The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

The worldwide Protein Data Bank (wwPDB) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive is a repository for the coordinates and related information for more than 38 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The founding members of the wwPDB are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan) [H.M. Berman, K. Henrick and H. Nakamura (2003) Nature Struct. Biol., 10, 980]. The BMRB group (USA) joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single archive of macromolecular structural data that are freely and publicly available to the global community. Additionally, the wwPDB provides a variety of services to a broad community of users. The wwPDB website at provides information about services provided by the individual member organizations and about projects undertaken by the wwPDB.

Tools for the automatic identification and classification of RNA base pairs

Three programs have been developed to aid in the classification and visualization of RNA structure. BPViewer provides a web interface for displaying three-dimensional (3D) coordinates of individual base pairs or base pair collections. A web server, RNAview, automatically identifies and classifies the types of base pairs that are formed in nucleic acid structures by various combinations of the three edges, Watson-Crick, Hoogsteen and the Sugar edge. RNAView produces two-dimensional (2D) diagrams of secondary and tertiary structure in either Postscript, VRML or RNAML formats. The application RNAMLview can be used to rearrange various parts of the RNAView 2D diagram to generate a standard representation (like the cloverleaf structure of tRNAs) or any layout desired by the user. A 2D diagram can be rapidly reformatted using RNAMLview since all the parts of RNA (like helices and single strands) are dynamically linked while moving the selected parts. With the base pair annotation and the 2D graphic display, RNA motifs are rapidly identified and classified. A survey has been carried out for 41 unique structures selected from the NDB database. The statistics for the occurrence of each edge and of each of the 12 bp families are given for the combinations of the four bases: A, G, U and C. The program also allows for visualization of the base pair interactions by using a symbolic convention previously proposed for base pairs. The web servers for BPViewer and RNAview are available at http://ndbserver.rutgers.edu/services/. The application RNAMLview can also be downloaded from this site. The 2D diagrams produced by RNAview are available for RNA structures in the Nucleic Acid Database (NDB) at http://ndbserver.rutgers.edu/atlas/.

The CCPN project: an interim report on a data model for the NMR community

A recent workshop discusses the progress toward integrating NMR data into a unifying data model.

Children and war: current understandings and future directions

During the last decade, the number of children whose lives have been disrupted by war, oppression, terror, and other forms of conflict has grown tremendously. When the United Nations High Commission for Refugees was first established during the 1950s to provide international protection to refugees following World War II, it was estimated that there were 1.5 million refugees and displaced persons. Today there are approximately 14 million, about three-fourths of whom are women and children. Although the experiences of refugee children and adolescents vary considerably, many have witnessed or experienced the death or murder of loved ones. Upon resettlement, they face numerous challenges. Research with this population is a relatively new area of investigation, but there is evidence that many of these young people experience long-term physical and emotional health problems. In this article, current research findings are reviewed, the widespread emphasis in the literature on post-traumatic stress disorder (PTSD) is critically examined, future research directions are suggested, and implications for public health nurses are addressed.

Metabolism of rat granular pneumocytes isolated in primary culture

Granular pneumocytes (GP) were isolated by trysinization of minced rat lungs followed by short-term primary culture. The yield from the lungs of one rat was approximately 3.5 X 10(6) GP representing 25 micrograms DNA and 0.5 mg protein. Depending on the method to remove cells from attachment to plastic, the purity was 82--92% GP of which > 90% excluded erythrosin B. Resting O2 consumption (37 degrees C) of cells was 202 +/- 29 (mean +/- SE, n = 3) nmol.h-1.(10(6) cells)-1 with a 2.5 times increase in the presence of an uncoupler of oxidative phosphorylation. ATP content of resting pneumocytes was 4.1 +/- 0.18 nmol.(10(6) cells)-1 and was markedly depressed by the "uncoupling" agent. During incubation with [U-14C]glucose, production of metabolites in nmol.h-1.(10(6) cells)-1 was lactate 58.0 +/- 7.9, pyruvate 25.8 +/- 3.2, and 14CO2 56.4 +/- 2.1, and glucose utilization was 104 +/- 38.5. Sonicated GP had higher activities of both lactate and succinate dehydrogenases compared with alveolar macrophages. Alkaline phosphatase activity was localized predominantly to GP, whereas macrophages contained predominantly acid phosphatase. The intracellular water space for granular pneumocytes was 0.55 +/- 0.05 ml.(10(6) cells)-1 and was 71% greater for alveolar macrophage. The presence of active glycolytic and oxidative pathways and appropriate responses to metabolic inhibitors and substrates suggest the presence of intact cell membranes and the retention of metabolic control mechanisms in this isolated lung epithelial cell preparation.

