The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies.

Viral metagenomics has fuelled a rapid change in our understanding of global viral diversity and ecology. Long-read sequencing and hybrid assembly approaches that combine long- and short-read technologies are now being widely implemented in bacterial genomics and metagenomics. However, the use of long-read sequencing to investigate viral communities is still in its infancy. While Nanopore and PacBio technologies have been applied to viral metagenomics, it is not known to what extent different technologies will impact the reconstruction of the viral community. Thus, we constructed a mock bacteriophage community of previously sequenced phage genomes and sequenced them using Illumina, Nanopore and PacBio sequencing technologies and tested a number of different assembly approaches. When using a single sequencing technology, Illumina assemblies were the best at recovering phage genomes. Nanopore- and PacBio-only assemblies performed poorly in comparison to Illumina in both genome recovery and error rates, which both varied with the assembler used. The best Nanopore assembly had errors that manifested as SNPs and INDELs at frequencies 41 and 157 % higher than found in Illumina only assemblies, respectively. While the best PacBio assemblies had SNPs at frequencies 12 and 78 % higher than found in Illumina-only assemblies, respectively. Despite high-read coverage, long-read-only assemblies recovered a maximum of one complete genome from any assembly, unless reads were down-sampled prior to assembly. Overall the best approach was assembly by a combination of Illumina and Nanopore reads, which reduced error rates to levels comparable with short-read-only assemblies. When using a single technology, Illumina only was the best approach. The differences in genome recovery and error rates between technology and assembler had downstream impacts on gene prediction, viral prediction, and subsequent estimates of diversity within a sample. These findings will provide a starting point for others in the choice of reads and assembly algorithms for the analysis of viromes.

Biomarkers of chronic kidney disease-mineral bone disorder (CKD-MBD) in the diabetic foot: A medical record review.

AIMS: Determine the prevalence and relative risk of having single and combinations of biomarkers of chronic kidney disease-mineral bone disorder (CKD-MBD) syndrome in the diabetic foot from an electronic medical record (EMR) review. METHODS: Review of 152 patients with one foot radiograph and diagnoses of both diabetes mellitus (DM) and chronic kidney disease (CKD) stages 1-5. Presence/absence of peripheral neuropathy (PN), targeted serum markers, and both pedal vessel calcification (PVC) and buckling ratio (BR) of 2nd and 5th metatarsals from radiographs were recorded. Prevalence of single and combinations of foot biomarkers are reported as count and percentage. Risk ratios (RR) with 95% confidence intervals (95% CI) were calculated to assess risk of foot biomarkers in each stage of CKD-MBD. RESULTS: Prevalence and RR of PVC, PN, and BR ≥ 3.5 biomarkers, both single and in combination, all increase with progression of CKD. The RR increases to 9.6 (95 % CI: 3, 26; p < 0.001) when all 3 biomarkers present in stage 5. CONCLUSIONS: PVC, PN, and BR ≥ 3.5 are prognostic biomarkers of CKD-MBD syndrome in the diabetic foot. Recognition of these foot biomarkers may allow earlier interventions to help reduce nontraumatic lower extremity amputation in individuals with diabetic CKD-MBD.

Multiscale anisotropy analysis of second-harmonic generation collagen imaging of human pancreatic cancer.

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers with a minority (< 10%) of patients surviving five years past diagnosis. This could be improved with the development of new imaging modalities for early differentiation of benign and cancerous fibrosis. This study intends to explore the application of a two-photon microscopy technique known as second harmonic generation to PDAC using the 2D Wavelet Transform Modulus Maxima (WTMM) Anisotropy method to quantify collagen organization in fibrotic pancreatic tissue. Forty slides from PDAC patients were obtained and eight images were captured per each tissue category on each slide. Brownian surface motion and white noise images were generated for calibration and testing of a new variable binning approach to the 2D WTMM Anisotropy method. The variable binning method had greater resistance to wavelet scaling effects and white noise images were found to have the lowest anisotropy factor. Cancer and fibrosis had greater anisotropy factors (Fa) at small wavelet scales than normal and normal adjacent tissue. At a larger scale of 21 µm this relationship changed with normal tissue having a higher Fa than all other tissue groups. White noise is the best representative image for isotropy and the 2D WTMM anisotropy method is sensitive to changes induced in collagen by PDAC.

