Articles

Neurogenetic interactions and aberrant behavioral co-morbidity of attention deficit hyperactivity disorder (ADHD): dispelling myths

Attention Deficit Hyperactivity Disorder, commonly referred to as ADHD, is a common, complex, predominately genetic but highly treatable disorder, which in its more severe form has such a profound effect on br...

Authors: David E Comings, Thomas JH Chen, Kenneth Blum, Julie F Mengucci, Seth H Blum and Brian Meshkin

A Global Workspace perspective on mental disorders

Recent developments in Global Workspace theory suggest that human consciousness can suffer interpenetrating dysfunctions of mutual and reciprocal interaction with embedding environments which will have early o...

Authors: Rodrick Wallace

Repolarization of the action potential enabled by Na⁺ channel deactivation in PSpice simulation of cardiac muscle propagation

In previous studies on propagation of simulated action potentials (APs) in cardiac muscle using PSpice modeling, we reported that a second black-box (BB) could not be inserted into the K⁺ leg of the basic membran...

Authors: Lakshminarayanan Ramasamy and Nicholas Sperelakis

Comment on and reply to "Analysis of variation of amplitudes in cell cycle gene expression" by Liu, Gaido and Wolfinger: On the analysis of gene expression during the normal, eukaryotic, cell cycle

The paper of Liu, Gaido and Wolfinger on gene expression during the division cycle of HeLa cells using the data of Whitfield et al. are discussed in order to see whether their analysis is related to gene expre...

Authors: Stephen Cooper

Analysis of variation of amplitudes in cell cycle gene expression

Variation in gene expression among cells in a population is often considered as noise produced from gene transcription and post-transcription processes and experimental artifacts. Most studies on noise in gene...

Authors: Delong Liu, Kevin W Gaido and Russ Wolfinger

Supply-demand balance in outward-directed networks and Kleiber's law

Recent theories have attempted to derive the value of the exponent α in the allometric formula for scaling of basal metabolic rate from the properties of distribution network models for arteries and capillarie...

Authors: Page R Painter

A mathematical model of the euglycemic hyperinsulinemic clamp

The Euglycemic Hyperinsulinemic Clamp (EHC) is the most widely used experimental procedure for the determination of insulin sensitivity, and in its usual form the patient is followed under insulinization for t...

Authors: Umberto Picchini, Andrea De Gaetano, Simona Panunzi, Susanne Ditlevsen and Geltrude Mingrone

Modeling the signaling endosome hypothesis: Why a drive to the nucleus is better than a (random) walk

Information transfer from the plasma membrane to the nucleus is a universal cell biological property. Such information is generally encoded in the form of post-translationally modified protein messengers. Text...

Authors: Charles L Howe

Hybrid dynamic/static method for large-scale simulation of metabolism

Many computer studies have employed either dynamic simulation or metabolic flux analysis (MFA) to predict the behaviour of biochemical pathways. Dynamic simulation determines the time evolution of pathway prop...

Authors: Katsuyuki Yugi, Yoichi Nakayama, Ayako Kinoshita and Masaru Tomita

Volume of the effect compartment in simulations of neuromuscular block

The study examines the role of the volume of the effect compartment in simulations of neuromuscular block (NMB) produced by nondepolarizing muscle relaxants.

Authors: Vladimir Nigrovic, Johannes H Proost, Anton Amann and Shashi B Bhatt

Uncertainty principle of genetic information in a living cell

Formal description of a cell's genetic information should provide the number of DNA molecules in that cell and their complete nucleotide sequences. We pose the formal problem: can the genome sequence forming t...

Authors: Pierluigi Strippoli, Silvia Canaider, Francesco Noferini, Pietro D'Addabbo, Lorenza Vitale, Federica Facchin, Luca Lenzi, Raffaella Casadei, Paolo Carinci, Maria Zannotti and Flavia Frabetti

Data from necropsy studies and in vitro tissue studies lead to a model for allometric scaling of basal metabolic rate

The basal metabolic rate (BMR) of a mammal of mass M is commonly described by the power function αM ^β where α and β are constants determined by linear regression of the logar...

