Scholarly Works, Biomedical Engineering and Mechanics

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Gradient descent optimization of acoustic holograms for transcranial focused ultrasound
Sallam, Ahmed; Cengiz, Ceren; Pewekar, Mihir; Hoffmann, Eric; Legon, Wynn; Vlaisavljevich, Eli; Shahab, Shima (AIP Publishing, 2024-10-08)
Acoustic holographic lenses, also known as acoustic holograms, can change the phase of a transmitted wavefront in order to shape and construct complex ultrasound pressure fields, often for focusing the acoustic energy on a target region. These lenses have been proposed for transcranial focused ultrasound (tFUS) to create diffraction-limited focal zones that target specific brain regions while compensating for skull aberration. Holograms are currently designed using time-reversal approaches in full-wave time-domain numerical simulations. Such simulations need time-consuming computations, which severely limits the adoption of iterative optimization strategies. In the time-reversal method, the number and distribution of virtual sources can significantly influence the final sound field. Because of the computational constraints, predicting these effects and determining the optimal arrangement is challenging. This study introduces an efficient method for designing acoustic holograms using a volumetric holographic technique to generate focused fields inside the skull. The proposed method combines a modified mixed-domain method for ultrasonic propagation with a gradient descent iterative optimization algorithm. The findings are further validated in underwater experiments with a realistic 3D-printed skull phantom. This approach enables substantially faster holographic computation than previously reported techniques. The iterative process uses explicitly defined loss functions to bias the ultrasound field’s optimization parameters to specific desired characteristics, such as axial resolution, transversal resolution, coverage, and focal region uniformity, while eliminating the uncertainty associated with virtual sources in time-reversal techniques. The proposed techniques enable more rapid hologram computation and more flexibility in tailoring ultrasound fields for specific therapeutic requirements.
Quantitative ultrasound assessment of fatty infiltration of the rotator cuff muscles using backscatter coefficient
Toto-Brocchi, Marco; Wu, Yuanshan; Jerban, Saeed; Han, Aiguo; Andre, Michael; Shah, Sameer B.; Chang, Eric Y. (2024-10-22)
Background: To prospectively evaluate ultrasound backscatter coefficients (BSCs) of the supraspinatus and infraspinatus muscles and compare with Goutallier classification on magnetic resonance imaging (MRI). Methods: Fifty-six participants had shoulder MRI exams and ultrasound exams of the supraspinatus and infraspinatus muscles. Goutallier MRI grades were determined and BSCs were measured. Group means were compared and the strength of relationships between the measures were determined. Using binarized Goutallier groups (0–2 versus 3–4), areas under the receiver operating characteristic curves (AUROCs) were calculated. The nearest integer cutoff value was determined using Youden’s index. Results: BSC values were significantly different among most Goutallier grades for the supraspinatus and infraspinatus muscles (both p < 0.001). Strong correlations were found between the BSC values and Goutallier grades for the supraspinatus (τb = 0.72, p < 0.001) and infraspinatus (τb = 0.79, p < 0.001) muscles. BSC showed excellent performance for classification of the binarized groups (0–2 versus 3–4) for both supraspinatus (AUROC = 0.98, p < 0.0001) and infraspinatus (AUROC = 0.98, p < 0.0001) muscles. Using a cutoff BSC value of −17 dB, sensitivity, specificity, and accuracy for severe fatty infiltration were 87.0%, 90.0%, and 87.5% for the supraspinatus muscle, and 93.6%, 87.5%, and 92.7% for the infraspinatus muscle. Conclusion: BSC can be applied to the rotator cuff muscles for assessment of fatty infiltration. For both the supraspinatus and infraspinatus muscles, BSC values significantly increased with higher Goutallier grades and showed strong performance in distinguishing low versus high Goutallier grades. Relevance statement: Fatty infiltration of the rotator cuff muscles can be quantified using BSC values, which are higher with increasing Goutallier grades. Key Points Ultrasound BSC measurements are reliable for the quantification of muscle fatty infiltration. BCS values increased with higher Goutallier MRI grades. BCS values demonstrated high performance for distinguishing muscle fatty infiltration groups.
