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Article ; Online: Licensing microgels prolong the immunomodulatory phenotype of mesenchymal stromal cells.

Patrick, Matthew D / Annamalai, Ramkumar T

2022 Volume 13, Page(s) 987032

Abstract: Mesenchymal stromal cells (MSC) are sensors of inflammation, and they exert immunomodulatory properties through the secretion of cytokines and exosomes and direct cell-cell interactions. MSC are routinely used in clinical trials and effectively resolve ... ...

Abstract	Mesenchymal stromal cells (MSC) are sensors of inflammation, and they exert immunomodulatory properties through the secretion of cytokines and exosomes and direct cell-cell interactions. MSC are routinely used in clinical trials and effectively resolve inflammatory conditions. Nevertheless, inconsistent clinical outcomes necessitate the need for more robust therapeutic phenotypes. The immunomodulatory properties of MSC can be enhanced and protracted by priming (aka licensing) them with IFNγ and TNFα. Yet these enhanced properties rapidly diminish, and prolonged stimulation could tolerize their response. Hence a balanced approach is needed to enhance the therapeutic potential of the MSC for consistent clinical performance. Here, we investigated the concentration-dependent effects of IFNγ and TNFα and developed gelatin-based microgels to sustain a licensed MSC phenotype. We show that IFNγ treatment is more beneficial than TNFα in promoting an immunomodulatory MSC phenotype. We also show that the microgels possess integrin-binding sites to support adipose tissue-derived MSC (AD-MSC) attachment and a net positive charge to sequester the licensing cytokines electrostatically. Microgels are enzymatically degradable, and the rate is dependent on the enzyme concentration and matrix density. Our studies show that one milligram of microgels by dry mass can sequester up to 641 ± 81 ng of IFNγ. Upon enzymatic degradation, microgels exhibited a sustained release of IFNγ that linearly correlated with their degradation rate. The AD-MSC cultured on the IFNγ sequestered microgels displayed efficient licensing potential comparable to or exceeding the effects of bolus IFNγ treatment. When cultured with proinflammatory M1-like macrophages, the AD-MSC-seeded on licensing microgel showed an enhanced immunomodulatory potential compared to untreated AD-MSC and AD-MSC treated with bolus IFNγ treatment. Specifically, the AD-MSC seeded on licensing microgels significantly upregulated
MeSH term(s)	Cytokines/metabolism ; Mesenchymal Stem Cells/metabolism ; Microgels ; Phenotype ; Tumor Necrosis Factor-alpha/metabolism
Chemical Substances	Cytokines ; Microgels ; Tumor Necrosis Factor-alpha
Language	English
Publishing date	2022-08-18
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2022.987032
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online: Exploring Software Reusability Metrics with Q&A Forum Data

Patrick, Matthew T.

2020

Abstract: Question and answer (Q&A) forums contain valuable information regarding software reuse, but they can be challenging to analyse due to their unstructured free text. Here we introduce a new approach (LANLAN), using word embeddings and machine learning, to ... ...

Abstract	Question and answer (Q&A) forums contain valuable information regarding software reuse, but they can be challenging to analyse due to their unstructured free text. Here we introduce a new approach (LANLAN), using word embeddings and machine learning, to harness information available in StackOverflow. Specifically, we consider two different kinds of user communication describing difficulties encountered in software reuse: 'problem reports' point to potential defects, while 'support requests' ask for clarification on software usage. Word embeddings were trained on 1.6 billion tokens from StackOverflow and applied to identify which Q&A forum messages (from two large open source projects: Eclipse and Bioconductor) correspond to problem reports or support requests. LANLAN achieved an area under the receiver operator curve (AUROC) of over 0.9; it can be used to explore the relationship between software reusability metrics and difficulties encountered by users, as well as predict the number of difficulties users will face in the future. Q&A forum data can help improve understanding of software reuse, and may be harnessed as an additional resource to evaluate software reusability metrics.
Keywords	Computer Science - Software Engineering
Subject code	028
Publishing date	2020-05-18
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Evolving information complexity of coarsening materials microstructures.

