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Biomedical Engineering


Biophysical metabolic modeling of complex bacterial colony morphology
I Dukovski, L Golden, J Zhang, M Osborne, D Segrè, K Korolev
bioRxiv, 2024.03. 13.584915 2024

Diversity in the Utilization of Different Molecular Classes of Dissolved Organic Matter by Heterotrophic Marine Bacteria
SH Givati, EJ Forchielli, D Aharonovich, N Barak, O Weissberg, N Belkin, ...  Daniel Segrè
bioRxiv, 2024.02. 13.580157 2024

Enhanced Multiscale Human Brain Imaging by Semi-supervised Digital Staining and Serial Sectioning Optical Coherence Tomography
L Tian, S Cheng, S Chang, Y Li, A Novoseltseva, S Lin, Y Wu, J Zhu, ...
Research Square DOI:10.21203/, 2024

Low-loss liquid metal interconnects for modular superconducting quantum systems
Z Yao, M Sandberg, DW Abraham, DJ Bishop
arXiv preprint: 2404.00770, 2024

Photothrombosis induced cortical stroke produces electrographic epileptic biomarkers in mice
DC Shaw, K Kondabolu, KG Walsh, W Shi, E Rillosi, M Hsiung, U Eden, ... Xue Han
bioRxiv, 2024.03. 01.582958, 2024

PhysMAP-interpretable in vivo neuronal cell type identification using multi-modal analysis of electrophysiological data
EK Lee, A Gul, G Heller, A Lakunina, S Jaramillo, P Przytycki, ...
bioRxiv, 2024.02. 28.582461 ,  2024

Tunable Universal OR-gated CAR T cells for AML
MY Siddiqui, J Chen, M Loffredo, S Lee, H Deng, Y Li, N Leemans, T Lu, ... WW Wong
bioRxiv, 2024.04. 13.589307 , 2024

Ultrasound pulse repetition frequency preferentially activates different neuron populations independent of cell type
J Sherman, E Bortz, E San Antonio, H Tseng, L Raiff, Xue Han
bioRxiv, 2024.03. 25.586645 2024

Unique growth and morphology properties of Clade 5 Clostridioides difficile strains revealed by single-cell time-lapse microscopy
JW Ribis, CA Nieto-Acuna, Q Dong, N DiBenedetto, A Mehra, IL Nagawa, ...
bioRxiv, 2024.02. 13.580212 2024

Visual stimulation drives retinotopic acetylcholine release in the mouse visual cortex
SG Knudstrup, C Martinez-Reyes, B Rauscher, PR Doran, ...
bioRxiv, 2024.02. 04.578821, 2024

Zeptonewton and Attotesla per Centimeter Metrology With Coupled Oscillators
I Bouche, J Javor, A Som, DK Campbell, DJ Bishop
arXiv preprint: 2402.14678, 2024

Article Databases


Adaptive Optics and Wavefront Control for Biological Systems X 
TG Bifano, N Ji, L Tian
Proc. of SPIE Vol 12851, 1285101-1, 2024 

Advances in Wearable High Density fNIRS and Utility for BCI 
D Boas, A von Lühmann, M Yücel, M Ning, S Duwadi, K Sen, ... 
2024 12th International Winter Conference on Brain-Computer Interface (BCI), 1-2, 2024 

Aged Tendons Exhibit Altered Mechanisms of Strain-Dependent Extracellular Matrix Remodeling 
AN Aggouras, EJ Stowe, SJ Mlawer, B Connizzo 
Journal of Biomechanical Engineering, 1-41, 2024 

Anti-CRISPR Anopheles mosquitoes inhibit gene drive spread under challenging behavioural conditions in large cages
R D’Amato, C Taxiarchi, M Galardini, A Trusso, RL Minuz, S Grilli, ...Ahmad S. Khalil
Nature Communications 15 (1), 952 2024

