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Article ; Online: Reprint of: Inversion of dynamical Bragg intensities to complex structure factors by iterated projections. For Ultramic. 2020. ("Pico" Festschrift, May 2021).

Spence, John C H / Donatelli, Jeffrey J

2021 Volume 231, Page(s) 113409

Abstract: A method for recovering complex structure factors from many simultaneously excited Bragg beam in- tensities is described. The method is applied to simulated transmission electron diffraction data over a wide range of crystal thickness and beam energies. ... ...

Abstract	A method for recovering complex structure factors from many simultaneously excited Bragg beam in- tensities is described. The method is applied to simulated transmission electron diffraction data over a wide range of crystal thickness and beam energies. The method is based on iterated projections between structure and scattering matrices, which are related by a matrix unit ary transformation, exponential, which we invert. The algorithm removes multiple-scattering perturbations from diffraction data and might be extended to other fields, including X-ray and neutron diffraction and cryo-electron microscopy. Because coherent multiple scattering involves interference between Bragg beams, the method also solves the phase problem. Unlike dynamical inversion from electron microscope images or ptychography data, the method, which starts with Bragg beam intensities, provides complex structure factors unaffected by focusing errors or resolution limitations imposed by lenses. We provide inversions from simulated data with 441 simultaneously excited Bragg beams over a range of thickness and beam energy. We discuss the retrieval of chirality information from enantiomorphs, the efficient incorporation of symmetry information using the irreducible representation of the group of structure matrices, and the effect of HOLZ lines to provide three-dimensional information.
Language	English
Publishing date	2021-10-28
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1479043-9
ISSN	1879-2723 ; 0304-3991
ISSN (online)	1879-2723
ISSN	0304-3991
DOI	10.1016/j.ultramic.2021.113409
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Article ; Online: Inversion of dynamical Bragg intensities to complex structure factors by iterated projections. For Ultramic. 2020. ("Pico" Festschrift, May 2021).

Spence, John C H / Donatelli, Jeffrey J

Ultramicroscopy

2021 Volume 222, Page(s) 113214

Abstract	A method for recovering complex structure factors from many simultaneously excited Bragg beam in- tensities is described. The method is applied to simulated transmission electron diffraction data over a wide range of crystal thickness and beam energies. The method is based on iterated projections between structure and scattering matrices, which are related by a matrix unit ary transformation, exponential, which we invert. The algorithm removes multiple-scattering perturbations from diffraction data and might be extended to other fields, including X-ray and neutron diffraction and cryo-electron microscopy. Because coherent multiple scattering involves interference between Bragg beams, the method also solves the phase problem. Unlike dynamical inversion from electron microscope images or ptychography data, the method, which starts with Bragg beam intensities, provides complex structure factors unaffected by focusing errors or resolution limitations imposed by lenses. We provide inversions from simulated data with 441 simultaneously excited Bragg beams over a range of thickness and beam energy. We discuss the retrieval of chirality information from enantiomorphs, the efficient incorporation of symmetry information using the irreducible representation of the group of structure matrices, and the effect of HOLZ lines to provide three-dimensional information.
Language	English
Publishing date	2021-01-26
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1479043-9
ISSN	1879-2723 ; 0304-3991
ISSN (online)	1879-2723
ISSN	0304-3991
DOI	10.1016/j.ultramic.2021.113214
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Article: XFELs for structure and dynamics in biology.

Spence, J C H

IUCrJ

2017 Volume 4, Issue Pt 4, Page(s) 322–339

Abstract: The development and application of the free-electron X-ray laser (XFEL) to structure and dynamics in biology since its inception in 2009 are reviewed. The research opportunities which result from the ability to outrun most radiation-damage effects are ... ...

