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Article ; Online: Publisher Correction: Expanding the arsenal of bacterial spearguns.

Righetto, Ricardo D / Engel, Benjamin D

Nature microbiology

2022 Volume 7, Issue 5, Page(s) 738

Language	English
Publishing date	2022-03-10
Publishing country	England
Document type	Published Erratum
ISSN	2058-5276
ISSN (online)	2058-5276
DOI	10.1038/s41564-022-01102-2
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Article ; Online: Expanding the arsenal of bacterial spearguns.

Righetto, Ricardo D / Engel, Benjamin D

Nature microbiology

2022 Volume 7, Issue 3, Page(s) 363–364

MeSH term(s)	Bacteria/genetics ; Bacteroidetes
Language	English
Publishing date	2022-03-04
Publishing country	England
Document type	Journal Article ; Comment
ISSN	2058-5276
ISSN (online)	2058-5276
DOI	10.1038/s41564-022-01078-z
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Article ; Online: Visualizing a Carbon-Fixing Nanowire Inside Bacteria

Ricardo D. Righetto / Benjamin D. Engel

CHIMIA, Vol 77, Iss

2023 Volume 5

Keywords	Anaerobic bacteria ; Carbon fixation ; Cyro-electron microscopy ; Electron transfer ; Enzyme ; Nanowire ; Chemistry ; QD1-999
Language	German
Publishing date	2023-05-01T00:00:00Z
Publisher	Swiss Chemical Society
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Chlorophyll biogenesis sees the light.

Wietrzynski, Wojciech / Engel, Benjamin D

Nature plants

2021 Volume 7, Issue 4, Page(s) 380–381

MeSH term(s)	Chlorophyll ; Chloroplasts ; Light-Harvesting Protein Complexes
Chemical Substances	Light-Harvesting Protein Complexes ; Chlorophyll (1406-65-1)
Language	English
Publishing date	2021-04-19
Publishing country	England
Document type	Journal Article ; Comment
ISSN	2055-0278
ISSN (online)	2055-0278
DOI	10.1038/s41477-021-00900-6
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Article ; Online: Integrating cellular electron microscopy with multimodal data to explore biology across space and time.

McCafferty, Caitlyn L / Klumpe, Sven / Amaro, Rommie E / Kukulski, Wanda / Collinson, Lucy / Engel, Benjamin D

Cell

2024 Volume 187, Issue 3, Page(s) 563–584

Abstract: Biology spans a continuum of length and time scales. Individual experimental methods only glimpse discrete pieces of this spectrum but can be combined to construct a more holistic view. In this Review, we detail the latest advancements in volume electron ...

Abstract	Biology spans a continuum of length and time scales. Individual experimental methods only glimpse discrete pieces of this spectrum but can be combined to construct a more holistic view. In this Review, we detail the latest advancements in volume electron microscopy (vEM) and cryo-electron tomography (cryo-ET), which together can visualize biological complexity across scales from the organization of cells in large tissues to the molecular details inside native cellular environments. In addition, we discuss emerging methodologies for integrating three-dimensional electron microscopy (3DEM) imaging with multimodal data, including fluorescence microscopy, mass spectrometry, single-particle analysis, and AI-based structure prediction. This multifaceted approach fills gaps in the biological continuum, providing functional context, spatial organization, molecular identity, and native interactions. We conclude with a perspective on incorporating diverse data into computational simulations that further bridge and extend length scales while integrating the dimension of time.
MeSH term(s)	Biology ; Cryoelectron Microscopy/methods ; Electron Microscope Tomography/methods ; Microscopy, Electron ; Microscopy, Fluorescence ; Time ; Computer Simulation
Language	English
Publishing date	2024-02-02
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2024.01.005
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Zs.A 1167: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Biologic Adjuvants to Rotator Cuff Repairs Induce Anti-Inflammatory Macrophage 2 Polarization and Reduce Inflammatory Macrophage 1 Polarization In Vitro.

Hawthorne, Benjamin C / Engel, Sam / McCarthy, Mary Beth R / Cote, Mark C / Mazzocca, Augustus D / Coyner, Katherine J

Arthroscopy : the journal of arthroscopic & related surgery : official publication of the Arthroscopy Association of North America and the International Arthroscopy Association

2024

Abstract: Purpose: To examine the effect of various biologic adjuvants on the polarization of macrophages in an in vitro model for rotator cuff tears.: Methods: Tissue was harvested from 6 patients undergoing arthroscopic rotator cuff repair. An in vitro model ...

