Pubmed

dysplastic and malignant IP, it may have a higher detection rate than another series which contains only nondysplastic IP. We hypothesize that the higher rates of HPV detection in dysplastic and malignant IP may be related to HPV integration. The implication of this is that HPV sub-type testing may identify patients at risk for recurrence, or progression to dysplasia and malignancy, and thus may impact surveillance protocols.

The purpose is to provide an update the Bone Metastases Guideline published in 2011 based on evidence complemented by expert opinion. The update will discuss new high-quality literature for the 8 key questions from the original guideline and implications for practice. Methods and materials: A systematic PubMed search from the last date included in the original Guideline yielded 414 relevant articles. Ultimately, 20 randomized controlled trials, 32 prospective nonrandomized studies, and 4 meta-analyses/pooled analyses were selected and abstracted into evidence tables. The authors synthesized the evidence and reached consensus on the included recommendations. Results: Available literature continues to support pain relief equivalency between single and multiple fraction regimens for bone metastases. High-quality data confirm single fraction radiation therapy may be delivered to spine lesions with acceptable late toxicity. One prospective, randomized trial confirms both peripheral and spine-based painful metastases can be successfully and safely palliated with retreatment for recurrence pain with adherence to published dosing constraints. Advanced radiation therapy techniques such as stereotactic body radiation therapy lack high-quality data, leading the panel to favor its use on a clinical trial or when results will be collected in a registry. The panel's conclusion remains that surgery, radionuclides, bisphosphonates, and kyphoplasty/vertebroplasty do not obviate the need for Supplementary material for this article (http://dx.doi.org/10.1016/j.prro.2016.08.001) can be found at www.practicalradonc.org. Conflicts of interest. Before initiating work on this guideline, all panelists completed disclosure statements and pertinent disclosures are published within this report. Where potential conflicts are detected, remedial measures to address them are taken and noted here. TB received research funding from Templeton Foundation and leads ongoing bone metastases study. S.Lo. participated in international oligometastases consortium partially funded by Elekta and received honoraria and travel expenses from Accuray and Varian. These disclosures were shared with the panel. The panel and guideline subcommittee chair reviewed these relationships and determined that the disclosure here is sufficient to manage potential conflicts.

Background: An increasing number of childhood cancer survivors need long-term follow-up care. Different models address this problem, including that of follow-up by general practitioners (GP). We describe models that involve GPs in follow-up for childhood cancer survivors, their advantages and disadvantages, clinics that employ these models, and the elements essential to high-quality, GP-led follow-up care.

Your assignment: Write a scholarly paper for a nursing course. What is your reaction? Panic!? Confusion? A need to get prepared! Most nursing students ask the following questions: "What is considered scholarly writing style?" "What should be included in the paper?" "Where do I find references?" "What references are appropriate?" "How are references cited?" "How should the paper be typed?" "Why do I need to write papers for nursing courses anyway?" These questions and anxieties are expressed by nursing students across the country, especially since undergraduate and graduate nursing students are asked to write scholarly papers throughout their nursing journey. Nursing papers are often written using the American Psychological Association (APA) (2001) style guidelines, and we've prepared this article so that you'll be on your way to writing a successful paper. We've included information on the APA format, with examples, so that you're not only developing your writing skills while at school but during your career as a professional nurse.

In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi. nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez

The treatment of anxiety is on the edge of a new era of combinations of pharmacologic and psychosocial interventions. A new wave of translational research has focused on the use of pharmacological agents as psychotherapy adjuvants using neurobiological insights into the mechanism of the action of certain psychological treatments such as exposure therapy. Recently, d-cycloserine (DCS) an antibiotic used to treat tuberculosis has been applied to enhance exposure-based treatment for anxiety and has proved to be a promising, but as yet unproven intervention. The present study aimed to evaluate the efficacy of DCS in the enhancement of exposure therapy in anxiety disorders. A systematic review/metaanalysis was conducted. Electronic searches were conducted in the databases ISI-Web of Science, Pubmed and PsycINFO. We included only randomized, double-blind, placebo-controlled trials with humans, focusing on the role of DCS in enhancing the action of exposure therapy for anxiety disorders. We identified 328 references, 13 studies were included in our final sample: 4 on obsessive-compulsive disorder, 2 on panic disorder, 2 on social anxiety disorder, 2 on posttraumatic stress disorder, one on acrophobia, and 2 on snake phobia. The results of the present meta-analysis show that DCS enhances exposure therapy in the treatment of anxiety disorders (Cohen d = 20.34; CI: 20.54 to 20.14), facilitating the specific process of extinction of fear. DCS seems to be effective when administered at a time close to the exposure therapy, at low doses and a limited number of times. DCS emerges as a potential new therapeutic approach for patients with refractory anxiety disorders that are unresponsive to the conventional treatments available. When administered correctly, DCS is a promising strategy for augmentation of CBT and could reduce health care costs, drop-out rates and bring faster relief to patients.

