21,650 results on '"Phillips A."'
Search Results
2. Ketone monoester attenuates declines in cognitive performance and oxygen saturation during acute severe hypoxic exposure under resting conditions
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Tyler S. McClure, Jeffrey Phillips, Andrew P. Koutnik, Kody Coleman, Ed Chappe, Gary R. Cutter, Brendan Egan, Todd Norell, Brianna J. Stubbs, Marcas M. Bamman, and Dawn Kernagis
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β‐hydroxybutyrate ,code substitution ,cognitive resilience ,exogenous ketosis ,Physiology ,QP1-981 - Abstract
Abstract Exogenous ketone supplements are a potential augmentation strategy for cognitive resilience during acute hypoxic exposure due to their capacity to attenuate the decline in oxygen (O2) availability, and by providing an alternative substrate for cerebral metabolism. Utilizing a single‐blind randomized crossover design, 16 male military personnel (age, 25.3 ± 2.4 year, body mass, 86.2 ± 9.3 kg) performed tests of cognitive performance at rest in three environments: room air (baseline), normoxia (20 min; 0 m; 20.9% O2) and hypoxia (20 min; 6096 m, 9.7% O2) using a reduced O2 breathing device (ROBD). (R)‐3‐Hydroxybutyl (R)‐3‐hydroxybutyrate (R‐BD R‐βHB) ketone monoester (KME; 650 mg/kg, split dose given at 30 min prior to each exposure) or taste‐matched placebo (PLA) was ingested prior to normoxia and hypoxic exposure. Blood R‐βHB and glucose concentrations, cognitive performance and O2 saturation (SpO2) were collected throughout. KME ingestion increased blood R‐βHB concentration, which was rapid and sustained (>4 mM 30 min post; P
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- 2024
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3. Mitigating disuse‐induced skeletal muscle atrophy in ageing: Resistance exercise as a critical countermeasure
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James McKendry, Giulia Coletta, Everson A. Nunes, Changhyun Lim, and Stuart M. Phillips
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anabolism ,catabolism ,muscle unloading ,physical activity ,sarcopenia ,Physiology ,QP1-981 - Abstract
Abstract The gradual deterioration of physiological systems with ageing makes it difficult to maintain skeletal muscle mass (sarcopenia), at least partly due to the presence of ‘anabolic resistance’, resulting in muscle loss. Sarcopenia can be transiently but markedly accelerated through periods of muscle disuse‐induced (i.e., unloading) atrophy due to reduced physical activity, sickness, immobilisation or hospitalisation. Periods of disuse are detrimental to older adults' overall quality of life and substantially increase their risk of falls, physical and social dependence, and early mortality. Disuse events induce skeletal muscle atrophy through various mechanisms, including anabolic resistance, inflammation, disturbed proteostasis and mitochondrial dysfunction, all of which tip the scales in favour of a negative net protein balance and subsequent muscle loss. Concerningly, recovery from disuse atrophy is more difficult for older adults than their younger counterparts. Resistance training (RT) is a potent anabolic stimulus that can robustly stimulate muscle protein synthesis and mitigate muscle losses in older adults when implemented before, during and following unloading. RT may take the form of traditional weightlifting‐focused RT, bodyweight training and lower‐ and higher‐load RT. When combined with sufficient dietary protein, RT can accelerate older adults' recovery from a disuse event, mitigate frailty and improve mobility; however, few older adults regularly participate in RT. A feasible and practical approach to improving the accessibility and acceptability of RT is through the use of resistance bands. Moving forward, RT must be prescribed to older adults to mitigate the negative consequences of disuse atrophy.
