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PubMed1982

The RNA operator theory.

The aim of the RNA Operator Theory is to propose a new explanation for the mechanism of certain biological control functions, including morphogenesis and brain function. It assumes the existence of a natural computing language, the vocabulary of which, in machine language form, is constituted of bytes of nucleotide bits. These are observable empirically as, inter alia, repeated sequences in genetic nucleic acid. The assumed computing language possesses a range of operators which act directly when coded as RNS to effect the positional manipulation of matter on a molecular level.

Animals↗
PubMed2002

Protein design is NP-hard.

Biologists working in the area of computational protein design have never doubted the seriousness of the algorithmic challenges that face them in attempting in silico sequence selection. It turns out that in the language of the computer science community, this discrete optimization problem is NP-hard. The purpose of this paper is to explain the context of this observation, to provide a simple illustrative proof and to discuss the implications for future progress on algorithms for computational protein design.

Algorithms↗
PubMed2004

A neuropsychological investigation of male premutation carriers of fragile X syndrome.

It is currently thought that fragile X syndrome (FraX; the most common inherited form of learning disability) results from having more than 200 cytosine-guanine-guanine (CGG) trinucleotide repeats, with consequent methylation of the fragile X mental retardation (FMR1) gene and loss of FMR1 protein (FMRP). It was also considered that premutation carriers (with 55-200 CGG repeats) are unaffected, although a tremor/ataxia syndrome has recently been described in older adult male carriers. We reported that premutation expansion of CGG trinucleotide repeats affects brain anatomy, which, together with other studies, indicates that the molecular model for FraX needs modification. However, there are few studies on the cognitive ability of adult male premutation carriers. Thus, we selected 20 male premutation carriers on the basis of their genetic phenotype, and compared them to 20 male controls matched on age, IQ and handedness. We investigated intellectual functioning, executive function, memory, attention, visual and spatial perception, and language and pragmatics. The premutation carriers had significant impairments on tests of executive function (Verbal Fluency, Trail Making Test and Tower of London) and memory (Names sub-test of the Doors and People, Verbal Paired Associates Immediate Recall and Visual Paired Associates Delayed Recall sub-tests of the WMS-R, and Category Fluency Test for natural kinds). We therefore suggest that CGG trinucleotide repeats in the premutation range affect specific neuronal circuits that are concordant with specific neuropsychological deficits; and that these deficits reflect an emerging neuropsychological phenotype of premutation FraX.

Adult↗
PubMed1984

Genome structure described by formal languages.

Nucleic acid sequences may be looked upon as words over the alphabet of nucleotides. Naturally occurring DNAs and RNAs form subsets of the set of all possible words. The use of formal languages is proposed to describe the structure of these subsets. Regular languages defined by finite automata are introduced to demonstrate the application of the concept on RNA-phages of group I. This approach permits a concise characterization of grammatical patterns in genetic information.

Base Sequence↗
PubMed2025

Deleterious, protein-altering variants in GSPT2 are putatively associated with an X-linked neurodevelopmental disorder with intellectual disability, language impairment, autism, and epilepsy.

PURPOSE: Approximately 6% of individuals with neurodevelopmental disorders are predicted to be X-linked, and the GSPT2 gene, located at Xp11.22, has not yet been associated with any Mendelian disease. METHODS: To establish genotype-phenotype associations between GSPT2 and neurodevelopmental disorders, clinical investigations were performed in unrelated individuals, genomic and functional studies were conducted on the participants' blood and heterologous cell system. RESULTS: We described 6 individuals from 6 unrelated families carrying hemizygous variants in GSPT2 with intellectual disability, delayed speech and language development, autism spectrum disorder, epilepsy, or abnormal fetal neurodevelopment. Structural molecular modeling revealed significant deleterious effects of the identified variants. GSPT2 is preferentially enriched in the brain and cerebellum compared with other tissues. GSPT2-deficient H4 neuroglioma cells slow down the proliferation and downregulate the expression of cell-cycle-related genes. Transcriptomics revealed that GABAergic and calcium-signaling-related genes were significantly downregulated in GSPT2-deficient cells. Consistent with the transcriptomic data, RT-PCR analysis verified the marked downregulation of critical genes (CACNA1B, etc) in GSPT2-knockout cells and further confirmed these findings with proteomic profiling. CONCLUSION: Our data suggest a putative GSPT2-related X-linked neurodevelopmental disorders through dysregulation of cell-cycle progression and calcium/GABAergic signaling pathways.

