Amino acid changes in the spike protein of feline coronavirus correlate with systemic spread of virus from the intestine and not with feline infectious peritonitis

Recent evidence suggests that a mutation in the spike protein gene of feline coronavirus (FCoV), which results in an amino acid change from methionine to leucine at position 1058, may be associated with feline infectious peritonitis (FIP). Tissue and faecal samples collected post mortem from cats diagnosed with or without FIP were subjected to RNA extraction and quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) to detect FCoV RNA. In cats with FIP, 95% of tissue, and 81% of faecal samples were PCR-positive, as opposed to 22% of tissue, and 60% of faecal samples in cats without FIP. Relative FCoV copy numbers were significantly higher in the cats with FIP, both in tissues (P < 0.001) and faeces (P = 0.02). PCR-positive samples underwent pyrosequencing encompassing position 1058 of the FCoV spike protein. This identified a methionine codon at position 1058, consistent with the shedding of an enteric form of FCoV, in 77% of the faecal samples from cats with FIP, and in 100% of the samples from cats without FIP. In contrast, 91% of the tissue samples from cats with FIP and 89% from cats without FIP had a leucine codon at position 1058, consistent with a systemic form of FCoV. These results suggest that the methionine to leucine substitution at position 1058 in the FCoV spike protein is indicative of systemic spread of FCoV from the intestine, rather than a virus with the potential to cause FIP

Carbon Free Boston: Transportation Technical Report

Part of a series of reports that includes: Carbon Free Boston: Summary Report; Carbon Free Boston: Social Equity Report; Carbon Free Boston: Technical Summary; Carbon Free Boston: Buildings Technical Report; Carbon Free Boston: Waste Technical Report; Carbon Free Boston: Energy Technical Report; Carbon Free Boston: Offsets Technical ReportOVERVIEW: Transportation connects Boston’s workers, residents and tourists to their livelihoods, health care, education, recreation, culture, and other aspects of life quality. In cities, transit access is a critical factor determining upward mobility. Yet many urban transportation systems, including Boston’s, underserve some populations along one or more of those dimensions. Boston has the opportunity and means to expand mobility access to all residents, and at the same time reduce GHG emissions from transportation. This requires the transformation of the automobile-centric system that is fueled predominantly by gasoline and diesel fuel. The near elimination of fossil fuels—combined with more transit, walking, and biking—will curtail air pollution and crashes, and dramatically reduce the public health impact of transportation. The City embarks on this transition from a position of strength. Boston is consistently ranked as one of the most walkable and bikeable cities in the nation, and one in three commuters already take public transportation. There are three general strategies to reaching a carbon-neutral transportation system: • Shift trips out of automobiles to transit, biking, and walking;1 • Reduce automobile trips via land use planning that encourages denser development and affordable housing in transit-rich neighborhoods; • Shift most automobiles, trucks, buses, and trains to zero-GHG electricity. Even with Boston’s strong transit foundation, a carbon-neutral transportation system requires a wholesale change in Boston’s transportation culture. Success depends on the intelligent adoption of new technologies, influencing behavior with strong, equitable, and clearly articulated planning and investment, and effective collaboration with state and regional partners.Published versio

Scattering by a semi-infinite periodic array and the excitation of surface waves

The two-dimensional problem of acoustic scattering of an incident plane wave by a semi-infinite array of either rigid or soft circular scatterers is solved. Solutions to the corresponding infinite array problems are used, together with a novel filtering approach, to enable accurate solutions to be computed efficiently. Particular attention is focussed on the determination of the amplitude of the Rayleigh–Bloch waves that can be excited along the array. In general, the far field away from the array consists of sum of a finite number of plane waves propagating in different directions (the number depending on the observation angle) and a circular wave emanating from the edge of the array. In certain resonant cases (characterised by one of the scattered plane waves propagating parallel to the array), a different far field pattern occurs, involving contributions that are neither circular waves nor plane waves. Uniform asymptotic expansions that vary continuously across all of the shadow boundaries that exist are given for both cases

A new approximation method for scattering by long finite arrays

The scattering of water waves by a long array of evenly spaced, rigid, vertical circular cylinders is analysed under the usual assumptions of linear theory. These assumptions permit the reduction of the problem to that of solving the Helmholtz equation in two dimensions, with appropriate circular boundaries. Our primary goal is to show how solutions obtained for semi-infinite arrays can be combined to provide accurate and numerically efficient solutions to problems involving long, but finite, arrays. The particular diffraction problem considered here has been chosen both for its theoretical interest and for its applicability. The design of offshore structures supported by cylindrical columns is commonplace and understanding how the multiple interactions between the waves and the supports affect the field is clearly important. The theoretical interest comes from the fact that, for wavelengths greater than twice the geometric periodicity, the associated infinite array can support Rayleigh–Bloch surface waves that propagate along the array without attenuation. For a long finite array, we expect to see these surface waves travelling back and forth along the array and interacting with the ends. For particular sets of parameters, near-trapping has previously been observed and we provide a quantitative explanation of this phenomenon based on the excitation and reflection of surface waves by the ends of the finite array