Stories and numbers: coexistence without compromise

Research methods are not paradigm specific but should be selected on the basis of whether they fit with the purposes of an investigation. In the postpositivist, interpretive, and critical paradigms, both qualitative and quantitative data or a combination of these may be used without violating paradigm assumptions. Attention to the four basic issues of quality of the data, investigator bias, quality of the research process, and usefulness of the finding is necessary to produce valid research. Although researchers in each paradigm deal with these differently, combining strategies across paradigms may enhance the scientific value of a study and result in new methodologies to address the health needs of all people.

Sexuality and the adolescent with a physical disability: understandings and misunderstandings

The purpose of this descriptive study was to examine the areas of sexual knowledge, sexual behavior, and beliefs about sexuality among adolescents with congenital physical disabilities. The sample consisted of 15 males and 14 females, ranging in age from 12 to 22 years. The Sexual Knowledge Interview Schedule (SKIS) was administered to all participants during face-to-face interviews. In addition, the participants were asked questions regarding their ability to engage in intimate relationships and their future childbearing potential. Overall, the findings suggested that these adolescents are uninformed or misinformed about general sexual knowledge, have many misconceptions about sexuality and their disability, and depend on health care professionals and parents for sex education. Implications of this research are discussed.

Metabolic syndrome in Argentinean patients with systemic lupus erythematosus

The objective was to determine the prevalence of the metabolic syndrome (MS) in patients with systemic lupus erythematosus (SLE) in Argentina, to assess the factors associated to it, and to compare the results with a control group with non-inflammatory disorders. The study included 147 patients with SLE and 119 controls. MS was defined according to criteria by the American Heart Association/National Heart, Lung, and Blood Institute (AHA/NHLBI) Scientific Statement. Demographic characteristics, Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) and Systemic Lupus International Collaborating Clinics/ACR Damage Index (SDI) were assessed as well as administration, maximum dose and cumulative dose of prednisone and hydroxychloroquine (HCQ). MS prevalence was 28.6% (CI 95%: 21.4-36.6) in patients with SLE and 16% in controls (P = 0.0019). Patients with SLE presented higher arterial hypertension frequency compared with controls (43 vs 25%, P = 0.007). When comparing lupus patients with MS (n = 41) and without MS (n = 106), no significant differences were observed regarding duration of the disease, SLEDAI or cumulative prednisone dose. Cumulative damage was associated independently with MS (OR 1.98; P = 0.021), whereas HCQ use was found to be protective (OR 0.13; P = 0.015). Patients with lupus presented higher MS prevalence than controls with non-inflammatory disorders, and occurrence of arterial hypertension was also higher. MS was associated with cumulative damage; the use of HCQ showed to be protective against presence of MS.

Combining stories and numbers: a methodologic approach for a critical nursing science

The critical paradigm is increasingly being recognized as an appropriate perspective for the development of nursing knowledge. While different research approaches including feminist, neo-Marxist, and participatory research have been described, all share the goals of empowerment, emancipation, and change. As a relatively new world-view for nursing, the concept of a critical nursing science faces much the same resistance as the interpretive paradigm did a decade ago. This article reviews the aims and assumptions of the critical paradigm; discusses the merits of combining stories and numbers for the agenda of change; and, using examples from our research, describes three strategies for combining stories and numbers in the critical paradigm.