Assessing neuroprotective effects of diroximel fumarate and siponimod via modulation of pacemaker channels in an experimental model of remyelination
L Vinnenberg, N Rychlik, T Oniani, B Williams, JA White, S Kovac, ...
Experimental Neurology 371, 114572, 2024

Association between air raids and reported incidence of cholera in Yemen, 2016–19: an ecological modelling study
MC Tarnas, N Al-Dheeb, MH Zaman, DM Parker
The Lancet, 2024

Camera selection for speckle contrast optical spectroscopy and validation against diffuse correlation spectroscopy 
TY Cheng, B Kim, BB Zimmermann, MR Robinson, M Renna, SA Carp, ... 
Dynamics and Fluctuations in Biomedical Photonics XXI 12841, 15-18, 2024 

Cationic tantalum oxide nanoparticle contrast agent for micro computed tomography reveals articular cartilage proteoglycan distribution and collagen architecture alterations
J Jäntti, A Joenathan, M Fugazzola, J Tuppurainen, JTJ Honkanen, ... Grinstaff, Mark W
Osteoarthritis and Cartilage 32 (3), 299-309 2024

Combined frequency domain near-infrared spectroscopy and diffuse correlation spectroscopy system for comprehensive metabolic monitoring of inspiratory muscles during loading
CA Gómez, L Brochard, EC Goligher, D Rozenberg, WD Reid, D Roblyer
Journal of Biomedical Optics 29 (3), 035002-035002 2024

Comparing the performance potential of speckle contrast optical spectroscopy and diffuse correlation spectroscopy for cerebral blood flow monitoring using Monte Carlo simulations in realistic head geometries
MB Robinson, TY Cheng, M Renna, MM Wu, B Kim, X Cheng, DA Boas, ... 
Neurophotonics 11 (1), 015004-015004, 2024 

Computational identification of antibody-binding epitopes from mimotope datasets
R Li, S Wilderotter, M Stoddard, D Van Egeren, A Chakravarty, ... D Joseph-Mccarthy
Frontiers in Bioinformatics 4, 1295972, 2024

Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2
AA Bekar-Cesaretli, O Khan, T Nguyen, D Kozakov, D Joseph-Mccarthy, ...
Journal of Chemical Information and Modeling  2024

Decreased Lung Metastasis in Triple Negative Breast Cancer Following Locally Delivered Supratherapeutic Paclitaxel-Loaded Polyglycerol Carbonate Nanoparticle Therapy
RC Sabatelle, NQ Chu, W Blessing, H Kharroubi, E Bressler, L Tsai, ... Grinstaff, Mark W
Biomacromolecules  2024

Deep model predictive control of gene expression in thousands of single cells 
JB Lugagne, CM Blassick, MJ Dunlop 
Nature Communications 15 (1), 2148 5, 2024 

Drinkable in situ-forming tough hydrogels for gastrointestinal therapeutics
GW Liu, MJ Pickett, JLP Kuosmanen, K Ishida, WAM Madani, GN White, ... Miguel Jimenez
Nature Materials, 1-8, 2024

Dynamic light scattering and laser speckle contrast imaging of the brain: theory of the spatial and temporal statistics of speckle pattern evolution 
B Liu, D Postnov, DA Boas, X Cheng 
Biomedical Optics Express 15 (2), 579-593, 2, 2024 

Effects of polydimethylsiloxane membrane surface treatments on human uterine smooth muscle cell strain response
EE Marr, BC Isenberg, JY Wong
Bioactive Materials 32, 415-426, 2024

Emergence of nanoscale viscoelasticity from single cancer cells to established tumors
M Hadzipasic, S Zhang, Z Huang, R Passaro, MS Sten, GM Shankar, ... HT Nia
Biomaterials 305, 122431, 2024

Engineered virus-like particles for transient delivery of prime editor ribonucleoprotein complexes in vivo 
M An, A Raguram, SW Du, S Banskota, JR Davis, GA Newby, PZ Chen, ... 
Nature biotechnology, 1-12, 2024 

