Object-oriented query language facilitating construction of new objects

In object-oriented database systems, messages can be used to manipulate the database; however, a query language is still a required component of any kind of database system. In the paper, we describe a query language for object-oriented databases where both objects as well as behaviour defined in them are handled. Not only existing objects are manipulated; the introduction of new relationships and new objects constructed out of existing ones is also facilitated. The operations supported in the described query language subsumes those of the relational algebra aiming at a more powerful query language than the relational algebra. Among the additional operators, there is an operator that handles the application of an aggregate function on objects in an operand while still having the result possessing the characteristics of an operand. The result of a query as well as the operands are considered to have a pair of sets, a set of objects and a set of message expressions; where a message expression is a sequence of messages. A message expression handles both stored and derived values and hence provides a full computational power without having an embedded query language with impedance mismatch. Therefore the closure property is maintained by having the result of a query possessing the characteristics of an operand. Furthermore, we define a set of objects and derive a set of message expressions for every class; hence any class can be an operand. Moreover, the result of a query has the characteristics of a class and its superclass/subclass relationships with the operands are established to make it persistent. © 1993

Combining Optimal Control Theory and Molecular Dynamics for Protein Folding

A new method to develop low-energy folding routes for proteins is presented. The novel aspect of the proposed approach is the synergistic use of optimal control theory with Molecular Dynamics (MD). In the first step of the method, optimal control theory is employed to compute the force field and the optimal folding trajectory for the atoms of a Coarse-Grained (CG) protein model. The solution of this CG optimization provides an harmonic approximation of the true potential energy surface around the native state. In the next step CG optimization guides the MD simulation by specifying the optimal target positions for the atoms. In turn, MD simulation provides an all-atom conformation whose positions match closely the reference target positions determined by CG optimization. This is accomplished by Targeted Molecular Dynamics (TMD) which uses a bias potential or harmonic restraint in addition to the usual MD potential. Folding is a dynamical process and as such residues make different contacts during the course of folding. Therefore CG optimization has to be reinitialized and repeated over time to accomodate these important changes. At each sampled folding time, the active contacts among the residues are recalculated based on the all-atom conformation obtained from MD. Using the new set of contacts, the CG potential is updated and the CG optimal trajectory for the atoms is recomputed. This is followed by MD. Implementation of this repetitive CG optimization - MD simulation cycle generates the folding trajectory. Simulations on a model protein Villin demonstrate the utility of the method. Since the method is founded on the general tools of optimal control theory and MD without any restrictions, it is widely applicable to other systems. It can be easily implemented with available MD software packages

Prediction of Optimal Folding Routes of Proteins That Satisfy the Principle of Lowest Entropy Loss: Dynamic Contact Maps and Optimal Control

An optimization model is introduced in which proteins try to evade high energy regions of the folding landscape, and prefer low entropy loss routes during folding. We make use of the framework of optimal control whose convenient solution provides practical and useful insight into the sequence of events during folding. We assume that the native state is available. As the protein folds, it makes different set of contacts at different folding steps. The dynamic contact map is constructed from these contacts. The topology of the dynamic contact map changes during the course of folding and this information is utilized in the dynamic optimization model. The solution is obtained using the optimal control theory. We show that the optimal solution can be cast into the form of a Gaussian Network that governs the optimal folding dynamics. Simulation results on three examples (CI2, Sso7d and Villin) show that folding starts by the formation of local clusters. Non-local clusters generally require the formation of several local clusters. Non-local clusters form cooperatively and not sequentially. We also observe that the optimal controller prefers “zipping” or small loop closure steps during folding. The folding routes predicted by the proposed method bear strong resemblance to the results in the literature

Imaging of articular cartilage [Kikirdak lezyonlarinda görüntüleme.]

PubMed ID: 18180582There have been many improvements in joint cartilage imaging in recent years with the development of new imaging methods. The purpose of cartilage imaging is to assess the integrity of the cartilage surface, the thickness and volume of the cartilage matrix and its relationship with the subchondral bone. Direct radiography, the conventional imaging method for the skeletal system, is not sufficient for assessing the joint cartilage, nor are arthrography, computed tomography, and arthrography together with computed tomography. Moreover, biomechanical changes in the joint cartilage cannot be assessed with these methods. Magnetic resonance imaging (MRI), with its superior contrast resolution and multiplanar imaging capability across tissues, has become the primary diagnostic method for assessment of joint pathologies. The morphological features of the joint cartilage can be assessed adequately with the use of MRI sequences specific to the cartilage. Appropriate use of MRI sequences to determine the type of cartilage damage, the presence and degree of accompanying pathologies in the subchondral bone will help minimize diagnostic errors. This article reviews cartilage imaging in the following aspects: the technique used in MRI for cartilage imaging, findings of cartilage pathology, and anticipation of future cartilage imaging

Imaging techniques in the diagnosis of soft tissue sarcoma

1st Congress of the Balkan-Union-of-Oncology -- JUL 03-07, 1996 -- ATHENS, GREECEWOS: A1996BG40Z00083Balkan Union Onco

Diagnostic imaging of the rotator cuff [Rotator manşet: Görüntüleme.]

PubMed ID: 14578661The importance of imaging modalities in the evaluation of the rotator cuff has increased thanks to the development of non-invasive methods. An optimum application of the technique, appreciation of the anatomical details and imaging pitfalls, and proper interpretation of clinical findings should be incorporated in order to increase diagnostic accuracy. Ultrasonography (US) and magnetic resonance imaging (MRI) are commonly used for rotator cuff pathologies. The former has a high diagnostic accuracy in full-thickness tears, but requires operator dependency and long-term training. Both US and MRI require sophisticated equipment and present difficulties in distinguishing between partial and small full-thickness tears. In full-thickness tears, MRI may be more appropriate if imaging findings are likely to alter the course of surgical treatment. However, it is not necessary in patients in whom US may clearly show tendinosis. Magnetic resonance imaging or MR arthrography may be required in order to evaluate partial tears or suspicious small full-thickness tears in patients unresponsive to conservative therapy. A close collaboration is essential between the radiologist and the shoulder surgeon in the interpretation of clinical findings. The diagnostic accuracy will increase if the examinations are performed by a musculoskeletal radiologist