCLUSIONS: The change in plasma tau was associated with delirium incidence and severity, and resolved over time in parallel with delirium features. The impact of this putative perioperative neuronal injury biomarker on long-term cognition merits further investigation. CLINICAL TRIAL REGISTRATION: NCT02926417 and NCT03124303

Hollow carbon spheres in microwaves: Bio inspired absorbing coating

This is the final version of the article. Available from American Institute of Physics (AIP)] via the DOI in this record.The electromagnetic response of a heterostructure based on a monolayer of hollow glassy carbon spheres packed in 2D was experimentally surveyed with respect to its response to microwaves, namely, the Ka-band (26-37 GHz) frequency range. Such an ordered monolayer of spheres mimics the well-known "moth-eye"-like coating structures, which are widely used for designing anti-reflective surfaces, and was modelled with the long-wave approximation. Based on the experimental and modelling results, we demonstrate that carbon hollow spheres may be used for building an extremely lightweight, almost perfectly absorbing, coating for Ka-band applications.This work was supported in part by FP7-PEOPLE-2013- IRSES-610875 NAmiceMC, FP7 Twinning Grant Inconet EaP_004

Cohort study of electroencephalography markers of amyloid-tau-neurodegeneration pathology

Electroencephalography signatures of amyloid-β, tau and neurodegenerative pathologies would aid in screening for, tracking progression of, and critically, understanding the pathogenesis of dementia. We hypothesized that slowing of the alpha peak frequency, as a signature of hyperpolarization-activated cyclic nucleotide gated ‘pacemaker’ channel activity, would correlate with amyloid and tau pathology burden measured by amyloid (Pittsburgh Compound B) and tau (MK-6240) positron emission tomography or CSF biomarkers. We also hypothesized that EEG power would be associated with neurodegeneration (CSF neurofilament light and hippocampal volume). Wakeful high-density EEG data were collected from 53 subjects. Both amyloid-β and tau pathology were associated with slowing in the alpha peak frequency [Pittsburgh Compound B (+) vs. Pittsburgh Compound B (−) subjects, P = 0.039 and MK-6240 (+) vs. MK-6240 (−) subjects, P = 0.019]. Furthermore, slowing in the peak alpha frequency correlated with CSF Aβ42/40 ratio (r2 = 0.270; P = 0.003), phosphoTau (pTau181, r2 = 0.290; P = 0.001) and pTau181/Aβ42 (r2 = 0.343; P < 0.001). Alpha peak frequency was not associated with neurodegeneration. Higher CSF neurofilament light was associated with lower total EEG power (r2 = 0.136; P = 0.018), theta power (r2 = 0.148; P = 0.014) and beta power (r2 = 0.216; P = 0.002); the latter was also associated with normalized hippocampal volume (r2 = 0.196; P = 0.002). Amyloid-tau and neurodegenerative pathologies are associated with distinct electrophysiological signatures that may be useful as mechanistic tools and diagnostic/treatment effect biomarkers in clinical trials

Middleborns disadvantaged? testing birth-order effects on fitness in pre-industrial finns

Parental investment is a limited resource for which offspring compete in order to increase their own survival and reproductive success. However, parents might be selected to influence the outcome of sibling competition through differential investment. While evidence for this is widespread in egg-laying species, whether or not this may also be the case in viviparous species is more difficult to determine. We use pre-industrial Finns as our model system and an equal investment model as our null hypothesis, which predicts that (all else being equal) middleborns should be disadvantaged through competition. We found no overall evidence to suggest that middleborns in a family are disadvantaged in terms of their survival, age at first reproduction or lifetime reproductive success. However, when considering birth-order only among same-sexed siblings, first-, middle-and lastborn sons significantly differed in the number of offspring they were able to rear to adulthood, although there was no similar effect among females. Middleborn sons appeared to produce significantly less offspring than first-or lastborn sons, but they did not significantly differ from lastborn sons in the number of offspring reared to adulthood. Our results thus show that taking sex differences into account is important when modelling birth-order effects. We found clear evidence of firstborn sons being advantaged over other sons in the family, and over firstborn daughters. Therefore, our results suggest that parents invest differentially in their offspring in order to both preferentially favour particular offspring or reduce offspring inequalities arising from sibling competition

Validation of the SF-36 in patients with endometriosis.

OBJECTIVES: Endometriosis presents with significant pain as the most common symptom. Generic health measures can allow comparisons across diseases or populations. However, the Medical Outcomes Study Short Form 36 (SF-36) has not been validated for this disease. The goal of this study was to validate the SF-36 (version 2) for endometriosis. METHODS: Using data from two clinical trials (N = 252 and 198) of treatment for endometriosis, a full complement of psychometric analyses was performed. Additional instruments included a pain visual analog scale (VAS); a physician-completed questionnaire based on patient interview (modified Biberoglu and Behrman--B&B); clinical global impression of change (CGI-C); and patient satisfaction with treatment. RESULTS: Bodily pain (BP) and the Physical Component Summary Score (PCS) were correlated with the pain VAS at baseline and over time and the B&B at baseline and end of study. In addition, those who had the greatest change in BP and PCS also reported the greatest change on CGI-C and patient satisfaction with treatment. Other subscales showed smaller, but significant, correlations with change in the pain VAS, CGI-C, and patient satisfaction with treatment. CONCLUSIONS: The SF-36--particularly BP and the PCS--appears to be a valid and responsive measure for endometriosis and its treatment

Proteostasis in pediatric pulmonary pathology.