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- 2024
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4. Body weight and composition endpoints in cancer cachexia clinical trials: Systematic Review 4 of the cachexia endpoints series
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Leo R. Brown, Mariana S. Sousa, Michael S. Yule, Vickie E. Baracos, Donald C. McMillan, Jann Arends, Trude R. Balstad, Asta Bye, Olav Dajani, Ross D. Dolan, Marie T. Fallon, Christine Greil, Marianne J. Hjermstad, Gunnhild Jakobsen, Matthew Maddocks, James McDonald, Inger O. Ottestad, Iain Phillips, Judith Sayers, Melanie R. Simpson, Ola M. Vagnildhaug, Tora S. Solheim, Barry J.A. Laird, Richard J.E. Skipworth, and the Cancer Cachexia Endpoints Working Group
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body composition ,cachexia ,cancer cachexia ,clinical trials ,Diseases of the musculoskeletal system ,RC925-935 ,Human anatomy ,QM1-695 - Abstract
Abstract Significant variation exists in the outcomes used in cancer cachexia trials, including measures of body composition, which are often selected as primary or secondary endpoints. To date, there has been no review of the most commonly selected measures or their potential sensitivity to detect changes resulting from the interventions being examined. The aim of this systematic review is to assess the frequency and diversity of body composition measures that have been used in cancer cachexia trials. MEDLINE, Embase and Cochrane Library databases were systematically searched between January 1990 and June 2021. Eligible trials examined adults (≥18 years) who had received an intervention aiming to treat or attenuate the effects of cancer cachexia for >14 days. Trials were also of a prospective controlled design and included body weight or at least one anthropometric, bioelectrical or radiological endpoint pertaining to body composition, irrespective of the modality of intervention (e.g., pharmacological, nutritional, physical exercise and behavioural) or comparator. Trials with a sample size of
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- 2024
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5. Implantable and transcutaneous photobiomodulation promote neuroregeneration and recovery of lost function after spinal cord injury
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Andrew R. Stevens, Mohammed Hadis, Alice Phillips, Abhinav Thareja, Michael Milward, Antonio Belli, William Palin, David J. Davies, and Zubair Ahmed
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medical devices ,neuroregeneration ,photobiomodulation ,spinal cord injury ,spinal cord stimulation ,Chemical engineering ,TP155-156 ,Biotechnology ,TP248.13-248.65 ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Abstract Spinal cord injury (SCI) is a cause of profound and irreversible damage, with no effective therapy to promote functional recovery. Photobiomodulation (PBM) may provide a viable therapeutic approach using red or near‐infrared light to promote recovery after SCI by mitigating neuroinflammation and preventing neuronal apoptosis. Our current study aimed to optimize PBM dose regimens and develop and validate the efficacy of an invasive PBM delivery paradigm for SCI. Dose optimization studies were performed using a serum withdrawal model of injury in cultures of primary adult rat dorsal root ganglion neurons (DRGN). Implantable and transcutaneous PBM delivery protocols were developed and validated using cadaveric modeling. The efficacy of PBM in promoting recovery after SCI in vivo was studied in a dorsal column crush injury model of SCI in adult rats. Optimal neuroprotection in vitro was achieved between 4 and 22 mW/cm2. 11 mW/cm2 for 1 min per day (0.66 J/cm2) increased cell viability by 45% over 5 days (p
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- 2024
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6. The effect of home‐based neuromuscular electrical stimulation‐resistance training and protein supplementation on lean mass in persons with spinal cord injury: A pilot study
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Sven Hoekstra, James A. King, Jordan Fenton, Natasha Kirk, Scott A. Willis, Stuart M. Phillips, Nick Webborn, Keith Tolfrey, Johan De Vogel‐Van Den Bosch, and Vicky L. Goosey‐Tolfrey
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exercise training ,muscle mass ,paralysis ,rehabilitation ,whey protein ,Physiology ,QP1-981 - Abstract
