A flow cytometric assay to quantify \u3ci\u3ein vivo\u3c/i\u3e bacterial uptake by alveolar macrophages

Our laboratory has developed a flow cytometric assay to quantify alveolar macrophage (MФ) phagocytosis of bacteria within a live animal. MФs collected by bronchoalveolar lavage from rats infected transtracheally with Syto 9-labeled bacteria are fluorescently labeled for identification and analyzed by flow cytometry to quantify their bacterial uptake

Tamm Review: Management of mixed-severity fire regime forests in Oregon, Washington, and Northern California

Increasingly, objectives for forests with moderate- or mixed-severity fire regimes are to restore successionally diverse landscapes that are resistant and resilient to current and future stressors. Maintaining native species and characteristic processes requires this successional diversity, but methods to achieve it are poorly explained in the literature. In the Inland Pacific US, large, old, early seral trees were a key historical feature of many young and old forest successional patches, especially where fires frequently occurred. Large, old trees are naturally fire-tolerant, but today are often threatened by dense understory cohorts that create fuel ladders that alter likely post-fire successional pathways. Reducing these understories can contribute to resistance by creating conditions where canopy trees will survive disturbances and climatic stressors; these survivors are important seed sources, soil protectors, and critical habitat elements. Historical timber harvesting has skewed tree size and age class distributions, created hard edges, and altered native patch sizes. Manipulating these altered forests to promote development of larger patches of older, larger, and more widely-spaced trees with diverse understories will increase landscape resistance to severe fires, and enhance wildlife habitat for underrepresented conditions. Closed-canopy, multi-layered patches that develop in hot, dry summer environments are vulnerable to droughts, and they increase landscape vulnerability to insect outbreaks and severe wildfires. These same patches provide habitat for species such as the northern spotted owl, which has benefited from increased habitat area. Regional and local planning will be critical for gauging risks, evaluating trade-offs, and restoring dynamics that can support these and other species. The goal will be to manage for heterogeneous landscapes that include variably-sized patches of (1) young, middle-aged, and old, closed canopy forests growing in upper montane, northerly aspect, and valley bottom settings, (2) a similar diversity of open-canopy, fire-tolerant patches growing on ridgetops, southerly aspects, and lower montane settings, and (3) significant montane chaparral and grassland areas. Tools to achieve this goal include managed wildfire, prescribed burning, and variable density thinning at small to large scales. Specifics on ‘‘how much and where?” will vary according to physiographic, topographic and historical templates, and regulatory requirements, and be determined by means of a socio-ecological process

Significance of signet ring cells in high-grade mucinous adenocarcinoma of the peritoneum from appendiceal origin

Significance of signet ring cells in mucinous adenocarcinoma of the peritoneum from appendiceal origin has never been specifically studied. We retrospectively reviewed cases of mucinous adenocarcinoma of the peritoneum from appendiceal origin (n = 55) and collected clinical follow-up data. Signet ring cells were identified in 29 of 55 cases. No low-grade mucinous adenocarcinoma case (n = 11) had signet ring cells, whereas 29 of 44 high-grade mucinous adenocarcinoma cases did. Cases of high-grade mucinous adenocarcinoma were subdivided into 3 groups: (1) high-grade mucinous adenocarcinoma without signet ring cells (n = 15), (2) high-grade mucinous adenocarcinoma with signet ring cells only within mucin pools (n = 20), and (3) high-grade mucinous adenocarcinoma with signet ring cells invading tissue (n = 9). Overall survival (OS) and progression-free survival were subsequently evaluated. Five-year OS for cases of high-grade mucinous adenocarcinoma without signet ring cells and high-grade mucinous adenocarcinoma with signet ring cells within mucin pools were similar at 31.8% (SE, 14.4%) and 35.8% (SE, 13.9%), respectively. A significant survival difference was seen for cases of high-grade mucinous adenocarcinoma with signet ring cells invading tissue with a median OS of 0.5 years versus 2.9 and 2.4 years (P = .04 and P = .03), respectively, for cases of high-grade mucinous adenocarcinoma without signet ring cells and high-grade mucinous adenocarcinoma with signet ring cells within mucin pools. Finding signet ring cells floating in extracellular mucin pools made no prognostic difference when compared with cases of high-grade mucinous adenocarcinoma without signet ring cells. In contrast, high-grade mucinous adenocarcinoma with signet ring cells invading tissue was significant for worse survival, and thus, we propose reporting signet ring cell tissue invasion particularly when extensive