Rickman, J M / Barmak, K / Chen, B Y / Patrick, Matthew

Scientific reports

2023 Volume 13, Issue 1, Page(s) 22390

Abstract: The temporal evolution of microstructural features in metals and ceramics has been the subject of intense investigation over many years because deviations from normal grain growth behavior are ubiquitous and strongly dictate observed mechanical and ... ...

Abstract	The temporal evolution of microstructural features in metals and ceramics has been the subject of intense investigation over many years because deviations from normal grain growth behavior are ubiquitous and strongly dictate observed mechanical and magnetic properties. To distinguish among different grain growth scenarios, we examine the time evolution of the information content of both synthetic and experimental coarsening microstructures as quantified by both a computable information density (CID) and a spectral entropy along with selected metrics and measures of shared information and interaction strength. In these approaches, microstructural evolution is described in terms of two time series representations, namely: (1) strings and their compressed counterparts that reflect the information contained in the configuration of a system over time, and (2) the spectra of graph Laplacians that embody the information contained in a coarsening grain network. These approaches permit one to characterize dynamically evolving microstructures and to identify correlation times associated with different coarsening scenarios. Moreover, as the information content of a system is a proxy for the entropy, a thermodynamic description of grain growth is also described.
Language	English
Publishing date	2023-12-16
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-49759-x
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Article ; Online: Termiticidal activity of oil from Jatropha curcas L. and Azadirachta indica A. Juss against Coptotermes sjostedti Holmgren (Isoptera

Simon Idoko Okweche / Patrick Matthew Hilili / Edache Ernest Ekoja

Bulletin of the National Research Centre, Vol 45, Iss 1, Pp 1-

Rhinotermitidae)

2021 Volume 8

Abstract: Abstract Background Coptotermes sjostedti Holmgren (Isoptera:Rhinotermitidae) is one of the major termite species found infesting woods and other plant materials in Africa. Bioassays were carried out at the Arboretum of the Department of Forestry and ... ...

Abstract	Abstract Background Coptotermes sjostedti Holmgren (Isoptera:Rhinotermitidae) is one of the major termite species found infesting woods and other plant materials in Africa. Bioassays were carried out at the Arboretum of the Department of Forestry and Wildlife Resources Management, University of Calabar, Nigeria to investigate the effect of oils from the kernel of Jatropha curcas L. and Azadirachta indica oils A. Juss against the African subterranean termite (Coptotermes sjostedti Holmgren). Treatments comprised of the plant oils and Solignum (a synthetic termiticide, serving as positive control) applied at the rate of 5, 10 and 15 mL per 100 cm3 of the wood from seven plant species. Untreated woods also served as control. Seven wood species were placed in a test arena and artificially infested with 50 termites per unit. The setup was a randomized complete block design with four replicates. Data on termite mortality and wood weight loss were recorded. Results The use of 10 and 15 mL of J. curcas oil caused more than 90% mortality of C. sjostedti, after 96 h, kept wood consumption by the insect below 6.0% after 3 months, and these outcomes were similar to that of Solignum at the same concentrations. About 35.0–65.2% reduction in weight was observed among untreated woods from the tested woods, indicating their susceptibility to C. sjostedti attacks. Correlation analysis shows a significant (r > − 0.900; P < 0.0001) negative association between termite mortality and the rate of wood consumption. Conclusion The use of J. curcas oil at 10 mL per 100 cm3 of wood could be a potent alternative to Solignum for the control of C. sjostedti.
Keywords	Termiticide ; Jatropha curcas ; Azadirachta indica solignum ; Wood consumption ; Termite mortality ; Science ; Q
Subject code	580
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	SpringerOpen
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: A Murine Delayed-Healing Model Associates Immune Response with Functional Bone Regeneration after Trauma.

Patrick, Matthew / Stromberg, Arnold / Ahn, Jaimo / Hankenson, Kurt / Annamalai, Ramkumar T

bioRxiv : the preprint server for biology

2023

Abstract: Nonunion and delayed-union fractures pose a significant clinical challenge, often leading to prolonged morbidity and impaired quality of life. Fracture-induced hematoma and acute inflammation are crucial for establishing the healing cascade. However, ... ...

