Year in review 2007: Critical Care – intensive care unit management

With the development of new technologies and drugs, health care is becoming increasisngly complex and expensive. Governments and health care providers around the world devote a large proportion of their budgets to maintaining quality of care. During 2007, Critical Care published several papers that highlight important aspects of critical care management, which can be subdivided into structure, processes and outcomes, including costs. Great emphasis was given to quality of life after intensive care unit stay, especially the impact of post-traumatic stress disorder. Significant attention was also given to staffing level, optimization of intensive care unit capacity, and drug cost-effectiveness, particularly that of recombinant human activated protein C. Managing costs and providing high-quality care simultaneously are emerging challenges that we must understand and meet

High-performance design patterns for modern Fortran

This paper presents ideas for using coordinate-free numerics in modern Fortran to achieve code flexibility in the partial differential equation (PDE) domain. We also show how Fortran, over the last few decades, has changed to become a language well-suited for state-of-the-art software development. Fortran’s new coarray distributed data structure, the language’s class mechanism, and its side-effect-free, pure procedure capability provide the scaffolding on which we implement HPC software. These features empower compilers to organize parallel computations with efficient communication. We present some programming patterns that support asynchronous evaluation of expressions comprised of parallel operations on distributed data. We implemented these patterns using coarrays and the message passing interface (MPI). We compared the codes’ complexity and performance. The MPI code is much more complex and depends on external libraries. The MPI code on Cray hardware using the Cray compiler is 1.5–2 times faster than the coarray code on the same hardware. The Intel compiler implements coarrays atop Intel’s MPI library with the result apparently being 2–2.5 times slower than manually coded MPI despite exhibiting nearly linear scaling efficiency. As compilers mature and further improvements to coarrays comes in Fortran 2015, we expect this performance gap to narrow.publishedVersio

High-Performance Design Patterns for Modern Fortran

This paper presents ideas for using coordinate-free numerics in modern Fortran to achieve code flexibility in the partial differential equation (PDE) domain. We also show how Fortran, over the last few decades, has changed to become a language well-suited for state-of-the-art software development. Fortran’s new coarray distributed data structure, the language’s class mechanism, and its side-effect-free, pure procedure capability provide the scaffolding on which we implement HPC software. These features empower compilers to organize parallel computations with efficient communication. We present some programming patterns that support asynchronous evaluation of expressions comprised of parallel operations on distributed data. We implemented these patterns using coarrays and the message passing interface (MPI). We compared the codes’ complexity and performance. The MPI code is much more complex and depends on external libraries. The MPI code on Cray hardware using the Cray compiler is 1.5–2 times faster than the coarray code on the same hardware. The Intel compiler implements coarrays atop Intel’s MPI library with the result apparently being 2–2.5 times slower than manually coded MPI despite exhibiting nearly linear scaling efficiency. As compilers mature and further improvements to coarrays comes in Fortran 2015, we expect this performance gap to narrow

A Configurationally-Resolved-Super-Transition-Arrays method for calculation of the spectral absorption coefficient in hot plasmas

A new method, 'Configurationally-Resolved-Super-Transition-Arrays', for calculation of the spectral absorption coefficient in hot plasmas is presented. In the new method, the spectrum of each Super-Transition-Array is evaluated as the Fourier transform of a single Complex Pseudo Partition Function, which represents the exact analytical sum of the contributions of all constituting unresolved transition arrays sharing the same set of one-electron solutions. Thus, in the new method, the spectrum of each Super-Transition-Array is resolved down to the level of the (unresolved) transition arrays. It is shown that the corresponding spectrum, evaluated by the traditional Super-Transition-Arrays (STA) method [A. Bar Shalom, J. Oreg, W.H. Goldstein, D. Shvarts and A. Zigler, Phys. Rev. A 40, 3183 (1989)], is just the coarse grained Gaussian approximation of the Configurationally-Resolved-Super-Transition-Array. A new computer program is presented, capable of evaluating the absorption coefficient by both the new configurationally resolved and the traditional Gaussian Super-Transition-Arrays methods. A numerical example of gold at temperature 1keV and density 0.5 gr/cm^{3}, is presented, demonstrating the simplicity, efficiency and accuracy of the new method

