313 results on '"Lawrence, Michael"'
Search Results
2. The tidyomics ecosystem: enhancing omic data analyses
- Author
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Hutchison, William J., Keyes, Timothy J., Crowell, Helena L., Serizay, Jacques, Soneson, Charlotte, Davis, Eric S., Sato, Noriaki, Moses, Lambda, Tarlinton, Boyd, Nahid, Abdullah A., Kosmac, Miha, Clayssen, Quentin, Yuan, Victor, Mu, Wancen, Park, Ji-Eun, Mamede, Izabela, Ryu, Min Hyung, Axisa, Pierre-Paul, Paiz, Paulina, Poon, Chi-Lam, Tang, Ming, Gottardo, Raphael, Morgan, Martin, Lee, Stuart, Lawrence, Michael, Hicks, Stephanie C., Nolan, Garry P., Davis, Kara L., Papenfuss, Anthony T., Love, Michael I., and Mangiola, Stefano
- Abstract
The growth of omic data presents evolving challenges in data manipulation, analysis and integration. Addressing these challenges, Bioconductor provides an extensive community-driven biological data analysis platform. Meanwhile, tidy R programming offers a revolutionary data organization and manipulation standard. Here we present the tidyomics software ecosystem, bridging Bioconductor to the tidy R paradigm. This ecosystem aims to streamline omic analysis, ease learning and encourage cross-disciplinary collaborations. We demonstrate the effectiveness of tidyomics by analyzing 7.5 million peripheral blood mononuclear cells from the Human Cell Atlas, spanning six data frameworks and ten analysis tools.
- Published
- 2024
- Full Text
- View/download PDF
3. Revisiting the use of structural similarity index in Hi-C
- Author
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Lee, Hanjun, Blumberg, Bruce, Lawrence, Michael S., and Shioda, Toshihiro
- Published
- 2023
- Full Text
- View/download PDF
4. Natural Walking Intensity in Persons With Parkinson Disease.
- Author
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Girnis, Jaimie L., Cavanaugh, James T., Baker, Teresa C., Duncan, Ryan P., Fulford, Daniel, LaValley, Michael P., Lawrence, Michael, Nordahl, Timothy, Porciuncula, Franchino, Rawson, Kerri S., Saint-Hilaire, Marie, Thomas, Cathi A., Zajac, Jenna A., Earhart, Gammon M., and Ellis, Terry D.
- Abstract
Background and Purpose: Few persons with Parkinson disease (PD) appear to engage in moderate-intensity walking associated with disease-modifying health benefits. How much time is spent walking at lower, yet still potentially beneficial, intensities is poorly understood. The purpose of this exploratory, observational study was to describe natural walking intensity in ambulatory persons with PD. Methods: Accelerometer-derived real-world walking data were collected for more than 7 days at baseline from 82 participants enrolled in a PD clinical trial. Walking intensity was defined according to the number of steps in each active minute (1-19, 20-39, 40-59, 60-79, 80-99, or ≥100 steps). Daily minutes of walking and duration of the longest sustained walking bout were calculated at each intensity. Number of sustained 10 to 19, 20 to 29, and 30-minute bouts and greater at any intensity also were calculated. Values were analyzed in the context of physical activity guidelines. Results: Most daily walking occurred at lower intensities (157.3 ± 58.1 min of 1-19 steps; 81.3 ± 32.6 min of 20-39 steps; 38.2 ± 21.3 min of 40-59 steps; 15.1 ± 11.5 min of 60-79 steps; 7.4 ± 7.0 min of 80-99 steps; 7.3 ± 9.6 min of ≥100 steps). The longest daily sustained walking bout occurred at the lowest intensity level (15.9 ± 5.2 min of 1-19 steps). Few bouts lasting 20 minutes and greater occurred at any intensity. Discussion and Conclusions: Despite relatively high daily step counts, participants tended to walk at remarkably low intensity, in bouts of generally short duration, with relatively few instances of sustained walking. The findings reinforced the need for health promotion interventions designed specifically to increase walking intensity. Video Abstract available for more insight from authors (see the Video, Supplemental Digital Content 1 available at: http://links.lww.com/JNPT/A426). [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
5. Women With Self-Reported Stress Urinary Incontinence Had Differences in Clinical Measures Depending on Whether Jumping Jacks Provoked Leakage.
- Author
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Hartigan, Erin, McAuley, J. Adrienne, Lawrence, Michael, Clarenbach, Megan, Sterling, Jessica, Quirion, Emily, and Lewis, Cara L.
- Subjects
HIP joint physiology ,RESEARCH ,EXERCISE tests ,RANGE of motion of joints ,MUSCLE contraction ,ANALYSIS of variance ,SELF-evaluation ,MUSCLES ,CROSS-sectional method ,WOMEN ,COMPARATIVE studies ,URINARY stress incontinence ,URINARY incontinence ,EXERCISE ,PELVIC floor ,QUESTIONNAIRES ,DATA analysis software - Published
- 2023
- Full Text
- View/download PDF
6. Diffuse calcification of pancreas impairs endocrine function and predicts poor outcome in total pancreatectomy with islet autotransplantation
- Author
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Darden, Carly, Kumano, Kenjiro, Liu, Yang, Mohamed, Asim, Mattke, Jordan, Lawrence, Michael, Gupta, Amar, Beecherl, Ernest, Lee, Seung Hee S., and Naziruddin, Bashoo
- Abstract
In patients with chronic pancreatitis, pancreatic calcification is a risk factor for diabetes development, poor islet yield, and metabolic outcomes after total pancreatectomy with islet autotransplantation (TPIAT). We investigated whether calcification pattern based on computed tomography is associated with outcomes using our database of 200 consecutive TPIAT procedures. Three groups were compared: noncalcification (NC); focal calcification, limited to the pancreas head, body, or tail; and diffuse calcification (DC), with calcification in >2 sections. Maximum changes in outcomes were seen in the DC vs focal calcification group. In the DC group, preoperative hemoglobin A1c levels were higher (P< .01), and stimulated C-peptide levels were lower (P< .01) than in the NC group. Islet isolation from the DC pancreas resulted in the lowest islet equivalent (IEQ) yield and IEQ/kg among the 3 groups (P< .0001), with no insulin independence 12 months posttransplant (P< .05 vs NC group). Notably, at 12 months, the DC group was 91.7% narcotic-free, significantly higher than the NC group (P< .05). Although DC is a sign of diabetes risk after TPIAT, the DC group showed exceptional pain relief. These findings suggest that TPIAT can be beneficial for patients with chronic pancreatitis with severe calcification.
- Published
- 2023
- Full Text
- View/download PDF
7. Therapy-induced APOBEC3A drives evolution of persistent cancer cells
- Author
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Isozaki, Hideko, Sakhtemani, Ramin, Abbasi, Ammal, Nikpour, Naveed, Stanzione, Marcello, Oh, Sunwoo, Langenbucher, Adam, Monroe, Susanna, Su, Wenjia, Cabanos, Heidie Frisco, Siddiqui, Faria M., Phan, Nicole, Jalili, Pégah, Timonina, Daria, Bilton, Samantha, Gomez-Caraballo, Maria, Archibald, Hannah L., Nangia, Varuna, Dionne, Kristin, Riley, Amanda, Lawlor, Matthew, Banwait, Mandeep Kaur, Cobb, Rosemary G., Zou, Lee, Dyson, Nicholas J., Ott, Christopher J., Benes, Cyril, Getz, Gad, Chan, Chang S., Shaw, Alice T., Gainor, Justin F., Lin, Jessica J., Sequist, Lecia V., Piotrowska, Zofia, Yeap, Beow Y., Engelman, Jeffrey A., Lee, Jake June-Koo, Maruvka, Yosef E., Buisson, Rémi, Lawrence, Michael S., and Hata, Aaron N.
- Abstract
Acquired drug resistance to anticancer targeted therapies remains an unsolved clinical problem. Although many drivers of acquired drug resistance have been identified1–4, the underlying molecular mechanisms shaping tumour evolution during treatment are incompletely understood. Genomic profiling of patient tumours has implicated apolipoprotein B messenger RNA editing catalytic polypeptide-like (APOBEC) cytidine deaminases in tumour evolution; however, their role during therapy and the development of acquired drug resistance is undefined. Here we report that lung cancer targeted therapies commonly used in the clinic can induce cytidine deaminase APOBEC3A (A3A), leading to sustained mutagenesis in drug-tolerant cancer cells persisting during therapy. Therapy-induced A3A promotes the formation of double-strand DNA breaks, increasing genomic instability in drug-tolerant persisters. Deletion of A3A reduces APOBEC mutations and structural variations in persister cells and delays the development of drug resistance. APOBEC mutational signatures are enriched in tumours from patients with lung cancer who progressed after extended responses to targeted therapies. This study shows that induction of A3A in response to targeted therapies drives evolution of drug-tolerant persister cells, suggesting that suppression of A3A expression or activity may represent a potential therapeutic strategy in the prevention or delay of acquired resistance to lung cancer targeted therapy.
- Published
- 2023
- Full Text
- View/download PDF
8. Women With Self-Reported Stress Urinary Incontinence Had Differences in Clinical Measures Depending on Whether Jumping Jacks Provoked Leakage
- Author
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Hartigan, Erin, McAuley, J. Adrienne, Lawrence, Michael, Clarenbach, Megan, Sterling, Jessica, Quirion, Emily, and Cara, L. Lewis
- Published
- 2023
- Full Text
- View/download PDF
9. Natural Walking Intensity in Persons With Parkinson Disease
- Author
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Girnis, Jaimie L., Cavanaugh, James T., Baker, Teresa C., Duncan, Ryan P., Fulford, Daniel, LaValley, Michael P., Lawrence, Michael, Nordahl, Timothy, Porciuncula, Franchino, Rawson, Kerri S., Saint-Hilaire, Marie, Thomas, Cathi A., Zajac, Jenna A., Earhart, Gammon M., and Ellis, Terry D.