Authors: Page R Painter

Targeting MDM2 by the small molecule RITA: towards the development of new multi-target drugs against cancer

The use of low-molecular-weight, non-peptidic molecules that disrupt the interaction between the p53 tumor suppressor and its negative regulator MDM2 has provided a promising alternative for the treatment of d...

Authors: L Michel Espinoza-Fonseca

A comparative study of a theoretical neural net model with MEG data from epileptic patients and normal individuals

The aim of this study was to compare a theoretical neural net model with MEG data from epileptic patients and normal individuals.

Authors: A Kotini, P Anninos, AN Anastasiadis and D Tamiolakis

Boundary effects influence velocity of transverse propagation of simulated cardiac action potentials

We previously demonstrated that transverse propagation of excitation (cardiac action potentials simulated with PSpice) could occur in the absence of low-resistance connections (gap – junction channels) between...

Authors: Nicholas Sperelakis, Bijoy Kalloor and Lakshminarayanan Ramasamy

Nucleic acid chaperons: a theory of an RNA-assisted protein folding

Proteins are assumed to contain all the information necessary for unambiguous folding (Anfinsen's principle). However, ab initio structure prediction is often not successful because the amino acid sequence its...

Authors: Jan C Biro

Review of "Systems Biology in Practice" by Edda Klipp, Ralf Hertwig, Axel Kowald, Christoph Wierling and Hans Lehrach

Authors: Paul S Agutter

Possible Cis-acting signal that could be involved in the localization of different mRNAs in neuronal axons

Messenger RNA (mRNA) comprises three major parts: a 5'-UTR (UnTranslated Region), a coding region, and a 3'-UTR. The 3'-UTR contains signal sequences involved in polyadenylation, degradation and localization/s...

Authors: Gonzalo E Aranda-Abreu, Ma Elena Hernández, Abraham Soto and Jorge Manzo

On the number of founding germ cells in humans

The number of founding germ cells (FGCs) in mammals is of fundamental significance to the fidelity of gene transmission between generations, but estimates from various methods vary widely. In this paper we obt...

Authors: Chang-Jiang Zheng, E Georg Luebeck, Breck Byers and Suresh H Moolgavkar

Allometric scaling of the maximum metabolic rate of mammals: oxygen transport from the lungs to the heart is a limiting step

The maximum metabolic rate (MMR) of mammals is approximately proportional to M ^0.9 , where M is the mammal's body weight. Therefore, MMR increases with body weight faster tha...

Authors: Page R Painter

The fractal geometry of nutrient exchange surfaces does not provide an explanation for 3/4-power metabolic scaling

A prominent theoretical explanation for 3/4-power allometric scaling of metabolism proposes that the nutrient exchange surface of capillaries has properties of a space-filling fractal. The theory assumes that ...

Authors: Page R Painter

Three subsets of sequence complexity and their relevance to biopolymeric information

Genetic algorithms instruct sophisticated biological organization. Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC). FSC alone provides algorithmic instru...

Authors: David L Abel and Jack T Trevors

Modelling of oedemous limbs and venous ulcers using partial differential equations

Oedema, commonly known as tissue swelling, occurs mainly on the leg and the arm. The condition may be associated with a range of causes such as venous diseases, trauma, infection, joint disease and orthopaedic...

Authors: Hassan Ugail and Michael J Wilson

Statistical distribution of blood serotonin as a predictor of early autistic brain abnormalities

A wide range of abnormalities has been reported in autistic brains, but these abnormalities may be the result of an earlier underlying developmental alteration that may no longer be evident by the time autism ...

Authors: Skirmantas Janušonis

The complexity of anatomical systems

The conception of anatomical entities as a hierarchy of infinitely graduated forms and the increase in the number of observed anatomical sub-entities and structural variables has generated a growing complexity, t...

Authors: Fabio Grizzi and Maurizio Chiriva-Internati

Identification and isolation of embryonic stem cells in reproductive endocrinology: theoretical protocols for conservation of human embryos derived from in vitro fertilization

Embryonic stem cells (ESC) are pluripotent cells obtained from the inner cell mass (ICM) of blastocysts derived from in vitro culture associated with reproductive endocrinology therapy. Human ESCs are regarded as...

