Chemistry by Mobile Phone (or how to justify more time at the bar)

By combining automatic environment monitoring with Java smartphones a system has been produced for the real-time monitoring of experiments whilst away from the lab. Changes in the laboratory environment are encapsulated as simple XML messages, which are published using an MQTT compliant broker. Clients subscribe to the MQTT stream, and produce a user display. An MQTT client written for the Java MIDP platform, can be run on a smartphone with a GPRS Internet connection, freeing us from the constraints of the lab. We present an overview of the technologies used, and how these are helping chemists make the best use of their time

The Combechem MQTT LEGO microscope: a grid enabled scientific apparatus demonstrator

Grid computing impacts directly on the experimental scientific laboratory in the areas of monitoring and remote control of experiments, and the storage, processing and dissemination of the resulting data. We highlight some of the issues in extending the use of an MQ Telemetry Transport (MQTT) broker from facilitating the remote monitoring of an experiment and its environment to the remote control of an apparatus. To demonstrate these techniques, an Intel-Play QX3 microscope has been "grid-enabled" using a combination of software to control the microscope imaging, and sample handling hardware built from LEGO Mindstorms. The whole system is controlled remotely by passing messages using an IBM WebSphere Message Broker. <br/

Collapse of the North American ice saddle 14,500 years ago caused widespread cooling and reduced ocean overturning circulation

Collapse of ice sheets can cause significant sea level rise and widespread climate change. We examine the climatic response to meltwater generated by the collapse of the Cordilleran-Laurentide ice saddle (North America) ~14.5 thousand years ago (ka) using a high-resolution drainage model coupled to an ocean-atmosphere-vegetation general circulation model. Equivalent to 7.26 m global mean sea level rise in 340 years, the meltwater caused a 6 sverdrup weakening of Atlantic Meridional Overturning Circulation (AMOC) and widespread Northern Hemisphere cooling of 1–5°C. The greatest cooling is in the Atlantic sector high latitudes during Boreal winter (by 5–10°C), but there is also strong summer warming of 1–3°C over eastern North America. Following recent suggestions that the saddle collapse was triggered by the Bølling warming event at ~14.7–14.5 ka, we conclude that this robust submillennial mechanism may have initiated the end of the warming and/or the Older Dryas cooling through a forced AMOC weakening

Development of Risk Prediction Equations for Incident Chronic Kidney Disease

IMPORTANCE ‐ Early identification of individuals at elevated risk of developing chronic kidney disease  could improve clinical care through enhanced surveillance and better management of underlying health  conditions.  OBJECTIVE – To develop assessment tools to identify individuals at increased risk of chronic kidney  disease, defined by reduced estimated glomerular filtration rate (eGFR).  DESIGN, SETTING, AND PARTICIPANTS – Individual level data analysis of 34 multinational cohorts from  the CKD Prognosis Consortium including 5,222,711 individuals from 28 countries. Data were collected  from April, 1970 through January, 2017. A two‐stage analysis was performed, with each study first  analyzed individually and summarized overall using a weighted average. Since clinical variables were  often differentially available by diabetes status, models were developed separately within participants  with diabetes and without diabetes. Discrimination and calibration were also tested in 9 external  cohorts (N=2,253,540). EXPOSURE Demographic and clinical factors.  MAIN OUTCOMES AND MEASURES – Incident eGFR <60 ml/min/1.73 m2.  RESULTS – In 4,441,084 participants without diabetes (mean age, 54 years, 38% female), there were  660,856 incident cases of reduced eGFR during a mean follow‐up of 4.2 years. In 781,627 participants  with diabetes (mean age, 62 years, 13% female), there were 313,646 incident cases during a mean follow‐up of 3.9 years. Equations for the 5‐year risk of reduced eGFR included age, sex, ethnicity, eGFR, history of cardiovascular disease, ever smoker, hypertension, BMI, and albuminuria. For participants  with diabetes, the models also included diabetes medications, hemoglobin A1c, and the interaction  between the two. The risk equations had a median C statistic for the 5‐year predicted probability of  0.845 (25th – 75th percentile, 0.789‐0.890) in the cohorts without diabetes and 0.801 (25th – 75th percentile, 0.750‐0.819) in the cohorts with diabetes. Calibration analysis showed that 9 out of 13 (69%) study populations had a slope of observed to predicted risk between 0.80 and 1.25. Discrimination was  similar in 18 study populations in 9 external validation cohorts; calibration showed that 16 out of 18 (89%) had a slope of observed to predicted risk between 0.80 and 1.25. CONCLUSIONS AND RELEVANCE – Equations for predicting risk of incident chronic kidney disease developed in over 5 million people from 34 multinational cohorts demonstrated high discrimination and  variable calibration in diverse populations