Tamm Review: Management of mixed-severity fire regime forests in Oregon, Washington, and Northern California

Increasingly, objectives for forests with moderate- or mixed-severity fire regimes are to restore successionally diverse landscapes that are resistant and resilient to current and future stressors. Maintaining native species and characteristic processes requires this successional diversity, but methods to achieve it are poorly explained in the literature. In the Inland Pacific US, large, old, early seral trees were a key historical feature of many young and old forest successional patches, especially where fires frequently occurred. Large, old trees are naturally fire-tolerant, but today are often threatened by dense understory cohorts that create fuel ladders that alter likely post-fire successional pathways. Reducing these understories can contribute to resistance by creating conditions where canopy trees will survive disturbances and climatic stressors; these survivors are important seed sources, soil protectors, and critical habitat elements. Historical timber harvesting has skewed tree size and age class distributions, created hard edges, and altered native patch sizes. Manipulating these altered forests to promote development of larger patches of older, larger, and more widely-spaced trees with diverse understories will increase landscape resistance to severe fires, and enhance wildlife habitat for underrepresented conditions. Closed-canopy, multi-layered patches that develop in hot, dry summer environments are vulnerable to droughts, and they increase landscape vulnerability to insect outbreaks and severe wildfires. These same patches provide habitat for species such as the northern spotted owl, which has benefited from increased habitat area. Regional and local planning will be critical for gauging risks, evaluating trade-offs, and restoring dynamics that can support these and other species. The goal will be to manage for heterogeneous landscapes that include variably-sized patches of (1) young, middle-aged, and old, closed canopy forests growing in upper montane, northerly aspect, and valley bottom settings, (2) a similar diversity of open-canopy, fire-tolerant patches growing on ridgetops, southerly aspects, and lower montane settings, and (3) significant montane chaparral and grassland areas. Tools to achieve this goal include managed wildfire, prescribed burning, and variable density thinning at small to large scales. Specifics on ‘‘how much and where?” will vary according to physiographic, topographic and historical templates, and regulatory requirements, and be determined by means of a socio-ecological process

VprBP binds full-length RAG1 and is required for B-cell development and V(D)J recombination fidelity

The N-terminus of full-length RAG1, though dispensable for RAG1/2 cleavage activity, is required for efficient V(D)J recombination. This region supports RING E3 ubiquitin ligase activity in vitro, but whether full-length RAG1 functions as a single subunit or a multi-subunit E3 ligase in vivo is unclear. We show the multi-subunit cullin RING E3 ligase complex VprBP/DDB1/Cul4A/Roc1 associates with full-length RAG1 through VprBP. This complex is assembled into RAG protein–DNA complexes, and supports in-vitro ubiquitylation activity that is insensitive to RAG1 RING domain mutations. Conditional B lineage-specific VprBP disruption arrests B-cell development at the pro-B-to-pre-B cell transition, but this block is bypassed by expressing rearranged immunoglobulin transgenes. Mice with a conditional VprBP disruption show modest reduction of D–JH rearrangement, whereas VH–DJH and Vκ–Jκ rearrangements are severely impaired. D–JH coding joints from VprBP-insufficent mice show longer junctional nucleotide insertions and a higher mutation frequency in D and J segments than normal. These data suggest full-length RAG1 recruits a cullin RING E3 ligase complex to ubiquitylate an unknown protein(s) to limit error-prone repair during V(D)J recombination