Abstract	Purpose: To examine the effect of various biologic adjuvants on the polarization of macrophages in an in vitro model for rotator cuff tears. Methods: Tissue was harvested from 6 patients undergoing arthroscopic rotator cuff repair. An in vitro model of the supraspinatus and subacromial bursa was created and treated with control, platelet rich plasma (PRP), autologous activated serum (AAS), or a combination of PRP+AAS. The effect of treatment on macrophage polarization between M1 pro-inflammatory macrophages or M2 anti-inflammatory macrophages was measured using gene expression, protein expression, flow cytometry and nitric oxide (NO) production. Results: Tendon and bursa treated with PRP, AAS and PRP+AAS significantly decreased the gene expression of M1 markers IL-12 and TNF-a, while significantly increasing the expression of M2 markers Arginase, IL-10 and TGF-b (p<0.05) compared to treatment with control. ELISA analysis of protein production demonstrated that compared to control, co-culture treated with PRP, AAS and PRP+AAS significantly decreased markers of M1-macrophages (IL-6, IL-12, and TNF-a), while significantly increasing the expression of markers of M2-macrophages (Arginase, IL-10, and TGF-b) (p<0.05). Flow cytometry analysis of surface markers demonstrated that compared to control, tendon and bursa treated with PRP, AAS and PRP+AAS significantly decreased markers of M1-macrophages (CD80, CD86, CD64, CD16), while significantly increasing the expression of markers of M2-macrophages (CD163 and CD206) (p<0.05). Treatment of the co-culture with PRP, AAS and PRP+AAS consistently demonstrated a decrease in NO production (p<0.05) compared to control. AAS and PRP+AAS demonstrated an increased macrophage shift to M2 compared to PRP alone, whereas there was not as uniform of a shift when comparing PRP+AAS to AAS alone. Conclusions: In an in vitro model of rotator cuff tears, the treatment of supraspinatus tendon and subacromial bursa with PRP, AAS and PRP+AAS demonstrated an increase in markers of anti-inflammatory M2-macrophages and a concomitant decrease in markers of pro-inflammatory M1-macrophages. AAS and PRP+AAS contributed to a large shift to macrophage polarization to the anti-inflammatory M2 compared to PRP.
Language	English
Publishing date	2024-05-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	632528-2
ISSN	1526-3231 ; 0749-8063
ISSN (online)	1526-3231
ISSN	0749-8063
DOI	10.1016/j.arthro.2024.04.031
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Article ; Online: Complex Total Hip Arthroplasty in a Patient with Klippel-Trénaunay Syndrome: A Case Report.

Morrison, Todd A / Streufert, Benjamin D / Engel, Corey C / Bernasek, Thomas L / Gill, Meera

JBJS case connector

2022 Volume 12, Issue 1

Abstract: Case: Klippel-Trénaunay syndrome (KTS) carries manifestations including skeletal dysplasia and prominent vascular malformations. This report details a case of hip dysplasia in the setting of KTS treated with total hip arthroplasty (THA) requiring ... ...

Abstract	Case: Klippel-Trénaunay syndrome (KTS) carries manifestations including skeletal dysplasia and prominent vascular malformations. This report details a case of hip dysplasia in the setting of KTS treated with total hip arthroplasty (THA) requiring preoperative embolization, intraoperative angiography for placement of an iliac artery occlusive balloon, and modular hip arthroplasty components for femoral and acetabular dysplasia. Perioperatively, the patient rehabilitated well and was walking painlessly and unassisted at 3 and 12 months postoperatively. Conclusion: Successful THA for dysplasia and degenerative changes associated with KTS is possible but requires a complex multidisciplinary perioperative approach.
MeSH term(s)	Arthroplasty, Replacement, Hip ; Hip Dislocation, Congenital/complications ; Humans ; Klippel-Trenaunay-Weber Syndrome/complications ; Klippel-Trenaunay-Weber Syndrome/surgery ; Lower Extremity/surgery ; Vascular Malformations
Language	English
Publishing date	2022-01-12
Publishing country	United States
Document type	Case Reports ; Journal Article
ISSN	2160-3251
ISSN (online)	2160-3251
DOI	e20.00488
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Article ; Online: Factors that influence the scope of practice of the chiropractic profession in Australia: a thematic analysis.

