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The present study aims to quantify the electron-induced inelastic and elastic processes for molecules of industrial relevance, furfural and p-benzoquinone. We have computed inelastic cross-sections (Qinel), elastic cross-sections (Qel) and total cross-sections (QT) through spherical complex optical potential (SCOP) formalism, from ionisation energy (IE) to 5000 eV. The continuum and discrete contributions of the Qinel have been calculated in terms of ionisation (Qion) and excitation (∑Qexc) cross-sections, respectively, by employing the complex scattering potential-ionisation contribution (CSP-iC) method. A novel 2-parameter semi-empirical method (2p-SEM), a useful approach applicable for the large molecules 55 < Z < 95 for calculating QT, has been proposed and validated. Computed results are compared with previous experimental and theoretical data. We have also estimated the dielectric constant (ε) using various methods and correlations with molecular ionisation for these applied molecules. [ABSTRACT FROM AUTHOR]

In this paper we aim to make a comparison between three types of heat pumps: air-to-water, water-to-water, ground-to-water. We show that, from a construction point of view, the difference between the three types of heat pumps is the source from which the additional heat is extracted. We point out that the heat pump is the installation that transfers heat from a colder medium to a warmer medium. Most often, pumps extract heat from water, air or ground/geothermal sources and transfer it into the home via underfloor heating, radiators, etc. Any decision to install heat pump equipment must be carefully considered, taking into account all four elements (energy consumption, installation costs, existence of the chosen heat source and its accessibility) that influence the technical and economic efficiency and the proper functioning of the equipment. [ABSTRACT FROM AUTHOR]

The article summarizes the results of the 25-year time horizon performance analysis of the ground source heat pump that serves as a heat source in a detached house in the climatic conditions that prevail in Wrocław, Poland. The main aim is to assess the potential of ground regeneration and reduction of CO2 emission by passive cooling application. The study adds value to similar research conducted worldwide for various conditions. The behavior of the lower source of the heat pump was simulated using EED software. The ground and borehole properties, heat pump characteristics, heating and cooling load, as well as the energy demand for domestic hot water preparation have been used as input data. Based on the brine temperatures for all analyzed cases including the ground with lower and higher values of conductivity and heat capacity, the borehole filler of inferior and superior thermal properties, and the passive cooling option turned on and off, the seasonal efficiencies of the heat pump have been calculated. The energy and emission savings calculations are based on the values obtained. The application of passive cooling reduces the brine temperature drop by 0.5 K to over 1.0 K in consecutive years in the analyzed cases and the thermal imbalance by 65.0% to 65.9%. Electric energy savings for heating and domestic hot water preparation reach 4.5%, but the greatest advantage of the system is the possibility of almost emission-free colling the living spaces which allows reducing around 33.7 GWh of electric energy and 1186–1830 kg of CO2 emission for cooling. [ABSTRACT FROM AUTHOR]

This article reports the electron scattering ionization cross sections for S 2 , S 3 , S 4 , S 5 , S 6 , S 7 , and S 8 target molecules essential to many fields like radiation chemistry, atmospheric, astrophysical, and astrochemical modeling. The theoretical approach utilizes a complex scattering potential ionization contribution method. The computation is carried from the ionization threshold of the target molecule to 5000 eV to investigate the entire energy range, which is significant to the ionization process of the molecules. A simple additivity rule is applied to study complex and non-spherical cases. Further, screening correction is implemented within the molecular system to reduce the overestimation in cross section values due to the overlapping charge density. A high correlation was obtained for the maximum ionization cross section value and the square root of the ratio of polarizability to the target molecule's ionization energy, indicating the present method's accuracy. Besides the Astro modeling applications, the cross section values also find utility in industrial plasma, sulfur lamps, lithium-sulfur batteries, and mass spectrometry. [Display omitted] • Electron interaction with sulfur clusters studied by quantum mechanical formalism. • EPS method helps to identify molecular charge density distribution. • Simple additivity applied to charge density and screening correction applied to refine CS. • Ionization data for S 4 to S 8 target molecules reported for the first time. • Correlation of maximum ionization CS with target parameters observed for clusters. [ABSTRACT FROM AUTHOR]

In this article, we report a detailed theoretical study on electron interactions with chlorobenzene with incident energies ranging from 0.1 to 5000 eV. Due to this wide range of impact energy, we are able to investigate a variety of processes and report data on resonances, differential cross-sections (DCS), momentum transfer cross-sections (MTCS), rate coefficient, vertical electronic excitations, dissociative electron attachment (DEA), total ionisation cross-sections and total scattering cross-sections (TCS). In order to compute the total scattering cross-sections, we have employed the ab-initio R-matrix method via Quantemol-N for the lower energy range (0.1 eV to 20 eV) and Spherical Complex Optical Potential (SCOP) beyond threshold energy of the target to 5000 eV. The R-matrix calculations are performed using a close-coupling method with the aid of 34 target states, 1667 configuration state functions, and 233 channels employing Configuration Interaction (CI) model. The present study reports evidence for electron scattering resonances through analysis of eigenphase diagrams fitting them to Breit-Wigner profile at low energies below the ionisation threshold. [ABSTRACT FROM AUTHOR]

This article is focused on the calculation of electron-induced ionisation and total scattering cross sections by Boron, Aluminium and Gallium trihalide molecules in the intermediate energy domain. The computational formalism, spherical complex optical potential has been employed for the study of these two scattering cross sections. The ionisation cross section has been derived from the inelastic cross section using a semi-empirical method called complex scattering potential-ionisation contribution (CSP-ic) method. We have also calculated the ionisation cross section using the BEB theory with Hartree-Fock and density functional theory (DFT- ωB97XD) orbitals so that a comparison can be made with the cross sections predicted by CSP-ic method. For this theoretical study, we have also calculated polarisability and bond length of some targets which were not found in literature using DFT/B3LYP in Gaussian 09 software. [ABSTRACT FROM AUTHOR]