Antimicrobial resistance in dairy slurry tanks: A critical point for measurement and control.

Waste from dairy production is one of the largest sources of contamination from antimicrobial resistant bacteria (ARB) and genes (ARGs) in many parts of the world. However, studies to date do not provide necessary evidence to inform antimicrobial resistance (AMR) countermeasures. We undertook a detailed, interdisciplinary, longitudinal analysis of dairy slurry waste. The slurry contained a population of ARB and ARGs, with resistances to current, historical and never-used on-farm antibiotics; resistances were associated with Gram-negative and Gram-positive bacteria and mobile elements (ISEcp1, Tn916, Tn21-family transposons). Modelling and experimental work suggested that these populations are in dynamic equilibrium, with microbial death balanced by fresh input. Consequently, storing slurry without further waste input for at least 60 days was predicted to reduce ARB spread onto land, with > 99 % reduction in cephalosporin resistant Escherichia coli. The model also indicated that for farms with low antibiotic use, further reductions are unlikely to reduce AMR further. We conclude that the slurry tank is a critical point for measurement and control of AMR, and that actions to limit the spread of AMR from dairy waste should combine responsible antibiotic use, including low total quantity, avoidance of human critical antibiotics, and choosing antibiotics with shorter half-lives, coupled with appropriate slurry storage.

Chemistry beyond the Hartree-Fock energy via quantum computed moments.

Quantum computers hold promise to circumvent the limitations of conventional computing for difficult molecular problems. However, the accumulation of quantum logic errors on real devices represents a major challenge, particularly in the pursuit of chemical accuracy requiring the inclusion of electronic correlation effects. In this work we implement the quantum computed moments (QCM) approach for hydrogen chain molecular systems up to H[Formula: see text]. On a superconducting quantum processor, Hamiltonian moments, [Formula: see text] are computed with respect to the Hartree-Fock state, which are then employed in Lanczos expansion theory to determine an estimate for the ground-state energy which incorporates electronic correlations and manifestly improves on the direct energy measurement. Post-processing purification of the raw QCM data takes the estimate below the Hartree-Fock energy to within 99.9% of the exact electronic ground-state energy for the largest system studied, H[Formula: see text]. Calculated dissociation curves indicate precision at about 10mH for this system and as low as 0.1mH for molecular hydrogen, H[Formula: see text], over a range of bond lengths. In the context of stringent precision requirements for chemical problems, these results provide strong evidence for the error suppression capability of the QCM method, particularly when coupled with post-processing error mitigation. While calculations based on the Hartree-Fock state are tractable to classical computation, these results represent a first step towards implementing the QCM method in a quantum chemical trial circuit. Greater emphasis on more efficient representations of the Hamiltonian and classical preprocessing steps may enable the solution of larger systems on near-term quantum processors.

Outlook for Implementation of Genomics-Based Selection in Public Cotton Breeding Programs.

Researchers have used quantitative genetics to map cotton fiber quality and agronomic performance loci, but many alleles may be population or environment-specific, limiting their usefulness in a pedigree selection, inbreeding-based system. Here, we utilized genotypic and phenotypic data on a panel of 80 important historical Upland cotton (Gossypium hirsutum L.) lines to investigate the potential for genomics-based selection within a cotton breeding program's relatively closed gene pool. We performed a genome-wide association study (GWAS) to identify alleles correlated to 20 fiber quality, seed composition, and yield traits and looked for a consistent detection of GWAS hits across 14 individual field trials. We also explored the potential for genomic prediction to capture genotypic variation for these quantitative traits and tested the incorporation of GWAS hits into the prediction model. Overall, we found that genomic selection programs for fiber quality can begin immediately, and the prediction ability for most other traits is lower but commensurate with heritability. Stably detected GWAS hits can improve prediction accuracy, although a significance threshold must be carefully chosen to include a marker as a fixed effect. We place these results in the context of modern public cotton line-breeding and highlight the need for a community-based approach to amass the data and expertise necessary to launch US public-sector cotton breeders into the genomics-based selection era.

Structural Origins of Voltage Hysteresis in the Na-Ion Cathode P2-Na0.67[Mg0.28Mn0.72]O2: A Combined Spectroscopic and Density Functional Theory Study.