Introduction: Reduced dopaminergic activity in the pre-frontal cortex may partially explain the negative symptoms of schizophrenia. Animal models have shown that adding an alpha-2 adrenergic receptor antagonist to a D2 antagonist can efflux dopamine into the frontal cortex increasing dopaminergic activity. Trials of alpha-2 antagonist add-on therapy in humans have been limited by small sample sizes. Therefore, a meta-analysis was conducted to determine if adding an alpha-2 antagonist to a D2 antagonist improves schizophrenia treatment by reducing negative symptoms. Methods: Randomized, placebo-controlled trials of the addition of an alpha-2 antagonist to a D2 antagonist were identified through a PubMed search. Treatment effects were measured using schizophrenia rating scales and meta-analyzed as standardized mean differences using random effects models. Results: Eight unique studies were identified, each including 18 to 41 patients and lasting four to eight weeks. The overall effect size of add-on alpha-2 therapy across the eight trials was an improvement of 0.16 (95% C.I., −.30 to 0.62) for positive symptoms, 0.84 (95% C.I., .17 to 1.51) for negative symptoms, 0.28 (95% C.I., −.08 to 0.64) for general symptoms, and .80 (95% C.I., .15 to 1.46) for symptoms overall. Negative symptom improvements were independent of improvements in depressive symptoms, measured using the Hamilton depression rating scale, for 3 of the 5 studies. Conclusions: Add-on agents with alpha-2 antagonist activity appear to improve the efficacy of D2 antagonists for the treatment of schizophrenia by reducing negative symptoms. These results support conducting a more definitive confirmatory clinical trial.

Substance abuse is the most prevalent comorbid psychiatric condition associated with schizophrenia, and cannabis is the illicit drug most often abused. Apart from worsening the course of schizophrenia, frequent cannabis use especially at an early age seems to be an important risk factor for developing schizophrenia. Although a large body of neuroimaging studies gives evidence for structural alterations in many different brain regions in schizophrenia patients, there is still limited knowledge of the impact of cannabis abuse on brain structure in schizophrenia. We performed a systematic review including structural magnetic resonance imaging studies comparing high-risk and schizophrenia patients with and without cannabis abuse and found inconclusive results. While there is some evidence that chronic cannabis abuse could alter brain morphology in schizophrenia in patients continuing their cannabis consumption, there is no convincing evidence that this alteration takes place before the onset of schizophrenia when looking at first-episode patients. There is some weak evidence that cannabis abuse could affect brain structures in high-risk subjects, but replication of these studies is needed.

Biocompatibility or tissue compatibility describes the ability of a material to perform with an appropriate host response when applied as intended. Poly-methylmethacrylate (PMMA) based resins are most widely used resins in dentistry, especially in fabrication of dentures and orthodontic appliances. They are considered cytotoxic on account of leaching of various potential toxic substances, most common being residual monomer. Various in vitro and in vivo experiments and cell based studies conducted on acrylic based resins or their leached components have shown them to have cytotoxic effects. They can cause mucosal irritation and tissue sensitization. These studies are not only important to evaluate the long term clinical effect of these materials, but also help in further development of alternate resins. This article reviews information from scientific full articles, reviews, or abstracts published in dental literature, associated with biocompatibility of PMMA resins and it is leached out components. Published materials were searched in dental literature using general and specialist databases, like the PubMED database. V C 2012 Wiley Periodicals, Inc. J Biomed Mater Res Part B:

Objectives: This article attempts to cover pragmatic clinical considerations involved in the use of cannabinergic medicines in pain practice, including geographical and historical considerations, pharmacokinetics, pharmacodynamics, adverse effects, drug interactions, indications, and contraindications. Topics include molecular considerations such as the 10-fold greater abundance of cannabinoid type 1 receptors compared to m-opioid receptors in the central nervous system and anatomic distributions of cannabinoid receptors in pain circuits.