This article reports various cross sections of electron scattering from C 5 H 10 isomers, viz. 1-pentene, 2-methyl-2-butene, cis-2-pentene, trans-2-pentene and 2-methyl-1-butene. These molecules are scarcely investigated in terms of such interactions, especially cis-2-pentene, trans-2-pentene and 2-methyl-1-butene molecules for which no previous cross section data is available. The results presented here are obtained by the quantum mechanical formalism using optical potential method, for a wide energy range from the ionization threshold of the target to 5000 eV. Geometrical screening correction is included in this calculation to account for the overlapping charge densities of different atoms present in a molecule. Most of the data presented here are reported for the first time. The effect of structural difference on cross section is investigated through isomeric effect. [Display omitted] • Theoretical studies of electron scattering from different C 5 H 10 isomers are reported. • Cross sections for different channels are computed using Complex Optical Potential. • Cross section of cis and trans-2-pentene and 2-methyl-1-butene are reported for the first time. • Geometric screening correction is employed to refine the cross section. • The isomeric effect is visualized by comparing cross section to 2-methyl-2-butene. [ABSTRACT FROM AUTHOR]

An analytical study is conducted to optimize the injection-port geometries of a vapor injection asymmetric scroll compressor operating under various climatic conditions. A numerical model was developed to predict the performance of the vapor injection asymmetric scroll compressor in the heating mode according to various operating parameters, and this numerical model was validated using data measured in a vapor injection heat pump. The effects of the location and number of injection ports on the performance of the asymmetric scroll compressor were analyzed using the numerical model. Both the optimal injection-port angle and required injection-port area increased as the outdoor temperature decreased in order to increase the injection mass flow rate. The optimized injection port designs were then proposed for the asymmetric scroll compressor in order to achieve the maximum SCOP (seasonal coefficient of performance) under various climatic conditions, improving the SCOP by 2%–6% relative to the baseline injection compressor. [ABSTRACT FROM AUTHOR]

Quantum cognition is an emergent area of research that applies quantum structures in cognitive situations where traditional approaches are problematic. Independently from quantum cognition, quantum approaches for the semantics of music interpretation and improvisation have been proposed in the context of quantum computational logic and standard quantum mechanics, respectively. These frameworks overcome the non-contextual and compositional approaches to the semantics of music. In this paper, we analyze the quantum approach to the semantics of music from the perspective of quantum cognition. We first introduce an operational framework, inspired by the Brussels-Geneva approach to the foundations of quantum theory, named state context property (SCoP) formalism, that has been applied in quantum cognition to model concepts. Next, we show that the quantum approaches to the semantics of music can be operationalized in SCoP. In particular, we apply the SCoP definitions of 'orthogonal property' and 'experiment-context' to operationalize the notions of 'vague meaning' and 'interpretation', and to characterize the structural differences between the semantics of music interpretation and improvisation. [ABSTRACT FROM AUTHOR]

This article reports electron impact ionisation cross sections for platinum-based drugs viz., cisplatin (H6N2Cl2Pt), carboplatin (C6H12N2O4Pt), oxaliplatin (C8H14N2O4Pt), nedaplatin (C2H8N2O3Pt) and satraplatin (C10H22ClN2O4Pt) complexes used in the cancer chemotherapy. The multi-scattering centre spherical complex optical potential formalism is used to obtain the inelastic cross section for these large molecules upon electron impact. The ionisation cross section is derived from the inelastic cross section employing complex scattering potential–ionisation contribution method. Comparison is made with previous results, where ever available and overall a reasonable agreement is observed. This is the first attempt to report total ionisation cross sections for nedaplatin and satraplatin complexes. [ABSTRACT FROM AUTHOR]

Climate control systems typically account for a substantial part of energy consumption in commercial buildings. The obligations established in global agreements as well as regulations and legislation that limit the energy consumption and greenhouse gases emissions gave a novel importance to the HVAC systems rating. This paper describes various indicators for assessing the energy performance of HVAC systems by defining the concepts involved and presenting calculation procedures. Various methods are used, from the basic indicators ( EER , COP ) to the most sophisticated ( SEER , SCOP ), which are due to the need to include more parameters to determine the level of energy efficiency accurately and to adjust it to the actual operation of the equipment. A case study is presented in order to calculate the indicators of actual systems in Europe and to assess developments by geographical location. A difference between the results of the various indicators when changing the geographical location and weather conditions that affect the systems was noticeable, which can lead to misconceptions regarding the energy efficiency. It is therefore important to correctly use the indicators that best fit the location, a task that is not usually performed by the manufacturers. [ABSTRACT FROM AUTHOR]

While calpain-1 activation is required for LTP induction by theta burst stimulation (TBS), calpain-2 activation limits its magnitude during the consolidation period. A selective calpain-2 inhibitor applied either before or shortly after TBS enhanced the degree of potentiation. In the present study, we tested whether the selective calpain-2 inhibitor, Z-Leu-Abu-CONH-CH2-C6H3 (3, 5-(OMe)2 (C2I), could enhance learning and memory in wild-type (WT) and calpain-1 knock-out (C1KO) mice. We first showed that C2I could reestablish TBS-LTP in hippocampal slices from C1KO mice, and this effect was blocked by PD98059, an inhibitor of ERK. TBS resulted in PTEN degradation in hippocampal slices from both WT and C1KO mice, and C2I treatment blocked this effect in both mouse genotypes. Systemic injection of C2I 30 min before training in the fear-conditioning paradigm resulted in a biphasic dose-response curve, with low doses enhancing and high doses inhibiting freezing behavior. The difference between the doses needed to enhance and inhibit learning matches the difference in concentrations producing inhibition of calpain-2 and calpain-1. A low dose of C2I also restored normal learning in a novel object recognition task in C1KO mice. Levels of SCOP, a ERK phosphatase known to be cleaved by calpain-1, were decreased in dorsal hippocampus early but not late following training in WT mice; C2I treatment did not affect the early decrease in SCOP levels but prevented its recovery at the later time-point and prolonged ERK activation. The results indicate that calpain-2 activation limits the extent of learning, an effect possibly due to temporal limitation of ERK activation, as a result of SCOP synthesis induced by calpain-2-mediated PTEN degradation. [ABSTRACT FROM AUTHOR]

We report here the total ionisation cross sections for CF3X and CF2X2(X = H, Cl, Br and I) molecules by electron impact from ionisation threshold to 5 keV. The total inelastic cross section is obtained employing a quantum mechanical approach called spherical complex optical potential formalism. Then, using a semi-empirical complex scattering potential-ionisation contribution method, the ionisation cross section is derived from the inelastic cross section. The results obtained are compared with previous measurements and theoretical values, wherever available and a satisfactorily agreement is observed. The ionisation cross section values for CF2I2molecule are reported for the first time. [ABSTRACT FROM PUBLISHER]