Detection, Isolation and Quantification of Myocardial Infarct with Four Different Histological Staining Techniques
Wu, Xiaobo; Meier, Linnea; Liu, Tom X.; Toldo, Stefano; Poelzing, Steven; Gourdie, Robert G. (MDPI, 2024-10-18)
Background/Objectives: The precise quantification of myocardial infarction is crucial for evaluating therapeutic strategies. We developed a robust, color-based semi-automatic algorithm capable of infarct region detection, isolation and quantification with four different histological staining techniques, and of the isolation and quantification of diffuse fibrosis in the heart. Methods: Our method is developed based on the color difference in the infarct and non-infarct regions after histological staining. Mouse cardiac tissues stained with Masson’s trichrome (MTS), hematoxylin and eosin (H&E), 2,3,5-Triphenyltetrazolium chloride and picrosirius red were included to demonstrate the performance of our method. Results: We demonstrate that our algorithm can effectively identify and produce a clear visualization of infarct tissue in the four staining techniques. Notably, the infarct region on an H&E-stained tissue section can be clearly visualized after processing. The MATLAB-based program we developed holds promise for infarct quantification. Additionally, our program can isolate and quantify diffuse fibrotic elements from an MTS-stained cardiac section, which suggests the algorithm’s potential for evaluating pathological cardiac fibrosis in diseased cardiac tissues. Conclusions: We demonstrate that this color-based algorithm is capable of accurately identifying, isolating and quantifying cardiac infarct regions with different staining techniques, as well as diffuse and patchy fibrosis in MTS-stained cardiac tissues.
Investigation of High Frequency Irreversible Electroporation for Canine Spontaneous Primary Lung Tumor Ablation
Hay, Alayna N.; Aycock, Kenneth N.; Lorenzo, Melvin F.; David, Kailee; Coutermarsh-Ott, Sheryl; Salameh, Zaid; Campelo, Sabrina N.; Arroyo, Julio P.; Ciepluch, Brittany; Daniel, Gregory; Davalos, Rafael V.; Tuohy, Joanne (MDPI, 2024-09-07)
In this study, the feasibility of treating canine primary lung tumors with high-frequency irreversible electroporation (H-FIRE) was investigated as a novel lung cancer treatment option. H-FIRE is a minimally invasive tissue ablation modality that delivers bipolar pulsed electric fields to targeted cells, generating nanopores in cell membranes and rendering targeted cells nonviable. In the current study, canine patients (n = 5) with primary lung tumors underwent H-FIRE treatment with an applied voltage of 2250 V using a 2-5-2 µs H-FIRE waveform to achieve partial tumor ablation prior to the surgical resection of the primary tumor. Surgically resected tumor samples were evaluated histologically for tumor ablation, and with immunohistochemical (IHC) staining to identify cell death (activated caspase-3) and macrophages (IBA-1, CD206, and iNOS). Changes in immunity and inflammatory gene signatures were also evaluated in tumor samples. H-FIRE ablation was evident by the microscopic observation of discrete foci of acute hemorrhage and necrosis, and in a subset of tumors (n = 2), we observed a greater intensity of cleaved caspase-3 staining in tumor cells within treated tumor regions compared to adjacent untreated tumor tissue. At the study evaluation timepoint of 2 h post H-FIRE, we observed differential gene expression changes in the genes IDO1, IL6, TNF, CD209, and FOXP3 in treated tumor regions relative to paired untreated tumor regions. Additionally, we preliminarily evaluated the technical feasibility of delivering H-FIRE percutaneously under CT guidance to canine lung tumor patients (n = 2). Overall, H-FIRE treatment was well tolerated with no adverse clinical events, and our results suggest H-FIRE potentially altered the tumor immune microenvironment.
