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Abstract Background This study explores the use of Unmanned Aerial Vehicles (UAVs) for estimating wheat biomass, focusing on the impact of phenotyping and analytical protocols in the context of late-stage variety selection programs. It emphasizes the importance of variable selection, model specificity, and sampling location within the experimental plot in predicting biomass, aiming to refine UAV-based estimation techniques for enhanced selection accuracy and throughput in variety testing programs. Results The research uncovered that integrating geometric and spectral traits led to an increase in prediction accuracy, whilst a recursive feature elimination (RFE) based variable selection workflowled to slight reductions in accuracy with the benefit of increased interpretability. Models, tailored to specific experiments were more accurate than those modelling all experiments together, while models trained for broad-growth stages did not significantly increase accuracy. The comparison between a permanent and a precise region of interest (ROI) within the plot showed negligible differences in biomass prediction accuracy, indicating the robustness of the approach across different sampling locations within the plot. Significant differences in the within-season repeatability (w2) of biomass predictions across different experiments highlighted the need for further investigation into the optimal timing of measurement for prediction. Conclusions The study highlights the promising potential of UAV technology in biomass prediction for wheat at a small plot scale. It suggests that the accuracy of biomass predictions can be significantly improved through optimizing analytical and modelling protocols (i.e., variable selection, algorithm selection, stage-specific model development). Future work should focus on exploring the applicability of these findings under a wider variety of conditions and from a more diverse set of genotypes.

Abstract Glycerol, a versatile and ubiquitous compound, plays a vital role in a plethora of metabolic pathways in both prokaryotes and eukarotyes. Relatively few glycerol analogues have previously been explored for their use as glycerol kinase inhibitors, in addition to their therapeutic potential, however their use as (pro)‐drugs in the context of parasitic diseases such as trypanosomiasis is unreported. The literature on glycerol metabolism and particular its synergic anti‐profilation behaviour with salicylhydroxamic acid (SHAM) in Trypanosoma brucei is extensive. However, utiliation of glycerol analogues has not been explored as possible superior combinatory compounds. This report describes the synthesis of various glycerol analogues and their subsequent biochemical pheotypic analysis for their effect on lipid metabolism and their possible synergic activity with SHAM on Trypanosoma brucei. The glycerol analogues caused morphological changes;, including detached flagella, cytokinesis defects and ‘big‐eye’ phenotype. All four compounds either matched or marginally increased the toxicity of SHAM when used in combination against Trypanosoma brucei. However, the compounds exhibited mostly an antagonistic relationship with SHAM rather than synergistic. This research highlights the potential of small molecule glycerol analogues for their combination use with SHAM for the treatment of parasitic disease, such as trypanosomiasis.

Abstract In the southwest Pacific, a meandering jet‐stream in the upper troposphere is sometimes found at ~30° S during austral winters and is usually treated as a sub‐tropical jet (STJ) due to its low latitude. For two contrasting cases, we have conducted analyses from two perspectives to identify the STJ and PFJ: first, using previously published qualitative criteria to identify jet‐cores and second, investigating the jet‐stream axes of STJ and PFJ identified using 2‐PVU curves. The results showed that the chosen meandering jet‐stream case at ~30° S was a merged, and for a time, a superposed STJ and PFJ. Downstream of the jet‐streak, the PFJ split to the south and the STJ to the east. This is in significant contrast to the horizontally well‐separated jet‐stream case chosen in this study. Some processes likely contributing to the superposition of the STJ and PFJ were analyzed and discussed. The movement of PFJ that was closely associated with the movement of the low over the Tasman Sea and the convection in and near the tropical region may have played dominant roles.

Abstract We perform a global QCD analysis of high energy scattering data within the JAM Monte Carlo framework, including a coupling to a dark photon that augments the Standard Model (SM) electroweak coupling via kinetic mixing with the hypercharge B boson. We first set limits on the dark photon mass and mixing parameter assuming that the SM is the true theory of Nature, taking into account also the effect on g – 2 of the muon. If instead we entertain the possibility that the dark photon may play a role in deep-inelastic scattering (DIS), we find that the best fit is preferred over the SM at 6.5σ, even after accounting for missing higher order uncertainties. The improvement in χ 2 with the dark photon is stable against all the tests we have applied, with the improvements in the theoretical predictions spread across a wide range of x and Q 2. The largest improvement corresponds to the fixed target and HERA DIS data, while the best fit yields a value of g – 2 which significantly reduces the disagreement with the latest experimental determination.