- Published
- 2023
- Full Text
- View/download PDF
10. ATR inhibition induces synthetic lethality in mismatch repair-deficient cells and augments immunotherapy
- Author
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Wang, Mingchao, Ran, Xiaojuan, Leung, Wendy, Kawale, Ajinkya, Saxena, Sneha, Ouyang, Jian, Patel, Parasvi S., Dong, Yuting, Yin, Tao, Shu, Jian, Manguso, Robert T., Lan, Li, Wang, Xiao-Fan, Lawrence, Michael S., and Zou, Lee
- Abstract
In this study, Wang et al. show that the inhibition of ATR kinase affords selective lethality to mismatch repair-deficient (MMR-d) cancer cells by promoting MUS81 nuclease- and replication-dependent DNA damage, increasing cytosolic DNA fragments, and activating cGAS signaling. The consequent interferon response potentially stimulates cytotoxic T-cell-dependent antitumor immunity and points to ATR inhibition as a notable strategy to augment PD-1 targeting immunotherapies against MMR-d cancers.
- Published
- 2023
- Full Text
- View/download PDF
11. Catch‐and‐Release Ice Fishing: Status, Issues, and Research Needs.
- Author
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Lawrence, Michael J., Jeffries, Ken M., Cooke, Steven J., Enders, Eva C., Hasler, Caleb T., Somers, Christopher M., Suski, Cory D., and Louison, Michael J.
- Abstract
Catch‐and‐release (C&R) ice fishing is a popular form of recreational angling. At present, there is a considerable deficiency in our understanding of how ice angling affects the physiology, behavior, and survival of fish. Thus, the purpose of this review was to summarize our current knowledge of the consequences of winter C&R fishing on fish biology and to identify key knowledge gaps. Our synthesis revealed that in addition to the typical stressors encountered from C&R fishing during the open‐water season, fish that are caught through the ice are subject to several unique challenges, including exposure to subzero air temperatures upon landing as well as unique gear types that are not commonly used in the summer (i.e., passive angling techniques). We currently understand that while C&R angling causes a generalized stress response, cold environments may mute or delay these effects and may also come with additional deleterious consequences, such as tissue freezing. Interestingly, reported mortality can be low following release but can be influenced by gear type, barotrauma, and hooking location. Postrelease behaviors and the spatial ecology of ice‐angled fish are poorly understood, but technologies such as telemetry and biologgers and an intensification of research on the topic are starting to produce new insights in this area. As it stands, research on the consequences of winter C&R angling is largely restricted to a handful of popular sport fish species, and these consequences are likely not being considered in management and conservation contexts. Given the increasing popularity of the sport, furthering our understanding of C&R impacts in the winter represents a timely and important area of inquiry and can be used to develop more informed and effective C&R guidelines and management practices. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
12. Dispersal Patterns of Largemouth Bass and Smallmouth Bass Following Early‐, Mid‐, and Late‐Season Fishing Tournaments in an Eastern Ontario Lake.
- Author
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Abrams, Alice E. I., Zolderdo, A. J., Lédée, Elodie J. I., Lawrence, Michael J., Holder, Peter E., and Cooke, Steven J.
- Subjects
TOURNAMENT fishing ,LARGEMOUTH bass ,BLACK bass fishing ,TOP predators ,LAKES - Abstract
Black bass fishing tournaments with conventional weigh‐ins tend to displace fish from their capture site and often release fish within close proximity to the weigh‐in site. Tournaments often include Largemouth Bass Micropterus salmoides and Smallmouth Bass M. dolomieu and occur throughout fishing seasons; however, there have yet to be any systematic congeneric comparisons across different seasons. Objectives of our study were to (1) assess post‐tournament dispersal of Largemouth Bass and Smallmouth Bass (i.e., short‐term stockpiling—accumulation of fish around weigh‐in site <1 month after tournament) across seasons, and (2) determine the success of return to the main basin. Research took place on Big Rideau Lake in eastern Ontario and included a preseason control (N = 30) where fish were captured, acoustically tagged, and released at the site of tournament weigh‐in (Rideau Ferry). Tournament‐caught bass (N = 88 total) were tagged at three tournaments that spanned June (early season), August (midseason), and October (late season). Our results indicated a brief short‐term stockpiling (within 300 m) in all seasons, and all detected fish eventually returned to the main basin. Tournament‐caught Largemouth Bass tended to take longer to disperse from the release site following the midseason tournament (4.6 d); Smallmouth Bass tended to disperse from release site <1 d following all treatments. Similarly, tournament‐caught Largemouth Bass exposed to the midseason tournament tended to take the longest to redistribute to the main basin (238 d) in comparison to other treatments. Although Smallmouth Bass tended to redistribute to the main basin faster than Largemouth Bass, late‐season Smallmouth Bass tended to redistribute the slowest (101 d) following tournament release. Although fish do survive and eventually return to the main basin, displacement may have broader ecological consequences (i.e., large‐scale displacement of top predators, adverse effects on recruitment) such that there would be merit in more catch–weigh–release formatted events. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
13. Catch‐and‐Release Ice Fishing: Status, Issues, and Research Needs
- Author
-
Lawrence, Michael J., Jeffries, Ken M., Cooke, Steven J., Enders, Eva C., Hasler, Caleb T., Somers, Christopher M., Suski, Cory D., and Louison, Michael J.
- Abstract
Catch‐and‐release (C&R) ice fishing is a popular form of recreational angling. At present, there is a considerable deficiency in our understanding of how ice angling affects the physiology, behavior, and survival of fish. Thus, the purpose of this review was to summarize our current knowledge of the consequences of winter C&R fishing on fish biology and to identify key knowledge gaps. Our synthesis revealed that in addition to the typical stressors encountered from C&R fishing during the open‐water season, fish that are caught through the ice are subject to several unique challenges, including exposure to subzero air temperatures upon landing as well as unique gear types that are not commonly used in the summer (i.e., passive angling techniques). We currently understand that while C&R angling causes a generalized stress response, cold environments may mute or delay these effects and may also come with additional deleterious consequences, such as tissue freezing. Interestingly, reported mortality can be low following release but can be influenced by gear type, barotrauma, and hooking location. Postrelease behaviors and the spatial ecology of ice‐angled fish are poorly understood, but technologies such as telemetry and biologgers and an intensification of research on the topic are starting to produce new insights in this area. As it stands, research on the consequences of winter C&R angling is largely restricted to a handful of popular sport fish species, and these consequences are likely not being considered in management and conservation contexts. Given the increasing popularity of the sport, furthering our understanding of C&R impacts in the winter represents a timely and important area of inquiry and can be used to develop more informed and effective C&R guidelines and management practices.
- Published
- 2022
- Full Text
- View/download PDF
14. Symmetric and asymmetric receptor conformation continuum induced by a new insulin
- Author
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Xiong, Xiaochun, Blakely, Alan, Kim, Jin Hwan, Menting, John G., Schäfer, Ingmar B., Schubert, Heidi L., Agrawal, Rahul, Gutmann, Theresia, Delaine, Carlie, Zhang, Yi Wolf, Artik, Gizem Olay, Merriman, Allanah, Eckert, Debbie, Lawrence, Michael C., Coskun, Ünal, Fisher, Simon J., Forbes, Briony E., Safavi-Hemami, Helena, Hill, Christopher P., and Chou, Danny Hung-Chieh
- Abstract
Cone snail venoms contain a wide variety of bioactive peptides, including insulin-like molecules with distinct structural features, binding modes and biochemical properties. Here, we report an active humanized cone snail venom insulin with an elongated A chain and a truncated B chain, and use cryo-electron microscopy (cryo-EM) and protein engineering to elucidate its interactions with the human insulin receptor (IR) ectodomain. We reveal how an extended A chain can compensate for deletion of B-chain residues, which are essential for activity of human insulin but also compromise therapeutic utility by delaying dissolution from the site of subcutaneous injection. This finding suggests approaches to developing improved therapeutic insulins. Curiously, the receptor displays a continuum of conformations from the symmetric state to a highly asymmetric low-abundance structure that displays coordination of a single humanized venom insulin using elements from both of the previously characterized site 1 and site 2 interactions.
- Published
- 2022
- Full Text
- View/download PDF
15. Do Carbonated Beverages Reduce Bleeding from Gill Injuries in Angled Northern Pike?
- Author
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Trahan, Alexandria T., Chhor, Auston D., Lawrence, Michael J., Brownscombe, Jacob W., Glassman, Daniel M., Reid, Connor H., Abrams, Alice E. I., Danylchuk, Andy J., and Cooke, Steven J.
- Subjects
CARBONATED beverages ,GILLS ,WOUNDS & injuries ,WATER temperature ,HEMORRHAGE ,BEVERAGE packaging - Abstract
The premise of catch‐and‐release recreational angling is that postrelease survival is high. Therefore, it is common for anglers, management agencies, and conservation organizations to share information on handling practices and other strategies that are believed to improve the welfare and survival of fish that are released. A recent surge in popularity has sensationalized the use of carbonated beverages to treat bleeding fish—an intervention that is purported to stop bleeding but has yet to be validated scientifically. We captured Northern Pike Esox lucius via hook and line and experimentally injured their gills in a standardized manner. Gill injuries were treated with Mountain Dew, Coca‐Cola, or carbonated lake water. The duration and intensity of bleeding as well as overall blood loss (using gill color as a proxy) were observed while the fish were held in a lake water bath. As a control, we used a group of experimentally injured fish that did not have liquid poured over their gills before the observation period. All treatments and the control were conducted at two different water temperatures (11–18°C and 24–27°C) to determine whether the effects of pouring carbonated beverages over injured gills are seasonally dependent. When compared to the control, we found that the duration and intensity of bleeding increased regardless of the type of carbonated beverage used in this study, and there was no effect of season. Use of chilled versus ambient‐temperature beverages similarly had no influence on outcomes. As such, there is no scientific evidence to support the use of carbonated beverages for reducing or stopping blood loss in fish that receive gill injuries during recreational angling based on the context studied here. Our study reinforces the need to scientifically test angler anecdotes and theories regarding best practices for catch‐and‐release fishing. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
16. Predictors of Response to an Upper Extremity Telerehabilitation-Home Practice Program after Stroke: An Interim Analysis.
