Escaping the fate of Sisyphus: assessing resistome hybridization baits for antimicrobial resistance gene capture.

Finding, characterizing and monitoring reservoirs for antimicrobial resistance (AMR) is vital to protecting public health. Hybridization capture baits are an accurate, sensitive and cost-effective technique used to enrich and characterize DNA sequences of interest, including antimicrobial resistance genes (ARGs), in complex environmental samples. We demonstrate the continued utility of a set of 19 933 hybridization capture baits designed from the Comprehensive Antibiotic Resistance Database (CARD)v1.1.2 and Pathogenicity Island Database (PAIDB)v2.0, targeting 3565 unique nucleotide sequences that confer resistance. We demonstrate the efficiency of our bait set on a custom-made resistance mock community and complex environmental samples to increase the proportion of on-target reads as much as >200-fold. However, keeping pace with newly discovered ARGs poses a challenge when studying AMR, because novel ARGs are continually being identified and would not be included in bait sets designed prior to discovery. We provide imperative information on how our bait set performs against CARDv3.3.1, as well as a generalizable approach for deciding when and how to update hybridization capture bait sets. This research encapsulates the full life cycle of baits for hybridization capture of the resistome from design and validation (both in silico and in vitro) to utilization and forecasting updates and retirement.

Measurement of the Charge-Averaged Elastic Lepton-Proton Scattering Cross Section by the OLYMPUS Experiment.

We report the first measurement of the average of the electron-proton and positron-proton elastic scattering cross sections. This lepton charge-averaged cross section is insensitive to the leading effects of hard two-photon exchange, giving more robust access to the proton's electromagnetic form factors. The cross section was extracted from data taken by the OLYMPUS experiment at DESY, in which alternating stored electron and positron beams were scattered from a windowless gaseous hydrogen target. Elastic scattering events were identified from the coincident detection of the scattered lepton and recoil proton in a large-acceptance toroidal spectrometer. The luminosity was determined from the rates of Møller, Bhabha, and elastic scattering in forward electromagnetic calorimeters. The data provide some selectivity between existing form factor global fits and will provide valuable constraints to future fits.

Measurement of the Vector and Tensor Asymmetries at Large Missing Momentum in Quasielastic (e[over →],e

We report the measurement of the beam-vector and tensor asymmetries A_{ed}^{V} and A_{d}^{T} in quasielastic (e[over →],e^{'}p) electrodisintegration of the deuteron at the MIT-Bates Linear Accelerator Center up to missing momentum of 500 MeV/c. Data were collected simultaneously over a momentum transfer range 0.1

Hard Two-Photon Contribution to Elastic Lepton-Proton Scattering Determined by the OLYMPUS Experiment.

The OLYMPUS Collaboration reports on a precision measurement of the positron-proton to electron-proton elastic cross section ratio, R_{2γ}, a direct measure of the contribution of hard two-photon exchange to the elastic cross section. In the OLYMPUS measurement, 2.01 GeV electron and positron beams were directed through a hydrogen gas target internal to the DORIS storage ring at DESY. A toroidal magnetic spectrometer instrumented with drift chambers and time-of-flight scintillators detected elastically scattered leptons in coincidence with recoiling protons over a scattering angle range of ≈20° to 80°. The relative luminosity between the two beam species was monitored using tracking telescopes of interleaved gas electron multiplier and multiwire proportional chamber detectors at 12°, as well as symmetric Møller or Bhabha calorimeters at 1.29°. A total integrated luminosity of 4.5 fb^{-1} was collected. In the extraction of R_{2γ}, radiative effects were taken into account using a Monte Carlo generator to simulate the convolutions of internal bremsstrahlung with experiment-specific conditions such as detector acceptance and reconstruction efficiency. The resulting values of R_{2γ}, presented here for a wide range of virtual photon polarization 0.456<ε<0.978, are smaller than some hadronic two-photon exchange calculations predict, but are in reasonable agreement with a subtracted dispersion model and a phenomenological fit to the form factor data.

An improved workflow for accurate and robust healthcare environmental surveillance using metagenomics.

