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  • UMCCTS Newsletter, April 2024

    UMass Center for Clinical and Translational Science (2024-04-01)
    This is the April 2024 issue of the UMass Center for Clinical and Translational Science Newsletter containing news and events of interest.
  • Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements

    Wirthlin, Morgan E; Schmid, Tobias A; Elie, Julie E; Zhang, Xiaomeng; Kowalczyk, Amanda; Redlich, Ruby; Shvareva, Varvara A; Rakuljic, Ashley; Ji, Maria B; Bhat, Ninad S; et al. (2024-03-29)
    Vocal production learning ("vocal learning") is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical, and neurophysiological data from the Egyptian fruit bat (Rousettus aegyptiacus) with analyses of the genomes of 215 placental mammals. First, we identified a set of proteins evolving more slowly in vocal learners. Then, we discovered a vocal motor cortical region in the Egyptian fruit bat, an emergent vocal learner, and leveraged that knowledge to identify active cis-regulatory elements in the motor cortex of vocal learners. Machine learning methods applied to motor cortex open chromatin revealed 50 enhancers robustly associated with vocal learning whose activity tended to be lower in vocal learners. Our research implicates convergent losses of motor cortex regulatory elements in mammalian vocal learning evolution.
  • Robust thalamic nuclei segmentation from T1-weighted MRI using polynomial intensity transformation

    Vidal, Julie P; Danet, Lola; Péran, Patrice; Pariente, Jérémie; Bach Cuadra, Meritxell; Zahr, Natalie M; Barbeau, Emmanuel J; Saranathan, Manojkumar (2024-03-28)
    Accurate segmentation of thalamic nuclei, crucial for understanding their role in healthy cognition and in pathologies, is challenging to achieve on standard T1-weighted (T1w) magnetic resonance imaging (MRI) due to poor image contrast. White-matter-nulled (WMn) MRI sequences improve intrathalamic contrast but are not part of clinical protocols or extant databases. In this study, we introduce histogram-based polynomial synthesis (HIPS), a fast preprocessing transform step that synthesizes WMn-like image contrast from standard T1w MRI using a polynomial approximation for intensity transformation. HIPS was incorporated into THalamus Optimized Multi-Atlas Segmentation (THOMAS) pipeline, a method developed and optimized for WMn MRI. HIPS-THOMAS was compared to a convolutional neural network (CNN)-based segmentation method and THOMAS modified for the use of T1w images (T1w-THOMAS). The robustness and accuracy of the three methods were tested across different image contrasts (MPRAGE, SPGR, and MP2RAGE), scanner manufacturers (PHILIPS, GE, and Siemens), and field strengths (3 T and 7 T). HIPS-transformed images improved intra-thalamic contrast and thalamic boundaries, and HIPS-THOMAS yielded significantly higher mean Dice coefficients and reduced volume errors compared to both the CNN method and T1w-THOMAS. Finally, all three methods were compared using the frequently travelling human phantom MRI dataset for inter- and intra-scanner variability, with HIPS displaying the least inter-scanner variability and performing comparably with T1w-THOMAS for intra-scanner variability. In conclusion, our findings highlight the efficacy and robustness of HIPS in enhancing thalamic nuclei segmentation from standard T1w MRI.
  • The 20th Annual Gerald F. Berlin Creative Writing Award Ceremony and Readings

    Lamar Soutter Library; Berlin, Richard M (2024-03-26)
    The Gerald F. Berlin Creative Writing Award is funded by a donation from Richard M. Berlin, M.D., a poet and Associate Professor of Psychiatry at UMass Chan Medical School. Dr. Berlin established the Award to encourage creative writing among UMass Chan students and residents, and to honor his father who struggled with a severe chronic illness. 2024 Awards: First Place: "Two True Stories" by Elizabeth (Liz) M. Irvin, MD Candidate, Class of 2026, UMass Chan Medical School. Second Place: "To Be a Body" by Hyein Sarah Lee (she/they), MD/PhD Candidate, GS1, UMass Chan Medical School. Third Place: "Hospital Food" by Abigail DeNike, MD Candidate, Class of 2027, UMass Chan Medical School. Honorable Mention: "Grief Sandwich" by Darya Herscovici, MD Candidate, Class of 2024, UMass Chan Medical School. Honorable Mention: "Shadow" by Alexander Hamel, MD Candidate, Class of 2027, UMass Chan Medical School. Honorable Mention: "His Name is Phil" by Melanie Fu (she/they), MD Candidate, Class of 2027, UMass Chan Medical School.
  • Celebrating and Congratulations!