P2-layered sodium-ion battery (NIB) cathodes are a promising class of Na-ion electrode materials with high Na+ mobility and relatively high capacities. In this work, we report the structural changes that take place in P2-Na0.67[Mg0.28Mn0.72]O2. Using ex situ X-ray diffraction, Mn K-edge extended X-ray absorption fine structure, and 23Na NMR spectroscopy, we identify the bulk phase changes along the first electrochemical charge-discharge cycle-including the formation of a high-voltage "Z phase", an intergrowth of the OP4 and O2 phases. Our ab initio transition state searches reveal that reversible Mg2+ migration in the Z phase is both kinetically and thermodynamically favorable at high voltages. We propose that Mg2+ migration is a significant contributor to the observed voltage hysteresis in Na0.67[Mg0.28Mn0.72]O2 and identify qualitative changes in the Na+ ion mobility.

Impact of Orientational Glass Formation and Local Strain on Photo-Induced Halide Segregation in Hybrid Metal-Halide Perovskites.

Band gap tuning of hybrid metal-halide perovskites by halide substitution holds promise for tailored light absorption in tandem solar cells and emission in light-emitting diodes. However, the impact of halide substitution on the crystal structure and the fundamental mechanism of photo-induced halide segregation remain open questions. Here, using a combination of temperature-dependent X-ray diffraction and calorimetry measurements, we report the emergence of a disorder- and frustration-driven orientational glass for a wide range of compositions in CH3NH3Pb(Cl x Br1-x )3. Using temperature-dependent photoluminescence measurements, we find a correlation between halide segregation under illumination and local strains from the orientational glass. We observe no glassy behavior in CsPb(Cl x Br1-x )3, highlighting the importance of the A-site cation for the structure and optoelectronic properties. Using first-principles calculations, we identify the local preferential alignment of the organic cations as the glass formation mechanism. Our findings rationalize the superior photostability of mixed-cation metal-halide perovskites and provide guidelines for further stabilization strategies.

Population structure and genetic diversity of the Pee Dee cotton breeding program.

Accelerated marker-assisted selection and genomic selection breeding systems require genotyping data to select the best parents for combining beneficial traits. Since 1935, the Pee Dee (PD) cotton germplasm enhancement program has developed an important genetic resource for upland cotton (Gossypium hirsutum L.), contributing alleles for improved fiber quality, agronomic performance, and genetic diversity. To date, a detailed genetic survey of the program's eight historical breeding cycles has yet to be undertaken. The objectives of this study were to evaluate genetic diversity across and within-breeding groups, examine population structure, and contextualize these findings relative to the global upland cotton gene pool. The CottonSNP63K array was used to identify 17,441 polymorphic markers in a panel of 114 diverse PD genotypes. A subset of 4597 markers was selected to decrease marker density bias. Identity-by-state pairwise distance varied substantially, ranging from 0.55 to 0.97. Pedigree-based estimates of relatedness were not very predictive of observed genetic similarities. Few rare alleles were present, with 99.1% of SNP alleles appearing within the first four breeding cycles. Population structure analysis with principal component analysis, discriminant analysis of principal components, fastSTRUCTURE, and a phylogenetic approach revealed an admixed population with moderate substructure. A small core collection (n < 20) captured 99% of the program's allelic diversity. Allele frequency analysis indicated potential selection signatures associated with stress resistance and fiber cell growth. The results of this study will steer future utilization of the program's germplasm resources and aid in combining program-specific beneficial alleles and maintaining genetic diversity.

Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens.