BACKGROUND: Effective surveillance of microbial communities in the healthcare environment is increasingly important in infection prevention. Metagenomics-based techniques are promising due to their untargeted nature but are currently challenged by several limitations: (1) they are not powerful enough to extract valid signals out of the background noise for low-biomass samples, (2) they do not distinguish between viable and nonviable organisms, and (3) they do not reveal the microbial load quantitatively. An additional practical challenge towards a robust pipeline is the inability to efficiently allocate sequencing resources a priori. Assessment of sequencing depth is generally practiced post hoc, if at all, for most microbiome studies, regardless of the sample type. This practice is inefficient at best, and at worst, poor sequencing depth jeopardizes the interpretation of study results. To address these challenges, we present a workflow for metagenomics-based environmental surveillance that is appropriate for low-biomass samples, distinguishes viability, is quantitative, and estimates sequencing resources. RESULTS: The workflow was developed using a representative microbiome sample, which was created by aggregating 120 surface swabs collected from a medical intensive care unit. Upon evaluating and optimizing techniques as well as developing new modules, we recommend best practices and introduce a well-structured workflow. We recommend adopting liquid-liquid extraction to improve DNA yield and only incorporating whole-cell filtration when the nonbacterial proportion is large. We suggest including propidium monoazide treatment coupled with internal standards and absolute abundance profiling for viability assessment and involving cultivation when demanding comprehensive profiling. We further recommend integrating internal standards for quantification and additionally qPCR when we expect poor taxonomic classification. We also introduce a machine learning-based model to predict required sequencing effort from accessible sample features. The model helps make full use of sequencing resources and achieve desired outcomes. Video Abstract CONCLUSIONS: This workflow will contribute to more accurate and robust environmental surveillance and infection prevention. Lessons gained from this study will also benefit the continuing development of methods in relevant fields.

Precise measurement of deuteron tensor analyzing powers with BLAST.

We report a precision measurement of the deuteron tensor analyzing powers T(20) and T(21) at the MIT-Bates Linear Accelerator Center. Data were collected simultaneously over a momentum transfer range Q=2.15-4.50 fm(-1) with the Bates Large Acceptance Spectrometer Toroid using a highly polarized deuterium internal gas target. The data are in excellent agreement with calculations in a framework of effective field theory. The deuteron charge monopole and quadrupole form factors G(C) and G(Q) were separated with improved precision, and the location of the first node of G(C) was confirmed at Q=4.19±0.05 fm(-1). The new data provide a strong constraint on theoretical models in a momentum transfer range covering the minimum of T(20) and the first node of G(C).

Infectious Period of Severe Acute Respiratory Syndrome Coronavirus 2 in 17 Nursing Home Residents-Arkansas, June-August 2020.

BACKGROUND: To estimate the infectious period of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in older adults with underlying conditions, we assessed duration of coronavirus disease 2019 (COVID-19) symptoms, reverse-transcription polymerase chain reaction (RT-PCR) positivity, and culture positivity among nursing home residents. METHODS: We enrolled residents within 15 days of their first positive SARS-CoV-2 test (diagnosis) at an Arkansas facility from July 7 to 15, 2020 and instead them for 42 days. Every 3 days for 21 days and then weekly, we assessed COVID-19 symptoms, collected specimens (oropharyngeal, anterior nares, and saliva), and reviewed medical charts. Blood for serology was collected on days 0, 6, 12, 21, and 42. Infectivity was defined by positive culture. Duration of culture positivity was compared with duration of COVID-19 symptoms and RT-PCR positivity. Data were summarized using measures of central tendency, frequencies, and proportions. RESULTS: We enrolled 17 of 39 (44%) eligible residents. Median participant age was 82 years (range, 58-97 years). All had ≥3 underlying conditions. Median duration of RT-PCR positivity was 22 days (interquartile range [IQR], 8-31 days) from diagnosis; median duration of symptoms was 42 days (IQR, 28-49 days). Of 9 (53%) participants with any culture-positive specimens, 1 (11%) severely immunocompromised participant remained culture-positive 19 days from diagnosis; 8 of 9 (89%) were culture-positive ≤8 days from diagnosis. Seroconversion occurred in 12 of 12 (100%) surviving participants with ≥1 blood specimen; all participants were culture-negative before seroconversion. CONCLUSIONS: Duration of infectivity was considerably shorter than duration of symptoms and RT-PCR positivity. Severe immunocompromise may prolong SARS-CoV-2 infectivity. Seroconversion indicated noninfectivity in this cohort.

Ethanol neurotoxicity: effects on neurite formation and neurotrophic factor production in vitro.

The effects of ethanol on chick embryo sensory and spinal cord neurons growing on one of several biological substrates (poly-D-lysine, laminin, or neuron-produced neurite-promoting materials) were examined. Ethanol inhibited process formation by the neurons in a dose-dependent manner and inhibited the production of neurotrophic factors. Neuronal attachment to the substrates, survival of attached neurons, and receptor interactions of sensory neurons with nerve growth factor were not influenced by ethanol. It appears that ethanol alters certain metabolic characteristics of developing neurons.

