The Bioperl toolkit: Perl modules for the life sciences

The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.     

Antifluoridationists Persist: the Constitutional Basis for Fluoridation

The controversy surrounding fluoridation persists. In recent years opponents of fluoridation have resorted to the courts with increasing frequency and have achieved a few victories in the trial courts. To date, however, no appellate court has ruled against fluoridation. This article discusses the constitutional basis for the court decisions upholding fluoridation and the main arguments put forth by the antifluoridationists. Five of the more recent cases are summarized, as is the first fluoridation case to be appealed to the US Supreme Court. The article concludes that the legal validity of fluoridation in the United States has been thoroughly tested in the courts and confirmed. It appears that the antifluoridationists will concentrate their future legal attacks on the "harmful effects" of fluoridation on health and the environment. If they can convince the courts that even a few people were truly harmed, the delicate balance between the rights of the state to fluoridate in order to protect the public's health and the rights of the individual not to be harmed could well shift. In closing, the question is raised whether the US Congress has the power to pass legislation either to mandate or forbid fluoridation.     

Effects of DFMO-induced polyamine depletion on human tumor cell sensitivity to antineoplastic DNA-crosslinking drugs

Summary We investigated the effect of pretreatment with difluoromethylornithine (DFMO), an ornithine decarboxylase inhibitor, on the cytocidal responses of four human adenocarcinoma cell lines to two alkylating and crosslinking agents: chlorambucil and N,N,N-triethylenethio-phosphoramide (thiotepa). The cell lines studied included HuTu-80 (duodenum), HT-29 (colon), ME-180 (cervix), and A-427 (lung). A 48- to 72-h pretreatment with DFMO reduced intracellular putrescine and spermidine contents to <10% and <1% of control levels. This treatment also caused a 30%–70% decline in spermine content. Survival of control and DFMO-pretreated cells after treatment with chlorambucil or thiotepa was measured by a plating efficiency assy. For three of the four lines studied, the DFMO-induced partial polyamine depletion significantly protected cells from the lethal effects of chlorambucil. In ME-180 cultures alone, DFMO pretreatment did not alter the cytocidal efficacy of chlorambucil. Addition of exogenous putrescine to cultures of HuTu-80, HT-29, or A-427 24 h after DFMO addition but 24 h before treatment with chlorambucil reversed the polyamine depletion and its protective effects on chlorambucil-induced cell kill. In contrast to the above observations, DFMO and partial polyamine depletion had no effect on cell survival after thiotepa treatment for any of the cell lines investigated.Abbreviations BCNU 1,3-bis (2-chloroethyl)-1-nitrosourea - CENU chloroethylnitrosourea - cis-Pt (II) cis-diamminedichloroplatinum (II) - DFMO difluoromethylornithine - ODC ornithine decarboxylase - PU putrescine - SD spermidine - SP spermine thiotepa - N,N,N triethylenethiophosphoramide This investigation was supported in part by PHS grant no. CA-32758 awarded by the National Cancer Institute, DHHS; by grant no. 82-6 from the American Cancer Society, Ill. Div., Inc.; and by a Biomedical Research Support Grant to Northwestern University Medical School from the US PHS, NIH (RR-05370)     

Anger Dimensions and Mental Health Following a Disaster: Distribution and Implications After a Major Bushfire

Anger is an important dimension of affect and a prominent feature of posttraumatic mental health, but it is commonly overlooked in postdisaster settings. We aimed to examine the distribution and implications of significant anger problems in the aftermath of a natural disaster, via analyses of Beyond Bushfires survey data from 736 residents of rural communities 5 years after the 2009 Black Saturday bushfires in Victoria, Australia. Assessments included the five‐item Dimensions of Anger Reaction (DAR‐5) scale along with measures of PTSD, depression, and significant mental illness, and indicators of life satisfaction, suicidality, hostile aggressive behavior, and violence exposure. The results indicated that approximately 10% of respondents from areas highly affected by the bushfires scored above the provisional cutoff criteria for significant anger problems on the DAR‐5, which was a more than 3‐fold increase, OR = 3.26, relative to respondents from areas of low‐to‐moderate bushfire impact. The rates were higher among women, younger participants, and those who were unemployed, and co‐occurred commonly, although not exclusively, with other postdisaster mental health problems. Anger problems were also associated with lower life satisfaction, β = ?.31, an 8‐fold increase in suicidal ideation, OR = 8.68, and a nearly 13‐fold increase in hostile aggressive behavior, OR = 12.98. There were associations with anger problems and violence exposure, which were reduced when controlling for covariates, including probable PTSD. The findings provide evidence indicating that anger is a significant issue for postdisaster mental health and should be considered routinely alongside other posttraumatic mental health issues.     

Surgical harvesting of bone graft from the ilium: point of view

Autologous bone harvested from the ilium is commonly used as a grafting material in surgical reconstructive and arthrodesis procedures to ensure a satisfactory postoperative outcome. However, operative removal of bone from the iliac crest requires an additional surgical procedure with a distinct set of postoperative complications. We provide a comprehensive literature synthesis of the incidence and severity of complications reported to be associated with this commonly practiced procedure. Most severe complications are rare, but chronic pain at the donor site exceeding three months in duration occurs frequently and can be particularly bothersome to patients. Alternative grafting materials that are safe and effective are sorely needed.