Anin numero study of glucose-insulin interaction

A mathematical model has been developed to simulate the glucose-insulin interaction following a glucose load such as occurs in an IVGTT. This model differs from earlier models in that the insulin response to glucose loading is a recurring all or none threshold response. The model has been simulated on a digital computer using the digital analog simulation language CSMP.     

Computational analysis of T cell receptor signaling and ligand discrimination--past, present, and future

Signaling through the T cell receptor for antigen (TCR) has been studied for years by conventional biochemical means. More recently, attempts have been made to develop computational models of signaling through this receptor, with a specific focus on understanding how this recognition system discriminates between closely related (self and non-self) ligands. Here we discuss recent advances centered on the role of feedback regulation, especially the key finding that a combination of digital and analog control circuits is fundamental to the discrimination properties of the TCR. We end by pointing to future, more biologically accurate models that incorporate spatial aspects of molecular organization in antigen-engaged T lymphocytes with this underlying biochemistry.     

Role of p53 in the ability of 1,2-diaminocyclohexane-diacetato-dichloro-Pt(IV) to circumvent cisplatin resistance

Several reports indicate that the mechanism of resistance to cisplatin is multifactorial. However, DNA damage tolerance appears to be the more significant mechanism. It is clear that resistance in general is a major clinical concern, and a number of approaches have been taken to circumvent this clinical impediment. One approach is through analog development, and we have identified 1,2-diaminocyclohexane-diacetatodichloro-platinum(IV) as an analog with activity in cisplatin resistance. The activity is greatest against ovarian tumor cell lines where the latent, non-inducible wild-type p53 function can be reactivated by the analog. This functional activation of p53 also corresponds to a reduced threshold for tolerance to DNA damage induced by the analog. Interestingly, cell lines with mutant or null p53 are cross-resistant to the analog. The data indicate that cisplatin resistance due to an increase in DNA damage tolerance can arise through a loss of p53 function, and that functional activation of latent wild-type p53 by the analog facilitates cell death and circumvents this resistance mechanism.     

Soluble and insoluble signals sculpt osteogenesis in angiogenesis

The basic tissue engineering paradigm is tissue induction and morphogenesis by combinatorial molecular protocols whereby soluble molecular signals are combined with insoluble signals or substrata. The insoluble signal acts as a three-dimensional scaffold for the initiation of de novo tissue induction and morphogenesis. The osteogenic soluble molecular signals of the transforming growth factor-β (TGF-β) supergene family, the bone morphogenetic/osteogenic proteins (BMPs/OPs) and, uniquely in the non-human primate Papio ursinus (P. ursinus), the three mammalian TGF-β isoforms induce bone formation as a recapitulation of embryonic development. In this paper, I discuss the pleiotropic activity of the BMPs/OPs in the non-human primate P. ursinus, the induction of bone by transitional uroepithelium, and the apparent redundancy of molecular signals initiating bone formation by induction including the three mammalian TGF-β isoforms. Amongst all mammals tested so far, the three mammalian TGF-β isoforms induce endochondral bone formation in the non-human primate P. ursinus only. Bone tissue engineering starts by erecting scaffolds of biomimetic biomaterial matrices that mimic the supramolecular assembly of the extracellular matrix of bone. The molecular scaffolding lies at the hearth of all tissue engineering strategies including the induction of bone formation. The novel concept of tissue engineering is the generation of newly formed bone by the implantation of "smart" intelligent biomimetic matrices that per se initiate the ripple-like cascade of bone differentiation by induction without exogenously applied BMPs/OPs of the TGF-β supergene family. A comprehensive digital iconographic material presents the modified tissue engineering paradigm whereby the induction of bone formation is initiated by intelligent smart biomimetic matrices that per se initiate the induction of bone formation without the exogenous application of the soluble osteogenic molecular signals. The driving force of the intrinsic induction of bone formation by bioactive biomimetic matrices is the shape of the implanted substratum. The language of shape is the language of geometry; the language of geometry is the language of a sequence of repetitive concavities, which biomimetizes the remodelling cycle of the primate osteonic bone.     

A high capacity data recording device based on a digital audio processor and a video cassette recorder.