- Author
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Rishe, Kelly, Goedeken, Susan, DiCarlo, Julie, McKiernan, Sydney, Hamilton, Taya, Lawrence, Michael, Friesen, Christopher, Ingram, Tony, and Lin, David
- Abstract
To examine whether baseline cognitive and motor impairments influence response to a 5-week paired telerehabilitation-home practice intervention and explore functional neuroimaging features related to motor gains. Prospective interventional pilot study with intervention delivered over five-weeks including pre- and post- assessments. Telerehabilitation. Adults with chronic ischemic or hemorrhagic stroke and UE motor deficits (Fugl-Meyer (FMA-UE) scores ≤ 56) were eligible to participate. Exclusion criteria included significant physical disability prior to stroke, Botox within 90 days, severe cognitive or language impairments (MoCA < 10, inability to understand instructions), or inability to use the portable fNIRS system. A two-part telerehabilitation intervention: synchronous sessions of task-practice and metacognitive strategy training with an occupational therapist two times per week, and asynchronous app-based exercise sessions while wearing a portable fNIRS device four times per week. Motor impairment was assessed pre- and post- intervention. FMA-UE. 10 participants (55.1 +/- 12.4 age, 27.2% female), in this interim analysis, completed the 5-week intervention. In bi-variate analyses, less severe UE motor impairment (t= 5.58, p=< 0.001) and less severe cognitive impairment (t= 2.9, p=.024) at baseline were each associated with greater response to the telerehabilitation-home practice program (i.e., UE motor gains; change in FMA-UE). Increased relative cortical activation (i.e., higher laterality) in the ipsilesional motor cortex (C3-C4) at baseline, as measured by portable fNIRS, was also related to UE motor gains. Response to an UE motor telerehabilitation-home practice program was greatest for individuals with less severe UE motor and cognitive impairments at baseline. Furthermore, portable functional neuroimaging technologies (i.e., fNIRS) may be useful in determining who would most benefit from therapeutic interventions. Together these factors could assist therapists in developing personalized telerehabilitation programs for patients after stroke. KR is a consultant for Constant Therapeutics and Constant Therapy. JAD is a consultant for Axem Neurotechnology. TH is a consultant for Axem Neurotechnology. CF, TI and ML are co-founders of and have stock ownership in Axem Neurotechnology. DJL – none. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
17. Dispersal Patterns of Largemouth Bass and Smallmouth Bass Following Early‐, Mid‐, and Late‐Season Fishing Tournaments in an Eastern Ontario Lake
- Author
-
Abrams, Alice E. I., Zolderdo, A. J., Lédée, Elodie J. I., Lawrence, Michael J., Holder, Peter E., and Cooke, Steven J.
- Abstract
Black bass fishing tournaments with conventional weigh‐ins tend to displace fish from their capture site and often release fish within close proximity to the weigh‐in site. Tournaments often include Largemouth Bass Micropterus salmoidesand Smallmouth Bass M. dolomieuand occur throughout fishing seasons; however, there have yet to be any systematic congeneric comparisons across different seasons. Objectives of our study were to (1) assess post‐tournament dispersal of Largemouth Bass and Smallmouth Bass (i.e., short‐term stockpiling—accumulation of fish around weigh‐in site <1 month after tournament) across seasons, and (2) determine the success of return to the main basin. Research took place on Big Rideau Lake in eastern Ontario and included a preseason control (N= 30) where fish were captured, acoustically tagged, and released at the site of tournament weigh‐in (Rideau Ferry). Tournament‐caught bass (N= 88 total) were tagged at three tournaments that spanned June (early season), August (midseason), and October (late season). Our results indicated a brief short‐term stockpiling (within 300 m) in all seasons, and all detected fish eventually returned to the main basin. Tournament‐caught Largemouth Bass tended to take longer to disperse from the release site following the midseason tournament (4.6 d); Smallmouth Bass tended to disperse from release site <1 d following all treatments. Similarly, tournament‐caught Largemouth Bass exposed to the midseason tournament tended to take the longest to redistribute to the main basin (238 d) in comparison to other treatments. Although Smallmouth Bass tended to redistribute to the main basin faster than Largemouth Bass, late‐season Smallmouth Bass tended to redistribute the slowest (101 d) following tournament release. Although fish do survive and eventually return to the main basin, displacement may have broader ecological consequences (i.e., large‐scale displacement of top predators, adverse effects on recruitment) such that there would be merit in more catch–weigh–release formatted events.
- Published
- 2021
- Full Text
- View/download PDF
18. Peer Review: The Volpe/Federal Highway Administration National Vehicle Miles Traveled Forecasting Models
- Author
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Cohen, Jeffrey, Vadali, Sharada, Lawrence, Michael F., Dave, Shikha, and Clark, Clayton
- Abstract
This paper describes the findings of an independent peer review of the modeling tools used by the Volpe National Transportation Systems Center to forecast national vehicle miles traveled (VMT) over the next 30 years. Overall, the VMT forecasting models, which use autoregressive distributed lag models for light-duty vehicle, single-unit truck, and combination truck VMT, work well to estimate travel demand. All model estimations were reviewed, and all models perform well against several validation and testing techniques. The study team was supported by an expert panel selected from academia, government, and industry with experience in econometric methods, transportation and economic data, and modeling methods. The panel reviewed model documentation as well as the report assessing the VMT forecasting models and provided insight into alternative model research. The paper is an effort to synthesize the approaches and the validation methods used. A complementary literature search was also conducted to test the validity and comparability of several estimated variable coefficients. The paper concludes by summarizing the key findings and making recommendations on future model improvements.
- Published
- 2021
- Full Text
- View/download PDF
19. Physiological Consequences of Different Fishing Tournament Culling Methods on Largemouth Bass.
- Author
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Chong, Daniel R., Abrams, Alice E. I., Zolderdo, Aaron J., Lawrence, Michael J., Reid, Connor H., and Cooke, Steven J.
- Subjects
TOURNAMENT fishing ,LARGEMOUTH bass ,BLOOD lactate ,BLOOD sugar ,BLOOD sampling - Abstract
In live‐release angling tournaments, fish are captured and typically held within onboard live‐well systems, where they are subsequently "culled" (i.e., released) as larger fish are captured. Anglers often mark individual fish to easily identify them based on weight and to reduce handling time. However, there is limited information about the physiological consequences of using different culling apparatus on fish. This study examined the physiological consequences associated with using four different types of culling apparatus (i.e., metal stringer through the jaw, pincher on the jaw, lasso around the caudal peduncle, and zippered mesh bag) on Largemouth Bass Micropterus salmoides relative to controls during a 2‐h live‐well retention period. Blood samples were taken afterwards and were analyzed for blood glucose, blood lactate, plasma cortisol, and osmolality. Compared to the baseline control (i.e., fish that were captured, subjected to blood sampling, and immediately released), blood parameters (except osmolality) were significantly elevated in all treatments. The pincher and lasso treatments tended to yield higher physiological disturbances than the other treatments, including fish that were held in the live well without any culling apparatus. Moreover, the lasso culling apparatus appeared to cause noticeable injury relative to the other culling devices. Our research provides valuable information to help guide the selection of culling gear that maintains the welfare status of retained fish during tournaments. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
20. Do Carbonated Beverages Reduce Bleeding from Gill Injuries in Angled Northern Pike?
- Author
-
Trahan, Alexandria T., Chhor, Auston D., Lawrence, Michael J., Brownscombe, Jacob W., Glassman, Daniel M., Reid, Connor H., Abrams, Alice E. I., Danylchuk, Andy J., and Cooke, Steven J.
- Abstract
The premise of catch‐and‐release recreational angling is that postrelease survival is high. Therefore, it is common for anglers, management agencies, and conservation organizations to share information on handling practices and other strategies that are believed to improve the welfare and survival of fish that are released. A recent surge in popularity has sensationalized the use of carbonated beverages to treat bleeding fish—an intervention that is purported to stop bleeding but has yet to be validated scientifically. We captured Northern Pike Esox luciusvia hook and line and experimentally injured their gills in a standardized manner. Gill injuries were treated with Mountain Dew, Coca‐Cola, or carbonated lake water. The duration and intensity of bleeding as well as overall blood loss (using gill color as a proxy) were observed while the fish were held in a lake water bath. As a control, we used a group of experimentally injured fish that did not have liquid poured over their gills before the observation period. All treatments and the control were conducted at two different water temperatures (11–18°C and 24–27°C) to determine whether the effects of pouring carbonated beverages over injured gills are seasonally dependent. When compared to the control, we found that the duration and intensity of bleeding increased regardless of the type of carbonated beverage used in this study, and there was no effect of season. Use of chilled versus ambient‐temperature beverages similarly had no influence on outcomes. As such, there is no scientific evidence to support the use of carbonated beverages for reducing or stopping blood loss in fish that receive gill injuries during recreational angling based on the context studied here. Our study reinforces the need to scientifically test angler anecdotes and theories regarding best practices for catch‐and‐release fishing.
- Published
- 2021
- Full Text
- View/download PDF
21. Women With and Without Self-reported Stress Urinary Incontinence Walk Differently Before and After 16-Ounce Water Consumption.