Domains are folded structures and evolutionary building blocks of protein molecules. Their three-dimensional atomic conformations, which define biological functions, can be coarse-grained into levels of a hierarchy. Here we build global dynamical models for the evolution of domains at fold and fold superfamily (FSF) levels. We fit the models with data from phylogenomic trees of domain structures and evaluate the distributions of the resulting parameters and their implications. The trees were inferred from a census of domain structures in hundreds of genomes from all three superkingdoms of life. The models used birth-death differential equations with the global abundances of structures as state variables, with one set of equations for folds and another for FSFs. Only the transitions present in the tree are assumed possible. Each fold or FSF diversifies in variants, eventually producing a new fold or FSF. The parameters specify rates of generation of variants and of new folds or FSFs. The equations were solved for the parameters by simplifying the trees to a comb-like topology, treating branches as emerging directly from a trunk. We found that the rate constants for folds and FSFs evolved similarly. These parameters showed a sharp transient change at about 1.5 Gyrs ago. This time coincides with a period in which domains massively combined in proteins and their arrangements distributed in novel lineages during the rise of organismal diversification. Our simulations suggest that exploration of protein structure space occurs through coarse-grained discoveries that undergo fine-grained elaboration. [ABSTRACT FROM AUTHOR]

• Forecast analysis of the behavior of air source heat pumps for the next 50 years for all climate zones. • The winter heating season is expected to shorten and the summer season to lengthen. • Winter operating hours will increase in very cold climates and decrease in temperate climates. • Rising temperatures will force air source heat pumps to work in extreme conditions for longer periods in hot climates. • Under extreme winter conditions, exceeding the TOL (operating limit temperature) occurs for an increasing number of hours. Climate change will impact the building sector, but the related consequences are not fully known, especially at energy system level. This paper investigates the effect of a changing climate on heat pumps, worldwide recognized as one of the most promising technology to decarbonize the building sector. Being highly dependent on outdoor temperature, the research aims to understand how air-source heat pumps (ASHPs) will perform within climate change depending on locations and scenarios. ASHPs are considered in several locations around the world selected to cover the climate variability of the Köppen-Geiger climate classification. Future projected climate scenarios to the years 2030, 2050, and 2070 are studied under three Representative Concentration Pathways (RCPs: 2.6, 4.5, 8.5) that reflect an increasing climate change severity. The forecast analysis is conducted in terms of ASHPs seasonal coefficients of performance, working hours, seasonal and annual energy consumption. Results show how a rising average temperature facilitates, in winter, the energy transition to the use of electric heat pumps to replace fossil fuels. However, differences are found among locations, scenarios, and RCPs. The research illustrates how the two effects of heating decrease and cooling increase offset or whether one seasonal consumption prevails and where this occurs. The general trend foresees a noteworthy reduction of winter energy consumption in all climate zones. Higher decreases are found for RCP 8.5 compared to RCP 2.6 and RCP 4.5 scenarios, for both radiant floor panels and fan coils, with most variations in Hanoi (-48,24 % in 2070) and Cairo (-39,59 % in 2070). Concurrently, a major rise is estimated in cooling consumption in almost each climate zone, with wider differences within RCP 8.5. In this scenario, the increase in summer energy consumption is more extreme, ranging from a minimum in Singapore (+4.20 %) and Mombasa (+4.66 %), to a maximum in Anchorage (+87.31 %), Reykjavik (+49.89 %) and Lethbridge (+56.53 %). This increase is only partly offset by the reduction in winter energy consumption, with an overall net increment in the forecasted building's energy consumption. [ABSTRACT FROM AUTHOR]

In this work, we propose a new distance measure for comparing two protein structures based on their contact map representations. We show that our novel measure, which we refer to as the maximum contact map overlap (max-CMO) metric, satisfies all properties of a metric on the space of protein representations. Having a metric in that space allows one to avoid pairwise comparisons on the entire database and, thus, to significantly accelerate exploring the protein space compared to no-metric spaces. We show on a gold standard superfamily classification benchmark set of 6759 proteins that our exact k-nearest neighbor (k-NN) scheme classifies up to 224 out of 236 queries correctly and on a larger, extended version of the benchmark with 60; 850 additional structures, up to 1361 out of 1369 queries. Our k-NN classification thus provides a promising approach for the automatic classification of protein structures based on flexible contact map overlap alignments. [ABSTRACT FROM AUTHOR]

Background: Since experimental techniques are time and cost consuming, in silico protein structure prediction is essential to produce conformations of protein targets. When homologous structures are not available, fragment-based protein structure prediction has become the approach of choice. However, it still has many issues including poor performance when targets' lengths are above 100 residues, excessive running times and sub-optimal energy functions. Taking advantage of the reliable performance of structural class prediction software, we propose to address some of the limitations of fragment-based methods by integrating structural constraints in their fragment selection process. Results: Using Rosetta, a state-of-the-art fragment-based protein structure prediction package, we evaluated our proposed pipeline on 70 former CASP targets containing up to 150 amino acids. Using either CATH or SCOP-based structural class annotations, enhancement of structure prediction performance is highly significant in terms of both GDT_TS (at least +2.6, p-values < 0.0005) and RMSD (-0.4, p-values < 0.005). Although CATH and SCOP classifications are different, they perform similarly. Moreover, proteins from all structural classes benefit from the proposed methodology. Further analysis also shows that methods relying on class-based fragments produce conformations which are more relevant to user and converge quicker towards the best model as estimated by GDT_TS (up to 10% in average). This substantiates our hypothesis that usage of structurally relevant templates conducts to not only reducing the size of the conformation space to be explored, but also focusing on a more relevant area. Conclusions: Since our methodology produces models the quality of which is up to 7% higher in average than those generated by a standard fragment-based predictor, we believe it should be considered before conducting any fragment-based protein structure prediction. Despite such progress, ab initio prediction remains a challenging task, especially for proteins of average and large sizes. Apart from improving search strategies and energy functions, integration of additional constraints seems a promising route, especially if they can be accurately predicted from sequence alone. [ABSTRACT FROM AUTHOR]

