| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)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. |
- Carneiro de Freitas, Rui, et al.
(author)
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Prevalence of Visual Impairment in Portugal : study design and initial results
- 2015
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In: Investigative Ophthalmology and Visual Science. - 0146-0404 .- 1552-5783. ; 56:7
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Journal article (peer-reviewed)abstract
- Purpose Information about the prevalence of visual impairment is fundamental to define policies that deal with vision loss. The aim of this study is to determine the prevalence of visual impairment (VI) in the population looking for eye care in public hospitals in Portugal.Methods We designed an observation, cross-sectional prospective study (Prevalence and Costs of Visual Impairment in Portugal: PC-VIP study) to investigate the prevalence of VI in patients attending outpatient appointments in four public hospitals in Portugal. Hospital selected provide from general eye care (3-6 ophthalmologists) to high-specialized eye care (40+ ophthalmologists) that in total have between 120-140K hospital appointments per year. Files of patients are analysed weekly to detect patients with VI. Inclusion criteria were: visual acuity equal or worse than 0.5 (USA definition 20/40) in the better eye and/or a visual field of less than 20deg. Cases are selected by trained hospital staff and inserted in a database. Data collected included demographic information, acuity from both eyes, qualitative information about visual field (good, reduced, requires investigation), main diagnosis, secondary diagnosis and comorbidities. Diagnoses were classified according with ICD9.Results We have now detected 2462 cases of VI that correspond to 4 to 33 weeks of data collection. The number of weeks is variable because collection did not start simultaneously in all sites. From the number of cases detected, 58% were female, 1.9% were under 20y, 8.2% were between 20y and 50y and 89.9% were ≥50y. The mean prevalence of visual impairment was 13.6% (SD=5.6) using the USA definition and it was 7.0%(SD=4.1) using the WHO definition (acuity equal or worse than 0.3 or ~20/63). With a methodology that controls for demographics the lowest and highest estimates were calculated. Considering the USA definition, the prevalence in the general population would be in the range 0.4 -0.4% (age<40y) and 0.8-2.4% (age>=40y). Considering WHO definition, it would be 0.2-0.5% (age<40y) and 0.4-1.0% (age>=40y).Conclusions A hospital-based study can provide effective estimates of the prevalence of visual impairment in a population. Estimates for the country are in agreement with the expected results that can be deducted from neighbour countries and self-reported visual impairment in census 2001.
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| 3. |
- Marques, Ana Patricia, et al.
(author)
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Productivity Losses and Their Explanatory Factors Amongst People with Impaired Vision
- 2019
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In: Ophthalmic Epidemiology. - : Taylor & Francis Group. - 0928-6586 .- 1744-5086. ; 26:6, s. 378-392
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Journal article (peer-reviewed)abstract
- Purpose: To estimate productivity losses amongst people with impaired vision in Portugal and to investigate explanatory factors associated with non-participation in the labour market.Methods: A total of 546 visually impaired individuals participated in face-to-face interviews. Participants were asked about their workforce participation to determine productivity (employment status questionnaire), their health-related quality of life – HRQoL (EQ-5D) and their visual acuity and visual ability (Activity Inventory). Productivity losses included absenteeism and reduction in workforce participation. Logistic regression was used to determine independent factors associated with participation in the labour market.Results: From the 546 participants, 50% were retired, 47% were of working age and 3% were students. The employment rate was 28%, and the unemployment rate was 21% for the working age sample. For those of working age, productivity losses were estimated at €1.51 million per year, mean of €5496 per participant. The largest contributor to productivity losses was reduced workforce participation, estimated from 159 early retired or unemployed participants. After controlling for visual acuity and ability, younger individuals, with more years of education, without comorbidities and high HRQoL had a higher probability of being employed.Conclusions: Our findings show a high unemployment rate and high productivity losses amongst people with impaired vision. The probability of being employed was associated with education, HRQoL and comorbidities. We speculate that promoting education and health through effective visual rehabilitation programs may help to increase participation in the labour market. These findings can inform decisions to intervene to reduce the burden of vision loss.
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| 4. |
- Abolfathi, Bela, et al.
(author)
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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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In: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 235:2
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Journal article (peer-reviewed)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. |
- Baptista, Antonio M. G., et al.