BACKGROUND: Viruses are the most abundant biological entities on Earth, known to be crucial components of microbial ecosystems. However, there is little information on the viral community within agricultural waste. There are currently ~ 2.7 million dairy cattle in the UK producing 7-8% of their own bodyweight in manure daily, and 28 million tonnes annually. To avoid pollution of UK freshwaters, manure must be stored and spread in accordance with guidelines set by DEFRA. Manures are used as fertiliser, and widely spread over crop fields, yet little is known about their microbial composition. We analysed the virome of agricultural slurry over a 5-month period using short and long-read sequencing. RESULTS: Hybrid sequencing uncovered more high-quality viral genomes than long or short-reads alone; yielding 7682 vOTUs, 174 of which were complete viral genomes. The slurry virome was highly diverse and dominated by lytic bacteriophage, the majority of which represent novel genera (~ 98%). Despite constant influx and efflux of slurry, the composition and diversity of the slurry virome was extremely stable over time, with 55% of vOTUs detected in all samples over a 5-month period. Functional annotation revealed a diverse and abundant range of auxiliary metabolic genes and novel features present in the community, including the agriculturally relevant virulence factor VapE, which was widely distributed across different phage genera that were predicted to infect several hosts. Furthermore, we identified an abundance of phage-encoded diversity-generating retroelements, which were previously thought to be rare on lytic viral genomes. Additionally, we identified a group of crAssphages, including lineages that were previously thought only to be found in the human gut. CONCLUSIONS: The cattle slurry virome is complex, diverse and dominated by novel genera, many of which are not recovered using long or short-reads alone. Phages were found to encode a wide range of AMGs that are not constrained to particular groups or predicted hosts, including virulence determinants and putative ARGs. The application of agricultural slurry to land may therefore be a driver of bacterial virulence and antimicrobial resistance in the environment. Video abstract.

A new family of "megaphages" abundant in the marine environment.

Megaphages, bacteriophages harbouring extremely large genomes, have recently been found to be ubiquitous, being described from a variety of microbiomes ranging from the animal gut to soil and freshwater systems. However, no complete marine megaphage has been identified to date. Here, using both short and long read sequencing, we assembled >900 high-quality draft viral genomes from water in the English Channel. One of these genomes included a novel megaphage, Mar_Mega_1 at >650 Kb, making it one of the largest phage genomes assembled to date. Utilising phylogenetic and network approaches, we found this phage represents a new family of megaphages. Genomic analysis showed Mar_Mega_1 shares relatively few homologues with its closest relatives, but, as with other megaphages Mar_Mega_1 contained a variety of auxiliary metabolic genes responsible for carbon metabolism and nucleotide biosynthesis, including a NADP-dependent isocitrate dehydrogenase [Idh] and nicotinamide-nucleotide amidohydrolase [PncC], which have not previously been identified in megaphages. Mar_Mega_1 was abundant in a marine virome sample and related phages are widely prevalent in the oceans.

INfrastructure for a PHAge REference Database: Identification of Large-Scale Biases in the Current Collection of Cultured Phage Genomes.

Background: With advances in sequencing technology and decreasing costs, the number of phage genomes that have been sequenced has increased markedly in the past decade. Materials and Methods: We developed an automated retrieval and analysis system for phage genomes (https://github.com/RyanCook94/inphared) to produce the INfrastructure for a PHAge REference Database (INPHARED) of phage genomes and associated metadata. Results: As of January 2021, 14,244 complete phage genomes have been sequenced. The INPHARED data set is dominated by phages that infect a small number of bacterial genera, with 75% of phages isolated on only 30 bacterial genera. There is further bias, with significantly more lytic phage genomes (∼70%) than temperate (∼30%) within our database. Collectively, this results in ∼54% of temperate phage genomes originating from just three host genera. With much debate on the carriage of antibiotic resistance genes and their potential safety in phage therapy, we searched for putative antibiotic resistance genes. Frequency of antibiotic resistance gene carriage was found to be higher in temperate phages than in lytic phages and again varied with host. Conclusions: Given the bias of currently sequenced phage genomes, we suggest to fully understand phage diversity, efforts should be made to isolate and sequence a larger number of phages, in particular temperate phages, from a greater diversity of hosts.

Magnetic Ordering in the Layered Cr(II) Oxide Arsenides Sr2CrO2Cr2As2 and Ba2CrO2Cr2As2.