Abstract	The development and application of the free-electron X-ray laser (XFEL) to structure and dynamics in biology since its inception in 2009 are reviewed. The research opportunities which result from the ability to outrun most radiation-damage effects are outlined, and some grand challenges are suggested. By avoiding the need to cool samples to minimize damage, the XFEL has permitted atomic resolution imaging of molecular processes on the 100 fs timescale under near-physiological conditions and in the correct thermal bath in which molecular machines operate. Radiation damage, comparisons of XFEL and synchrotron work, single-particle diffraction, fast solution scattering, pump-probe studies on photosensitive proteins, mix-and-inject experiments, caged molecules, pH jump and other reaction-initiation methods, and the study of molecular machines are all discussed. Sample-delivery methods and data-analysis algorithms for the various modes, from serial femtosecond crystallo-graphy to fast solution scattering, fluctuation X-ray scattering, mixing jet experiments and single-particle diffraction, are also reviewed.
Language	English
Publishing date	2017-05-10
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2754953-7
ISSN	2052-2525
ISSN	2052-2525
DOI	10.1107/S2052252517005760
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Article ; Online: Latent tuberculosis infection testing practices in a large U.S. integrated healthcare system.

Ku, Jennifer H / Fischer, Heidi / Qian, Lei X / Li, Kris / Skarbinski, Jacek / Shaw, Sally / Bruxvoort, Katia J / Lewin, Bruno J / Spence, Brigitte C / Tartof, Sara Y

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

2024

Abstract: ... 1.13, 1.09-1.16], hepatitis B [1.45, 1.34-1.57], hepatitis C [1.54, 1.44-1.66], and birth ...

Abstract	Purpose: Tuberculosis (TB) is a public health threat with >80% of active TB in the U.S. occurring due to reactivation of latent tuberculosis infection (LTBI). We may be under-screening those with high risk for LTBI and over-testing those at lower risk. A better understanding of gaps in current LTBI testing practices in relation to LTBI test positivity is needed. Methods: This study, conducted between 01/01/2008 and 12/31/2019 at Kaiser Permanente Southern California, included individuals ≥18 years of age without a history of active TB. We examined factors associated with LTBI testing and LTBI positivity. Results: Among 3,816,884 adults (52% female, 37% White, 37% Hispanic, mean age 43.5 years [S.D. 16.1]), 706,367 (19%) were tested for LTBI, among whom 60,393 (9%) had ≥1 positive result. Among 1,211,971 individuals meeting ≥1 screening criteria for LTBI, 210,025 (17%) were tested for LTBI. Factors associated with higher adjusted odds (aOR) of testing positive included male sex [aOR: 1.32, 95% CI:1.30-1.35], Asian/Pacific Islander [2.78, 2.68-2.88], current smoking [1.24, 1.20-1.28], diabetes [1.13, 1.09-1.16], hepatitis B [1.45, 1.34-1.57], hepatitis C [1.54, 1.44-1.66], and birth in a country with an elevated TB rate [3.40, 3.31-3.49]). Despite being risk factors for testing positive for LTBI, none of these factors were associated with higher odds of LTBI testing. Conclusions: Current LTBI testing practices may be missing individuals at high risk of LTBI. Additional work is needed to refine and implement screening guidelines that appropriately target testing for those at highest risk for LTBI.
Language	English
Publishing date	2024-01-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	1099781-7
ISSN	1537-6591 ; 1058-4838
ISSN (online)	1537-6591
ISSN	1058-4838
DOI	10.1093/cid/ciae015
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Article ; Online: Inversion of Many-Beam Bragg Intensities for Phasing by Iterated Projections: Removal of Multiple Scattering Artifacts from Diffraction Data.

Donatelli, Jeffrey J / Spence, John C H

Physical review letters

2020 Volume 125, Issue 6, Page(s) 65502

Abstract: An iterated projection algorithm (N-Phaser) is developed that reconstructs a scattering potential from N-beam multiple Bragg scattered intensities. The method may be used to eliminate multiple scattering artifacts from electron diffraction data, solving ... ...

Abstract	An iterated projection algorithm (N-Phaser) is developed that reconstructs a scattering potential from N-beam multiple Bragg scattered intensities. The method may be used to eliminate multiple scattering artifacts from electron diffraction data, solving the phase problem and increasing the thicknesses of samples used in materials science, solid-state chemistry, and small molecule crystallography. For high-energy transmission electron diffraction, we show that the algorithm recovers accurate complex structure factors from a wide range of thicknesses, orientations, and relativistic beam energies, and does not require known thickness or atomic-resolution data if sufficient multiple scattering occurs. Extensions to Cryo-electron microscopy and Micro-electron diffraction are suggested.
Language	English
Publishing date	2020-08-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.125.065502
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Article ; Online: Physical activity, screen time and dietary behaviours in New Zealand adolescents prior to and following the onset of the COVID-19 pandemic.