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require data management plans for publicly funded research. Furthermore, the value of data increases exponentially when they are properly stored, described, integrated and shared, so that they can be easily utilized in future analyses. AgBioData (https://www.agbiodata.org) is a consortium of people working at agricultural biological databases, data archives and knowledgbases who strive to identify common issues in database development, curation and management, with the goal of creating database products that are more Findable, Accessible, Interoperable and Reusable. We strive to promote authentic, detailed, accurate and explicit communication between all parties involved in scientific data. As a step toward this goal, we present the current state of biocuration, ontologies, metadata and persistence, database platforms, programmatic (machine) access to data, communication and sustainability with regard to data curation. Each section describes challenges and opportunities for these topics, along with recommendations and best practices

Predominant expression of Alzheimer’s disease-associated BIN1 in mature oligodendrocytes and localization to white matter tracts

BIN1 is not expressed in human brain microglial cells. (A) Immunohistochemical staining of adjacent sections of normal human brain cortex with antibodies against BIN1 or Iba1 reveals that BIN1 immunoreactive cells that are morphologically distinct from microglia. The boxed region is shown at a higher magnification on the right. (B) Single and two-color immunostaining of the human brain using antibodies against BIN1 and CD45 reveals that perivenular CD45-positive cells of the hematopoietic lineage do not express BIN1. (TIFF 4392 kb

The Cayman Crab Fly Revisited — Phylogeny and Biology of Drosophila endobranchia

BACKGROUND: The majority of all known drosophilid flies feed on microbes. The wide spread of microorganisms consequently mean that drosophilids also can be found on a broad range of substrates. One of the more peculiar types of habitat is shown by three species of flies that have colonized land crabs. In spite of their intriguing lifestyle, the crab flies have remained poorly studied. Perhaps the least investigated of the three crab flies is the Cayman Island endemic Drosophila endobranchia. Apart from its life cycle very little is known about this species, including its phylogenetic position, which has remained unresolved due to a cryptic set of characteristics. PRINCIPAL FINDINGS: Based on molecular data, corroborated by a re-analysis of the morphological make up, we have resolved the phylogenetic position of D. endobranchia and show that it somewhat surprisingly belongs to the large Neotropical repleta radiation, and should be considered as an aberrant member of the canalinea species group. Furthermore we also provide additional data on the behavior of these remarkable flies. CONCLUSION: Our findings reveal that the two Caribbean crab flies are not as distantly related as first thought, as both species are members of the derived repleta radiation. That this lineage has given rise to two species with the same odd type of breeding substrate is curious and prompts the question of what aspects of their shared ancestry has made these flies suitable for a life on (and inside) land crabs. Knowledge of the phylogenetic position of D. endobranchia will allow for comparative explorations and will aid in efforts aimed at understanding processes involved in drastic host shifts and extreme specialization

Aristotle's Peculiarly Human Psychology

For Aristotle, human cognition has a lot in common both with non-human animal cognition and with divine cognition. With non-human animals, humans share a non-rational part of the soul and non-rational cognitive faculties (DA 427b6–14, NE 1102b29 and EE 1219b24–6). With gods, humans share a rational part of the soul and rational cognitive faculties (NE 1177b17– 1178a8). The rational part and the non-rational part of the soul, however, coexist and cooperate only in human souls (NE 1102b26–9, EE 1219b28–31). In this chapter, I show that a study of this cooperation helps to uncover some distinctive aspects of human cognition and desire