En este documento se explica de manera detallada como obtener información en la base de datos PUBMED.

PubMed es una base de datos gratis creada y mantenida por la Biblioteca Nacional de Medicina de los Estados Unidos. Esta base de datos incluye más de 26 millones de citas en las áreas de medicina, enfermería, odontología, medicina veterinaria, el sistema de salud, y las ciencias preclínicas.

The COVID-19 pandemic requires a fast response from researchers to help address biological, medical and public health issues to minimize its impact. In this rapidly evolving context, scholars, professionals and the public may need to quickly identify important new studies. In response, this paper assesses the coverage of scholarly databases and impact indicators during 21 March to 18 April 2020. The results confirm a rapid increase in the volume of research, which particularly accessible through Google Scholar and Dimensions, and less through Scopus, the Web of Science, PubMed. A few COVID-19 papers from the 21,395 in Dimensions were already highly cited, with substantial news and social media attention. For this topic, in contrast to previous studies, there seems to be a high degree of convergence between articles shared in the social web and citation counts, at least in the short term. In particular, articles that are extensively tweeted on the day first indexed are likely to be highly read and relatively highly cited three weeks later. Researchers needing wide scope literature searches (rather than health focused PubMed or medRxiv searches) should start with Google Scholar or Dimensions and can use tweet and Mendeley reader counts as indicators of likely importance.

BACKGROUND CONTEXT: Spine trauma is relatively common, and each year approximately 10,000 to 17,000 people in the United States will sustain a spinal cord injury and approximately 150,000 to 160,000 will fracture their spinal column. Posttraumatic spinal deformity is a common potential complication of spinal injury and poses one of the greatest challenges in spinal surgery. PURPOSE: To provide a comprehensive and current review of posttraumatic deformity focusing on the epidemiology, clinical and radiographical presentation, treatment options, and prognosis. STUDY DESIGN/SETTING: A thorough review of the English literature on the management of posttraumatic deformity was performed. Pertinent articles were identified by using PubMed and a review of publications by the American Academy of Orthopaedic Surgeons. METHODS: Each article was reviewed, and findings were analyzed to formulate a concise review of current treatment methods for posttraumatic deformity. RESULTS: Successful treatment of posttraumatic deformity is dependent on careful patient selection and appropriate surgical intervention, which should be considered in the presence of significant or increasing deformity, increasing back and/or leg pain, ''breakdown'' at levels above or below the deformity, pseudarthrosis or malunion, and increasing neurological deficit. The goals of surgery should be to decompress the neural elements if neurological claudication or a neurological deficit is present, to recreate normal sagittal contours and balance, and to optimize the chances for successful fusion; these goals can be achieved through an all-anterior, all-posterior, or a combined anterior/ posterior approach assuming that close attention is paid to using the appropriate bone-grafting techniques, selecting technically sound segmental instrumentation, and providing appropriate biomechanical environment for maintenance of correction and successful fusion. CONCLUSIONS: Posttraumatic spinal deformity is a common complication of spinal injury, and it is therefore essential for patients with vertebral column injuries to have a careful initial evaluation, close follow-up, and early intervention when needed. Once posttraumatic deformity is present, successful outcome is achievable assuming a thorough, systematic, and technically well-executed surgical intervention is performed. Ó

Background: Focus group studies are increasingly published in health related journals, but we know little about how researchers use this method, particularly how they determine the number of focus groups to conduct. The methodological literature commonly advises researchers to follow principles of data saturation, although practical advise on how to do this is lacking. Our objectives were firstly, to describe the current status of sample size in focus group studies reported in health journals. Secondly, to assess whether and how researchers explain the number of focus groups they carry out. Methods: We searched PubMed for studies that had used focus groups and that had been published in open access journals during 2008, and extracted data on the number of focus groups and on any explanation authors gave for this number. We also did a qualitative assessment of the papers with regard to how number of groups was explained and discussed.