Humans↗
PubMed2005

A model-based scan statistic for identifying extreme chromosomal regions of gene expression in human tumors.

MOTIVATION: The analysis of gene expression data in its chromosomal context has been a recent development in cancer research. However, currently available methods fail to account for variation in the distance between genes, gene density and genomic features (e.g. GC content) in identifying increased or decreased chromosomal regions of gene expression. RESULTS: We have developed a model-based scan statistic that accounts for these aspects of the complex landscape of the human genome in the identification of extreme chromosomal regions of gene expression. This method may be applied to gene expression data regardless of the microarray platform used to generate it. To demonstrate the accuracy and utility of this method, we applied it to a breast cancer gene expression dataset and tested its ability to predict regions containing medium-to-high level DNA amplification (DNA ratio values >2). A classifier was developed from the scan statistic results that had a 10-fold cross-validated classification rate of 93% and a positive predictive value of 88%. This result strongly suggests that the model-based scan statistic and the expression characteristics of an increased chromosomal region of gene expression can be used to accurately predict chromosomal regions containing amplified genes. AVAILABILITY: Functions in the R-language are available from the author upon request. CONTACT: fcouples@umich.edu.

Base Composition↗
PubMed1998

A cost analysis of long term antibiotic prophylaxis for spontaneous bacterial peritonitis in cirrhosis.

OBJECTIVE: The aim of this study was to perform a cost analysis of different strategies of long term antibiotic prophylaxis for spontaneous bacterial peritonitis (SBP) in patients with cirrhosis and ascites. The study involved a cost analysis using a decision analysis model and patients with cirrhosis and ascites who are at risk for developing SBP. METHODS: Two different strategies of antibiotic prophylaxis were compared with a "no prophylaxis" strategy in patients with cirrhosis and ascites using a decision analysis model. In strategy I, antibiotic prophylaxis was administered in all patients with cirrhosis and ascites and in strategy II, patients were stratified into a low risk and a high risk group on the basis of serum bilirubin and ascitic fluid protein levels; only patients in the high risk group received antibiotic prophylaxis. The cost per patient treated for 1 yr was the outcome measure compared in the different strategies. Clinical input probabilities and ranges used were obtained by searching the MEDLINE database for English language articles. Cost estimates were obtained from a university hospital setting. Cost analysis was done with a societal perspective, and only direct costs were taken into account. Sensitivity analyses were performed to evaluate the effect of variations in the key clinical probabilities and cost estimates ranging from a best case to a worst case scenario on the outcome measure. RESULTS: The estimated cost per patient treated in strategy I, strategy II, and strategy III (the strategy of "no prophylaxis") were $1311, $1123, and $3509, respectively. Over a broad range of clinical and cost variables, the strategy of risk stratification and restriction of antibiotic prophylaxis to the subgroup of patients with cirrhosis and ascites who were at high risk for SBP (as identified by serum bilirubin >2.5 mg/dl and ascitic fluid protein <1 g/dl) was the most favored strategy. However, when the cost of prophylaxis was low or the probability of a primary episode of SBP was at the lower end of the range reported in the literature, administering antibiotic prophylaxis to all patients with cirrhosis and ascites was the least costly strategy. CONCLUSION: This cost analysis indicates that antibiotic prophylaxis particularly when restricted to a subgroup of patients who, by simple laboratory parameters, are identified to be at high risk for SBP, is very cost-effective in the prevention of SBP in patients with cirrhosis and ascites.

