Identifying Ligand Binding Conformations of the β2-Adrenergic Receptor by Using Its Agonists as Computational Probes

Recently available G-protein coupled receptor (GPCR) structures and biophysical studies suggest that the difference between the effects of various agonists and antagonists cannot be explained by single structures alone, but rather that the conformational ensembles of the proteins need to be considered. Here we use an elastic network model-guided molecular dynamics simulation protocol to generate an ensemble of conformers of a prototypical GPCR, β2-adrenergic receptor (β2AR). The resulting conformers are clustered into groups based on the conformations of the ligand binding site, and distinct conformers from each group are assessed for their binding to known agonists of β2AR. We show that the select ligands bind preferentially to different predicted conformers of β2AR, and identify a role of β2AR extracellular region as an allosteric binding site for larger drugs such as salmeterol. Thus, drugs and ligands can be used as "computational probes" to systematically identify protein conformers with likely biological significance. © 2012 Isin et al

ABCD Neurocognitive Prediction Challenge 2019: Predicting individual fluid intelligence scores from structural MRI using probabilistic segmentation and kernel ridge regression

We applied several regression and deep learning methods to predict fluid intelligence scores from T1-weighted MRI scans as part of the ABCD Neurocognitive Prediction Challenge (ABCD-NP-Challenge) 2019. We used voxel intensities and probabilistic tissue-type labels derived from these as features to train the models. The best predictive performance (lowest mean-squared error) came from Kernel Ridge Regression (KRR; $\lambda=10$), which produced a mean-squared error of 69.7204 on the validation set and 92.1298 on the test set. This placed our group in the fifth position on the validation leader board and first place on the final (test) leader board.Comment: Winning entry in the ABCD Neurocognitive Prediction Challenge at MICCAI 2019. 7 pages plus references, 3 figures, 1 tabl

Inference of population splits and mixtures from genome-wide allele frequency data

Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In this model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication, and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and "ancient" Asian breeds. Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.comComment: 28 pages, 6 figures in main text. Attached supplement is 22 pages, 15 figures. This is an updated version of the preprint available at http://precedings.nature.com/documents/6956/version/

Nitrogen transfer from forage legumes to nine neighbouring plants in a multi-species grassland

Legumes play a crucial role in nitrogen supply to grass-legume mixtures for ruminant fodder. To quantify N transfer from legumes to neighbouring plants in multi-species grasslands we established a grass-legume-herb mixture on a loamy-sandy site in Denmark. White clover (Trifolium repens L.), red clover (Trifolium pratense L.) and lucerne (Medicago sativa L.) were leaf-labelled with 15N enriched urea during one growing season. N transfer to grasses (Lolium perenne L. and xfestulolium), white clover, red clover, lucerne, birdsfoot trefoil (Lotus corniculatus L.), chicory (Cichorium intybus L.), plantain (Plantago lanceolata L.), salad burnet (Sanguisorba minor L.)and caraway (Carum carvi L.) was assessed. Neighbouring plants contained greater amounts of N derived from white clover (4.8 gm-2) compared with red clover (2.2 gm-2) and lucerne (1.1 gm-2). Grasses having fibrous roots received greater amounts of N from legumes than dicotyledonous plants which generally have taproots. Slurry application mainly increased N transfer from legumes to grasses. During the growing season the three legumes transferred approximately 40 kg N ha-1 to neighbouring plants. Below-ground N transfer from legumes to neighbouring plants differed among nitrogen donors and nitrogen receivers and may depend on root characteristics and regrowth strategies of plant species in the multi-species grassland

A hybrid Constraint Programming/Mixed Integer Programming framework for the preventive signaling maintenance crew scheduling problem

This research has been carried out as part of the PhD research project funded by Technical University of Denmark and Banedanmark company which is responsible for the operation and maintenance of the Danish railway network. This work has been partially funded by the DAASE project, EPSRC programme grant EP/J017515/1

Serum-neuroproteins, near-infrared spectroscopy, and cognitive outcome after beach-chair shoulder surgery: observational cohort study analyses