Este artículo busca ilustrar a profesionales de la salud sobre la importancia y utilidad de la Medicina Basada en la Evidencia (MBE) como un método para la toma de decisiones clínicas en el ejercicio actual de la medicina y se enfoca en el primer paso: ¿Cómo estructurar una pregunta clínica de manera que se facilite el acceso a la respuesta en las bases de literatura biomédica como PubMED y la Librería Cochrane? El empleo de preguntas estructuradas permiten ahorrar tiempo en la recuperación de las referencias de la literatura científica pertinentes a la pregunta de intervención o tratamiento y consta de cuatro componentes: Pacientes, intervención, comparación y resultados (Outcomes). Los términos de la pregunta estructurada y la combinación de los mismos constituyen uno de los elementos de la estrategia de búsqueda, que también es de utilidad en la construcción de un estado del arte o un marco teórico en un proyecto de investigación.

Background: With the increased knowledge of biological risk factors, interest in including this information in forensic assessments is growing. Currently, forensic assessments are predominantly focused on psychosocial factors. A better understanding of the neurobiology of violent criminal behaviour and biological risk factors could improve forensic assessments.

Background: The goal of the gene normalization task is to link genes or gene products mentioned in the literature to biological databases. This is a key step in an accurate search of the biological literature. It is a challenging task, even for the human expert; genes are often described rather than referred to by gene symbol and, confusingly, one gene name may refer to different genes (often from different organisms). For BioCreative II, the task was to list the Entrez Gene identifiers for human genes or gene products mentioned in PubMed/MEDLINE abstracts. We selected abstracts associated with articles previously curated for human genes. We provided 281 expert-annotated abstracts containing 684 gene identifiers for training, and a blind test set of 262 documents containing 785 identifiers, with a gold standard created by expert annotators. Inter-annotator agreement was measured at over 90%.

The distribution of scientific citations for publications selected with different rules (author, topic, institution, country, journal, etc…) collapse on a single curve if one plots the citations relative to their mean value. We find that the distribution of "shares" for the Facebook posts rescale in the same manner to the very same curve with scientific citations. This finding suggests that citations are subjected to the same growth mechanism with Facebook popularity measures, being influenced by a statistically similar social environment and selection mechanism. In a simple master-equation approach the exponential growth of the number of publications and a preferential selection mechanism leads to a Tsallis-Pareto distribution offering an excellent description for the observed statistics. Based on our model and on the data derived from PubMed we predict that according to the present trend the average citations per scientific publications exponentially relaxes to about 4.

Objective: Male, non-barrier, contraceptive options are limited to vasectomy and inadequate methods such as withdrawal and periodic abstinence. Herein we give an overview of current research on male contraception by pharmacological means. Methods: Literature search of PubMed documented publications and abstracts from meetings. Results: Cross-cultural surveys show men's willingness to carry contraceptive responsibility. Clinical trials substantiate that hormonal contraception involving suppression of gonadotropins holds the best promise to provide a male pharmacological contraceptive. Androgens have been demonstrated to induce reversible infertility particularly in combination with certain progestins and GnRH antagonists. Advances in non-endocrine contraception include intervention with triptolide derivatives, alkylated imino sugars, and immunization by eppin. Conclusion: The prospect of a pharmacological, male contraceptive has been considerably advanced in recent years. Long-term studies involving a greater number of subjects may result in a safe, reversible and effective means. Asia is likely to be the first market for male, hormonal contraceptive methods. The clinical evaluation of nonendocrine approaches may ultimately lead to an alternative to hormone-based male contraception. #

The BRENDA (BRaunschweig ENzyme DAtabase) (http://www.brenda-enzymes.org) represents the largest freely available information system containing a huge amount of biochemical and molecular information on all classified enzymes as well as software tools for querying the database and calculating molecular properties. The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. The data in BRENDA are manually curated from more than 79 000 primary literature references. Each entry is clearly linked to a literature reference, the origin organism and, where available, to the protein sequence of the enzyme protein. A new search option provides the access to proteinspecific data. FRENDA (Full Reference ENzyme DAta) and AMENDA (Automatic Mining of ENzyme DAta) are additional databases created by continuously improved text-mining procedures. These databases ought to provide a complete survey on enzyme data of the literature collection of PubMed. The web service via a SOAP (Simple Object Access Protocol) interface for access to the BRENDA data has been further enhanced.

