In-vehicle communication networks : a literature survey

The increasing use of electronic systems in automobiles instead of mechanical and hydraulic parts brings about advantages by decreasing their weight and cost and providing more safety and comfort. There are many electronic systems in modern automobiles like antilock braking system (ABS) and electronic brakeforce distribution (EBD), electronic stability program (ESP) and adaptive cruise control (ACC). Such systems assist the driver by providing better control, more comfort and safety. In addition, future x-by-wire applications aim to replace existing braking, steering and driving systems. The developments in automotive electronics reveal the need for dependable, efficient, high-speed and low cost in-vehicle communication. This report presents the summary of a literature survey on in-vehicle communication networks. Different in-vehicle system domains and their requirements are described and main invehicle communication networks that have been used in automobiles or are likely to be used in the near future are discussed and compared with key references

Mental disorders frequency alternative and complementary medicine usage among patients with hypertension and type 2 diabetes mellitus

Objectives: Diabetes mellitus (DM) and hypertension (HT) are chronic disorders with which mental disorders may coexist and for which patients may resort to alternative medicine use. Alternative and complementary medicine is a treatment option that patients tend to use. This study is to determine the prevalence of mental disorders among patients diagnosed with DM and HT and their use of alternative medicine methods.Materials and Methods The study was conducted in a primary care setting. The data were collected from the Family Health Center No. 4 at Çankaya, Ankara, Turkey. It involved patients aged between 18 and 65, who were on follow‑up treatment for DM and HT. Patients accepted to participate in the study were administered the sociodemographic data form, the Primary Care Evaluation of Mental Disorders (PRIME‑MD) questionnaire and the alternative medicine inquiry form.Participants: One hundred and sixteen patients with HT and 119 patients with DM (type 2) were recruited for the study.Results: In this study, 47.4% of HT patients and 53.8% of the DM patients were diagnosed with a PRIME‑MD. The most commonly encountered disorder was mood disorders, in 37.1% of the HT patients and 45.4% of the DM patients. In this study, four HT patients (0.3%) and no DM patients stated that they resorted to complimentary medicine, which can use be used alongside conventional medical treatment and may help to feel better and cope better with any chronic condition. All four HT patients were using multivitamin combinations to support the treatment. As the alternative medicine usage was described as treatment used instead of conventional medical treatment we did not find any patient using alternative medicine.Conclusions: Mental disorders may coexist with HT and DM. Some of the HT and DM patients suffering from a mental disorder seek psychiatric support, while others do not. We believe that it is important to examine patients for mental disorders, while being followed‑up for a chronic disease.Keywords: Alternative medicine, diabetes mellitus, hypertension, mental disorde

Minimum Configuration Insensitive Multifunctional Current-Mode Biquad Using Current Conveyors and All-Grounded Passive Components

This paper proposes a new current conveyorbased high-output impedance single-input three-output current mode filter with minimum configuration. It contains two dual output second generation current conveyors, one third generation dual output current conveyor, and four grounded resistors and capacitors. The circuit simultaneously provides low-pass, band-pass, and high-pass filtering outputs, without any passive component matching conditions and restrictions on input signals. Additionally, the proposed circuit offers following advantages: Minimum active and passive element count, high output and low input impedances, suitable for cascading identical currentmode sections, all passive elements are grounded (no virtual grounding), low natural frequency and Q-factor sensitivities. The influences of non-ideal current conveyors on the proposed circuit are researched in the last

Specialized dynamical properties of promiscuous residues revealed by simulated conformational ensembles

The ability to interact with different partners is one of the most important features in proteins. Proteins that bind a large number of partners (hubs) have been often associated with intrinsic disorder. However, many examples exist of hubs with an ordered structure, and evidence of a general mechanism promoting promiscuity in ordered proteins is still elusive. An intriguing hypothesis is that promiscuous binding sites have specific dynamical properties, distinct from the rest of the interface and pre-existing in the protein isolated state. Here, we present the first comprehensive study of the intrinsic dynamics of promiscuous residues in a large protein data set. Different computational methods, from coarse-grained elastic models to geometry-based sampling methods and to full-atom Molecular Dynamics simulations, were used to generate conformational ensembles for the isolated proteins. The flexibility and dynamic correlations of interface residues with a different degree of binding promiscuity were calculated and compared considering side chain and backbone motions, the latter both on a local and on a global scale. The study revealed that (a) promiscuous residues tend to be more flexible than nonpromiscuous ones, (b) this additional flexibility has a higher degree of organization, and (c) evolutionary conservation and binding promiscuity have opposite effects on intrinsic dynamics. Findings on simulated ensembles were also validated on ensembles of experimental structures extracted from the Protein Data Bank (PDB). Additionally, the low occurrence of single nucleotide polymorphisms observed for promiscuous residues indicated a tendency to preserve binding diversity at these positions. A case study on two ubiquitin-like proteins exemplifies how binding promiscuity in evolutionary related proteins can be modulated by the fine-tuning of the interface dynamics. The interplay between promiscuity and flexibility highlighted here can inspire new directions in protein-protein interaction prediction and design methods. © 2013 American Chemical Society