Antibiotic Prophylaxis↗
PubMed2005

Unsupervised learning of natural languages.

We address the problem, fundamental to linguistics, bioinformatics, and certain other disciplines, of using corpora of raw symbolic sequential data to infer underlying rules that govern their production. Given a corpus of strings (such as text, transcribed speech, chromosome or protein sequence data, sheet music, etc.), our unsupervised algorithm recursively distills from it hierarchically structured patterns. The adios (automatic distillation of structure) algorithm relies on a statistical method for pattern extraction and on structured generalization, two processes that have been implicated in language acquisition. It has been evaluated on artificial context-free grammars with thousands of rules, on natural languages as diverse as English and Chinese, and on protein data correlating sequence with function. This unsupervised algorithm is capable of learning complex syntax, generating grammatical novel sentences, and proving useful in other fields that call for structure discovery from raw data, such as bioinformatics.

Algorithms↗
PubMed1995

Who wrote the book of life? Information and the transformation of molecular biology, 1945-55.

This paper focuses on the opening of a discursive space: the emergence of informational and scriptural representations of life and hereditiy and their self-negating consequences for the construction of biological meaning. It probes the notion of writing and the book of life and shows how molecular biology's claims to a status of language and texuality undermines its own objective of control. These textual significations were historically contingent. The informational representations of heredity and life were not an outcome of the internal cognitive momentum of molecular biology; they were not a logical necessity of the unravelling of the base-pairing of the DNA double-helix. They were transported into molecular biology still within the protein paradigm of the gene in the 1940s and permeated nearly every discipline in the life and social sciences. These information-based models, metaphors, linguistic, and semiotic tools which were central to the formulation of the genetic code were transported into molecular biology from cybernetics, information theory, electronic computing, and control and communication systems--technosciences that were deeply embedded with the military experiences of World War II and the Cold War. The information discourse thus became fixed in molecular biology not because it worked in the narrow epistemic sense (it did not), but because it positioned molecular biology within postwar discourse and culture, perhaps within the transition to a post-modern information-based society.

History, 20th Century↗
PubMedDate not supplied

[Simulation of liquid transcapillary exchanges].

The exchange between capillaries and the interstitial spaces are analysed using Wiederhielm's technique, and programmed in Basic language. The physiological variants represented are the hydrostatic pressures: arteriolar, venular and interstitial, and the oncotic, plasmatic and interstitial pressures. This technique enables us to analyses the relations between filtration, reabsorption. Plasmatic protein leaks, and lymphatic flux. It also enables us to simulate oedema of venous obstruction or lymphatic oedema, or protein deficiency oedema.

Arterioles↗
PubMed2006

Agents in bioinformatics, computational and systems biology.

The adoption of agent technologies and multi-agent systems constitutes an emerging area in bioinformatics. In this article, we report on the activity of the Working Group on Agents in Bioinformatics (BIOAGENTS) founded during the first AgentLink III Technical Forum meeting on the 2nd of July, 2004, in Rome. The meeting provided an opportunity for seeding collaborations between the agent and bioinformatics communities to develop a different (agent-based) approach of computational frameworks both for data analysis and management in bioinformatics and for systems modelling and simulation in computational and systems biology. The collaborations gave rise to applications and integrated tools that we summarize and discuss in context of the state of the art in this area. We investigate on future challenges and argue that the field should still be explored from many perspectives ranging from bio-conceptual languages for agent-based simulation, to the definition of bio-ontology-based declarative languages to be used by information agents, and to the adoption of agents for computational grids.

Artificial Intelligence↗
PubMed1994

SORTEZ: a relational translator for NCBI's ASN.1 database.