- Author
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Hartigan, Erin, McAuley, J. Adrienne, and Lawrence, Michael
- Subjects
ANALYSIS of variance ,BIOMECHANICS ,DIAGNOSIS ,DRINKING (Physiology) ,EXPERIMENTAL design ,GAIT in humans ,QUESTIONNAIRES ,RESEARCH ,RESEARCH funding ,STATISTICAL sampling ,SELF-evaluation ,STATISTICS ,T-test (Statistics) ,URINARY stress incontinence ,WATER ,WOMEN'S health ,DATA analysis ,REPEATED measures design ,CASE-control method ,DATA analysis software ,DESCRIPTIVE statistics - Abstract
Supplemental Digital Content is Available in the Text. Background: Women with stress urinary incontinence (SUI) use different hip biomechanics during gait than women without SUI. Objective: To compare hip angles, moments, and temporal-spatial parameters during gait between women with and without SUI from a control to full-bladder condition. Study Design: Case-control study with a repeated-measures design. Methods: Hip angles and moments (net forces) of 19 women with SUI and 23 women without SUI were analyzed during the weight acceptance phase of the gait. Mixed-model analyses of variance were used to compare between groups (SUI, without SUI), conditions (control, full bladder), and limbs (dominant [D], nondominant [ND]). Significance: P <.05. Results: Women with SUI were older (P <.001), more active (P =.022), produced more offspring (P <.001), used lesser adduction (P =.035; D-limb only), and minimum (P =.01) and peak flexion angles (P =.01), compared with women without SUI. Hip angles (internal rotation [IR]: ND > D, P <.001; external rotation [ER]: D > ND, P =.001), and moments (IR: ND < D, P =.001) differed between limbs. For ER moments, post hoc testing revealed that ND > D were found for women without SUI (P <.001, both conditions) and women with SUI during the control condition only (P =.001). From the control to full-bladder condition, ER angles decreased (P =.012), abduction moments increased (without SUI only; P =.027), extension moments increased (P =.003; D-limb only), step time increased (P =.006), and cadence decreased (P =.007). Conclusions: Women with SUI did not use different hip moments but used different hip positions during gait compared with women without SUI. Women with and without SUI altered force generation differently in response to bladder stress. A Video Abstract for this article is available at http://links.lww.com/JWHPT/A41. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
22. Hip Angles, Joint Moments, and Muscle Activity During Gait in Women With and Without Self-reported Stress Urinary Incontinence.
- Author
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Hartigan, Erin, McAuley, J. Adrienne, Lawrence, Michael, Brucker, Willis, King, Adam, Tryon, Brooks, and DeSilva, Mary
- Subjects
MUSCLE physiology ,PELVIC floor physiology ,HIP joint physiology ,BIOMECHANICS ,COMPARATIVE studies ,GAIT in humans ,RESEARCH methodology ,QUESTIONNAIRES ,SELF-evaluation ,URINARY stress incontinence ,WOMEN'S health ,GLUTEAL muscles - Published
- 2020
- Full Text
- View/download PDF
23. Effects of Tibiofibular and Ankle Joint Manipulation on Hip Strength and Muscle Activation.
- Author
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Lawrence, Michael A., Raymond, Jamie T., Look, Amy E., Woodard, Nicholas M., Schicker, Christina M., and Swanson, Brian T.
- Subjects
ANKLE injury treatment ,SKELETAL muscle physiology ,ANALYSIS of variance ,ANKLE ,HIP joint ,LEG ,MANIPULATION therapy ,MUSCLE strength ,RESEARCH funding ,SPRAINS ,STATISTICS ,T-test (Statistics) ,STATISTICAL power analysis ,DATA analysis ,GLUTEAL muscles ,TREATMENT effectiveness ,REPEATED measures design ,DATA analysis software ,MUSCLE weakness ,DESCRIPTIVE statistics ,RECTUS femoris muscles ,SUBTALAR joint - Abstract
The purpose of this study was to determine whether high-velocity, low-amplitude ankle region manipulations could increase force output and muscle activation of hip musculature in individuals with a history of ankle sprain and unilateral tensor fascia latae (TFL) weakness during muscle testing. This investigation used a single-arm repeated measures design. Twenty-five participants' force outputs were tested at three time points (before manipulation, immediately after manipulation, and 48 hours after manipulation), and muscle activation of the rectus femoris, gluteus medius, and TFL was measured before and immediately after manipulation. Manipulations were applied to the talocrural, subtalar, proximal, and distal tibiofibular joints of the weaker limb. No contralateral manipulations were applied. Two-way repeated measures analysis of variance was used to compare maximal and average force production for each limb. In addition, paired t tests were used to compare muscle activation before and after manipulations. There was a significant limb × time interaction. The involved limb average force increased from before manipulation (65.7 N) to 48 hours after manipulation (77.8 N; P =.014), maximal force increased (76.9 N) 48 hours after manipulation (87.8 N; P =.030), and gluteus medius activation increased (9.8% maximum, 12.2% average) immediately after manipulation. No significant differences were found in the uninvolved limb. The results of this study suggest that high-velocity, low-amplitude ankle region manipulations might improve hip abductor strength in individuals with a history of ankle sprain and unilateral weakness during a TFL muscle test. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
24. Comparative Behavior of Wild Bluegill Captured Inside and Outside of a Long‐Standing Aquatic Protected Area.
- Author
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Moynes, Emily N., Lawrence, Michael J., Zolderdo, Aaron J., Prystay, Tanya S., Abrams, Alice E.I., Holder, Peter, and Cooke, Steven J.
- Abstract
In recreational fisheries it is understood that individual fish that exhibit bolder personality traits have a tendency to be removed from the population (i.e., fishing mortality via harvest or catch‐and‐release mortality), while more timid individuals remain. The use of aquatic protected areas (APAs) has been promoted as a means of offsetting the negative consequences that are associated with fishing mortality by protecting the full suite of phenotypes. However, little work has investigated whether APAs are able to maintain heterogeneity in behavioral traits in wild fish. We attempted to address this question by using wild Bluegill Lepomis macrochirus from Lake Opinicon, a freshwater system consisting of both an APA and heavily fished areas. The Bluegill were obtained via angling from three zones in the lake: the main lake area (i.e., fished), the APA (which has been in place since the 1940s), and a transitional zone between these two areas. In the laboratory, the Bluegill were subjected to two behavioral assessments, a Z‐maze and a flight‐initiation‐distance (FID) test, to address differences in boldness and risk‐taking between these populations. No significant effects of capture zone were detected for any of the behavioral metrics that were assessed in the maze trial. However, individuals that originated from the main lake population had significantly higher FID scores than the fish from the transitional zone and the APA did, indicating that they were more timid. Our results suggest that fisheries activities may only be acting only on specific traits, which may explain some of the null results that are presented here. Nevertheless, our study provides evidence that APAs are providing a reservoir of less timid individuals, which is consistent with an evolutionarily enlightened management strategy. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
25. Subependymal giant cell astrocytomas are characterized by mTORC1 hyperactivation, a very low somatic mutation rate, and a unique gene expression profile
- Author
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Giannikou, Krinio, Zhu, Zachary, Kim, Jaegil, Winden, Kellen D., Tyburczy, Magdalena E., Marron, David, Parker, Joel S., Hebert, Zachary, Bongaarts, Anika, Taing, Len, Long, Henry W., Pisano, William V., Alexandrescu, Sanda, Godlewski, Brianna, Nellist, Mark, Kotulska, Katarzyna, Jozwiak, Sergiusz, Roszkowski, Marcin, Mandera, Marek, Thiele, Elizabeth A., Lidov, Hart, Getz, Gad, Devinsky, Orrin, Lawrence, Michael S., Ligon, Keith L., Ellison, David W., Sahin, Mustafa, Aronica, Eleonora, Meredith, David M., and Kwiatkowski, David J.
- Abstract
Subependymal giant-cell astrocytomas (SEGAs) are slow-growing brain tumors that are a hallmark feature seen in 5–10% of patients with Tuberous Sclerosis Complex (TSC). Though histologically benign, they can cause serious neurologic symptoms, leading to death if untreated. SEGAs consistently show biallelic loss of TSC1or TSC2. Herein, we aimed to define other somatic events beyond TSC1/TSC2loss and identify potential transcriptional drivers that contribute to SEGA formation. Paired tumor-normal whole-exome sequencing was performed on 21 resected SEGAs from 20 TSC patients. Pathogenic variants in TSC1/TSC2were identified in 19/21 (90%) SEGAs. Copy neutral loss of heterozygosity (size range: 2.2–46?Mb) was seen in 76% (16/21) of SEGAs (44% chr9q and 56% chr16p). An average of 1.4 other somatic variants (range 0–7) per tumor were identified, unlikely of pathogenic significance. Whole transcriptome RNA-sequencing analyses revealed 190 common differentially expressed genes in SEGA (n?=?16, 13 from a prior study) in pairwise comparison to each of: low grade diffuse gliomas (n?=?530) and glioblastoma (n?=?171) from The Cancer Genome Atlas (TCGA) consortium, ganglioglioma (n?=?10), TSC cortical tubers (n?=?15), and multiple normal tissues. Among these, homeobox transcription factors (TFs) HMX3, HMX2, VAX1, SIX3;and TFs IRF6and EOMESwere all expressed >12-fold higher in SEGAs (FDR/q-value?0.05). Immunohistochemistry supported the specificity of IRF6, VAX1, SIX3 for SEGAs in comparison to other tumor entities and normal brain. We conclude that SEGAs have an extremely low somatic mutation rate, suggesting that TSC1/TSC2loss is sufficient to drive tumor growth. The unique and highly expressed SEGA-specific TFs likely reflect the neuroepithelial cell of origin, and may also contribute to the transcriptional and epigenetic state that enables SEGA growth following two-hit loss of TSC1or TSC2and mTORC1 activation.
- Published
- 2021
- Full Text
- View/download PDF
26. Physiological Consequences of Different Fishing Tournament Culling Methods on Largemouth Bass
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Chong, Daniel R., Abrams, Alice E. I., Zolderdo, Aaron J., Lawrence, Michael J., Reid, Connor H., and Cooke, Steven J.
- Abstract
In live‐release angling tournaments, fish are captured and typically held within onboard live‐well systems, where they are subsequently “culled” (i.e., released) as larger fish are captured. Anglers often mark individual fish to easily identify them based on weight and to reduce handling time. However, there is limited information about the physiological consequences of using different culling apparatus on fish. This study examined the physiological consequences associated with using four different types of culling apparatus (i.e., metal stringer through the jaw, pincher on the jaw, lasso around the caudal peduncle, and zippered mesh bag) on Largemouth Bass Micropterus salmoidesrelative to controls during a 2‐h live‐well retention period. Blood samples were taken afterwards and were analyzed for blood glucose, blood lactate, plasma cortisol, and osmolality. Compared to the baseline control (i.e., fish that were captured, subjected to blood sampling, and immediately released), blood parameters (except osmolality) were significantly elevated in all treatments. The pincher and lasso treatments tended to yield higher physiological disturbances than the other treatments, including fish that were held in the live well without any culling apparatus. Moreover, the lasso culling apparatus appeared to cause noticeable injury relative to the other culling devices. Our research provides valuable information to help guide the selection of culling gear that maintains the welfare status of retained fish during tournaments.
