A journal (through French from late Latin diurnalis, daily) has several related meanings:

• a daily record of events or business; a private journal is usually referred to as a diary.
• a newspaper or other periodical, in the literal sense of one published each day;
• however, some publications issued at stated intervals, such as a magazine or the record of the transactions of society such as a scientific journal or academic journals in general, are called a journal. Journal, then, is sometimes used as a synonym for "magazine".

The word "journalist" for one whose business is writing for the public press has been in use since the end of the 17th century.

"Journal" is also applied to the record, day by day, of the business and proceedings of a public body:

• The journals of the British Houses of Parliament contain an official record of the business transacted day by day in either house. The record does not take note of speeches, though some of the earlier volumes contain references to them. The journals are a lengthened account written from the "Votes and Proceedings" (in the House of Lords called "Minutes of Proceedings"), made day by day by the Clerks at the Table, and printed on the responsibility of the Clerk of the House. In the Commons the Votes and Proceedings, but not the Journal, bear the Speaker's signature in fulfilment of a former order that he should "peruse" them before publication. The journals of the British House of Commons begin in the first year of the reign of Edward VI in 1547, and are complete, except for a short interval under Elizabeth I. Those of the House of Lords date from the first year of Henry VIII in 1509. Before that date the proceedings in parliament were entered in the rolls of parliament, which extend from 1278 to 1503. The journals of the Lords are "records" in the judicial sense, those of the Commons are not (see Erskine May, Parliamentary Practice, 1906, pp. 201-202).
• Section 5 of Article I of the United States Constitution requires the Congress of the United States to keep a journal of its proceedings. This journal, the Congressional Record is published by the Government Printing Office.

Journals of this sort are also often referred to as minutes.

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Theoretical Biology and Medical Modelling - Latest articles

Feature context-dependency and complexity-reduction in probability landscapes for integrative genomics
Annick Lesne and Arndt Benecke Wed, 10 Sep 2008 00:00:00 -0000
Background: The question of how to integrate heterogeneous sources of biological information into a coherent framework that allows the gene regulatory code in eukaryotes to be systematically investigated is one of the major challenges faced by systems biology. Probability landscapes, which include as reference set the probabilistic representation of the genomic sequence, have been proposed as a possible approach to the systematic discovery and analysis of correlations amongst initially heterogeneous and un-relatable descriptions and genome-wide measurements. Much of the available experimental sequence and genome activity information is de facto, but not necessarily obviously, context dependent. Furthermore, the context dependency of the relevant information is itself dependent on the biological question addressed. It is hence necessary to develop a systematic way of discovering the context-dependency of functional genomics information in a flexible, question-dependent manner. Results: We demonstrate here how feature context-dependency can be systematically investigated using probability landscapes. Furthermore, we show how different feature probability profiles can be conditionally collapsed to reduce the computational and formal, mathematical complexity of probability landscapes. Interestingly, the possibility of complexity reduction can be linked directly to the analysis of context-dependency. Conclusion: These two advances in our understanding of the properties of probability landscapes not only simplify subsequent cross-correlation analysis in hypothesis-driven model building and testing, but also provide additional insights into the biological gene regulatory problems studied. Furthermore, insights into the nature of individual features and a classification of features according to their minimal context-dependency are achieved. The formal structure proposed contributes to a concrete and tangible basis for attempting to formulate novel mathematical structures for describing gene regulation in eukaryotes on a genome-wide scale.
Extracting key information from historical data to quantify the transmission dynamics of smallpox
Hiroshi Nishiura, Stefan O Brockmann and Martin Eichner Wed, 20 Aug 2008 00:00:00 -0000
Background: Quantification of the transmission dynamics of smallpox is crucial for optimizing intervention strategies in the event of a bioterrorist attack. This article reviews basic methods and findings in mathematical and statistical studies of smallpox which estimate key transmission parameters from historical data.Main findingsFirst, critically important aspects in extracting key information from historical data are briefly summarized. We mention different sources of heterogeneity and potential pitfalls in utilizing historical records. Second, we discuss how smallpox spreads in the absence of interventions and how the optimal timing of quarantine and isolation measures can be determined. Case studies demonstrate the following. (1) The upper confidence limit of the 99th percentile of the incubation period is 22.2 days, suggesting that quarantine should last 23 days. (2) The highest frequency (61.8%) of secondary transmissions occurs 3–5 days after onset of fever so that infected individuals should be isolated before the appearance of rash. (3) The U-shaped age-specific case fatality implies a vulnerability of infants and elderly among non-immune individuals. Estimates of the transmission potential are subsequently reviewed, followed by an assessment of vaccination effects and of the expected effectiveness of interventions. Conclusion: Current debates on bio-terrorism preparedness indicate that public health decision making must account for the complex interplay and balance between vaccination strategies and other public health measures (e.g. case isolation and contact tracing) taking into account the frequency of adverse events to vaccination. In this review, we summarize what has already been clarified and point out needs to analyze previous smallpox outbreaks systematically.
Utility of a single adjusting compartment: a novel methodology for whole body physiologically-based pharmacokinetic modelling
Hirotaka Ando, Shigeru Izawa, Wataru Hori and Ippei Nakagawa Fri, 08 Aug 2008 00:00:00 -0000
Background: There are various methods for predicting human pharmacokinetics. Among these, a whole body physiologically-based pharmacokinetic (WBPBPK) model is useful because it gives a mechanistic description. However, WBPBPK models cannot predict human pharmacokinetics with enough precision. This study was conducted to elucidate the primary reason for poor predictions by WBPBPK models, and to enable better predictions to be made without reliance on complex concepts. Methods: The primary reasons for poor predictions of human pharmacokinetics were investigated using a generic WBPBPK model that incorporated a single adjusting compartment (SAC), a virtual organ compartment with physiological parameters that can be adjusted arbitrarily. The blood flow rate, organ volume, and the steady state tissue-plasma partition coefficient of a SAC were calculated to fit simulated to observed pharmacokinetics in the rat. The adjusted SAC parameters were fixed and scaled up to the human using a newly developed equation. Using the scaled-up SAC parameters, human pharmacokinetics were simulated and each pharmacokinetic parameter was calculated. These simulated parameters were compared to the observed data. Simulations were performed to confirm the relationship between the precision of prediction and the number of tissue compartments, including a SAC. Results: Increasing the number of tissue compartments led to an improvement of the average-fold error (AFE) of total body clearances (CLtot) and half-lives (T1/2) calculated from the simulated human blood concentrations of 14 drugs. The presence of a SAC also improved the AFE values of a ten-organ model from 6.74 to 1.56 in CLtot, and from 4.74 to 1.48 in T1/2. Moreover, the within-2-fold errors were improved in all models; incorporating a SAC gave results from 0 to 79% in CLtot, and from 14 to 93% in T1/2 of the ten-organ model. Conclusion: By using a SAC in this study, we were able to show that poor prediction resulted mainly from such physiological factors as organ blood flow rate and organ volume, which were not satisfactorily accounted for in previous WBPBPK models. The SAC also improved precision in the prediction of human pharmacokinetics. This finding showed that the methodology of our study may be useful for functionally reinforcing a WBPBPK model.

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