Wiggins, Desmond / Downie, Aron / Engel, Roger / Grace, Sandra / Brown, Benjamin T

Chiropractic & manual therapies

2024 Volume 32, Issue 1, Page(s) 18

Abstract: Scope of practice has been defined as the activities that an individual health care practitioner is allowed to undertake within a specific profession. The chiropractic profession in Australia does not currently have a documented scope of practice. ... ...

Abstract	Scope of practice has been defined as the activities that an individual health care practitioner is allowed to undertake within a specific profession. The chiropractic profession in Australia does not currently have a documented scope of practice. Informed discussions around scope of practice are hampered by a paucity of literature in this area. Acknowledging this void in the literature, we chose to investigate the factors that influence scope of practice of the chiropractic profession. A knowledge of the factors will facilitate discussion on the topic and help the profession to work towards establishing a scope of practice.Aim The aim of this study was to identify the factors that influence scope of practice of chiropractic in Australia from the perspective of 4 stakeholder groups within the profession.Methods This study employed semi-structured, online-interviews. Open-ended questions, guided by a flexible interview protocol, and augmented by supplemental questions, probes and comments, were used to gather data on the research question. Data were analysed using reflexive thematic analysis.Results Six factors that influenced scope of practice of chiropractic were identified in this study: education, evidence (research-derived and practice-based), political influence, community expectations, entrepreneurial business models, and geographical location.Conclusion Knowledge of the factors that influence scope of practice of chiropractic in Australia is important for establishing a scope of practice for the profession. This knowledge is also of value to a range of stakeholders including patients, health care providers (within and outside the profession), professional associations, and policymakers.
MeSH term(s)	Chiropractic ; Humans ; Australia ; Scope of Practice ; Qualitative Research ; Attitude of Health Personnel
Language	English
Publishing date	2024-05-27
Publishing country	England
Document type	Journal Article
ZDB-ID	2590836-4
ISSN	2045-709X ; 2045-709X
ISSN (online)	2045-709X
ISSN	2045-709X
DOI	10.1186/s12998-024-00535-2
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Article ; Online: MemBrain: A deep learning-aided pipeline for detection of membrane proteins in Cryo-electron tomograms.

Lamm, Lorenz / Righetto, Ricardo D / Wietrzynski, Wojciech / Pöge, Matthias / Martinez-Sanchez, Antonio / Peng, Tingying / Engel, Benjamin D

Computer methods and programs in biomedicine

2022 Volume 224, Page(s) 106990

Abstract: Background and objective: Cryo-electron tomography (cryo-ET) is an imaging technique that enables 3D visualization of the native cellular environment at sub-nanometer resolution, providing unpreceded insights into the molecular organization of cells. ... ...

Abstract	Background and objective: Cryo-electron tomography (cryo-ET) is an imaging technique that enables 3D visualization of the native cellular environment at sub-nanometer resolution, providing unpreceded insights into the molecular organization of cells. However, cryo-electron tomograms suffer from low signal-to-noise ratios and anisotropic resolution, which makes subsequent image analysis challenging. In particular, the efficient detection of membrane-embedded proteins is a problem still lacking satisfactory solutions. Methods: We present MemBrain - a new deep learning-aided pipeline that automatically detects membrane-bound protein complexes in cryo-electron tomograms. After subvolumes are sampled along a segmented membrane, each subvolume is assigned a score using a convolutional neural network (CNN), and protein positions are extracted by a clustering algorithm. Incorporating rotational subvolume normalization and using a tiny receptive field simplify the task of protein detection and thus facilitate the network training. Results: MemBrain requires only a small quantity of training labels and achieves excellent performance with only a single annotated membrane (F1 score: 0.88). A detailed evaluation shows that our fully trained pipeline outperforms existing classical computer vision-based and CNN-based approaches by a large margin (F1 score: 0.92 vs. max. 0.63). Furthermore, in addition to protein center positions, MemBrain can determine protein orientations, which has not been implemented by any existing CNN-based method to date. We also show that a pre-trained MemBrain program generalizes to tomograms acquired using different cryo-ET methods and depicting different types of cells. Conclusions: MemBrain is a powerful and annotation-efficient tool for the detection of membrane protein complexes in cryo-ET data, with the potential to be used in a wide range of biological studies. It is generalizable to various kinds of tomograms, making it possible to use pretrained models for different tasks. Its efficiency in terms of required annotations also allows rapid training and fine-tuning of models. The corresponding code, pretrained models, and instructions for operating the MemBrain program can be found at: https://github.com/CellArchLab/MemBrain.
MeSH term(s)	Cryoelectron Microscopy/methods ; Deep Learning ; Electron Microscope Tomography/methods ; Electrons ; Image Processing, Computer-Assisted/methods ; Membrane Proteins
Chemical Substances	Membrane Proteins
Language	English
Publishing date	2022-07-01
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	632564-6
ISSN	1872-7565 ; 0169-2607
ISSN (online)	1872-7565
ISSN	0169-2607
DOI	10.1016/j.cmpb.2022.106990
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Article ; Online: The burden of laboratory-confirmed pertussis in low- and middle-income countries since the inception of the Expanded Programme on Immunisation (EPI) in 1974: a systematic review and meta-analysis.