Milk is a biofluid with various functions, containing carbohydrates, lipids, proteins, vitamins, and minerals. Owing to its importance and availability of vast proteomics information, our research group designed a database for bovine milk proteins (N = 3159) containing the primary and secondary information called BoMiProt. Due to the gaining interest and intensively published literature in the last three years, BoMiProt has been upgraded with newer identified proteins (N = 7459) from peer-reviewed journals, significantly expanding the database from different milk fractions (e.g., whey, fat globule membranes, and exosomes). Additionally, class, architecture, topology, and homology, structural classification of proteins, known and predicted disorder, predicted transmembrane helices, and structures have been included. Each protein entry in the database is thoroughly cross-referenced, including 1392 BoMiProt defined proteins provided with secondary information, such as protein function, biochemical properties, post-translational modifications, significance in milk, domains, fold, AlphaFold predicted models and crystal structures. The proteome data in the database can be retrieved using several search parameters using protein name, accession IDs, and FASTA sequence. Overall, BoMiProt represents an extensive compilation of newer proteins, including structural, functional, and hierarchical information, to help researchers better understand mammary gland pathophysiology, including their potential application in improving the nutritional quality of dairy products. [Display omitted] • BoMiProt version 2.0, comprises 10,642 new bovine milk proteins. • Heirarchial classification, fold information, biochemical functions, and milk fractions have been included. • Over 1392 BoMiProt defined proteins have been added with well-defined secondary information. • For 1288 proteins, structures have been predicted using AlphaFold. • SCOP and CATH, known and predicted disorder, predicted transmembrane helices, and structures have been included. [ABSTRACT FROM AUTHOR]

The present article reports total ionization cross section for W, WO, WO 2 , WO 3 , U, UO, UO 2 and UO 3 targets by electron impact. Tungsten is used as a wall coating element in fusion reactors and are found as impurities in the fusion edge plasma along with their oxides. Uranium and its oxides are found especially in nuclear reactors. In both cases, electron induced collision and ionization are the most probable reaction that can take place in such environments. Hence, the knowledge of electron impact cross section data is very important for the modelling of these reactors. The total inelastic cross sections for these targets were calculated using spherical complex optical potential (SCOP) formalism. Then by employing complex scattering potential ionization contribution (CSP-ic) method, total ionization cross sections is derived from inelastic cross section. The present results show reasonable agreement with previous theories and experiments, wherever available. A linear relation between the ionization potential and peak of ionization cross section was also obtained confirming the consistency of the data reported here. The total ionization cross sections for UO, UO 2 and UO 3 presented in this work is reported for the first time. [ABSTRACT FROM AUTHOR]

Contact sites between amino acids characterize important structural features of a protein. We investigated characteristics of contact sites in a representative set of proteins and their relations between protein class or topology. For this purpose, we used a non-redundant set of 5872 protein domains, identically categorized by CATH and SCOP databases. The proteins represented alpha, beta, and alpha+beta classes. Contact maps of protein structures were obtained for a selected set of physical distances in the main backbone and separations in protein sequences. For each set a dependency between contact degree and distance parameters was quantified. We indicated residues forming contact sites most frequently and unique amino acid pairs which created contact sites most often within each structural class. Contact characteristics of specific topologies were compared to the characteristics of their protein classes showing protein groups with a distinguished contact characteristic. We showed that our results could be used to improve the performance of recent top contact predictor - direct coupling analysis. Our work provides values of contact site propensities that can be involved in bioinformatic databases. [ABSTRACT FROM AUTHOR]

There is already a common place the affirmation that adolescence constitutes a crucial point for the human being in the process of development. The identity starts to take a certain shape; the youth becomes more aware in what concerns his relation with the world which is seen even at a cosmic level. It is the age which re-discovers the essential philosophical questions: Who am I? Where am I from? What is behind?... This behind is experienced by the adolescent on multiple planes, of which, he is seldom not aware. Depending on the cultural background which could be religious or laic, the developing personality searches for solutions, usually in philosophy or religion. In fact, is actually the same domain - the field of spirituality? The paper presents the results of a research in this field and takes up the topic of the spiritual cooperation between the psychological counselling and the philosophical one. [ABSTRACT FROM AUTHOR]

We report total scattering cross sections for C2H4 molecule by electron impact. Calculations are performed by using two different quantum mechanical methods and they cover the energy range from 1 to 2000 eV. For low energy calculations up to 15 eV, UK molecular R-matrix code through QUANTEMOL-N software is used, while intermediate to high energy (15-2000 eV) calculations were carried out by applying spherical complex optical potential formalism. Comparison is made with earlier measurements and theoretical data wherever available. A shape resonance is detected around 2 eV due to the 2B2g symmetry of an electronic state that corresponds to the temporary negative ion formation of ethylene. The differential cross sections are also calculated for the energy range from 1 to15 eV for the scattering angles between 0º and 180º. © 2013 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Protein domains that can fold in isolation are significant targets in diverse area of proteomics research as they are often readily analyzed by high-throughput methods. Here, we report IS-Dom, a dataset of Independent Structural Domains (ISDs) that are most likely to fold in isolation. IS-Dom was constructed by filtering domains from SCOP, CATH, and DomainParser using quantitative structural measures, which were calculated by estimating inter-domain hydrophobic clusters and hydrogen bonds from the full length protein's atomic coordinates. The ISD detection protocol is fully automated, and all of the computed interactions are stored in the server which enables rapid update of IS-Dom. We also prepared a standard IS-Dom using parameters optimized by maximizing the Youden's index. The standard IS-Dom, contained 54,860 ISDs, of which 25.5 % had high sequence identity and termini overlap with a Protein Data Bank (PDB) cataloged sequence and are thus experimentally shown to fold in isolation [coined autonomously folded domain (AFDs)]. Furthermore, our ISD detection protocol missed less than 10 % of the AFDs, which corroborated our protocol's ability to define structural domains that are able to fold independently. IS-Dom is available through the web server (), and users can either, download the standard IS-Dom dataset, construct their own IS-Dom by interactively varying the parameters, or assess the structural independence of newly defined putative domains. [ABSTRACT FROM AUTHOR]