Individuals with hematologic malignancy have increased risk of latent tuberculosis infection (LTBI) reactivation and Strongyloides stercoralis (SS) dissemination. However, screening prior to chemotherapy or corticosteroids is not routine. We conducted a LTBI and SS screening intervention amongst patients with hematologic malignancies. Over one-third immigrated from countries with high TB incidence and SS prevalence, and some had additional risk factors (HIV, HTLV-1, eosinophilia). The intervention increased screening rates but universal screening was not achieved. Screening positivity was similar pre- and post-intervention. We demonstrate a population with increased indolent infection reactivation risk. Specific infectious screening guidelines are needed to prevent significant morbidity.

ABSTRACTIn response to microbiota colonization, the intestinal epithelia of many animals exhibit increased rates of cell proliferation. We used gnotobiotic larval zebrafish to identify a secreted factor from the mutualist Aeromonas veronii that is sufficient to promote intestinal epithelial cell proliferation. This secreted A. veronii protein is a homologue of the Vibrio cholerae GlcNAc binding protein GbpA, which was identified as a chitin-binding colonization factor in mice. GbpA was subsequently shown to be a lytic polysaccharide monooxygenase (LPMO) that can degrade recalcitrant chitin. Our phenotypic characterization of gbpA deficient A. veronii found no alterations in these cells’ biogeography in the zebrafish intestine and only a modest competitive disadvantage in chitin-binding and colonization fitness when competed against the wild-type strain. These results argue against the model of GbpA being a secreted adhesin that binds simultaneously to bacterial cells and GlcNAc, and instead suggests that GbpA is part of a bacterial GlcNAc utilization program. We show that the host proliferative response to GbpA occurs in the absence of bacteria upon exposure of germ-free zebrafish to preparations of native GbpA secreted from either A. veronii or V. cholerae or recombinant A. veronii GbpA. Furthermore, domain 1 of A. veronii GbpA, containing the predicted LPMO activity, is sufficient to stimulate intestinal epithelial proliferation. We propose that intestinal epithelial tissues upregulate their rates of renewal in response to secreted bacterial GbpA proteins as an adaptive strategy for coexisting with bacteria that can degrade glycan constituents of the protective intestinal lining.

Abstract Ongoing climatic changes have altered growing conditions for plants by limiting water availability and inducing unprecedented temperature increases, eliciting plant functional responses that compromise floral trait expression, reduce pollen production and promote early self‐pollination. In a controlled greenhouse study, plants of Collinsia heterophylla, an annual mixed‐mated hermaphrodite, were grown under temperature and water stresses. Floral trait responses and related effects on plant reproductive success were recorded. Plants grown under temperature and water stresses were shorter and had fewer leaves at flowering than control plants. Temperature‐stressed plants flowered earlier and had smaller flowers that produced fewer per capita pollen grains than control and water‐stressed plants. While lifetime flower production in plants experiencing temperature stress alone or water stress alone was similar to control plants, those receiving combined temperature and water stresses had significantly lower lifetime flower production. Abiotic stress did not affect investment in female traits such as ovule number per flower, but impacted male traits seen as fewer pollen grains per flower. In plants experiencing abiotic stress, an increase in autonomous self‐pollination was facilitated through a compromise in herkogamy, a sexual interference mechanism that promotes cross‐pollination. Spatial separation between stigma and anther, a measure of herkogamy was zero or negative in stressed plants. Thus, abiotic stress responses in plants did not compromise plant reproductive success as autonomous selfing was augmented. In nature, such responses will likely reduce available nutrition for pollinators through decreased flower and pollen production.

Dark-field X-ray imaging is sensitive to the microstructure of a material. Here, the authors combine this with a neural network algorithm to provide efficient material discrimination, e.g., of explosives vs non-threat materials.

Recent advances in modelling capabilities and data processing combined with vastly improved observation tools and networks have resulted in the expansion of available weather and climate information, from historical observations to seasonal climate forecasts, as well as decadal climate predictions and multi-decadal climate change projections. However, it remains a key challenge to ensure this information reaches the intended climate-sensitive sectors (e.g. water, energy, agriculture, health), and is fit-for-purpose to guarantee the usability of climate information for these downstream users. Climate information can be produced on demand via climate resilience information systems which are existing in various forms. To optimise the efficiency and establish better information exchange between these systems, standardisation is necessary. Here, standards and deployment options are described for how scientific methods can be be deployed in climate resilience information systems, respecting the principles of being findable, accessible, interoperable and reusable. Besides the general description of OGC-API Standards and OGC-API Processes based on existing building blocks, ongoing developments in AI-enhanced services for climate services are described.