Strange magnetism and the anapole structure of the proton.

The violation of mirror symmetry in the weak force provides a powerful tool to study the internal structure of the proton. Experimental results have been obtained that address the role of strange quarks in generating nuclear magnetism. The measurement reported here provides an unambiguous constraint on strange quark contributions to the proton's magnetic moment through the electron-proton weak interaction. We also report evidence for the existence of a parity-violating electromagnetic effect known as the anapole moment of the proton. The proton's anapole moment is not yet well understood theoretically, but it could have important implications for precision weak interaction studies in atomic systems such as cesium.

Corticotropin releasing hormone modulates endotoxin-induced inflammatory cytokine expression in human trophoblast cells.

Recent studies have suggested a significant increase in corticotropin releasing hormone (CRH) in maternal plasma and placenta during the course of maternal infection. The aim of this study was to examine the possible role of CRH in lipopolysaccharide (LPS)-induced pro-inflammatory cytokine expression using the well-established human extravillous trophoblast cell line HTR-8/SVneo. Exposure of the HTR-8/SVneo cells to LPS resulted in increased secretion of tumour necrosis factor alpha (TNF-alpha) and interleukin (IL)-8. Pre-treatment of the cells with CRH prior to LPS exposure significantly enhanced LPS induced TNF-alpha and IL-8 secretion. This effect was inhibited by the CRH antagonist astressin. Stimulation of the cells with CRH caused a rapid and transient phosphorylation of p38/MAPK while CRH had no effect on ERK1/2 activation. The effect of CRH on p38/MAPK activation was suppressed by astressin and by the p38/MAPK inhibitor SB203580. Exposure of the cells to CRH resulted in increased expression of TLR-4 and this effect was also inhibited by astressin. Taken together, these findings suggest that CRH augments LPS induced cytokine secretion in human trophoblast cells. Modulation of LPS induced immune responses by CRH may be mediated through regulation of TLR-4 and selective activation of the p38/MAPK signalling pathway.

Surfactant utilization and short-term outcomes in an era of non-invasive respiratory support in Canadian neonatal intensive care units.

OBJECTIVE: Increased use of non-invasive respiratory support (NRS) in the delivery room management of preterm neonates has resulted in delayed surfactant treatment, yet the short-term effects of this change are unknown. The aim of this study was to comparatively evaluate the use of surfactant and the short-term outcomes prior to and after the implementation of early routine use of NRS. STUDY DESIGN: Eligible infants of <29 weeks gestational age (GA) admitted to a Canadian tertiary neonatal center during two time periods (2005 to 2008 and 2010 to 2013) were included in this retrospective cohort study. Timing of surfactant (prophylactic vs therapeutic) and short-term outcomes were compared between the two groups. Univariate and multivariate regression analysis was performed to determine the adjusted odds ratio (AOR) along with 95% confidence interval (CI) of receiving exogenous surfactant and developing bronchopulmonary dysplasia (BPD) using the later cohort as the reference group. Subgroup analyses were also performed for infants <26 and 26 to 286/7 weeks GA, respectively. RESULTS: A total of 3980 and 5137 infants were included in the first and second time periods, respectively. There was no significant difference in overall surfactant utilization between the two time periods (AOR 1.00, 95% CI 0.89, 1.13). However, between 2005 and 2008, a lower proportion of neonates received therapeutic surfactant compared with the later cohort (47.1% vs 56.9%, P<0.01) but were more likely to receive prophylactic surfactant (52.9% vs 43.1%, P<0.01). BPD overall was significantly higher in the earlier cohort (AOR 1.19, 95% CI 1.07, 1.33), particularly among the <26 weeks gestation subgroup (AOR 1.34, 95% CI 1.08, 1.66). CONCLUSION: Early routine use of NRS did not impact overall surfactant utilization rate, although therapeutic surfactant administration rates were higher with a concomitant decrease in BPD rates.

Results of allergen-specific immunotherapy in 117 dogs with atopic dermatitis.

The success of the treatment of 117 dogs with atopic dermatitis with allergen-specific immunotherapy for up to 48 months was assessed. An excellent response (remission with exclusive immunotherapy) was recorded in 18 of the dogs, a good response (more than 50 per cent reduction in medication and improvement of clinical signs) was recorded in 57, a moderate response was recorded in 24 and a poor response in 18. The mould antigens in the allergen extract were stored in a separate vial before administration and the success rate of the immunotherapy including mould antigens was much higher than in an earlier study in which mould and pollen antigens had been stored in one vial. The success rate was not affected significantly by the age of the dogs when the disease developed, or by their age or the period for which they had shown clinical signs when the treatment began; it was also unaffected by whether pollens, moulds or dust mites were used as antigens, or by whether the offending allergens had been identified by intradermal testing or by serum testing for allergen-specific immunoglobulin E.