This paper reports computational results of the total (complete) and total ionization cross- sections, for electron impact on Uracil (C4H4N2O2) and PO3OH for impact energies from the ionization threshold to 2 keV. The total cross-section is evaluated using quantum mechanical approach using Spherical Complex Optical Potential (SCOP) presented as sum of the elastic and inelastic cross-sections. The ionization cross-sections are extracted from total inelastic cross-section using Complex Optical Potential–ionization contribution (CSP-ic) method. The present results are, in general, found to be in good agreement with previous theoretical results. In absence of any theoretical or experimental data, present results for PO3OH will serve to fill the void in the data base and may also inspire the experimentalists for some measurements as it is very important target. [ABSTRACT FROM PUBLISHER]

The functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. The molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden Markov models of structural recognition. Here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. We find there is a remarkable conservation in the distribution of domains with respect to the molecular functions they perform in the three superkingdoms of life. In general, most of the protein repertoire is spent in functions related to metabolic processes but there are significant differences in the usage of domains for regulatory and extra-cellular processes both within and between superkingdoms. Our results support the hypotheses that the proteomes of superkingdom Eukarya evolved via genome expansion mechanisms that were directed towards innovating new domain architectures for regulatory and extra/intracellular process functions needed for example to maintain the integrity of multicellular structure or to interact with environmental biotic and abiotic factors (e.g., cell signaling and adhesion, immune responses, and toxin production). Proteomes of microbial superkingdoms Archaea and Bacteria retained fewer numbers of domains and maintained simple and smaller protein repertoires. Viruses appear to play an important role in the evolution of superkingdoms. We finally identify few genomic outliers that deviate significantly from the conserved functional design. These include Nanoarchaeum equitans, proteobacterial symbionts of insects with extremely reduced genomes, Tenericutes and Guillardia theta. These organisms spend most of their domains on information functions, including translation and transcription, rather than on metabolism and harbor a domain repertoire characteristic of parasitic organisms. In contrast, the functional repertoire of the proteomes of the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum was no different than the rest of bacteria, failing to support claims of them representing a separate superkingdom. In turn, Protista and Bacteria shared similar functional distribution patterns suggesting an ancestral evolutionary link between these groups. [ABSTRACT FROM AUTHOR]

This review deals with structural and functional features of glycoside hydrolases, a widespread group of enzymes present in almost all living organisms. Their catalytic domains are grouped into 120 amino acid sequence-based families in the international classification of the carbohydrate-active enzymes (CAZy database). At a higher hierarchical level some of these families are combined in 14 clans. Enzymes of the same clan have common evolutionary origin of their genes and share the most important functional characteristics such as composition of the active center, anomeric configuration of cleaved glycosidic bonds, and molecular mechanism of the catalyzed reaction (either inverting, or retaining). There are now extensive data in the literature concerning the relationship between glycoside hydrolase families belonging to different clans and/or included in none of them, as well as information on phylogenetic protein relationship within particular families. Summarizing these data allows us to propose a multilevel hierarchical classification of glycoside hydrolases and their homologs. It is shown that almost the whole variety of the enzyme catalytic domains can be brought into six main folds, large groups of proteins having the same three-dimensional structure and the supposed common evolutionary origin. [ABSTRACT FROM AUTHOR]

Abstract: The geometrical arrangement of the aromatic rings of phenylalanine, tyrosine, tryptophan and histidine has been analyzed at a database level using the X-ray crystal structure of proteins from PDB in order to find out the aromatic–aromatic (π–π) networks in proteins and to understand how these aromatic rings are connected with each-other in a specific π–π network. A stringent examination of the 7848 proteins indicates that close to 89% of the proteins have occurrence of at least a network of 2π or a higher π–π network. The occurrence of π–π networks in various protein superfamilies based on SCOP, CATH and EC classifiers has also been probed in the present work. In general, we find that multidomain and membrane proteins as well as lyases show a more number of these networks. Analysis of the distribution of angle between planes of two proximal aromatic rings (ϕ) distribution indicates that at a larger cutoff distance (between centroid of two aromatic rings), above 5Å, C–H⋯π interactions (T-shaped orientation) are more prevalent, while π–π interactions (stacked orientation) are more prevalent at a smaller cutoff distance. The connectivity patterns of π–π networks propose strong propensity of finding arrangement of aromatic residues as clusters rather than linear arrangement. We have also made a public domain database “Aromatic–Aromatic Interactions Database” (A2ID) comprising of all types of π–π networks and their connectivity pattern present in proteins. It can be accessed by url http://203.199.182.73/gnsmmg/databases/aidb/aidb.html. [Copyright &y& Elsevier]

Several descriptors of protein structure at the sequence and residue levels have been recently proposed. They are widely adopted in the analysis and prediction of structural and functional characteristics of proteins. Numerous in silico methods have been developed for sequence-based prediction of these descriptors. However, many of them do not have a public web-server and only a few integrate multiple descriptors to improve the predictions. We introduce iFC (integrated prediction of fold, class, and content) server that is the first to integrate three modern predictors of sequence-level descriptors. They concern fold type (PFRES), structural class (SCEC), and secondary structure content (PSSC-core). The server exploits relations between the three descriptors to implement a cross-evaluation procedure that improves over the predictions of the individual methods. The iFC annotates fold and class predictions as potentially correct/incorrect. When tested on datasets with low-similarity chains, for the fold prediction iFC labels 82% of the PFRES predictions as correct and the accuracy of these predictions equals 72%. The accuracy of the remaining 28% of the PFRES predictions equals 38%. Similarly, our server assigns correct labels for over 79% of SCEC predictions, which are shown to be 98% accurate, while the remaining SCEC predictions are only 15% accurate. These results are shown to be competitive when contrasted against recent relevant web-servers. Predictions on CASP8 targets show that the content predicted by iFC is competitive when compared with the content computed from the tertiary structures predicted by three best-performing methods in CASP8. The iFC server is available at . [ABSTRACT FROM AUTHOR]

Abstract: Existing protein structure classifications group proteins by overall structural similarity at the highest level and by evolutionary relationships at the lowest level, deriving higher-level groups by pairwise structure comparison. For this to be successful requires that large changes in structure are relatively rare in evolution and that proteins with no detectable evolutionary relationship do not converge on similar global chain conformations since this creates conflicts between structural and evolutionary consistency. Analysis of global structural changes using core topological descriptions for 4261 domains from classes C and D of the SCOP database and new measures of topological distance and consistency of classification showed that the topological consistency of SCOP folds is highly variable with some folds having no consistent description and significant overlaps between groups including some members of separate folds with identical topological descriptions. Topological clustering shows that including sufficient indels to allow family members to be joined would also require joining several distinct folds. We conclude that evolutionary changes in the global topology of protein domains are the root cause of many difficulties for present approaches to structure classification using pairwise comparison. As a resolution we propose that a purely structural classification should be created using an approach similar to that adopted by the Gene Ontology in which proteins are assigned labels describing structure. [ABSTRACT FROM AUTHOR]

