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Article ; Online: Becoming a PA: Reflections from Johnson & Wales University Students.

Africo, Ariana / Pazienza, Alysse / Dacosta, Matthew J / Denis, Kayla

Rhode Island medical journal (2013)

2018 Volume 101, Issue 6, Page(s) 23–24

MeSH term(s)	Humans ; Physician Assistants/education ; Rhode Island ; Students/psychology ; Universities
Language	English
Publishing date	2018-08-01
Publishing country	United States
Document type	Journal Article ; Personal Narratives
ZDB-ID	2707068-2
ISSN	2327-2228 ; 2327-2228
ISSN (online)	2327-2228
ISSN	2327-2228
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Article ; Online: py4DSTEM: A Software Package for Four-Dimensional Scanning Transmission Electron Microscopy Data Analysis.

Savitzky, Benjamin H / Zeltmann, Steven E / Hughes, Lauren A / Brown, Hamish G / Zhao, Shiteng / Pelz, Philipp M / Pekin, Thomas C / Barnard, Edward S / Donohue, Jennifer / Rangel DaCosta, Luis / Kennedy, Ellis / Xie, Yujun / Janish, Matthew T / Schneider, Matthew M / Herring, Patrick / Gopal, Chirranjeevi / Anapolsky, Abraham / Dhall, Rohan / Bustillo, Karen C /

Ercius, Peter / Scott, Mary C / Ciston, Jim / Minor, Andrew M / Ophus, Colin

Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada

2021 Volume 27, Issue 4, Page(s) 712–743

Abstract: Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a full two- ... ...

Abstract	Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a full two-dimensional (2D) image of the diffracted electron beam at each probe position, typically a 2D grid of probe positions. These 4D-STEM datasets are rich in information, including signatures of the local structure, orientation, deformation, electromagnetic fields, and other sample-dependent properties. However, extracting this information requires complex analysis pipelines that include data wrangling, calibration, analysis, and visualization, all while maintaining robustness against imaging distortions and artifacts. In this paper, we present py4DSTEM, an analysis toolkit for measuring material properties from 4D-STEM datasets, written in the Python language and released with an open-source license. We describe the algorithmic steps for dataset calibration and various 4D-STEM property measurements in detail and present results from several experimental datasets. We also implement a simple and universal file format appropriate for electron microscopy data in py4DSTEM, which uses the open-source HDF5 standard. We hope this tool will benefit the research community and help improve the standards for data and computational methods in electron microscopy, and we invite the community to contribute to this ongoing project.
Language	English
Publishing date	2021-05-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	1385710-1
ISSN	1435-8115 ; 1431-9276
ISSN (online)	1435-8115
ISSN	1431-9276
DOI	10.1017/S1431927621000477
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Article ; Online: Economic burden and health-related quality-of-life among infants with respiratory syncytial virus infection: A multi-country prospective cohort study in Europe.

Mao, Zhuxin / Li, Xiao / Dacosta-Urbieta, Ana / Billard, Marie-Noëlle / Wildenbeest, Joanne / Korsten, Koos / Martinón-Torres, Federico / Heikkinen, Terho / Cunningham, Steve / Snape, Matthew D / Robinson, Hannah / Pollard, Andrew J / Postma, Maarten / Dervaux, Benoit / Hens, Niel / Bont, Louis / Bilcke, Joke / Beutels, Philippe

Vaccine

2023 Volume 41, Issue 16, Page(s) 2707–2715

Abstract: Background: Respiratory syncytial virus (RSV) causes a considerable disease burden in young children globally, but reliable estimates of RSV-related costs and health-related quality-of-life (HRQoL) are scarce. This study aimed to evaluate the RSV- ... ...