- Published
- 2021
- Full Text
- View/download PDF
27. Subependymal giant cell astrocytomas are characterized by mTORC1 hyperactivation, a very low somatic mutation rate, and a unique gene expression profile
- Author
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Giannikou, Krinio, Zhu, Zachary, Kim, Jaegil, Winden, Kellen D., Tyburczy, Magdalena E., Marron, David, Parker, Joel S., Hebert, Zachary, Bongaarts, Anika, Taing, Len, Long, Henry W., Pisano, William V., Alexandrescu, Sanda, Godlewski, Brianna, Nellist, Mark, Kotulska, Katarzyna, Jozwiak, Sergiusz, Roszkowski, Marcin, Mandera, Marek, Thiele, Elizabeth A., Lidov, Hart, Getz, Gad, Devinsky, Orrin, Lawrence, Michael S., Ligon, Keith L., Ellison, David W., Sahin, Mustafa, Aronica, Eleonora, Meredith, David M., and Kwiatkowski, David J.
- Abstract
Subependymal giant-cell astrocytomas (SEGAs) are slow-growing brain tumors that are a hallmark feature seen in 5–10% of patients with Tuberous Sclerosis Complex (TSC). Though histologically benign, they can cause serious neurologic symptoms, leading to death if untreated. SEGAs consistently show biallelic loss of TSC1or TSC2. Herein, we aimed to define other somatic events beyond TSC1/TSC2loss and identify potential transcriptional drivers that contribute to SEGA formation. Paired tumor-normal whole-exome sequencing was performed on 21 resected SEGAs from 20 TSC patients. Pathogenic variants in TSC1/TSC2were identified in 19/21 (90%) SEGAs. Copy neutral loss of heterozygosity (size range: 2.2–46 Mb) was seen in 76% (16/21) of SEGAs (44% chr9q and 56% chr16p). An average of 1.4 other somatic variants (range 0–7) per tumor were identified, unlikely of pathogenic significance. Whole transcriptome RNA-sequencing analyses revealed 190 common differentially expressed genes in SEGA (n= 16, 13 from a prior study) in pairwise comparison to each of: low grade diffuse gliomas (n= 530) and glioblastoma (n= 171) from The Cancer Genome Atlas (TCGA) consortium, ganglioglioma (n= 10), TSC cortical tubers (n= 15), and multiple normal tissues. Among these, homeobox transcription factors (TFs) HMX3, HMX2, VAX1, SIX3;and TFs IRF6and EOMESwere all expressed >12-fold higher in SEGAs (FDR/q-value < 0.05). Immunohistochemistry supported the specificity of IRF6, VAX1, SIX3 for SEGAs in comparison to other tumor entities and normal brain. We conclude that SEGAs have an extremely low somatic mutation rate, suggesting that TSC1/TSC2loss is sufficient to drive tumor growth. The unique and highly expressed SEGA-specific TFs likely reflect the neuroepithelial cell of origin, and may also contribute to the transcriptional and epigenetic state that enables SEGA growth following two-hit loss of TSC1or TSC2and mTORC1 activation.
- Published
- 2021
- Full Text
- View/download PDF
28. Grafting Islets to a Dissected Peritoneal Pouch to Improve Transplant Survival and Function
- Author
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Kumano, Kenjiro, Vasu, Srividya, Liu, Yang, Lo, Su-Tang, Mulgaonkar, Aditi, Pennington, Jenelle, Darden, Carly M., Sun, Xiankai, Lawrence, Michael C., and Naziruddin, Bashoo
- Abstract
Supplemental Digital Content is available in the text.
- Published
- 2020
- Full Text
- View/download PDF
29. Women With and Without Self-reported Stress Urinary Incontinence Walk Differently Before and After 16-Ounce Water Consumption
- Author
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Hartigan, Erin, McAuley, J. Adrienne, and Lawrence, Michael
- Abstract
Supplemental Digital Content is Available in the Text.
- Published
- 2020
- Full Text
- View/download PDF
30. Field Implementation of Remote Ischemic Conditioning in ST-Segment–Elevation Myocardial Infarction: The FIRST Study
- Author
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Cheskes, Sheldon, Koh, Maria, Turner, Linda, Heslegrave, Ronald, Verbeek, Richard, Dorian, Paul, Scales, Damon C., Singh, Bob, Amlani, Shy, Natarajan, Madhu, Morrison, Laurie J., Kakar, Priya, Nowickyj, Roman, Lawrence, Michael, Cameron, Jennifer, and Ko, Dennis T.
- Abstract
Remote ischemic conditioning (RIC) is a noninvasive therapeutic strategy that uses brief cycles of blood pressure cuff inflation and deflation to protect the myocardium against ischemia-reperfusion injury. We sought to compare major adverse cardiovascular events (MACE) for patients who received RIC before PCI for ST-segment–elevation myocardial infarction (STEMI) compared with standard care.
- Published
- 2020
- Full Text
- View/download PDF
31. Hip Angles, Joint Moments, and Muscle Activity During Gait in Women With and Without Self-reported Stress Urinary Incontinence
- Author
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Hartigan, Erin, McAuley, J. Adrienne, Lawrence, Michael, Brucker, Willis, King, Adam, Tryon, Brooks, and DeSilva, Mary
- Abstract
Supplemental Digital Content is Available in the Text.
- Published
- 2020
- Full Text
- View/download PDF
32. A structurally minimized yet fully active insulin based on cone-snail venom insulin principles
- Author
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Xiong, Xiaochun, Menting, John G., Disotuar, Maria M., Smith, Nicholas A., Delaine, Carlie A., Ghabash, Gabrielle, Agrawal, Rahul, Wang, Xiaomin, He, Xiao, Fisher, Simon J., MacRaild, Christopher A., Norton, Raymond S., Gajewiak, Joanna, Forbes, Briony E., Smith, Brian J., Safavi-Hemami, Helena, Olivera, Baldomero, Lawrence, Michael C., and Chou, Danny Hung-Chieh
- Abstract
Human insulin and its current therapeutic analogs all show propensity, albeit varyingly, to self-associate into dimers and hexamers, which delays their onset of action and makes blood glucose management difficult for people with diabetes. Recently, we described a monomeric, insulin-like peptide in cone-snail venom with moderate human insulin-like bioactivity. Here, with insights from structural biology studies, we report the development of mini-Ins—a human des-octapeptide insulin analog—as a structurally minimal, full-potency insulin. Mini-Ins is monomeric and, despite the lack of the canonical B-chain C-terminal octapeptide, has similar receptor binding affinity to human insulin. Four mutations compensate for the lack of contacts normally made by the octapeptide. Mini-Ins also has similar in vitro insulin signaling and in vivo bioactivities to human insulin. The full bioactivity of mini-Ins demonstrates the dispensability of the PheB24–PheB25–TyrB26 aromatic triplet and opens a new direction for therapeutic insulin development.
- Published
- 2020
- Full Text
- View/download PDF
33. Mutational dynamics and immune evasion in diffuse large B-cell lymphoma explored in a relapse-enriched patient series
- Author
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Wise, Jillian F., Nakken, Sigve, Steen, Chloé B., Vodák, Daniel, Trøen, Gunhild, Johannessen, Bjarne, Lingjærde, Ole Christian, Hilden, Vera, Blaker, Yngvild Nuvin, Bai, Baoyan, Aasheim, Lars Birger, Pasanen, Annika, Lorenz, Susanne, Sveen, Anita, Lothe, Ragnhild A., Myklebost, Ola, Leppä, Sirpa, Meza-Zepeda, Leonardo A., Beiske, Klaus, Lawrence, Michael S., Hovig, Eivind, Myklebust, June Helen, Smeland, Erlend B., and Holte, Harald
- Published
- 2020
- Full Text
- View/download PDF
34. Mutational dynamics and immune evasion in diffuse large B-cell lymphoma explored in a relapse-enriched patient series
- Author
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Wise, Jillian F., Nakken, Sigve, Steen, Chloé B., Vodák, Daniel, Trøen, Gunhild, Johannessen, Bjarne, Lingjærde, Ole Christian, Hilden, Vera, Blaker, Yngvild Nuvin, Bai, Baoyan, Aasheim, Lars Birger, Pasanen, Annika, Lorenz, Susanne, Sveen, Anita, Lothe, Ragnhild A., Myklebost, Ola, Leppä, Sirpa, Meza-Zepeda, Leonardo A., Beiske, Klaus, Lawrence, Michael S., Hovig, Eivind, Myklebust, June Helen, Smeland, Erlend B., and Holte, Harald
- Abstract
•Diagnostic and relapse diffuse large B-cell lymphoma (DLBCL) biopsies reveal increased mutational burden/loss of heterozygosity in HLA-A.•Serially sampled tumor biopsies provide insight into therapeutic targets and evolutionary divergence in relapsed/refractory DLBCL.
- Published
- 2020
- Full Text
- View/download PDF
35. Comparative Behavior of Wild Bluegill Captured Inside and Outside of a Long‐Standing Aquatic Protected Area
- Author
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Moynes, Emily N., Lawrence, Michael J., Zolderdo, Aaron J., Prystay, Tanya S., Abrams, Alice E.I., Holder, Peter, and Cooke, Steven J.
- Abstract
In recreational fisheries it is understood that individual fish that exhibit bolder personality traits have a tendency to be removed from the population (i.e., fishing mortality via harvest or catch‐and‐release mortality), while more timid individuals remain. The use of aquatic protected areas (APAs) has been promoted as a means of offsetting the negative consequences that are associated with fishing mortality by protecting the full suite of phenotypes. However, little work has investigated whether APAs are able to maintain heterogeneity in behavioral traits in wild fish. We attempted to address this question by using wild Bluegill Lepomis macrochirusfrom Lake Opinicon, a freshwater system consisting of both an APAand heavily fished areas. The Bluegill were obtained via angling from three zones in the lake: the main lake area (i.e., fished), the APA(which has been in place since the 1940s), and a transitional zone between these two areas. In the laboratory, the Bluegill were subjected to two behavioral assessments, a Z‐maze and a flight‐initiation‐distance (FID) test, to address differences in boldness and risk‐taking between these populations. No significant effects of capture zone were detected for any of the behavioral metrics that were assessed in the maze trial. However, individuals that originated from the main lake population had significantly higher FIDscores than the fish from the transitional zone and the APAdid, indicating that they were more timid. Our results suggest that fisheries activities may only be acting only on specific traits, which may explain some of the null results that are presented here. Nevertheless, our study provides evidence that APAs are providing a reservoir of less timid individuals, which is consistent with an evolutionarily enlightened management strategy.