Mandic, Sandra / Khan, Asaduzzaman / García Bengoechea, Enrique / Coppell, Kirsten J / Spence, John C / Smith, Melody

BMC public health

2024 Volume 24, Issue 1, Page(s) 188

Abstract: ... of moderate-to-vigorous physical activity), outside school screen time (≤ 2 h/day) and fruit and vegetable ... 9; p < 0.001) and weekend days (6.9 ± 3.5 vs. 6.1 ± 3.6 h/day; p < 0.001). Reported frequency ...

Abstract	Background: Insufficient physical activity, high screen time, and unhealthy dietary patterns among adolescents may have worsened during the pandemic, but data are lacking. This study compared physical activity, screen time and fruit and vegetable intake in adolescents from Dunedin, New Zealand, 5-6 years before (Study 1) and during (Study 2) the COVID-19 pandemic. Methods: Adolescents completed an online survey as part of the Built Environment and Active Transport to School (BEATS) studies in 2014/2015 (Study 1; n = 1,266; age: 15.3 ± 1.4 years; 54.6% female) and 2021/2022 (Study 2; n = 819; age: 15.2 ± 1.4 years; 47.4% female). The proportion of adolescents meeting guidelines for physical activity (≥ 60 min/day of moderate-to-vigorous physical activity), outside school screen time (≤ 2 h/day) and fruit and vegetable intake (> 1 serving/day for both fruit and vegetables) was calculated. Data were analysed using multivariable linear and logistic regression modelling. Results: Few adolescents met recommended health behaviour guidelines. Compared to Study 1, significantly greater proportions of adolescents at Study 2 met guidelines for physical activity (16.7% vs. 23.1%; p < 0.001) and outside school screen time (13.3% vs. 18.3%; p < 0.001) while fruit and vegetable intake was not different (29.6% vs. 27.0%; p = 0.322). Compared to Study 1, average outside school screen time at Study 2 was lower on both weekdays (5.0 ± 2.9 vs. 4.6 ± 2.9; p < 0.001) and weekend days (6.9 ± 3.5 vs. 6.1 ± 3.6 h/day; p < 0.001). Reported frequency of consuming sweets was higher and soft drinks lower at Study 2 versus Study 1. Conclusions: Despite observed higher levels of physical activity and lower levels of outside school screen time during the pandemic compared to the pre-pandemic levels, few adolescents met health behaviour guidelines at both time points. Therefore, comprehensive health promotion that aims to improve physical activity levels, screen time and dietary patterns for adolescents is still necessary to prevent chronic health conditions adulthood.
MeSH term(s)	Humans ; Female ; Adolescent ; Adult ; Male ; Pandemics ; Screen Time ; New Zealand/epidemiology ; COVID-19/epidemiology ; Diet ; Exercise
Language	English
Publishing date	2024-01-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2041338-5
ISSN	1471-2458 ; 1471-2458
ISSN (online)	1471-2458
ISSN	1471-2458
DOI	10.1186/s12889-024-17688-7
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Article ; Online: FGF18 promotes human lung branching morphogenesis through regulating mesenchymal progenitor cells.

Danopoulos, Soula / Belgacemi, Randa / Hein, Renee F C / Miller, Alyssa J / Deutsch, Gail H / Glass, Ian / Spence, Jason R / Al Alam, Denise

American journal of physiology. Lung cellular and molecular physiology

2023 Volume 324, Issue 4, Page(s) L433–L444

Abstract: Fibroblast growth factor (FGF) signaling is known to play an important role in lung organogenesis. However, we recently demonstrated that FGF10 fails to induce branching in human fetal lungs as is observed in mouse. Our previous human fetal lung RNA ... ...