Abstract	Background: Respiratory syncytial virus (RSV) causes a considerable disease burden in young children globally, but reliable estimates of RSV-related costs and health-related quality-of-life (HRQoL) are scarce. This study aimed to evaluate the RSV-associated costs and HRQoL effects in infants and their caregivers in four European countries. Methods: Healthy term-born infants were recruited at birth and actively followed up in four European countries. Symptomatic infants were systematically tested for RSV. Caregivers recorded the daily HRQoL of their child and themselves, measured by a modified EQ-5D with Visual Analogue Scale, for 14 consecutive days or until symptoms resolved. At the end of each RSV episode, caregivers reported healthcare resource use and work absenteeism. Direct medical costs per RSV episode were estimated from a healthcare payer's perspective and indirect costs were estimated from a societal perspective. Means and 95% confidence intervals (CI) of direct medical costs, total costs (direct costs + productivity loss) and quality-adjusted life-day (QALD) loss per RSV episode were estimated per RSV episode, as well as per subgroup (medical attendance, country). Results: Our cohort of 1041 infants experienced 265 RSV episodes with a mean symptom duration of 12.5 days. The mean (95% CI) cost per RSV episode was €399.5 (242.3, 584.2) and €494.3 (317.7, 696.1) from the healthcare payer's and societal perspective, respectively. The mean QALD loss per RSV episode of 1.9 (1.7, 2.1) was independent of medical attendance (in contrast to costs, which also differed by country). Caregiver and infant HRQoL evolved similarly. Conclusion: This study fills essential gaps for future economic evaluations by prospectively estimating direct and indirect costs and HRQoL effects on healthy term infants and caregivers separately, for both medically attended (MA) and non-MA laboratory-confirmed RSV episodes. We generally observed greater HRQoL losses than in previous studies which used non-community and/or non-prospective designs.
MeSH term(s)	Child ; Infant, Newborn ; Humans ; Infant ; Child, Preschool ; Respiratory Syncytial Virus Infections/epidemiology ; Financial Stress ; Prospective Studies ; Patient Care ; Health Care Costs ; Surveys and Questionnaires ; Quality of Life ; Europe/epidemiology ; Respiratory Syncytial Virus, Human ; Hospitalization
Language	English
Publishing date	2023-03-21
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	605674-x
ISSN	1873-2518 ; 0264-410X
ISSN (online)	1873-2518
ISSN	0264-410X
DOI	10.1016/j.vaccine.2023.03.024
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Article ; Online: A hydrazine- and phosgene-free synthesis of tetrazinanones, precursors to 1,5-dialkyl-6-oxoverdazyl radicals.

Bancerz, Matthew / Youn, Beom / DaCosta, Matthew V / Georges, Michael K

The Journal of organic chemistry

2012 Volume 77, Issue 5, Page(s) 2415–2421

Abstract: A complementary approach to published synthetic methods for tetrazinanones, precursors to verdazyl radicals, is described herein. This approach uses carbohydrazide, a commercially available reagent, as a common starting material. Unlike previous methods ... ...

Abstract	A complementary approach to published synthetic methods for tetrazinanones, precursors to verdazyl radicals, is described herein. This approach uses carbohydrazide, a commercially available reagent, as a common starting material. Unlike previous methods described in the literature, this synthetic scheme does not rely on phosgene, phosgene substitutes, or the limited pool of commercially available monosubstituted hydrazines for its execution. A large variety of alkyl substitution patterns at the N-1 and N-5 positions of verdazyl radicals are possible, including both symmetrically and unsymmetrically substituted products. An initial condensation reaction of carbohydrazide with a specific aldehyde introduces the desired C-3 substituent in the final verdazyl radical product and protects the NH(2) groups during the subsequent N-1 and N-5 alkylation reactions. A succeeding methanolysis and concomitant ring-closing reaction gives the tetrazinanone. A number of known oxidation methods can then be employed to form the final verdazyl radical product.
MeSH term(s)	Free Radicals/chemical synthesis ; Free Radicals/chemistry ; Hydrazines/chemistry ; Molecular Structure ; Phosgene/chemistry ; Tetrazoles/chemical synthesis ; Tetrazoles/chemistry
Chemical Substances	Free Radicals ; Hydrazines ; Tetrazoles ; Phosgene (117K140075) ; hydrazine (27RFH0GB4R) ; carbohydrazide (W8V7FYY4WH)
Language	English
Publishing date	2012-03-02
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	123490-0
ISSN	1520-6904 ; 0022-3263
ISSN (online)	1520-6904
ISSN	0022-3263
DOI	10.1021/jo300027b
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Article ; Online: Phylogenomics clarifies biogeographic and evolutionary history, and conservation status of West Indian tremblers and thrashers (Aves: Mimidae).

DaCosta, Jeffrey M / Miller, Matthew J / Mortensen, Jennifer L / Reed, J Michael / Curry, Robert L / Sorenson, Michael D

Molecular phylogenetics and evolution

2019 Volume 136, Page(s) 196–205

Abstract: The West Indian avifauna has provided fundamental insights into island biogeography, taxon cycles, and the evolution of avian behavior. Our interpretations, however, should rely on robust hypotheses of evolutionary relationships and consistent ... ...

