| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Blanton, Michael R., et al.
(författare)
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Sloan Digital Sky Survey IV : Mapping the Milky Way, Nearby Galaxies, and the Distant Universe
- 2017
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Ingår i: Astronomical Journal. - : IOP Publishing Ltd. - 0004-6256 .- 1538-3881. ; 154:1
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Tidskriftsartikel (refereegranskat)abstract
- We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and. high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median z similar to 0.03). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between z similar to 0.6 and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs. and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the. Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July.
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| 3. |
- Hoshino, Ayuko, et al.
(författare)
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Extracellular Vesicle and Particle Biomarkers Define Multiple Human Cancers
- 2020
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Ingår i: Cell. - : CELL PRESS. - 0092-8674 .- 1097-4172. ; 182:4, s. 1044-
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Tidskriftsartikel (refereegranskat)abstract
- There is an unmet clinical need for improved tissue and liquid biopsy tools for cancer detection. We investigated the proteomic profile of extracellular vesicles and particles (EVPs) in 426 human samples from tissue explants (TEs), plasma, and other bodily fluids. Among traditional exosome markers, CD9, HSPA8, ALIX, and HSP90AB1 represent pan-EVP markers, while ACTB, MSN, and RAP1B are novel pan-EVP markers. To confirm that EVPs are ideal diagnostic tools, we analyzed proteomes of TE- (n =151) and plasma-derived (n =120) EVPs. Comparison of TE EVPs identified proteins (e.g., VCAN, TNC, and THBS2) that distinguish tumors from normal tissues with 90% sensitivity/94% specificity. Machine-learning classification of plasma-derived EVP cargo, including immunoglobulins, revealed 95% sensitivity/90% specificity in detecting cancer Finally, we defined a panel of tumor-type-specific EVP proteins in TEs and plasma, which can classify tumors of unknown primary origin. Thus, EVP proteins can serve as reliable biomarkers for cancer detection and determining cancer type.
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| 4. |
- Abolfathi, Bela, et al.
(författare)
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The Fourteenth Data Release of the Sloan Digital Sky Survey : First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment
- 2018
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Ingår i: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 235:2
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Tidskriftsartikel (refereegranskat)abstract
- The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014-2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V.
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| 5. |
- Hill, Rebecca M., et al.
(författare)
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Combined MYC and P53 Defects Emerge at Medulloblastoma Relapse and Define Rapidly Progressive, Therapeutically Targetable Disease
- 2015
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Ingår i: Cancer Cell. - : Elsevier BV. - 1535-6108 .- 1878-3686. ; 27:1, s. 72-84
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Tidskriftsartikel (refereegranskat)abstract
- We undertook a comprehensive clinical and biological investigation of serial medulloblastoma biopsies obtained at diagnosis and relapse. Combined MYC family amplifications and P53 pathway defects commonly emerged at relapse, and all patients in this group died of rapidly progressive disease postrelapse. To study this interaction, we investigated a transgenic model of MYCN-driven medulloblastoma and found spontaneous development of Trp53 inactivating mutations. Abrogation of p53 function in this model produced aggressive tumors that mimicked characteristics of relapsed human tumors with combined P53-MYC dysfunction. Restoration of p53 activity and genetic and therapeutic suppression of MYCN all reduced tumor growth and prolonged survival. Our findings identify P53-MYC interactions at medulloblastoma relapse as biomarkers of clinically aggressive disease that may be targeted therapeutically.
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| 6. |
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| 7. |
- Hunsicker, Mary E., et al.
(författare)
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Functional responses and scaling in predator-prey interactions of marine fishes : contemporary issues and emerging concepts
- 2011
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Ingår i: Ecology Letters. - : Wiley-Blackwell. - 1461-023X .- 1461-0248. ; 14:12, s. 1288-1299
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Forskningsöversikt (refereegranskat)abstract
- Predatorprey interactions are a primary structuring force vital to the resilience of marine communities and sustainability of the worlds oceans. Human influences on marine ecosystems mediate changes in species interactions. This generality is evinced by the cascading effects of overharvesting top predators on the structure and function of marine ecosystems. It follows that ecological forecasting, ecosystem management, and marine spatial planning require a better understanding of food web relationships. Characterising and scaling predatorprey interactions for use in tactical and strategic tools (i.e. multi-species management and ecosystem models) are paramount in this effort. Here, we explore what issues are involved and must be considered to advance the use of predatorprey theory in the context of marine fisheries science. We address pertinent contemporary ecological issues including (1) the approaches and complexities of evaluating predator responses in marine systems; (2) the scaling up of predatorprey interactions to the population, community, and ecosystem level; (3) the role of predatorprey theory in contemporary fisheries and ecosystem modelling approaches; and (4) directions for the future. Our intent is to point out needed research directions that will improve our understanding of predatorprey interactions in the context of the sustainable marine fisheries and ecosystem management.