Entorhinal‐based path integration selectively predicts midlife risk of Alzheimer's disease
C Newton, M Pope, C Rua, R Henson, Z Ji, N Burgess, CT Rodgers, ...  Matthias Stangl
Alzheimer's & Dementia, Vol.20 (4), p.2779-2793, 2024

Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites
O Khan, G Jones, M Lazou, D Joseph-McCarthy, D Kozakov, D Beglov, ...
Journal of Chemical Information and Modeling 2024

Expanding the reach of label-free diffuse optics with frequency domain shortwave infrared imaging
D Roblyer
Molecular-Guided Surgery: Molecules, Devices, and Applications X, PC1282508, 2024

Fast volumetric imaging in tissue
Jerome Mertz 
Proc. SPIE PC12848, Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXXI, PC1284805, March 2024

Final Technical Report: High-throughput chemical imaging for optimizing biofuel synthesis using synthetic biology 
M Dunlop 

OSTI/Boston University, 2024 

fNIRS dataset during complex scene analysis
M Ning, S Duwadi, MA Yücel, A Von Lühmann, DA Boas, K Sen
Frontiers in Human Neuroscience 18, 1329086 2024

Geometry and length control of 3D engineered heart tissues using direct laser writing 
MÇ Karakan, JK Ewoldt, AJ Segarra, S Sundaram, MC Wang, AE White, ... 
Lab on a Chip, 2024 

Identification of a druggable site on GRP78 at the GRP78-SARS-CoV-2 interface and virtual screening of compounds to disrupt that interface
M Lazou, JR Hutton, A Chakravarty, D Joseph-McCarthy
Journal of Computer-Aided Molecular Design 38 (1), 6 2024

An improved image analysis method for micropattern traction microscopy: dot tracking and traction force calculation script protocols
KA Bunde, W Fan, D Stamenovic, PE Barbone, ML Smith

Improving gonorrhoea molecular diagnostics: Genome mining-based identification of identical multi-repeat sequences (IMRS) in Neisseria gonorrhoeae
C Shiluli, S Kamath, BN Kanoi, R Kimani, M Maina, H Waweru, M Kamita, ...
Heliyon 10 (6) 2024

In vivo voltage imaging with targeted illumination confocal (TICO) microscopy 
S Xiao, WJ Cunningham, K Kondabolu, E Lowet, MV Moya, R Mount, ... Jerome Mertz
Proc. SPIE PC12828, Neural Imaging and Sensing 2024,

Ischemic and hemorrhagic stroke lesion environments differentially alter the glia repair potential of neural progenitor cell and immature astrocyte grafts
HO Adewumi, GI Berniac, EA McCarthy, TM O'Shea
Experimental Neurology 374, 114692, 2024

Label-free imaging and quantitative analysis of lipofuscin aggregates in human brain tissue  
A Abdelhakeem, S Chang, A Novoseltseva, G Kureli, AC Mckee, B Huber, ... 
Label-free Biomedical Imaging and Sensing (LBIS) 2024, PC1285412, 2024 

Length of stay prediction for hospital management using domain adaptation
LNW Momo, N Moorosi, EO Nsoesie, F Rademakers, B De Moor
Engineering Applications of Artificial Intelligence 133, 108088

Light-inducible protein degradation in E. coli with the LOVdeg tag 
N Tague, C Coriano-Ortiz, MB Sheets, MJ Dunlop 
Elife 12, RP87303 2 2024 

Local fractal dimension of collagen detects increased spatial complexity in fibrosis
DT Casey, KG Lahue, V Mori, J Herrmann, JK Hall, B Suki, ...
Histochemistry and cell biology 161 (1), 29-42, 2024