Muloiwa, Rudzani / Kagina, Benjamin M / Engel, Mark E / Hussey, Gregory D

BMC medicine

2020 Volume 18, Issue 1, Page(s) 233

Abstract: Background: An effective vaccine against Bordetella pertussis was introduced into the Expanded Programme on Immunisation (EPI) by WHO in 1974, leading to a substantial global reduction in pertussis morbidity and mortality. In low- and middle-income ... ...

Abstract	Background: An effective vaccine against Bordetella pertussis was introduced into the Expanded Programme on Immunisation (EPI) by WHO in 1974, leading to a substantial global reduction in pertussis morbidity and mortality. In low- and middle-income countries (LMICs), however, the epidemiology of pertussis remains largely unknown. This impacts negatively on pertussis control strategies in these countries. This study aimed to systematically and comprehensively review published literature on the burden of laboratory-confirmed pertussis in LMICs over the 45 years of EPI. Methods: Electronic databases were searched for relevant literature (1974 to December 2018) using common and MeSH terms for pertussis. Studies using PCR, culture or paired serology to confirm Bordetella pertussis and parapertussis in symptomatic individuals were included if they had clearly defined numerators and denominators to determine prevalence and mortality rates. Results: Eighty-two studies (49,167 participants) made the inclusion criteria. All six WHO regions were represented with most of the studies published after 2010 and involving mainly upper middle-income countries (n = 63; 77%). PCR was the main diagnostic test after the year 2000. The overall median point prevalence of PCR-confirmed Bordetella pertussis was 11% (interquartile range (IQR), 5-27%), while culture-confirmed was 3% (IQR 1-9%) and paired serology a median of 17% (IQR 3-23%) over the period. On average, culture underestimated prevalence by 85% (RR = 0.15, 95% CI, 0.10-0.22) compared to PCR in the same studies. Risk of pertussis increased with HIV exposure [RR, 1.4 (95% CI, 1.0-2.0)] and infection [RR, 2.4 (95% CI, 1.1-5.1)]. HIV infection and exposure were also related to higher pertussis incidences, higher rates of hospitalisation and pertussis-related deaths. Pertussis mortality and case fatality rates were 0.8% (95% CI, 0.4-1.4%) and 6.5% (95% CI, 4.0-9.5%), respectively. Most deaths occurred in infants less than 6 months of age. Conclusions: Despite the widespread use of pertussis vaccines, the prevalence of pertussis remains high in LMIC over the last three decades. There is a need to increase access to PCR-based diagnostic confirmation in order to improve surveillance. Disease control measures in LMICs must take into account the persistent significant infant mortality and increased disease burden associated with HIV infection and exposure.
MeSH term(s)	Bordetella pertussis/pathogenicity ; Developing Countries ; Female ; History, 20th Century ; Humans ; Immunization Programs/methods ; Male ; Whooping Cough/epidemiology
Language	English
Publishing date	2020-08-28
Publishing country	England
Document type	Historical Article ; Journal Article ; Meta-Analysis ; Systematic Review
ISSN	1741-7015
ISSN (online)	1741-7015
DOI	10.1186/s12916-020-01699-3
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