(author)
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Causes of Vision Impairment in Portugal : A hospital based study
- 2015
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In: Investigative Ophthalmology and Visual Science. - 0146-0404 .- 1552-5783. ; 56:7
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Journal article (peer-reviewed)abstract
- Purpose Causes of vision impairment (VI) are influenced by factors such as race or socio-economic circumstances. Because of this collecting national information is important for planning reduction of vision loss. The aim of this study was to determine causes of vision impairment in a population visiting ophthalmology departments in public hospitals in Portugal.Methods This study was designed according with the guidelines of the Vancouver Economic Burden of Vision Loss Group (IOVS, 2010, V51/4/1801). Recommendations are to collect hospital data during 1 year to determine causes of VI. We selected four public hospitals that are expected to have over 120-140K appointments per year. Files are analysed weekly to detect patients with vision impairment. Inclusion criteria are: visual acuity with the current refractive correction equal or less than 0.5 (20/40) in the better-seeing eye and/or a visual field of less than 20 degrees. Patients were selected by trained hospital staff (medics and orthoptists) and inserted in a database. Diagnoses were classified according the ICD9. Data collected included fundamental demographic information, main diagnosis, secondary diagnosis and comorbidities.Results We have now 2462 patients selected that correspond to 4 to 33 weeks of data collection. The number of weeks is variable because we did not start all hospitals simultaneously. From the current number of cases detected, 58% are female, 1.9% are under 20, 8.2% are between 20 and 50 and 89.9% are 50 years or older. The leading causes of vision impairment among these patients are diabetic retinopathy (DR), cataract (C), glaucoma (GC) and age-related macular degeneration (AMD). Using the North American definition of VI the proportions are 26.8% for DR, 25.5% for C, 10.4% for GC and 8.2% for AMD. The remaining causes of VI have percentages below 5% and in total they correspond to approximately 29% of the cases detected.Conclusions Our results show that the most common causes of vision impairment are eye diseases related with systemic conditions and aging of the population. Vision impairment was relatively low under the age of 20 and the causes were mostly inherited diseases. Numbers reported now will be more accurate at the end of the study but they already highlight the importance of targeting conditions such as diabetes.
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| 6. |
- Blanton, Michael R., et al.
(author)
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Sloan Digital Sky Survey IV : Mapping the Milky Way, Nearby Galaxies, and the Distant Universe
- 2017
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In: Astronomical Journal. - : IOP Publishing Ltd. - 0004-6256 .- 1538-3881. ; 154:1
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Journal article (peer-reviewed)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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| 7. |
- Hernández-Moreno, Laura, et al.
(author)
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Cost‐effectiveness of basic vision rehabilitation (The basic VRS‐effect study): study protocol for a randomised controlled trial
- 2020
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In: Ophthalmic & physiological optics. - : John Wiley & Sons. - 0275-5408 .- 1475-1313. ; 40:3, s. 350-364
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Journal article (peer-reviewed)abstract
- Abstract Purpose To investigate the cost-effectiveness of a basic vision rehabilitation service (basic-VRS) in Portugal. We designed a parallel group, randomised controlled trial whose aim is to compare the effects and costs of ?usual low vision care? with a ?basic-VRS intervention? on self-reported visual ability and other psychosocial and health-related quality-of-life outcomes. Methods The trial will recruit participants that meet the following inclusion criteria: (1) visual acuity between 0.4?1.0 logMAR in the better-seeing eye, (2) cause of vision loss is diabetic retinopathy or age-related macular degeneration, (3) 18 years or older and iv) live in the community (not in nursing homes or other type of institution). Participants will be randomised to one of the study arms consisting of immediate intervention and delayed intervention. The delayed intervention group will receive ?usual care? or no intervention in the first 12 weeks. Visual acuity, contrast sensitivity and retinal structure will be assessed during the study. Results The primary outcome measure is visual ability, which will be evaluated with the Massof Activity Inventory, we expect that the intervention will raise the overall person measure or visual ability. Reading, health-related quality-of-life, anxiety and depression and social support will be also assessed. The analysis will be undertaken on an intention-to-treat basis. A cost-effectiveness analysis will be performed to provide information about the cost per unit of utility. To evaluate the cost-effectiveness of the intervention we will adopt the perspective of the healthcare system. Conclusion This study will provide additional evidence about the effects of basic-VRS on self-reported visual ability. Findings from this study should also contribute to better planning of low vision provision and, consequently, may contribute to reduce barriers to basic-VRS.
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| 8. |
- Hernández-Moreno, Laura, et al.
(author)
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The Portuguese version of the activity inventory
- 2015
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In: Investigative Ophthalmology and Visual Science. - 0146-0404 .- 1552-5783. ; 56:7
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Journal article (peer-reviewed)abstract
- Purpose: To characterize interventions needed by the population with visual impairment or to assess interventions in vision rehabilitation validated and standardized instruments used in different cultural contexts are necessary. The aim of this work was to characterize the functional status of a sample of people with visual impairment with the Portuguese version of the activity inventory (AI)Methods: A group of participants in the study Prevalence and Costs of Visual Impairment in Portugal (PC-VIP) was recruit to face-to-face interviews and the activity inventory was administered. The AI examines 50 goals split between three objectives: social functioning, recreation and daily living. Goals rated ‘not important’ were skipped, but for all other goals the participant was asked to rate its difficulty on a five point scale ranging from ‘not difficult’ to ‘impossible without help’. The difficulty responses were Rasch analysed (Winsteps v3.81.0) to produce a continuous measure of visual ability (AI score). Additional information about distance and near visual acuity (ETDRS scale), contrast sensitivity (MARS test) and critical print size (MNREAD test) was collected.Results: A total of 94 persons participated in this study. Some participants were not able to read or recognize letters due to their poor vision or poor literacy and were excluded from further analysis. Data reported here are from 62 participants, median age 63y (range=12-85) and the most common cause of visual impairment were retinal diseases. Mean presenting acuity in the better eye was 0.93logMAR (SD=0.5). The mean difficulty (item measure) in the AI was -0.33 logits (SD=0.96). The most difficult items were "sew or do needlework", "read the newspaper", "drive" and the easiest items were "provide care for a pet", "eat your meals", "use the restroom in a public place". The mean ability score (person measures) was 1.11 logits (SD=2.04). The ability measures in the AI were correlated with distance visual acuity (r=-0.57, p<.001), near visual acuity (r=-0.66, p<0.001), contrast sensitivity (r=0.62, p<.001) and critical print size (r=-0.60, p<.001).Conclusions: Our results indicate that the AI scores in a sample of people Portuguese people with visual impairment were in line with what has been found in other cultural contexts. The visual ability measured by the AI was correlated with visual function assessed by different visual tests, which shows that this instrument can be used with confidence.