Swift X-Ray Observations of Classical Novae. II. The Super Soft Source sample

The Swift GRB satellite is an excellent facility for studying novae. Its rapid response time and sensitive X-ray detector provides an unparalleled opportunity to investigate the previously poorly sampled evolution of novae in the X-ray regime. This paper presents Swift observations of 52 Galactic/Magellanic Cloud novae. We included the XRT (0.3-10 keV) X-ray instrument count rates and the UVOT (1700-8000 Angstroms) filter photometry. Also included in the analysis are the publicly available pointed observations of 10 additional novae the X-ray archives. This is the largest X-ray sample of Galactic/Magellanic Cloud novae yet assembled and consists of 26 novae with super soft X-ray emission, 19 from Swift observations. The data set shows that the faster novae have an early hard X-ray phase that is usually missing in slower novae. The Super Soft X-ray phase occurs earlier and does not last as long in fast novae compared to slower novae. All the Swift novae with sufficient observations show that novae are highly variable with rapid variability and different periodicities. In the majority of cases, nuclear burning ceases less than 3 years after the outburst begins. Previous relationships, such as the nuclear burning duration vs. t_2 or the expansion velocity of the eject and nuclear burning duration vs. the orbital period, are shown to be poorly correlated with the full sample indicating that additional factors beyond the white dwarf mass and binary separation play important roles in the evolution of a nova outburst. Finally, we confirm two optical phenomena that are correlated with strong, soft X-ray emission which can be used to further increase the efficiency of X-ray campaigns.Comment: Accepted to ApJ Supplements. Full data for Table 2 and Figure 17 available in the electronic edition. New version of the previously posted paper since the earlier version was all set in landscape mod

LSST: from Science Drivers to Reference Design and Anticipated Data Products

(Abridged) We describe here the most ambitious survey currently planned in the optical, the Large Synoptic Survey Telescope (LSST). A vast array of science will be enabled by a single wide-deep-fast sky survey, and LSST will have unique survey capability in the faint time domain. The LSST design is driven by four main science themes: probing dark energy and dark matter, taking an inventory of the Solar System, exploring the transient optical sky, and mapping the Milky Way. LSST will be a wide-field ground-based system sited at Cerro Pach\'{o}n in northern Chile. The telescope will have an 8.4 m (6.5 m effective) primary mirror, a 9.6 deg$^2$ field of view, and a 3.2 Gigapixel camera. The standard observing sequence will consist of pairs of 15-second exposures in a given field, with two such visits in each pointing in a given night. With these repeats, the LSST system is capable of imaging about 10,000 square degrees of sky in a single filter in three nights. The typical 5$\sigma$ point-source depth in a single visit in $r$ will be $\sim 24.5$ (AB). The project is in the construction phase and will begin regular survey operations by 2022. The survey area will be contained within 30,000 deg$^2$ with $\delta<+34.5^\circ$, and will be imaged multiple times in six bands, $ugrizy$, covering the wavelength range 320--1050 nm. About 90\% of the observing time will be devoted to a deep-wide-fast survey mode which will uniformly observe a 18,000 deg$^2$ region about 800 times (summed over all six bands) during the anticipated 10 years of operations, and yield a coadded map to $r\sim27.5$. The remaining 10\% of the observing time will be allocated to projects such as a Very Deep and Fast time domain survey. The goal is to make LSST data products, including a relational database of about 32 trillion observations of 40 billion objects, available to the public and scientists around the world.Comment: 57 pages, 32 color figures, version with high-resolution figures available from https://www.lsst.org/overvie

Exploring Variation and Predictors of Residential Fine Particulate Matter Infiltration

Although individuals spend the majority of their time indoors, most epidemiological studies estimate personal air pollution exposures based on outdoor levels. This almost certainly results in exposure misclassification as pollutant infiltration varies between homes. However, it is often not possible to collect detailed measures of infiltration for individual homes in large-scale epidemiological studies and thus there is currently a need to develop models that can be used to predict these values. To address this need, we examined infiltration of fine particulate matter (PM2.5) and identified determinants of infiltration for 46 residential homes in Toronto, Canada. Infiltration was estimated using the indoor/outdoor sulphur ratio and information on hypothesized predictors of infiltration were collected using questionnaires and publicly available databases. Multiple linear regression was used to develop the models. Mean infiltration was 0.52 ± 0.21 with no significant difference across heating and non-heating seasons. Predictors of infiltration were air exchange, presence of central air conditioning, and forced air heating. These variables accounted for 38% of the variability in infiltration. Without air exchange, the model accounted for 26% of the variability. Effective modelling of infiltration in individual homes remains difficult, although key variables such as use of central air conditioning show potential as an easily attainable indicator of infiltration