The National Center for Biotechnology Information (NCBI) has created a database collection that includes several protein and nucleic acid sequence databases, a biosequence-specific subset of MEDLINE, as well as value-added information such as links between similar sequences. Information in the NCBI database is modeled in Abstract Syntax Notation 1 (ASN.1) an Open Systems Interconnection protocol designed for the purpose of exchanging structured data between software applications rather than as a data model for database systems. While the NCBI database is distributed with an easy-to-use information retrieval system, ENTREZ, the ASN.1 data model currently lacks an ad hoc query language for general-purpose data access. For that reason, we have developed a software package, SORTEZ, that transforms the ASN.1 database (or other databases with nested data structures) to a relational data model and subsequently to a relational database management system (Sybase) where information can be accessed through the relational query language, SQL. Because the need to transform data from one data model and schema to another arises naturally in several important contexts, including efficient execution of specific applications, access to multiple databases and adaptation to database evolution this work also serves as a practical study of the issues involved in the various stages of database transformation. We show that transformation from the ASN.1 data model to a relational data model can be largely automated, but that schema transformation and data conversion require considerable domain expertise and would greatly benefit from additional support tools.

Algorithms↗
PubMed1990

An object-oriented database for protein structure analysis.

An object-oriented database system has been developed which is being used to store protein structure data. The database can be queried using the logic programming language Prolog or the query language Daplex. Queries retrieve information by navigating through a network of objects which represent the primary, secondary and tertiary structures of proteins. Routines written in both Prolog and Daplex can integrate complex calculations with the retrieval of data from the database, and can also be stored in the database for sharing among users. Thus object-oriented databases are better suited to prototyping applications and answering complex queries about protein structure than relational databases. This system has been used to find loops of varying length and anchor positions when modelling homologous protein structures.

Amino Acid Sequence↗
PubMed2004

CRANK: new methods for automated macromolecular crystal structure solution.

CRANK is a novel suite for automated macromolecular structure solution and uses recently developed programs for substructure detection, refinement, and phasing. CRANK utilizes methods for substructure detection and phasing and combines them with existing crystallographic programs for density modification and automated model building in a convenient and easy-to-use CCP4i graphical interface. The data model used conforms to the XML eXtensible Markup Language specification and works as a common language to communicate data between many different applications inside and outside of the suite. The application of CRANK on various test cases has yielded promising results: with minimal user input, CRANK can produce better quality solutions over currently available programs.

Crystallography↗
PubMed2006

Effects of aerobic exercise on C-reactive protein, body composition, and maximum oxygen consumption in adults: a meta-analysis of randomized controlled trials.

The aim of the study was to use the meta-analytic approach to examine the effects of aerobic exercise on C-reactive protein (CRP) in adults. Secondary outcomes included changes in body weight in kilograms, percentage of body fat, and maximum oxygen consumption (VO2max) in mL kg(-1) min(-1). Studies were retrieved using computerized literature searches, cross-referencing, and hand searching. Inclusion criteria were assessment of CRP in randomized controlled trials published in the English language between January 1, 1990, and January 1, 2006. Studies were also limited to aerobic exercise interventions lasting 4 weeks or more in adults 18 years or older. Five studies representing 323 male and female subjects (171 exercise, 152 control) and 6 outcomes for CRP were available for pooling. A nonsignificant reduction of approximately 3% was observed for CRP in the exercise groups (mean +/- SEM, -0.11 +/- 0.14 mg/L; 95% confidence interval [CI], -0.39 to 0.17 mg/L) using a random-effects model. Statistically significant reductions of approximately 4% were found for body weight (mean +/- SEM, -3.4 +/- 1.0 kg; 95% CI, -5.3 to -1.5 kg) and percentage of body fat (mean +/- SEM, -1.4% +/- 0.4%; 95% CI, -2.3% to -0.6%), whereas a statistically significant increase of 12% was found for VO2max (mean +/- SEM, 3.3 +/- 0.9 mL kg(-1) min(-1); 95% CI, 1.5 to 5.1 mL kg(-1) min(-1)). The results of our study suggest that aerobic exercise does not reduce CRP levels in adults, but does improve measures of body composition and physical fitness.

Adult↗
PubMed2006

Assessing semantic similarity measures for the characterization of human regulatory pathways.

