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Article ; Online: Data-driven dynamical coarse-graining for condensed matter systems.

Del Razo, Mauricio J / Crommelin, Daan / Bolhuis, Peter G

2024 Volume 160, Issue 2

Abstract: Simulations of condensed matter systems often focus on the dynamics of a few distinguished components but require integrating the full system. A prime example is a molecular dynamics simulation of a (macro)molecule in a solution, where the molecule(s) ... ...

Abstract	Simulations of condensed matter systems often focus on the dynamics of a few distinguished components but require integrating the full system. A prime example is a molecular dynamics simulation of a (macro)molecule in a solution, where the molecule(s) and the solvent dynamics need to be integrated, rendering the simulations computationally costly and often unfeasible for physically/biologically relevant time scales. Standard coarse graining approaches can reproduce equilibrium distributions and structural features but do not properly include the dynamics. In this work, we develop a general data-driven coarse-graining methodology inspired by the Mori-Zwanzig formalism, which shows that macroscopic systems with a large number of degrees of freedom can be described by a few relevant variables and additional noise and memory terms. Our coarse-graining method consists of numerical integrators for the distinguished components, where the noise and interaction terms with other system components are substituted by a random variable sampled from a data-driven model. The model is parameterized using data from multiple short-time full-system simulations, and then, it is used to run long-time simulations. Applying our methodology to three systems-a distinguished particle under a harmonic and a bistable potential and a dimer with two metastable configurations-the resulting coarse-grained models are capable of reproducing not only the equilibrium distributions but also the dynamic behavior due to temporal correlations and memory effects. Remarkably, our method even reproduces the transition dynamics between metastable states, which is challenging to capture correctly. Our approach is not constrained to specific dynamics and can be extended to systems beyond Langevin dynamics, and, in principle, even to non-equilibrium dynamics.
Language	English
Publishing date	2024-01-09
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	10.1063/5.0177553
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Article ; Online: Cage doping of Ti, Zr, and Hf-based 13-atom nanoclusters: two sides of the same coin.

Piotrowski, Maurício J / Palheta, João Marcos T / Fournier, René

Physical chemistry chemical physics : PCCP

2024 Volume 26, Issue 17, Page(s) 13172–13181

Abstract: Transition metal nanoclusters can exhibit unique and tunable properties which result not only from their chemical composition but also from their atomic packing and quantized electronic structures. Here, we introduce a promising family of bimetallic TM@ ... ...

Abstract	Transition metal nanoclusters can exhibit unique and tunable properties which result not only from their chemical composition but also from their atomic packing and quantized electronic structures. Here, we introduce a promising family of bimetallic TM@Ti
Language	English
Publishing date	2024-05-01
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d4cp00518j
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Article: Extraforaminal lumbar herniated disc mimicking foraminal tumor: Case report, literature review, and the role for minimally invasive approach for resection.

Avila, Mauricio J / Chua, Richard V

Journal of craniovertebral junction & spine

2022 Volume 13, Issue 1, Page(s) 101–105

Abstract: Herniated discs in the lumbar spine are common, however, extraforaminal disc herniations are less frequently encountered. Occasionally, rare disc herniations can mimic other pathologies such as nerve tumor. We present such case and a review of similar ... ...

Abstract	Herniated discs in the lumbar spine are common, however, extraforaminal disc herniations are less frequently encountered. Occasionally, rare disc herniations can mimic other pathologies such as nerve tumor. We present such case and a review of similar cases in the scientific literature. A 71-year-old male who presented with back pain and right-side sciatic pain. Magnetic resonance imaging revealed a fusiform enhancing 3 cm × 2 cm lesion that was concerning for a nerve sheath tumor. A minimally invasive lateral trans-psoas approach was performed for a biopsy that revealed disc fragments and a full resection was performed. The patient's symptoms improved at follow-up. Although uncommon, extraforaminal disc herniations can be mistaken for peripheral nerve tumors on imaging. The spine surgeon should remain vigilant about these entities and plan the surgical treatment accordingly.
Language	English
Publishing date	2022-03-09
Publishing country	India
Document type	Case Reports
ZDB-ID	2573344-8
ISSN	0976-9285 ; 0974-8237
ISSN (online)	0976-9285
ISSN	0974-8237
DOI	10.4103/jcvjs.jcvjs_105_21
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Article: Temperature variability and metabolic adaptation in terrestrial and aquatic ectotherms.