    Silk, Hugh (2024-03-21)
    Introduction: This week I am celebrating, along with my colleagues, our very successful match into family medicine (and to our residencies)! With 14.02% of UMass Chan students matching into Family Medicine, we exceeded the national average of 12.7% (per AAFP). Family Medicine Proud! This quote from Dr. Victor Johnson, known as the founding father of the College of General Practitioners now the College of Family Physicians in Canada, summarizes their future impact. "I became convinced that the medical profession would be saved not by its organization but by the sum total of the common sense and humanity of its individual practicing members. General practitioners... are the doctors closest to [the] people. They heal more of the broken hearted, repair more of the injured and deprived, and live with the poor and dying who are without influence and hope. As Family Physicians, you are ideally positioned in the health care system to understand patients and their family and community context, and to provide for them a deep connection, compassion, and care." The picture below says it best. These individuals are way more than a statistic. They will make us proud in the way Victor Johnson wanted family doctors to be. Congratulations to these future family physicians and to all who taught, challenged, mentored, coached, consoled, and encouraged them. Take a moment and congratulate yourselves too! Be well.
  • A machine learning approach for diagnostic and prognostic predictions, key risk factors and interactions

    Nasir, Murtaza; Summerfield, Nichalin S.; Carreiro, Stephanie; Berlowitz, Dan; Oztekin, Asil (2024-03-18)
    Machine learning (ML) has the potential to revolutionize healthcare, allowing healthcare providers to improve patient-care planning, resource planning and utilization. Furthermore, identifying key-risk-factors and interaction-effects can help service-providers and decision-makers to institute better policies and procedures. This study used COVID-19 electronic health record (EHR) data to predict five crucial outcomes: positive-test, ventilation, death, hospitalization days, and ICU days. Our models achieved high accuracy and precision, with AUC values of 91.6%, 99.1%, and 97.5% for the first three outcomes, and MAE of 0.752 and 0.257 days for the last two outcomes. We also identified interaction effects, such as high bicarbonate in arterial blood being associated with longer hospitalization in middle-aged patients. Our models are embedded in a prototype of an online decision support tool that can be used by healthcare providers to make more informed decisions.
  • Over Fartsgrensen

    Gracey, Kristina (2024-03-14)
    Introduction: This week I am grateful to Kristina Gracey, faculty at Barre Family Health Center, for her essay that is both personal and informative. She is an avid and successful runner. Which can be dangerous. She has been thinking about this element of risk and adds a public health perspective to her reflection that I personally admire. Food for thought for possible collective advocacy by us all on this topic.
  • Dual Layer vs Single Layer Woven EndoBridge Device in the Treatment of Intracranial Aneurysms: A Propensity Score-Matched Analysis

    Dmytriw, Adam A; Salim, Hamza; Musmar, Basel; Aslan, Assala; Cancelliere, Nicole M; McLellan, Rachel M; Algin, Oktay; Ghozy, Sherief; Dibas, Mahmoud; Lay, Sovann V; et al. (2024-03-14)
    Background: The Woven EndoBridge (WEB) devices have been used for treating wide neck bifurcation aneurysms (WNBAs) with several generational enhancements to improve clinical outcomes. The original device dual-layer (WEB DL) was replaced by a single-layer (WEB SL) device in 2013. This study aimed to compare the effectiveness and safety of these devices in managing intracranial aneurysms. Methods: A multicenter cohort study was conducted, and data from 1,289 patients with intracranial aneurysms treated with either the WEB SL or WEB DL devices were retrospectively analyzed. Propensity score matching was utilized to balance the baseline characteristics between the two groups. Outcomes assessed included immediate occlusion rate, complete occlusion at last follow-up, retreatment rate, device compaction, and aneurysmal rupture. Results: Before propensity score matching, patients treated with the WEB SL had a significantly higher rate of complete occlusion at the last follow-up and a lower rate of retreatment. After matching, there was no significant difference in immediate occlusion rate, retreatment rate, or device compaction between the WEB SL and DL groups. However, the SL group maintained a higher rate of complete occlusion at the final follow-up. Regression analysis showed that SL was associated with higher rates of complete occlusion (OR: 0.19; CI: 0.04 to 0.8, p = 0.029) and lower rates of retreatment (OR: 0.12; CI: 0 to 4.12, p = 0.23). Conclusion: The WEB SL and DL devices demonstrated similar performances in immediate occlusion rates and retreatment requirements for intracranial aneurysms. The SL device showed a higher rate of complete occlusion at the final follow-up.
  • Reinjury Following Return to Play