Genetic and epigenetic changes in mammary epithelial cells identify a subpopulation of cells involved in early carcinogenesis

Morphologically normal foci of epithelial cells exhibiting p16 inactivation have been found in several tissues and may be precursors to cancer. Our previous work demonstrates that cells lacking p16(INK4A) activity exhibit phenotypes associated with malignancy (Romanov et al. 2001). The acquisition of genomic instability occurs through the activation of telomeric and centrosomal dysfunction. Additionally, the activation of stress pathways such as COX-2 provides these cells with the mutagenic potential to survive adverse environments as well as the ability to migrate, evade apoptosis and immune surveillance, and summon sustaining vasculature. Examination of archived tissue from women with DCIS (ductal carcinoma in situ) reveals epithelial cells that overexpress markers of premalignant stress activation pathways and mirror the distinctive expression patterns of these markers observed in vitro. These epithelial cells are found within the premalignant lesion as well as in the field of morphologically normal tissue that surrounds the lesion. Here, we show that p16(INK4A)-silenced vHMEC cells exhibit a gene expression profile which is distinct, reproducible, and extends beyond the changes mediated by p16(INK4A) inactivation. The present work suggests that cells lacking p16(INK4A) activity exhibit critical activities which allow cells to evade differentiation processes that would be expected to terminate proliferation. All of these properties are critical to malignancy. These events may be useful biomarkers to detect the earliest events in breast cancer.

Sexual harassment: everyday violence in the lives of girls and women

Sexual harassment is one of the most insidious, yet pervasive, forms of violence that affects all girls, not merely those traditionally thought to be vulnerable or at risk. Although harassment in the workplace has been the focus of considerable attention during the last decade, there is a growing recognition that girls experience varied forms of sexual harassment, and that this behavior begins at a surprisingly early age. This article examines the plight of the "girl child" and presents findings from the first phase of a national action research project currently being conducted by the Canadian Alliance of Five Research Centres on Violence. A major objective of this project is to examine how violence becomes "normalized" in the lives of girls and young women. Implications for nurses, including strategies aimed at encouraging resistance among this population, are addressed.

Treatment of colorectal hepatic metastases by intrahepatic chemotherapy alone or as an adjuvant to complete or partial removal of metastatic disease

Because of the wide variation in reported benefits from the use of intrahepatic chemotherapy for colorectal hepatic metastases, the authors performed their own phase II studies comparing the use of intrahepatic chemotherapy alone and intrahepatic chemotherapy as an adjuvant to complete or partial removal of metastatic colorectal cancer to the liver. Techniques for partial removal included unilateral and bilateral wedge resection, peripheral presinusoidal embolization of the liver, and portal vein branch ligation. Patients were staged using the per cent hepatic replacement method of Pettavel and Taylor, and patients with bilateral metastases were included in the study. Twenty-seven patients, mean age 60.3 years, were examined. There were 19 males, mean age 60.4 years, and eight females, mean age 60 years. The patients were divided into four groups. Group A had an implantable pump only; Group B had an implantable pump and resection; Group C had an implantable pump and arterial embolization and portal vein branch ligation; and Group D had an implantable pump, partial resection, arterial embolization, and portal vein branch ligation. Kaplan-Meyer survival curves were calculated for all of these groups. A separate analysis was carried out for each of the stages, and a comparison was made. The study indicated that the overall median survival time was 18 months and that the more radical the treatment in addition to chemotherapy, the better the results. Such results were not totally dependent on the staging of the tumor volume but were dependent on the degree of extirpation of the tumor. In Group C, consisting primarily of Stage IIa, IIIa, and IV patients (i.e., unresectable patients), a doubling of expected median survival to 12 months could be achieved, compared to those in Group A, which achieved a median survival of only 6 months.