A lone spike in blood glucose can enhance the thrombo-inflammatory response in cortical venules 
I Shaked, C Foo, P Mächler, R Liu, Y Cui, X Ji, T Broggini, T Kaminski, ...  Anna Devor
Journal of Cerebral Blood Flow & Metabolism 44 (2), 252-271 2 2024 

Mapping a Way to Displaced Persons’ Access to Quality Medicines
C Ching, MH Zaman
AMA Journal of Ethics 26 (4), 341-347, 2024

MicroBundleCompute: Automated segmentation, tracking, and analysis of subdomain deformation in cardiac microbundles 
H Kobeissi, J Jilberto, MÇ Karakan, X Gao, SJ DePalma, SL Das, L Quach, ... 
Plos one 19 (3), e0298863 3 2024 

A missed opportunity: A scoping review of the effect of sex and age on osteoarthritis using large animal models 
HL Stewart, D Gilbert, D Stefanovski, Z Garman, MB Albro, M Bais, ... 
Osteoarthritis and Cartilage, 2024 

Multi-Attribute Subset Selection enables prediction of representative phenotypes across microbial populations
K Herbst, T Wang, EJ Forchielli, M Thommes, IC Paschalidis, D Segrè
Communications Biology 7 (1), 407 2024

Multiscale elasticity mapping of biological samples in 3D at optical resolution
K Regan, R LeBourdais, R Banerji, S Zhang, J Muhvich, S Zheng, HT Nia
Acta Biomaterialia 176, 250-266 1 2024

Multiscale Imaging and Spectroscopy V
PJ Campagnola, DM Roblyer, AJ Walsh
Proc. of SPIE Vol 12827, 1282701-1 2024

Multiscale mechanics of polydimethylsiloxane: A comparison of meso‐and micro‐cyclic deformation behavior 
L Lou, N Bacca, MS Ma, P Nautiyal, TG Bifano, A Agarwal 
Journal of Applied Polymer Science, e55546 , 2024  

Nanoscale structural mapping of protein aggregates in live cells modeling Huntington's disease by mid-infrared photothermal microscopy
Z Guo, G Chiesa, J Yin, A Sanford, S Meier, AS Khalil, JX Cheng
Advanced Chemical Microscopy for Life Science and Translational Medicine … 2024

Obesity Differs from Diabetes Mellitus in Antibody and T Cell Responses Post COVID-19 Recovery
M Ali, S Longet, I Neale, P Rongkard, FUH Chowdhury, J Hill, A Brown, ... A Tomic
Clinical and Experimental Immunology, uxae030, 2024

Open-source spatial frequency domain imaging from the near-infrared to the shortwave infrared
D Roblyer

Optical Interactions with Tissue and Cells XXXV, PC128400H, 2024
SPIE Conference presentation

Orthogonal inducible control of Cas13 circuits enables programmable RNA regulation in mammalian cells
Y Ding, C Tous, J Choi, J Chen, WW Wong
Nature Communications 15 (1), 1572 1 2024

Preliminary design of a handheld spatial frequency domain imager for quantitative scleroderma skin assessment
A Mehendale, K Karrobi, A Pilvar, A Bujor, D Roblyer
Multiscale Imaging and Spectroscopy V, PC1282709, 2024

Preliminary investigation of non-invasive blood pressure estimation using speckle contrast optical spectroscopy
A Garrett, B Kim, NZ Gurel, F Marsili, E Sie, D Boas, D Roblyer
Proceedings Volume PC12850, Optical Diagnostics and Sensing XXIV: Toward Point-of-Care Diagnostics; PC128500B (2024)

A Protein‐Adsorbent Hydrogel with Tunable Stiffness for Tissue Culture Demonstrates Matrix‐Dependent Stiffness Responses 
L Li, ME Griebel, M Uroz, SY Bubli, KA Gagnon, B Trappmann, BM Baker, ... Christopher S. Chen
Advanced Functional Materials, 2309567, 2024 