ABSTRACT Applied metagenomics is a powerful emerging capability enabling the untargeted detection of pathogens, and its application in clinical diagnostics promises to alleviate the limitations of current targeted assays. While metagenomics offers a hypothesis-free approach to identify any pathogen, including unculturable and potentially novel pathogens, its application in clinical diagnostics has so far been limited by workflow-specific requirements, computational constraints, and lengthy expert review requirements. To address these challenges, we developed UltraSEQ, a first-of-its-kind accurate and scalable metagenomic bioinformatic tool for potential clinical diagnostics and biosurveillance utility. Here, we present the results of the evaluation of our novel UltraSEQ pipeline using an in silico-synthesized metagenome, mock microbial community data sets, and publicly available clinical data sets from samples of different infection types, including both short-read and long-read sequencing data. Our results show that UltraSEQ successfully detected all expected species across the tree of life in the in silico sample and detected all 10 bacterial and fungal species in the mock microbial community data set. For clinical data sets, even without requiring data set-specific configuration setting changes, background sample subtraction, or prior sample information, UltraSEQ achieved an overall accuracy of 91%. Furthermore, as an initial demonstration with a limited patient sample set, we show UltraSEQ’s ability to provide antibiotic resistance and virulence factor genotypes that are consistent with phenotypic results. Taken together, the above-described results demonstrate that the UltraSEQ platform offers a transformative approach for microbial and metagenomic sample characterization, employing a biologically informed detection logic, deep metadata, and a flexible system architecture for the classification and characterization of taxonomic origin, gene function, and user-defined functions, including disease-causing infections. IMPORTANCE Traditional clinical microbiology-based diagnostic tests rely on targeted methods that can detect only one to a few preselected organisms or slow, culture-based methods. Although widely used today, these methods have several limitations, resulting in rates of cases of an unknown etiology of infection of >50% for several disease types. Massive developments in sequencing technologies have made it possible to apply metagenomic methods to clinical diagnostics, but current offerings are limited to a specific disease type or sequencer workflow and/or require laboratory-specific controls. The limitations associated with current clinical metagenomic offerings result from the fact that the backend bioinformatic pipelines are optimized for the specific parameters described above, resulting in an excess of unmaintained, redundant, and niche tools that lack standardization and explainable outputs. In this paper, we demonstrate that UltraSEQ uses a novel, information-based approach that enables accurate, evidence-based predictions for diagnosis as well as the functional characterization of a sample.

Coral reef health in the U.S. Virgin Islands (USVI) is in decline due to land-based sources of pollution associated with watershed development and global climate change. Water quality is a good indicator of stress in these nearshore environments as it plays a key role in determining the health and distribution of coral reef communities. Conventional water quality assessment methods based on in situ measurements are both time consuming and costly, and they lack the spatial coverage and temporal resolution that can be achieved using satellite remote sensing techniques. Water quality parameters (WQPs) such as Chlorophyll a (Chl-a), can be studied remotely using models that account for the inherent optical properties (IOPs) of the water. In this study, empirical based standard ocean color algorithm (OC4) and two semi-analytical algorithms, the Garver–Siegel–Maritorena (GSM) and the Generalized Inherent Optical Properties (GIOP) model, were evaluated in retrieving Chl-a in the nearshore waters of the USVI. GSM and GIOP were also evaluated for modeling inherent optical properties such as absorption coefficient of phytoplankton (aph (443)). Analysis of the results from each model using a field database from six cruises during May/June and December between 2016 and 2018, showed that the OC4 performed poorly with R2 of 0.14 and RMSE = 0.15. Effects of suspended particulates and benthic reflectance most likely contributed to the poor performance of the algorithm. GSM is a slightly better estimator for aph (443) and Chl-a (R2 = 0.55, RMSE = 0.04; R2 = 0.60, RMSE = 0.09) than GIOP (R2 = 0.52, RMSE = 0.05; R2 = 0.17, RMSE = 0.15). Performance of the semi-analytical models are limited in estimating particulate back scattering (bbp (443)) also due to the benthic albedo effects in the shallow waters. The calibrated GSM model was applied to Landsat 8 OLI satellite imagery spanning 2016–2018 to develop a time series of the spatial changes in Chl-a concentrations in the coastal waters of the USVI. The Landsat GSM Chl-a model produced promising results of R2 = 0.45, RMSE = 0.07, in an environment where signal-to-noise ratio is significantly low.

Abstract Phospholipases are esterases involved in lipid catabolism. In pathogenic micro-organisms (bacteria, fungi, parasites) they often play a critical role in virulence and pathogenicity. A few phospholipases (PL) have been characterised so far at the gene and protein level in unicellular parasites including African trypanosomes (AT). They could play a role in different processes such as host–pathogen interaction, antigenic variation, intermediary metabolism. By mining the genome database of AT we found putative new phospholipase candidate genes and here we provided biochemical evidence that one of these has lipolytic activity. This protein has a unique non-canonical glycosome targeting signal responsible for its dual localisation in the cytosol and the peroxisomes-related organelles named glycosomes. We also show that this new phospholipase is excreted by these pathogens and that antibodies directed against this protein are generated during an experimental infection with T. brucei gambiense, a subspecies responsible for infection in humans. This feature makes this protein a possible tool for diagnosis.

