Genometrics as an essential tool for the assembly of whole genome sequences: the example of the chromosome of Bifidobacterium longum NCC2705.

BACKGROUND: Analysis of the first reported complete genome sequence of Bifidobacterium longum NCC2705, an actinobacterium colonizing the gastrointestinal tract, uncovered its proteomic relatedness to Streptomyces coelicolor and Mycobacterium tuberculosis. However, a rapid scrutiny by genometric methods revealed a genome organization totally different from all so far sequenced high-GC Gram-positive chromosomes. RESULTS: Generally, the cumulative GC- and ORF orientation skew curves of prokaryotic genomes consist of two linear segments of opposite slope: the minimum and the maximum of the curves correspond to the origin and the terminus of chromosome replication, respectively. However, analyses of the B. longum NCC2705 chromosome yielded six, instead of two, linear segments, while its dnaA locus, usually associated with the origin of replication, was not located at the minimum of the curves. Furthermore, the coorientation of gene transcription with replication was very low. Comparison with closely related actinobacteria strongly suggested that the chromosome of B. longum was misassembled, and the identification of two pairs of relatively long homologous DNA sequences offers the possibility for an alternative genome assembly proposed here below. By genometric criteria, this configuration displays all of the characters common to bacteria, in particular to related high-GC Gram-positives. In addition, it is compatible with the partially sequenced genome of DJO10A B. longum strain. Recently, a corrected sequence of B. longum NCC2705, with a configuration similar to the one proposed here below, has been deposited in GenBank, confirming our predictions. CONCLUSION: Genometric analyses, in conjunction with standard bioinformatic tools and knowledge of bacterial chromosome architecture, represent fast and straightforward methods for the evaluation of chromosome assembly.

Instrument for assessing the quality of mobile emergency pre-hospital care: content validation

OBJECTIVES To validate an instrument to assess quality of mobile emergency pre-hospital care. METHOD A methodological study where 20 professionals gave their opinions on the items of the proposed instrument. The analysis was performed using Kappa test (K) and Content Validity Index (CVI), considering K> 0.80 and CVI ≥ 0.80. RESULTS Three items were excluded from the instrument: Professional Compensation; Job Satisfaction and Services Performed. Items that obtained adequate K and CVI indexes and remained in the instrument were: ambulance conservation status; physical structure; comfort in the ambulance; availability of material resources; user/staff safety; continuous learning; safety demonstrated by the team; access; welcoming; humanization; response time; costumer privacy; guidelines on care; relationship between professionals and costumers; opportunity for costumers to make complaints and multiprofessional conjunction/actuation. CONCLUSION The instrument to assess quality of care has been validated and may contribute to the evaluation of pre-hospital care in mobile emergency services.

Temozolomide: a milestone in neuro-oncology and beyond?

Temozolomide (Temodal, Temodar), an imidazol derivative, is a second-generation alkylating agent. The orally available prodrug with the capacity of crossing the blood-brain barrier received accelerated US FDA approval in 1999. Three pivotal Phase II trials showed modest activity in the treatment of recurrent anaplastic astrocytoma glioblastoma. In 2005, the FDA and the European Agency for the Evaluation of Medicinal Products approved temozolomide for use in newly diagnosed glioblastoma, in conjunction with radiotherapy, based on an European Organisation for Research and Treatment of Cancer/National Cancer Institute of Canada Phase III trial. The adverse events associated with temozolomide are mild-to-moderate and generally predictable; the most serious are noncumulative and reversible myelosuppression and, in particular, thrombocytopenia, which occurs in less than 5% of patients. Continuous temozolomide administration is associated with profound CD4-selective lymphocytopenia. Molecular studies have suggested that the benefit of temozolomide chemotherapy is restricted to patients whose tumors have a methylated methylguanine methyltransferase gene promotor and are thus unable to repair some of the chemotherapy-induced DNA damage. Temozolomide is under investigation for other disease entities, in particular lower-grade glioma, brain metastases and melanoma.

Nursing care in the anesthetic procedure: an integrative review

Abstract OBJECTIVE To search for the scientific evidence available on nursing professional actions during the anesthetic procedure. METHOD An integrative review of articles in Portuguese, English and Spanish, indexed in MEDLINE/PubMed, CINAHL, LILACS, National Cochrane, SciELO databases and the VHL portal. RESULTS Seven studies were analyzed, showing nurse anesthetists' work in countries such as the United States and parts of Europe, with the formulation of a plan for anesthesia and patient care regarding the verification of materials and intraoperative controls. The barriers to their performance involved working in conjunction with or supervised by anesthesiologists, the lack of government guidelines and policies for the legal exercise of the profession, and the conflict between nursing and the health system for maintenance of the performance in places with legislation and defined protocols for the specialty. Conclusion Despite the methodological weaknesses found, the studies indicated a wide diversity of nursing work. Furthermore, in countries absent of the specialty, like Brazil, the need to develop guidelines for care during the anesthetic procedure was observed.

