A systematic review of interventions by healthcare professionals to improve management of non-communicable diseases and communicable diseases requiring long-term care in adults who are homeless

Objective: Identify, describe and appraise trials of interventions delivered by healthcare professionals to manage non-communicable diseases (NCDs) and communicable diseases that require long-term care or treatment (LT-CDs), excluding mental health and substance use disorders, in homeless adults. Design: Systematic review of randomised controlled trials (RCTs), non-RCTs and controlled before–after studies. Interventions characterised using Effective Practice and Organisation of Care (EPOC) taxonomy. Quality assessed using EPOC risk of bias criteria. Data sources: Database searches (MEDLINE, Embase, PsycINFO, Scopus, Cumulative Index to Nursing and Allied Health Literature (CINAHL), Applied Social Sciences Index and Abstracts (ASSIA) and Cochrane Central Register of Controlled Trials), hand searching reference lists, citation searches, grey literature and contact with study authors. Setting: Community. Participants: Adults (≥18 years) fulfilling European Typology of Homelessness criteria. Intervention: Delivered by healthcare professionals managing NCD and LT-CDs. Outcomes: Primary outcome: unscheduled healthcare utilisation. Secondary outcomes: mortality, biological markers of disease control, adherence to treatment, engagement in care, patient satisfaction, knowledge, self-efficacy, quality of life and cost-effectiveness. Results: 11 studies were included (8 RCTs, 2 quasi-experimental and 1 feasibility) involving 9–520 participants (67%–94% male, median age 37–49 years). Ten from USA and one from UK. Studies included various NCDs (n=3); or focused on latent tuberculosis (n=4); HIV (n=2); hepatitis C (n=1) or type 2 diabetes (n=1). All interventions were complex with multiple components. Four described theories underpinning intervention. Three assessed unscheduled healthcare utilisation: none showed consistent reduction in hospitalisation or emergency department attendance. Six assessed adherence to specific treatments, of which four showed improved adherence to latent tuberculosis therapy. Three concerned education case management, all of which improved disease-specific knowledge. No improvements in biological markers of disease (two studies) and none assessed mortality. Conclusions: Evidence for management of NCD and LT-CDs in homeless adults is sparse. Educational case-management interventions may improve knowledge and medication adherence. Large trials of theory-based interventions are needed, assessing healthcare utilisation and outcomes as well as assessment of biological outcomes and cost-effectiveness

Interventions by healthcare professionals to improve management of physical long-term conditions in adults who are homeless: a systematic review protocol

Introduction People experiencing homelessness are at increased risk of, and have poorer outcomes from, a range of physical long-term conditions (LTCs). It is increasingly recognised that interventions targeting people who are homeless should be tailored to the specific needs of this population. This systematic review aims to identify, describe and appraise trials of interventions that aim to manage physical LTCs in homeless adults and are delivered by healthcare professionals. Methods and analysis Seven electronic databases (Medline, EMBASE, Cochrane Central Register of Controlled Trials, Assia, Scopus, PsycINFO and CINAHL) will be searched from 1960 (or inception) to October 2016 and supplemented by forward citation searching, handsearching of reference lists and searching grey literature. Two reviewers will independently review titles, abstract and full-texts using DistillerSR software. Inclusion criteria include (1) homeless adults with any physical LTC, (2) interventions delivered by a healthcare professional (any professional trained to provide any form of healthcare, but excluding social workers and professionals without health-related training), (3) comparison with usual care or an alternative intervention, (4) report outcomes such as healthcare usage, physical and psychological health or well-being or cost-effectiveness, (5) randomised controlled trials, non-randomised controlled trials, controlled before-after studies. Quality will be assessed using the Cochrane EPOC Risk of Bias Tool. A meta-analysis will be performed if sufficient data are identified; however, we anticipate a narrative synthesis will be performed. Ethics and dissemination This review will synthesise existing evidence for interventions delivered by healthcare professionals to manage physical LTCs in adults who are homeless. The findings will inform the development of future interventions and research aiming to improve the management of LTCs for people experiencing homelessness. Ethical approval will not be required for this systematic review as it does not contain individual patient data. We will disseminate the results of this systematic review via conference presentations, healthcare professional networks, social media and peer-reviewed publication