Abstract Background Patellar instability is a relatively common condition that leads to disability and restriction of activities. People with recurrent instability may be given the option of physiotherapy or surgery though this is largely driven by clinician preference rather than by a strong evidence base. We sought to determine the feasibility of conducting a definitive trial comparing physiotherapy with surgical treatment for people with recurrent patellar instability. Methods This was a pragmatic, open-label, two-arm feasibility randomised control trial (RCT) with an embedded interview component recruiting across three NHS sites comparing surgical treatment to a package of best conservative care; ‘Personalised Knee Therapy’ (PKT). The primary feasibility outcome was the recruitment rate per centre (expected rate 1 to 1.5 participants recruited each month). Secondary outcomes included the rate of follow-up (over 80% expected at 12 months) and a series of participant-reported outcomes taken at 3, 6 and 12 months following randomisation, including the Norwich Patellar Instability Score (NPIS), the Kujala Patellofemoral Disorder Score (KPDS), EuroQol-5D-5L, self-reported global assessment of change, satisfaction at each time point and resources use. Results We recruited 19 participants. Of these, 18 participants (95%) were followed-up at 12 months and 1 (5%) withdrew. One centre recruited at just over one case per month, one centre was unable to recruit, and one centre recruited at over one case per month after a change in participant screening approach. Ten participants were allocated into the PKT arm, with nine to the surgical arm. Mean Norwich Patellar Instability Score improved from 40.6 (standard deviation 22.1) to 28.2 (SD 25.4) from baseline to 12 months. Conclusion This feasibility trial identified a number of challenges and required a series of changes to ensure adequate recruitment and follow-up. These changes helped achieve a sufficient recruitment and follow-up rate. The revised trial design is feasible to be conducted as a definitive trial to answer this important clinical question for people with chronic patellar instability. Trial registration The trial was prospectively registered on the International Standard Randomised Controlled Trial Number registry on the 22/12/2016 (reference number: ISRCTN14950321). http://www.isrctn.com/ISRCTN14950321

Abstract Data assimilation (DA) is integrated with machine learning in order to perform entirely data‐driven online state estimation. To achieve this, recurrent neural networks (RNNs) are implemented as pretrained surrogate models to replace key components of the DA cycle in numerical weather prediction (NWP), including the conventional numerical forecast model, the forecast error covariance matrix, and the tangent linear and adjoint models. It is shown how these RNNs can be initialized using DA methods to directly update the hidden/reservoir state with observations of the target system. The results indicate that these techniques can be applied to estimate the state of a system for the repeated initialization of short‐term forecasts, even in the absence of a traditional numerical forecast model. Further, it is demonstrated how these integrated RNN‐DA methods can scale to higher dimensions by applying domain localization and parallelization, providing a path for practical applications in NWP.

The COVID-19 pandemic has infected tens of millions of people worldwide causing many deaths. Healthcare systems have been stretched caring for the most seriously ill and lockdown measures to interrupt COVID-19 transmission have had adverse economic and societal impacts. Large-scale population vaccination is seen as the solution.In the UK, a network of sites to deploy vaccines comprised National Health Service hospitals, primary care and new mass vaccination centres. Due to the pace at which mass vaccination centres were established and the scale of vaccine deployment, some sites experienced problems with queues and waiting times. To address this, one site used the Lean systematic improvement approach to make rapid operational improvements to reduce process times and improve flow.The case example identifies obstacles to flow experienced by a mass vaccination centre and how they were addressed using Lean concepts and techniques. Process cycle times were used as a proxy metric for efficiency and flow. Based on daily demand volume and open hours, takt time was calculated to give a process completion rate to achieve flow through the vaccination centre.The mass vaccination centre achieved its aim of reducing process times and improving flow. Administrative and clinical cycle times were reduced sufficiently to increase throughput and the number of queues and queueing time were reduced improving client experience.The design and operational management of vaccination centre processes contribute to client experience, efficiency and throughput. Lean provides a systematic approach that can improve operational processes and facilitate client flow through mass vaccination centres.