Abstract	Nonunion and delayed-union fractures pose a significant clinical challenge, often leading to prolonged morbidity and impaired quality of life. Fracture-induced hematoma and acute inflammation are crucial for establishing the healing cascade. However, aberrant inflammatory phenotypes can suppress healing and cause bone resorption. Elucidating these mechanisms is necessary to develop potent immunomodulatory therapies and prevent nonunion. Here, we report a delayed fracture healing model enabling the modulation of interfragmentary strain that mimics the etiology of hypertrophic nonunions to elucidate the role of dysregulated immune response in poor healing outcomes. High interfragmentary strain (>15%) was associated with larger callus volumes but delayed bone healing, increased inflammation, and inferior healing outcomes, while lower strain levels (<5%) corresponded to normal bone healing. In addition, we found distinct differences in the ossification, chondrification, and fibrosis patterns between high and low-strain groups, underscoring the significant impact of strain on the healing process. A comprehensive analysis of the systemic immune response revealed dynamic alterations in immune cell populations and factors, particularly within the early hours and days post-fracture. Several immune factors exhibited significant correlations with various functional healing outcomes, indicating their potential as predictive markers for assessing fracture healing progression. Our results also highlighted the significance of timely resolution of proinflammatory signals and the elevation of pro-regenerative immune cell phenotypes in promoting bone regeneration. Multivariate analysis revealed that CD25+ T-regulatory cells were influential in predicting proper bone healing, followed by CD206+ macrophages, underscoring the pivotal role of immune cell populations in the bone healing process. In conclusion, our study provides valuable insights into the intricate interplay between interfragmentary strain, immune response, and the ultimate outcomes of fracture healing. By shedding light on the underlying mechanisms that drive hypertrophic nonunion pathogenesis, our research lays the foundation for enhanced surgical management of nonunions and offers a promising avenue for developing targeted therapeutic interventions and personalized treatment strategies for individuals suffering from fracture nonunion.
Language	English
Publishing date	2023-10-31
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.10.26.564177
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Article ; Online: Large-scale epidemiological analysis of common skin diseases to identify shared and unique comorbidities and demographic factors.

Li, Qinmengge / Patrick, Matthew T / Sreeskandarajan, Sutharzan / Kang, Jian / Kahlenberg, J Michelle / Gudjonsson, Johann E / He, Zhi / Tsoi, Lam C

Frontiers in immunology

2024 Volume 14, Page(s) 1309549

Abstract: Introduction: The utilization of large-scale claims databases has greatly improved the management, accessibility, and integration of extensive medical data. However, its potential for systematically identifying comorbidities in the context of skin ... ...

Abstract	Introduction: The utilization of large-scale claims databases has greatly improved the management, accessibility, and integration of extensive medical data. However, its potential for systematically identifying comorbidities in the context of skin diseases remains unexplored. Methods: This study aims to assess the capability of a comprehensive claims database in identifying comorbidities linked to 14 specific skin and skin-related conditions and examining temporal changes in their association patterns. This study employed a retrospective case-control cohort design utilizing 13 million skin/skin-related patients and 2 million randomly sampled controls from Optum's de-identified Clinformatics Results: Using the established type-2 diabetes (T2D) and psoriasis comorbidity as example, we demonstrated the association is significant (P-values<1x10 Discussion: The findings highlight the potential of utilizing comprehensive claims databases in advancing research and improving patient care in dermatology.
MeSH term(s)	Humans ; Celiac Disease ; Crohn Disease ; Retrospective Studies ; Comorbidity ; Lupus Erythematosus, Systemic/epidemiology ; Diabetes Mellitus, Type 2 ; Hidradenitis Suppurativa ; Leprosy ; Demography
Language	English
Publishing date	2024-01-08
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2023.1309549
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Article ; Online: Orthopaedic fracture surgery in polytraumatized patients while on extracorporeal membrane oxygenation (ECMO): A report of two cases.

