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Cells that register logical relationships among proteins.

Two-hybrid methods have augmented the classical genetic techniques biologists use to assign function to genes. Here, we describe construction of a two-bait interaction trap that uses yeast cells to register more complex protein relationships than those detected in existing two-hybrid systems. We show that such cells can identify bridge or connecting proteins and peptide aptamers that discriminate between closely related allelic variants. The protein relationships detected by these cells are analogous to classical genetic relationships, but lend themselves to systematic application to the products of entire genomes and combinatorial libraries. We show that, by performing logical operations on the phenotypic outputs of these complex cells and existing two-hybrid cells, we can make inferences about the topology and order of protein interactions. Finally, we show that cells that register such relationships can perform logical operations on protein inputs. Thus these cells will be useful for analysis of gene and allele function, and may also define a path for construction of biological computational devices.

Alleles↗

A count-rate model for PET scanners using pixelated Anger-logic detectors with different scintillators.

A high count-rate simulation (HCRSim) model has been developed so that all results are derived from fundamental physics principles. Originally developed to study the behaviour of continuous sodium iodide (NaI(Tl)) detectors, this model is now applied to PET scanners based on pixelated Anger-logic detectors using lanthanum bromide (LaBr(3)), gadolinium orthosilicate (GSO) and lutetium orthosilicate (LSO) scintillators. This simulation has been used to study the effect on scanner deadtime and pulse pileup at high activity levels due to the scintillator stopping power (mu), decay time (tau) and energy resolution. Simulations were performed for a uniform 20 cm diameter x 70 cm long cylinder (NEMA NU2-2001 standard) in a whole-body scanner with an 85 cm ring diameter and a 25 cm axial field-of-view. Our results for these whole-body scanners demonstrate the potential of a pixelated Anger-logic detector and the relationship of its performance with the scanner NEC rate. Faster signal decay and short coincidence timing window lead to a reduction in deadtime and randoms fraction in the LaBr(3) and LSO scanners compared to GSO. The excellent energy resolution of LaBr(3) leads to the lowest scatter fraction for all scanners and helps compensate for reduced sensitivity compared to the GSO and LSO scanners, leading to the highest NEC values at high activity concentrations. The LSO scanner has the highest sensitivity of all the scanner designs investigated here, therefore leading to the highest peak NEC value but at a lower activity concentration than that of LaBr(3).

Bromides↗

Characterizing the regulatory logic of transcriptional control at the DNA sequence level by ensembles of thermodynamic models.

MOTIVATION: Understanding how the genome encodes the regulatory logic of transcription is a main challenge of the post-genomic era, and can be overcome with the aid of customized computational tools. RESULTS: We report an automated framework for analyzing an ensemble of fits to data of a thermodynamics-based sequence-level model for transcriptional regulation. The fits are clustered accordingly with their intrinsic regulatory logic. A multiscale analysis enables visualization of quantitative features resulting from the deconvolution of the regulatory profile provided by multiple transcription factors interacting with the locus of a gene. Quantitative experimental data on reporters driven by the whole locus of the even-skipped gene in the blastoderm of Drosophila embryos was used for validating our approach. A few clusters of highly active DNA binding sites within the enhancers collectively modulate even-skipped gene transcription. Analysis of variable enhancers' length shows the importance of bound protein-protein interactions for transcriptional regulation. The interplay between activation and quenching enables function conservation of enhancers despite length variations. AVAILABILITY AND IMPLEMENTATION: The transcription factor level data used for performing the reported study is accessible in the input files in Zenodo and GitHub as well the full code. Additional data from formerly FlyEx database will be available under request.

Thermodynamics↗

A cellular logic for G protein-coupled ion channel pathways.

A vast array of cellular signal transduction processes arise from combinations of many different types of agonists, receptors, effectors, and coupling molecules such as heterotrimeric G proteins or protein kinases that connect receptors to effectors. Receptors, effectors, G proteins, and kinases are being newly identified at bewildering speeds and in the process it seems that our understanding of how cells respond to specific stimuli may have diminished just as we lose sight of the forest when we are buried in the trees. Evolution would suggest that there may be a logic to the response provoked by a given stimulus and, using our recently acquired knowledge of G protein pathways between receptors and ion channel effectors, I will attempt to decipher what the underlying logic might be.