Nonoverlapping closed loops of around 25-35 amino acids formed via nonlocal interactions at the loop ends have been proposed as an important unit of protein structure. This hypothesis is significant as such short loops can fold quickly and so would not be bound by the Leventhal paradox, giving insight into the possible nature of the funnel in protein folding. Previously, these closed loops have been identified either by sequence analysis (conservation and autocorrelation) or studies of the geometry of individual proteins. Given the potential significance of the closed loop hypothesis, we have explored a new strategy for determining closed loops from the insertions identified by the structural alignment of proteins sharing the same overall fold. We determined the locations of the closed loops in 37 pairs of proteins and obtained excellent agreement with previously published closed loops. The relevance of NMR structures to closed loop determination is briefly discussed. For cytochrome c, cytochrome b562 and triosephophate isomerase, independent folding units have been determined on the basis of hydrogen exchange experiments and misincorporation proton-alkyl exchange experiments. The correspondence between these experimentally derived foldons and the theoretically derived closed loops indicates that the closed loop hypothesis may provide a useful framework for analyzing such experimental data. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [ABSTRACT FROM AUTHOR]

One of the major research directions in bioinformatics is that of predicting the protein superfamily in large databases and classifying a given set of protein domains into superfamilies. The classification reflects the structural, evolutionary and functional relatedness. These relationships are embodied in hierarchical classification such as Structural Classification of Protein (SCOP), which is manually curated. Such classification is essential for the structural and functional analysis of proteins. Yet, a large number of proteins remain unclassified. We have proposed an unsupervised machine-learning FuzzyART neural network algorithm to classify a given set of proteins into SCOP superfamilies. The proposed method is fast learning and uses an atypical non-linear pattern recognition technique. In this approach, we have constructed a similarity matrix from p-values of BLAST all-against-all, trained the network with FuzzyART unsupervised learning algorithm using the similarity matrix as input vectors and finally the trained network offers SCOP superfamily level classification. In this experiment, we have evaluated the performance of our method with existing techniques on six different datasets. We have shown that the trained network is able to classify a given similarity matrix of a set of sequences into SCOP superfamilies at high classification accuracy. [ABSTRACT FROM AUTHOR]

Abstract: In this article we report calculations of the total elastic, Q el , total ionization, Q ion , and total (complete), Q T , cross-sections for the targets Li, Na, K having low ionization thresholds and high polarizability upon electron impact for energies from circa threshold to 2000eV. We have employed the well-known spherical complex optical potential (SCOP) formalism, which provides total elastic cross-section (Q el ) and its inelastic counterpart (Q inel ). The sum of Q el and Q inel gives the total (complete) cross-section, Q T , which is found to be very high at the lower energies (around 5eV). This is attributed to high polarizabilities and low ionization thresholds of these atoms. Q inel includes Q ion and we have developed a semi-empirical method, called complex scattering potential-ionization contribution (CSP-ic) to extract ionization cross-sections from calculated total inelastic cross-section. Present calculations also provide information on the total excitation processes of these targets. The calculated cross-sections are examined as functions of incident electron energy along with available comparison and overall good agreement is observed. [Copyright &y& Elsevier]

Abstract: In protein fold recognition, the main disadvantage of hidden Markov models (HMMs) is the employment of large-scale model architectures which require large data sets and high computational resources for training. Also, HMMs must consider sequential information about secondary structures of proteins, to improve prediction performance and reduce model parameters. Therefore, we propose a novel method for protein fold recognition based on a hidden Markov model, called a 9-state HMM. The method can (i) reduce the number of states using secondary structure information about proteins for each fold and (ii) recognize protein folds more accurately than other HMMs. [Copyright &y& Elsevier]

Abstract: In this study protein chains were characterized based on alignment-independent protein descriptors using three types of structural and sequence data; (i) C-α atom Euclidean distances, (ii) protein backbone ψ and φ angles and (iii) amino acid physicochemical properties (zz-scales). The descriptors were analyzed using principal component analysis (PCA) and further elucidated using the multivariate methods partial least-squares projections to latent structures discriminant-analysis (PLS-DA) and hierarchical-PLS-DA. The descriptors were applied to three protein chain datasets: (i) 82 chains classified, according to the structural classification of proteins (SCOP) scheme, as either all-α or all-β; (ii) 96 chains classified as either α + β or α/β and (iii) 6590 chains of all aforementioned classes selected from the PDB-select database. Results showed that the descriptors related to the secondary structure of the chains. The C-α Euclidean distances, and as expected, the protein backbone angles were found to be most important for the characterization and classification of chains. Assignment of SCOP classes using PLS-DA based on all descriptor types was satisfactory for all-α and all-β chains with more than 93% correct classifications of a large external test set, while the protein chains of types α/β and α + β was harder to discriminate between, resulting in 74% and 54% correct classifications, respectively. [Copyright &y& Elsevier]

Abstract: In this article we report calculations of the total elastic Q el, total ionization, Q ion, and total (complete), Q T, cross-sections for the germanium hydrides GeH X (X =1–4) and digermane (Ge2H6) upon electron impact for energies from circa threshold to 2000eV. Spherical Complex Optical Potential (SCOP) formalism is employed to evaluate Q el, Q inel and Q T. Total ionization cross-sections, Q ion, are derived from the total inelastic cross-sections, Q inel, using a semi-empirical formulation developed by us called ‘Complex Spherical Potential-ionization contribution’ (CSP-ic) method. A comparison of the various cross-sections is provided to show their relative contribution to the total cross-section Q T. Present results are compared with available experimental and theoretical data wherever possible and overall agreement is good. However, no experimental data on the Q ion are available for the germanium hydrides, GeH X , X =1–3 or digermane. [Copyright &y& Elsevier]