Carter, Mauricio J / Cortes, Pablo A / Rezende, Enrico L

Journal of thermal biology

2023 Volume 115, Page(s) 103565

Abstract: Thermodynamics is a major factor determining rates of energy expenditure, rates of biochemical dynamics, and ultimately the biological and ecological processes linked with resilience to global warming in ectothermic organisms. Nonetheless, whether ... ...

Abstract	Thermodynamics is a major factor determining rates of energy expenditure, rates of biochemical dynamics, and ultimately the biological and ecological processes linked with resilience to global warming in ectothermic organisms. Nonetheless, whether ectothermic organisms exhibit general adaptive metabolic responses to cope with worldwide variation in thermal conditions has remained as an open question. Here we combine a model comparison approach with a global dataset of standard metabolic rates (SMR), including 1,160 measurements across 788 species of aquatic invertebrates, insects, fishes, amphibians and reptiles, to investigate the association between metabolic rates and environmental temperatures in their respective habitats. Our analyses suggest that variation in SMR after removing allometric and thermodynamic effects is best explained by the temperature range encountered across seasons, which always provided a better fit than the average temperature for the hottest and coldest month and mean annual temperatures. This pattern was consistent across taxonomic groups and robust to sensitivity analyses. Nonetheless, aquatic and terrestrial lineages responded differently to seasonality, with SMR declining - 6.8% °C
MeSH term(s)	Animals ; Temperature ; Adaptation, Physiological ; Body Temperature Regulation/physiology ; Acclimatization ; Cold Temperature
Language	English
Publishing date	2023-04-24
Publishing country	England
Document type	Journal Article
ZDB-ID	1498364-3
ISSN	1879-0992 ; 0306-4565
ISSN (online)	1879-0992
ISSN	0306-4565
DOI	10.1016/j.jtherbio.2023.103565
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Article ; Online: Prosthetic valve endocarditis secondary to Tropheryma whipplei in a patient with chronic polyarthritis.

Kahn, Mauricio J / Ennis, David M / Delgado, Dennis G

Journal of cardiothoracic surgery

2023 Volume 18, Issue 1, Page(s) 169

Abstract: Background: Whipple's disease is a chronic multisystemic infectious disease that rarely presents as culture-negative endocarditis. Most patients reported with Tropheryma whipplei endocarditis involve a native valve and few describe prosthetic valve ... ...

Abstract	Background: Whipple's disease is a chronic multisystemic infectious disease that rarely presents as culture-negative endocarditis. Most patients reported with Tropheryma whipplei endocarditis involve a native valve and few describe prosthetic valve disease. Case presentation: A patient with chronic polyarthritis and previous mitral valve replacement developed decompensated heart failure without fever. Transesophageal echocardiography revealed a prosthetic mitral valve vegetation and he underwent prosthetic mitral valve replacement. Blood and prosthetic mitral valve cultures were unrevealing. Broad-range polymerase chain reaction (PCR) of the extracted valve and subsequent Periodic-acid-Schiff (PAS) staining established the diagnosis of T. whipplei prosthetic valve endocarditis. Conclusion: Whipple's disease may present as culture-negative infective endocarditis and affect prosthetic valves. Histopathology with PAS staining and broad-range PCR of excised valves are essential for the diagnosis. Greater clinical awareness and implementation of these diagnostic procedures should result in an increased reported incidence of this rare disease.
MeSH term(s)	Male ; Humans ; Endocarditis, Bacterial/complications ; Endocarditis, Bacterial/diagnosis ; Endocarditis, Bacterial/surgery ; Aortic Valve/surgery ; Tropheryma ; Whipple Disease/complications ; Whipple Disease/diagnosis ; Whipple Disease/pathology ; Heart Valve Prosthesis/adverse effects ; Arthritis/complications
Language	English
Publishing date	2023-04-28
Publishing country	England
Document type	Case Reports ; Journal Article
ZDB-ID	2227224-0
ISSN	1749-8090 ; 1749-8090
ISSN (online)	1749-8090
ISSN	1749-8090
DOI	10.1186/s13019-023-02287-1
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Article ; Online: Fructose promotes liver cancer via microbial acetate-induced O-GlcNAcylation.