Abstract Background Long-term outcome in multiple sclerosis (MS) depends on early treatment. In patients with acute optic neuritis (ON), an early inflammatory event, we investigated markers in cerebrospinal fluid (CSF), which may predict a diagnosis of MS. Methods Forty patients with acute ON were recruited in a prospective population-based cohort with median 29 months (range 19–41) of follow-up. Paired CSF and serum samples were taken within 14 days (range 2–38), prior to treatment. Prospectively, 16/40 patients were by a uniform algorithm diagnosed with MS (MS-ON) and 24 patients continued to manifest isolated ON (ION) during follow-up. Levels of cytokines and neurofilament light chain (NF-L) were measured at the onset of acute ON and compared to healthy controls (HC). Significance levels were corrected for multiple comparisons (“q”). The predictive value of biomarkers was determined with multivariable prediction models using nomograms. Results CSF TNF-α, IL-10, and CXCL13 levels were increased in MS-ON compared to those in ION patients (q = 0.021, 0.004, and 0.0006, respectively). MS-ON patients had increased CSF pleocytosis, IgG indices, and oligoclonal bands (OCBs) compared to ION (q = 0.0007, q = 0.0058, and q = 0.0021, respectively). CSF levels of IL-10, TNF-a, IL-17A, and CXCL13 in MS-ON patients correlated with leukocyte counts (r > 0.69 and p 0.55, p

Erbium doped GaN (Er:GaN) is a promising candidate as a novel gain medium for solid-state high energy lasers (HELs) due to its superior physical properties over a synthetic garnet such as Nd:YAG. Er:GaN emits in the 1.5 µm region, which is retina-safe and has a high transmission in the air. We report photoluminescence (PL) studies performed on Er:GaN epilayers synthesized by the hydride vapor phase epitaxy (HVPE) technique. The room temperature PL spectra of HVPE grown Er:GaN epilayers resolved as many as 11 and seven emission lines in the 1.5 µm and 1.0 µm wavelength regions, respectively, corresponding to the intra-4f shell transitions between Stark levels from the first (4I13/2) and the second (4I11/2) excited states to the ground state (4I15/2) of Er3+ in GaN. The observed peak positions of these transitions enabled the construction of the detailed energy levels in Er:GaN. The results agree well with those of the calculation based on a crystal field analysis. Precise determination of the detailed energy levels of the Stark levels in the 4I11/2, 4I13/2, and 4I15/5 states is critically important for the realization of HELs based on Er:GaN.

Objectives Informing research participants of the results of studies in which they took part is viewed as an ethical imperative. However, there is little guidance in the literature about how to do this. The Fluoxetine Or Control Under Supervision trial randomised 3127 patients with a recent acute stroke to 6 months of fluoxetine or placebo and was published in the Lancet on 5 December 2018. The trial team decided to inform the participants of the results at exactly the same time as the Lancet publication, and also whether they had been allocated fluoxetine or placebo. In this report, we describe how we informed participants of the results.Design In the 6-month and 12-month follow-up questionnaires, we invited participants to provide an email address if they wished to be informed of the results of the trial. We re-opened our trial telephone helpline between 5 December 2018 and 31 March 2019.Setting UK stroke services.Participants 3127 participants were randomised. 2847 returned 6-month follow-up forms and 2703 returned 12-month follow-up forms; the remaining participants had died (380), withdrawn consent or did not respond.Results Of those returning follow-up questionnaires, a total of 1845 email addresses were provided and a further 50 people requested results to be sent by post. Results were sent to all email and postal addresses provided; 309 emails were returned unrecognised. Seventeen people replied, of whom three called the helpline and the rest responded by email.Conclusion It is feasible to disseminate results of large trials to research participants, though only around 60% of those randomised wanted to receive the results. The system we developed was efficient and required very little resource, and could be replicated by trialists in the future.Trial registration number ISRCTN83290762; Post-results.

Abstract Background To determine the prevalence of intestinal S. aureus colonization of patients at a large teaching hospital and determine the molecular characteristics of the identified strains. The second objective of this research was to determine risk factors associated with S. aureus intestinal colonization. Methods A cross-sectional study of 781 specimens from inpatients and outpatients at the University of Iowa Hospitals and Clinics Clinical Microbiology Laboratory was conducted. S. aureus was identified using traditional culture methodologies. Methicillin-resistance was determined via PCR of the mecA gene. PVL PCR, spa typing, and antimicrobial sensitivity testing were also done. A nested case-control study was done on a subset of patients with all colonized patients defined as cases and non-colonized controls. Medical record abstractions were done to identify risk factors for intestinal colonization in the nested study. Results Out of 625 patients included in the final study, 58 were positive for S. aureus (9.3%). One isolate was positive for the PVL gene. A high number of isolates were resistant to multiple antibiotics including oxacillin (43.1%), erythromycin (51.7%), and levofloxacin (41.4%). All isolates were susceptible to vancomycin, daptomycin, linezolid, and quinupristin-dalfopristin. In the nested study, having a disease or condition of the gastrointestinal tract significantly increased the odds of intestinal colonization (OR: 1.96, 95% CI: 1.04–3.7; aOR: 13.9, 95% CI: 1.67–115.7). No other variables were significantly associated with increased odds of colonization. Conclusions S. aureus was identified from the stool of patients at the University of Iowa Hospitals and Clinics, with a large number of those isolates being resistant to antibiotics and may serve a reservoir for subsequent infections as well as asymptomatic transmission.