Quantifying cerebral microvasculature alterations in neurodegenerative diseases 
Mackenzie Hyman, Shuaibin Chang, Jairui Yang, Anna Novoseltseva, Gulce Küreli, Ann C. McKee, Irving J. BigioDavid A. Boas, Hui Wang
Label-free Biomedical Imaging and Sensing (LBIS) 2024, PC128540A, 2024 

Randomized Trial of the Insulin-Only iLet Bionic Pancreas for the Treatment of Cystic Fibrosis–Related Diabetes 
JS Sherwood, LE Castellanos, MY O’Connor, CA Balliro, MA Hillard, ... 
Diabetes care 47 (1), 101-108, 2024 

Rapid, multiplexed, and enzyme-free nucleic acid detection using programmable aptamer-based RNA switches 
Zhaoqing Yan, Amit Eshed, Anli A Tang, Nery R Arevalos, Zackary M Ticktin, Soma Chaudhary, Duo Ma, Griffin McCutcheon, Yudan Li, Kaiyue Wu, Sanchari Saha, Jonathan Alcantar-Fernandez, Jose L Moreno-Camacho, Abraham Campos-Romero, James J Collins, Peng Yin, Alexander A Green 
Chem April, 2024 

Relatively Rare Populations of Invasive Cells Drive Progression of Heterogeneous Tumors
SE Leggett, MC Brennan, S Martinez, J Tien, CM Nelson
Cellular and Molecular Bioengineering, 1-18, 2024

Spatial frequency domain imaging (SFDI) for the assessment of disease progression in scleroderma
A Mehendale, A Pilvar, K Karrobi, H Vo, A Bujor, DM Roblyer
Proceedings Volume PC12816, Photonics in Dermatology and Plastic Surgery 2024; 
SPIE Conference presentation

Spike ripples localize the epileptogenic zone best: an international intracranial study
W Shi, D Shaw, KG Walsh, Xue Han, UT Eden, RM Richardson, SV Gliske, ...
Brain, awae037 3 2024

Structural maturation of myofilaments in engineered 3D cardiac microtissues characterized using small angle X-ray scattering 
G van Dover, J Javor, JK Ewoldt, M Zhernenkov, P Wąsik, G Freychet, ... 
Physical Biology 21 (3), 036001 ,2024 

Targeted micro-fiber arrays for measuring and manipulating localized multi-scale neural dynamics over large, deep brain volumes during behavior 
MAT Vu, EH Brown, MJ Wen, CA Noggle, Z Zhang, KJ Monk, S Bouabid, ... 
Neuron 2, 2024 

Trial-history biases in evidence accumulation can give rise to apparent lapses in decision-making 
D Gupta, B DePasquale, CD Kopec, CD Brody 
Nature communications 15 (1), 662, 2024 

Transmission Dynamics and Rare Clustered Transmission Within an Urban University Population Before Widespread Vaccination
J Turcinovic, K Kuhfeldt, M Sullivan, L Landaverde, JT Platt, YO Alekseyev, ...
The Journal of Infectious Diseases 229 (2), 485-492 1 2024

Triple contrast computed tomography reveals site‐specific biomechanical differences in the human knee joint—A proof of concept study
H Orava, P Paakkari, J Jäntti, MKM Honkanen, JTJ Honkanen, T Virén, ... Grinstaff, Mark W
Journal of Orthopaedic Research® 42 (2), 415-424, 2024

Understanding the nervous system: lessons from Frontiers in Neurophotonics
Y De Koninck, J Alonso, S Bancelin, JC Béïque, E Bélanger, C Bouchard, ...
Neurophotonics 11 (1), 014415-014415 1 2024

Use of an elastic-scattering spectroscopy and artificial intelligence device in the assessment of lesions suggestive of skin cancer: A comparative effectiveness study 
D Manolakos, G Patrick, JK Geisse, H Rabinovitz, K Buchanan, P Hoang, ... 
JAAD international 14, 52-58, 2024