Sequence verification of synthetic DNA by assembly of sequencing reads

Gene synthesis attempts to assemble user-defined DNA sequences with base-level precision. Verifying the sequences of construction intermediates and the final product of a gene synthesis project is a critical part of the workflow, yet one that has received the least attention. Sequence validation is equally important for other kinds of curated clone collections. Ensuring that the physical sequence of a clone matches its published sequence is a common quality control step performed at least once over the course of a research project. GenoREAD is a web-based application that breaks the sequence verification process into two steps: the assembly of sequencing reads and the alignment of the resulting contig with a reference sequence. GenoREAD can determine if a clone matches its reference sequence. Its sophisticated reporting features help identify and troubleshoot problems that arise during the sequence verification process. GenoREAD has been experimentally validated on thousands of gene-sized constructs from an ORFeome project, and on longer sequences including whole plasmids and synthetic chromosomes. Comparing GenoREAD results with those from manual analysis of the sequencing data demonstrates that GenoREAD tends to be conservative in its diagnostic. GenoREAD is available at www.genoread.or

Ice nucleating particles carried from below a phytoplankton bloom to the arctic atmosphere

Author Posting. © American Geophysical Union, 2019. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 46(14), (2019): 8572-8581, doi: 10.1029/2019GL083039.As Arctic temperatures rise at twice the global rate, sea ice is diminishing more quickly than models can predict. Processes that dictate Arctic cloud formation and impacts on the atmospheric energy budget are poorly understood, yet crucial for evaluating the rapidly changing Arctic. In parallel, warmer temperatures afford conditions favorable for productivity of microorganisms that can effectively serve as ice nucleating particles (INPs). Yet the sources of marine biologically derived INPs remain largely unknown due to limited observations. Here we show, for the first time, how biologically derived INPs were likely transported hundreds of kilometers from deep Bering Strait waters and upwelled to the Arctic Ocean surface to become airborne, a process dependent upon a summertime phytoplankton bloom, bacterial respiration, ocean dynamics, and wind‐driven mixing. Given projected enhancement in marine productivity, combined oceanic and atmospheric transport mechanisms may play a crucial role in provision of INPs from blooms to the Arctic atmosphere.We sincerely thank the U.S. Coast Guard and crew of the Healy for assistance with equipment installation and guidance, operation of the underway and CTD systems, and general operation of the vessel during transit and at targeted sampling stations. We would also like to thank Allan Bertram, Meng Si, Victoria Irish, and Benjamin Murray for providing INP data from their previous studies. J. M. C., R. P., P. L., L. T., and E. B. were funded by the National Oceanic and Atmospheric Administration (NOAA)’s Arctic Research Program. J. C. was supported by the NOAA Experiential Research & Training Opportunities (NERTO) program. T. A. and N. C. were supported through the NOAA Earnest F. Hollings Scholarship program. A. P. was funded by the National Science Foundation under Grant PLR‐1303617. Russel C. Schnell and Michael Spall are acknowledged for insightful discussions during data analysis and interpretation. There are no financial conflicts of interest for any author. INP data are available in the supporting information, while remaining DBO‐NCIS data presented in the manuscript are available online (at https://www2.whoi.edu/site/dboncis/).2020-01-1

Coordinated Sampling of Microorganisms Over Freshwater and Saltwater Environments Using an Unmanned Surface Vehicle (USV) and a Small Unmanned Aircraft System (sUAS)