MOTIVATION: Pathway modeling requires the integration of multiple data including prior knowledge. In this study, we quantitatively assess the application of Gene Ontology (GO)-derived similarity measures for the characterization of direct and indirect interactions within human regulatory pathways. The characterization would help the integration of prior pathway knowledge for the modeling. RESULTS: Our analysis indicates information content-based measures outperform graph structure-based measures for stratifying protein interactions. Measures in terms of GO biological process and molecular function annotations can be used alone or together for the validation of protein interactions involved in the pathways. However, GO cellular component-derived measures may not have the ability to separate true positives from noise. Furthermore, we demonstrate that the functional similarity of proteins within known regulatory pathways decays rapidly as the path length between two proteins increases. Several logistic regression models are built to estimate the confidence of both direct and indirect interactions within a pathway, which may be used to score putative pathways inferred from a scaffold of molecular interactions.

Databases, Protein↗
PubMed2026

Shielding the First 24 Postnatal Months of Life: A Proposal for a Prospective Cohort Study of Early-Life Electromagnetic Exposure and Autism Risk.

BACKGROUND: Autism Spectrum Disorder (ASD) involves Mirror Neuron System (MNS) dysfunction, driving core social and imitative impairments. Systemic physiological alterations such as autonomic dysregulation, mitochondrial dysfunction and neuroinflammation are known to impair synchronization and plasticity of neuronal clusters. A less-evident environmental cofactor, coinciding with rising ASD prevalence, is the considerable world-wide increase in electromagnetic radiation (EMR) overall exposure among children. Experimental evidence shows how low-intensity EMR influences cellular processes, via voltage-gated calcium channels (VGCCs), oxidative stress, and mitochondrial metabolism. The Resonant Convergence framework, allow to predict how chronic EMR exposure during the first 24 postnatal months of life can act as a factor in ASD pathogenesis. The best candidate mechanism is chronic Ion Cyclotron Resonance (ICR) detuning the Ca2+-calmodulin pathway, thus disrupting MNS synchronization. METHODS AND ANALYSIS: A prospective observational pilot cohort study (24-month follow-up) proposes to enroll 1000 full-term newborns into two arms: an EMR-reduced cohort (n = 500, rest and sleep-phase Faraday shielding) and a standard exposure cohort (n = 500). Exposure is quantified via radiofrequency (RF)/extremely low frequency(ELF) measurements, proximity analysis, device inventories and wearable dosimetry. The primary endpoint is a continuous neurodevelopmental trajectory score (joint attention, language, electroencephalogram (EEG) mu-rhythm); binary ASD diagnosis (Autism Diagnostic Observation Schedule, Second Edition (ADOS-2), Autism Diagnostic Interview-Revised (ADI-R)) is a secondary, exploratory endpoint. Moreover, an optional genomic screening will evaluate gene-environment interactions within extremely low-frequency electromagnetic field (ELF-EMF) vulnerable pathways, including ASD-associated genes upregulated by RF via bromodomain and extraterminal protein (BET)-mediated epigenetic mechanisms. Analyses will employ risk ratios, Fisher's exact tests and logistic regression adjusted for confounders; mixed-effects and Bayesian modeling will evaluate longitudinal outcomes and exposure reduction effects. Given a 2-3% baseline prevalence, approximately 20-30 ASD cases are expected. The study is therefore powered for exploratory signal detection rather than definitive causal inference, providing the critical baseline data required to justify and design future confirmatory trials. Sex-stratified modeling will address the 4:1 male-to-female prevalence ratio. ETHICS AND DISSEMINATION: Ethics committee approval is not yet sought; full protocol review and approval will be obtained prior to the study initiation, in strict accordance with the Declaration of Helsinki. Written parental informed consent will be mandatory for all participants prior to enrollment. Study findings and methodological milestones will be disseminated through peer-reviewed international scientific publications. This protocol provides a structured methodological framework for the first prospective investigation of sleep-phase EMR reduction as a potential modulator of ASD incidence during early neurodevelopment. Results will inform adequately powered confirmatory trials in electromagnetic neurodevelopmental epidemiology.

autism spectrum disorder↗
PubMed2005

Association of insulin-like growth factor I and insulin-like growth factor-binding protein-3 with intelligence quotient among 8- to 9-year-old children in the Avon Longitudinal Study of Parents and Children.