The connexin 43 carboxyl terminal mimetic peptide αCT1 prompts differentiation of a collagen scar matrix in humans resembling unwounded skin
Montgomery, Jade; Richardson, William J.; Marsh, Spencer; Rhett, J. Matthew; Bustos, Francis; Degen, Katherine; Ghatnekar, Gautam S.; Grek, Christina L.; Jourdan, L. Jane; Holmes, Jeffrey W.; Gourdie, Robert G. (Wiley, 2021-07-10)
Phase II clinical trials have reported that acute treatment of surgical skin wounds with the therapeutic peptide alpha Connexin Carboxy-Terminus 1 (αCT1) improves cutaneous scar appearance by 47% 9-month postsurgery. While Cx43 and ZO-1 have been identified as molecular targets of αCT1, the mode-of-action of the peptide in scar mitigation at cellular and tissue levels remains to be further characterized. Scar histoarchitecture in αCT1 and vehicle-control treated skin wounds within the same patient were compared using biopsies from a Phase I clinical trial at 29-day postwounding. The sole effect on scar structure of a range of epidermal and dermal variables examined was that αCT1-treated scars had less alignment of collagen fibers relative to control wounds—a characteristic that resembles unwounded skin. The with-in subject effect of αCT1 on scar collagen order observed in Phase I testing in humans was recapitulated in Sprague–Dawley rats and the IAF hairless guinea pig. Transient increase in histologic collagen density in response to αCT1 was also observed in both animal models. Mouse NIH 3T3 fibroblasts and primary human dermal fibroblasts treated with αCT1 in vitro showed more rapid closure in scratch wound assays, with individual cells showing decreased directionality in movement. An agent-based computational model parameterized with fibroblast motility data predicted collagen alignments in simulated scars consistent with that observed experimentally in human and the animal models. In conclusion, αCT1 prompts decreased directionality of fibroblast movement and the generation of a 3D collagen matrix postwounding that is similar to unwounded skin—changes that correlate with long-term improvement in scar appearance.
Tmem65 is critical for the structure and function of the intercalated discs in mouse hearts
Teng, Allen C. T.; Gu, Liyang; Di Paola, Michelle; Lakin, Robert; Williams, Zachary J.; Au, Aaron; Chen, Wenliang; Callaghan, Neal; Zadeh, Farigol Hakem; Zhou, Yu-Qing; Fatah, Meena; Chatterjee, Diptendu; Jourdan, L. Jane; Liu, Jack; Simmons, Craig A.; Kislinger, Thomas; Yip, Christopher M.; Backx, Peter H.; Gourdie, Robert G.; Hamilton, Robert M.; Gramolini, Anthony O. (Nature Portfolio, 2022-10-18)
The intercalated disc (ICD) is a unique membrane structure that is indispensable to normal heart function, yet its structural organization is not completely understood. Previously, we showed that the ICD-bound transmembrane protein 65 (Tmem65) was required for connexin43 (Cx43) localization and function in cultured mouse neonatal cardiomyocytes. Here, we investigate the functional and cellular effects of Tmem65 reductions on the myocardium in a mouse model by injecting CD1 mouse pups (3–7 days after birth) with recombinant adeno-associated virus 9 (rAAV9) harboring Tmem65 shRNA, which reduces Tmem65 expression by 90% in mouse ventricles compared to scrambled shRNA injection. Tmem65 knockdown (KD) results in increased mortality which is accompanied by eccentric hypertrophic cardiomyopathy within 3 weeks of injection and progression to dilated cardiomyopathy with severe cardiac fibrosis by 7 weeks post-injection. Tmem65 KD hearts display depressed hemodynamics as measured echocardiographically as well as slowed conduction in optical recording accompanied by prolonged PR intervals and QRS duration in electrocardiograms. Immunoprecipitation and super-resolution microscopy demonstrate a physical interaction between Tmem65 and sodium channel β subunit (β1) in mouse hearts and this interaction appears to be required for both the establishment of perinexal nanodomain structure and the localization of both voltage-gated sodium channel 1.5 (NaV1.5) and Cx43 to ICDs. Despite the loss of NaV1.5 at ICDs, whole-cell patch clamp electrophysiology did not reveal reductions in Na+ currents but did show reduced Ca2+ and K+ currents in Tmem65 KD cardiomyocytes in comparison to control cells. We conclude that disrupting Tmem65 function results in impaired ICD structure, abnormal cardiac electrophysiology, and ultimately cardiomyopathy.
Epigenomic tomography for probing spatially defined chromatin state in the brain
Liu, Zhengzhi; Deng, Chengyu; Zhou, Zirui; Ya, Xiao; Jiang, Shan; Zhu, Bohan; Naler, Lynette B.; Jia, Xiaoting; Yao, Danfeng (Daphne); Lu, Chang (Cell Press, 2024-03-25)
Spatially resolved epigenomic profiling is critical for understanding biology in the mammalian brain. Singlecell spatial epigenomic assays were developed recently for this purpose, but they remain costly and labor intensive for examining brain tissues across substantial dimensions and surveying a collection of brain samples. Here, we demonstrate an approach, epigenomic tomography, that maps spatial epigenomes of mouse brain at the scale of centimeters. We individually profiled neuronal and glial fractions of mouse neocortex slices with 0.5 mm thickness. Tri-methylation of histone 3 at lysine 27 (H3K27me3) or acetylation of histone 3 at lysine 27 (H3K27ac) features across these slices were grouped into clusters based on their spatial variation patterns to form epigenomic brain maps. As a proof of principle, our approach reveals striking dynamics in the frontal cortex due to kainic-acid-induced seizure, linked with transmembrane ion transporters, exocytosis of synaptic vesicles, and secretion of neurotransmitters. Epigenomic tomography provides a powerful and cost-effective tool for characterizing brain disorders based on the spatial epigenome.