Design of a data model for developing laboratory information management and analysis systems for protein production

Data management has emerged as one of the central issues in the high-throughput processes of taking a protein target sequence through to a protein sample. To simplify this task, and following extensive consultation with the international structural genomics community, we describe here a model of the data related to protein production. The model is suitable for both large and small facilities for use in tracking samples, experiments, and results through the many procedures involved. The model is described in Unified Modeling Language (UML). In addition, we present relational database schemas derived from the UML. These relational schemas are already in use in a number of data management projects.

Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction

One goal of the CASP community wide experiment on the critical assessment of techniques for protein structure prediction is to identify the current state of the art in protein structure prediction and modeling. A fundamental principle of CASP is blind prediction on a set of relevant protein targets, that is, the participating computational methods are tested on a common set of experimental target proteins, for which the experimental structures are not known at the time of modeling. Therefore, the CASP experiment would not have been possible without broad support of the experimental protein structural biology community. In this article, several experimental groups discuss the structures of the proteins which they provided as prediction targets for CASP9, highlighting structural and functional peculiarities of these structures: the long tail fiber protein gp37 from bacteriophage T4, the cyclic GMP-dependent protein kinase Iβ dimerization/docking domain, the ectodomain of the JTB (jumping translocation breakpoint) transmembrane receptor, Autotaxin in complex with an inhibitor, the DNA-binding J-binding protein 1 domain essential for biosynthesis and maintenance of DNA base-J (β-D-glucosyl-hydroxymethyluracil) in Trypanosoma and Leishmania, an so far uncharacterized 73 residue domain from Ruminococcus gnavus with a fold typical for PDZ-like domains, a domain from the phycobilisome core-membrane linker phycobiliprotein ApcE from Synechocystis, the heat shock protein 90 activators PFC0360w and PFC0270w from Plasmodium falciparum, and 2-oxo-3-deoxygalactonate kinase from Klebsiella pneumoniae.

Nurses' beliefs about family involvement in a children's hospital

Children's hospitals throughout North America have implemented many changes during the past 15 years. In recognition of the central role of parents in the lives of their children, policies and procedures have been implemented to enable parents to participate in various aspects of their children's care. However, the extent to which attitudes of nurses have changed to support a more active parental role is less evident. In a project to formulate a philosophy of nursing for a children's hospital, 22 nurses were asked a wide range of questions about nursing and family-centered care. Although all nurses expressed explicit support for the concept of family-centered care, some of their practices and beliefs suggested otherwise. This article describes their responses and suggests recommendations for future research, education, and nursing practice.

Stories of growing up amid violence by refugee children of war and children of battered women living in Canada

PURPOSE

To explore how two groups of children who grew up amid violence "make sense" of their experience. As violence has become a common element of some societies, growing numbers of children have been forced to live in dangerous environments. Although considerable research has been conducted with children who are abused or neglected, the needs of those who witness violence have been largely overlooked.

DESIGN

Critical narrative and descriptive. Data were collected, 1995-1996, in Canada from a convenience sample of 16 refugee children of war and 16 children of battered women.

METHODS

Participants were asked open-ended questions about the violence in their lives, their feelings about what occurred, their thoughts about the reasons for violence, and their ways of surviving and growing. Common themes were identified and validated.

FINDINGS

Despite differences in the children's stories, many parallels were evident. Both groups of youngsters endured pain, suffering, and feelings of betrayal. Both used creative strategies to survive. The way the children endured growing up amid violence was mediated by social, political, and cultural constructions of violence. Because these meanings were unique, violence was experienced in several ways.

CONCLUSIONS

Although the children showed remarkable strength and insight, they face many challenges. Despite a common perception that children are unable to talk about deeply troubling experiences, this research demonstrated that children not only want to discuss their experience, but also welcome the opportunity to do so.