Abstract In persons with a spinal cord injury (SCI), resistance training using neuromuscular electrical stimulation (NMES‐RT) increases lean mass in the lower limbs. However, whether protein supplementation in conjunction with NMES‐RT further enhances this training effect is unknown. In this randomized controlled pilot trial, 15 individuals with chronic SCI engaged in 3 times/week NMES‐RT, with (NMES+PRO, n = 8) or without protein supplementation (NMES, n = 7), for 12 weeks. Before and after the intervention, whole body and regional body composition (DXA) and fasting glucose and insulin concentrations were assessed in plasma. Adherence to the intervention components was ≥96%. Thigh lean mass was increased to a greater extent after NMES+PRO compared to NMES (0.3 (0.2, 0.4) kg; p
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- 2024
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7. Iron Corrole‐Catalyzed Intramolecular Amination Reactions of Alkyl Azides. Spectroscopic Characterization and Reactivity of [FeV(Cor)(NAd)]
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Tingjie You, Ka‐Pan Shing, Liangliang Wu, Kai Wu, Hua‐Hua Wang, Yungen Liu, Lili Du, Runhui Liang, David Lee Phillips, Xiao‐Yong Chang, Jie‐Sheng Huang, and Chi‐Ming Che
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C─H activation ,corrole ,imido complexes ,iron ,N‐heterocycles ,Science - Abstract
Abstract As nitrogen analogues of iron‐oxo species, high‐valent iron‐imido species have attracted great interest in the past decades. FeV‐alkylimido species are generally considered to be key reaction intermediates in Fe(III)‐catalyzed C(sp3)─H bond aminations of alkyl azides but remain underexplored. Here, it is reported that iron‐corrole (Cor) complexes can catalyze a wide range of intramolecular C─H amination reactions of alkyl azides to afford a variety of 5‐, 6‐ and 7‐membered N‐heterocycles, including alkaloids and natural product derivatives, with up to 3880 turnover numbers (TONs) and excellent diastereoselectivity (>99:1 d.r.). Mechanistic studies including density functional theory (DFT) calculations and intermolecular hydrogen atom abstraction (HAA) reactions reveal key reactive FeV‐alkylimido intermediates. The [FeV(Cor)(NAd)] (Ad = adamantyl) complex is independently prepared and characterized through electron paramagnetic resonance (EPR), resonance Raman (rR) measurement, and X‐ray photoelectron spectroscopy (XPS). This complex is reactive toward HAA reactions with kinetic isotope effects (KIEs) similar to [Fe(Cor)]‐catalyzed intramolecular C─H amination of alkyl azides.
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- 2024
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8. Patient perspectives on international multidisciplinary consensus criteria for chronic rhinosinusitis disease control
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Ryan A. Cotter, Firas A. Houssein, Rebecca K. Reinert, Katie M. Phillips, and Ahmad R. Sedaghat
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chronic rhinosinusitis ,consensus ,disease control ,patient perspectives ,qualitative study ,Otorhinolaryngology ,RF1-547 ,Surgery ,RD1-811 - Abstract
Abstract Objectives Recently, a set of consensus criteria and near‐consensus criteria for the evaluation of chronic rhinosinusitis (CRS) disease control was identified by an international multidisciplinary panel of key stakeholders. The objective of this study is to evaluate patient perspectives on these disease control criteria. Methods This is a qualitative phenomenological study using constant comparative methodology. Twenty‐one one‐on‐one interviews, ranging from 6 to 15 min and based on a standardized semi‐structured script, with CRS patients from diverse backgrounds were performed. The authors analyzed transcripts of the interviews to identify recurrent themes in patient responses. Conclusions were drawn based on these themes. Results All participants agreed with the consensus criteria (overall symptom severity, nasal obstruction severity, patients' self‐assessed CRS control, and need for CRS‐related oral corticosteroids), and most participants agreed with near‐consensus criteria (nasal endoscopy, smell loss and nasal drainage severities, impairment of day‐to‐day activities, and overall quality of life) identified by the international multidisciplinary panel. Some patients disagreed with inclusion of smell loss due to common etiologies—such as post‐viral or iatrogenic causes—that would not necessarily be an indicator of active sinonasal inflammation. One theme that emerged was the need for a facial pain/pressure criterion to be added. Conclusions CRS patients overwhelmingly affirmed recently described consensus and near‐consensus criteria for CRS disease control with the caveat that a question asking about facial pain/pressure should be included as well. Recently, identified consensus criteria for CRS disease control should be interpreted within the context of patient perspectives.