    Watts, George J.; Tai, Ryan; Joshi, Ganesh; Garwood, Elisabeth R; Saha, Debajyoti (2024-03-14)
    Radiologists are frequently called on for guidance regarding return to play (RTP) for athletes and active individuals after sustaining a musculoskeletal injury. Avoidance of reinjury is of particular importance throughout the rehabilitative process and following resumption of competitive activity. Understanding reinjury risk estimation, imaging patterns, and correlation of clinical and surgical findings will help prepare the radiologist to identify reinjuries correctly on diagnostic imaging studies and optimize management for a safe RTP.
  • Sampling of healthcare professionals' perspective on point-of-care technologies from 2019-2021: A survey of benefits, concerns, and development

    Orwig, Taylor; Sutaria, Shiv; Wang, Ziyue; Howard-Wilson, Sakeina; Dunlap, Denise; Lilly, Craig M; Buchholz, Bryan; McManus, David D; Hafer, Nathaniel (2024-03-08)
    Point-of-care technology (POCT) plays a vital role in modern healthcare by providing a fast diagnosis, improving patient management, and extending healthcare access to remote and resource-limited areas. The objective of this study was to understand how healthcare professionals in the United States perceived POCTs during 2019-2021 to assess the decision-making process of implementing these newer technologies into everyday practice. A 5-point Likert scale survey was sent to respondents to evaluate their perceptions of benefits, concerns, characteristics, and development of point-of-care technologies. The 2021 survey was distributed November 1st, 2021- February 15th, 2022, with a total of 168 independent survey responses received. Of the respondents, 59% identified as male, 73% were white, and 48% have been in practice for over 20 years. The results showed that most agreed that POCTs improve patient management (94%) and improve clinician confidence in decision making (92%). Healthcare professionals were most concerned with potentially not being reimbursed for the cost of the POCT (37%). When asked to rank the top 3 important characteristics of POCT, respondents chose accuracy, ease of use, and availability. It is important to note this survey was conducted during the COVID-19 pandemic. To achieve an even greater representation of healthcare professionals' point of view on POCTs, further work to obtain responses from a larger, more diverse population of providers is needed.
  • Normative modeling of thalamic nuclear volumes [preprint]

    Young, Taylor; Kumar, Vinod Jangid; Saranathan, Manojkumar (2024-03-08)
    Thalamic nuclei have been implicated in neurodegenerative and neuropsychiatric disorders. Normative models for thalamic nuclear volumes have not been proposed thus far. The aim of this work was to establish normative models of thalamic nuclear volumes and subsequently investigate changes in thalamic nuclei in cognitive and psychiatric disorders. Volumes of the bilateral thalami and 12 nuclear regions were generated from T1 MRI data using a novel segmentation method (HIPS-THOMAS) in healthy control subjects (n=2374) and non-control subjects (n=695) with early and late mild cognitive impairment (EMCI, LMCI), Alzheimer's disease (AD), Early psychosis and Schizophrenia, Bipolar disorder, and Attention deficit hyperactivity disorder. Three different normative modelling methods were evaluated while controlling for sex, intracranial volume, and site. Z-scores and extreme z-score deviations were calculated and compared across phenotypes. GAMLSS models performed the best. Statistically significant shifts in z-score distributions consistent with atrophy were observed for most phenotypes. Shifts of progressively increasing magnitude were observed bilaterally from EMCI to AD with larger shifts in the left thalamic regions. Heterogeneous shifts were observed in psychiatric diagnoses with a predilection for the right thalamic regions. Here we present the first normative models of thalamic nuclear volumes and highlight their utility in evaluating heterogenous disorders such as Schizophrenia.
  • Distribution and bulk flow analyses of the intraflagellar transport (IFT) motor kinesin-2 support an "on-demand" model for Chlamydomonas ciliary length control

