An Exact Algorithm for Side-Chain Placement in Protein Design

Computational protein design aims at constructing novel or improved functions on the structure of a given protein backbone and has important applications in the pharmaceutical and biotechnical industry. The underlying combinatorial side-chain placement problem consists of choosing a side-chain placement for each residue position such that the resulting overall energy is minimum. The choice of the side-chain then also determines the amino acid for this position. Many algorithms for this NP-hard problem have been proposed in the context of homology modeling, which, however, reach their limits when faced with large protein design instances. In this paper, we propose a new exact method for the side-chain placement problem that works well even for large instance sizes as they appear in protein design. Our main contribution is a dedicated branch-and-bound algorithm that combines tight upper and lower bounds resulting from a novel Lagrangian relaxation approach for side-chain placement. Our experimental results show that our method outperforms alternative state-of-the art exact approaches and makes it possible to optimally solve large protein design instances routinely

How the Kano model contributes to Kansei engineering in services

Recent studies show that products and services hold great appeal if they are attractively designed to elicit emotional feelings from customers. Kansei engineering (KE) has good potential to provide a competitive advantage to those able to read and translate customer affect and emotion in actual product and services. This study introduces an integrative framework of the Kano model and KE, applied to services. The Kano model was used and inserted into KE to exhibit the relationship between service attribute performance and customer emotional response. Essentially, the Kano model categorises service attribute quality into three major groups (must-be [M], one-dimensional [O] and attractive [A]). The findings of a case study that involved 100 tourists who stayed in luxury 4- and 5-star hotels are presented. As a practical matter, this research provides insight on which service attributes deserve more attention with regard to their significant impact on customer emotional needs. Statement of Relevance: Apart from cognitive evaluation, emotions and hedonism play a big role in service encounters. Through a focus on delighting qualities of service attributes, this research enables service providers and managers to establish the extent to which they prioritise their improvement efforts and to always satisfy their customer emotions beyond expectation. Keywords: Kansei engineering, emotional feelings, Kano model, service

This advert makes me cry: Disclosure of emotional response to advertisement on Facebook

As social media is transforming how consumers interact with brands and how brand-related content is consumed, this paper aims to investigate if and how Facebook users express their emotions towards advertisements of brand share on the site. Seven hundred and three comments about the Lloyds 250th Anniversary advertisement on Facebook were analysed as positive, negative or neutral attitude towards the advert. Facebook users found the advertisement emotionally appealing and voluntarily report their emotion of love, pride and in some cases anger. The presence of an iconic image like the black horse and the cover music was found to be emotionally appealing. The background music as well aroused positive emotions and engaging. This study introduces the possibility of analysing Facebook comments on brand content to understand consumers’ emotional responses and attitudes to the brand. Managers can explore these opportunities to identify what consumers find interesting in advertisements and how best to develop their creative strategies. It also offers the opportunity to allocate resources better to engage consumers with creative advertisement. Unlike interviews or surveys, this is a pioneering study on measuring emotional responses to advertisement through users’ self-report on social media

Towards ensemble asteroseismology of the young open clusters Chi Persei and NGC 6910

As a result of the variability survey in Chi Persei and NGC6910, the number of Beta Cep stars that are members of these two open clusters is increased to twenty stars, nine in NGC6910 and eleven in Chi Persei. We compare pulsational properties, in particular the frequency spectra, of Beta Cep stars in both clusters and explain the differences in terms of the global parameters of the clusters. We also indicate that the more complicated pattern of the variability among B type stars in Chi Persei is very likely caused by higher rotational velocities of stars in this cluster. We conclude that the sample of pulsating stars in the two open clusters constitutes a very good starting point for the ensemble asteroseismology of Beta Cep-type stars and maybe also for other B-type pulsators.Comment: 4 pages, Astronomische Nachrichten, HELAS IV Conference, Arecife, Lanzarote, Feb 2010, submitte