Esquea, Emily M / Young, Riley G / Reginato, Mauricio J

Trends in endocrinology and metabolism: TEM

2023 Volume 35, Issue 2, Page(s) 88–90

Abstract: High dietary fructose consumption is linked to multiple disease states, including cancer. Zhou and colleagues recently reported a novel mechanism where high dietary fructose levels increase acetate production by the gut microbiome increasing post- ... ...

Abstract	High dietary fructose consumption is linked to multiple disease states, including cancer. Zhou and colleagues recently reported a novel mechanism where high dietary fructose levels increase acetate production by the gut microbiome increasing post-translational modification O-GlcNAcylation in liver cells, which contributes to disease progression in mouse models of hepatocellular carcinoma.
MeSH term(s)	Mice ; Animals ; Fructose/adverse effects ; Liver Neoplasms/pathology ; Carcinoma, Hepatocellular/pathology ; Protein Processing, Post-Translational ; Acetates
Chemical Substances	Fructose (30237-26-4) ; Acetates
Language	English
Publishing date	2023-12-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	1042384-9
ISSN	1879-3061 ; 1043-2760
ISSN (online)	1879-3061
ISSN	1043-2760
DOI	10.1016/j.tem.2023.12.002
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Article ; Online: Improved detection and phylogenetic analysis of plant proteins containing LysM domains.

Dallachiesa, Dardo / Aguilar, O Mario / Lozano, Mauricio J

Functional plant biology : FPB

2023 Volume 51, Issue 1, Page(s) NULL

Abstract: Plants perceive N-acetyl-d-glucosamine-containing oligosaccharides that play a role in the interaction with bacteria and fungi, through cell-surface receptors containing a tight bundle of three LysM domains in their extracellular region. However, the ... ...

Abstract	Plants perceive N-acetyl-d-glucosamine-containing oligosaccharides that play a role in the interaction with bacteria and fungi, through cell-surface receptors containing a tight bundle of three LysM domains in their extracellular region. However, the identification of LysM domains of receptor-like kinases (RLK)/receptor-like proteins (RLP) using sequence based methods has led to some ambiguity, as some proteins have been annotated with only one or two LysM domains. This missing annotation was likely produced by the failure of the LysM hidden Markov model (HMM) from the Pfam database to correctly identify some LysM domains in proteins of plant origin. In this work, we provide improved HMMs for LysM domain detection in plants, that were built from the structural alignment of manually curated LysM domain structures from the Protein Data Bank and AlphaFold Protein Structure Database. Furthermore, we evaluated different sets of ligand-specific HMMs that were able to correctly classify a limited set of fully characterised RLK/Ps by their ligand specificity. In contrast, the phylogenetic analysis of the extracellular region of RLK/Ps, or of their individual LysM domains, was unable to discriminate these proteins by their ligand specificity. The HMMs reported here will allow a more sensitive detection of plant proteins containing LysM domains and help improve their characterisation.
MeSH term(s)	Plant Proteins/genetics ; Plant Proteins/metabolism ; Phylogeny ; Ligands ; Fungi/metabolism ; Receptors, Cell Surface
Chemical Substances	Plant Proteins ; Ligands ; Receptors, Cell Surface
Language	English
Publishing date	2023-10-28
Publishing country	Australia
Document type	Journal Article
ZDB-ID	2071582-1
ISSN	1445-4416 ; 1445-4408
ISSN (online)	1445-4416
ISSN	1445-4408
DOI	10.1071/FP23131
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Article ; Online: Editorial

Edward R. Ivimey-Cook / Pablo A. Cortes / Mauricio J. Carter

Frontiers in Ecology and Evolution, Vol

Ecological and evolutionary relevance of phenotypic plasticity in a changing world

2023 Volume 11

Keywords	phenotypic plasticity ; global change ; evolutionary ecology ; biodiversity ; climate change ; Evolution ; QH359-425 ; Ecology ; QH540-549.5
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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Article ; Online: Central Cord Syndrome Redefined.