A modified digital audio processor, a video cassette recorder, and some simple added circuitry are assembled into a recording device of high capacity. The unit converts two analog channels into digital form at 44-kHz sampling rate and stores the information in digital form in a common video cassette. Bandwidth of each channel is from direct current to approximately 20 kHz and the dynamic range is close to 90 dB. The total storage capacity in a 3-h video cassette is 2 Gbytes. The information can be retrieved in analog or digital form.     

Robust Models for Optic Flow Coding in Natural Scenes Inspired by Insect Biology

The extraction of accurate self-motion information from the visual world is a difficult problem that has been solved very efficiently by biological organisms utilizing non-linear processing. Previous bio-inspired models for motion detection based on a correlation mechanism have been dogged by issues that arise from their sensitivity to undesired properties of the image, such as contrast, which vary widely between images. Here we present a model with multiple levels of non-linear dynamic adaptive components based directly on the known or suspected responses of neurons within the visual motion pathway of the fly brain. By testing the model under realistic high-dynamic range conditions we show that the addition of these elements makes the motion detection model robust across a large variety of images, velocities and accelerations. Furthermore the performance of the entire system is more than the incremental improvements offered by the individual components, indicating beneficial non-linear interactions between processing stages. The algorithms underlying the model can be implemented in either digital or analog hardware, including neuromorphic analog VLSI, but defy an analytical solution due to their dynamic non-linear operation. The successful application of this algorithm has applications in the development of miniature autonomous systems in defense and civilian roles, including robotics, miniature unmanned aerial vehicles and collision avoidance sensors.     

Capacities of digital mammography in screening

The purpose of the study was to estimate the capacities of digital mammography in screening in women followed up by a mammologist in the Surgut Clinical Perinatal Center. The results of analog and digital mammography were compared using a Senographe DS in 1772 subjects who had been followed up by a mammologist in the Surgut Clinical Perinatal Center for 3-7 years. Females in whom mammography was first made as a basic study on a digital mammography were identified in an individual group of 887 subjects. Analysis of the capacities of analog and digital mammography indicated many advantages of the latter.     

Auxin-regulated changes in protein phosphorylation in pea epicotyls

Auxins regulate various aspects of plant growth and development. However, the mechanism by which these hormones elicit diverse physiological processes is not clear. We present evidence for the role of auxin in protein phosphorylation and the possible involvement of calmodulin in auxin-induced changes. In the presence of auxin, phosphorylation of 23,000, 82,000, 105,000 and 110,000 molecular weight polypeptides markedly decreased whereas phosphorylation of 19,000, 24,000 and 28,000 molecular weight polypeptides increased. These results open up a new experimental approach in understanding the molecular mechanism by which auxins regulate various physiological processes in plants.     

The digital language of amino acids

Summary. The subject of this paper is a digital approach to the investigation of the biochemical basis of genetic processes. The digital mechanism of nucleic acid and protein bio-syntheses, the evolution of biomacromolecules and, especially, the biochemical evolution of genetic language have been analyzed by the application of cybernetic methods, information theory and system theory, respectively. This paper reports the discovery of new methods for developing the new technologies in genetics. It is about the most advanced digital technology which is based on program, cybernetics and informational systems and laws. The results in the practical application of the new technology could be useful in bioinformatics, genetics, biochemistry, medicine and other natural sciences.     

Prescribing diatom morphology: toward genetic engineering of biological nanomaterials

The formation of inorganic materials with complex form is a widespread biological phenomenon (biomineralization). Among the most spectacular examples of biomineralization is the production by diatoms (a group of eukaryotic microalgae) of intricately nanopatterned to micropatterned cell walls made of silica (SiO2). Understanding the molecular mechanisms of diatom silica biomineralization is not only a fundamental biological problem, but also of great interest in materials engineering, as the biological self-assembly of three-dimensional (3D) inorganic nanomaterials has no man-made analog. Recently, insight into the molecular mechanism of diatom silica formation has been obtained by structural and functional analysis of biomolecules that are involved in this process. Furthermore, the rapid development of diatom molecular genetics has provided new tools for investigating the silica forming machinery of diatoms and for manipulating silica biogenesis. This has opened the door for the production, through genetic engineering, of unique 3D nanomaterials with designed structures and functionalities.     