Correlating tire traction performance on snow with measured parameters of ASTM F1805 using regression analysis
Shenvi, Mohit Nitin; Sandu, Corina; Untaroiu, Costin D.; Pierce, Eric (Elsevier, 2023-09)
Winter tires sold in North America are often tested using the ASTM F1805 testing process to determine if they can be labeled with the ‘mountain snowflake’ symbol which indicates better performance for snow usage. The standard dictates the requirements for testing and necessary track preparation methodologies. In addition, the requirements of the standard dictate the range of three major conditions for tests to be carried out, namely the CTI penetration measurement, the snow temperature, and the ambient temperature. However, these parameters cannot be directly used in the simulation stage of snow modeling for better evaluation of prototypes. It is well-known that snow properties depend on a wide variety of parameters, making the creation of an accurate and robust snow material model, and, consequently, applying a simulation-based approach for tire design, difficult. This work focuses on the analysis of a dataset of five winter seasons of a 14-in. Standard Reference Test Tire on snow used to benchmark the performance of a potential winter tire. The blinded data measured at Smithers Winter Test Center were used in the analysis to train regression models for predicting the traction coefficient and evaluating the extent to which the measured parameters affect the variation in the traction coefficient. This study utilized twenty-six different modeling approaches and implementation of principal component analysis. The findings of this study highlight the relative importance of the compression and shear characteristics of the snow on the traction of the tire. It was found that regression methods based on Gaussian processes were better at predicting the traction coefficient. The study also highlights the importance of utilizing a single physical tire as the reference tire for benchmarking according to the ASTM F1805.
Leveraging an Open-Access Digital Design Notebook for Graduate Biomedical Engineering Education in Nigeria
Casserly, Padraic; Dare, Ademola; Onuh, Joy; Baah, Williams; Taylor, Ashley R. (Springer, 2024-03-15)
Amidst the dual challenges of an eight-month university closure from nationwide public university strikes in Nigeria and the lingering impacts of the Covid-19 pandemic, we needed to innovate the delivery of BME graduate curriculum to ensure graduate students continued to progress in their studies. To ensure BME graduate students were engaging in team-based, clinician-identified engineering design challenges, we developed a digital design notebook (DDN) using Google Sites as an open-access, collaborative tool for scaffolding and documenting the engineering design process. Student design teams remotely uploaded digital content documenting their project work onto scaffolded DDNs created by program instructors. DDNs were purposefully designed to shepherd students through the design process such that each phase of the design process corresponded to an editable "page" of the DDN. Video lectures, learning resources, assignments, and other program information were embedded into the DDN for students to access throughout their design challenge. Project mentors and program instructors remotely monitored and assessed students' work using the DDN. At the end of the design challenge, students effectively created an e-portfolio which showcased the work they conducted to build a biomedical prototype. Designing and implementing the DDN builds on previous research which demonstrates that "structured" design notebooks can be used as effective tools in engineering design and design thinking education. Our work also leverages educational frameworks for infusing engineering design into existing graduate biomedical engineering curriculum in Nigeria.