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- 2024
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9. Co‐Designing a Palliative Dementia Care Framework to Support Holistic Assessment and Decision Making: The EMBED‐Care Framework
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Nathan Davies, Elizabeth L. Sampson, Jesutofunmi Aworinde, Juliet Gillam, Charlotte Kenten, Kirsten Moore, Bethan Phillips, Catherine Harvey, Janet Anderson, Jane Ward, Catherine J. Evans, Clare Ellis‐Smith, and EMBED‐Care Team
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co‐design ,decision making ,dementia ,palliative care ,Medicine (General) ,R5-920 ,Public aspects of medicine ,RA1-1270 - Abstract
ABSTRACT Background People with dementia have complex palliative care needs that are often unmet, including physical and psycho‐social needs. It is essential to empower people with dementia, family carers and professionals to better assess and manage care needs. We aimed to co‐design a palliative dementia care Framework delivered through a digital app to support holistic assessment and decision making for care in the community and care homes—the EMBED‐Care Framework. Methods A systematic co‐design approach was adopted to develop the EMBED‐Care Framework across three stages: 1) Framework analysis to synthesise data from preceding evidence reviews, large routine clinical data and cohort studies of unmet palliative dementia care need; 2) Co‐design using iterative workshops with people with dementia, family carers and health and social care professionals to construct the components, design of the app and implementation requirements; and 3) User testing to refine the final Framework and app, and strengthen use for clinical practice and methods of evaluation. Results The Framework was co‐designed for delivery through an app delivered by aTouchAway. It comprised five main components: 1) holistic assessment of palliative care needs using the Integrated Palliative care Outcome Scale‐Dementia (IPOS‐Dem); 2) alert system of IPOS‐Dem scores to highlight unmet needs; 3) IPOS‐Dem scores and alerts enable shared decision making between the practitioner, patient and/or carer to support priority setting and goals of care; 4) evidence‐informed clinical decision support tools automatically linked with identified needs to manage care; and 5) Training package for users incorporating face‐to‐face sessions, clinical champions who received additional face‐to‐face sessions, animated videos and manual covering the main intervention components and email and telephone support from the research team. Conclusions This is a novel digital palliative dementia care intervention to link holistic assessment with clinical decision support tools that are practical and easy to use but address the complexity of palliative dementia care. The Framework is ready for feasibility testing and pilot studies for people with dementia residing at home or in a care home. Patient or Public Contribution We were guided by our Patient and Public Involvement (PPI) group consisting of three people with mild dementia, including younger onset dementia, and seven family carers throughout the project. They supported the overall development of the Framework, including planning of workshops, interpreting findings and testing the framework in our PPI meetings.
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- 2024
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10. Narwhal (Monodon monoceros) associations with Greenland summer meltwater release
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Kristin L. Laidre, Marie J. Zahn, Malene Simon, Michael Ladegaard, Kathleen M. Stafford, Elizabeth Phillips, Twila Moon, Harry L. Stern, and Benjamin Cohen
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glacier ,Greenland ,habitat modeling ,narwhal ,passive acoustics ,Ecology ,QH540-549.5 - Abstract
Abstract Climate change is rapidly transforming the coastal margins of Greenland. At the same time, there is increasing recognition that marine‐terminating glaciers provide unique and critical habitats to ice‐associated top predators. We investigated the connection between a top predator occupying glacial fjord systems in Northwest Greenland and the properties of Atlantic‐origin water and marine‐terminating glaciers through a multiyear interdisciplinary project. Using passive acoustic monitoring, we quantified the summer presence and autumn departure of narwhals (Monodon monoceros) at glacier fronts in Melville Bay and modeled what glacier fjord physical attributes are associated with narwhal occurrence. We found that narwhals are present at glacier fronts after Greenland Ice Sheet peak summer runoff and they remain there during the period when the water column is becoming colder and fresher. Narwhals occupied glacier fronts when ocean temperatures ranged from −0.6 to 0.8°C and salinities between 33.2 and 34.0 psu at around 200 m depth and they departed on their southbound migration between October and November. Narwhals' departure was approximately 4 weeks later in 2019 than in 2018, after an extreme 2019 summer heatwave event that also delayed sea ice formation by 2 months. Our study provides further support for the niche conservative narwhal's preference for cold ocean temperatures. These results may inform projections about how future changes will impact narwhal subpopulations, especially those occupying Greenland glacial fjords.