- Published
- 2020
- Full Text
- View/download PDF
36. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
- Author
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Rheinbay, Esther, Nielsen, Morten Muhlig, Abascal, Federico, Wala, Jeremiah A., Shapira, Ofer, Tiao, Grace, Hornshøj, Henrik, Hess, Julian M., Juul, Randi Istrup, Lin, Ziao, Feuerbach, Lars, Sabarinathan, Radhakrishnan, Madsen, Tobias, Kim, Jaegil, Mularoni, Loris, Shuai, Shimin, Lanzós, Andrés, Herrmann, Carl, Maruvka, Yosef E., Shen, Ciyue, Amin, Samirkumar B., Bandopadhayay, Pratiti, Bertl, Johanna, Boroevich, Keith A., Busanovich, John, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Craft, David, Dhingra, Priyanka, Diamanti, Klev, Fonseca, Nuno A., Gonzalez-Perez, Abel, Guo, Qianyun, Hamilton, Mark P., Haradhvala, Nicholas J., Hong, Chen, Isaev, Keren, Johnson, Todd A., Juul, Malene, Kahles, Andre, Kahraman, Abdullah, Kim, Youngwook, Komorowski, Jan, Kumar, Kiran, Kumar, Sushant, Lee, Donghoon, Lehmann, Kjong-Van, Li, Yilong, Liu, Eric Minwei, Lochovsky, Lucas, Park, Keunchil, Pich, Oriol, Roberts, Nicola D., Saksena, Gordon, Schumacher, Steven E., Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stewart, Chip, Tamborero, David, Tubio, Jose M. C., Umer, Husen M., Uusküla-Reimand, Liis, Wadelius, Claes, Wadi, Lina, Yao, Xiaotong, Zhang, Cheng-Zhong, Zhang, Jing, Haber, James E., Hobolth, Asger, Imielinski, Marcin, Kellis, Manolis, Lawrence, Michael S., von Mering, Christian, Nakagawa, Hidewaki, Raphael, Benjamin J., Rubin, Mark A., Sander, Chris, Stein, Lincoln D., Stuart, Joshua M., Tsunoda, Tatsuhiko, Wheeler, David A., Johnson, Rory, Reimand, Jüri, Gerstein, Mark, Khurana, Ekta, Campbell, Peter J., López-Bigas, Núria, Weischenfeldt, Joachim, Beroukhim, Rameen, Martincorena, Iñigo, Pedersen, Jakob Skou, and Getz, Gad
- Abstract
The discovery of drivers of cancer has traditionally focused on protein-coding genes1–4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium5of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers6,7, raise doubts about others and identify novel candidates, including point mutations in the 5′ region of TP53, in the 3′ untranslated regions of NFKBIZand TOB1, focal deletions in BRD4and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available.
- Published
- 2020
- Full Text
- View/download PDF
37. Using the locus of slack logic to determine whether the output form of inhibition of return affects an early or late stage of processing
- Author
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Klein, Raymond M., Kavyani, Maryam, Farsi, Alireza, and Lawrence, Michael A.
- Abstract
Slower reaction times to targets presented at a previously cued or attended location are often attributed to inhibition of return (IOR). It has been suggested that IOR affects a process at the output end of processing continuum when it is generated while the oculomotor system is activated. Following the path set by Kavyani, Farsi, Abdoli, and Klein (2017)we used the locus of slack logic embedded in the psychological refractory period (PRP) paradigm to test this idea. We generated what we expected would be the output form of IOR by beginning each with participants making a target directed saccade which was followed by two tasks. Task 1, was a 2-choice auditory discrimination task and Task 2 was a 2-choice visual localization task. We varied the interval between the onsets of the two targets associated with these two tasks (using TTOAs of 200, 400, or 800 msec). As expected the visual task suffered from a robust PRP effect (substantially delayed RTs at the shorter TTOAs). There was also a robust IOR effect with RTs to localize visual targets being slower when the targets were presented at a previously fixated location. Importantly, and in striking to our previous results wherein we generated the input form of IOR, in the present study there was an additive effect between IOR and TTOA on RT2. As implied by the locus of slack logic, we therefore conclude that the form of IOR generated when the oculomotor system is activated affects a late stage of processing. Converging evidence for this conclusion, from a variety of neuroscientific methods, is presented and the dearth of such evidence about the input form of IOR is noted.
- Published
- 2020
- Full Text
- View/download PDF
38. plyranges: a grammar of genomic data transformation
- Author
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Lee, Stuart, Cook, Dianne, and Lawrence, Michael
- Abstract
Bioconductor is a widely used R-based platform for genomics, but its host of complex genomic data structures places a cognitive burden on the user. For most tasks, the GRanges object would suffice, but there are gaps in the API that prevent its general use. By recognizing that the GRanges class follows “tidy” data principles, we create a grammar of genomic data transformation, defining verbs for performing actions on and between genomic interval data and providing a way of performing common data analysis tasks through a coherent interface to existing Bioconductor infrastructure. We implement this grammar as a Bioconductor/R package called plyranges.
- Published
- 2019
- Full Text
- View/download PDF
39. GTP-Dependent Formation of Multimeric G‑Quadruplexes.
- Author
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Kolesnikova, Sofia, Srb, Pavel, Vrzal, Lukáš, Lawrence, Michael S., Veverka, Václav, and Curtis, Edward A.
- Published
- 2019
- Full Text
- View/download PDF
40. SELF-ASSESSMENT DURING JUMP SHOT DRILLS TRANSLATES TO DECREASED VERTICAL GROUND REACTION FORCES DURING SINGLE LIMB DROP JUMP LANDING.
- Author
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Hartigan, Erin, Coleman, Kelly, Brooks, Jaclyn, Frisbee, Hailey, Lawrence, Michael, Hawke, Katie, and Breslen, Gwenyth
- Subjects
ANTERIOR cruciate ligament injury prevention ,ANALYSIS of variance ,ATHLETES ,ATHLETIC ability ,AUDIOVISUAL materials ,BASKETBALL ,COMPUTER software ,CONFIDENCE intervals ,GROUND reaction forces (Biomechanics) ,JUMPING ,SCIENTIFIC observation ,POCKET computers ,QUESTIONNAIRES ,RESEARCH funding ,STATISTICAL sampling ,SELF-evaluation ,SPORTS sciences ,STATISTICS ,DATA analysis ,TASK performance ,BODY movement ,PRE-tests & post-tests ,CASE-control method ,EVALUATION of human services programs ,DATA analysis software - Abstract
Background: Prevention programs reduce hard and stiff landings associated with risk of anterior cruciate ligament (ACL) injury, yet cost and time are barriers to implementation. Providing feedback about landing mechanics during shooting drills at practices using minimal resources and time may improve adherence to educating athletes how to avoid risky mechanics associated with ACL injury when landing. Implementing video, auditory, written, and pictorial feedback into basketball practices to cue athletes on landing mechanics after taking a jump shot may soften the landing. Purpose: The purpose of this study was to test whether implementing video, auditory, written, and pictorial feedback into a basketball practice jump shot drill fie., double limb drop jump landing task) will result in lesser vertical ground reaction force (vGRP) during a single limb drop jump landing without decreasing maximal jump height. Study Design: Observational, Case-control Study Methods: During a summer league, 16 female high school basketball players were assigned to an intervention (Int) OT control (Con) group. The Int group (n = S) utilized delayed video feedback and task cards (written and pictorial cues) at six practices while the Con group (n=B) received typical coaching only. Cost and compliance with the intervention were measured. Pre- and post-season data collections included five single limb drop jumps from a 31 cm high box onto force plates. The vGRF impulses over the first 10% of landing were calculated for each limb. Data did not differ between limbs, thus data for both limbs were pooled. Two mixed model ANOVAs were used to compare groups over time (p<0 OS) for vGRF and maximum jump height, respectively Results: Compliance with the intervention was 100% and did not increase the time of drills. The implementation cost was less than S10 A time group interaction (p=0.04; Int significantly decreased vGKF over time), main effect of time (p = 0.004), and no main effect of group (p=0.412) were found foT vGRF during single limb drop jump landings. A time'group interaction (p = 0.03; Int significantly decreased max jump height over time), no main effect of time (p = 0.10) and no main effect of group [p = 0.32) were found for max jump height. Conclusion: Athletes landed more softly and jumped less high during a single limb drop jump landing task after receiving feedback during jump shot drills. High team compliance may occur since the intervention required minimal resources and addressed different learning styles Level of Evidence: Level 3b [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
41. Calibration and Validation of S3F Sensor for Measuring Normal and Shear Stresses in Soil
- Author
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Alqrinawi, Hussein, Lin, Hai, Chen, Shengli, Rogoshchchenkov, Nikolay, Lawrence, Michael, Ryan, Colleen, and Palluconi, Steve
- Abstract
Innovative sensors can provide new capabilities to monitor and understand the behavior of soil, rock, and geo-structures and help geotechnical engineers make informed decisions about the construction and maintenance of geo-structures. This study introduced, calibrated, and validated one such sensor, the Surface Stress Sensitive Film (S3F) point sensor, for both normal and shear stress measurements in soil and along the soil–structure interface. The measurements of the S3F sensor rely on the deformation of an elastic film that is monitored by a magnetic floating element embedded in the elastic film and a Hall effect sensor. This sensor provides measurements of the 3-D deformation of the film, which are converted to normal and shear stresses using an a priori calibration. The calibrations of the S3F sensor were performed considering the effect of the loading areas, loading and unloading conditions, and soil particle sizes. Then, the performance of the S3F sensor to measure the normal stresses in soil and shear stresses at the soil–wooden block interface under static tension and pull-out conditions was evaluated. It was found that the normal stress calibration curves depended on the sizes of the loading areas because of the stiff housing boundary effect. However, the shear stress calibration curves were independent of the loading areas. The S3F sensor showed an ability to measure normal stresses in three different types of soils, including two silica sands from Ottawa, Illinois, with particle sizes ranging between sieve No. 20 and 30 (Ottawa 20/30 sand) and sieve No. 50 and 70 (Ottawa 50/70 sand) and finely ground silica silt (Sil-Co-Sil). The S3F sensor also showed an ability to measure the shear stresses at the soil–structure interface, which match well with the theoretical shear stresses. The S3F sensor has potential for stress measurements at the soil–structure interfaces in foundations, tunnels, pipes, and retaining systems.