Consistent patterns of common species across tropical tree communities

Trees structure the Earth’s most biodiverse ecosystem, tropical forests. The vast number of tree species presents a formidable challenge to understanding these forests, including their response to environmental change, as very little is known about most tropical tree species. A focus on the common species may circumvent this challenge. Here we investigate abundance patterns of common tree species using inventory data on 1,003,805 trees with trunk diameters of at least 10 cm across 1,568 locations1,2,3,4,5,6 in closed-canopy, structurally intact old-growth tropical forests in Africa, Amazonia and Southeast Asia. We estimate that 2.2%, 2.2% and 2.3% of species comprise 50% of the tropical trees in these regions, respectively. Extrapolating across all closed-canopy tropical forests, we estimate that just 1,053 species comprise half of Earth’s 800 billion tropical trees with trunk diameters of at least 10 cm. Despite differing biogeographic, climatic and anthropogenic histories7, we find notably consistent patterns of common species and species abundance distributions across the continents. This suggests that fundamental mechanisms of tree community assembly may apply to all tropical forests. Resampling analyses show that the most common species are likely to belong to a manageable list of known species, enabling targeted efforts to understand their ecology. Although they do not detract from the importance of rare species, our results open new opportunities to understand the world’s most diverse forests, including modelling their response to environmental change, by focusing on the common species that constitute the majority of their trees.Publisher PDFPeer reviewe

Formulation, stabilisation and encapsulation of bacteriophage for phage therapy

Against a backdrop of global antibiotic resistance and increasing awareness of the importance of the human microbiota, there has been resurgent interest in the potential use of bacteriophages for therapeutic purposes, known as phage therapy. A number of phage therapy phase I and II clinical trials have concluded, and shown phages don’t present significant adverse safety concerns. These clinical trials used simple phage suspensions without any formulation and phage stability was of secondary concern. Phages have a limited stability in solution, and undergo a significant drop in phage titre during processing and storage which is unacceptable if phages are to become regulated pharmaceuticals, where stable dosage and well defined pharmacokinetics and pharmacodynamics are de rigueur. Animal studies have shown that the efficacy of phage therapy outcomes depend on the phage concentration (i.e. the dose) delivered at the site of infection, and their ability to target and kill bacteria, arresting bacterial growth and clearing the infection. In addition, in vitro and animal studies have shown the importance of using phage cocktails rather than single phage preparations to achieve better therapy outcomes. The in vivo reduction of phage concentration due to interactions with host antibodies or other clearance mechanisms may necessitate repeated dosing of phages, or sustained release approaches. Modelling of phage-bacterium population dynamics reinforces these points. Surprisingly little attention has been devoted to the effect of formulation on phage therapy outcomes, given the need for phage cocktails, where each phage within a cocktail may require significantly different formulation to retain a high enough infective dose. This review firstly looks at the clinical needs and challenges (informed through a review of key animal studies evaluating phage therapy) associated with treatment of acute and chronic infections and the drivers for phage encapsulation. An important driver for formulation and encapsulation is shelf life and storage of phage to ensure reproducible dosages. Other drivers include formulation of phage for encapsulation in micro- and nanoparticles for effective delivery, encapsulation in stimuli responsive systems for triggered controlled or sustained release at the targeted site of infection. Encapsulation of phage (e.g. in liposomes) may also be used to increase the circulation time of phage for treating systemic infections, for prophylactic treatment or to treat intracellular infections. We then proceed to document approaches used in the published literature on the formulation and stabilisation of phage for storage and encapsulation of bacteriophage in micro- and nanostructured materials using freeze drying (lyophilization), spray drying, in emulsions e.g. ointments, polymeric microparticles, nanoparticles and liposomes. As phage therapy moves forward towards Phase III clinical trials, the review concludes by looking at promising new approaches for micro- and nanoencapsulation of phages and how these may address gaps in the field