Animals↗

Haemodynamic basis for the development of left ventricular failure in systolic hypertension and for its logical therapy.

In youth, properties of the human arterial system are such that pulse pressure generated by ventricular ejection is low, and the major component of wave reflection returns to the heart after the aortic valve has shut, so making no contribution to ventricular load, but boosting pressure throughout diastole and so aiding coronary perfusion. That constitutes optimal arterial function and optimal vascular/ventricular interaction. With ageing, the aorta and elastic arteries stiffen, so that aortic pulse pressure is markedly increased. This is a consequence of a direct stiffening effect on the aorta itself, and of an indirect effect caused by early return of wave reflection consequent upon stiffening of the whole arterial system with an increase in its pulse wave velocity. There is a change in contour of the aorta pressure wave with wave generation of a late systolic peak and disappearance of the diastolic wave; the reflected wave moves from diastole and systole. Because the lowest diastolic pressure remains relatively constant [1,10], increased pulse pressure causes a substantial increase in aortic systolic pressure. Increased aortic systolic pressure is associated with increased left ventricular pressure and leads to left ventricular hypertrophy. Sustained elevation in systolic pressure and persistent left ventricular hypertrophy are associated with progressive degenerative changes in the hypertrophied myocytes such that these weaken, developing less force with each contraction. The weakened, hypertrophied fibres lengthen and the ventricle dilates, with force and cardiac output initally being maintained at greater muscle length and ventricular volume through the Frank-Starling mechanism. Ultimately compensation is lost. The hypertrophied ventricle normally functions as a flow source, which is capable of generating flow even against very high pressure. With the development of cardiac failure through muscle weakening, the ventricle comes to act as a pressure source, with ventricular output very sensitive to pressure and to changes in pressure. The normal ventricle functions in an intermediate position, even though it is closer in behaviour to a flow than to a pressure source. Wave reflection adds to pressure but subtracts from flow. In youth, wave reflection returns to the heart during diastole when the aortic valve is shut. Negative flow is not possible, so wave reflection is apparent only as a secondary pressure wave in the ascending aorta. In older subjects, when the left ventricle is beating powerfully, return of wave reflection during systole has less obvious an effect on the ascending aortic flow wave, but causes an obvious secondary boost to pressure in the ascending aorta and left ventricle. Hence, under normal circumstances, wave reflection at the heart is apparent as a positive secondary pressure wave, either because the aortic valve is shut when this wave returns, or because the ventricle possesses enough power that it virtually overcomes any negative influence on flow when reflection returns during systole. When the myocardium weakens and the heart fails, the heart starts to behave like a pressure source, and wave reflection starts to have a far greater effect on flow; wave reflection is manifested more as a negative influence on flow than as a positive influence on pressure. As heart failure develops, there is a progressive change in flow wave contour, with early deceleration of aortic flow and ultimately, abbreviation of systolic ejection duration with fall in stroke volume. Early wave reflection is the major factor in the genesis of systolic hypertension. Early wave reflection remains a major factor when heart failure develops, although its effect is apparent in reduction of late systolic flow rather than as a boost to late systolic pressure. Reduction in wave reflection through use of vasodilatory agents is a logical strategy in treatment of systolic hypertension. That type of therapy is equally logical in treatment

Animals↗

Experimental logical gates in a reaction-diffusion medium: the XOR gate and beyond.

We exploit the particulars of diffusive wave front interactions in certain types of two-reactant reaction-diffusion medium to construct a laboratory prototype of an XOR gate. In the design, the values of the logic variables are represented by the presence or absence of a precipitate, "wires" are constructed of a substrate loaded gel, and the computation is based on diffusive wave dynamics. We also discuss implementation of AND gate and study a three-valued composition, derived from the gate dynamic, and discuss possible logics that could be derived from this composition.

Journal Article↗

Exact soliton solutions of coupled nonlinear Schrödinger equations: shape-changing collisions, logic gates, and partially coherent solitons.