Abstract: Here, we present an automatic assignment of potential cognate ligands to domains of enzymes in the CATH and SCOP protein domain classifications on the basis of structural data available in the wwPDB. This procedure involves two steps; firstly, we assign the binding of particular ligands to particular domains; secondly, we compare the chemical similarity of the PDB ligands to ligands in KEGG in order to assign cognate ligands. We find that use of the Enzyme Commission (EC) numbers is necessary to enable efficient and accurate cognate ligand assignment. The PROCOGNATE database currently has cognate ligand mapping for 3277 (4118) protein structures and 351 (302) superfamilies, as described by the CATH and (SCOP) databases, respectively. We find that just under half of all ligands are only and always bound by a single domain, with 16% bound by more than one domain and the remainder of the ligands showing a variety of binding modes. This finding has implications for domain recombination and the evolution of new protein functions. Domain architecture or context is also found to affect substrate specificity of particular domains, and we discuss example cases. The most popular PDB ligands are all found to be generic components of crystallisation buffers, highlighting the non-cognate ligand problem inherent in the PDB. In contrast, the most popular cognate ligands are all found to be universal cellular currencies of reducing power and energy such as NADH, FADH2 and ATP, respectively, reflecting the fact that the vast majority of enzymatic reactions utilise one of these popular co-factors. These ligands all share a common adenine ribonucleotide moiety, suggesting that many different domain superfamilies have converged to bind this chemical framework. [Copyright &y& Elsevier]

Abstract: This paper addresses computational prediction of protein structural classes. Although in recent years progress in this field was made, the main drawback of the published prediction methods is a limited scope of comparison procedures, which in same cases were also improperly performed. Two examples include using protein datasets of varying homology, which has significant impact on the prediction accuracy, and comparing methods in pairs using different datasets. Based on extensive experimental work, the main aim of this paper is to revisit and reevaluate state of the art in this field. To this end, this paper performs a first-of-its-kind comprehensive and multi-goal study, which includes investigation of eight prediction algorithms, three protein sequence representations, three datasets with different homologies and finally three test procedures. Quality of several previously unused prediction algorithms, newly proposed sequence representation, and a new-to-the-field testing procedure is evaluated. Several important conclusions and findings are made. First, the logistic regression classifier, which was not previously used, is shown to perform better than other prediction algorithms, and high quality of previously used support vector machines is confirmed. The results also show that the proposed new sequence representation improves accuracy of the high quality prediction algorithms, while it does not improve results of the lower quality classifiers. The study shows that commonly used jackknife test is computationally expensive, and therefore computationally less demanding 10-fold cross-validation procedure is proposed. The results show that there is no statistically significant difference between these two procedures. The experiments show that sequence homology has very significant impact on the prediction accuracy, i.e. using highly homologous datasets results in higher accuracies. Thus, results of several past studies that use homologous datasets should not be perceived as reliable. The best achieved prediction accuracy for low homology datasets is about 57% and confirms results reported by Wang and Yuan [How good is the prediction of protein structural class by the component-coupled method?. Proteins 2000;38:165–175]. For a highly homologous dataset instance based classification is shown to be better than the previously reported results. It achieved 97% prediction accuracy demonstrating that homology is a major factor that can result in the overestimated prediction accuracy. [Copyright &y& Elsevier]

We propose a novel technique for automatically generating the SCOP classification of a protein structure with high accuracy. We achieve accurate classification by combining the decisions of multiple methods using the consensus of a committee (or an ensemble) classifier. Our technique, based on decision trees, is rooted in machine learning which shows that by judicially employing component classifiers, an ensemble classifier can be constructed to outperform its components. We use two sequence- and three structure-comparison tools as component classifiers. Given a protein structure and using the joint hypothesis, we first determine if the protein belongs to an existing category (family, superfamily, fold) in the SCOP hierarchy. For the proteins that are predicted as members of the existing categories, we compute their family-, superfamily-, andfold-level classifications using the consensus classifier. We show that we can significantly improve the classification accuracy compared to the individual component classifiers. In particular, we achieve error rates that are 3–12 times less than the individual classifiers' error rates at the family level, 1.5–4.5 times less at the superfamily level, and 1.1–2.4 times less at the fold level. [ABSTRACT FROM AUTHOR]

Abstract: Amphetamine abuse may be associated with adaptive changes in gene expression. In the present study, we used a newly developed cDNA array system comprising mouse KIAA (mKIAA) cDNA clones to examine changes in gene expression after chronic methamphetamine (MAP) treatment. Mice were daily treated with saline or MAP (2 mg/kg, ip) for 2 weeks. Approximately 800 mKIAA clones were blotted onto a nylon membrane and hybridized with 33P-labeled DNA derived from mRNAs from mouse whole brain. MAP-induced changes were found in several clones by using whole brain mRNA. Since gene expression of Per2, one of the period protein-related proteins, was the most affected by MAP treatment, its expression was further analyzed in pooled hippocampi from 20 mice that had been treated with saline or MAP (2 mg/kg, ip) for 2 weeks. The gene expression and protein expression of Per2 in the hippocampus were increased by MAP treatment. In the hippocampus, Per2 gene expression was under the regulation of circadian rhythm and increases in Per2 expression were due to the phase shift induced by chronic MAP treatment. These findings suggest that unique expression changes of period protein-related proteins in the hippocampus occur in MAP abuse. [Copyright &y& Elsevier]

Present article reports calculation of elastic, momentum transfer, ionization, and total cross sections for electron scattering from C 2 N 2 , C 4 N 2 , C 6 N 2 , and HC 5 N molecules, relevant to Titan's atmosphere. The cross sections are predicted using spherical complex optical potential and complex potential ionization contribution method in the energy range from ionization threshold of the molecules to 5 keV. The cross section data reported here consider geometrical screening correction to avoid overestimation of cross section due to the overlap of charge density. A strong correlation is observed between Q i o n m a x and (α / I) 1 2 for C 2 N 2 , C 4 N 2 , and C 6 N 2 molecular systems, which confirms the consistency of predicted ionization data. The cross sections reported here are important for mass spectrometry, especially in modelling Titan's atmosphere due the presence of these molecules along with abundant electrons in its environment. Most of the data are reported for the first time. [Display omitted] • Electron induced collision channels are studied for C 2 N 2 , C 4 N 2 , C 6 N 2 , and HC 5 N using quantum mechanical formalism. • Cross section values for important channels like total, elastic, momentum transfer and ionization are calculated using the same methodology reducing errors. • The computations are performed for a wide energy range and scattering centres are decided on the basis of electrostatic potential surface method. • Geometrical screening correction is included to reduce overestimation arising from group additivity rule. [ABSTRACT FROM AUTHOR]