Financial protection of patients through compensation of providers: the impact of health equity funds in Cambodia

Public providers have no financial incentive to respect their legal obligation to exempt the poor from user fees. Health Equity Funds (HEFs) aim to make exemptions effective by giving NGOs responsibility for assessing eligibility and compensating providers for lost revenue. We use the geographic spread of HEFs in Cambodia to identify their impact on out-of-pocket (OOP) payments. Among households with some OOP payment, HEFs reduce the amount by 29%, on average. The effect is larger for households that are poorer, mainly use public health care and live closer to a district hospital. HEFs are more effective in reducing OOP payments when they are operated by a NGO, rather than the government, and when they operate in conjunction with the contracting of public health services. HEFs reduce households' health-related debt by around 25%, on average. There is no significant impact on non-medical consumption and health care utilisation

Iowa Comprehensive Annual Financial Report, 2005

In accordance with Iowa Code Section 8A.502(8) we are pleased to submit the Comprehensive Annual Financial Report (CAFR) for the State of Iowa for the fiscal year ended June 30, 2005. The report is presented in three sections as follows: • The Introductory Section includes this transmittal letter, the Government Finance Officers Association (GFOA) Certificate of Achievement for the fiscal year 2004 CAFR, an organizational chart of State government, and a list of principal State officials. • The Financial Section contains the independent auditor’s report on the Basic Financial Statements, Management’s Discussion and Analysis (MD&A), the Basic Financial Statements, and Notes to the Financial Statements. The Financial Section also contains Required Supplementary Information (RSI), other than the MD&A, and supplementary information in the form of combining financial statements and schedules. This letter is intended to be read in conjunction with the MD&A. • The Statistical Section highlights selected financial and demographic information, generally presented on a multi-year basis. The Department of Administrative Services is responsible for both the accuracy of the presented data, and the completeness and fairness of the presentation. We believe the information presented is accurate in all material respects and the necessary disclosures have been made which enable the reader to obtain an understanding of the State’s financial activity. This report has been prepared in accordance with U.S. generally accepted accounting principles (GAAP) for governments as promulgated by the Governmental Accounting Standards Board (GASB). As a part of the statewide accounting system upgrade during fiscal year 2005, the implementation team performed a comprehensive review of the adequacy of internal controls and budgetary controls of the system. The team determined that internal controls continue to be in place to provide reasonable, but not absolute, assurance that assets are safeguarded against unauthorized use or disposition, and that financial records from all appropriate sources are reliable for preparing financial statements and maintaining accountability. The concept of reasonable assurance recognizes the cost of internal controls should not exceed the benefits likely to be derived from their use. To monitor the adequacy of internal controls, the Auditor of State reviews internal control procedures as an integral part of departmental audits.

Off-resonance angiography: a new method to depict vessels--phantom and rabbit studies.

PURPOSE: To evaluate the utility of inversion recovery with on-resonant water suppression (IRON) in combination with injection of the long-circulating monocrystalline iron oxide nanoparticle (MION)-47 for contrast material-enhanced magnetic resonance (MR) angiography. MATERIALS AND METhods: Experiments were approved by the institutional animal care committee. Eleven rabbits were imaged at baseline before injection of a contrast agent and then serially 5-30 minutes, 2 hours, 1 day, and 3 days after a single intravenous bolus injection of 80 micromol of MION-47 per kilogram of body weight (n = 6) or 250 micromol/kg MION-47 (n = 5). Conventional T1-weighted MR angiography and IRON MR angiography were performed on a clinical 3.0-T imager. Signal-to-noise and contrast-to-noise ratios were measured in the aorta of rabbits in vivo. Venous blood was obtained from the rabbits before and after MION-47 injection for use in phantom studies. RESULTS: In vitro blood that contained MION-47 appeared signal attenuated on T1-weighted angiograms, while characteristic signal-enhanced dipolar fields were observed on IRON angiograms. In vivo, the vessel lumen was signal attenuated on T1-weighted MR angiograms after MION-47 injection, while IRON supported high intravascular contrast by simultaneously providing positive signal within the vessels and suppressing background tissue (mean contrast-to-noise ratio, 61.9 +/- 12.4 [standard deviation] after injection vs 1.1 +/- 0.4 at baseline, P < .001). Contrast-to-noise ratio was higher on IRON MR angiograms than on conventional T1-weighted MR angiograms (9.0 +/- 2.5, P < .001 vs IRON MR angiography) and persisted up to 24 hours after MION-47 injection (76.2 +/- 15.9, P < .001 vs baseline). CONCLUSION: IRON MR angiography in conjunction with superparamagnetic nanoparticle administration provides high intravascular contrast over a long time and without the need for image subtraction.