Authors: Eric Scott Sills, Takumi Takeuchi, Noriko Tanaka, Queenie V Neri and Gianpiero D Palermo

Vasculature deprivation – induced osteonecrosis of the rat femoral head as a model for therapeutic trials

The authors' experience with experimentally produced femoral capital osteonecrosis in rats is reviewed: incising the periosteum at the base of the neck of the femur and cutting the ligamentum teres leads to co...

Authors: Jacob Bejar, Eli Peled and Jochanan H Boss

Predicting transcription factor activities from combined analysis of microarray and ChIP data: a partial least squares approach

The study of the network between transcription factors and their targets is important for understanding the complex regulatory mechanisms in a cell. Unfortunately, with standard microarray experiments it is no...

Authors: Anne-Laure Boulesteix and Korbinian Strimmer

The ups and downs of biological timers

The need to execute a sequence of events in an orderly and timely manner is central to many biological processes, including cell cycle progression and cell differentiation. For self-perpetuating systems, such ...

Authors: Noa Rappaport, Shay Winter and Naama Barkai

A new journal – "Theoretical Biology and Medical Modelling"

Biology has a conceptual basis that allows one to build models and theorize across many life sciences, including medicine and medically-related disciplines. A dearth of good venues for publication has been per...

Authors: Denys N Wheatley

Promoter addresses: revelations from oligonucleotide profiling applied to the Escherichia coli genome

Transcription is the first step in cellular information processing. It is regulated by cis-acting elements such as promoters and operators in the DNA, and trans-acting elements such as transcription factors and s...

Authors: Karthikeyan Sivaraman, Aswin Sai Narain Seshasayee, Krishnakumar Swaminathan, Geetha Muthukumaran and Gautam Pennathur

Quantification of the glycogen cascade system: the ultrasensitive responses of liver glycogen synthase and muscle phosphorylase are due to distinctive regulatory designs

Signaling pathways include intricate networks of reversible covalent modification cycles. Such multicyclic enzyme cascades amplify the input stimulus, cause integration of multiple signals and exhibit sensitiv...

Authors: Vivek K Mutalik and KV Venkatesh

Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition

Cell simulation, which aims to predict the complex and dynamic behavior of living cells, is becoming a valuable tool. In silico models of human red blood cell (RBC) metabolism have been developed by several la...

Authors: Yoichi Nakayama, Ayako Kinoshita and Masaru Tomita

An ETP model (exclusion-tolerance-progression) for multi drug resistance

It is known that sensitivity or resistance of tumor cells to a given chemotherapeutic agent is an acquired characteristic(s), depending on the heterogeneity of the tumor mass subjected to the treatment. The cl...

Authors: Subburaj Kannan

Breakdown of accommodation in nerve: a possible role for persistent sodium current

Accommodation and breakdown of accommodation are important elements of information processing in nerve fibers, as they determine how nerve fibers react to natural slowly changing stimuli or electrical stimulat...

Authors: Kristian Hennings, Lars Arendt-Nielsen and Ole K Andersen

Location of DNA damage by charge exchanging repair enzymes: effects of cooperativity on location time

How DNA repair enzymes find the relatively rare sites of damage is not known in great detail. Recent experiments and molecular data suggest that individual repair enzymes do not work independently of each other, ...

Authors: Kasper Astrup Eriksen

Hyperbolastic growth models: theory and application

Mathematical models describing growth kinetics are very important for predicting many biological phenomena such as tumor volume, speed of disease progression, and determination of an optimal radiation and/or c...

Authors: Mohammad Tabatabai, David Keith Williams and Zoran Bursac

Mathematical model of blunt injury to the vascular wall via formation of rouleaux and changes in local hemodynamic and rheological factors. Implications for the mechanism of traumatic myocardial infarction

Blood viscosity is fundamentally important in clinical practice yet the apparent viscosity at very low shear rates is not well understood. Various conditions such as blunt trauma may lead to the appearance of ...