- Published
- 2024
- Full Text
- View/download PDF
42. Comparing Immobilization, Recovery, and Stress Indicators Associated with Electric Fish Handling Gloves and a Portable Electrosedation System.
- Author
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Abrams, Alice E. I., Rous, Andrew M., Brooks, Jill L., Lawrence, Michael J., Midwood, Jonathan D., Doka, Susan E., and Cooke, Steven J.
- Abstract
Abstract: Fish sedation facilitates safer handling of fish during scientific research or fisheries assessment practices, thus limiting risk of injury to fish and reducing stress responses. In recent years, there has been growing interest in using electricity to sedate fish; two methods include (1) lower‐voltage, non‐pulsed‐DC fish handling gloves (FHGs) that tend to only sedate fish while the gloves are touching the animal; and (2) a comparatively high‐voltage, pulsed‐DC Portable Electrosedation System (PES) that leads to galvanonarcosis. This study compared the physiological consequences of exposure to FHGs and PES in teleost fish. Bluegills
Lepomis macrochirus and Largemouth BassMicropterus salmoides were exposed to FHGs, PES, or a handling control for a 3‐min simulated surgery. Blood was then sampled at 0.5 and 4.5 h postexposure and was analyzed for blood glucose, blood lactate, and plasma cortisol concentrations. Opercular rates were monitored during surgery, at 2 min postsurgery, and 0.5 h postsurgery. At 24 h postsurgery, time to exhaustion (via a standardized swimming chase protocol) was assessed. Fish exposed to FHGs tended to exhibit lower opercular rates than fish that were sedated with the PES during simulated surgery. Cortisol levels of Largemouth Bass treated with FHGs were higher than those of fish sedated with the PES. Glucose levels recorded for Bluegills at 4.5 h postsurgery were higher with FHGs than with the PES. In both species, lactate was lower for fish treated with FHGs than for those treated with the PES. At 24 h posttreatment, Bluegills sedated with FHGs exhibited a longer time to exhaustion than those subjected to the PES, whereas Largemouth Bass sedated with the PES exhibited a longer time to exhaustion than those sedated with FHGs. Physiological responses to treatments were inconsistent between species. Further investigation to determine the optimal electrosedation method is required. [ABSTRACT FROM AUTHOR]- Published
- 2018
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43. GTP-Dependent Formation of Multimeric G-Quadruplexes
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Kolesnikova, Sofia, Srb, Pavel, Vrzal, Lukáš, Lawrence, Michael S., Veverka, Václav, and Curtis, Edward A.
- Abstract
G-Quadruplexes are noncanonical nucleic acid structures made up of stacked guanosine tetrads connected by short loops. They are frequently used building blocks in synthetic biology and thought to play widespread biological roles. Multimerization can change the functional properties of G-quadruplexes, and understanding the factors that modulate this process remains an important goal. Here, we report the discovery of a novel mechanism by which the formation of multimeric G-quadruplexes can be controlled using GTP. We show that GTP likely inhibits multimer formation by becoming incorporated into a tetrad in the monomeric form of the structure and define the sequence requirements of G-quadruplexes that form GTP-dependent structures. These experiments provide new insights into the small molecule control of G-quadruplex multimerization. They also suggest possible roles for GTP-dependent multimeric G-quadruplexes in both synthetic and natural biological systems.
- Published
- 2019
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44. Next-generation characterization of the Cancer Cell Line Encyclopedia
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Ghandi, Mahmoud, Huang, Franklin, Jané-Valbuena, Judit, Kryukov, Gregory, Lo, Christopher, McDonald, E., Barretina, Jordi, Gelfand, Ellen, Bielski, Craig, Li, Haoxin, Hu, Kevin, Andreev-Drakhlin, Alexander, Kim, Jaegil, Hess, Julian, Haas, Brian, Aguet, François, Weir, Barbara, Rothberg, Michael, Paolella, Brenton, Lawrence, Michael, Akbani, Rehan, Lu, Yiling, Tiv, Hong, Gokhale, Prafulla, de Weck, Antoine, Mansour, Ali, Oh, Coyin, Shih, Juliann, Hadi, Kevin, Rosen, Yanay, Bistline, Jonathan, Venkatesan, Kavitha, Reddy, Anupama, Sonkin, Dmitriy, Liu, Manway, Lehar, Joseph, Korn, Joshua, Porter, Dale, Jones, Michael, Golji, Javad, Caponigro, Giordano, Taylor, Jordan, Dunning, Caitlin, Creech, Amanda, Warren, Allison, McFarland, James, Zamanighomi, Mahdi, Kauffmann, Audrey, Stransky, Nicolas, Imielinski, Marcin, Maruvka, Yosef, Cherniack, Andrew, Tsherniak, Aviad, Vazquez, Francisca, Jaffe, Jacob, Lane, Andrew, Weinstock, David, Johannessen, Cory, Morrissey, Michael, Stegmeier, Frank, Schlegel, Robert, Hahn, William, Getz, Gad, Mills, Gordon, Boehm, Jesse, Golub, Todd, Garraway, Levi, and Sellers, William
- Abstract
Large panels of comprehensively characterized human cancer models, including the Cancer Cell Line Encyclopedia (CCLE), have provided a rigorous framework with which to study genetic variants, candidate targets, and small-molecule and biological therapeutics and to identify new marker-driven cancer dependencies. To improve our understanding of the molecular features that contribute to cancer phenotypes, including drug responses, here we have expanded the characterizations of cancer cell lines to include genetic, RNA splicing, DNA methylation, histone H3 modification, microRNA expression and reverse-phase protein array data for 1,072 cell lines from individuals of various lineages and ethnicities. Integration of these data with functional characterizations such as drug-sensitivity, short hairpin RNA knockdown and CRISPR–Cas9 knockout data reveals potential targets for cancer drugs and associated biomarkers. Together, this dataset and an accompanying public data portal provide a resource for the acceleration of cancer research using model cancer cell lines. The original Cancer Cell Line Encyclopedia (CCLE) is expanded with deeper characterization of over 1,000 cell lines, including genomic, transcriptomic, and proteomic data, and integration with drug-sensitivity and gene-dependency data.
- Published
- 2019
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45. DGKα/ζ inhibitors combine with PD-1 checkpoint therapy to promote T cell–mediated antitumor immunity
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Wichroski, Michael, Benci, Joseph, Liu, Si-Qi, Chupak, Louis, Fang, Jie, Cao, Carolyn, Wang, Cindy, Onorato, Joelle, Qiu, Hongchen, Shan, Yongli, Banas, Dana, Powles, Ryan, Locke, Gregory, Witt, Abigail, Stromko, Caitlyn, Qi, Huilin, Zheng, Xiaofan, Martin, Scott, Ding, Min, Gentles, Robert, Meanwell, Nicholas, Velaparthi, Upender, Olson, Richard, Wee, Susan, Tenney, Daniel, Parker, Christopher G., Cravatt, Benjamin F., Lawrence, Michael, Borzilleri, Robert, and Lees, Emma
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- 2023
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46. Macroeconomic impacts of proposed climate change mitigation strategies for transportation in Southern California.
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Lawrence, Michael F., Wei, Dan, Rose, Adam, Williamson, Scott, and Cartwright-Smith, Devon
- Abstract
We evaluate the potential regional macroeconomic impacts of a set of eighteen greenhouse gas (GHG) mitigation policy options intended to enable the Southern California Association of Governments (SCAG) to comply with the California's emission reduction targets related to transportation and land use. The Regional Economic Models, Inc. (REMI) Policy Insight Plus (PI+) and TranSight (TS) Models were applied in the analysis by carefully linking technical and microeconomic aspects of each mitigation option to the workings of the regional economy. We account for key considerations, such as the extent to which investment in mitigation options would be generated from new revenue sources or would displace ordinary private business investment. Our results indicate that the combined eighteen policies could generate an employment gain of almost 14 thousand jobs per year and result in an increase in GDP of $22 billion over the entire planning period from now to 2035. Sensitivity analyses of key assumptions and parameters for the transportation and land use policies indicate that the results are robust. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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47. Exploring the Effects of Using an Oral Appliance to Reduce Movement Dysfunction in an Individual With Parkinson Disease: A Single-Subject Design Study.
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Lane, Hillary, Rose, Lindsey E., Woodbrey, Megan, Arghavani, David, Lawrence, Michael, and Cavanaugh, James T.