BACKGROUND: Insulin-like growth factor I (IGF-I) is a hormone that mediates the effects of growth hormone and plays a critical role in somatic growth regulation and organ development. It is hypothesized that it also plays a key role in human brain development. Previous studies have investigated the association of low IGF-I levels attributable to growth hormone receptor deficiency with intelligence but produced mixed results. We are aware of no studies that investigated the association of IGF-I levels with IQ in population samples of normal children. OBJECTIVES: To investigate the association of circulating levels of IGF-I and its principle binding protein, IGF-binding protein-3 (IGFBP-3), in childhood with subsequent measures of IQ. METHODS: The cohort study was based on data for 547 white singleton boys and girls, members of the Avon Longitudinal Study of Parents and Children, with IGF-I and IGFBP-3 measurements (obtained at a mean age of 8.0 years) and IQ measured with the Wechsler Intelligence Scale for Children (at a mean age of 8.7 years). We also investigated associations with measures of speech and language based on the Wechsler Objective Reading Dimensions test (measured at an age of 7.5 years) and the Wechsler Objective Language Dimensions test (listening comprehension subtest only, measured at an age of 8.7 years). For some children (n = 407), IGF-I (but not IGFBP-3) levels had been measured at approximately 5 years of age in a previous study. Linear regression models were used to investigate associations of the IGF-I system with the measures of cognitive function. RESULTS: Three hundred one boys and 246 girls were included in the sample. IGF-I levels (mean +/- SD) were 142.6 +/- 53.9 ng/mL for boys and 154.4 +/- 51.6 ng/mL for girls. IQ scores (mean +/- SD) were 106.05 +/- 16.6 and 105.27 +/- 15.6 for boys and girls, respectively. IGF-I levels were associated positively with intelligence. For every 100 ng/mL increase in IGF-I, IQ increased by 3.18 points (95% confidence interval [CI]: 0.52 to 5.84 points). These positive associations were seen in relation to the verbal component (coefficient: 4.27; 95% CI: 1.62 to 6.92), rather than the performance component (coefficient: 1.06; 95% CI: -1.67 to 3.78), of IQ. There was no evidence that associations with overall IQ differed between boys and girls. In a data set with complete information on confounders (n = 484), controlling for birth weight (adjusted for gestation), breastfeeding, and BMI slightly strengthened the associations of IGF-I levels with IQ. Additionally controlling for maternal education and IGFBP-3 levels attenuated the associations (change in IQ for every 100 ng/mL increase in IGF-I levels: 2.51 points; 95% CI: -0.42 to 5.44 points). The weakening of associations in models controlling for markers of parental socioeconomic position and education could reflect shared influences of parental IGF levels on parents' own educational attainment and their offspring's IGF-I levels. In unadjusted models examining associations of Wechsler Objective Reading Dimensions and Wechsler Objective Language Dimensions test scores with IGF-I levels, there was no strong evidence that performance on either of these tests was associated with circulating IGF-I levels, although positive associations were seen with both measures. Associations between IGF-I levels measured at age 5 and Wechsler Intelligence Scale for Children scores (n = 407) were similar to those for IGF-I levels measured at age 7 to 8. For every 100 ng/mL increase in IGF-I levels at 5 years of age, IQ increased by 2.3 points (95% CI: -0.21 to 4.89 points). CONCLUSIONS: This study provides some preliminary evidence that IGF-I is associated with brain development in childhood. Additional longitudinal research is required to clarify the role of IGF-I in neurodevelopment. Because IGF-I levels are modifiable through diet and other environmental exposures, this may be one pathway through which the childhood environment may influence neurodevelopment.

Birth Weight↗