Phosphoryl transfer by a concerted reaction mechanism in UMP/CMP-kinase

The reaction mechanism of phosphoryl transfer catalyzed by UMP/CMP-kinase from Dictyostelium discoideum was investigated by semiempirical AM1 molecular orbital computations of an active site model system derived from crystal structures that contain a transition state analog or a bisubstrate inhibitor. The computational results suggest that the nucleoside monophosphate must be protonated for the forward reaction while it is unprotonated in the presence of aluminium fluoride, a popular transition state analog for phosphoryl transfer reactions. Furthermore, a compactification of the active site model system during the reaction and for the corresponding complex containing AlF3 was observed. For the active site residues that are part of the LID domain, conformational flexibility during the reaction proved to be crucial. On the basis of the calculations, a concerted phosphoryl transfer mechanism is suggested that involves the synchronous shift of a proton from the monophosphate to the transferred PO3-group. The proposed mechanism is thus analogous to the phosphoryl transfer mechanism in cAMP-dependent protein kinase that phosphorylates the hydroxyl groups of serine residues.     

Eight-parameter PC-AT based flow cytometric data system

An 8-parameter flow cytometric data system is described using an IBM-AT compatible personal computer (PC) and a commercial analog to digital conversion (ADC) board. A dedicated pulse processing interface adapts the flow cytometric pulses to the ADC board and controls the number of parameters to be taken up and the trigger conditions. The trigger thresholds are automatically held at a level immediately above the noise level. For the timing of kinetic measurements a linear voltage ramp of adjustable rise time is available. A built-in precision voltage source can be used for an overall calibration. The data system is operated by software written in assembly language. Data may be collected and processed in 1-8-parameter listmode or 1-3-parameter histogram mode. Functions are available for graphical color displays, numerical integration, multiparameter gating, and printing.     

Autophagy: from basic research to its application in food biotechnology

Autophagy is a catabolic process by which the cytoplasm is sequestered into double-membrane vesicles and delivered to the lysosome/vacuole for breaking down and recycling of the low molecular weight degradation products. The isolation in the yeast Saccharomyces cerevisiae of many of the genes involved in autophagy constituted a milestone in understanding the molecular bases of this pathway. The identification of ortholog genes in other eukaryotic models revealed that the mechanism of autophagy is conserved among all eukaryotes. This pathway has been shown to be involved in a growing number of physiological processes and conversely, its deregulation may contribute to the development of several diseases. Recent reports have also shown that autophagy may play an important role in biotechnological processes related with the food industry. In this review we discuss current knowledge of the molecular mechanism of autophagy, including some applied aspects of autophagy in the field of food biotechnology.     

Sources of variation in developmental language disorders: evidence from eye-tracking studies of sentence production

Skilled sentence production involves distinct stages of message conceptualization (deciding what to talk about) and message formulation (deciding how to talk about it). Eye-movement paradigms provide a mechanism for observing how speakers accomplish these aspects of production in real time. These methods have recently been applied to children with autism spectrum disorder (ASD) and specific language impairment (LI) in an effort to reveal qualitative differences between groups in sentence production processes. Findings support a multiple-deficit account in which language production is influenced not only by lexical and syntactic constraints, but also by variation in attention control, inhibition and social competence. Thus, children with ASD are especially vulnerable to atypical patterns of visual inspection and verbal utterance. The potential to influence attentional focus and prime appropriate language structures are considered as a mechanism for facilitating language adaptation and learning.     

Why a Constant Number of Vertebrae? Digital Control of Segmental Identity during Vertebrate Development

It is not understood how the numbers and identities of vertebrae are controlled during mammalian development. The remarkable robustness and conservation of segmental numbers may suggest the digital nature of the underlying process. The study proposes a mechanism that allows cells to obtain and store the segmental information in digital form, and to produce a pattern of chromatin accessibility that in turn regulates Hox gene expression specific to the metameric segment. The model requires that a regulatory element be present such that the number of occurrences of the motif between two consecutive Hox genes equals the number of segments under the control of the anterior gene. This is true for the recently discovered hydroxyl radical cleavage 3bp-periodic (HRC3) motif, associated with histone modifications and developmental genes. The finding not only allows the correct prediction of the numbers of segments using only sequence information, but also resolves the 40-year-old enigma of the function of temporal and spatial collinearity of Hox genes. The logic of the mechanism is illustrated in the attached animated video. How different aspects of the proposed mechanism can be tested experimentally is also discussed.     