Biological aerosols (bioaerosols) are ubiquitous in terrestrial and aquatic environments and may influence cloud formation and precipitation processes. Little is known about the aerosolization and transport of bioaerosols from aquatic environments. We designed and deployed a bioaerosol-sampling system onboard an unmanned surface vehicle (USV; a remotely operated boat) to collect microbes and monitor particle sizes in the atmosphere above a salt pond in Falmouth, MA, United States and a freshwater lake in Dublin, VA, United States. The bioaerosol-sampling system included a series of 3D-printed impingers, two different optical particle counters, and a weather station. A small unmanned aircraft system (sUAS; a remotely operated airplane) was used in a coordinated effort with the USV to collect microorganisms on agar media 50 m above the surface of the water. Samples from the USV and sUAS were cultured on selective media to estimate concentrations of culturable microorganisms (bacteria and fungi). Concentrations of microbes from the sUAS ranged from 6 to 9 CFU/m3 over saltwater, and 12 to 16 CFU/m3 over freshwater (over 10-min sampling intervals) at 50 m above ground level (AGL). Concentrations from the USV ranged from 0 (LOD) to 42,411 CFU/m3 over saltwater, and 0 (LOD) to 56,809 CFU/m3 over freshwater (over 30-min sampling intervals) in air near the water surface. Particle concentrations recorded onboard the USV ranged from 0 (LOD) to 288 μg/m3 for PM1, 1 to 290 μg/m3 for PM2.5, and 1 to 290 μg/m3 for PM10. A general trend of increasing concentration with an increase in particle size was recorded by each sensor. Through laboratory testing, the collection efficiency of the 3D-printed impingers was determined to be 75% for 1 μm beads and 99% for 3 μm beads. Additional laboratory tests were conducted to determine the accuracy of the miniaturized optical particle counters used onboard the USV. Future work aims to understand the distribution of bioaerosols above aquatic environments and their potential association with cloud formation and precipitation processes

Infection and genotype remodel the entire soybean transcriptome

<p>Abstract</p> <p>Background</p> <p>High throughput methods, such as high density oligonucleotide microarray measurements of mRNA levels, are popular and critical to genome scale analysis and systems biology. However understanding the results of these analyses and in particular understanding the very wide range of levels of transcriptional changes observed is still a significant challenge. Many researchers still use an arbitrary cut off such as two-fold in order to identify changes that may be biologically significant. We have used a very large-scale microarray experiment involving 72 biological replicates to analyze the response of soybean plants to infection by the pathogen <it>Phytophthora sojae </it>and to analyze transcriptional modulation as a result of genotypic variation.</p> <p>Results</p> <p>With the unprecedented level of statistical sensitivity provided by the high degree of replication, we show unambiguously that almost the entire plant genome (97 to 99% of all detectable genes) undergoes transcriptional modulation in response to infection and genetic variation. The majority of the transcriptional differences are less than two-fold in magnitude. We show that low amplitude modulation of gene expression (less than two-fold changes) is highly statistically significant and consistent across biological replicates, even for modulations of less than 20%. Our results are consistent through two different normalization methods and two different statistical analysis procedures.</p> <p>Conclusion</p> <p>Our findings demonstrate that the entire plant genome undergoes transcriptional modulation in response to infection and genetic variation. The pervasive low-magnitude remodeling of the transcriptome may be an integral component of physiological adaptation in soybean, and in all eukaryotes.</p

Sequence verification of synthetic DNA by assembly of sequencing reads

Gene synthesis attempts to assemble user-defined DNA sequences with base-level precision. Verifying the sequences of construction intermediates and the final product of a gene synthesis project is a critical part of the workflow, yet one that has received the least attention. Sequence validation is equally important for other kinds of curated clone collections. Ensuring that the physical sequence of a clone matches its published sequence is a common quality control step performed at least once over the course of a research project. GenoREAD is a web-based application that breaks the sequence verification process into two steps: the assembly of sequencing reads and the alignment of the resulting contig with a reference sequence. GenoREAD can determine if a clone matches its reference sequence. Its sophisticated reporting features help identify and troubleshoot problems that arise during the sequence verification process. GenoREAD has been experimentally validated on thousands of gene-sized constructs from an ORFeome project, and on longer sequences including whole plasmids and synthetic chromosomes. Comparing GenoREAD results with those from manual analysis of the sequencing data demonstrates that GenoREAD tends to be conservative in its diagnostic. GenoREAD is available at www.genoread.org.This is the publisher’s final pdf. The published article is copyrighted by Oxford University Press and can be found at: http://www.oxfordjournals.org/Keywords: Bioinformatics, Gene synthesis, Genome, Retrieval, Biology, Alignmen