The different dynamical features underlying soliton interactions in coupled nonlinear Schrödinger equations, which model multimode wave propagation under varied physical situations in nonlinear optics, are studied. In this paper, by explicitly constructing multisoliton solutions (up to four-soliton solutions) for two-coupled and arbitrary N-coupled nonlinear Schrödinger equations using the Hirota bilinearization method, we bring out clearly the various features underlying the fascinating shape changing (intensity redistribution) collisions of solitons, including changes in amplitudes, phases and relative separation distances, and the very many possibilities of energy redistributions among the modes of solitons. However, in this multisoliton collision process the pairwise collision nature is shown to be preserved in spite of the changes in the amplitudes and phases of the solitons. Detailed asymptotic analysis also shows that when solitons undergo multiple collisions, there exists the exciting possibility of shape restoration of at least one soliton during interactions of more than two solitons represented by three- and higher-order soliton solutions. From an application point of view, we have shown from the asymptotic expressions how the amplitude (intensity) redistribution can be written as a generalized linear fractional transformation for the N-component case. Also we indicate how the multisolitons can be reinterpreted as various logic gates for suitable choices of the soliton parameters, leading to possible multistate logic. In addition, we point out that the various recently studied partially coherent solitons are just special cases of the bright soliton solutions exhibiting shape-changing collisions, thereby explaining their variable profile and shape variation in collision process.

Journal Article↗

Demonstration of nondeterministic quantum logic operations using linear optical elements.

Knill, Laflamme, and Milburn [Nature (London) 409, 46 (2001)] recently showed that nondeterministic quantum logic operations could be performed using linear optical elements, additional photons (ancilla), and postselection based on the output of single-photon detectors. Here we report the experimental demonstration of two logic devices of this kind, a destructive controlled-NOT (CNOT) gate and a quantum parity check. These two devices can be combined with a pair of entangled photons to implement a conventional (nondestructive) CNOT that succeeds with a probability of 1/4.

Journal Article↗

A logical state model of reentrant ventricular activation.

The ventricular surface of the heart was modeled as two-dimensional, 4096 element, network of cells connected logically to each other. An ischemic area was represented by a central core of prolonged refractoriness, distributed into eccentrically-layered elliptical contours such that refractoriness declined along varying gradients to the surrounding normal area. Propagation of cardiac action potentials was stimulated by five sequential states ranging from activation to inactivation. Reentrant activation was induced by premature stimulation of the network and resembled a "figure 8" type reentry seen experimentally. Activation patterns of reentry appeared as two propagation wavefronts which traveled around the ends of a continuous line of functional conduction block, merged into a single wavefront, then conducted slowly along a retrograde path to reactivate a region proximal to the block. Reentry could be prevented by modifying the distribution of recovery of excitability through stimulation at two strategically located sites during basic rhythm. Prevention occurred when the second site was situated in an area of prolonged refractoriness, just distal to the line of block. These simulations indicate that reentrant activation is characterized by the formation of long lines of conduction block which occur along a border of steeply graded refractoriness, and retrograde slow conduction which occurs along a more shallow refractory gradient. The occurrence of reentry is dependent on: 1) the coupling interval of the premature stimulus, 2) the location of the stimulus relative to the maximum refractory gradient, and 3) the activation sequence of the basic paced beats. Thus, this paper presents an efficient logical state model of cardiac activation which simulates experimentally observed activation patterns of reentry and its prevention.

Action Potentials↗

All-optical biomolecular parallel logic gates with bacteriorhodopsin.

All-optical two input parallel logic gates with bacteriorhodopsin (BR) protein have been designed based on nonlinear intensity-induced excited-state absorption. Amplitude modulation of a continuous wave (CW) probe laser beam transmission at 640 nm corresponding to the peak absorption of O intermediate state through BR, by a modulating CW pump laser beam at 570 nm corresponding to the peak absorption of initial BR state has been analyzed considering all six intermediate states in its photocycle using the rate equation approach. The transmission characteristics have been shown to exhibit a dip, which is sensitive to normalized small-signal absorption coefficient (beta), rate constants of O and N intermediate states and absorption of the O state at 570 nm. There is an optimum value of beta for a given pump intensity range for which maximum modulation can be achieved. It is shown that 100% modulation can be achieved if the initial state of BR does not absorb the probe beam. The results have been used to design low-power all-optical parallel NOT, AND, OR, XNOR, and the universal NAND and NOR logic gates for two cases: 1) only changing the output threshold and 2) considering a common threshold with different beta values.

Bacteriorhodopsins↗

Evaluating children's rehabilitation services: an application of a programme logic model.

