23 research outputs found
Bilateral intralobar pulmonary sequestration : a case report
Bronchopulmonary sequestration is a congenital lung malformation consisting of a non-functioning lung segment. Arterial supply to such a segment is found to be systemic rather than pulmonary, and by definition there is no communication with the tracheobronchial tree. It accounts for about 6% of all congenital pulmonary malformations. Bilateral bronchopulmonary sequestration is yet more uncommon. These malformations can be classified as either intralobar sequestration (the commoner type), or extralobar sequestration (in 14- 25%).peer-reviewe
Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis
BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London
The khmer software package: enabling efficient nucleotide sequence analysis
The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/
The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations]
The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/
Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study
Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world.
Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231.
Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001).
Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication
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Genomics of Antarctic Cyanobacteria from Lakes Fryxell and Vanda: Sulfide Tolerant Oxygenic Photosynthesis, Implications of Polar Light Cycles, and Biogeography with Large-Scale k-mer Searching
Antarctic cyanobacteria form microbial mats in perennially ice-covered lakes in the McMurdo Dry Valleys, Antarctica. These mats demonstrate a variety of ecological and metabolic behaviors consistent with Antarctic conditions as well as specific challenges between and within the lakes. In this thesis, I explore the survival of cyanobacteria in Antarctic conditions focusing on sulfide stress, polar light availability, and their biogeographical distribution in other environments.In Lake Fryxell, Antarctica, the benthic, filamentous cyanobacterium Phormidium pseudopriestleyi creates a 1-2 mm thick layer of 50 µmol L-1 O2 in otherwise sulfidic water, demonstrating that it sustains oxygenic photosynthesis in the presence of sulfide. Sulfide inhibits oxygenic photosynthesis by blocking electron transfer between H2O and the oxygen-evolving complex in the D1 protein of Photosystem II. The ability of cyanobacteria to counter this effect has implications for understanding the productivity of benthic microbial mats in sulfidic environments throughout Earth history. A metagenome-assembled genome (MAG) of P. pseudopriestleyi indicates a genetic capacity for oxygenic photosynthesis, including multiple copies of psbA (encoding the D1 protein of Photosystem II), and anoxygenic photosynthesis with a copy of sqr (encoding the sulfide quinone reductase protein that oxidizes sulfide). The genomic content of P. pseudopriestleyi is consistent with sulfide tolerance mechanisms including increasing psbA expression or directly oxidizing sulfide with sulfide quinone reductase. However, it is unknown whether the organism can perform anoxygenic photosynthesis using sqr and PS I while PS II is sulfide-inhibited.
The seasonal light availability of polar environments has implications for the functioning of circadian clocks in Antarctic cyanobacteria. However, polar cyanobacteria are underrepresented in available genomic data, limiting opportunities to study their genetic adaptations to this and other polar challenges. Chapter 2 presents four new Antarctic cyanobacteria MAGs, bringing the total number of polar MAGs and genomes to ten. These new cyanobacteria are from microbial mats in Lake Vanda located in the McMurdo Dry Valleys in Antarctica. The four MAGs were taxonomically categorized as a Leptolyngyba, Pseudanabaena, Microcoleus, and Neosynechococcus. The sizes of these MAGs range from 2.76 Mpb – 6.07 Mbp and the bin completion ranges from 74.2% – 92.57%. Furthermore, the four novel cyanobacteria have ANIs below 90% with each other and below 77% with existing polar cyanobacteria MAGs and genomes, which demonstrates genomic diversity among polar cyanobacteria genomes. Analysis of the gene content of all ten polar cyanobacteria demonstrates that they have metabolic capacity for photosynthesis and various cold tolerance mechanisms. Standard circadian rhythm genes are present in the majority of cyanobacteria studied with the Leptolyngbya and Neosynechococcus containing kaiB3, a divergent homolog of kaiB.