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| 9. |
- Lima Ramos, Pedro, et al.
(author)
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A review of capture-recapture methods and its possibilities in ophthalmology and vision sciences
- 2020
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In: Ophthalmic Epidemiology. - : Taylor & Francis. - 0928-6586 .- 1744-5086. ; 27:4, s. 310-324
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Research review (peer-reviewed)abstract
- Epidemiological information is expected to be used to develop key aspects of eye care such as to control and minimise the impact of diseases, to allocate resources, to monitor public health actions, to determine the best treatment options and to forecast the consequence of diseases in populations. Epidemiological studies are expected to provide information about the prevalence and/or incidence of eye diseases or conditions. To determine prevalence is necessary to perform a cross-sectional screening of the population at risk to ascertain the number of cases.The aim of this review is to describe and evaluate capture-recapture methods (or models) to ascertaining the number of individuals with a disease (e.g. diabetic retinopathy) or condition (e.g. vision impairment) in the population.The review covers the fundamental aspects of capture-recapture methods that would enable non-experts in epidemiology to use it in ophthalmic studies. The review provides information about theoretical aspects of the method with examples of studies in ophthalmology in which it has been used. We also provide a problem/solution approach for limitations arising from the lists obtained from registers or other reliable sources.We concluded that capture-recapture models can be considered reliable to estimate the total number of cases with eye conditions using incomplete information from registers. Accordingly, the method may be used to maintain updated epidemiological information about eye conditions helping to tackle the lack of surveillance information in many regions of the globe.
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| 10. |
- Lima Ramos, Pedro, et al.
(author)
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Cross-sectional study investigating the prevalence and causes of vision impairment in Northwest Portugal using capture–recapture: [SV] Tvärsnittsstudie som undersöker prevalensen och orsakerna till synnedsättning i nordvästra Portugal med hjälp av infångning-återfångst[PT] Estudo transversal que investiga a prevalência e as causas da deficiência visual no Noroeste de Portugal utilizando captura-recaptura
- 2022
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In: BMJ Open. - : BMJ Publishing Group Ltd. - 2044-6055. ; 12:9
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Journal article (peer-reviewed)abstract
- Objectives: The aim of this study was to estimate the prevalence and causes of vision impairment (VI) in Portugal.Setting Information about people with VI was obtained from primary care centres, blind association (ACAPO) and from hospitals (the PCVIP study) in the Northwest of Portugal during a period spanning years 2014–2015. Causes of VI were obtained from hospitals.Participants Administrative and medical records of people with visual acuity in the better seeing eye of 0.5 decimal (0.30logMAR) or worse and/or visual field less than 20° were investigated. Capture–recapture with log-linear models was applied to estimate the number of individuals missing from lists of cases obtained from available sources.Primary and secondary outcome measures Log-linear models were used to estimate the crude prevalence and the category specific prevalence of VI.Results Crude prevalence of VI was 1.97% (95% CI 1.56% to 2.54%), and standardised prevalence was 1% (95% CI 0.78% to 1.27%). The age-specific prevalence was 3.27% (95% CI 2.36% to 4.90%), older than 64 years, 0.64% (95% CI 0.49% to 0.88%), aged 25–64 years, and 0.07% (95% CI 0.045% to 0.13%), aged less than 25 years. The female-to-male ratio was 1.3, that is, higher prevalence among females. The five leading causes of VI were diabetic retinopathy, cataract, age-related macular degeneration, glaucoma and disorders of the globe.Conclusions The prevalence of VI in Portugal was within the expected range and in line with other European countries. A significant number of cases of VI might be due to preventable cases and, therefore, a reduction of the prevalence of VI in Portugal seems possible. Women and old people were more likely to have VI and, therefore, these groups require extra attention. Future studies are necessary to characterise temporal changes in prevalence of VI in Portugal.No data are available. Raw data can be requested from the first author.
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