    Patel, Mansi B; Griffin, Paul J; Olson, Spencer F; Dai, Jin; Hou, Yuqing; Malik, Tara; Das, Poulomi; Zhang, Gui; Zhao, Winston; Witman, George B.; et al. (2024-03-08)
    Most cells tightly control the length of their cilia. The regulation likely involves intraflagellar transport (IFT), a bidirectional motility of multi-subunit particles organized into trains that deliver building blocks into the organelle. In Chlamydomonas, the anterograde IFT motor kinesin-2 consists of the motor subunits FLA8 and FLA10 and the nonmotor subunit KAP. KAP dissociates from IFT at the ciliary tip and diffuses back to the cell body. This observation led to the diffusion-as-a-ruler model of ciliary length control, which postulates that KAP is progressively sequestered into elongating cilia because its return to the cell body will require increasingly more time, limiting motor availability at the ciliary base, train assembly, building block supply, and ciliary growth. Here, we show that Chlamydomonas FLA8 also returns to the cell body by diffusion. However, more than 95% of KAP and FLA8 are present in the cell body and, at a given time, just ~1% of the motor participates in IFT. After repeated photobleaching of both cilia, IFT of fluorescent kinesin subunits continued indicating that kinesin-2 cycles from the large cell-body pool through the cilia and back. Furthermore, growing and full-length cilia contained similar amounts of kinesin-2 subunits and the size of the motor pool at the base changed only slightly with ciliary length. These observations are incompatible with the diffusion-as-a-ruler model, but rather support an "on-demand model," in which the cargo load of the trains is regulated to assemble cilia of the desired length.
  • Photos of Meaningful Things and Places

    Penumetcha, Venkata "Sai Sri"; Isaac, Tamika; Coderre, Danielle; Silk, Hugh (2024-03-07)
    Introduction: This week I have a visual treat. Last week Sara Shields and I had a session with the PGY1s on the topic of medical humanities and one of the prompts was to go into the hospital and return with a photo of something that is meaningful to you - can be a piece, a thing, a person. The discussion that ensued from these photos was wonderful! I am sharing some of the photos here for you with their title. Enjoy.
  • UMCCTS Newsletter, March 2024

    UMass Center for Clinical and Translational Science (2024-03-01)
    This is the March 2024 issue of the UMass Center for Clinical and Translational Science Newsletter containing news and events of interest.
  • Adjustment for Renal Function Improves the Prognostic Performance of Urinary Thromboxane Metabolites

    Barton, Bruce A; Kronsberg, Shari S; Hariri, Essa; Vasan, Ramachandran S; Rade, Grace A; Xanthakis, Vanessa; Kickler, Thomas S; Rade, Jeffrey J (2024-02-28)
    Background: Systemic thromboxane A2 generation, assessed by quantifying the concentration of stable thromboxane B2 metabolites (TXB2-M) in the urine adjusted for urinary creatinine, is strongly associated with mortality risk. We sought to define optimal TXB2-M cutpoints for aspirin users and nonusers and determine if adjusting TXB2-M for estimated glomerular filtration rate (eGFR) in addition to urinary creatinine improved mortality risk assessment. Methods: Urinary TXB2-M were measured by competitive ELISA in 1363 aspirin users and 1681 nonusers participating in the Framingham Heart Study. Cutpoints were determined for TXB2-M and TXB2-M/eGFR using log-rank statistics and used to assess mortality risk by Cox proportional hazard modeling and restricted mean survival time. Multivariable models were compared using the Akaike Information Criterion (AIC). A cohort of 105 aspirin users with heart failure was used for external validation. Results: Optimized cutpoints of TXB2-M were 1291 and 5609 pg/mg creatinine and of TXB2-M/eGFR were 16.6 and 62.1 filtered prostanoid units (defined as pg·min/creatinine·mL·1.73 m2), for aspirin users and nonusers, respectively. TXB2-M/eGFR cutpoints provided more robust all-cause mortality risk discrimination than TXB2-M cutpoints, with a larger unadjusted hazard ratio (2.88 vs 2.16, AIC P < 0.0001) and greater differences in restricted mean survival time between exposure groups (1.46 vs 1.10 years), findings that were confirmed in the external validation cohort of aspirin users. TXB2-M/eGFR cutpoints also provided better cardiovascular/stroke mortality risk discrimination than TXB2-M cutpoints (unadjusted hazard ratio 3.31 vs 2.13, AIC P < 0.0001). Conclusion: Adjustment for eGFR strengthens the association of urinary TXB2-M with long-term mortality risk irrespective of aspirin use.
  • Adulting Shorts: Let’s Talk About Workplace Accommodations