Sr2CrO2Cr2As2 and Ba2CrO2Cr2As2 with Cr2+ ions in CrO2 sheets and in CrAs layers crystallize with the Sr2Mn3Sb2O2 structure (space group I4/mmm, Z = 2) and lattice parameters a = 4.00800(2) Å, c = 18.8214(1) Å (Sr2CrO2Cr2As2) and a = 4.05506(2) Å, c = 20.5637(1) Å (Ba2CrO2Cr2As2) at room temperature. Powder neutron diffraction reveals checkerboard-type antiferromagnetic ordering of the Cr2+ ions in the arsenide layers below TN1_Sr, of 600(10) K (Sr2CrO2Cr2As2) and TN1_Ba 465(5) K (Ba2CrO2Cr2As2) with the moments initially directed perpendicular to the layers in both compounds. Checkerboard-type antiferromagnetic ordering of the Cr2+ ions in the oxide layer below 230(5) K for Ba2CrO2Cr2As2 occurs with these moments also perpendicular to the layers, consistent with the orientation preferences of d4 moments in the two layers. In contrast, below 330(5) K in Sr2CrO2Cr2As2, the oxide layer Cr2+ moments are initially oriented in the CrO2 plane; but on further cooling, these moments rotate to become perpendicular to the CrO2 planes, while the moments in the arsenide layers rotate by 90° with the moments on the two sublattices remaining orthogonal throughout [behavior recently reported independently by Liu et al. [Liu et al. Phys. Rev. B 2018, 98, 134416]]. In Sr2CrO2Cr2As2, electron diffraction and high resolution powder X-ray diffraction data show no evidence for a structural distortion that would allow the two Cr2+ sublattices to couple, but high resolution neutron powder diffraction data suggest a small incommensurability between the magnetic structure and the crystal structure, which may account for the coupling of the two sublattices and the observed spin reorientation. The saturation values of the Cr2+ moments in the CrO2 layers (3.34(1) µB (for Sr2CrO2Cr2As2) and 3.30(1) µB (for Ba2CrO2Cr2As2)) are larger than those in the CrAs layers (2.68(1) µB for Sr2CrO2Cr2As2 and 2.298(8) µB for Ba2CrO2Cr2As2) reflecting greater covalency in the arsenide layers.

Honeycomb-shaped carbon nanotube supports for BiVO4 based solar water splitting.

Advances in the synthesis and assembly of nanomaterials offer a unique opportunity to purposefully design structures according to the requirements of the targeted applications. This paper shows a process to create robust 3D carbon nanotube (CNT) structures, which provide an electrically conductive support for nanoparticle coating. We describe a process to reliably fabricate robust honeycomb structures with walls made out of aligned CNTs. We present a design of experimental analysis of this fabrication process and discuss methods to coat these honeycombs with BiVO4 for solar fuel applications. The proposed honeycomb structure allows for an efficient transport of electrons through the electrode, as well as an enhanced light-electrode interaction. Finally, we demonstrate that the developed CNT electrodes can survive harsh BiVO4 synthesis conditions and can subsequently be used as photoelectrodes for solar water splitting.

Carbohydrate-restricted Diet and High-intensity Interval Training Exercise Improve Cardio-metabolic and Inflammatory Profiles in Metabolic Syndrome: A Randomized Crossover Trial.

Introduction One approach to slow the pandemic of obesity and chronic disease is to look to our evolutionary past for clues of the changing behaviors contributing to the emergence of 'diseases of civilization'. Modern humans have deviated from the lifestyle behaviors of our ancestors that have introduced pressures (i.e. diet and activity changes) quicker than our genetic ability to respond. This caused a 'mismatch' between our biological systems and environment, leading to 'man-made' chronic diseases. Purpose The purpose of the study was to investigate the effects of a short-term evolutionarily informed dietary and lifestyle intervention on inflammatory and cardio-metabolic profiles in individuals characterized as having metabolic syndrome (MetS). Methods Twelve subjects with MetS followed a crossover design with two, four-week interventions, including a carbohydrate (CHO)-restricted Paleolithic-based diet (CRPD; <50g CHO) with sedentary activity (CRPD-Sed) and CRPD with high-intensity interval training (CRPD-Ex), separated by a four-week washout period. The HIIT exercise consisted of 10 X 60 seconds (s) cycling intervals interspersed with 60s of active recovery three d/wk for four weeks. The effects of a diet with sedentary activity as compared to a diet with exercise on body composition, as well as the cardiovascular, inflammatory, and metabolic profiles, were assessed. A two-way analysis of variance (ANOVA) with repeated measures was performed with a post-hoc analysis using a simple effects analysis with a Bonferroni adjustment. The level of statistical significance was established a priori as p < 0.05. Results Compared to baselines, CRPD-Sed and CRPD-Ex improved cardio-metabolic markers, including reductions in waist adiposity (-15%, -18%), body mass (-3%, -5%), body fat % (BF%; -7%, -12%), fasting plasma glucose (GLU; -20%, -27%), triglycerides (TG; -47%, -52%), fasting insulin (-34%, -39%), insulin resistance (-35%, -46%), and increased HDL-C (+22%, +36%) and VO2max (+22% and +29%), respectively. CRPD-Sed and CRPD-Ex also reduced inflammatory markers, including hsCRP (-32% and-36%), TNF-alpha (-35% and -41%), IL-6 (-29% and -40%), and ICAM-1 (-19%, -23%), respectively, when compared to baseline. Conclusion Adopting behaviors from our evolutionary past, including diet and exercise, shows favorable cardio-metabolic and inflammatory profiles in those individuals characterized with MetS.

