Quest for certainty regarding early discharge in paediatric low-risk febrile neutropenia : a multicentre qualitative focus group discussion study involving patients, parents and healthcare professionals in the UK

OBJECTIVES: A systematic review of paediatric low-risk febrile neutropenia found that outpatient care is safe, with low rates of treatment failure. However, this review, and a subsequent meta-ethnography, suggested that early discharge of these patients may not be acceptable to key stakeholders. This study aimed to explore experiences and perceptions of patients, parents and healthcare professionals involved in paediatric febrile neutropenia care in the UK. SETTING: Three different centres within the UK, purposively selected from a national survey on the basis of differences in their service structure and febrile neutropenia management. PARTICIPANTS: Thirty-two participants were included in eight focus group discussions. PRIMARY OUTCOMES: Experiences and perceptions of paediatric febrile neutropenia care, including possible future reductions in therapy. RESULTS: Participants described a quest for certainty, in which they attempted to balance the uncertainty involved in understanding, expressing and negotiating risk with the illusion of certainty provided by strict protocols. Participants assessed risk using both formal and informal stratification tools, overlaid with emotional reactions to risk and experiences of risk within other situations. The benefits of certainty provided by protocols were counterbalanced by frustration at their strict constraints. The perceived benefits and harms of previous inpatient care informed participants' appraisals of future treatment strategies. CONCLUSIONS: This study highlighted the previously underestimated harms of admission for febrile neutropenia and the paternalistic nature of decision making, along with the frustrations and challenges for all parties involved in febrile neutropenia care. It demonstrates how the same statistics, generated by systematic reviews, can be used by key stakeholders to interpret risk differently, and how families in particular can view the harms of therapeutic options as different from the outcomes used within the literature. It justifies a reassessment of current treatment strategies for these children and further exploration of the potential to introduce shared decision making

Isolation and Characterization of Bacteria That Degrade Phosphonates in Marine Dissolved Organic Matter

Semi-labile dissolved organic matter (DOM) accumulates in surface waters of the oligotrophic ocean gyres and turns over on seasonal to annual timescales. This reservoir of DOM represents an important source of carbon, energy, and nutrients to marine microbial communities but the identity of the microorganisms and the biochemical pathways underlying the cycling of DOM remain largely uncharacterized. In this study we describe bacteria isolated from the North Pacific Subtropical Gyre (NPSG) near Hawaii that are able to degrade phosphonates associated with high molecular weight dissolved organic matter (HMWDOM), which represents a large fraction of semi-labile DOM. We amended dilution-to-extinction cultures with HMWDOM collected from NPSG surface waters and with purified HMWDOM enriched with polysaccharides bearing alkylphosphonate esters. The HMWDOM-amended cultures were enriched in Roseobacter isolates closely related to Sulfitobacter and close relatives of hydrocarbon-degrading bacteria of the Oceanospirillaceae family, many of which encoded phosphonate degradation pathways. Sulfitobacter cultures encoding C-P lyase were able to catabolize methylphosphonate and 2-hydroxyethylphosphonate, as well as the esters of these phosphonates found in native HMWDOM polysaccharides to acquire phosphorus while producing methane and ethylene, respectively. Conversely, growth of these isolates on HMWDOM polysaccharides as carbon source did not support robust increases in cell yields, suggesting that the constituent carbohydrates in HMWDOM were not readily available to these individual isolates. We postulate that the complete remineralization of HMWDOM polysaccharides requires more complex microbial inter-species interactions. The degradation of phosphonate esters and other common substitutions in marine polysaccharides may be key steps in the turnover of marine DOM.Gordon and Betty Moore Foundation (Award GBMF3298)Simons Foundation (Grant 329108

Targeted optogenetic stimulation and recording of neurons in vivo using cell-type-specific expression of Channelrhodopsin-2

A major long-term goal of systems neuroscience is to identify the different roles of neural subtypes in brain circuit function. The ability to causally manipulate selective cell types is critical to meeting this goal. This protocol describes techniques for optically stimulating specific populations of excitatory neurons and inhibitory interneurons in vivo in combination with electrophysiology. Cell type selectivity is obtained using Cre-dependent expression of the light-activated channel Channelrhodopsin-2. We also describe approaches for minimizing optical interference with simultaneous extracellular and intracellular recording. These optogenetic techniques provide a spatially and temporally precise means of studying neural activity in the intact brain and allow a detailed examination of the effect of evoked activity on the surrounding local neural network. Injection of viral vectors requires 30–45 min, and in vivo electrophysiology with optogenetic stimulation requires 1–4 h.National Institutes of Health (U.S.)National Science Foundation (U.S.)Simons FoundationNational Institutes of Health (U.S.). Pioneer AwardNational Eye Institue (K99 Award)Knut and Alice Wallenberg Foundation (Postdoctoral Fellowship)Brain & Behavior Research Foundation. Young Investigator AwardThomas F. Peterse

Recalculation of dose for each fraction of treatment on TomoTherapy.