In this paper, a descriptive and detailed theoretical analysis is carried out on electron scattering of formyl fluoride (HFCO) covering a wide impact energy range of 0.1 eV–5000 eV. Due to such a wide impact energy range, we were able to calculate the variety of interaction processes such as eigen phase study to infer about the resonances, vertical electron excitations, differential cross-sections, momentum transfer cross-sections, ionization cross-sections and total scattering cross-sections for electron impact on formyl fluoride. To compute these cross-sections for this energy range, we have used an amalgamation of two theoretical methodologies namely R-matrix via. Quantemol-N, valid for the low energy calculations from 0.1 eV to 20 eV and the Spherical Complex Optical Potential (SCOP) applicable from ionization threshold of the target to 5000 eV. There is a smooth cross over of total cross-sections observed between these two methods at the incident energy just below 20 eV. The present study becomes more important as it presents the electron impact cross-sections on HFCO for the first time and thus provides a reference data set for HFCO over an extensive impact energy range. The data set is important as Hydrofluorocarbons (HFCs) are one class of potential chlorofluorocarbons (CFC) substituents which mainly reacts with the OH radical in the atmosphere leading to the formation of the dominant intermediate product HFCO. • The study provides reference data for HFCO over a wide energy range of 0.1eV-5keV. • Maiden theoretical attempt to find electron impact cross-sectional data for HFCO. • Total cross sections are computed using R-matrix and SCOP for e-HFCO. • Compared the contribution of elastic and inelastic cross sections for e-HFCO. • First attempt to estimate partial ionization cross-sections for HFCO. [ABSTRACT FROM AUTHOR]

• An ASHP coupled with an EAHX system is proposed and modelled. • The ASHP- EAHX behaviour is tested in four locations with different climates. • The model has been validated with a real case. • The ASHP- EAHX allows to use ASHP also with lower external temperatures. • For cold extremely climate, the reduction of the shutdown periods of ASHP. Geothermal energy has a huge potential in building applications. This paper proposes the use of an Air-Source Heat Pump (ASHP) system coupled with a Horizontal Earth-To-Air Heat Exchanger (EAHX) to reduce energy consumption in buildings. The novelty is to geothermally pre-heat or pre-cool the air source of the ASHP through the EAHX, reducing the electric power needed, keeping constant heating/cooling capacity. The behaviour of ASHP-EAHX system has been investigated by a numerical model implemented in TRNSYS. A total of 54 combinations have been obtained and tested varying ground thermal properties, burial depth, air flow rate and pipe length. The model has been validated with a real case showing a good agreement between simulated and monitored data. The study is focused on the city of Turin (North of Italy), compared with Brindisi (South of Italy), and extremely cold and hot climates like Tromsø (Norway) and Béchar (Algeria), respectively. The ASHP-EAXH performance has been investigated, by the comparison with the traditional ASHP, using different coefficients, such as the Coefficient of Performance (COP), the Energy Efficiency Ratio (EER), the Seasonal Coefficient of Performance (SCOP), and the Seasonal Energy Efficiency Ratio (SEER). The paper reveals how the ASHP-EAHX system show higher performance compared to the traditional ASHP, in all seasons. The overall merit is, for cold extremely climate, the reduction of the shutdown periods, when the outside temperature is below the limit operating temperature, and to allow the extension of the use of the heat pump to locations, where it is currently not convenient for the average outside temperature lower than the limit operating temperature of the heat pump. [ABSTRACT FROM AUTHOR]

• The Present work focus on the theoretical calculation of the electron impact on iodine diatomic molecule. The prime interesting point is the complexity involved in the calculation of the high order electronic excited state. The work presents the cross-sectional data for merely all possible scattering phenomena occurring at low energy regime 0.1 eV to 20 eV. The highlighted data is the DEA cross sections and the Total cross sections using two different approaches. We also provide the study on the resonance using two different methodology indicating pros and cons of the methods. A theoretical analysis is performed for electron interactions with the Iodine molecule (I 2) for incident energies ranging from 0.1 eV to 20 eV. The calculations were carried out using Quantemol-N package, which uses the UK Molecular R-matrix Codes. Electron interactions with the I 2 molecule have been studied with several target models in its equilibrium geometry, and the results are reported for the optimized target model. Scattering calculations are performed to provide resonance parameters along with Dissociative Electron Attachment (DEA) Cross-Sections. In addition, the study also focussed on the estimation of various cross-sections such as elastic, electronic excitation, differential, momentum transfer, ionization and total cross-sections. Many of these cross-sections reported here are for the first time for electron interaction with the iodine molecule to the best of our knowledge. [ABSTRACT FROM AUTHOR]

A concept of Air-Cooled Heat Pump (ACHP) coupled with a Horizontal Air-Ground Heat Exchanger (HAGHE), also called Horizontal Earth-To-Air Heat Exchanger (EAHX), has been proposed. The Air-Cooled Heat Pump is a system which transfers heat from outside source (air) to inside sink (water) and vice versa in summertime. The innovation is to provide a geothermal treatment of pre-heating/cooling of air before meeting the evaporator in winter or the condenser in summer of the heat pump. Besides, it is known that the variations of the ground temperature, respect to the external air one, are mitigated already in the first layers of the ground throughout the year, due to the high thermal inertia of the ground, letting the heat pump work with more mitigated conditions, improving the performances. The behaviour of HAGHE has been investigated by varying the length and the installation depth of the probes, the air flow rate and the ground thermal properties. All the combinations have been implemented using TRNSYS 17 software (Transient System Simulation Program) to obtain the outlet temperatures from HAGHE, resulting from the 54 configurations. The results are compared in terms of Coefficient of Performance (COP) in wintertime and Energy Efficiency Ratio (EER) in summertime between configurations with and without the coupling with HAGHE. In addition, two seasonal performance SCOP and SEER coefficients have been calculated considering, not only the inlet air temperatures into the Air-Cooled Heat Pump, but also their frequency of occurrence, the off-set external temperature (16 °C), the nominal external temperature and heating and cooling loads. [ABSTRACT FROM AUTHOR]