A global heat flux model based on a fractional derivative of plasma pressure is proposed for the heat transport in fusion plasmas. The degree of the fractional derivative of the heat flux, α, is defined through the power balance analysis of the steady state. The model was used to obtain the experimental values of α for a large database of the Joint European Torus (JET) carbon-wall as well as ITER like-wall plasmas. The fractional degrees of the electron heat flux are found to be α

Attitudes toward the environment are understood in psychological science as the result of separate mental systems, one conscious and the other unconscious, and capable of affecting behavior outside of awareness. For example, the common incongruity between what people say about global sustainability and what they do about the environment has been explicated by the influence of implicit environmental attitudes. This study examined the operational adequacy of the commonly used Implicit Association Test (IAT) by directly asking participants to report their recognition of behavioral influences whilst performing an IAT. An analytic technique of awareness assessment was introduced to improve on traditional post-experimental questioning, by requiring a constrained report that provided introspective access to task-related knowledge in awareness. Results revealed participants were very aware of their IAT response latencies, they accurately recognized IAT features that produced those latencies, and the validity of this awareness predicted their test scores, challenging the claim to attitude effects of which individuals are unaware. Thus, the critical evaluation showed the IAT method to be inadequate as a measure of environmental attitudes that are implicit. Applications of the awareness assessment technique are discussed for evaluating tests of implicit cognition, and for promoting individual mindfulness of one’s own environmental attitude.

Nanoscale processes may directly impact macroscopic mechanical behaviour. Here authors describe a ‘phase-transformation strengthening’ mechanism in nickel-based high temperature alloys, allowing suppression of deleterious deformation processes at elevated temperatures by specific alloying elements.

This paper describes a blended sea-surface temperature (SST) data set that is part of the National Oceanic and Atmospheric Administration (NOAA) Climate Data Record (CDR) program product suite. Using optimum interpolation (OI), in situ and satellite observations are combined on a daily and 0.25° spatial grid to form an SST analysis, i.e., a spatially complete field. A large-scale bias adjustment of the input infrared SSTs is made using buoy and ship observations as a reference. This is particularly important for the time periods when volcanic aerosols from the El Chichón and Mt. Pinatubo eruptions are widespread globally. The main source of SSTs is the Advanced Very High Resolution Radiometer (AVHRR), available from late 1981 to the present, which is also the temporal span of this CDR. The input and processing choices made to ensure a consistent data set that meets the CDR requirements are summarized. A brief history and an explanation of the forward production schedule for the preliminary and science-quality final product are also provided. The data set is produced and archived at the newly formed National Centers for Environmental Information (NCEI) in Network Common Data Form (netCDF) at doi:10.7289/V5SQ8XB5.

ABSTRACT The bacterial intracellular second messenger, cyclic dimeric GMP (c-di-GMP), regulates biofilm formation for many bacteria. The binding of c-di-GMP by the inner membrane protein LapD controls biofilm formation, and the LapD receptor is central to a complex network of c-di-GMP-mediated biofilm formation. In this study, we examine how c-di-GMP signaling specificity by a diguanylate cyclase (DGC), GcbC, is achieved via interactions with the LapD receptor and by small ligand sensing via GcbC’s calcium channel chemotaxis (CACHE) domain. We provide evidence that biofilm formation is stimulated by the environmentally relevant organic acid citrate (and a related compound, isocitrate) in a GcbC-dependent manner through enhanced GcbC-LapD interaction, which results in increased LapA localization to the cell surface. Furthermore, GcbC shows little ability to synthesize c-di-GMP in isolation. However, when LapD is present, GcbC activity is significantly enhanced (~8-fold), indicating that engaging the LapD receptor stimulates the activity of this DGC; citrate-enhanced GcbC-LapD interaction further stimulates c-di-GMP synthesis. We propose that the I-site of GcbC serves two roles beyond allosteric control of this enzyme: promoting GcbC-LapD interaction and stabilizing the active conformation of GcbC in the GcbC-LapD complex. Finally, given that LapD can interact with a dozen different DGCs of Pseudomonas fluorescens, many of which have ligand-binding domains, the ligand-mediated enhanced signaling via LapD-GcbC interaction described here is likely a conserved mechanism of signaling in this network. Consistent with this idea, we identify a second example of ligand-mediated enhancement of DGC-LapD interaction that promotes biofilm formation. IMPORTANCE In many bacteria, dozens of enzymes produce the dinucleotide signal c-di-GMP; however, it is unclear how undesired cross talk is mitigated in the context of this soluble signal and how c-di-GMP signaling is regulated by environmental inputs. We demonstrate that GcbC, a DGC, shows little ability to synthesize c-di-GMP in the absence of its cognate receptor LapD; GcbC-LapD interaction enhances c-di-GMP synthesis by GcbC, likely mediated by the I-site of GcbC. We further show evidence for a ligand-mediated mechanism of signaling specificity via increased physical interaction of a DGC with its cognate receptor. We envision a scenario wherein a “cloud” of weakly active DGCs can increase their activity by specific interaction with their receptor in response to appropriate environmental signals, concomitantly boosting c-di-GMP production, ligand-specific signaling, and biofilm formation.