The Long-Term Outcomes after Radical Prostatectomy of Patients with Pathologic Gleason 8–10 Disease

Background. We explored the long-term clinical outcomes including metastases-free survival and prostate cancer-specific survival (PCSS) in patients with pathologic Gleason 8–10 disease after radical prostatectomy (RP). Methods. We report on 91 patients with PCSS data with a median followup of 8.2 years after RP performed between 1988 and 1997. Cox regression and Kaplan-Meier analysis were used to evaluate year of surgery, pathologic stage, and surgical margin status as predictors of PCSM. Results. Median age was 65 years (IQR: 61–9), and median PSA was 9.7 ng/ml (IQR: 6.1–13.4). Of all patients, 62 (68.9%) had stage T3 disease or higher, and 48 (52.7%) had a positive surgical margin. On multivariate analysis, none of the predictors were statistically significant. Of all patients, the predicted 10-year BCR-free survival, mets-free survival, and PCSS were 59% (CI: 53%–65%), 88% (CI: 84%–92%), and 94% (CI: 91%–97%), respectively. Conclusions. We have demonstrated that cancer control is durable even 10 years after RP in those with pathologic Gleason 8–10 disease. Although 40% will succumb to BCR, only 6% of patients died of their disease. These results support the use of RP for patients with high-risk localized prostate cancer

Bod1, a novel kinetochore protein required for chromosome biorientation

We have combined the proteomic analysis of Xenopus laevis in vitro–assembled chromosomes with RNA interference and live cell imaging in HeLa cells to identify novel factors required for proper chromosome segregation. The first of these is Bod1, a protein conserved throughout metazoans that associates with a large macromolecular complex and localizes with kinetochores and spindle poles during mitosis. Small interfering RNA depletion of Bod1 in HeLa cells produces elongated mitotic spindles with severe biorientation defects. Bod1-depleted cells form syntelic attachments that can oscillate and generate enough force to separate sister kinetochores, suggesting that microtubule–kinetochore interactions were intact. Releasing Bod1-depleted cells from a monastrol block increases the frequency of syntelic attachments and the number of cells displaying biorientation defects. Bod1 depletion does not affect the activity or localization of Aurora B but does cause mislocalization of the microtubule depolymerase mitotic centromere- associated kinesin and prevents its efficient phosphorylation by Aurora B. Therefore, Bod1 is a novel kinetochore protein that is required for the detection or resolution of syntelic attachments in mitotic spindles

Modeling the economic value of carbon sequestration by wetlands in the Delaware Estuary : historic estimates and future projections

© The Author(s), 2017. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Journal of Environmental Management 206 (2018): 40-50, doi:10.1016/j.jenvman.2017.10.018.Coastal wetlands sequester large amounts of carbon in their soils, effectively removing carbon dioxide from the atmosphere and acting as a carbon sink. In this paper, we estimate the economic value of carbon sequestered by wetlands in the Delaware Estuary. We estimate the value of the current stock of wetlands, the value of the historic loss of wetlands, and under a range of different scenarios the expected future loss. We use historical topographic maps and Land Cover inventories of the Delaware Estuary to measure the acreage of tidal wetlands in nine distinct time periods from 1778 to 2011. Using these data, we estimate an annual rate of wetland loss of 1.03km2. Coupling observed land cover change with exogenous factors including sea-level rise, population pressure, and channel dredging, we estimate changes in tidal wetland area under a range of future scenarios for our expected future economic loss estimates.This research is supported by NSF Coastal SEES Grant No. 1325136

Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb

We demonstrate a new scheme of spectromicroscopy in the extreme ultraviolet (EUV) spectral range, where the spectral response of the sample at different wavelengths is imaged simultaneously. It is enabled by applying ptychographical information multiplexing (PIM) to a tabletop EUV source based on high harmonic generation, where four spectrally narrow harmonics near 30 nm form a spectral comb structure. Extending PIM from previously demonstrated visible wavelengths to the EUV/X-ray wavelengths promises much higher spatial resolution and more powerful spectral contrast mechanism, making PIM an attractive spectromicroscopy method in both the microscopy and the spectroscopy aspects. Besides the sample, the multicolor EUV beam is also imaged in situ, making our method a powerful beam characterization technique. No hardware is used to separate or narrow down the wavelengths, leading to efficient use of the EUV radiation