Abstract	The West Indian avifauna has provided fundamental insights into island biogeography, taxon cycles, and the evolution of avian behavior. Our interpretations, however, should rely on robust hypotheses of evolutionary relationships and consistent conclusions about taxonomic status in groups with many endemic island populations. Here we present a phylogenetic study of the West Indian thrashers, tremblers, and allies, an assemblage of at least 5 species found on 29 islands, including what is considered the Lesser Antilles' only avian radiation. We improve on previous phylogenetic studies of this group by using double-digest restriction site-associated DNA sequencing (ddRAD-seq) to broadly sample loci scattered across the nuclear genome. A variety of analyses, based on either nucleotide variation in 2223 loci recovered in all samples or at 13,282 loci confidently scored as present or absent in all samples, converged on a single well-supported phylogenetic hypothesis. Results indicate that the resident West Indian taxa form a monophyletic group, exclusive of the Neotropical-Nearctic migratory Gray Catbird Dumetella carolinensis, which breeds in North America; this outcome differs from earlier studies suggesting that Gray Catbird was nested within a clade of island resident species. Thus, our findings imply a single colonization of the West Indies without the need to invoke a subsequent 'reverse colonization' of the mainland by West Indian taxa. Additionally, our study is the first to sample both endemic subspecies of the endangered White-breasted Thrasher Ramphocinclus brachyurus. We find that these subspecies have a long history of evolutionary independence with no evidence of gene flow, and are as genetically divergent from each other as other genera in the group. These findings support recognition of R. brachyurus (restricted to Martinique) and the Saint Lucia Thrasher R. sanctaeluciae as two distinct, single-island endemic species, and indicate the need to re-evaluate conservation plans for these taxa. Our results demonstrate the utility of phylogenomic datasets for generating robust systematic hypotheses.
MeSH term(s)	Animals ; Base Sequence ; Conserved Sequence ; DNA, Mitochondrial/genetics ; Passeriformes/classification ; Passeriformes/genetics ; Phylogeny ; Phylogeography ; Restriction Mapping ; Sequence Analysis, DNA ; Species Specificity ; West Indies
Chemical Substances	DNA, Mitochondrial
Language	English
Publishing date	2019-04-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	33610-5
ISSN	1095-9513 ; 1055-7903
ISSN (online)	1095-9513
ISSN	1055-7903
DOI	10.1016/j.ympev.2019.04.016
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Article: A Hydrazine- and Phosgene-Free Synthesis of Tetrazinanones, Precursors to 1,5-Dialkyl-6-Oxoverdazyl Radicals

Bancerz, Matthew / DaCosta Matthew V / Georges Michael K / Youn Beom

Journal of organic chemistry. 2012 Mar. 02, v. 77, no. 5

2012

Abstract	A complementary approach to published synthetic methods for tetrazinanones, precursors to verdazyl radicals, is described herein. This approach uses carbohydrazide, a commercially available reagent, as a common starting material. Unlike previous methods described in the literature, this synthetic scheme does not rely on phosgene, phosgene substitutes, or the limited pool of commercially available monosubstituted hydrazines for its execution. A large variety of alkyl substitution patterns at the N-1 and N-5 positions of verdazyl radicals are possible, including both symmetrically and unsymmetrically substituted products. An initial condensation reaction of carbohydrazide with a specific aldehyde introduces the desired C-3 substituent in the final verdazyl radical product and protects the NHâ groups during the subsequent N-1 and N-5 alkylation reactions. A succeeding methanolysis and concomitant ring-closing reaction gives the tetrazinanone. A number of known oxidation methods can then be employed to form the final verdazyl radical product.
Keywords	aldehydes ; alkylation ; chemical structure ; condensation reactions ; free radicals ; hydrazines ; methanolysis ; organic chemistry ; oxidation
Language	English
Dates of publication	2012-0302
Size	p. 2415-2421.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	123490-0
ISSN	1520-6904 ; 0022-3263
ISSN (online)	1520-6904
ISSN	0022-3263
DOI	10.1021%2Fjo300027b
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Article ; Online: The burden of respiratory syncytial virus in healthy term-born infants in Europe: a prospective birth cohort study.