Averting biodiversity collapse in tropical forest protected areas

The rapid disruption of tropical forests probably imperils global biodiversity more than any other contemporary phenomenon¹⁻³. With deforestation advancing quickly, protected areas are increasingly becoming final refuges for threatened species and natural ecosystem processes. However, many protected areas in the tropics are themselves vulnerable to human encroachment and other environmental stresses⁴⁻⁹. As pressures mount, it is vital to know whether existing reserves can sustain their biodiversity. A critical constraint in addressing this question has been that data describing a broad array of biodiversity groups have been unavailable for a sufficiently large and representative sample of reserves. Here we present a uniquely comprehensive data set on changes over the past 20 to 30 years in 31 functional groups of species and 21 potential drivers of environmental change, for 60 protected areas stratified across the world’s major tropical regions. Our analysis reveals great variation in reserve ‘health’: about half of all reserves have been effective or performed passably, but the rest are experiencing an erosion of biodiversity that is often alarmingly widespread taxonomically and functionally. Habitat disruption, hunting and forest-product exploitation were the strongest predictors of declining reserve health. Crucially, environmental changes immediately outside reserves seemed nearly as important as those inside in determining their ecological fate, with changes inside reserves strongly mirroring those occurring around them. These findings suggest that tropical protected areas are often intimately linked ecologically to their surrounding habitats, and that a failure to stem broad-scale loss and degradation of such habitats could sharply increase the likelihood of serious biodiversity declines.Keywords: Ecology, Environmental scienc

Methods for re-imagining social tools in new contexts

Digital exclusion refers to a lack of access to technological facilities, including the blossoming arena of social interaction. People without mobile phones or PCs cannot access email, SMS or social networking websites; this includes many groups, such as the elderly, who can become vulnerable without good social contact. These people could partake in such interactions if we could enable multimodal access to social networks through a wider variety of communication channels (for example, television and telephone). This poster describes how we have used methods from HCI and Social Theory to better understand social technology

Sensor Networks and Grid Middleware for Laboratory Monitoring

By combining automatic environment sensing and experimental data collection with broker based messaging middleware, a system has been produced for the real-time monitoring of experiments whilst away from the lab. Changes in the laboratory environment are encapsulated as simple messages, which are published using an MQTT compliant broker. Clients subscribe to the MQTT stream, and perform a data transform on the messages; this may be to produce a user display or to change the format of the message for republishing. For example, an MQTT client written for the Java MIDP platform can be run on a smart-phone with a GPRS Internet connection, freeing us from the constraints of the network. We present an overview of the technologies used, and ho

Timing of meltwater pulse 1a and climate responses to meltwater injections

The temporal relationship between meltwater pulse 1a (mwp-1a) and the climate history of the last deglaciation remains a subject of debate. By combining the Greenland Ice Core Project d18O ice core record on the new Greenland ice core chronology 2005 timescale with the U/Th-dated Barbados coral record, we conclusively derive that mwp-1a did not coincide with the sharp Bølling warming but instead with the abrupt cooling of the Older Dryas. To evaluate whether there is a relationship between meltwater injections, North Atlantic Deep Water (NADW) formation, and climate change, we present a high-resolution record of NADW flow intensity from Eirik Drift through the last deglaciation. It indicates only a relatively minor 200-year weakening of NADW flow, coincident with mwp-1a. Our compilation of records also indicates that during Heinrich event 1 and the Younger Dryas there were no discernible sea level rises, and yet these periods were characterized by intense NADW slowdowns/shutdowns. Clearly, deepwater formation and climate are not simply controlled by the magnitude or rate of meltwater addition. Instead, our results emphasize that the location of meltwater pulses may be more important, with NADW formation being particularly sensitive to surface freshening in the Arctic/Nordic Seas