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- 2024
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11. Preclinical Direct Endoluminal Assessment of Endothelialization After Flow Diversion With Microangioscopy
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Visish M. Srinivasan, Roberto L. Garcia, Oleg Shekhtman, Ariadna Robledo, Tyler Lazaro, Abhijit Rao, Sean O'Leary, Adam Husain, Michael M. Covell, Michael Phillips, Phillip Cooper, Richard Forrest Duncan, Oscar Bolanos, Marco Colasurdo, Gautam Edhayan, Stephen R. Chen, Robert Fahed, and Peter Kan
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angiography ,angioscopy ,flow diversion ,flow diverter ,microangioscope ,microangioscopy ,Neurology. Diseases of the nervous system ,RC346-429 ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Background Direct endoluminal imaging, such as with our previously described microangioscope, is an emerging adjunct in endovascular cerebral aneurysm management that enables clinicians to delineate between thrombi and visualize neoepithelialization after stent placement with high resolution. The present study sought to study flow diversion in vivo under direct endoluminal imaging, and to validate our findings with histopathology. Methods In a rabbit model, we implanted each left common carotid artery with a shielded flow diverter (FD) (Medtronic Pipeline Vantage) and nonshielded FD (Medtronic Pipeline Flex) in the right common carotid artery. We studied 9 animals in 3 groups: (1) no periprocedural antiplatelet therapy, (2) aspirin 81 mg daily, and (3) aspirin 81 mg and clopidogrel 75 mg daily. FD thrombosis, stenosis, malapposition, and neoepithelialization were all evaluated by diagnostic cerebral angiography and microangioscopy after 30 days. Diagnostic cerebral angiography and angioscopic video were analyzed by independent evaluators and compared with histopathologic analysis. Results In the aspirin and dual antiplatelet therapy groups, there were no significant observed differences in stent thrombosis, stenosis, malapposition, or neoepithelialization between the shielded and non‐shielded FD groups. There was significantly more thrombus formation in Group 1. Neointimal thickness as measured by the microangioscope was highly correlated with histology (r = 0.72; P = 0.016). Interrater agreement of microangioscope videos was highest for FD thrombosis and stenosis. Conclusion In‐stent thrombosis, stenosis, malapposition, and neopithelialization demonstrated no significant difference between shielded and non‐shielded FDs. Microangioscopy measurements for neointimal thickness were highly correlated with pathology and may be a helpful adjunct to diagnostic cerebral angiography in FD follow‐up.
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- 2024
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12. Tolerance, adherence, and acceptability of a ketogenic 2.5:1 ratio, nutritionally complete, medium chain triglyceride‐containing liquid feed in children and adults with drug‐resistant epilepsy following a ketogenic diet
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Corbin Griffen, Natasha E. Schoeler, Robert Browne, Tracy Cameron, Martin Kirkpatrick, Seema Thowfeek, Judith Munn, Helena Champion, Nicole Mills, Siân Phillips, Linda Air, Anita Devlin, Claire Nicol, Susan Macfarlane, Victoria Bittle, Phillipa Thomas, Lisa Cooke, Julia Ackril, Astrid Allford, Vanessa Appleyard, Clare Szwec, Kiranjit Atwal, Gary P. Hubbard, and Rebecca J. Stratton
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enteral feed ,gastrointestinal tolerance ,ketogenic diet ,medium chain triglycerides ,seizures ,Neurology. Diseases of the nervous system ,RC346-429 - Abstract
Abstract Objective To investigate incorporating a ready‐to‐use 2.5:1 ratio liquid feed into a ketogenic diet (KD) in children and adults with drug‐resistant epilepsy. Methods Following a three‐day baseline, patients (n = 19; age: 19 years [SD 13], range: 8–46 years) followed a KD for 28 days (control period), then incorporated ≥200 mL/day of a ready‐to‐use liquid feed, made with a ratio of 2.5 g of fat to 1 g of protein plus carbohydrate and including medium chain triglycerides ([MCTs]; 25.6% of total fat/100 mL) for 28 days as part of their KD (intervention period). Outcome measures (control vs intervention period) included gastrointestinal (GI) tolerance, adherence to KD and intervention feed, dietary intake, blood ß‐hydroxybutyrate (BHB) concentration, seizure outcomes, health‐related quality of life (HRQoL), acceptability and safety. Results Compared to the control period, during the intervention period, the percentage of patients reporting no GI symptoms increased (+5% [SD 5], p = 0.02); adherence to the KD prescription was similar (p = 0.92) but higher in patients (n = 5) with poor adherence (