Positive contrast visualization of iron oxide-labeled stem cells using inversion-recovery with ON-resonant water suppression (IRON)

In proton magnetic resonance imaging (MRI) metallic substances lead to magnetic field distortions that often result in signal voids in the adjacent anatomic structures. Thus, metallic objects and superparamagnetic iron oxide (SPIO)-labeled cells appear as hypointense artifacts that obscure the underlying anatomy. The ability to illuminate these structures with positive contrast would enhance noninvasive MR tracking of cellular therapeutics. Therefore, an MRI methodology that selectively highlights areas of metallic objects has been developed. Inversion-recovery with ON-resonant water suppression (IRON) employs inversion of the magnetization in conjunction with a spectrally-selective on-resonant saturation prepulse. If imaging is performed after these prepulses, positive signal is obtained from off-resonant protons in close proximity to the metallic objects. The first successful use of IRON to produce positive contrast in areas of metallic spheres and SPIO-labeled stem cells in vitro and in vivo is presented.

What comes to mind

We present a model of intuitive inference, called local thinking, in which anagent combines data received from the external world with information retrieved frommemory to evaluate a hypothesis. In this model, selected and limited recall ofinformation follows a version of the respresentativeness heuristic. The model canaccount for some of the evidence on judgment biases, including conjunction anddisjunction fallacies, but also for several anomalies related to demand for insurance.

Measuring ecological niche overlap from occurrence and spatial environmental data

1. Aim - Concerns over how global change will influence species distributions, in conjunction with increased emphasis on understanding niche dynamics in evolutionary and community contexts, highlight the growing need for robust methods to quantify niche differences between or within taxa. We propose a statistical framework to describe and compare environmental niches from occurrence and spatial environmental data.¦2. Location - Europe, North America, South America¦3. Methods - The framework applies kernel smoothers to densities of species occurrence in gridded environmental space to calculate metrics of niche overlap and test hypotheses regarding niche conservatism. We use this framework and simulated species with predefined distributions and amounts of niche overlap to evaluate several ordination and species distribution modeling techniques for quantifying niche overlap. We illustrate the approach with data on two well-studied invasive species.¦4. Results - We show that niche overlap can be accurately detected with the framework when variables driving the distributions are known. The method is robust to known and previously undocumented biases related to the dependence of species occurrences on the frequency of environmental conditions that occur across geographic space. The use of a kernel smoother makes the process of moving from geographical space to multivariate environmental space independent of both sampling effort and arbitrary choice of resolution in environmental space. However, the use of ordination and species distribution model techniques for selecting, combining and weighting variables on which niche overlap is calculated provide contrasting results.¦5. Main conclusions - The framework meets the increasing need for robust methods to quantify niche differences. It is appropriate to study niche differences between species, subspecies or intraspecific lineages that differ in their geographical distributions. Alternatively, it can be used to measure the degree to which the environmental niche of a species or intraspecific lineage has changed over time.

Asset pricing with idiosyncratic risk and overlapping generations

A number of existing studies have concluded that risk sharing allocations supported by competitive, incomplete markets equilibria are quantitatively close to first-best. Equilibrium asset prices in these models have been difficult to distinguish from those associated with a complete markets model, the counterfactual features of which have been widely documented. This paper asks if life cycle considerations, in conjunction with persistent idiosyncratic shocks which become more volatile during aggregate downturns, can reconcile the quantitative properties of the competitive asset pricing framework with those of observed asset returns. We begin by arguing that data from the Panel Study on Income Dynamics support the plausibility of such a shock process. Our estimates suggest a high degree of persistence as well as a substantial increase in idiosyncratic conditional volatility coincident with periods of low growth in U.S. GNP. When these factors are incorporated in a stationary overlapping generations framework, the implications for the returns on risky assets are substantial. Plausible parameterizations of our economy are able to generate Sharpe ratios which match those observed in U.S. data. Our economy cannot, however, account for the level of variability of stock returns, owing in large part to the specification of its production technology.