Authors: Rovshan M Ismailov

Tyrosine phosphorylation of myosin heavy chain during skeletal muscle differentiation: an integrated bioinformatics approach

Previously it has been shown that insulin-mediated tyrosine phosphorylation of myosin heavy chain is concomitant with enhanced association of C-terminal SRC kinase during skeletal muscle differentiation. We so...

Authors: DF Harney, RK Butler and RJ Edwards

A topological model of biofeedback based on catecholamine interactions

The present paper describes a topological model of biofeedback. This model incorporates input from a sensory organ and a transduction phase mediated through catecholamine production in the feedback path. The t...

Authors: Tapas K Basak, Suman Halder, Madona Kumar, Renu Sharma and Bijoylaxmi Midya

The Estradiol-Dihydrotestosterone model of prostate cancer

The exact relationship between hormonal activity and prostate cancer(PCa) has not yet been clearly defined. One of the key hormones associated with PCa is testosterone(T). However, both in vitro and in vivo studi...

Authors: A Edward Friedman

The quantitation of buffering action II. Applications of the formal & general approach

The paradigm of "buffering" originated in acid-base physiology, but was subsequently extended to other fields and is now used for a wide and diverse set of phenomena. In the preceding article, we have presente...

Authors: Bernhard M Schmitt

The quantitation of buffering action I. A formal & general approach

Although "buffering" as a homeostatic mechanism is a universal phenomenon, the quantitation of buffering action remains controversial and problematic. Major shortcomings are: lack of a buffering strength unit ...

Authors: Bernhard M Schmitt

High-Temperature unfolding of a trp-Cage mini-protein: a molecular dynamics simulation study

Trp cage is a recently-constructed fast-folding miniprotein. It consists of a short helix, a 3,10 helix and a C-terminal poly-proline that packs against a Trp in the alpha helix. It is known to fold within 4 ns.

Authors: Aswin Sai Narain Seshasayee

Volume-based non-continuum modeling of bone functional adaptation

Bone adapts to mechanical strain by rearranging the trabecular geometry and bone density. The common finite element methods used to simulate this adaptation have inconsistencies regarding material properties a...

Authors: Zhengyuan Wang and Adrian Mondry

Propagated repolarization of simulated action potentials in cardiac muscle and smooth muscle

Propagation of repolarization is a phenomenon that occurs in cardiac muscle. We wanted to test whether this phenomenon would also occur in our model of simulated action potentials (APs) of cardiac muscle (CM) ...

Authors: Nicholas Sperelakis, Lakshminarayanan Ramasamy and Bijoy Kalloor

Single cell studies of the cell cycle and some models

Analysis of growth and division often involves measurements made on cell populations, which tend to average data. The value of single cell analysis needs to be appreciated, and models based on findings from si...

Authors: JM Mitchison

In vitro bioassay as a predictor of in vivo response

There is a substantial discrepancy between in vitro and in vivo experiments. The purpose of the present work was development of a theoretical framework to enable improved prediction of in vivo response from in vi...

Authors: Ross Barnard and Konstantin G Gurevich

Construction of predictive promoter models on the example of antibacterial response of human epithelial cells

Binding of a bacteria to a eukaryotic cell triggers a complex network of interactions in and between both cells. P. aeruginosa is a pathogen that causes acute and chronic lung infections by interacting with the p...

Authors: Ekaterina Shelest and Edgar Wingender

Human embryonal epithelial cells of the developing small intestinal crypts can express the Hodgkin-cell associated antigen Ki-1 (CD30) in spontaneous abortions during the first trimester of gestation

Ki-1 (CD30) antigen expression is not found on peripheral blood cells but its expression can be induced in vitro on T and B lymphocytes by viruses and lectins. Expression of CD30 in normal tissues is very limi...

Authors: Demetrio Tamiolakis, John Venizelos, Maria Lambropoulou, Silva Nikolaidou, Sophia Bolioti, Maria Tsiapali, Dionysios Verettas, Panagiotis Tsikouras, Athanasios Chatzimichail and Nikolas Papadopoulos