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| 8. |
- Vowles, Kevin E., et al.
(författare)
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Initial evaluation of the Chronic Pain Acceptance Questionnaire-2
- 2020
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Ingår i: European Journal of Pain. - : WILEY. - 1090-3801 .- 1532-2149. ; 24:10, s. 2027-2036
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Tidskriftsartikel (refereegranskat)abstract
- Greater acceptance of chronic pain is associated with lesser levels of pain-related distress and disability and better overall functioning. Pain acceptance is most often assessed using the Chronic Pain Acceptance Questionnaire (CPAQ), which includes both an eight-item short form (CPAQ-8) and a twenty item parent measure (CPAQ-20). This study derived a two-item CPAQ for use in busy clinical settings and for repeated measurement during treatment, the CPAQ-2. An Item Response Theory (IRT) approach was used to identify the strongest items from the CPAQ-20, one from each of its two subscales. Next, regression analyses were conducted to evaluate the utility of the CPAQ-2 by examining variance accounted for in the CPAQ-8, CPAQ-20, and in measures of depression, pain-related fear, physical disability, and psychosocial disability. Four clinical databases were combined (N = 1,776) for the analyses. Items 9 and 14 were identified as the strongest CPAQ-20 items in the IRT analyses. The sum score of these two items accounted for over 60% of the variance in the CPAQ-8 and CPAQ-20. Furthermore, this score accounted for significant variance in measures of depression, pain-related fear, physical disability, and psychosocial disability after controlling for data collection method (i.e. in clinic or online), participant age, education, pain duration and usual pain. Finally, the amount of variance accounted for by the CPAQ-2 was comparable to that accounted for by both the CPAQ-8 and CPAQ-20. These results provide initial support for the CPAQ-2 and suggest that it is well-suited as a brief assessment of chronic pain acceptance. Significance The most frequently used measure of pain acceptance is the CPAQ, which includes both an eight-item short form, the CPAQ-8, and a longer twenty item parent measure, the CPAQ-20. The present study sought to derive a two-item measure of the CPAQ for use in busy clinical settings and for repeated measurement during treatment, the CPAQ-2. An IRT approach was used to identify the strongest items from the CPAQ-20, one from each of its two subscales in a large sample of 1,776 individuals with chronic pain. The two item measure accounted for significant variance in measures of depression, pain-related fear, physical disability, and psychosocial disability. The brief measure will be useful in assessing pain acceptance in busy clinical setting and longitudinal designs.
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| 9. |
- Vowles, Kevin E., et al.
(författare)
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The Pain Anxiety Symptom Scale : Initial Development and Evaluation of 4 and 8 Item Short Forms
- 2024
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Ingår i: Journal of Pain. - : Elsevier. - 1526-5900 .- 1528-8447. ; 25:1, s. 176-186
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Tidskriftsartikel (refereegranskat)abstract
- Elevated levels of anxiety in relation to chronic pain have been consistently associated with greater distress and disability. Thus, accurate measurement of pain-related anxiety is an important requirement in modern pain services. The Pain Anxiety Symptom Scale (PASS) was introduced over 30 years ago, with a shortened 20-item version introduced 10 years later. Both versions of the PASS were derived using Principal Components Analysis, an established method of measure development with roots in classical test theory. Item Response Theory (IRT) is a complementary approach to measure development that can reduce the number of items needed and maximize item utility with minimal loss of statistical and clinical information. The present study used IRT to shorten the 20-item PASS (PASS-20) in a large sample of people with chronic pain (N = 2,669). Two shortened versions were evaluated, 1 composed of the single best-performing item from each of its 4 subscales (PASS-4) and the other with the 2 best-performing items from each subscale (PASS-8). Several supplementary analyses were performed, including comparative item convergence evaluations based on sample characteristics (ie, female or male sex; clinical or online sample), factor invariance testing, and criterion validity evaluation of the 4, 8, and 20-item versions of the PASS in hierarchical regression models predicting pain-related distress and interference. Overall, both shortened PASS versions performed adequately across these supplemental tests, although the PASS-4 had more consistent item convergence between samples, stronger evidence for factor invariance, and accounted for 83% of the variance accounted for by the PASS-20% and 92% of the variance accounted for by the PASS-8 in criterion variables. Consequently, the PASS-4 is recommended for use in situations where a briefer evaluation of pain-related anxiety is appropriate.
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