OBJECTIVE: The VoxTox study, linking delivered dose to toxicity requires recalculation of typically 20-37 fractions per patient, for nearly 2000 patients. This requires a non-interactive interface permitting batch calculation with multiple computers. METHODS: Data are extracted from the TomoTherapy(®) archive and processed using the computational task-management system GANGA. Doses are calculated for each fraction of radiotherapy using the daily megavoltage (MV) CT images. The calculated dose cube is saved as a digital imaging and communications in medicine RTDOSE object, which can then be read by utilities that calculate dose-volume histograms or dose surface maps. The rectum is delineated on daily MV images using an implementation of the Chan-Vese algorithm. RESULTS: On a cluster of up to 117 central processing units, dose cubes for all fractions of 151 patients took 12 days to calculate. Outlining the rectum on all slices and fractions on 151 patients took 7 h. We also present results of the Hounsfield unit (HU) calibration of TomoTherapy MV images, measured over an 8-year period, showing that the HU calibration has become less variable over time, with no large changes observed after 2011. CONCLUSION: We have developed a system for automatic dose recalculation of TomoTherapy dose distributions. This does not tie up the clinically needed planning system but can be run on a cluster of independent machines, enabling recalculation of delivered dose without user intervention. ADVANCES IN KNOWLEDGE: The use of a task management system for automation of dose calculation and outlining enables work to be scaled up to the level required for large studies.JES is supported by Cancer Research UK through the Cambridge Cancer Centre. MR, AB and KH are supported by Cancer Research UK through the VoxTox Research Programme. NGB is supported by the NIHR Cambridge Biomedical Research Centre.This is the author accepted manuscript. The final version is available from British Institute of Radiology via http://dx.doi.org/10.1259/bjr.2015077

Distinct dissolved organic matter sources induce rapid transcriptional responses in coexisting populations of Prochlorococcus, Pelagibacter and the OM60 clade

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Environmental Microbiology 16 (2014): 2815-2830, doi:10.1111/1462-2920.12254.A considerable fraction of the Earth's organic carbon exists in dissolved form in seawater. To investigate the roles of planktonic marine microbes in the biogeochemical cycling of this dissolved organic matter (DOM), we performed controlled seawater incubation experiments and followed the responses of an oligotrophic surface water microbial assemblage to perturbations with DOM derived from an axenic culture of Prochlorococcus, or high-molecular weight DOM concentrated from nearby surface waters. The rapid transcriptional responses of both Prochlorococcus and Pelagibacter populations suggested the utilization of organic nitrogen compounds common to both DOM treatments. Along with these responses, both populations demonstrated decreases in gene transcripts associated with nitrogen stress, including those involved in ammonium acquisition. In contrast, responses from low abundance organisms of the NOR5/OM60 gammaproteobacteria were observed later in the experiment, and included elevated levels of gene transcripts associated with polysaccharide uptake and oxidation. In total, these results suggest that numerically dominant oligotrophic microbes rapidly acquire nitrogen from commonly available organic sources, and also point to an important role for carbohydrates found within the DOM pool for sustaining the less abundant microorganisms in these oligotrophic systems.This work was supported by a National Science Foundation Science and Technology Center Award EF0424599 (E.F.D and D.M.K.), grants to D.M.K., D.J.R and E.F.D from the Gordon and Betty Moore Foundation, a gift from the Agouron Institute (to E.F.D.) and a fellowship (202180) to A.K.S. from the Canadian Institutes of Health Research (CIHR)

Clarifying the Dominant Sources and Mechanisms of Cirrus Cloud Formation

Formation of cirrus clouds depends on the availability of ice nuclei to begin condensation of atmospheric water vapor. Although it is known that only a small fraction of atmospheric aerosols are efficient ice nuclei, the critical ingredients that make those aerosols so effective have not been established. We have determined in situ the composition of the residual particles within cirrus crystals after the ice was sublimated. Our results demonstrate that mineral dust and metallic particles are the dominant source of residual particles, whereas sulfate and organic particles are underrepresented, and elemental carbon and biological materials are essentially absent. Further, composition analysis combined with relative humidity measurements suggests that heterogeneous freezing was the dominant formation mechanism of these clouds.National Science Foundation (U.S.) (NSF AGS-0840732)National Science Foundation (U.S.) (NSF grant AGS-1036275)United States. National Aeronautics and Space Administration (NASA Earth and Space Science Graduate Fellowship)United States. National Aeronautics and Space Administration (NASA Radiation Sciences Program award number NNX07AL11G)United States. National Aeronautics and Space Administration (NASA Radiation Sciences Program award number NNX08AH57G)United States. National Aeronautics and Space Administration (NASA Earth Science Division Atmospheric Composition program award number NNH11AQ58UI

Transposon mutagenesis screen in <i>Klebsiella pneumoniae</i> identifies genetic determinants required for growth in human urine and serum