Novas Pragas Agrícolas na Ilha de São Nicolau - Cabo Verde - Tuta absoluta (Meyrick) (Lep - Gelechiidae) e Bactrocera invadens (Drew, Tsuruta & White) (Dipt - Tephritidae)

Em algumas das ilhas do Arquipélago de Cabo Verde entraram, nos últimos dois anos, espécies invasoras que constituem pragas de culturas agrícolas e que têm apresentado elevada repercussão económica. Entre elas contam-se a traça do tomateiro, Tuta absoluta (Meyrick) (Lepidoptera: Gelechidae) e Bactrocera invadens (Drew, Tsuruta & White) (Diptera: Tephritidae). Com o objectivo de avaliar a presença destas pragas na ilha de São Nicolau, foram instaladas armadilhas com atractivos em quatro zonas com bananeiras (Ribeira Prata, Fajã, Maiama e Campo de Preguiça) para a monitorização da mosca da fruta. Foram também instaladas ensaios em seis parcelas de tomateiro para a comparação de estratégias de protecção contra T. absoluta, armadilha com feromona sexual para captura em massa em conjunto com Bacillus thuringiensis e tratamento com deltametrina. Das quatro zonas monitorizadas, B. invadens só foi encontrada no Vale da Fajã. No que diz respeito a T. absoluta, fez-se a comparação entre a população presente em três estratos do tomateiro e não se encontraram diferenças significativas. As estratégias de protecção contra T. absoluta também não diferiram significativamente no que se refere ao número de minas nas folhas e frutos furados. Nesidiocoris tenuis foi identificado como inimigo natural de T. absoluta presente na ilha.

Death and resurrection of the human IRGM gene

Immunity-related GTPases (IRG) play an important role in defense against intracellular pathogens. One member of this gene family in humans, IRGM, has been recently implicated as a risk factor for Crohn's disease. We analyzed the detailed structure of this gene family among primates and showed that most of the IRG gene cluster was deleted early in primate evolution, after the divergence of the anthropoids from prosimians ( about 50 million years ago). Comparative sequence analysis of New World and Old World monkey species shows that the single-copy IRGM gene became pseudogenized as a result of an Alu retrotransposition event in the anthropoid common ancestor that disrupted the open reading frame (ORF). We find that the ORF was reestablished as a part of a polymorphic stop codon in the common ancestor of humans and great apes. Expression analysis suggests that this change occurred in conjunction with the insertion of an endogenous retrovirus, which altered the transcription initiation, splicing, and expression profile of IRGM. These data argue that the gene became pseudogenized and was then resurrected through a series of complex structural events and suggest remarkable functional plasticity where alleles experience diverse evolutionary pressures over time. Such dynamism in structure and evolution may be critical for a gene family locked in an arms race with an ever-changing repertoire of intracellular parasites.

Recreating the South Sea bubble: Lessons from an experiment in financial history

Major bubble episodes are rare events. In this paper, we examine what factors might cause some asset price bubbles to become very large. We recreate, in a laboratory setting, some of the specific institutional features investors in the South Sea Company faced in 1720. Several factors have been proposed as potentially contributing to one of the greatest periods of asset overvaluation in history: an intricate debt-for-equity swap, deferred payment for these shares, and the possibility of default on the deferred payments. We consider which aspect might have had the most impact in creating the South Sea bubble. The results of the experiment suggest that the company?s attempt to exchange its shares for government debt was the single biggest contributor to the stock price explosion, because of the manner in which the swap affected fundamental value. Issuing new shares with only partial payments required, in conjunction with the debt-equity swap, also had a significant effect on the size of the bubble. Limited contract enforcement, on the other hand, does not appear to have contributed significantly.

Effects of the playing surface on plantar pressures during the first serve in tennis.

PURPOSE: This study aimed at examining the influence of different playing surfaces on in-shoe loading patterns in each foot (back and front) separately during the first serve in tennis. METHODS: Ten competitive tennis players completed randomly five first (ie, flat) serves on two different playing surfaces: clay vs GreenSet. Maximum and mean force, peak and mean pressure, mean area, contact area and relative load were recorded by Pedar insoles divided into 9 areas for analysis. RESULTS: Mean pressure was significantly lower (123 ± 30 vs 98 ± 26 kPa; -18.5%; P < .05) on clay than on GreenSet when examining the entire back foot. GreenSet induced higher mean pressures under the medial forefoot, lateral forefoot and hallux of the back foot (+9.9%, +3.5% and +15.9%, respectively; both P < .01) in conjunction with a trend toward higher maximal forces in the back hallux (+15.1%, P = .08). Peak pressures recorded under the central and lateral forefoot (+21.8% and +25.1%; P < .05) of the front foot but also the mean area values measured on the back medial and lateral midfoot were higher (P < .05) on clay. No significant interaction between foot region and playing surface on relative load was found. CONCLUSIONS: It is suggested that in-shoe loading parameters characterizing the first serve in tennis are adjusted according to the ground type surface. A lesser asymmetry in peak (P < .01) and mean (P < .001) pressures between the two feet was found on clay, suggesting a greater need for stability on this surface.