Carbohydrate-restricted Diet and Exercise Increase Brain-derived Neurotrophic Factor and Cognitive Function: A Randomized Crossover Trial.

Introduction Metabolic syndrome (MetS) has been recognized as one of the most important clinical challenges and global health issues of today. Growing evidence suggests that mechanisms of energy metabolism may also play a key role in mediating aspects of cognitive function. Brain-derived neurotrophic factor (BDNF) is one such factor well known for its critical role in neuronal plasticity, including memory and learning, and more recently metabolic processes. BDNF levels have been shown separately to be dependent on diet and exercise programming. Purpose The purpose of this study was to investigate the effect of diet and exercise on BDNF levels and cognitive functioning with any metabolic association in individuals characterized with MetS. Methods Twelve subjects with MetS followed a randomized crossover design with two four-week interventions, including a carbohydrate (CHO)-restricted Paleolithic-based diet (CRPD; <50gCHO) with sedentary activity (CRPD-Sed) and CRPD with high intensity interval training (HIIT; CRPD-Sed), separated by a four-week washout period. The HIIT exercise consisted of 10 x 60 s cycling intervals interspersed with 60 s of active recovery 3 day/week for four-week. Serum BDNF was detected and quantified via enzyme-linked immunosorbent assay (ELISA). Cognitive executive function (Stroop Test) and self-perceived cognitive symptoms and function (MOS-CFS) were quantified. A two-way analysis of variance with repeated measures was performed with post-hoc analysis using simple effects analysis with a Bonferroni adjustment. The level of statistical significance was established a priori as P < 0.05. Results Compared to baseline, CRPD-Sed and CRPD-Ex improved variables for cognitive function, including increased peripheral serum BDNF levels (20% and 38%), psychomotor speed and cognitive flexibility (-14%, -14%), and self-perceived cognitive symptoms and functioning (+8%, +16%), respectively. BDNF inversely correlated with %body fat (r = -0.35, P < 0.05), fasting glucose (r = -0.64, P < 0.05), triglycerides (r = -0.55, P < 0.05), and insulin sensitivity (r = -0.25, P < 0.05). Conclusion This study shows the short-term beneficial effects of carbohydrate-restricted diet on serum BDNF and executive function in those individuals characterized with MetS. We have shown that the addition of exercise can further improve neuroprotection and cognitive function beyond the results of diet alone.

Short-range ordering in a battery electrode, the 'cation-disordered' rocksalt Li1.25Nb0.25Mn0.5O2.

Cation order, with a local structure related to γ-LiFeO2, is observed in the nominally cation-disordered Li-excess rocksalt Li1.25Nb0.25Mn0.5O2via X-ray diffraction, neutron pair distribution function analysis, magnetic susceptibility and NMR spectroscopy. The correlation length of ordering depends on synthesis conditions and has implications for the electrochemistry of these phases.

A Computational Model for Assessing the Population Health Impact of Introducing a Modified Risk Claim on an Existing Smokeless Tobacco Product.