Wildenbeest, Joanne G / Billard, Marie-Noëlle / Zuurbier, Roy P / Korsten, Koos / Langedijk, Annefleur C / van de Ven, Peter M / Snape, Matthew D / Drysdale, Simon B / Pollard, Andrew J / Robinson, Hannah / Heikkinen, Terho / Cunningham, Steve / O'Neill, Thomas / Rizkalla, Bishoy / Dacosta-Urbieta, Ana / Martinón-Torres, Federico / van Houten, Marlies A / Bont, Louis J

The Lancet. Respiratory medicine

2022 Volume 11, Issue 4, Page(s) 341–353

Abstract: Background: Respiratory syncytial virus (RSV) is a major cause of hospitalisation in infants. The burden of RSV infection in healthy term infants has not yet been established. Accurate health-care burden data in healthy infants are necessary to ... ...

Abstract	Background: Respiratory syncytial virus (RSV) is a major cause of hospitalisation in infants. The burden of RSV infection in healthy term infants has not yet been established. Accurate health-care burden data in healthy infants are necessary to determine RSV immunisation policy when RSV immunisation becomes available. Methods: We performed a multicentre, prospective, observational birth cohort study in healthy term-born infants (≥37 weeks of gestation) in five sites located in different European countries to determine the health-care burden of RSV. The incidence of RSV-associated hospitalisations in the first year of life was determined by parental questionnaires and hospital chart reviews. We performed active RSV surveillance in a nested cohort to determine the incidence of medically attended RSV infections. The study is registered with ClinicalTrials.gov, NCT03627572. Findings: In total, 9154 infants born between July 1, 2017, and April 1, 2020, were followed up during the first year of life and 993 participated in the nested active surveillance cohort. The incidence of RSV-associated hospitalisations in the total cohort was 1·8% (95% CI 1·6-2·1). There were eight paediatric intensive care unit admissions, corresponding to 5·5% of 145 RSV-associated hospitalisations and 0·09% of the total cohort. Incidence of RSV infection in the active surveillance cohort confirmed by any diagnostic assay was 26·2% (24·0-28·6) and that of medically attended RSV infection was 14·1% (12·3-16·0). Interpretation: RSV-associated acute respiratory infection causes substantial morbidity, leading to the hospitalisation of one in every 56 healthy term-born infants in high-income settings. Immunisation of pregnant women or healthy term-born infants during their first winter season could have a major effect on the health-care burden caused by RSV infections. Funding: Innovative Medicines Initiative 2 Joint Undertaking, with support from the EU's Horizon 2020 research and innovation programme and European Federation of Pharmaceutical Industries and Associations.
MeSH term(s)	Child ; Female ; Humans ; Infant ; Pregnancy ; Cohort Studies ; Europe/epidemiology ; Hospitalization ; Prospective Studies ; Respiratory Syncytial Virus Infections ; Respiratory Syncytial Virus, Human
Language	English
Publishing date	2022-11-10
Publishing country	England
Document type	Journal Article ; Multicenter Study ; Observational Study ; Research Support, Non-U.S. Gov't
ZDB-ID	2686754-0
ISSN	2213-2619 ; 2213-2600
ISSN (online)	2213-2619
ISSN	2213-2600
DOI	10.1016/S2213-2600(22)00414-3
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Article: Phylogenomics clarifies biogeographic and evolutionary history, and conservation status of West Indian tremblers and thrashers (Aves: Mimidae)

DaCosta, Jeffrey M / Miller, Matthew J / Mortensen, Jennifer L / Reed, J. Michael / Curry, Robert L / Sorenson, Michael D