OBJECTIVES: To apply a programme logic model to evaluate the effectiveness of a new therapy service for children with special needs who were in transition from pre-school to kindergarten. SETTING: A children's outpatient rehabilitation centre in Ontario, Canada. MAIN OUTCOMES: The short-term outcomes included parents' perceptions of the transition process itself and the information they required, the children's skill development for the transition to kindergarten, and parents' perceptions of services and satisfaction with resources. METHODS: A combination of quantitative methods [Goal Attainment Scaling (GAS), Measure of Processes of Care (MPOC), Client Satisfaction Questionnaire (CSQ)] and qualitative interviews were used to evaluate both the process ('Outputs') and outcomes ('Short-term objectives') of the new therapy service. RESULTS: The children involved in the evaluation met or exceeded goals that were set by therapists and parents. Parents' perceptions of, and satisfaction with, the new service were higher than the provincial average. Qualitative data from interviews with parents and service providers supported the findings from standardized measures, and provided suggestions for future service delivery. CONCLUSIONS: The programme logic model provided researchers and service providers a collaborative and systematic approach to conducting programme evaluation in a relatively short-time frame. It appears to be a useful option for evaluation of other children's services.

Attitude to Health↗

The individualised birthweight ratio: a more logical outcome measure of pregnancy than birthweight alone.

OBJECTIVE: To provide a new outcome measure for pregnancy specifically related to the individual. DESIGN: Computer analysis of physiological factors affecting birthweight. SETTING: Two provincial teaching hospitals (University and City Hospitals, Nottingham) and an associated district general hospital (Derby City Hospital) serving a defined catchment area in the East Midlands. SUBJECTS: All women delivering in the above hospitals since the start of computerised obstetric records: 31,561 women with gestational age verified by early pregnancy ultrasound scan data. MAIN OUTCOME MEASURES: Calculation of the predicted birthweight taking into account maternal and fetal physiological factors. Derivation of the individualised birthweight ratio (actual birthweight divided by predicted birthweight expressed as a percentage) for each individual baby. RESULTS: The individualised birthweight ratio redefines as normally grown 41% of babies below the 10th centile of crude birthweight for gestation. Other babies previously regarded as normal are redefined as growth retarded. At the upper end of the distribution 46% of those above the 90th centile of birthweight for gestation are redefined as normally grown. CONCLUSIONS: The predicted birthweight can be calculated for an individual pregnancy at a given gestation. The standardised comparison between this predicted birthweight and the actual birthweight is a more logical reflection of the normality of intrauterine growth and therefore more logical as an outcome measure for pregnancy than crude birthweight for gestation.

Adolescent↗

The logical levels of complementary, symmetrical, and parallel interaction classes in family dyads.

It was postulated that the parallel interaction class is a higher logical order than complementary and symmetrical interaction, which appear to be of the same logical type. Father-mother, father-child, and mother-child dyads of 48 families were categorized into complementary, symmetrical, and parallel classes using the Relationship Styles Inventory. Each of the dyads in these three categories was then randomly assigned to one of two experimental conditions in which they jointly resolved a moral dilemma. In one condition, the dyads were asked to follow complementary rules, while in the second condition they were instructed to follow symmetrical rules. Results indicated that parallel dyads adjusted to both the complementary and symmetrical conditions, whereas symmetrical and complementary dyads did not successfully accomodate rules outside their own class. The implications in terms of therapeutic intervention and further research are discussed.

Adolescent↗

Fuzzy logic in medicine and bioinformatics.

The purpose of this paper is to present a general view of the current applications of fuzzy logic in medicine and bioinformatics. We particularly review the medical literature using fuzzy logic. We then recall the geometrical interpretation of fuzzy sets as points in a fuzzy hypercube and present two concrete illustrations in medicine (drug addictions) and in bioinformatics (comparison of genomes).

Journal Article↗

Detection, diagnosing, monitoring and logical treatment of occlusal caries in relation to lesion activity and severity: an in vivo examination with histological validation.