Computational models are valuable tools for predicting the population effects prior to Food and Drug Administration (FDA) authorization of a modified risk claim on a tobacco product. We have developed and validated a population model using best modeling practices. Our model consists of a Markov compartmental model based on cohorts starting at a defined age and followed up to a specific age accounting for 29 tobacco-use states based on a cohort members transition pathway. The Markov model is coupled with statistical mortality models and excess relative risk ratio estimates to determine survival probabilities from use of smokeless tobacco. Our model estimates the difference in premature deaths prevented by comparing Base Case ("world-as-is") and Modified Case (the most likely outcome given that a modified risk claim is authorized) scenarios. Nationally representative transition probabilities were used for the Base Case. Probabilities of key transitions for the Modified Case were estimated based on a behavioral intentions study in users and nonusers. Our model predicts an estimated 93,000 premature deaths would be avoided over a 60-year period upon authorization of a modified risk claim. Our sensitivity analyses using various reasonable ranges of input parameters do not indicate any scenario under which the net benefit could be offset entirely.

Anthropogenic environmental drivers of antimicrobial resistance in wildlife.

The isolation of antimicrobial resistant bacteria (ARB) from wildlife living adjacent to humans has led to the suggestion that such antimicrobial resistance (AMR) is anthropogenically driven by exposure to antimicrobials and ARB. However, ARB have also been detected in wildlife living in areas without interaction with humans. Here, we investigated patterns of resistance in Escherichia coli isolated from 408 wild bird and mammal faecal samples. AMR and multi-drug resistance (MDR) prevalence in wildlife samples differed significantly between a Sewage Treatment Plant (STP; wastes of antibiotic-treated humans) and a Farm site (antibiotic-treated livestock wastes) and Central site (no sources of wastes containing anthropogenic AMR or antimicrobials), but patterns of resistance also varied significantly over time and between mammals and birds. Over 30% of AMR isolates were resistant to colistin, a last-resort antibiotic, but resistance was not due to the mcr-1 gene. ESBL and AmpC activity were common in isolates from mammals. Wildlife were, therefore, harbouring resistance of clinical relevance. AMR E. coli, including MDR, were found in diverse wildlife species, and the patterns and prevalence of resistance were not consistently associated with site and therefore different exposure risks. We conclude that AMR in commensal bacteria of wildlife is not driven simply by anthropogenic factors, and, in practical terms, this may limit the utility of wildlife as sentinels of spatial variation in the transmission of environmental AMR.

Systemic and cardiac susceptibility of immune compromised mice to doxorubicin.

BACKGROUND: Anthracycline chemotherapy is an effective and widely used treatment for solid tumors and hematological malignancies regardless of its known cardiotoxicity. The mechanisms of the cardiotoxicity are not fully understood and methods to protect the heart during or following anthracycline chemotherapy are currently unclear. In order to examine the efficacy of human cell based therapy in anthracycline-induced injury, we characterized a mouse model using an immune compromised strain of mice capable of accepting human cells. METHODS: Immune compromised mice (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) were repeatedly exposed to pharmaceutical grade doxorubicin (0.5 mg/kg - 4 mg/kg). Cardiotoxicity was assessed by echocardiography and µCT imaging of the coronary vascular bed as well as by flow cytometry and by histological assessments of anthracycline-induced cardiac tissue damage. RESULTS: The immune compromised mice were highly susceptible to doxorubicin treatment. Doxorubicin induced both systemic and cardiac toxicities. Gastrointestinal and hepatic injury occurred at 4 mg/kg and 1.5 mg/kg dosing while mice receiving 0.5 mg/kg weekly only displayed hepatic damage. Repeated exposure to 0.5 mg/kg anthracyclines resulted in cardiac toxicity. Flow cytometric analysis of hearts indicated a loss in endothelial and cardiac progenitor cells after doxorubicin treatment. This endothelial loss is corroborated by the lack of small vessels detected by µCT in the hearts of mice exposed to doxorubicin. Histological assessment shows no overt cardiomyocyte injury but livers from mice treated with doxorubicin show marked hepatic plate atrophy with intracytoplasmic and canalicular cholestasis, rare pericentral hepatocellular necrosis and significant zone 3 iron accumulation, likely an indication of metabolic injury due to doxorubicin toxicity. CONCLUSIONS: Immune compromised mice are sensitive to doxorubicin therapy resulting in systemic complications in addition to cardiovascular toxicity. Anthracycline-induced cardiotoxicity is observed at very low doses in NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mice.