The evolution of the electronic age has led to the development of numerous medical databases on the World Wide Web, offering search facilities on a particular subject and the ability to perform citation analysis. We compared the content coverage and practical utility of PubMed, Scopus, Web of Science, and Google Scholar. The official Web pages of the databases were used to extract information on the range of journals covered, search facilities and restrictions, and update frequency. We used the example of a keyword search to evaluate the usefulness of these databases in biomedical information retrieval and a specific published article to evaluate their utility in performing citation analysis. All databases were practical in use and offered numerous search facilities. PubMed and Google Scholar are accessed for free. The keyword search with PubMed offers optimal update frequency and includes online early articles; other databases can rate articles by number of citations, as an index of importance. For citation analysis, Scopus offers about 20% more coverage than Web of Science, whereas Google Scholar offers results of inconsistent accuracy. PubMed remains an optimal tool in biomedical electronic research. Scopus covers a wider journal range, of help both in keyword searching and citation analysis, but it is currently limited to recent articles (published after 1995) compared with Web of Science. Google Scholar, as for the Web in general, can help in the retrieval of even the most obscure information but its use is marred by inadequate, less often updated, citation information.-Falagas, M. E., Pitsouni, E I., Malietzis, G. A., and Pappas, G. Comparison of Pub Med, Scopus, Web of Science, and Google Scholar: strengths and weaknesses. FASEB J. 22, 338 -342 (2008)

The management of chronic pain remains a challenge because of its complexity and unpredictable response to pharmacological treatment. In addition, accurate pain management may be hindered by the prejudice of physicians and patients that strong opioids, classified as step 3 medications in the World Health Organization ladder for cancer pain management, are reserved for the end stage of life. Recent information indicates the potential value of strong opioids in the treatment of chronic nonmalignant pain. There are, up until now, insufficient data to provide indications about which opioid to use to initiate treatment or the dose to be used for any specific pain syndrome. The strong inter-patient variability in opioid receptor response and in the pharmacokinetic and pharmacodynamic behavior of strong opioids justifies an individual selection of the appropriate opioid and stepwise dose titration. Clinical experience shows that switching from one opioid to another may optimize pain contro...

Background Child abuse presents in many different forms: physical, sexual, psychological, and neglect. The orthopaedic surgeon is involved mostly with physical abuse but should be aware of the other forms. There is limited training regarding child abuse, and the documentation is poor when a patient is at risk for abuse. There is a considerable risk to children when abuse is not recognized. Questions/purposes In this review, we (1) define abuse, (2) describe the incidence and demographic characteristics of abuse, (3) describe the orthopaedic manifestations of abuse, and (4) define the orthopaedic surgeon's role in cases of abuse.

The effect of bisphenol A (BPA) exposure on human brain and behavior is a relatively new issue, and particular concerns have been raised about its potential impact on children. The primary objective of this review was to analyze the current state of knowledge on the association of environmental BPA exposure during pregnancy and/or childhood with child cognitive and/or behavior outcomes. All scientific publications until March 2015 that include examination of this relationship have been reviewed using the MEDLINE/PubMed database. Although research on this issue has not been abundant, an association with altered neurobehavior was reported by eight out of the twelve available articles, including aggressive behavior, attention deficit, hyperactivity disorder, depression and anxiety impairments, mostly in children exposed in utero, indicating disruption of the brain during this critical window of development. Despite the reduced number of studies and their heterogeneity, the results suggest that prenatal BPA exposure may have a negative impact on neurobehavioral functioning in children and that the effects may be sex-dependent. It is therefore necessary to be vigilant towards the potential adverse effects of ubiquitous low-level BPA exposure, although more studies in humans are required to convincingly confirm or rule out the association between BPA exposure and health. Meanwhile, it is desirable to inform women planning or undergoing pregnancy about measures to reduce or avoid exposure to BPA. We discuss some key aspects of the relationship between exposure and neurobehavioral outcomes.

Background: Advances in biotechnology and in high-throughput methods for gene analysis have contributed to an exponential increase in the number of scientific publications in these fields of study. While much of the data and results described in these articles are entered and annotated in the various existing biomedical databases, the scientific literature is still the major source of information. There is, therefore, a growing need for text mining and information retrieval tools to help researchers find the relevant articles for their study. To tackle this, several tools have been proposed to provide alternative solutions for specific user requests.