Kakalecik, Jaquelyn / Frantz, Amanda M / Talerico, Michael T / Krupko, Thomas A / Hagen, Jennifer E / Patrick, Matthew R

Trauma case reports

2024 Volume 51, Page(s) 101020

Abstract: Extracorporeal membrane oxygenation (ECMO) has become a salvage therapy for patients with severe acute respiratory distress syndrome (ARDS). The management of orthopaedic trauma in ECMO-supported patients with ARDS remains an evolving area of interest. ... ...

Abstract	Extracorporeal membrane oxygenation (ECMO) has become a salvage therapy for patients with severe acute respiratory distress syndrome (ARDS). The management of orthopaedic trauma in ECMO-supported patients with ARDS remains an evolving area of interest. Orthopaedic injuries are often temporized with external fixators, skeletal traction, or splints due to hemodynamic instability as well as concerns of exacerbating underlying pulmonary injury. However, patients requiring ECMO support do not rely on their pulmonary system for oxygenation, the need for delayed fixation may not apply. However, patients utilizing ECMO therapy can have external cardiac and pulmonary support depending on their cannulation strategy, bypassing the need for delayed fixation. We present a case series of two polytrauma patients with ARDS who underwent surgical management of pelvic ring and femoral shaft fractures while receiving ECMO support. Both patients underwent surgical management without complication and were able to be weaned from ECMO and ventilator support postoperatively. These cases highlight the potential benefits to orthopaedic fixation and underscore the need for further clinical research.
Language	English
Publishing date	2024-04-08
Publishing country	Netherlands
Document type	Case Reports
ZDB-ID	2835433-3
ISSN	2352-6440 ; 2352-6440
ISSN (online)	2352-6440
ISSN	2352-6440
DOI	10.1016/j.tcr.2024.101020
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Article ; Online: Wafer-scale development, characterization, and high temperature stabilization of epitaxial Cr2O3 films grown on Ru(0001).

Cumston, Quintin / Patrick, Matthew / Hegazy, Ahmed R / Zangiabadi, Amirali / Daughtry, Maximillian / Coffey, Kevin R / Barmak, Katayun / Kaden, William E

The Journal of chemical physics

2024 Volume 160, Issue 14

Abstract: This work outlines conditions suitable for the heteroepitaxial growth of Cr2O3(0001) films (1.5-20 nm thick) on a Ru(0001)-terminated substrate. Optimized growth is achieved by sputter deposition of Cr within a 4 mTorr Ar/O2 20% ambient at Ru ... ...

Abstract	This work outlines conditions suitable for the heteroepitaxial growth of Cr2O3(0001) films (1.5-20 nm thick) on a Ru(0001)-terminated substrate. Optimized growth is achieved by sputter deposition of Cr within a 4 mTorr Ar/O2 20% ambient at Ru temperatures ranging from 450 to 600 °C. The Cr2O3 film adopts a 30° rotated honeycomb configuration with respect to the underlying Ru(0001) substrate and exhibits a hexagonal lattice parameter consistent with that for bulk Cr2O3(0001). Heating to 700 °C within the same environment during film preparation leads to Ru oxidation. Exposure to temperatures at or above 400 °C in a vacuum, Ar, or Ar/H2 3% leads to chromia film degradation characterized by increased Ru 3d XPS intensity coupled with concomitant Cr 2p and O 1s peak attenuations when compared to data collected from unannealed films. An ill-defined but hexagonally well-ordered RuxCryOz surface structure is noted after heating the film in this manner. Heating within a wet Ar/H2 3% environment preserves the Cr2O3(0001)/Ru(0001) heterolayer structure to temperatures of at least 950 °C. Heating an Ru-Cr2O3-Ru heterostacked film to 950 °C within this environment is shown by cross-sectional scanning/transmission electron microscopy (S/TEM) to provide clear evidence of retained epitaxial bicrystalline oxide interlayer structure, interlayer immiscibility, and epitaxial registry between the top and bottom Ru layers. Subtle effects marked by O enrichment and O 1s and Cr 2p shifts to increased binding energies are noted by XPS in the near-Ru regions of Cr2O3(0001)/Ru(0001) and Ru(0001)/Cr2O3(0001)/Ru(0001) films after annealing to different temperatures in different sets of environmental conditions.
Language	English
Publishing date	2024-04-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0201818
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Article ; Online: Sex-Specific Systemic Inflammatory Responses in Mice Infected with a SARS-CoV-2-like Virus and Femur Fracture