Although some work has been done on the biogeography of cyanobacteria within Antarctica, the global distribution of polar cyanobacteria is not well understood. It is not known if polar cyanobacteria are specialists of their environments or opportunists that tolerate survival in the cryosphere. These questions can be addressed by identifying the distribution of Antarctic cyanobacteria across global locations, but this is logistically complicated to do using 16S amplicon sequences, which is standard for biogeography studies. However, novel sourmash MAGsearch software based on large-scale k-mer searching allows for MAGs of interest to be identified in publicly available metagenomic data. Chapter 3 used five Antarctic cyanobacteria MAGs from Lake Vanda (Microcoleus, Neosynechococcus, Leptolyngbya, and Pseudanabaena) and Lake Fryxell (P. pseudopriestleyi), as search queries. The sourmash MAGsearch revealed that the Microcoleus MAG was widely dispersed in a variety of environmental conditions, the P. pseudopriestleyi MAG was present in harsh environments, and the Neosynechococcus, Leptolyngbya, and Pseudanabaena MAGs were present in polar and a few non-polar environments. The search technique can be used to search for any organism present in metagenomes and has exciting implications for future biogeography studies
Draft genome of tule elk Cervus canadensis nannodes [version 2; referees: 2 approved]
This paper presents the first draft genome of the tule elk (Cervus elaphus nannodes), a subspecies native to California that underwent an extreme genetic bottleneck in the late 1800s. The genome was generated from Illumina HiSeq 3000 whole genome sequencing of four individuals, resulting in the assembly of 2.395 billion base pairs (Gbp) over 602,862 contigs over 500 bp and N50 = 6,885 bp. This genome provides a resource to facilitate future genomic research on elk and other cervids
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Draft genome of tule elk Cervus canadensis nannodes.
This paper presents the first draft genome of the tule elk ( Cervus elaphus nannodes), a subspecies native to California that underwent an extreme genetic bottleneck in the late 1800s. The genome was generated from Illumina HiSeq 3000 whole genome sequencing of four individuals, resulting in the assembly of 2.395 billion base pairs (Gbp) over 602,862 contigs over 500 bp and N50 = 6,885 bp. This genome provides a resource to facilitate future genomic research on elk and other cervids
Structural Chemistry and Properties of Metal Oxalates Containing a Long-Spanning Dipyridyl Ligand: Chain, Interpenetrated Diamondoid, Threaded-Loop Layer, and Self-Penetrated Topologies
Hydrothermal reaction of metal oxalate
(ox) salts and bis(4-pyridylmethyl)piperazine
(bpmp) afforded a series of coordination polymers that were structurally
characterized by single-crystal X-ray diffraction. {[Cd(H<sub>2</sub>O)<sub>4</sub>(bpmp)](ox)}<sub><i>n</i></sub> (<b>1</b>) and {[Co(H<sub>2</sub>O)<sub>4</sub>(bpmp)](ox)}<sub><i>n</i></sub> (<b>2</b>) show isostructural cationic one-dimensional
(1D) coordination polymer chain motifs with unligated ox anions. A
higher temperature polymorph of <b>2</b>, {[Co(ox)(bpmp)]·3H<sub>2</sub>O}<sub><i>n</i></sub> (<b>3</b>), possesses
a system of threefold interpenetrated three-dimensional (3D) diamondoid
nets. {[Mn(H<sub>2</sub>O)<sub>4</sub>(bpmp)] [Mn<sub>2</sub>(ox)<sub>3</sub>]·5H<sub>2</sub>O}<sub><i>n</i></sub> (<b>4</b>) manifests a unique 1D + 2D → 3D polyrotaxane coordination
polymer structure with 1D cationic [Mn(H<sub>2</sub>O)<sub>4</sub>(bpmp)]<sub><i>n</i></sub> chains threaded through apertures
coursing through parallel stacks of anionic [Mn<sub>2</sub>(ox)<sub>3</sub>]<sub><i>n</i></sub> two-dimensional (2D) hexagonal
layers. {[Cu<sub>2</sub>(ox)<sub>2</sub>(bpmp)]·6H<sub>2</sub>O}<sub><i>n</i></sub> (<b>5</b>) possesses 2D [Cu<sub>2</sub>(ox)<sub>2</sub>]<sub><i>n</i></sub> layers pillared
by bpmp ligands into a 3D [Cu<sub>2</sub>(ox)<sub>2</sub>(bpmp)]<sub><i>n</i></sub> coordination polymer network with an unprecedented
4,4-connected self-penetrated (5<sup>3</sup>8<sup>3</sup>)<sub>2</sub>(5<sup>4</sup>8<sup>2</sup>) topology. Variable temperature magnetic
susceptibility studies showed weak antiferromagnetic coupling along
[Co(ox)]<sub><i>n</i></sub> chain submotifs in <b>3</b> with concomitant zero-field splitting (<i>J</i> = −4.1(7)
cm<sup>–1</sup>, <i>D</i> = 34.5(6) cm<sup>–1</sup>), weak antiferromagnetic coupling within the [Mn<sub>2</sub>(ox)<sub>3</sub>]<sub><i>n</i></sub> hexagonal layers in <b>4</b> (<i>J</i> ∼ −0.5 cm<sup>–1</sup>),
and strong antiferromagnetic coupling within the 2D [Cu<sub>2</sub>(ox)<sub>2</sub>]<sub><i>n</i></sub> layers in <b>5</b> (<i>J</i> = −220(6) cm<sup>–1</sup>)