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At least 649 records · Page 36Linked to original sources
PubMedDate not supplied

Discovering H-bonding rules in crystals with inductive logic programming.

In the domain of crystal engineering, various schemes have been proposed for the classification of hydrogen bonding (H-bonding) patterns observed in 3D crystal structures. In this study, the aim is to complement these schemes with rules that predict H-bonding in crystals from 2D structural information only. Modern computational power and the advances in inductive logic programming (ILP) can now provide computational chemistry with the opportunity for extracting structure-specific rules from large databases that can be incorporated into expert systems. ILP technology is here applied to H-bonding in crystals to develop a self-extracting expert system utilizing data in the Cambridge Structural Database of small molecule crystal structures. A clear increase in performance was observed when the ILP system DMax was allowed to refer to the local structural environment of the possible H-bond donor/acceptor pairs. This ability distinguishes ILP from more traditional approaches that build rules on the basis of global molecular properties.

Artificial Intelligence↗
PubMed2006

Medium scale integration of molecular logic gates in an automaton.

The assembly of molecular automata that perform increasingly complex tasks, such as game playing, presents an unbiased test of molecular computation. We now report a second-generation deoxyribozyme-based automaton, MAYA-II, which plays a complete game of tic-tac-toe according to a perfect strategy. In silicon terminology, MAYA-II represents the first "medium-scale integrated molecular circuit", integrating 128 deoxyribozyme-based logic gates, 32 input DNA molecules, and 8 two-channel fluorescent outputs across 8 wells.

Algorithms↗
PubMed2005

9-(cycloheptatrienylidene)-fluorene derivative: remarkable ratiometric pH sensor and computing switch with NOR logic gate.

2,7-Bis(4-dimethylaminophenyl)-9-(cycloheptatrienylidene)fluorene (1) was synthesized and characterized. 1 could be used as a fluorescent sensor either for pH or for pyridinium halide. Integrated with the ratiometric method and an NOR logic gate, a tunable two-input/multi-output system was presented on the basis of this single molecule. [structure: see text]

Journal Article↗
PubMed1997

The discovery of indicator variables for QSAR using inductive logic programming.

A central problem in forming accurate regression equations in QSAR studies is the selection of appropriate descriptors for the compounds under study. We describe a novel procedure for using inductive logic programming (ILP) to discover new indicator variables (attributes) for QSAR problems, and show that these improve the accuracy of the derived regression equations. ILP techniques have previously been shown to work well on drug design problems where there is a large structural component or where clear comprehensible rules are required. However, ILP techniques have had the disadvantage of only being able to make qualitative predictions (e.g. active, inactive) and not to predict real numbers (regression). We unify ILP and linear regression techniques to give a QSAR method that has the strength of ILP at describing steric structure, with the familiarity and power of linear regression. We evaluated the utility of this new QSAR technique by examining the prediction of biological activity with and without the addition of new structural indicator variables formed by ILP. In three out of five datasets examined the addition of ILP variables produced statistically better results (P < 0.01) over the original description. The new ILP variables did not increase the overall complexity of the derived QSAR equations and added insight into possible mechanisms of action. We conclude that ILP can aid in the process of drug design.

Animals↗
PubMedDate not supplied

One axon, many kinesins: What's the logic?

A large number of membrane-bounded organelles, protein complexes, and mRNAs are transported along microtubules to different locations within the neuronal axon. Axonal transport in the anterograde direction is carried out by members of a superfamily of specialized motor proteins, the kinesins. All kinesins contain a conserved motor domain that hydrolyses ATP to generate movement along microtubules. Regions outside the motor domain are responsible for cargo binding and regulation of motor activity. Present in a soluble, inactive form in the cytoplasm, kinesins are activated upon cargo binding. Selective targeting of different types of kinesin motors to specific cargoes is directed by amino acid sequences situated in their variable tails. Cargo proteins with specific function at their destination, bind directly to specific kinesins for transport. Whereas most kinesins move to microtubule plus-ends, a small number of them move to microtubule minus-ends, and may participate in retrograde axonal transport. Axonal transport by kinesins has a logic: Fully assembled, multisubunit, functional complexes (e.g., ion channel complexes, signaling complexes, RNA-protein complexes) are transported to their destination by kinesin motors that interact transiently (i.e., during transport only) with one of the complexes' subunits.

Animals↗
PubMed1999

The estrogen receptor: a logical target for the prevention of breast cancer with antiestrogens.

A strategy for the prevention of breast cancer has been refined over the last century beginning with the first observation that oophorectomy caused disease regression in some patients, to the identification of the estrogen receptor some 60 years later, and finally to the synthesis of the first nonsteroidal antiestrogen. Tamoxifen was the first clinically useful antiestrogen and has been used for the treatment of breast cancer for the last twenty-one years in the United States. It is therefore a logical progression that antiestrogens are now recognized as useful agents for the prevention of breast cancer. We will discuss the estrogen receptor as a target for the treatment and now the prevention of breast cancer. Data from the National Surgical and Bowel Project (NSABP)4 tamoxifen prevention trial will be discussed with the preliminary results of two other European studies. The status of breast cancer prevention to date involves the comparison of the current standard of prevention, tamoxifen, with the osteoporosis prevention drug, raloxifene in an ongoing trial called Study of Tamoxifen and Raloxifene (STAR).

Animals↗
PubMed2003

Persecutors or victims? The moral logic at the heart of eating disorders.