Patrick, Matthew D / Foster, Austin / Aneja, Arun / Annamalai, Ramkumar T.

bioRxiv

Abstract: This study investigates the systemic inflammatory response in mice infected with a murine coronavirus (MHV), which shares a common genus with SARS-CoV-2, and sustaining a fracture. The study reveals that the combined inflammatory incidents of MHV ... ...

Abstract	This study investigates the systemic inflammatory response in mice infected with a murine coronavirus (MHV), which shares a common genus with SARS-CoV-2, and sustaining a fracture. The study reveals that the combined inflammatory incidents of MHV infection and fracture disrupt the systemic immune response in both female and male mice, likely leading to immune dysregulation, altered cell recruitment, and disruption of the typical inflammatory cascade. Notably, the study uncovers sex-specific responses that modulate circulating immune factors. Females exhibit elevated levels of inflammatory factors, whereas males demonstrate a diminished response. This divergence is mirrored in cell populations, suggesting that the quantity of immune factors released may contribute to these discrepancies. The findings suggest that an overproduction of proinflammatory cytokines may induce a dysregulated immune response, contributing to the observed poorer prognosis in comorbid cases. These insights could pave the way for therapeutic advancements and treatment strategies aimed at reducing mortality rates in COVID-19 patients with fractures.
Keywords	covid19
Language	English
Publishing date	2023-12-04
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2023.12.04.567060
Database	COVID19

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Article ; Online: Toward Next‐Generation Lava Flow Forecasting: Development of a Fast, Physics‐Based Lava Propagation Model

Hyman, David M. R. / Dietterich, Hannah R. / Patrick, Matthew R.

Journal of Geophysical Research: Solid Earth. 2022 Oct., v. 127, no. 10 p.e2022JB024998-

2022

Abstract: During effusive volcanic crises, the eruption and propagation of lava flows pose a significant hazard to nearby populations, homes, and infrastructure. Consequently, timely lava flow forecasts are a critical need for volcano observatory and emergency ... ...

Abstract	During effusive volcanic crises, the eruption and propagation of lava flows pose a significant hazard to nearby populations, homes, and infrastructure. Consequently, timely lava flow forecasts are a critical need for volcano observatory and emergency management operations. Previous lava flow modeling tools are typically either too slow to produce timely forecasts, or are fast, but lack critical aspects of lava physics or important forecasting outputs. In particular, the strong thermal stratification present in laminar, high‐Prandtl number flows has generally been neglected. Bulk rheological changes have previously been computed from cell‐averaged temperatures, assuming that the flow is thermally mixed. Here, we detail the development and initial testing of Lava2d, a new two‐dimensional depth‐averaged finite volume model of lava flow propagation over natural terrain which accounts for bulk rheological changes due to thermorheological stratification. We use a novel approach to energy conservation based on tracking cooling and solidifying at the flow base and at the moving flow surface, allowing for the estimation of more realistic vertical thermorheological profiles, while maintaining computational efficiency, producing very timely model runs. We validate our approach with three examples: comparison with theoretical propagation of crust‐dominated lava flows, comparison with a large‐scale molten basalt experiment from the Syracuse University Lava Project, and efficiency testing and comparison with the initial phase of the 1984 Mauna Loa lava flows. Our model is shown to produce rapid, realistic forecasts, making it a good candidate for operationalization in active volcanic regions such as in Hawai'i.
Keywords	Hawaii ; basalt ; cooling ; energy conservation ; geophysics ; infrastructure ; landscapes ; lava ; models ; research ; temperature profiles
Language	English
Dates of publication	2022-10
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ISSN	2169-9313
DOI	10.1029/2022JB024998
Database	NAL-Catalogue (AGRICOLA)

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