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- 2024
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13. Developing a comparative photon‐proton planning service in Victoria: the experience at Peter MacCallum Cancer Centre
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Roshini Gunewardena, Lisa Hall, Michelle Li, Gabrielle Drum, Dianna Le, Emily Nigro, Bridget Houlder, Claire Phillips, Greg Wheeler, Kirsty Wiltshire, Tomas Kron, and Adam Yeo
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Medical physics. Medical radiology. Nuclear medicine ,R895-920 - Abstract
Abstract Proton‐beam therapy (PBT) is a cutting‐edge radiation therapy modality that is currently not available in Australia. Comparative photon‐proton (CPP) planning is required for the medical treatment overseas programme (MTOP) and will be required for access to PBT in Australia in the future. Comparative planning brings professional development benefits to all members of the radiation therapy team. This service was also created to support future proposals for a PBT facility in Victoria. We report our experience developing an in‐house CPP service at Peter MacCallum Cancer Centre. A set of resources to support CPP planning was established. Training of relevant staff was undertaken after which an in‐house training programme was developed. A standard protocol for PBT planning parameters was established. All CPP plans were reviewed. Future goals for the CPP planning programme were described. In total, 62 cases were comparatively planned over 54 months. Of these, 60% were paediatric cases, 14% were adolescents and young adults (15–25 years) and 26% were adults. The vast majority (over 75%) of patients comparatively planned required irradiation to the central nervous system including brain and cranio‐spinal irradiation. A variety of proton plans were reviewed by international PBT experts to confirm their deliverability. Our team at Peter MacCallum Cancer Centre has gained significant experience in CPP planning and will continue to develop this further. Local expertise will help support decentralisation of patient selection for proton treatments in the near future and the PBT business case in Victoria.
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- 2024
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14. Is proton beam therapy always better than photon irradiation? Lessons from two cases
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Michelle P Li, Adam Yeo, Roshini Gunewardena, Gabrielle Drum, Kirsty Wiltshire, Claire Phillips, Joseph Sia, Greg Wheeler, and Lisa Hall
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Comparative treatment planning ,ependymoma ,optic pathway glioma ,paediatric radiotherapy ,proton beam therapy ,proton therapy ,Medical physics. Medical radiology. Nuclear medicine ,R895-920 - Abstract
Abstract Proton beam therapy (PBT) is increasingly used to treat cancers, especially in the paediatric and adolescent and young adult (AYA) population. As PBT becomes more accessible, determining when PBT should be used instead of photon irradiation can be difficult. There is a need to balance patient, tumour and treatment factors when making this decision. Comparing the dosimetry between these two modalities plays an important role in this process. PBT can reduce low to intermediate doses to organs at risk (OAR), but photon irradiation has its dosimetric advantages. We present two cases with brain tumours, one paediatric and one AYA, in which treatment plan comparison between photons and protons showed dosimetric advantages of photon irradiation. The first case was an 18‐month‐old child diagnosed with posterior fossa ependymoma requiring adjuvant radiotherapy. Photon irradiation using volumetric modulated arc therapy (VMAT) had lower doses to the hippocampi but higher doses to the pituitary gland. The second case was a 21‐year‐old with an optic pathway glioma. There was better sparing of the critical optic structures and pituitary gland using fractionated stereotactic radiation therapy over PBT. The dosimetric advantages of photon irradiation over PBT have been demonstrated in these cases. This highlights the role of proton‐to‐photon comparative treatment planning to better understand which patients might benefit from photon irradiation versus PBT.