Eating Disorders, particularly anorexia and bulimia, are of immense contemporary importance and interest. News stories depicting the tragic effects of eating disorders command wide attention. Almost everybody in society has been touched by eating disorders in one way or another, and contemporary obsession with body image and diet fuels fascination with this problem. It is unclear why people develop eating disorders. Clinical and sociological studies have provided important information relating to the relational systems in which eating disorders are mainly found. This paper shows that their explanations are not conclusive and points out that the reasons why people develop eating disorders should not be found in the dysfunctional interactions occurring in both familial and social systems, but in the moral beliefs that underlie these interactions. Eating disorders are impossible to understand or explain, unless they are viewed in the light of these beliefs. A moral logic, that is a way of thinking of interpersonal relations in moral terms, gives shape to and justifies the clinical condition, and finds consistent expression in abnormal eating behaviour. The analysis offered here is not mainstream either in philosophy (eating disorders are in fact seldom the subject of philosophical investigation) or in clinical psychology (the methods of philosophical analysis are in fact seldom utilised in clinical psychology). However, this paper offers a important contribution to the understanding of such a dramatic and widespread condition, bringing to light the deepest reasons, which are moral in nature, that contribute to the explanation of this complex phenomenon.

Culture↗
PubMed1979

A fuzzy logical model of letter identification.

Stimuli were generated by factorially varying two sets of features that distinguish between two letter patterns. Subjects rated the degree to which each stimulus was an instance of one letter rather than the alternative. The obtained ratings were relatively continuous and systematic functions of the feature manipulations. The results were well accounted for by a model in which (a) each feature has an associated fuzzy predicate that is used to independently evaluate the degree to which it is true that the feature is present in the stimulus; (b) the featural truth values are integrated according to fuzzy logical expressions that correspond directly to propositional descriptions of each letter pattern; and (c) the resulting goodness of match to the stimulus for each letter is compared to that of the alternatives to determine the final identification.

Discrimination Learning↗
PubMed1998

A new logic for DNA engineering using recombination in Escherichia coli.

A straightforward way to engineer DNA in E. coli using homologous recombination is described. The homologous recombination reaction uses RecE and RecT and is transferable between E. coli strains. Several target molecules were manipulated, including high copy plasmids, a large episome and the E. coli chromosome. Sequential steps of homologous or site-specific recombination were used to demonstrate a new logic for engineering DNA, unlimited by the disposition of restriction endonuclease cleavage sites or the size of the target DNA.

Bacterial Proteins↗
PubMed2000

Alternative dielectrics to silicon dioxide for memory and logic devices

The silicon-based microelectronics industry is rapidly approaching a point where device fabrication can no longer be simply scaled to progressively smaller sizes. Technological decisions must now be made that will substantially alter the directions along which silicon devices continue to develop. One such challenge is the need for higher permittivity dielectrics to replace silicon dioxide, the properties of which have hitherto been instrumental to the industry's success. Considerable efforts have already been made to develop replacement dielectrics for dynamic random-access memories. These developments serve to illustrate the magnitude of the now urgent problem of identifying alternatives to silicon dioxide for the gate dielectric in logic devices, such as the ubiquitous field-effect transistor.

Journal Article↗
PubMed2006

Evolution of alternative transcriptional circuits with identical logic.

Evolution of gene regulation is an important contributor to the variety of life. Here, we analyse the evolution of a combinatorial transcriptional circuit composed of sequence-specific DNA-binding proteins that are conserved among all eukaryotes. This circuit regulates mating in the ascomycete yeast lineage. We first identify a group of mating genes that was transcriptionally regulated by an activator in a fungal ancestor, but is now transcriptionally regulated by a repressor in modern bakers' yeast. Despite this change in regulatory mechanism, the logical output of the overall circuit remains the same. By examining the regulation of mating in modern yeasts that are related to different extents, we deduce specific, sequential changes in both cis- and trans-regulatory elements that constitute the transition from positive to negative regulation. These changes indicate specific mechanisms by which fitness barriers were traversed during the transition.

Amino Acid Sequence↗
PubMed2003

Relationship between habitual breakfast and intellectual performance (logical reasoning) in well-nourished schoolchildren of Madrid (Spain).

OBJECTIVE: To determine the relationships between habitual breakfast habits and performance in verbal aptitude, logical reasoning and mathematical tests in a group of well-nourished scholars from Madrid. DESIGN: The study subjects were 180 children between 9 and 13 y of age. A dietetic study was undertaken using a 7-day food record. Scholastic aptitude was examined using the scholastic aptitude test (SAT-1) test. RESULTS: Breakfast made up 19.1% of total daily intake. No differences were found between subjects in terms of personal data or total diet with respect to whether they habitually took adequate breakfasts (AB) (ie, more than 20% of daily energy being provided by this meal) or inadequate breakfasts (IB) (less than 20%). However, AB subjects achieved better reasoning scores in the SAT-1 test. CONCLUSIONS: The normal breakfast habits of schoolchildren should be taken into account when studying diet-mental function relationships, even when studying well-nourished populations.

Adolescent↗
PubMed2005

A switchable macrocycle-clip complex that functions as a NOR logic gate.

We have synthesized a new molecular switch-based on a macrocycle-clip complex-whose switching behavior not only can be controlled through the use of either K+-[2,2,2]cryptand or NH4+-Et3N systems but also provides color changes that are visible to the naked eye; consequently, this system operates as a two-input NOR functioning molecular logic gate.

Journal Article↗