Different mechanisms are involved in a complex network of interactions resulting in the painful and impairing disorder, complex regional pain syndrome (CRPS). There is convincing evidence that inflammation plays a pivotal role in the pathophysiology of CRPS. Immunomodulating medication reduces the manifestation of inflammation by acting on the mediators of inflammation. Therefore, as inflammation is involved in the pathophysiology of CRPS, immunomodulating medication in CRPS patients may prove beneficial. To describe the current empirical evidence for the efficacy of administering the most commonly used immunomodulating medication (ie, glucocorticoids, tumor necrosis factor-α antagonists, thalidomide, bisphosphonates, and immunoglobulins) in CRPS patients. PubMed was searched for original articles that investigated CRPS and the use of one of the abovementioned immunomodulating agents. The search yielded 39 relevant articles: from these, information on study design, sample size, duration of disease, type and route of medication, primary outcome measures, and results was examined. Theoretically, the use of immunomodulating medication could counteract the ongoing inflammation and might be an important step in improving a disabled hand or foot, leading to further recovery. However, more high-quality intervention studies are needed.

Objective: Propriospinal myoclonus (PSM) is a rare disorder with repetitive, usually flexor arrhythmic brief jerks of the trunk, hips, and knees in a fixed pattern. It has a presumed generation in the spinal cord and diagnosis depends on characteristic features at polymyography. Recently, a historical paradigm shift took place as PSM has been reported to be a functional (or psychogenic) movement disorder (FMD) in most patients. This review aims to characterize the clinical features, etiology, electrophysiologic features, and treatment outcomes of PSM.

Effective access to the vast biomedical knowledge present in the scientific literature is challenging. Semantic relations are increasingly used in knowledge management applications supporting biomedical research to help address this challenge. We describe SemMedDB, a repository of semantic predications (subject-predicate-object triples) extracted from the entire set of PubMed citations. We propose the repository as a knowledge resource that can assist in hypothesis generation and literature-based discovery in biomedicine as well as in clinical decision-making support. Availability and implementation: The SemMedDB repository is available as a MySQL database for non-commercial use at http://skr3. nlm.nih.gov/SemMedDB. An UMLS Metathesaurus license is required. Contact:

The present study provides a meta-analysis of cognitive rehabilitation literature (K 115, N 2,014) that was originally reviewed by K. D. Cicerone et al. (2000, 2005) for the purpose of providing evidence-based practice guidelines for persons with acquired brain injury. The analysis yielded a small treatment effect size (ES .30, d statistic) directly attributable to cognitive rehabilitation. A larger treatment effect (ES .71) was found for single-group pretest to posttest outcomes; however, modest improvement was observed for nontreatment control groups as well (ES .41). Correction for this effect, which was not attributable to cognitive treatments, resulted in the small, but significant, overall estimate. Treatment effects were moderated by cognitive domain treated, time postinjury, type of brain injury, and age. The meta-analysis revealed sufficient evidence for the effectiveness of attention training after traumatic brain injury and of language and visuospatial training for aphasi...

The goal of the gene normalization task is to link genes or gene products mentioned in the literature to biological databases. This is a key step in an accurate search of the biological literature. It is a challenging task, even for the human expert; genes are often described rather than referred to by gene symbol and, confusingly, one gene name may refer to different genes (often from different organisms). For BioCreative II, the task was to list the Entrez Gene identifiers for human genes or gene products mentioned in PubMed/MEDLINE abstracts. We selected abstracts associated with articles previously curated for human genes. We provided 281 expert-annotated abstracts containing 684 gene identifiers for training, and a blind test set of 262 documents containing 785 identifiers, with a gold standard created by expert annotators. Inter-annotator agreement was measured at over 90%. The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2008/9/S2/S3 Genome Biology 2008, 9(Suppl 2):S3 http://genomebiology.com/2008/9/S2/S3 Genome Biology 2008, Volume 9, Suppl 2, Article S3 Morgan et al. S3.2

The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology 'revolutionizes' molecular biology and 'transcends' its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology's use of modelling and bioinformatics, and by its scale enlargement.