A scoping review on examination approaches for identifying tactile deficits at the upper extremity in individuals with stroke
Paul, Arco P.; Nayak, Karan; Sydnor, Lindsey C.; Kalantaryardebily, Nahid; Parcetich, Kevin M.; Miner, Daniel G.; Wafford, Q. E.; Sullivan, Jane E.; Gurari, Netta (2024-06-08)
Purpose: Accurate perception of tactile stimuli is essential for performing and learning activities of daily living. Through this scoping review, we sought to summarize existing examination approaches for identifying tactile deficits at the upper extremity in individuals with stroke. The goal was to identify current limitations and future research needs for designing more comprehensive examination tools. Methods: A scoping review was conducted in accordance with the Joanna Briggs Institute methodological framework and the PRISMA for Scoping Reviews (PRISMA-ScR) guidelines. A database search for tactile examination approaches at the upper extremity of individuals with stroke was conducted using Medline (Ovid), The Cochrane Library (Wiley), CINAHL Plus with Full Text (Ebsco), Scopus (Elsevier), PsycInfo (Ebsco), and Proquest Dissertations and Theses Global. Original research and review articles that involved adults (18 years or older) with stroke, and performed tactile examinations at the upper extremity were eligible for inclusion. Data items extracted from the selected articles included: if the examination was behavioral in nature and involved neuroimaging, the extent to which the arm participated during the examination, the number of possible outcomes of the examination, the type(s) of tactile stimulation equipment used, the location(s) along the arm examined, the peripheral nerves targeted for examination, and if any comparison was made with the non-paretic arm or with the arms of individuals who are neurotypical. Results: Twenty-two articles met the inclusion criteria and were accepted in this review. Most examination approaches were behavioral in nature and involved self-reporting of whether a tactile stimulus was felt while the arm remained passive (i.e., no volitional muscle activity). Typically, the number of possible outcomes with these behavioral approaches were limited (2-3), whereas the neuroimaging approaches had many more possible outcomes (> 15). Tactile examinations were conducted mostly at the distal locations along the arm (finger or hand) without targeting any specific peripheral nerve. Although a majority of articles compared paretic and non-paretic arms, most did not compare outcomes to a control group of individuals who are neurotypical. Discussion: Our findings noted that most upper extremity tactile examinations are behavioral approaches, which are subjective in nature, lack adequate resolution, and are insufficient to identify the underlying neural mechanisms of tactile deficits. Also, most examinations are administered at distal locations of the upper extremity when the examinee’s arm is relaxed (passive). Further research is needed to develop better tactile examination tools that combine behavioral responses and neurophysiological outcomes, and allow volitional tactile exploration. Approaches that include testing of multiple body locations/nerves along the upper extremity, provide higher resolution of outcomes, and consider normative comparisons with individuals who are neurotypical may provide a more comprehensive understanding of the tactile deficits occurring following a stroke.
The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level in fruit flies
Afanasyev, Alexander Y.; Kim, Yoonjin; Tolokh, Igor S.; Sharakhov, Igor V.; Onufriev, Alexey V. (2024-05-06)
Background: Multiple studies have demonstrated a negative correlation between gene expression and positioning of genes at the nuclear envelope (NE) lined by nuclear lamina, but the exact relationship remains unclear, especially in light of the highly stochastic, transient nature of the gene association with the NE. Results: In this paper, we ask whether there is a causal, systematic, genome-wide relationship between the expression levels of the groups of genes in topologically associating domains (TADs) of Drosophila nuclei and the probabilities of TADs to be found at the NE. To investigate the nature of this possible relationship, we combine a coarse-grained dynamic model of the entire Drosophila nucleus with genome-wide gene expression data; we analyze the TAD averaged transcription levels of genes against the probabilities of individual TADs to be in contact with the NE in the control and lamins-depleted nuclei. Our findings demonstrate that, within the statistical error margin, the stochastic positioning of Drosophila melanogaster TADs at the NE does not, by itself, systematically affect the mean level of gene expression in these TADs, while the expected negative correlation is confirmed. The correlation is weak and disappears completely for TADs not containing lamina-associated domains (LADs) or TADs containing LADs, considered separately. Verifiable hypotheses regarding the underlying mechanism for the presence of the correlation without causality are discussed. These include the possibility that the epigenetic marks and affinity to the NE of a TAD are determined by various non-mutually exclusive mechanisms and remain relatively stable during interphase. Conclusions: At the level of TADs, the probability of chromatin being in contact with the nuclear envelope has no systematic, causal effect on the transcription level in Drosophila. The conclusion is reached by combining model-derived time-evolution of TAD locations within the nucleus with their experimental gene expression levels.