Digit morphogenesis: Is the tip different?

Digit formation is the last step in the skeletal patterning of developing limbs. This process involves important aspects such as determination of chondrogenic versus interdigital areas; growth of digital rays with periodic segmentation to form joints and thus phalanges, and finally tip formation. Traditionally it was believed that the properties of digital rays were fixed at earlier stages, but recently a surprising plasticity of digit primordia at the time of condensation has been demonstrated. This implies the presence of local interactions that are able to modulate the particular programs that make a given digit, but we don't fully understand how they operate. An involvement of signaling from the interdigital spaces and from the apical ectodermal ridge has been proposed. Another interesting question is the formation of the last limb structure, digit tips, which may involve a specific molecular and cellular program. Indeed, the expression of several developmentally important genes is restricted to digit tips at late stages of limb development. Understanding the molecular and cellular interactions that lead to digit morphogenesis has important implications not only in the context of embryonic development (for example, how early cues received by cells are translated into anatomy or what are the mechanisms that control the cease of activity of signaling regions) but also in terms of limb diversification during evolution.     

Origin and diversification of a metabolic cycle in oligomer world

Based on the oligomer-world hypothesis we propose an abstract model where the molecular recognition among oligomers is described in the shape space. The origin of life in the oligomer world is regarded as the establishment of a metabolic cycle in a primitive cell. The cycle is sustained by the molecular recognition. If an original cell acquires the ability of the replication of oligomers, the relationship among oligomers changes due to the poor fidelity of the replication. This change leads to the diversification of metabolic cycles. The selection among diverse cycles is the basis of the evolution. The evolvability is one of the essential characters of life. We demonstrate the origin and diversification of the metabolic cycle by the computer simulation of our model. Such a simulation is expected to be the simplified demonstration of what actually occurred in the primordial soup. Our model describes an analog era preceding the digital era based on the genetic code.     

Short latency somatosensory and spinal evoked potentials: Power spectra and comparison between high pass analog and digital filter

Medium nerve somatosensory evoked potentials (SSEPs) and intraoperative spinal evoked potentials were analyzed using different analog and zero phase shift digital high pass filter and by power spectrum. Additionally, high pass analog and digital filtering was performed on various sine, triangular and rectangular waves manufactured by a wave form generator. Recordings were also transformed to the 1st and 2nd time derivatives.The great abundance of spectral energy for scalp recorded median nerve SSEPs was below 125 c/sec but lower energy fast frequency components consistently extended to 500 c/sec. Power spectrum of the Erb's point compound nerve action potential revealed a wide band of spectral energy commencing at about 50–100 c/sec, peaking at about 250–270 c/sec and extending to nearly 1000 c/sec. This suggests that synchronous axonal activity generates predominantly faster frequencies above 100 c/sec.High pass analog filter confers phase non-linearity which results in various distortions including latency shift and a morphological change which may be visually similar to the 1st or 2nd time derivatives. High pass zero phase shift digital filter removes selected low frequencies without accompanying phase distortion. This accentuates fast peaks seen at open bandpass as well as transition points between baseline and component ascent or descent. Zero phase shift digital filter may also generate peaks that are not visualized at open pass but which reflect the sum of frequencies which were not removed by filtering. These peaks do not necessarily correspond to discrete singular neuroanatomical structures.Although peaks observed in high pass analog and digital filter appear similar and comparable, their underlying activity may be of different origin. This is because high pass analog filter projects a considerable amount of overlap from earlier onto later waves.For clinical correlation it is important that restricted bandpass analog or digitally filtered recordings be compared with open pass data. Only those peaks visualized in both open and restricted bandpass can be considered authentic. Examples of spinal and scalp SSEPs indicate that selective filtering may, under certain circumstances, distinguish axonal or lemniscal from synaptic generators.