Protein homeostasis describes the tight supervision of protein synthesis, correct protein maturation and folding, as well as the timely disposal of unwanted and damaged proteins by the ubiquitin-proteasome pathway or the lysosome-autophagy route. The cellular processes involved in preservation of protein homeostasis are collectively called proteostasis. Dysregulation of proteostasis is an emerging common pathomechanism for chronic lung diseases in the adult and aged patient. There is also rising evidence that impairment of protein homeostasis contributes to early sporadic disease onset in pediatric lung diseases beyond the well-known hereditary proteostasis disorders such as cystic fibrosis and alpha-1 antitrypsin (AAT) deficiency. Identifying the pathways that contribute to impaired proteostasis will provide new avenues for therapeutic interference with the pathogenesis of chronic lung diseases in the young and adult. Here, we introduce the concept of proteostasis and summarize available evidence on dysregulation of proteostasis pathways in pediatric and adult chronic lung diseases

Cigarette smoke extract affects mitochondrial function in alveolar epithelial cells.

Cigarette smoke is the main risk factor for chronic obstructive pulmonary disease (COPD). Exposure of cells to cigarette smoke induces an initial adaptive cellular stress response involving increased oxidative stress and induction of inflammatory signaling pathways. Exposure of mitochondria to cellular stress alters their fusion/fission dynamics. While mild stress induces a pro-survival response termed stress induced mitochondrial hyperfusion, severe stress results in mitochondrial fragmentation and mitophagy. In the present study, we analyzed the mitochondrial response to mild and non-toxic doses of cigarette smoke extract (CSE) in alveolar epithelial cells. We characterized mitochondrial morphology, expression of mitochondrial fusion and fission genes, markers of mitochondrial proteostasis as well as mitochondrial functions such as membrane potential and oxygen consumption. Murine lung epithelial (MLE)12, as well as primary mouse alveolar epithelial cells revealed pronounced mitochondrial hyperfusion upon treatment with CSE, accompanied by increased expression of the mitochondrial fusion protein mitofusin (MFN) 2 and increased metabolic activity. We did not observe any alterations in mitochondrial proteostasis, i.e. induction of the mitochondrial unfolded protein response or mitophagy. Therefore, our data indicate an adaptive pro-survival response of mitochondria of alveolar epithelial cells to non-toxic concentrations of CSE. A hyperfused mitochondrial network, however, renders the cell more vulnerable to additional stress such as sustained cigarette smoke exposure. As such cigarette smoke induced mitochondrial hyperfusion - although being part of a beneficial adaptive stress response in the first place - may contribute to the pathogenesis of COPD

Visualization of Delay Uncertainty and its Impact on Train Trip Planning: A Design Study

Uncertainty about possible train delays has an impact on train trips, as the exact arrival time is unknown during trip planning. Delays can lead to missing a connecting train at the transfer station, or to coming too late to an appointment at the destination. Facing this uncertainty, the traveler may wish to use an earlier train or a different connection arriving well before the appointment. Currently, train trip planning is based on scheduled times of connections between two stations. Information about approximate delays is only available shortly before train departure. Although several visualization approaches can show temporal uncertainty, we are not aware of any visual design specifically supporting trip planning, which can show delay uncertainty and its impact on the connections. We propose and evaluate a visual design which extends train trip planning with delay uncertainty. It shows the scheduled train connections together with their expected train delays as well as their impacts on both the arrival time, and the potential of missing a transfer. The visualization also includes information about alternative connections in case of these critical transfers. In this way the user is able to judge which train connection is suitable for a trip. We conducted a user study with 76 participants to evaluate our design. We compared it to two alternative presentations that are prominent in Germany. The study showed that our design performs comparably well for tasks concerning train schedules. The additional uncertainty display as well as the visualization of alternative connections was appreciated and well understood. The participants were able to estimate when they would likely arrive at their destination despite possible train delays while they were unable to estimate this with existing presentations. The users would prefer to use the new design for their trip planning

Interactive Input and Visualization for Planning with Temporal Uncertainty

Data with temporal uncertainty is ubiquitous in everyone’s life. Popular examples are holiday planning or train trips. There are several approaches to visualize temporal uncertainty, but common research usually does not take uncertainty into account, neither as input nor output. We propose a new approach that provides both an interactive drawing for data with temporal uncertainty and their respective visualizations. The user can draw both variable and fixed activities and also has the possibility to set probability distributions and enter indefinite activities. A quantitative user study shows the need and suitability of our new approach