Abstract	Fibroblast growth factor (FGF) signaling is known to play an important role in lung organogenesis. However, we recently demonstrated that FGF10 fails to induce branching in human fetal lungs as is observed in mouse. Our previous human fetal lung RNA sequencing data exhibited increased FGF18 during the pseudoglandular stage of development, suggestive of its importance in human lung branching morphogenesis. Whereas it has been previously reported that FGF18 is critical during alveologenesis, few studies have described its implication in lung branching, specifically in human. Therefore, we aimed to determine the role of FGF18 in human lung branching morphogenesis. Human fetal lung explants within the pseudoglandular stage of development were treated with recombinant human FGF18 in air-liquid interface culture. Explants were analyzed grossly to assess differences in branching pattern, as well as at the cellular and molecular levels. FGF18 treatment promoted branching in explant cultures and demonstrated increased epithelial proliferation as well as maintenance of the double positive SOX2/SOX9 distal bud progenitor cells, confirming its role in human lung branching morphogenesis. In addition, FGF18 treated explants displayed increased expression of SOX9, FN1, and COL2A1 within the mesenchyme, all factors that are important to chondrocyte differentiation. In humans, cartilaginous airways extend deep into the lung up to the 12th generation of branching whereas in mouse these are restricted to the trachea and main bronchi. Therefore, our data suggest that FGF18 promotes human lung branching morphogenesis through regulating mesenchymal progenitor cells.
MeSH term(s)	Animals ; Humans ; Mice ; Fibroblast Growth Factors/genetics ; Lung/metabolism ; Mesenchymal Stem Cells ; Morphogenesis/physiology ; Organogenesis/genetics
Chemical Substances	Fibroblast Growth Factors (62031-54-3) ; fibroblast growth factor 18
Language	English
Publishing date	2023-02-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1013184-x
ISSN	1522-1504 ; 1040-0605
ISSN (online)	1522-1504
ISSN	1040-0605
DOI	10.1152/ajplung.00316.2022
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Article ; Online: A new solution to the curved Ewald sphere problem for 3D image reconstruction in electron microscopy.

Chen, J P J / Schmidt, K E / Spence, J C H / Kirian, R A

Ultramicroscopy

2021 Volume 224, Page(s) 113234

Abstract: We develop an algorithm capable of imaging a three-dimensional object given a collection of two-dimensional images of that object that are significantly influenced by the curvature of the Ewald sphere. These two-dimensional images cannot be approximated ... ...

Abstract	We develop an algorithm capable of imaging a three-dimensional object given a collection of two-dimensional images of that object that are significantly influenced by the curvature of the Ewald sphere. These two-dimensional images cannot be approximated as projections of the object. Such an algorithm is useful in cryo-electron microscopy where larger samples, higher resolution, or lower energy electron beams are desired, all of which contribute to the significance of Ewald curvature.
Language	English
Publishing date	2021-02-21
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1479043-9
ISSN	1879-2723 ; 0304-3991
ISSN (online)	1879-2723
ISSN	0304-3991
DOI	10.1016/j.ultramic.2021.113234
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Article: Working Memory Maintenance of Visual and Auditory Spatial Information Relies on Supramodal Neural Codes in the Dorsal Frontoparietal Cortex.

Rizza, Aurora / Pedale, Tiziana / Mastroberardino, Serena / Olivetti Belardinelli, Marta / Van der Lubbe, Rob H J / Spence, Charles / Santangelo, Valerio

Brain sciences

2024 Volume 14, Issue 2

Abstract: The frontoparietal attention network plays a pivotal role during working memory (WM) maintenance, especially under high-load conditions. Nevertheless, there is ongoing debate regarding whether this network relies on supramodal or modality-specific neural ...