    Seward, Hannah (2024-02-27)
    Work can be hard! If you have a mental health condition, you might need to ask for an accommodation at work. An accommodation is a change to the way your job is done to allow you to do your job well when you have a disability. This comic by the NIDILRR-funded Learning & Working RRTC shares some real-world experiences young adults with lived experience of mental health conditions when working. For more information about requesting accommodations at work, please read our Accommodations at Work tip sheet.
  • Fleischner Society: Glossary of Terms for Thoracic Imaging

    Bankier, Alexander A; MacMahon, Heber; Colby, Thomas; Gevenois, Pierre Alain; Goo, Jin Mo; Leung, Ann N C; Lynch, David A; Schaefer-Prokop, Cornelia M; Tomiyama, Noriyuki; Travis, William D; et al. (2024-02-27)
    Members of the Fleischner Society have compiled a glossary of terms for thoracic imaging that replaces previous glossaries published in 1984, 1996, and 2008, respectively. The impetus to update the previous version arose from multiple considerations. These include an awareness that new terms and concepts have emerged, others have become obsolete, and the usage of some terms has either changed or become inconsistent to a degree that warranted a new definition. This latest glossary is focused on terms of clinical importance and on those whose meaning may be perceived as vague or ambiguous. As with previous versions, the aim of the present glossary is to establish standardization of terminology for thoracic radiology and, thereby, to facilitate communications between radiologists and clinicians. Moreover, the present glossary aims to contribute to a more stringent use of terminology, increasingly required for structured reporting and accurate searches in large databases. Compared with the previous version, the number of images (chest radiography and CT) in the current version has substantially increased. The authors hope that this will enhance its educational and practical value. All definitions and images are hyperlinked throughout the text. Click on each figure callout to view corresponding image. © RSNA, 2024 Supplemental material is available for this article. See also the editorials by Bhalla and Powell in this issue.
  • Hippocampal subfields and thalamic nuclei associations with clinical outcomes in multiple sclerosis: An ultrahigh field MRI study

    Santini, Tales; Chen, Chenyi; Zhu, Wen; Liou, Jr-Jiun; Walker, Elizabeth; Venkatesh, Shruthi; Farhat, Nadim; Sajewski, Andrea; Alkhateeb, Salem; Saranathan, Manojkumar; et al. (2024-02-27)
    Background: Previous studies have shown that thalamic and hippocampal neurodegeneration is associated with clinical decline in Multiple Sclerosis (MS). However, contributions of the specific thalamic nuclei and hippocampal subfields require further examination. Objective: Using 7 Tesla (7T) magnetic resonance imaging (MRI), we investigated the cross-sectional associations between functionally grouped thalamic nuclei and hippocampal subfields volumes and T1 relaxation times (T1-RT) and subsequent clinical outcomes in MS. Methods: High-resolution T1-weighted and T2-weighted images were acquired at 7T (n=31), preprocessed, and segmented using the Thalamus Optimized Multi Atlas Segmentation (THOMAS, for thalamic nuclei) and the Automatic Segmentation of Hippocampal Subfields (ASHS, for hippocampal subfields) packages. We calculated Pearson correlations between hippocampal subfields and thalamic nuclei volumes and T1-RT and subsequent multi-modal rater-determined and patient-reported clinical outcomes (∼2.5 years after imaging acquisition), correcting for confounders and multiple tests. Results: Smaller volume bilaterally in the anterior thalamus region correlated with worse performance in gait function, as measured by the Patient Determined Disease Steps (PDDS). Additionally, larger volume in most functional groups of thalamic nuclei correlated with better visual information processing and cognitive function, as measured by the Symbol Digit Modalities Test (SDMT). In bilateral medial and left posterior thalamic regions, there was an inverse association between volumes and T1-RT, potentially indicating higher tissue degeneration in these regions. We also observed marginal associations between the right hippocampal subfields (both volumes and T1-RT) and subsequent clinical outcomes, though they did not survive correction for multiple testing. Conclusion: Ultrahigh field MRI identified markers of structural damage in the thalamic nuclei associated with subsequently worse clinical outcomes in individuals with MS. Longitudinal studies will enable better understanding of the role of microstructural integrity in these brain regions in influencing MS outcomes.
  • Incidence and clinical outcomes of perforations during mechanical thrombectomy for medium vessel occlusion in acute ischemic stroke: A retrospective, multicenter, and multinational study