Molecular phylogenetics and evolution. 2019 July, v. 136

2019

Abstract	The West Indian avifauna has provided fundamental insights into island biogeography, taxon cycles, and the evolution of avian behavior. Our interpretations, however, should rely on robust hypotheses of evolutionary relationships and consistent conclusions about taxonomic status in groups with many endemic island populations. Here we present a phylogenetic study of the West Indian thrashers, tremblers, and allies, an assemblage of at least 5 species found on 29 islands, including what is considered the Lesser Antilles’ only avian radiation. We improve on previous phylogenetic studies of this group by using double-digest restriction site-associated DNA sequencing (ddRAD-seq) to broadly sample loci scattered across the nuclear genome. A variety of analyses, based on either nucleotide variation in 2223 loci recovered in all samples or at 13,282 loci confidently scored as present or absent in all samples, converged on a single well-supported phylogenetic hypothesis. Results indicate that the resident West Indian taxa form a monophyletic group, exclusive of the Neotropical–Nearctic migratory Gray Catbird Dumetella carolinensis, which breeds in North America; this outcome differs from earlier studies suggesting that Gray Catbird was nested within a clade of island resident species. Thus, our findings imply a single colonization of the West Indies without the need to invoke a subsequent ‘reverse colonization’ of the mainland by West Indian taxa. Additionally, our study is the first to sample both endemic subspecies of the endangered White-breasted Thrasher Ramphocinclus brachyurus. We find that these subspecies have a long history of evolutionary independence with no evidence of gene flow, and are as genetically divergent from each other as other genera in the group. These findings support recognition of R. brachyurus (restricted to Martinique) and the Saint Lucia Thrasher R. sanctaeluciae as two distinct, single-island endemic species, and indicate the need to re-evaluate conservation plans for these taxa. Our results demonstrate the utility of phylogenomic datasets for generating robust systematic hypotheses.
Keywords	Mimidae ; avifauna ; biogeography ; birds ; breeds ; conservation status ; data collection ; gene flow ; genetic variation ; geographical distribution ; indigenous species ; islands ; loci ; migratory behavior ; monophyly ; nuclear genome ; sequence analysis ; Caribbean ; Martinique ; North America ; Saint Lucia
Language	English
Dates of publication	2019-07
Size	p. 196-205.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	33610-5
ISSN	1095-9513 ; 1055-7903
ISSN (online)	1095-9513
ISSN	1055-7903
DOI	10.1016/j.ympev.2019.04.016
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Lanthanide upconversion nanoparticles and applications in bioassays and bioimaging: a review.

DaCosta, Matthew V / Doughan, Samer / Han, Yi / Krull, Ulrich J

Analytica chimica acta

2014 Volume 832, Page(s) 1–33

Abstract: Through the process of photon upconversion, trivalent lanthanide doped nanocrystals convert long-wavelength excitation radiation in the infrared or near infrared region to higher energy emission radiation from ultraviolet to infrared. Such materials ... ...

Abstract	Through the process of photon upconversion, trivalent lanthanide doped nanocrystals convert long-wavelength excitation radiation in the infrared or near infrared region to higher energy emission radiation from ultraviolet to infrared. Such materials offer potential for numerous advantages in analytical applications in comparison to molecular fluorophores and quantum dots. The use of IR radiation as an excitation source reduces autofluorescence and scattering of excitation radiation, which leads to a reduction of background in optical experiments. The upconverting nanocrystals offer excellent photostability and are composed of materials that are not particularly toxic to biological organisms. Excitation at long wavelengths also minimizes damage to biological materials. In this review, the different mechanisms responsible for the upconversion process, and methods that are used to synthesize and decorate upconverting nanoparticles are presented to indicate how absorption and emission can be tuned. Examples of recent applications of upconverting nanoparticles in bioassays for the detection of proteins, nucleic acids, metabolites and metal ions offer indications of analytical advantages in the development of methods of analysis. Examples include multi-color and multi-modal imaging, and the use of upconverting nanoparticles in theranostics.
MeSH term(s)	Animals ; Biological Assay/methods ; Humans ; Lanthanoid Series Elements/chemistry ; Luminescence ; Molecular Imaging/methods ; Nanoparticles/chemistry
Chemical Substances	Lanthanoid Series Elements
Language	English
Publishing date	2014-06-17
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1483436-4
ISSN	1873-4324 ; 0003-2670
ISSN (online)	1873-4324
ISSN	0003-2670
DOI	10.1016/j.aca.2014.04.030
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Book ; Online: py4DSTEM

a software package for multimodal analysis of four-dimensional scanning transmission electron microscopy datasets

2020

Abstract	Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a full 2D image of the diffracted electron beam at each probe position, typically a 2D grid of probe positions. These 4D-STEM datasets are rich in information, including signatures of the local structure, orientation, deformation, electromagnetic fields and other sample-dependent properties. However, extracting this information requires complex analysis pipelines, from data wrangling to calibration to analysis to visualization, all while maintaining robustness against imaging distortions and artifacts. In this paper, we present py4DSTEM, an analysis toolkit for measuring material properties from 4D-STEM datasets, written in the Python language and released with an open source license. We describe the algorithmic steps for dataset calibration and various 4D-STEM property measurements in detail, and present results from several experimental datasets. We have also implemented a simple and universal file format appropriate for electron microscopy data in py4DSTEM, which uses the open source HDF5 standard. We hope this tool will benefit the research community, helps to move the developing standards for data and computational methods in electron microscopy, and invite the community to contribute to this ongoing, fully open-source project. Comment: 32 pages, 18 figures
Keywords	Condensed Matter - Materials Science ; Condensed Matter - Mesoscale and Nanoscale Physics ; Physics - Applied Physics
Subject code	669
Publishing date	2020-03-20
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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