Drone-based Water Sampling and Characterization of Three Freshwater Harmful Algal Blooms in the United States

Freshwater harmful algal blooms (HABs), caused mostly by toxic cyanobacteria, produce a range of cyanotoxins that threaten the health of humans and domestic animals. Climate conditions and anthropogenic influences such as agricultural run-off can alter the onset and intensity of HABs. Little is known about the distribution and spread of freshwater HABs. Current sampling protocols in some lakes involve teams of researchers that collect samples by hand from a boat and/or from the shoreline. Water samples can be collected from the surface, from discrete-depth collections, and/or from depth-integrated intervals. These collections are often restricted to certain months of the year, and generally are only performed at a limited number of collection sites. In lakes with active HABs, surface samples are generally sufficient for HAB water quality assessments. We used a unique DrOne Water Sampling SystEm (DOWSE) to collect water samples from the surface of three different HABs in Ohio (Grand Lake St Marys, GLSM and Lake Erie) and Virginia (Lake Anna), United States in 2019. The DOWSE consisted of a 3D-printed sampling device tethered to a drone (uncrewed aerial system, or UAS), and was used to collect surface water samples at different distances (10–100 m) from the shore or from an anchored boat. One hundred and eighty water samples (40 at GLSM, 20 at Lake Erie, and 120 at Lake Anna) were collected and analyzed from 18 drone flights. Our methods included testing for cyanotoxins, phycocyanin, and nutrients from surface water samples. Mean concentrations of microcystins (MCs) in drone water samples were 15.00, 1.92, and 0.02 ppb for GLSM, Lake Erie, and Lake Anna, respectively. Lake Anna had low levels of anatoxin in nearly all (111/120) of the drone water samples. Mean concentrations of phycocyanin in drone water samples were 687, 38, and 62 ppb for GLSM, Lake Erie, and Lake Anna, respectively. High levels of total phosphorus were observed in the drone water samples from GLSM (mean of 0.34 mg/L) and Lake Erie (mean of 0.12 mg/L). Lake Anna had the highest variability of total phosphorus with concentrations that ranged from 0.01 mg/L to 0.21 mg/L, with a mean of 0.06 mg/L. Nitrate levels varied greatly across sites, inverse with bloom biomass, ranging from below detection to 3.64 mg/L, with highest mean values in Lake Erie followed by GLSM and Lake Anna, respectively. Drones offer a rapid, targeted collection of water samples from virtually anywhere on a lake with an active HAB without the need for a boat which can disturb the surrounding water. Drones are, however, limited in their ability to operate during inclement weather such as rain and heavy winds. Collectively, our results highlight numerous opportunities for drone-based water sampling technologies to track, predict, and respond to HABs in the future

Sequence verification of synthetic DNA by assembly of sequencing reads

This is the publisher’s final pdf. The published article is copyrighted by Oxford University Press and can be found at: http://www.oxfordjournals.org/Gene synthesis attempts to assemble user-defined DNA sequences with base-level precision. Verifying the sequences of construction intermediates and the final product of a gene synthesis project is a critical part of the workflow, yet one that has received the least attention. Sequence validation is equally important for other kinds of curated clone collections. Ensuring that the physical sequence of a clone matches its published sequence is a common quality control step performed at least once over the course of a research project. GenoREAD is a web-based application that breaks the sequence verification process into two steps: the assembly of sequencing reads and the alignment of the resulting contig with a reference sequence. GenoREAD can determine if a clone matches its reference sequence. Its sophisticated reporting features help identify and troubleshoot problems that arise during the sequence verification process. GenoREAD has been experimentally validated on thousands of gene-sized constructs from an ORFeome project, and on longer sequences including whole plasmids and synthetic chromosomes. Comparing GenoREAD results with those from manual analysis of the sequencing data demonstrates that GenoREAD tends to be conservative in its diagnostic. GenoREAD is available at www.genoread.org