    Dmytriw, Adam A; Musmar, Basel; Salim, Hamza; Ghozy, Sherief; Siegler, James E; Kobeissi, Hassan; Shaikh, Hamza; Khalife, Jane; Abdalkader, Mohamad; Klein, Piers; et al. (2024-02-26)
    Background: Mechanical thrombectomy (MT) has revolutionized the treatment of acute ischemic stroke (AIS) due to large vessel occlusion (LVO), but its efficacy and safety in medium vessel occlusion (MeVO) remain less explored. This multicenter, retrospective study aims to investigate the incidence and clinical outcomes of vessel perforations (confirmed by extravasation during an angiographic series) during MT for AIS caused by MeVO. Methods: Data were collected from 37 academic centers across North America, Asia, and Europe between September 2017 and July 2021. A total of 1373 AIS patients with MeVO underwent MT. Baseline characteristics, procedural details, and clinical outcomes were analyzed. Results: The incidence of vessel perforation was 4.8% (66/1373). Notably, our analysis indicates variations in perforation rates across different arterial segments: 8.9% in M3 segments, 4.3% in M2 segments, and 8.3% in A2 segments (p = 0.612). Patients with perforation had significantly worse outcomes, with lower rates of favorable angiographic outcomes (TICI 2c-3: 23% vs 58.9%, p < 0.001; TICI 2b-3: 56.5% vs 88.3%, p < 0.001). Functional outcomes were also worse in the perforation group (mRS 0-1 at 3 months: 22.7% vs 36.6%, p = 0.031; mRS 0-2 at 3 months: 28.8% vs 53.9%, p < 0.001). Mortality was higher in the perforation group (30.3% vs 16.8%, p = 0.008). Conclusion: This study reveals that while the occurrence of vessel perforation in MT for AIS due to MeVO is relatively rare, it is associated with poor functional outcomes and higher mortality. The findings highlight the need for increased caution and specialized training in performing MT for MeVO. Further prospective research is required for risk mitigation strategies.
  • Silencing Parkinson's risk allele Rit2 sex-specifically compromises motor function and dopamine neuron viability

    Kearney, Patrick J; Zhang, Yuanxi; Liang, Marianna; Tan, Yanglan; Kahuno, Elizabeth; Conklin, Tucker L; Fagan, Rita R; Pavchinskiy, Rebecca G; Shaffer, Scott A; Yue, Zhenyu; et al. (2024-02-23)
    Parkinson's disease (PD) is the second most prevalent neurodegenerative disease and arises from dopamine (DA) neuron death selectively in the substantia nigra pars compacta (SNc). Rit2 is a reported PD risk allele, and recent single cell transcriptomic studies identified a major RIT2 cluster in PD DA neurons, potentially linking Rit2 expression loss to a PD patient cohort. However, it is still unknown whether Rit2 loss itself impacts DA neuron function and/or viability. Here we report that conditional Rit2 silencing in mouse DA neurons drove motor dysfunction that occurred earlier in males than females and was rescued at early stages by either inhibiting the DA transporter (DAT) or with L-DOPA treatment. Motor dysfunction was accompanied by decreased DA release, striatal DA content, phenotypic DAergic markers, DA neurons, and DAergic terminals, with increased pSer129-alpha synuclein and pSer935-LRRK2 expression. These results provide clear evidence that Rit2 loss is causal for SNc cell death and motor dysfunction, and reveal key sex-specific differences in the response to Rit2 loss.

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