Human Cancer Protein-Protein Interaction Network: A Structural Perspective

Protein-protein interaction networks provide a global picture of cellular function and biological processes. Some proteins act as hub proteins, highly connected to others, whereas some others have few interactions. The dysfunction of some interactions causes many diseases, including cancer. Proteins interact through their interfaces. Therefore, studying the interface properties of cancer-related proteins will help explain their role in the interaction networks. Similar or overlapping binding sites should be used repeatedly in single interface hub proteins, making them promiscuous. Alternatively, multi-interface hub proteins make use of several distinct binding sites to bind to different partners. We propose a methodology to integrate protein interfaces into cancer interaction networks (ciSPIN, cancer structural protein interface network). The interactions in the human protein interaction network are replaced by interfaces, coming from either known or predicted complexes. We provide a detailed analysis of cancer related human protein-protein interfaces and the topological properties of the cancer network. The results reveal that cancer-related proteins have smaller, more planar, more charged and less hydrophobic binding sites than non-cancer proteins, which may indicate low affinity and high specificity of the cancer-related interactions. We also classified the genes in ciSPIN according to phenotypes. Within phenotypes, for breast cancer, colorectal cancer and leukemia, interface properties were found to be discriminating from non-cancer interfaces with an accuracy of 71%, 67%, 61%, respectively. In addition, cancer-related proteins tend to interact with their partners through distinct interfaces, corresponding mostly to multi-interface hubs, which comprise 56% of cancer-related proteins, and constituting the nodes with higher essentiality in the network (76%). We illustrate the interface related affinity properties of two cancer-related hub proteins: Erbb3, a multi interface, and Raf1, a single interface hub. The results reveal that affinity of interactions of the multi-interface hub tends to be higher than that of the single-interface hub. These findings might be important in obtaining new targets in cancer as well as finding the details of specific binding regions of putative cancer drug candidates

SCOWLP classification: Structural comparison and analysis of protein binding regions

<p>Abstract</p> <p>Background</p> <p>Detailed information about protein interactions is critical for our understanding of the principles governing protein recognition mechanisms. The structures of many proteins have been experimentally determined in complex with different ligands bound either in the same or different binding regions. Thus, the structural interactome requires the development of tools to classify protein binding regions. A proper classification may provide a general view of the regions that a protein uses to bind others and also facilitate a detailed comparative analysis of the interacting information for specific protein binding regions at atomic level. Such classification might be of potential use for deciphering protein interaction networks, understanding protein function, rational engineering and design.</p> <p>Description</p> <p>Protein binding regions (PBRs) might be ideally described as well-defined separated regions that share no interacting residues one another. However, PBRs are often irregular, discontinuous and can share a wide range of interacting residues among them. The criteria to define an individual binding region can be often arbitrary and may differ from other binding regions within a protein family. Therefore, the rational behind protein interface classification should aim to fulfil the requirements of the analysis to be performed.</p> <p>We extract detailed interaction information of protein domains, peptides and interfacial solvent from the SCOWLP database and we classify the PBRs of each domain family. For this purpose, we define a similarity index based on the overlapping of interacting residues mapped in pair-wise structural alignments. We perform our classification with agglomerative hierarchical clustering using the complete-linkage method. Our classification is calculated at different similarity cut-offs to allow flexibility in the analysis of PBRs, feature especially interesting for those protein families with conflictive binding regions.</p> <p>The hierarchical classification of PBRs is implemented into the SCOWLP database and extends the SCOP classification with three additional family sub-levels: Binding Region, Interface and Contacting Domains. SCOWLP contains 9,334 binding regions distributed within 2,561 families. In 65% of the cases we observe families containing more than one binding region. Besides, 22% of the regions are forming complex with more than one different protein family.</p> <p>Conclusion</p> <p>The current SCOWLP classification and its web application represent a framework for the study of protein interfaces and comparative analysis of protein family binding regions. This comparison can be performed at atomic level and allows the user to study interactome conservation and variability. The new SCOWLP classification may be of great utility for reconstruction of protein complexes, understanding protein networks and ligand design. SCOWLP will be updated with every SCOP release. The web application is available at <url>http://www.scowlp.org</url>.</p

Structural Similarity and Classification of Protein Interaction Interfaces

Interactions between proteins play a key role in many cellular processes. Studying protein-protein interactions that share similar interaction interfaces may shed light on their evolution and could be helpful in elucidating the mechanisms behind stability and dynamics of the protein complexes. When two complexes share structurally similar subunits, the similarity of the interaction interfaces can be found through a structural superposition of the subunits. However, an accurate detection of similarity between the protein complexes containing subunits of unrelated structure remains an open problem

Beauty Is in the Eye of the Beholder: Proteins Can Recognize Binding Sites of Homologous Proteins in More than One Way

Understanding the mechanisms of protein–protein interaction is a fundamental problem with many practical applications. The fact that different proteins can bind similar partners suggests that convergently evolved binding interfaces are reused in different complexes. A set of protein complexes composed of non-homologous domains interacting with homologous partners at equivalent binding sites was collected in 2006, offering an opportunity to investigate this point. We considered 433 pairs of protein–protein complexes from the ABAC database (AB and AC binary protein complexes sharing a homologous partner A) and analyzed the extent of physico-chemical similarity at the atomic and residue level at the protein–protein interface. Homologous partners of the complexes were superimposed using Multiprot, and similar atoms at the interface were quantified using a five class grouping scheme and a distance cut-off. We found that the number of interfacial atoms with similar properties is systematically lower in the non-homologous proteins than in the homologous ones. We assessed the significance of the similarity by bootstrapping the atomic properties at the interfaces. We found that the similarity of binding sites is very significant between homologous proteins, as expected, but generally insignificant between the non-homologous proteins that bind to homologous partners. Furthermore, evolutionarily conserved residues are not colocalized within the binding sites of non-homologous proteins. We could only identify a limited number of cases of structural mimicry at the interface, suggesting that this property is less generic than previously thought. Our results support the hypothesis that different proteins can interact with similar partners using alternate strategies, but do not support convergent evolution