DAS Preprocessing Workflow

This report addresses deliverable D1.4 of the DigiMon project, which covers the preprocessing workflow for datasets acquired by Distributed Acoustic Systems (DAS). The workflow seeks to capture the key stages required to prepare the raw seismic data for the main processing stages and demonstrates their application using both synthetic and real-world data. A description of the synthetic datasets can be found in DigiMon deliverable D1.3 report, while details of the real-world datasets are included in DigiMon reports D1.1 and D1.2

Developing an e-infrastructure for social science

We outline the aims and progress to date of the National Centre for e-Social Science e-Infrastructure project. We examine the challenges faced by the project, namely in ensuring outputs are appropriate to social scientists, managing the transition from research projects to service and embedding software and data within a wider infrastructural framework. We also provide pointers to related work where issues which have ramifications for this and similar initiatives are being addressed

Molecular antimicrobial resistance surveillance for neisseria gonorrhoeae, Northern Territory, Australia

Neisseria gonorrhoeae antimicrobial resistance (AMR) is a globally recognized health threat; new strategies are needed to enhance AMR surveillance. The Northern Territory of Australia is unique in that 2 different first-line therapies, based primarily on geographic location, are used for gonorrhea treatment. We tested 1,629 N. gonorrhoeae nucleic acid amplification test–positive clinical samples, collected from regions where ceftriaxone plus azithromycin or amoxicillin plus azithromycin are recommended first-line treatments, by using 8 N. gonorrhoeae AMR PCR assays. We compared results with those from routine culture-based surveillance data. PCR data confirmed an absence of ceftriaxone resistance and a low level of azithromycin resistance (0.2%), and that penicillin resistance was \u3c5% in amoxicillin plus azithromycin regions. Rates of ciprofloxacin resistance and penicillinase-producing N. gonorrhoeae were lower when molecular methods were used. Molecular methods to detect N. gonorrhoeae AMR can increase the evidence base for treatment guidelines, particularly in settings where culture-based surveillance is limited

DAS synthetic dataset

Deliverable D1.3 of the ACT DigiMon project is a synthetic microseismic distributed acoustic sensins (DAS) dataset. There are a number of possible uses for such a dataset; for example supporting the development and testing of DAS processing algorithms, testing the efficacy of different array geometries in detecting and characterising events, or simulating a field experiment to better understand observed processes. Given the large number of possible uses it was decided that rather than simply delivering a collection of files of synthetic seismic events, it would be more valuable to deliver a modelling framework from which synthetic data can be generated as the need arises, combined with a small example dataset of a few events to demonstrate the capabilities. DAS systems record seismic wavefields and ground motion due to their sensitivity to strain along the axis of the fibre. To understand the response of DAS it is necessary to understand (1) the seismic source, (2) the path effects and (3) the site and instrument effects. In this report we discuss the modelling of the first two contributions of the DAS response; the source and path effects. We simulate the resulting particle motion and strain at the fibre location, resulting from realistic microseismic sources in geological models representative of the North Sea. The third contribution; site and instrument effects, is contained in the transfer function, which describes the mathematical relationship between the wavefield properties at the cable location to the recorded DAS output. The form of the transfer function is a key unanswered question which will be addressed in Task 1.2 of the DigiMon project

Extreme Dysbiosis of the Microbiome in Critical Illness.

Critical illness is hypothesized to associate with loss of "health-promoting" commensal microbes and overgrowth of pathogenic bacteria (dysbiosis). This dysbiosis is believed to increase susceptibility to nosocomial infections, sepsis, and organ failure. A trial with prospective monitoring of the intensive care unit (ICU) patient microbiome using culture-independent techniques to confirm and characterize this dysbiosis is thus urgently needed. Characterizing ICU patient microbiome changes may provide first steps toward the development of diagnostic and therapeutic interventions using microbiome signatures. To characterize the ICU patient microbiome, we collected fecal, oral, and skin samples from 115 mixed ICU patients across four centers in the United States and Canada. Samples were collected at two time points: within 48 h of ICU admission, and at ICU discharge or on ICU day 10. Sample collection and processing were performed according to Earth Microbiome Project protocols. We applied SourceTracker to assess the source composition of ICU patient samples by using Qiita, including samples from the American Gut Project (AGP), mammalian corpse decomposition samples, childhood (Global Gut study), and house surfaces. Our results demonstrate that critical illness leads to significant and rapid dysbiosis. Many taxons significantly depleted from ICU patients versus AGP healthy controls are key "health-promoting" organisms, and overgrowth of known pathogens was frequent. Source compositions of ICU patient samples are largely uncharacteristic of the expected community type. Between time points and within a patient, the source composition changed dramatically. Our initial results show great promise for microbiome signatures as diagnostic markers and guides to therapeutic interventions in the ICU to repopulate the normal, "health-promoting" microbiome and thereby improve patient outcomes. IMPORTANCE Critical illness may be associated with the loss of normal, "health promoting" bacteria, allowing overgrowth of disease-promoting pathogenic bacteria (dysbiosis), which, in turn, makes patients susceptible to hospital-acquired infections, sepsis, and organ failure. This has significant world health implications, because sepsis is becoming a leading cause of death worldwide, and hospital-acquired infections contribute to significant illness and increased costs. Thus, a trial that monitors the ICU patient microbiome to confirm and characterize this hypothesis is urgently needed. Our study analyzed the microbiomes of 115 critically ill subjects and demonstrated rapid dysbiosis from unexpected environmental sources after ICU admission. These data may provide the first steps toward defining targeted therapies that correct potentially "illness-promoting" dysbiosis with probiotics or with targeted, multimicrobe synthetic "stool pills" that restore a healthy microbiome in the ICU setting to improve patient outcomes