Effects of 4-deoxy-L-threo-pentose, a novel carbohydrate, on neural cell proteoglycan synthesis and function.

A novel carbohydrate, 4-deoxy-L-threo-pentose (4-deoxyxylose), was synthesized by way of reductive dechlorination of a chlorodeoxy sugar. This carbohydrate, an analogue of xylose which is required for the initiation of glycosaminoglycan (GAG) synthesis, was used to explore the function of GAG side chains in neurite outgrowth on a laminin substrate. 4-Deoxyxylose inhibited the incorporation of 35SO4 into the GAGs of neuronal and astrocytic proteoglycans, with no effect being seen on the incorporation of [3H]glucosamine into proteoglycan. Direct analysis of the heparan sulphate fraction from such cells using nitrous acid digestion confirmed that the GAGs were undersulphated. No inhibition of either 35SO4 or [3H]glucosamine incorporation was observed in primary mouse hepatocytes exposed to 4-deoxyxylose. 4-Deoxyxylose produced a direct dose-dependent inhibition of neurite outgrowth by sensory neurons, and medium conditioned by neurons or astrocytes in the presence of 4-deoxyxylose displayed less laminin-complexed neurite-promoting activity than medium conditioned in its absence. These data suggest that 4-deoxyxylose inhibits neurite outgrowth by altering the sulphation of the GAGs of heparan sulphate proteoglycans.

Retinopathy of prematurity: Risk factors and variability in Canadian neonatal intensive care units.

OBJECTIVE: To identify predictors of severe retinopathy of prematurity (ROP) in a large population-based cohort and to examine risk-adjusted variations across units. STUDY DESIGN: Retrospective analysis of Canadian Neonatal Network data on neonates with birth weight <1500 g who were screened for ROP between 2003 and 2010. Characteristics of infants with and without ROP were compared and a risk-adjusted model for severe ROP was developed. Rates of severe ROP were compared between sites. RESULTS: 1163 of 9187 (12.7%) infants developed severe ROP. Lower gestational age, male sex, small for gestational age, patent ductus arteriosus, late onset sepsis, more than two blood transfusions, inotrope use, and outborn status were associated with an increased risk of severe ROP. Severe ROP rates varied significantly between units. CONCLUSION: Younger, smaller and sicker male infants had higher adjusted risks of severe ROP and rates varied significantly among sites.

Pregnancy after breast-conserving surgery and radiation therapy for breast cancer.

Since the incidence of breast cancer is increasing in young women and young women are more commonly delaying child-bearing, the issue of considering a pregnancy subsequent to the diagnosis and treatment of breast cancer is becoming more common. The impact of a subsequent pregnancy on disease progression and quality of life is, however, not well defined. We evaluated treatment outcome and quality of life among 23 breast cancer patients treated with conservative surgery and radiation among the 1624 patients treated at the Joint Center for Radiation Therapy between 1968 and 1985 who had subsequent pregnancies as compared with 23 patients without subsequent pregnancy matched by age and stage at diagnosis and time to pregnancy without recurrence. Quality of life was evaluated using two self-report measures, Ferrans and Powers Quality of Life Index and the Adaptation to Surviving Cancer Profile, and a measure of parenting stress (Parenting Stress Index). Results showed no differences in recurrence or distant metastasis between the matched groups. In addition, subjects with subsequent pregnancy perceived that family issues had the greatest impact on quality of life and were not at higher risk for parental stress due to breast cancer than the normal population. Both groups of young women perceived that they were able to adjust well after treatment. Study results are consistent with other clinical studies comparing patients with and without subsequent pregnancy who have failed to demonstrate a survival disadvantage.(ABSTRACT TRUNCATED AT 250 WORDS)

Effects of neuronal proteoglycans on activity-dependent growth responses of fetal hippocampal neurons.