The aims of the present study were to investigate the ability of 3 experienced clinicians to detect occlusal carious lesions, assess their depth, diagnose their activity and define a logical management for each lesion. The material consisted of 35 third molars scheduled for extraction or surgical removal making it possible to validate the accuracy of the clinical recordings histologically. Examinations were carried out at baseline and after 4 months in order to monitor lesion progression. At the first visit a radiograph was taken; the number of filled surfaces was counted and the oral hygiene assessed generally and by disclosing occlusal plaque of the tooth under examination. After cleaning the occlusal surface caries was recorded in a selected investigation site using a visual ranked caries scoring system, as well as an electrical conductance recording (ECM). Apart from counting fillings and taking new radiographs the same procedure was performed at the second visit, which then was followed by extraction of the tooth. After sectioning the tooth lesion depth was recorded, and lesion activity, based on acid production, was assessed using methyl red dye. Lesion activity was also judged by means of polarized light microscopic examinations of the sections. Results showed strong relationships between the visual, ECM and radiographic assessments and both lesion depth and lesion activity. In contrast, all other parameters were poorly related to lesion activity. Changes in visual assessments and in conductance readings from first to second examination were poorly associated with lesion activity. In conclusion, clinicians are able to detect lesions, predict activity and severity and define a logical management of occlusal caries on the basis of a single examination.

Acids↗

Relationship between aortic stiffening and microvascular disease in brain and kidney: cause and logic of therapy.

A close relationship has been established between microvascular damage in brain and kidney and indices of age and hypertension (pulse pressure, aortic pulse wave velocity, and augmentation index). The mechanism of such association has not been established, nor has rationale for prevention and treatment of microvascular damage. A logical pathophysiological explanation can be offered on the basis of differential input impedance in the brain and kidney compared with other systemic vascular beds. Torrential flow and low resistance to flow in these organs exposes small arterial vessels to the high-pressure fluctuations that exist in the carotid, vertebral, and renal arteries. Such fluctuations, measurable as central pulse pressure, increase 3- to 4-fold with age. Exposure of small vessels to highly pulsatile pressure and flow explains microvascular damage and resulting renal insufficiency and intellectual deterioration, according to the mechanism established by Byrom >50 years ago. The logical approach to prevention and treatment requires reduction of central pulse pressure. Because the aorta and large arteries are not directly affected by drugs, this entails reduction of wave reflection by dilation of conduit arteries elsewhere in the body. This can be accomplished by regular exercise and by drugs such as nitrates, calcium channel blockers, angiotensin-converting enzyme inhibitors, and angiotensin receptor blockers. The explanation given here accounts for greater and earlier vascular damage in diabetes mellitus (relative microvascular fragility) and is similar to that given for vascular changes of pulmonary hypertension caused by ventricular septal defects and other congenital vascular shunts.

Aorta↗

Evidence, logic, the rule and the exception in Renaissance law and medicine.

This article sets out to investigate aspects of the uptake of Renaissance law and medicine from some of the logical and natural-philosophical components of the university arts course. Medicine is shown to have a much laxer operative logic than law, reflecting its commitment to the theory of idiosyncrasy as opposed to the demands made upon the law by the need for a uniform application of justice. Symptomatic of the different uptake are the contrasting meanings of "regulariter" and "generaliter" in the two disciplines. Whereas the law treats the rule as inviolable and the exception as only valid if made explicit in due legal form, medicine is able to conceive of a nature as a field of knowledge broader than that encompassed by its rules of art. Both law and medicine approach evidence in ways which reflect their attempts to keep apart the process of information-gathering from that of interpretation; this is exemplified by the legal computation of competing testimony on the one hand and by the various medical modes of sign interpretation on the other.

Europe↗

A majority-logic nanodevice using a balanced pair of single-electron boxes.

This paper describes a majority-logic gate device that will be useful in developing single-electron integrated circuits. The gate device consists of two identical single-electron boxes combined to form a balanced pair. It accepts three inputs and produces a majority-logic output by using imbalances caused by the input signals; it produces a 1 output if two or three inputs are 1, and a 0 output if two or three inputs are 0. We combine these gate devices into two subsystems, a shift register and an adder, and demonstrate their operation by computer simulation. We also propose a method of fabricating the unit element of the gate device, a minute dot with four coupling arms. We demonstrate by experiments that it is possible to arrange these unit elements on a GaAs substrate, in a self-organizing manner, by means of a process technology that is based on selective-area metalorganic vapor-phase epitaxy.

Aluminum↗