Reconstructing Air Shower Parameters with MGMR3D

Measuring the radio emission from cosmic ray particle cascades has proven to be a very efficient method to determine their properties such as the mass composition. Efficient modeling of the radio emission from air showers is crucial in order to extract the cosmic ray physics parameters from the measured radio emission. MGMR3D is a fast semi-analytic code that calculates the complete radio footprint, i.e.\ intensity, polarization, and pulse shapes, for a parametrized shower-current density and can be used in a chi-square optimization to fit a given radio data. It is many orders of magnitude faster than its Monte Carlo counterparts. We provide a detailed comparative study of MGMR3D to Monte Carlo simulations, where, with improved parametrizations, the shower maximum \Xmax is found to have very strong agreement with a small dependency on the incoming zenith angle of the shower. Another interesting feature we observe with MGMR3D is sensitivity to the shape of the longitudinal profile in addition to \Xmax. This is achieved by probing the distinguishable radio footprint produced by a shower having a different longitudinal profile than usual. Furthermore, for the first time, we show the results of reconstructing shower parameters for LOFAR data using MGMR3D, and obtaining a \Xmax resolution of 22 g/cm$^2$ and energy resolution of 19\%

PBP-A, a cyanobacterial dd-peptidase with high specificity for amidated muropeptides, exhibits pH-dependent promiscuous activity harmful to <em>Escherichia coli</em>

\ua9 The Author(s) 2024. Penicillin binding proteins (PBPs) are involved in biosynthesis, remodeling and recycling of peptidoglycan (PG) in bacteria. PBP-A from Thermosynechococcus elongatus belongs to a cyanobacterial family of enzymes sharing close structural and phylogenetic proximity to class A β-lactamases. With the long-term aim of converting PBP-A into a β-lactamase by directed evolution, we simulated what may happen when an organism like Escherichia coli acquires such a new PBP and observed growth defect associated with the enzyme activity. To further explore the molecular origins of this harmful effect, we decided to characterize deeper the activity of PBP-A both in vitro and in vivo. We found that PBP-A is an enzyme endowed with dd-carboxypeptidase and dd-endopeptidase activities, featuring high specificity towards muropeptides amidated on the d-iso-glutamyl residue. We also show that a low promiscuous activity on non-amidated peptidoglycan deteriorates E. coli’s envelope, which is much higher under acidic conditions where substrate discrimination is mitigated. Besides expanding our knowledge of the biochemical activity of PBP-A, this work also highlights that promiscuity may depend on environmental conditions and how it may hinder rather than promote enzyme evolution in nature or in the laboratory

Tillage erosion as an important driver of in‐field biomass patterns in an intensively used hummocky landscape

Tillage erosion causes substantial soil redistribution that can exceed water erosion especially in hummocky landscapes under highly mechanized large field agriculture. Consequently, truncated soil profiles can be found on hill shoulders and top slopes, whereas colluvial material is accumulated at footslopes, in depressions, and along downslope field borders. We tested the hypothesis that soil erosion substantially affects in-field patterns of the enhanced vegetation index (EVI) of different crop types on landscape scale. The interrelation between the EVI (RAPIDEYE satellite data; 5 m spatial resolution) as a proxy for crop biomass and modeled total soil erosion (tillage and water erosion modeled using SPEROS-C) was analyzed for the Quillow catchment (size: 196 km2) in Northeast Germany in a wet versus normal year for four crop types (winter wheat, maize, winter rapeseed, winter barley). Our findings clearly indicate that eroded areas had the lowest EVI values, while the highest EVI values were found in depositional areas. The differences in the EVI between erosional and depositional sites are more pronounced in the analyzed normal year. The net effect of total erosion on the EVI compared to areas without pronounced erosion or deposition ranged from −10.2% for maize in the normal year to +3.7% for winter barley in the wet year. Tillage erosion has been identified as an important driver of soil degradation affecting in-field crop biomass patterns in a hummocky ground moraine landscape. While soil erosion estimates are to be made, more attention should be given toward tillage erosion.ISSN:1085-3278ISSN:1099-145

Physical activity to improve cognition in older adults: can physical activity programs enriched with cognitive challenges enhance the effects? A systematic review and meta-analysis

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