The Information Coded in the Yeast Response Elements Accounts for Most of the Topological Properties of Its Transcriptional Regulation Network

The regulation of gene expression in a cell relies to a major extent on transcription factors, proteins which recognize and bind the DNA at specific binding sites (response elements) within promoter regions associated with each gene. We present an information theoretic approach to modeling transcriptional regulatory networks, in terms of a simple “sequence-matching” rule and the statistics of the occurrence of binding sequences of given specificity in random promoter regions. The crucial biological input is the distribution of the amount of information coded in these cognate response elements and the length distribution of the promoter regions. We provide an analysis of the transcriptional regulatory network of yeast Saccharomyces cerevisiae, which we extract from the available databases, with respect to the degree distributions, clustering coefficient, degree correlations, rich-club coefficient and the k-core structure. We find that these topological features are in remarkable agreement with those predicted by our model, on the basis of the amount of information coded in the interaction between the transcription factors and response elements

Defining traumatic brain injury in children and youth using International Classification of Diseases version 10 codes: a systematic review protocol

BACKGROUND: Although healthcare administrative data are commonly used for traumatic brain injury research, there is currently no consensus or consistency on using the International Classification of Diseases version 10 codes to define traumatic brain injury among children and youth. This protocol is for a systematic review of the literature to explore the range of International Classification of Diseases version 10 codes that are used to define traumatic brain injury in this population. METHODS/DESIGN: The databases MEDLINE, MEDLINE In-Process, Embase, PsychINFO, CINAHL, SPORTDiscus, and Cochrane Database of Systematic Reviews will be systematically searched. Grey literature will be searched using Grey Matters and Google. Reference lists of included articles will also be searched. Articles will be screened using predefined inclusion and exclusion criteria and all full-text articles that meet the predefined inclusion criteria will be included for analysis. The study selection process and reasons for exclusion at the full-text level will be presented using a PRISMA study flow diagram. Information on the data source of included studies, year and location of study, age of study population, range of incidence, and study purpose will be abstracted into a separate table and synthesized for analysis. All International Classification of Diseases version 10 codes will be listed in tables and the codes that are used to define concussion, acquired traumatic brain injury, head injury, or head trauma will be identified. DISCUSSION: The identification of the optimal International Classification of Diseases version 10 codes to define this population in administrative data is crucial, as it has implications for policy, resource allocation, planning of healthcare services, and prevention strategies. It also allows for comparisons across countries and studies. This protocol is for a review that identifies the range and most common diagnoses used to conduct surveillance for traumatic brain injury in children and youth. This is an important first step in reaching an appropriate definition using International Classification of Diseases version 10 codes and can inform future work on reaching consensus on the codes to define traumatic brain injury for this vulnerable population

Defining pediatric traumatic brain injury using International Classification of Diseases Version 10 Codes: A systematic review

Background: Although healthcare administrative data are commonly used for traumatic brain injury (TBI) research, there is currently no consensus or consistency on the International Classification of Diseases Version 10 (ICD-10) codes used to define TBI among children and youth internationally. This study systematically reviewed the literature to explore the range of ICD-10 codes that are used to define TBI in this population. The identification of the range of ICD-10 codes to define this population in administrative data is crucial, as it has implications for policy, resource allocation, planning of healthcare services, and prevention strategies. Methods: The databases MEDLINE, MEDLINE In-Process, Embase, PsychINFO, CINAHL, SPORTDiscus, and Cochrane Database of Systematic Reviews were systematically searched. Grey literature was searched using Grey Matters and Google. Reference lists of included articles were also searched for relevant studies. Two reviewers independently screened all titles and abstracts using pre-defined inclusion and exclusion criteria. A full text screen was conducted on articles that met the first screen inclusion criteria. All full text articles that met the pre-defined inclusion criteria were included for analysis in this systematic review. Results: A total of 1,326 publications were identified through the predetermined search strategy and 32 articles/reports met all eligibility criteria for inclusion in this review. Five articles specifically examined children and youth aged 19 years or under with TBI. ICD-10 case definitions ranged from the broad injuries to the head codes (ICD-10 S00 to S09) to concussion only (S06.0). There was overwhelming consensus on the inclusion of ICD-10 code S06, intracranial injury, while codes S00 (superficial injury of the head), S03 (dislocation, sprain, and strain of joints and ligaments of head), and S05 (injury of eye and orbit) were only used by articles that examined head injury, none of which specifically examined children and youth. Conclusion: This review provides evidence for discussion on how best to use ICD codes for different goals. This is an important first step in reaching an appropriate definition and can inform future work on reaching consensus on the ICD-10 codes to define TBI for this vulnerable population