Excitatory amino-acid (EAA) neurotransmitters act as molecular signals influencing the structure of neurons during development. However, the signal transduction and effector mechanisms responsible for these effects have yet to be fully elucidated. We have previously provided evidence that EAA agonists induce the synthesis and release of proteoglycans (PGs) with neurite-promoting activity from fetal hippocampal neurons. In the present studies exposure of fetal hippocampal neurons to glutamate (100 microM) for 5 min resulted in increases in the neuron-specific growth-associated genes T alpha 1 alpha-tubulin (T alpha 1), microtubule-associated protein-2 (MAP-2) and growth-associated protein-43 (GAP-43). mRNA levels peaked at between 8 and 12 h following exposure as determined by competitive reverse transcription polymerase chain reaction (RT-PCR). Increases in neurite growth as measured by axonal length, the total length of dendrites, the number of branches per axon, the total length of branches per axon and the total neurite length were also observed 48 h after glutamate exposure. The increase in T alpha 1, MAP-2 and GAP-43 mRNA levels following glutamate exposure was mediated via both N-methyl-D-aspartate and metabotropic receptor activation. Heparin, which inhibits the neurite growth-promoting effects of PGs in vitro, and heparitinase, which catalyzes the cleavage of heparan sulphate, also inhibited the glutamate-dependent induction of T alpha 1, MAP-2 and GAP-43 mRNA expression and neurite growth when added to culture medium following glutamate exposure. Chondroitin sulphate and chondroitinase AC had no effects on the mRNA levels tested or on neurite growth. Therefore, these studies suggest that neuronal PGs regulated by activation of EAA receptors mediate neuronal growth responses.

Novel neurite growth-inhibitory properties of an astrocyte proteoglycan.

Conditioned medium (CM) of primary cultures of GFAP-positive adherent astrocytes from neonatal rat neocortex contained a chondroitin sulphate/dermatan sulphate proteoglycan (CDSPG) that co-eluted with a heparan sulphate proteoglycan (HSPG) by ion-exchange chromatography. The CDSPG was resolved from the HSPG by molecular sieve chromatography, which indicated that the molecular mass of the HSPG was greater than 300 kDa, while that of the CDSPG was approximately 50 kDa. Specific lyase digestion and urea/polyacrylamide gel electrophoresis established the homogeneity of the CDSPG and suggested molecular masses of the core protein and glycosylated protein as 54 kDa and 58 kDa respectively. Virtually all of the poly-D-lysine substrate-bound proteoglycan-associated neurite growth-promoting activity of astrocyte CM was accounted for by the HSPG. On poly-D-lysine the immobilized CDSPG displayed little neurite growth-stimulatory activity relative to the HSPG. However, the CDSPG inhibited the potent growth-promoting activity of the HSPG by displacing it from the poly-D-lysine substrate. Differential cellular regulation of production of growth-modulatory proteins with different binding avidity for the substrate of growth may determine the success of a regenerative axonal response by fully competent neurons.

Parity violation in elastic electron-proton scattering and the Proton's strange magnetic form factor

We report a new measurement of the parity-violating asymmetry in elastic electron scattering from the proton at backward scattering angles. This asymmetry is sensitive to the strange magnetic form factor of the proton as well as electroweak axial radiative corrections. The new measurement of A = -4.92+/-0.61+/-0.73 ppm provides a significant constraint on these quantities. The implications for the strange magnetic form factor are discussed in the context of theoretical estimates for the axial corrections.

Measurement of tensor polarization in elastic electron-deuteron scattering at large momentum transfer

Tensor polarization observables ( t(20), t(21), and t(22)) have been measured in elastic electron-deuteron scattering for six values of momentum transfer between 0.66 and 1.7 (GeV/c)(2). The experiment was performed at the Jefferson Laboratory in Hall C using the electron High Momentum Spectrometer, a specially designed deuteron magnetic channel and the recoil deuteron polarimeter POLDER. The new data determine to much larger Q2 the deuteron charge form factors G(C) and G(Q). They are in good agreement with relativistic calculations and disagree with perturbative QCD predictions.

Ethanol inhibits NMDA-stimulated neurite growth by sensory neurons in vitro.

N-methyl-D-aspartate (NMDA) produced dose dependent neurite growth from 8 day chick embryo sensory neurons in-vitro on a laminin substrate. NMDA-stimulated neurite growth was blocked by the competitive antagonist D-2-amino-5-phosphonovaleric acid (APV), by an antagonist of the glycine modulatory site kynurenate, and by the NMDA ion channel antagonist Mg2+. Ethanol blocked the NMDA-mediated neurotrophic effect in a manner that was additive with the effects of Mg2+, but non-additive with the inhibitory influences of APV and kynurenate. Thus the influences of ethanol were mediated at the NMDA receptor/modulatory site. These observations have implications for the understanding of adverse influences of ethanol on neuronal development and connectivity and on activity-dependent enduring changes in synaptic changes in synaptic function.