Biomass Derived, Hierarchically Porous, Activated Starbons® as Adsorbents for Volatile Organic Compounds

The use of potassium hydroxide activated Starbons® derived from starch and alginic acid as adsorbents for 29 volatile organic compounds (VOCs) was investigated. In every case, the alginic acid derived Starbon (A800K2) was found to be the optimal adsorbent, significantly outperforming both commercial activated carbon and starch derived, activated Starbon (S800K2). The saturated adsorption capacity of A800K2 depends on both the size of the VOC and the functional groups it contains. The highest saturated adsorption capacities were obtained with small VOCs. For VOC's of similar size, the presence of polarizable electrons in lone pairs or π-bonds within non-polar VOCs was beneficial. Analysis of porosimetry data suggests that the VOC's are being adsorbed within the pore structure of A800K2 rather than just on its surface. The adsorption was completely reversible by thermal treatment of the saturated Starbon under vacuum

Management of Gastroschisis: Results From the NETS2G Study, a Joint British, Irish, and Canadian Prospective Cohort Study of 1268 Infants.

OBJECTIVE: In infants with gastroschisis, outcomes were compared between those where operative reduction and fascial closure were attempted ?24?hours of age (PC), and those who underwent planned closure of their defect >24?hours of age following reduction with a pre-formed silo (SR). SUMMARY OF BACKGROUND DATA: Inadequate evidence exists to determine how best to treat infants with gastroschisis. METHODS: A secondary analysis was conducted of data collected 2006-2008 using the British Association of Pediatric Surgeons Congenital Anomalies Surveillance System, and 2005-2016 using the Canadian Pediatric Surgery Network.28-day outcomes were compared between infants undergoing PC and SR. Primary outcome was number of gastrointestinal complications. Interactions were investigated between infant characteristics and treatment to determine whether intervention effect varied in sub-groups of infants. RESULTS: Data from 341 British and Irish infants (27%) and 927 Canadian infants (73%) were used. 671 infants (42%) underwent PC and 597 (37%) underwent SR. The effect of SR on outcome varied according to the presence/absence of intestinal perforation, intestinal matting and intestinal necrosis. In infants without these features, SR was associated with fewer gastrointestinal complications [aIRR 0.25 (95% CI 0.09-0.67, P = 0.006)], more operations [aIRR 1.40 (95% CI 1.22-1.60, P < 0.001)], more days PN [aIRR 1.08 (95% CI 1.03-1.13, P < 0.001)], and a higher infection risk [aOR 2.06 (95% CI 1.10-3.87, P = 0.025)]. In infants with these features, SR was associated with a greater number of operations [aIRR 1.30 (95% CI 1.17-1.45, P < 0.001)], and more days PN [aIRR 1.06 (95% CI 1.02-1.10, P = 0.003)]. CONCLUSIONS: In infants without intestinal perforation, matting, or necrosis, the benefits of SR outweigh its drawbacks. In infants with these features, the opposite is true. Treatment choice should be based upon these features

Comment on: “Peatland carbon stocks and burn history: blanket bog peat core evidence highlights charcoal impacts on peat physical properties and long-term carbon storage,” by A. Heinemeyer, Q. Asena, W.L. Burn and A.L. Jones (Geo: Geography and Environment 2018; e00063)

A recent paper by Heinemeyer et al. (2018) in this journal has suggested that the use of prescribed fire may enhance carbon accumulation in UK upland blanket bogs. We challenge this finding based on a number of concerns with the original manuscript including the lack of an unburned control, insufficient replication, unrecognised potential confounding factors, and potentially large inaccuracies in the core dating approach used to calculate carbon accumulation rates. We argue that burn‐management of peatlands is more likely to lead to carbon loss than carbon gain

Global disparities in SARS-CoV-2 genomic surveillance

Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing intensity and turnaround times on variant detection in 189 countries. In the first two years of the pandemic, 78% of high-income countries sequenced >0.5% of their COVID-19 cases, while 42% of low- and middle-income countries reached that mark. Around 25% of the genomes from high income countries were submitted within 21 days, a pattern observed in 5% of the genomes from low- and middle-income countries. We found that sequencing around 0.5% of the cases, with a turnaround time <21 days, could provide a benchmark for SARS-CoV-2 genomic surveillance. Socioeconomic inequalities undermine the global pandemic preparedness, and efforts must be made to support low- and middle-income countries improve their local sequencing capacity

An Association of Cancer Physicians' strategy for improving services and outcomes for cancer patients.

The Association of Cancer Physicians in the United Kingdom has developed a strategy to improve outcomes for cancer patients and identified the goals and commitments of the Association and its members.The ACP is very grateful to all of its members who have expressed views on the development of the strategy and to the sponsors of our workshops and publications, especially Cancer Research UK and Macmillan Cancer SupportThis is the final version of the article. It was first available from Cancer Intelligence via http://dx.doi.org/10.3332/ecancer.2016.60