Klebsiella pneumoniae is a global public health concern due to the rising myriad of hypervirulent and multidrug-resistant clones both alarmingly associated with high mortality. The molecular mechanisms underpinning these recalcitrant K. pneumoniae infection, and how virulence is coupled with the emergence of lineages resistant to nearly all present-day clinically important antimicrobials, are unclear. In this study, we performed a genome-wide screen in K. pneumoniae ECL8, a member of the endemic K2-ST375 pathotype most often reported in Asia, to define genes essential for growth in a nutrient-rich laboratory medium (Luria-Bertani [LB] medium), human urine, and serum. Through transposon directed insertion-site sequencing (TraDIS), a total of 427 genes were identified as essential for growth on LB agar, whereas transposon insertions in 11 and 144 genes decreased fitness for growth in either urine or serum, respectively. These studies not only provide further knowledge on the genetics of this pathogen but also provide a strong impetus for discovering new antimicrobial targets to improve current therapeutic options for K. pneumoniae infections

Terahertz Emission of Gallium Arsenide on Textured p-type Silicon (100) Substrates Grown via Molecular Beam Epitaxy

This study presents the terahertz (THz) emission of molecular beam epitaxy (MBE)-grown Gallium Arsenide (GaAs) on surface textured p-type Silicon (p- Si) (100) substrates. Surface texturing was achieved by anisotropic wet chemical etching using 5% wt Potassium Hydroxide (KOH): Isopropyl alcohol (IPA) (50:1) solution for 15, 30, 45, and 60 minutes. Reflectivity measurements for the textured p-Si(100) substrates indicated that the overall texturing increases with longer etching times. Raman spectroscopy of the post-growth samples confirmed GaAs growth. The THz emission intensities were the same order of magnitude. The GaAs grown on p-Si(100) textured for 60 minutes exhibited the most intense THz emission attributed to the increased absorption from a larger surface-to-volume ratio due to surface texturing. All GaAs on textured p-Si(100) samples had frequency bandwidth of ~2.5 THz

Implementing GitHub Actions Continuous Integration to Reduce Error Rates in Ecological Data Collection

Accurate field data are essential to understanding ecological systems and forecasting their responses to global change. Yet, data collection errors are common, and data analysis often lags far enough behind its collection that many errors can no longer be corrected, nor can anomalous observations be revisited. Needed is a system in which data quality assurance and control (QA/QC), along with the production of basic data summaries, can be automated immediately following data collection. Here, we implement and test a system to satisfy these needs. For two annual tree mortality censuses and a dendrometer band survey at two forest research sites, we used GitHub Actions continuous integration (CI) to automate data QA/QC and run routine data wrangling scripts to produce cleaned datasets ready for analysis. This system automation had numerous benefits, including (1) the production of near real-time information on data collection status and errors requiring correction, resulting in final datasets free of detectable errors, (2) an apparent learning effect among field technicians, wherein original error rates in field data collection declined significantly following implementation of the system, and (3) an assurance of computational reproducibility—that is, robustness of the system to changes in code, data and software. By implementing CI, researchers can ensure that datasets are free of any errors for which a test can be coded. The result is dramatically improved data quality, increased skill among field technicians, and reduced need for expert oversight. Furthermore, we view CI implementation as a first step towards a data collection and analysis pipeline that is also more responsive to rapidly changing ecological dynamics, making it better suited to study ecological systems in the current era of rapid environmental change

Driving fast-spiking cells induces gamma rhythm and controls sensory responses,”

Cortical gamma oscillations (20280 Hz) predict increases in focused attention, and failure in gamma regulation is a hallmark of neurological and psychiatric disease. Current theory predicts that gamma oscillations are generated by synchronous activity of fast-spiking inhibitory interneurons, with the resulting rhythmic inhibition producing neural ensemble synchrony by generating a narrow window for effective excitation. We causally tested these hypotheses in barrel cortex in vivo by targeting optogenetic manipulation selectively to fast-spiking interneurons. Here we show that light-driven activation of fast-spiking interneurons at varied frequencies (82200 Hz) selectively amplifies gamma oscillations. In contrast, pyramidal neuron activation amplifies only lower frequency oscillations, a cell-type-specific double dissociation. We found that the timing of a sensory input relative to a gamma cycle determined the amplitude and precision of evoked responses. Our data directly support the fast-spiking-gamma hypothesis and provide the first causal evidence that distinct network activity states can be induced in vivo by cell-type-specific activation. Brain states characterized by rhythmic electrophysiological activity have been studied intensively for more than 80 years Cell-type-specific expression of channelrhodopsin-2 To test directly the hypothesis that FS interneuron activity in an in vivo cortical circuit is sufficient to induce gamma oscillations, we used the light-sensitive bacteriorhodopsin Chlamydomonas reinhardtii channelrhodopsin-2 (ChR2), a cation channel activated by ,470 nm blue ligh