Applying Proteomics and Computational Approaches to Identify Novel Targets in Blast-Associated Post-Traumatic Epilepsy
Browning, Jack L.; Wilson, Kelsey A.; Shandra, Oleksii; Wei, Xiaoran; Mahmutovic, Dzenis; Maharathi, Biswajit; Robel, Stefanie; VandeVord, Pamela J.; Olsen, Michelle L. (MDPI, 2024-03-01)
Traumatic brain injury (TBI) can lead to post-traumatic epilepsy (PTE). Blast TBI (bTBI) found in Veterans presents with several complications, including cognitive and behavioral disturbances and PTE; however, the underlying mechanisms that drive the long-term sequelae are not well understood. Using an unbiased proteomics approach in a mouse model of repeated bTBI (rbTBI), this study addresses this gap in the knowledge. After rbTBI, mice were monitored using continuous, uninterrupted video-EEG for up to four months. Following this period, we collected cortex and hippocampus tissues from three groups of mice: those with post-traumatic epilepsy (PTE⁺), those without epilepsy (PTE⁻), and the control group (sham). Hundreds of differentially expressed proteins were identified in the cortex and hippocampus of PTE⁺ and PTE⁻ relative to sham. Focusing on protein pathways unique to PTE⁺, pathways related to mitochondrial function, post-translational modifications, and transport were disrupted. Computational metabolic modeling using dysregulated protein expression predicted mitochondrial proton pump dysregulation, suggesting electron transport chain dysregulation in the epileptic tissue relative to PTE⁻. Finally, data mining enabled the identification of several novel and previously validated TBI and epilepsy biomarkers in our data set, many of which were found to already be targeted by drugs in various phases of clinical testing. These findings highlight novel proteins and protein pathways that may drive the chronic PTE sequelae following rbTBI.
Scaling analysis of taenidia in beetle tracheae
Staples, Anne; Wilmsen, Sara; Zaslavsky, Sasha; Hopkins, Devyn; Khan, Saadbin; Socha, John (2024-01-04)
Comparison of the Biomechanics of the Mouse Astrocytic Lamina Cribrosa Between Glaucoma and Optic Nerve Crush Models
Korneva, Arina; Kimball, Elizabeth C.; Johnson, Thomas V.; Quillen, Sarah E.; Pease, Mary E.; Quigley, Harry A.; Nguyen, Thao D. (Association for Research in Vision and Ophthalmology (ARVO), 2023-12-13)
PURPOSE. The strain response of the mouse astrocytic lamina (AL) to an ex vivo mechanical test was compared between two protocols: eyes that underwent sustained intraocular pressure (IOP) increase and eyes after optic nerve crush. METHODS. Chronic IOP elevation was induced by microbead injection or the optic nerve was crushed in mice with widespread green fluorescence. After 3 days or 6 weeks, eyes were inflation tested by a published method of two-photon fluorescence to image the AL. Digital volume correlation was used to calculate strains. Optic nerve axon damage was also evaluated. RESULTS. In the central AL but not the peripheral AL, four strains were greater in eyes at the 3-day glaucoma time point than control (P from 0.029 to 0.049, n = 8 eyes per group). Also, at this time point, five strains were greater in the central AL compared to the peripheral AL (P from 0.041 to 0.00003). At the 6-week glaucoma time point, the strains averaged across the specimen, in the central AL, and the peripheral AL were indistinguishable from the respective controls. Strains were not significantly different between controls and eyes 3 days or 6 weeks after crush (n = 8 and 16). CONCLUSIONS. We found alterations in the ex vivo mechanical behavior in eyes from mice with experimental glaucoma but not in those with crushed optic nerves. The results of this study demonstrate that significant axon injury does not directly affect mechanical behavior of the astrocytic lamina.
Effects of Covid-19 Pandemic and Response on Student Performance in Large Foundational Mechanics Courses
Lord, James; Thompson, M. K. (ASEE Conferences, 2023-06-25)
In Spring 2020, institutions were forced to make rapid changes to their teaching, attendance, assessment, and academic relief policies. Our institution moved all classes and assessment online, removed most attendance policies, extended the drop deadline, and allowed students to alter their grading system from A-F to credit/no-credit. Most classes and assessments continued to be online in Fall 2020 and Spring 2021, before returning to typical pre-pandemic scheduling in Fall 2021. These accommodations were necessary to respond to public health advice, student and faculty illness, and ongoing uncertainty at the time. However, there are growing concerns about the effect that the pandemic and associated policies had on student learning and preparation for follow-on courses. We analyze student grade data and withdrawal rate for three large multi-section foundational mechanics courses between Fall 2015 - Fall 2022: Statics (91 sections), Mechanics of Deformable Bodies ('Deformables') (79 sections), and Dynamics (73 sections). Specifically, we look at Grade Point Average (GPA) and the proportion of students receiving either D grades, F grades, or withdrawing from each course (collectively known as the DFW rate). We separate our data into 4 time periods and compare results across these periods: Fall 2015 - Fall 2019 ('pre-pandemic'), Spring 2020 ('early-pandemic'), Fall 2020 - Spring 2021 ('mid-pandemic'), and Fall 2021 - Fall 2022 ('post-pandemic'). We find a significant increase in GPA and decrease in DFW rate in the Spring 2020 semester when classes were moved online and institutional polices were very lenient around grading and drop policies. Since Fall 2021 (when both course modality and institutional policies largely reverted) GPA and DFW rates in Statics have been virtually identical to pre-pandemic rates. However, we see significant decreases in GPA and significant increases in DFW rate in both Deformables and Dynamics. Statics is a prerequisite for both of these courses. This general trend was observed for almost all faculty members who taught classes across this time period, although the size of the effect varied. One section of Deformables has been offered asynchronously online since Fall 2015. This class also saw the same trends in GPA and DFW rate across the study period. We do not explicitly explore the reasons for these changes in this paper, but our experience in these classes suggests that students who took Statics mid-pandemic are not as well prepared for follow-on courses as students were pre-pandemic. The changes in GPA and DFW rate are a concern that is likely to extend to higher level courses. We intend to continue to track student progress through these courses and report on longer-term trends. Larger studies are warranted to help explain these trends.