Iron and ferritin accumulate in separate cellular locations in Phaseolus seeds

<p>Abstract</p> <p>Background</p> <p>Iron is an important micronutrient for all living organisms. Almost 25% of the world population is affected by iron deficiency, a leading cause of anemia. In plants, iron deficiency leads to chlorosis and reduced yield. Both animals and plants may suffer from iron deficiency when their diet or environment lacks bioavailable iron. A sustainable way to reduce iron malnutrition in humans is to develop staple crops with increased content of bioavailable iron. Knowledge of where and how iron accumulates in seeds of crop plants will increase the understanding of plant iron metabolism and will assist in the production of staples with increased bioavailable iron.</p> <p>Results</p> <p>Here we reveal the distribution of iron in seeds of three <it>Phaseolus </it>species including thirteen genotypes of <it>P. vulgaris</it>, <it>P. coccineus</it>, and <it>P. lunatus</it>. We showed that high concentrations of iron accumulate in cells surrounding the provascular tissue of <it>P. vulgaris </it>and <it>P. coccineus </it>seeds. Using the Perls' Prussian blue method, we were able to detect iron in the cytoplasm of epidermal cells, cells near the epidermis, and cells surrounding the provascular tissue. In contrast, the protein ferritin that has been suggested as the major iron storage protein in legumes was only detected in the amyloplasts of the seed embryo. Using the non-destructive micro-PIXE (Particle Induced X-ray Emission) technique we show that the tissue in the proximity of the provascular bundles holds up to 500 μg g^-1of iron, depending on the genotype. In contrast to <it>P. vulgaris </it>and <it>P. coccineus</it>, we did not observe iron accumulation in the cells surrounding the provascular tissues of <it>P. lunatus </it>cotyledons. A novel iron-rich genotype, NUA35, with a high concentration of iron both in the seed coat and cotyledons was bred from a cross between an Andean and a Mesoamerican genotype.</p> <p>Conclusions</p> <p>The presented results emphasize the importance of complementing research in model organisms with analysis in crop plants and they suggest that iron distribution criteria should be integrated into selection strategies for bean biofortification.</p

Evaluation of the effect of sodium–glucose co‐transporter 2 inhibition with empagliflozin on morbidity and mortality of patients with chronic heart failure and a reduced ejection fraction: rationale for and design of the EMPEROR‐Reduced trial

Drugs that inhibit the sodium–glucose co‐transporter 2 (SGLT2) have been shown to reduce the risk of hospitalizations for heart failure in patients with type 2 diabetes. In populations that largely did not have heart failure at the time of enrolment, empagliflozin, canagliflozin and dapagliflozin decreased the risk of serious new‐onset heart failure events by ≈30%. In addition, in the EMPA‐REG OUTCOME trial, empagliflozin reduced the risk of both pump failure and sudden deaths, the two most common modes of death among patients with heart failure. In none of the three trials could the benefits of SGLT2 inhibitors on heart failure be explained by the actions of these drugs as diuretics or anti‐hyperglycaemic agents. These observations raise the possibility that SGLT2 inhibitors could reduce morbidity and mortality in patients with established heart failure, including those without diabetes. The EMPEROR‐Reduced trial is enrolling ≈3600 patients with heart failure and a reduced left ventricular ejection fraction (≤ 40%), half of whom are expected not to have diabetes. Patients are being randomized to placebo or empagliflozin 10 mg daily, which is added to all appropriate treatment with inhibitors of the renin–angiotensin system and neprilysin, beta‐blockers and mineralocorticoid receptor antagonists. The primary endpoint is the time‐to‐first event analysis of the combined risk of cardiovascular death and hospitalization for heart failure, but the trial will also evaluate the effects of empagliflozin on renal function, cardiovascular death, all‐cause mortality, and recurrent hospitalization events. By adjusting eligibility based on natriuretic peptide levels to the baseline ejection fraction, the trial will preferentially enrol high‐risk patients. A large proportion of the participants is expected to have an ejection fraction &lt; 30%, and the estimated annual event rate is expected to be at least 15%. The EMPEROR‐Reduced trial is well‐positioned to determine if the addition of empagliflozin can add meaningfully to current approaches that have established benefits in the treatment of chronic heart failure with left ventricular systolic dysfunction