Avila, Mauricio J / Hurlbert, R John

Neurosurgery clinics of North America

2021 Volume 32, Issue 3, Page(s) 353–363

Abstract: This article reviews the historical origins of central cord syndrome (CCS), the mechanism of injury, pathophysiology, and clinical implications. CCS is the most common form of incomplete spinal cord injury. CCS involves a spectrum of neurologic deficits ... ...

Abstract	This article reviews the historical origins of central cord syndrome (CCS), the mechanism of injury, pathophysiology, and clinical implications. CCS is the most common form of incomplete spinal cord injury. CCS involves a spectrum of neurologic deficits preferentially affecting the hands and arms. Evidence suggests that in the twenty-first century CCS has become the most common form of spinal cord injury overall. In an era of big data and the need to standardize this particular diagnosis to unite outcome data, we propose redefining CCS as any adult cervical spinal cord injury in the absence of fracture/dislocation.
MeSH term(s)	Adult ; Central Cord Syndrome/diagnosis ; Central Cord Syndrome/epidemiology ; Central Cord Syndrome/surgery ; Cervical Vertebrae ; Humans ; Spinal Cord Injuries
Language	English
Publishing date	2021-05-07
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1196855-2
ISSN	1558-1349 ; 1042-3680
ISSN (online)	1558-1349
ISSN	1042-3680
DOI	10.1016/j.nec.2021.03.007
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Article ; Online: Utility of Magnetic Resonance Imaging for Ligamentous Injury in Cervical Spine Trauma: A 2-Year Consecutive Case Cohort.

Avila, Mauricio J / Dumont, Travis M / Ganapathy, Venkat / Hurlbert, R John

World neurosurgery

2023 Volume 183, Page(s) e339–e344

Abstract: Background: Magnetic resonance imaging (MRI) is increasingly used as an adjunct to spinal soft tissue evaluation in cervical spine (C-spine) trauma; however, the utility of this information remains controversial. In this consecutive observational study, ...

Abstract	Background: Magnetic resonance imaging (MRI) is increasingly used as an adjunct to spinal soft tissue evaluation in cervical spine (C-spine) trauma; however, the utility of this information remains controversial. In this consecutive observational study, we reviewed the utility of MRI in patients with C-spine trauma. Methods: We identified patients in real time over a 2-year period as they presented to our level 1 trauma center for C-spine computed tomography (CT) scan followed by MRI. MRI was obtained by the trauma team prior to the spine service consultation if (1) they were unable to clear the C-spine according to protocol or (2) if the on-call radiologist reported a concern for ligamentous integrity from the CT findings. Results: Thirty-three patients, including 19 males (58%) and 14 females, with a mean age of 54 years, were referred to the spine service for concerns of ligamentous instability. The most common mechanisms of injury were motor vehicle accidents (n = 13) and falls (n = 11). MRI demonstrated ligamentous signal change identified by the radiologist as potentially unstable in all patients. Fifteen patients (45%) had multiple C-spine ligaments affected. The interspinous ligament was involved most frequently (28%), followed by the ligamentum flavum (21%) and supraspinous ligament (15%). All patients underwent dynamic upright C-spine X-rays that were interpreted by both the ordering surgeon and radiologist. There was no evidence of instability in any patient; concurrence between X-ray interpretation was 100%. The cervical collar was successfully removed in all cases. No patients required late surgical intervention, and there were no return visits to the emergency department of a spinal nature. Conclusions: MRI signal change within the ligaments of the C-spine should be interpreted with caution in the setting of trauma. To physicians less familiar with spinal biomechanics, MRI findings may be perceived in an inadvertently alarming manner. Bony alignment and, when indicated, dynamic upright X-rays remain the gold standard for evaluating the ligamentous integrity of the C-spine.
MeSH term(s)	Female ; Humans ; Male ; Middle Aged ; Cervical Vertebrae/pathology ; Ligaments, Articular/pathology ; Magnetic Resonance Imaging/methods ; Neck Injuries ; Observational Studies as Topic ; Radiography ; Spinal Injuries/diagnostic imaging ; Spinal Injuries/pathology
Language	English
Publishing date	2023-12-22
Publishing country	United States
Document type	Journal Article ; Observational Study
ZDB-ID	2534351-8
ISSN	1878-8769 ; 1878-8750
ISSN (online)	1878-8769
ISSN	1878-8750
DOI	10.1016/j.wneu.2023.12.098
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