Abstract	The frontoparietal attention network plays a pivotal role during working memory (WM) maintenance, especially under high-load conditions. Nevertheless, there is ongoing debate regarding whether this network relies on supramodal or modality-specific neural signatures. In this study, we used multi-voxel pattern analysis (MVPA) to evaluate the neural representation of visual versus auditory information during WM maintenance. During fMRI scanning, participants maintained small or large spatial configurations (low- or high-load trials) of either colour shades or sound pitches in WM for later retrieval. Participants were less accurate in retrieving high- vs. low-load trials, demonstrating an effective manipulation of WM load, irrespective of the sensory modality. The frontoparietal regions involved in maintaining high- vs. low-load spatial maps in either sensory modality were highlighted using a conjunction analysis. Widespread activity was found across the dorsal frontoparietal network, peaking on the frontal eye fields and the superior parietal lobule, bilaterally. Within these regions, MVPAs were performed to quantify the pattern of distinctness of visual vs. auditory neural codes during WM maintenance. These analyses failed to reveal distinguishable patterns in the dorsal frontoparietal regions, thus providing support for a common, supramodal neural code associated with the retention of either visual or auditory spatial configurations.
Language	English
Publishing date	2024-01-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2651993-8
ISSN	2076-3425
ISSN	2076-3425
DOI	10.3390/brainsci14020123
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Article ; Online: Is there an athlete's artery? A comparison of brachial and femoral artery structure and function in male strength, power and endurance athletes.

Naylor, Louise H / Spence, Angela L / Donker, Stijn C M / Thijssen, Dick H J / Green, Daniel J

Journal of science and medicine in sport

2021 Volume 24, Issue 7, Page(s) 635–640

Abstract: Objectives: Exercise places physiological demands upon the cardiovascular system, subsequently leading to adaptations in structure and function. Different exercise modalities (endurance, strength and power) lead to distinct hemodynamic demands and, ... ...

Abstract	Objectives: Exercise places physiological demands upon the cardiovascular system, subsequently leading to adaptations in structure and function. Different exercise modalities (endurance, strength and power) lead to distinct hemodynamic demands and, possibly, different patterns of adaptation. Our aim was to assess and compare brachial and femoral artery function and structure in elite level athletes engaged in endurance, strength and power sports. Design: cross sectional comparison. Methods: 30 male elite athletes (runners n=10, powerlifters n=11, weightlifters n=9) and 23 healthy controls were recruited. Brachial and femoral arterial diameters were assessed using ultrasound. Arterial function (brachial and femoral arteries) was determined using the flow mediated dilation (FMD) technique and body composition using body mass index (BMI) and body surface area (BSA). Results: Weightlifters had significantly larger brachial arterial diameters compared to controls (4.39±0.34 vs 3.86±0.42mm, p<0.01). As weightlifter and power athletes had significantly higher body mass, BMI and BSA, we adjusted diameter for BSA. BSA-correction ameliorated differences in brachial artery resting diameters between athletes and controls. However, BSA-corrected femoral artery diameter was significantly larger in runners compared to controls (3.51±0.28 vs 3.25±0.34mm, p<0.05). There were no differences in brachial FMD between groups. Femoral artery FMD was significantly higher in runners and weightlifters compared to controls (p<0.05 for both groups). Conclusions: Heterogeneous, limb-specific structural and functional vascular adaptation is evident in athletes, which may be influenced by exercise modality. Further, vascular remodelling relates to differences in body shape, specifically body composition, which should be accounted for when comparing athletes.
MeSH term(s)	Adaptation, Physiological ; Adult ; Body Mass Index ; Body Surface Area ; Brachial Artery/anatomy & histology ; Brachial Artery/diagnostic imaging ; Brachial Artery/physiology ; Cross-Sectional Studies ; Endothelium, Vascular/anatomy & histology ; Endothelium, Vascular/physiology ; Femoral Artery/anatomy & histology ; Femoral Artery/diagnostic imaging ; Femoral Artery/physiology ; Humans ; Male ; Muscle Strength ; Physical Conditioning, Human/physiology ; Physical Endurance/physiology ; Running/physiology ; Ultrasonography ; Vascular Remodeling ; Vasodilation ; Weight Lifting/physiology
Language	English
Publishing date	2021-02-26
Publishing country	Australia
Document type	Journal Article
ZDB-ID	1437829-2
ISSN	1878-1861 ; 1440-2440
ISSN (online)	1878-1861
ISSN	1440-2440
DOI	10.1016/j.jsams.2021.02.010
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