Animal locomotion: Wing-like femoral lobes help orchid mantid nymphs glide
Socha, John J.; Khandelwal, Pranav C. (Elsevier, 2024-02)
The femoral lobes of the orchid mantis give this fierce predator a flower-like appearance, but they also assist in gliding, showing that form can match function in more ways than one.
A Year at the Forefront of Gliding Locomotion
Khandelwal, Pranav C.; Zakaria, Mohamed A.; Socha, John J. (Company of Biologists, 2023-08-15)
This review highlights the largely understudied behavior of gliding locomotion, which is exhibited by a diverse range of animals spanning vertebrates and invertebrates, in air and in water. The insights in the literature gained from January 2022 to December 2022 continue to challenge the previously held notion of gliding as a relatively simple form of locomotion. Using advances in field/lab data collection and computation, the highlighted studies cover gliding in animals including seabirds, flying lizards, flying snakes, geckos, dragonflies, damselflies, and dolphins. Altogether, these studies present gliding as a sophisticated behavior resulting from the interdependent aspects of morphology, sensing, environment, and likely selective pressures. This review uses these insights as inspiration to encourage researchers to revisit gliding locomotion, both in the animal's natural habitat and in the laboratory, and to investigate questions spanning gliding biomechanics, ecology, sensing, and the evolution of animal flight.
A biologically accurate model of directional hearing in the parasitoid fly Ormia ochracea
Mikel-Stites, Max R.; Salcedo, Mary K.; Socha, John J.; Marek, Paul E.; Staples, Anne E. (Cold Spring Harbor Laboratory, 2021-09-17)
Although most binaural organisms localize sound sources using neurological structures to amplify the sounds they hear, some animals use mechanically coupled hearing organs instead. One of these animals, the parasitoid fly Ormia ochracea, has astoundingly accurate sound localization abilities and can locate objects in the azimuthal plane with a precision of 2°, equal to that of humans. This is accomplished despite an intertympanal distance of only 0.5 mm, which is less than 1/100th of the wavelength of the sound emitted by the crickets that it parasitizes. In 1995, Miles et al. developed a model of hearing mechanics in O. ochracea, which works well for incoming sound angles of less than ±30°, but suffers from reduced accuracy (up to 60% error) at higher angles. Even with this limitation, it has served as the basis for multiple bio-inspired microphone designs for decades. Here, we present critical improvements to the classic O. ochracea hearing model based on information from 3D reconstructions of O. ochracea’s tympana. The 3D images reveal that the tympanal organ has curved lateral faces in addition to the flat front-facing prosternal membranes represented in the Miles model. To mimic these faces, we incorporated spatially-varying spring and damper coefficients that respond asymmetrically to incident sound waves, making a new quasi-two-dimensional (q2D) model. The q2D model has high accuracy (average errors of less than 10%) for the entire range of incoming sound angles. This improved biomechanical hearing model can inform the development of new technologies and may help to play a key role in developing improved hearing aids. Significance Statement: The ability to identify the location of sound sources is critical to organismal survival and for technologies that minimize unwanted background noise, such as directional microphones for hearing aids. Because of its exceptional auditory system, the parasitoid fly Ormia ochracea has served as an important model for binaural hearing and a source of bioinspiration for building tiny directional microphones with outsized sound localization abilities. Here, we performed 3D imaging of the fly’s tympanal organs and used the morphological information to improve the current model for hearing in O. ochracea. This model greatly expands the range of biological accuracy from ±30° to all incoming sound angles, providing a new avenue for studies of binaural hearing and further inspiration for fly-inspired technologies.