Thin films of CuGaSe were deposited on n-Si (1 0 0) by rf magnetron sputtering from a stoichiometric CuGaSe2 target. The objective of this study was to characterize the thin film/Si heterojunction for potential photovoltaic applications, evaluate possible candidates for metal contacts and to establish whether heteroepitaxial growth could be achieved, particularly as the mismatch of lattice parameters corresponding to the base of the copper gallium selenide (CGS) tetragonal cell is quite close to that of Si, with a 2.9% mismatch. For this study, Si substrates were prepared by the standard Radio Corporation of America (RCA) cleaning procedure immediately followed by the deposition of CGS by sputtering at a substrate temperature of 600°C. The deposited thin-film stoichiometry and morphology were characterized by Rutherford backscattering spectroscopy (RBS) and transmission electron microscopy (TEM). Rutherford back scattering (RBS) analysis indicated a thin-film composition of Cu1Ga1Se1 indicating that the films were Se deficient, although channeling was not observed. The polycrystalline nature of the deposited thin film was established by cross-sectional TEM. An estimated 1.5-nm thick layer likely to be SiO x was observed at the CGS–Si interface. It is believed that this interfacial layer prevented heteroepitaxy CGS on Si. Additionally, circular metal contacts were deposited on the thin films and characterized by capacitance and current–voltage measurements. It was observed that Al and Ag contacts were rectifying, from which the thin-film carrier density was estimated to be ~5 × 1015 and ~7.68 × 1015 cm−3 with Al and Ag contacts, respectively. Au, Pt, W and Cr were ohmic, and Mo and Ni provided semi-ohmic contacts to CGS films.

The aim of this study was to determine medium and long management of phosphorus fertilization with two application methods on the maize. An experiment was established in El Ejido, Panama, from 2004 to 2013 on Udic Haplustalf soil. Two factors were evaluated in a 5 x 4 factorial arrangement of split plot under a randomized block design with three replications. The main plot was the broadcast application of P in rates of 0, 25, 50, 75, and 100 kgP/ha (applied only the first year), while in sub-plots applied P in band, for ten years, together with N and K doses of 0, 10, 20 and 30 kgP/ha. The maximum grain yield was achieved by applying average 304 kg (average of 30.4 kgP/year). It was observed that the residual effect broadcast applications of 0 and 25 kgP/ha had a relative yield below 80%. Treatment of 50 kgP/ha remained at 82%, while 75 kgP/ha declined from the year 2007 and is at a value close to 80%. Treatment of 100 kgP/ha broadcast presents a relative yield close to 100%. The results indicate that the broadcast application over 50 kgP/ha did not differ from the response obtained with annual applications of 30 P/ha in the first five years. These results suggest that the residual effect of phosphorus broadcast and incorporated before planting, on the type of soil used, varies according doses applied initially, where dosages above 50 kg/ha should be repeated after six years to maintain good productivity, since, from this time the residual effect is drastically reduced.

Human saliva is clinically informative of both oral and general health. Since next generation shotgun sequencing (NGS) is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the Human Microbiome Project, along with a control dataset containing short NGS reads from bacterial species representative of the bacterial flora of human saliva. GENIUS, a system designed to identify and quantify bacterial species using unassembled short NGS reads was used to identify the bacterial species comprising the microbiomes of the saliva samples and datasets. Results, achieved within minutes and at greater than 90% accuracy, showed more than 175 bacterial species comprised the bacterial flora of human saliva, including bacteria known to be commensal human flora but also Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, and Gamma proteobacteria. Basic Local Alignment Search Tool (BLASTn) analysis in parallel, reported ca. five times more species than those actually comprising the in silico sample. Both GENIUS and BLAST analyses of saliva samples identified major genera comprising the bacterial flora of saliva, but GENIUS provided a more precise description of species composition, identifying to strain in most cases and delivered results at least 10,000 times faster. Therefore, GENIUS offers a facile and accurate system for identification and quantification of bacterial species and/or strains in metagenomic samples.