BACKGROUND: Cerebral hypoxia may occur during surgery but currently used cerebral oxygenation saturation (rSO2) monitors remain controversial with respect to improving clinical outcome. Novel neuroprotein biomarkers are potentially released into systemic circulation and combined with near-infrared spectroscopy (NIRS) could clarify the presence of per-operative cerebral hypoxia. We investigated changes to serum-neuroprotein concentrations postsurgically, paired with NIRS and cognitive outcome, in patients operated in the beach chair position (BCP). METHODS: A prospective cohort in 28 shoulder surgery patients placed in the BCP. Blood samples were collected before induction of anaesthesia, and 2 hours and 3-5 days postoperatively. We analysed blood-levels of biomarkers including tau and neurofilament light (NFL). We post hoc assessed the cross-wise relationship between biomarker levels and postsurgical changes in cognitive function and intraoperatively monitored rSO2 from NIRS. RESULTS: Serum-NFL decreased from 24.2 pg/mL to 21.5 (P=0.02) 2 hours postoperatively, then increased to 27.7 pg/mL on day 3-5 (P=0.03). Conversely, s-tau increased from 0.77 pg/mL to 0.98 (2 h), then decreased to 0.81 on day 3-5 (P=0.08). In 14/28 patients, episodic rSO2 below 55% occurred, and the duration <55% was correlated to change in s-tau (P<0.05). The cognitive function z-score at 1 week and 3 mo. correlated to the change in tau (P=0.01), but not to NFL. CONCLUSION: Some biomarkers were significantly changed with surgery in the beach chair position. The change was at some points associated to postoperative cognitive decline, and to intraoperative low rSO2. (237)

High-temperature performance of ferritic steels in fireside corrosion regimes: temperature and deposits

The paper reports high temperature resistance of ferritic steels in fireside corrosion regime in terms of temperature and deposits aggressiveness. Four candidate power plant steels: 15Mo3, T22, T23 and T91 were exposed under simulated air-fired combustion environment for 1000 h. The tests were conducted at 600, 650 and 700 °C according to deposit-recoat test method. Post-exposed samples were examined via dimensional metrology (the main route to quantify metal loss), and mass change data were recorded to perform the study of kinetic behavior at elevated temperatures. Microstructural investigations using ESEM-EDX were performed in order to investigate corrosion degradation and thickness of the scales. The ranking of the steels from most to the least damage was 15Mo3 > T22 > T23 > T91 in all three temperatures. The highest rate of corrosion in all temperatures occurred under the screening deposit

Stress factors and stress management interventions: the heuristic of “bottom up” an update from a systematic review

Organizations have increasingly sought to adopt innovative interventions to prevent stress-related issues. In the field of manufacturing, however, the effectiveness of these interventions remains unclear because a systematic and specific review of existing primary evidence has not been undertaken. The present systematic literature review sought to address the foregoing limitation in the literature by summarizing the main source of stress and effectiveness of stress management interventions as grounded in the context of manufacturing. Our review was limited to only randomized clinical trials (RCTs) and quasi-experimental studies and concerned employees from the manufacturing sector. Twenty-two studies on primary, secondary and tertiary interventions across four continents (Asia, Europe, USA and South America) were selected and analyzed in terms of stress factors, methodological properties and outcomes. Most of these were RCT studies (68% Vs 32%) with a majority of secondary interventions (N = 11, 50%), followed by primary (N = 5, 22%), tertiary (N = 3, 13%), and two (9%) mixed interventions. The main outcomes included an improvement of psychological wellbeing, decreased stress reactivity and an increment of general health. There was a predominance of interventions utilizing skills programs and/or cognitive-behavioral techniques. The main source of stress reported related to professional identity, organizational deficiencies, interpersonal conflicts, physical complaints and poor work environment. Taken together, the findings provide important theoretical and practical implications for advancing the study of stress factors and the use of stress management interventions in the workplace. The prerequisite for a successful intervention is to address the real problems experienced by professionals and help them to cope with their difficult situations. The strategy of “bottom-up” offers a potential means of enhancing employees’ health and well-being; however, the most effective means of implementing these interventions needs to be understood better

Positive selection inhibits gene mobilization and transfer in soil bacterial communities

Horizontal gene transfer (HGT) between bacterial lineages is a fundamental evolutionary process that accelerates adaptation. Sequence analyses show that conjugative plasmids are principal agents of HGT in natural communities. However, we lack understanding of how the ecology of bacterial communities and their environments affect the dynamics of plasmid-mediated gene mobilization and transfer. Here we show, in simple experimental soil bacterial communities containing a conjugative mercury resistance plasmid, the repeated, independent mobilization of transposon-borne genes from chromosome to plasmid, plasmid to chromosome and, in the absence of mercury selection, interspecific gene transfers from the chromosome of one species to the other via the plasmid. By reducing conjugation, positive selection for plasmid-encoded traits, like mercury resistance, can consequently inhibit HGT. Our results suggest that interspecific plasmid-mediated gene mobilization is most likely to occur in environments where plasmids are infectious, parasitic elements rather than those where plasmids are positively selected, beneficial elements