3D X-ray analysis of the subterranean burrowing depth and pupal chamber size of Laricobius (Coleoptera: Derodontidae), a specialist predator of Adelges tsugae (Hemiptera: Adelgidae)
Hillen, Ashleigh P.; Foley, Jeremiah R.; Salcedo, Mary K.; Socha, John J.; Salom, Scott M. (Oxford University Press, 2023-05-01)
The non-native hemlock woolly adelgid (HWA), Adelges tsugae Annand (Hemiptera: Adelgidae), has caused a significant decline of eastern hemlock, Tsuga canadensis L. (Pinales: Pinaceae), and Carolina hemlock, Tsuga caroliniana Engelmann (Pinales: Pinaceae), in eastern North America. Biological control of HWA has focused on the use of 2 Laricobius spp. (Coleoptera: Derodontidae), natural predators of HWA, which require arboreal and subterranean life phases to complete their development. In its subterranean phase, Laricobius spp. are subject to abiotic factors including soil compaction or soil-applied insecticides used to protect hemlock from HWA. This study used 3D X-ray microcomputed tomography (micro-CT) to identify the depth at which Laricobius spp. burrows during its subterranean lifecycle, characterize pupal chamber volume, and determine whether soil compaction had a significant effect on these variables. The mean burrowing depth in the soil of individuals was 27.0 mm ± 14.8 (SD) and 11.4 mm ± 11.8 (SD) at compaction levels of 0.36 and 0.54 g/ cm3, respectively. The mean pupal chamber volume was 11.15 mm3 ± 2.8 (SD) and 7.65 mm3 ± 3.5 (SD) in soil compacted at 0.36 and 0.54 g/cm3, respectively. These data show that soil compaction influences burrowing depth and pupal chamber size for Laricobius spp.This information will help us better identify the effect of soil-applied insecticide residues on estivating Laricobius spp. and soil-applied insecticide residues in the field. Additionally, these results demonstrate the utility of 3D micro-CT in assessing subterranean insect activity in future studies.
Pregnancy-induced remodeling of the murine reproductive tract: a longitudinal in vivo magnetic resonance imaging study
Suarez, Aileen C.; Gimenez, Clara J.; Russell, Serena R.; Wang, Maosen; Munson, Jennifer M.; Myers, Kristin M.; Miller, Kristin S.; Abramowitch, Steven D.; De Vita, Rafaella (Springer, 2024-01-05)
Mammalian pregnancy requires gradual yet extreme remodeling of the reproductive organs to support the growth of the embryos and their birth. After delivery, the reproductive organs return to their non-pregnant state. As pregnancy has traditionally been understudied, there are many unknowns pertaining to the mechanisms behind this remarkable remodeling and repair process which, when not successful, can lead to pregnancy-related complications such as maternal trauma, pre-term birth, and pelvic floor disorders. This study presents the first longitudinal imaging data that focuses on revealing anatomical alterations of the vagina, cervix, and uterine horns during pregnancy and postpartum using the mouse model. By utilizing advanced magnetic resonance imaging (MRI) technology, T1-weighted and T2-weighted images of the reproductive organs of three mice in their in vivo environment were collected at five time points: non-pregnant, mid-pregnant (gestation day: 9–10), late pregnant (gestation day: 16–17), postpartum (24–72 h after delivery) and three weeks postpartum. Measurements of the vagina, cervix, and uterine horns were taken by analyzing MRI segmentations of these organs. The cross-sectional diameter, length, and volume of the vagina increased in late pregnancy and then returned to non-pregnant values three weeks after delivery. The cross-sectional diameter of the cervix decreased at mid-pregnancy before increasing in late pregnancy. The volume of the cervix peaked at late pregnancy before shortening by 24–72 h postpartum. As expected, the uterus increased in cross-sectional diameter, length, and volume during pregnancy. The uterine horns decreased in size postpartum, ultimately returning to their average non-pregnant size three weeks postpartum. The newly developed methods for acquiring longitudinal in vivo MRI scans of the murine reproductive system can be extended to future studies that evaluate functional and morphological alterations of this system due to pathologies, interventions, and treatments.

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