- Abstract
Background and Purpose: Clinical reports suggest that wearing an oral appliance can improve the gait and balance of an individual with Parkinson disease (PD). Our primary purpose was to systematically explore this effect using a single-subject study design and quantitative motion analysis. Secondarily, we sought to examine the quality-of-life outcomes following 1-month of routine oral appliance wear. Methods: The participant was a 73-year-old ambulatory man with mid-stage PD. Using an A-B-A design, for which a custom-made oral appliance served as the intervention, kinematic and kinetic data were captured during performance of Four Square Step Test, serpentine walk, and tandem walk tasks. Grip strength was quantified with a dynamometer. Quality-of-life outcomes were collected after 1 month of appliance wear using the Parkinson Disease Questionnaire-39 (PDQ-39). Perceived changes in balance, mobility, and quality of life were captured from the participant using an 11-point Global Rate of Change (GRC) scale. Results: Changes in mobility, postural control, and grip strength during appliance wear were suggestive of reduced movement dysfunction. The PDQ-39 revealed a significant improvement in quality of life, primarily related to increased emotional well-being, decreased stigma, and increased communication. GRC scores indicated a clinically significant improvement in ease of movement in the community (+3), ease of movement during the performance of activities of daily living (+4), and in standing balance while performing activities of daily living (+4). Discussion and Conclusions: Study findings provided quantitative evidence supporting the effectiveness of oral appliance wear for reducing movement dysfunction in a patient with mid-stage PD. Video Abstract available for more insights from the authors (see Supplemental Digital Content 1, http://links.lww.com/JNPT/A155 ). [ABSTRACT FROM AUTHOR]
- Published
- 2017
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48. Early TLR4 Blockade Attenuates Sterile Inflammation-mediated Stress in Islets During Isolation and Promotes Successful Transplant Outcomes
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Chang, Charles A., Murphy, Kayla, Kane, Robert R., Lawrence, Michael C., and Naziruddin, Bashoo
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TLR4 blockade with TAK-242, a small molecular inhibitor, protects islets from sterile inflammation-mediated stress in a syngeneic transplant model using a marginal mass of islets transplanted intraportally into mice with streptozotocin-induced diabetes. Supplemental digital content is available in the text.
- Published
- 2018
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49. Integrated Molecular Characterization of Testicular Germ Cell Tumors
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Shen, Hui, Shih, Juliann, Hollern, Daniel P., Wang, Linghua, Bowlby, Reanne, Tickoo, Satish K., Thorsson, Vésteinn, Mungall, Andrew J., Newton, Yulia, Hegde, Apurva M., Armenia, Joshua, Sánchez-Vega, Francisco, Pluta, John, Pyle, Louise C., Mehra, Rohit, Reuter, Victor E., Godoy, Guilherme, Jones, Jeffrey, Shelley, Carl S., Feldman, Darren R., Vidal, Daniel O., Lessel, Davor, Kulis, Tomislav, Cárcano, Flavio M., Leraas, Kristen M., Lichtenberg, Tara M., Brooks, Denise, Cherniack, Andrew D., Cho, Juok, Heiman, David I., Kasaian, Katayoon, Liu, Minwei, Noble, Michael S., Xi, Liu, Zhang, Hailei, Zhou, Wanding, ZenKlusen, Jean C., Hutter, Carolyn M., Felau, Ina, Zhang, Jiashan, Schultz, Nikolaus, Getz, Gad, Meyerson, Matthew, Stuart, Joshua M., Wang, Linghua, Xi, Liu, Wheeler, David, Hughes, Daniel, Covington, Kyle, Jayaseelan, Joy C., Korchina, Viktoriya, Lewis, Lora, Hu, Jianhong, Doddapaneni, HarshaVardhan, Muzny, Donna, Gibbs, Richard, Hoadley, Katherine A., Hollern, Daniel, Vincent, Benjamin G., Chai, Shengjie, Smith, Christof C., Auman, J. Todd, Shi, Yan, Meng, Shaowu, Skelly, Tara, Tan, Donghui, Veluvolu, Umadevi, Mieczkowski, Piotr A., Jones, Corbin D., Wilkerson, Matthew D., Balu, Saianand, Bodenheimer, Tom, Hoyle, Alan P., Jefferys, Stuart R., Mose, Lisle E., Simons, Janae V., Soloway, Matthew G., Roach, Jeffrey, Parker, Joel S., Hayes, D. Neil, Perou, Charles M., Shih, Juliann, Cherniack, Andrew D., Meyerson, Matthew, Saksena, Gordon, Cibulskis, Carrie, Schumacher, Steven E., Beroukhim, Rameen, Gabriel, Stacey B., Bowlby, Reanne, Mungall, Andrew J., Brooks, Denise, Kasaian, Katayoon, Ally, Adrian, Balasundaram, Miruna, Carlsen, Rebecca, Cheung, Dorothy, Chuah, Eric, Dhalla, Noreen, Holt, Robert A., Jones, Steven J.M., Ma, Yussanne, Mayo, Michael, Moore, Richard A., Robertson, A. Gordon, Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Wong, Tina, Marra, Marco A., Shen, Hui, Zhou, Wanding, Laird, Peter W., Weisenberger, Daniel J., Van Den Berg, David J., Lai, Phillip H., Berrios, Mario, Holbrook, Andrea, Bootwalla, Moiz S., Maglinte, Dennis T., Armenia, Joshua, Sánchez-Vega, Francisco, Schultz, Nikolaus, Chakravarty, Debyani, Gao, Jianjiong, Heins, Zachary, Kundra, Ritika, Ochoa, Angelica, Liu, Minwei, Sander, Chris, Ladanyi, Marc, Thorsson, Vesteinn, Radenbaugh, Amie J., Newton, Yulia, Stuart, Joshua M., Cho, Juok, Heiman, David I., Noble, Michael S., Zhang, Hailei, Getz, Gad, Gehlenborg, Nils, Saksena, Gordon, Voet, Doug, Lin, Pei, Frazer, Scott, Kim, Jaegil, Lawrence, Michael S., Meier, Sam, Defreitas, Timothy, Chin, Lynda, Hegde, Apurva M., Akbani, Rehan, Weinstein, John N., Liu, Wenbin, Mills, Gordon B., Lu, Yiling, Pyle, Louise C., Pluta, John, Nathanson, Katherine L., Tickoo, Satish K., Reuter, Victor E., Mehra, Rohit, Looijenga, Leendert, Bryce, Alan H., Cárcano, Flavio M., Carvalho, André L., Cortessis, Victoria K., Feldman, Darren, Godoy, Guilherme, Ittmann, Michael, Jones, Jeffrey, Kulis, Tomislav, Lerner, Seth, Lessel, Davor, Nathanson, Katherine L., Shelley, Carl S., Vidal, Daniel O., Leraas, Kristen M., Lichtenberg, Tara M., Bowen, Jay, Gastier-Foster, Julie M., Gerken, Mark, Helsel, Carmen, Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Cottingham, Sandra, Chesla, David, Saller, Charles, Tarvin, Katherine, Lopes, Luiz Fernando, Scapulatempo-Neto, Cristovam, Aredes, Natália D.A., Oosterhuis, Wolter, Gillis, Ad, Stoop, Hans, Eijkenboom, Wil, Sandusky, George, Martin, Sue Ellen, Aron, Manju, Daneshmand, Siamak, Djaladat, Hooman, Quinn, David, Dorff, Tanya, Lennerz, Jochen K., Thorne, Leigh B., Gamulin, Marija, Kastelan, Zeljko, Hudolin, Tvrtko, Kubisch, Christian, Boice, Lori, Huang, Mei, Perou, Amy H., Rathmell, W. Kimryn, Pihl, Todd, Wan, Yunhu, Sun, Qiang, Naresh, Rashi, Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Wu, Ye, Ferguson, Martin L., Zenklusen, Jean C., Felau, Ina, Zhang, Jiashan (Julia), Sheth, Margi, Demchok, John A., Yang, Liming, Wang, Zhining, Tarnuzzer, Roy, Hutter, Carolyn M., Sofia, Heidi J., Davidsen, Tanja M., Akbani, Rehan, Wheeler, David A., Laird, Peter W., Nathanson, Katherine L., Cortessis, Victoria K., and Hoadley, Katherine A.
- Abstract
We studied 137 primary testicular germ cell tumors (TGCTs) using high-dimensional assays of genomic, epigenomic, transcriptomic, and proteomic features. These tumors exhibited high aneuploidy and a paucity of somatic mutations. Somatic mutation of only three genes achieved significance—KIT, KRAS, and NRAS—exclusively in samples with seminoma components. Integrated analyses identified distinct molecular patterns that characterized the major recognized histologic subtypes of TGCT: seminoma, embryonal carcinoma, yolk sac tumor, and teratoma. Striking differences in global DNA methylation and microRNA expression between histology subtypes highlight a likely role of epigenomic processes in determining histologic fates in TGCTs. We also identified a subset of pure seminomas defined by KITmutations, increased immune infiltration, globally demethylated DNA, and decreased KRAScopy number. We report potential biomarkers for risk stratification, such as miRNA specifically expressed in teratoma, and others with molecular diagnostic potential, such as CpH (CpA/CpC/CpT) methylation identifying embryonal carcinomas.
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- 2018
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50. Islet damage during isolation as assessed by miRNAs and the correlation of miRNAlevels with posttransplantation outcome in islet autotransplantation
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Saravanan, Prathab Balaji, Kanak, Mazhar A., Chang, Charles A., Darden, Carly, Yoshimatsu, Gumpei, Lawrence, Michael C., and Naziruddin, Bashoo
- Abstract
High‐quality pancreatic islets are essential for better posttransplantation endocrine function in total pancreatectomy with islet autotransplantation (TPIAT), yet stress during the isolation process affects quality and yield. We analyzed islet‐enriched microRNAs (miRNAs) ‐375 and ‐200c released during isolation to assess damage and correlated the data with posttransplantation endocrine function. The absolute concentration of miR‐375, miR‐200c, and C‐peptide was measured in various islet isolation steps, including digestion, dilution, recombination, purification, and bagging, in 12 cases of TPIAT. Posttransplantation glycemic control was monitored through C‐peptide, hemoglobin A1c, insulin requirement, and SUITOindex. The amount of miR‐375 released was significantly higher during enzymatic digestion followed by the islet bagging (P <.001). Mir‐200c mirrored these changes, albeit at lower concentrations. In contrast, the C‐peptide amount was significantly higher in the purification and bagging steps (P <.001). Lower amounts of miR‐375 were associated with a lower 6‐month insulin requirement (P =.01) and lower hemoglobin A1c(P =.04). Measurement of the absolute quantity of miRNA‐375 and ‐200c released during islet isolation is a useful tool to assess islet damage. The quantity of released miRNAis indicative of posttransplantation endocrine function in TPIATpatients. Quantification of microRNA‐375 released during islet isolation procedures demonstrates islet damage and indicates posttransplant endocrine function in patients undergoing total pancreatectomy with islet autotransplantation.
- Published
- 2018
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