Plasma cholesteryl ester (CE) synthesis by lecithin cholesterol acyltransferase (LCAT) is activated by apolipoprotein (apo)A-I. We studied the effect of plasma apoA-I concentration on LCAT activation, using normal, heterozygous or homozygous apoA-I-deficient mice made by gene targeting. Plasma esterified cholesterol concentrations of mice fed chow diets were ordered (mean +/- SEM): 105 +/- 7 (normal) > 70 +/- 5 (heterozygotes) > 26 +/- 2 (homozygotes) mg/dl. Plasma free cholesterol concentrations were similar among the three genotypes. Endogenous LCAT activity, measured as the decrease in plasma free cholesterol after a 1 h incubation at 37 degrees C, was ordered: 44 +/- 3 (normal) > 21 +/- 2 (heterozygotes) > 5 +/- 1 (homozygotes) nmol CE formed/h per ml plasma. Using a recombinant exogenous substrate consisting of egg yolk phospholipid, [14C]cholesterol, and apoA-I, CE formation of normals and heterozygotes was similar (27.4 +/- 0.6 and 28.8 +/- 1.3 nmol/h per ml plasma, respectively), but was significantly less for homozygotes (19.2 +/- 1.7 nmol/h per ml plasma). However, using a small unilamellar vesicle substrate particle containing phospholipid and [14C]cholesterol, CE formation was ordered: 1.6 +/- 0.1 (normal) = 1.6 +/- 0.1 (heterozygotes) > 0.6 +/- 0.1 (homozygotes) nmol/h per ml plasma; addition of apoA-I to the plasma of homozygous animals restored CE formation to normal levels (1.6 +/- 0.1). CE fatty acid analysis demonstrated that plasma from homozygous mice contained significantly more saturated and monounsaturated and fewer polyunsaturated fatty acids compared to normal and heterozygous mice.(ABSTRACT TRUNCATED AT 250 WORDS)

The aim of the present study was to assess, through an epidemiological study, whether suicide risk is increased in patients with motor neuron disease (MND). The study involved 116 patients with MND. In the study period 92 patients died, 47 males and 45 females. No patients committed suicide. The number of expected suicides was 0.27 for males and 0.12 for females, a total of 0.38. The difference between observed and expected suicides was not statistically significant for males and females.

In 2010, nuclear power accounted for 27% of electricity production in Japan. The March 2011 disaster at the Fukushima Daiichi power station resulted in the closure of all of Japan’s nuclear power plants and it remains an open question as to how many will reopen. Even before the loss of nuclear capacity, there were efforts in Japan to foster the use of renewable energy, including large scale solar power. Nuclear power plants in Japan provided more than just base-load by storing energy in large scale pumped hydroelectric storage systems, which was then released to provide some peaking capacity. If this storage were instead coupled to current generation rooftop solar systems in Tokyo, the combined system could help to meet peak requirements while at the same time providing ∼26.5% of the electricity Tokyo used to get from nuclear output, and do so 91% of the time. Data from a study of rooftop space and a 34 yr data set of average daily irradiance in the Tokyo metropolitan area were used. Using pumped hydroelectric storage with 5.6 times this rooftop area could completely provide for TEPCO’s nuclear capacity.

Superconducting radio-frequency electron guns are viewed by many as the preferred technology for generating the high-quality, high-current beams needed for future high power free-electron lasers and energy recovery linacs. All previous guns of this type have employed elliptical cavities, but there are potential advantages associated with other geometries. Here we describe the design, commissioning, and initial results from a superconducting radio-frequency electron gun employing a quarter-wave resonator configuration, the first such device to be built and tested. In initial operation, the gun has generated beams with bunch charge in excess of 78 pC, energy of 469 keV, and normalized rms emittances of about 4.9 μm. Currently, bunch charge is limited by the available drive laser energy, and beam energy is limited by x-ray production and the available rf power. No fundamental limits on beam charge or energy have been encountered, and no high-field quenching events have been observed.

High precision fundamental neutron physics experiments have been proposed for the intense pulsed spallation neutron beams at JSNS, LANSCE, and SNS to test the standard model and search for new physics. Certain systematic effects in some of these experiments have to be controlled at the few ppb level. The NPDGamma experiment, a search for the small parity-violating γ-ray asymmetry A_{γ} in polarized cold neutron capture on parahydrogen, is one example. For the NPDGamma experiment we developed a radio-frequency resonant spin rotator to reverse the neutron polarization in a 9.5 cm×9.5 cm pulsed cold neutron beam with high efficiency over a broad cold neutron energy range. The effect of the spin reversal by the rotator on the neutron beam phase space is compared qualitatively to rf neutron spin flippers based on adiabatic fast passage. We discuss the design of the spin rotator and describe two types of transmission-based neutron spin-flip efficiency measurements where the neutron beam was both polarized and analyzed by optically polarized ^{3}He neutron spin filters. The efficiency of the spin rotator was measured at LANSCE to be 98.8±0.5% for neutron energies from 3 to 20 meV over the full phase space of the beam. Systematic effects that the rf spin rotator introduces to the NPDGamma experiment are considered.