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- 2024
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15. Tau maturation in the clinicopathological spectrum of Lewy body and Alzheimer's disease
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Sanaz Arezoumandan, Katheryn A.Q. Cousins, Daniel T. Ohm, MaKayla Lowe, Min Chen, James Gee, Jeffrey S. Phillips, Corey T. McMillan, Kelvin C. Luk, Andres Deik, Meredith A. Spindler, Thomas F. Tropea, Daniel Weintraub, David A. Wolk, Murray Grossman, Virginia Lee, Alice S. Chen‐Plotkin, Edward B. Lee, and David J. Irwin
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Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 ,Neurology. Diseases of the nervous system ,RC346-429 - Abstract
Abstract Objective Alzheimer's disease neuropathologic change and alpha‐synucleinopathy commonly co‐exist and contribute to the clinical heterogeneity of dementia. Here, we examined tau epitopes marking various stages of tangle maturation to test the hypotheses that tau maturation is more strongly associated with beta‐amyloid compared to alpha‐synuclein, and within the context of mixed pathology, mature tau is linked to Alzheimer's disease clinical phenotype and negatively associated with Lewy body dementia. Methods We used digital histology to measure percent area‐occupied by pathology in cortical regions among individuals with pure Alzheimer's disease neuropathologic change, pure alpha‐synucleinopathy, and a co‐pathology group with both Alzheimer's and alpha‐synuclein pathologic diagnoses. Multiple tau monoclonal antibodies were used to detect early (AT8, MC1) and mature (TauC3) epitopes of tangle progression. We used linear/logistic regression to compare groups and test the association between pathologies and clinical features. Results There were lower levels of tau pathology (β = 1.86–2.96, p
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- 2024
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16. The PI3Kδ inhibitor zandelisib on intermittent dosing in relapsed/refractory follicular lymphoma: Results from a global phase 2 study
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Andrew D. Zelenetz, Wojciech Jurczak, Vincent Ribrag, Kim Linton, Graham P. Collins, Javier L. Jiménez, Mark Bishton, Bhagirathbhai Dholaria, Andrea Mengarelli, Tycel J. Phillips, Nagendraprasad Sungala, Gerardo Musuraca, Oonagh Sheehy, Eric Van Den Neste, Mitsuhiko Odera, Lu Miao, Daniel P. Gold, Richard G. Ghalie, and Pier L. Zinzani
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Diseases of the blood and blood-forming organs ,RC633-647.5 - Abstract
Abstract In this global phase 2 study in patients with relapsed/refractory follicular lymphoma (FL), zandelisib was administered on intermittent dosing to mitigate immune‐related adverse events and infections that have been reported with oral PI3Kδ inhibitors administered daily continuously. Eligible patients with measurable disease and progression after at least two prior therapies were administered zandelisib until disease progression or intolerability. The primary efficacy endpoint was objective response rate (ORR) and the key secondary efficacy endpoint was duration of response (DOR). We report on 121 patients with FL administered zandelisib on intermittent dosing after 8 weeks of daily dosing for tumor debulking. The median number of prior therapies was 3 (range, 2–8) and 45% of patients had refractory disease. The ORR was 73% (95% confidence interval [CI], 63.9–80.4), the complete response (CR) rate was 38% (95% CI, 29.3–47.3), and the median DOR was 16.4 months (95% CI, 9.5–not reached). With a median follow‐up of 14.3 months (range, 1–30.5), the median progression‐free survival was 11.6 months (95% CI, 8.3–not reached). Twenty‐one patients (17%) discontinued therapy due to an adverse event. Grade 3–4 class‐related toxicities included 6% diarrhea, 5% lung infections, 3% colitis (confirmed by biopsy or imaging), 3% rash, 2% AST elevation, and 1% non‐infectious pneumonitis. Zandelisib achieved a high rate of durable responses in heavily pretreated patients with relapsed/refractory FL. The intermittent dosing resulted in a relatively low incidence of severe class‐related toxicities, which supports the evaluation of zandelisib as a single agent and in combination with indolent B‐cell malignancies.
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- 2024
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17. Vitamin B12 as a source of variability in isotope effects for chloroform biotransformation by Dehalobacter
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Elizabeth Phillips, Katherine Picott, Steffen Kümmel, Olivia Bulka, Elizabeth Edwards, Po‐Hsiang Wang, Matthias Gehre, Ivonne Nijenhuis, and Barbara S. Lollar
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biotransformation ,compound‐specific isotope analysis ,dual‐isotope analysis ,enzyme kinetics ,organohalide respiration ,reductive dechlorination ,Microbiology ,QR1-502 - Abstract
Abstract Carbon and chlorine isotope effects for biotransformation of chloroform by different microbes show significant variability. Reductive dehalogenases (RDase) enzymes contain different cobamides, affecting substrate preferences, growth yields, and dechlorination rates and extent. We investigate the role of cobamide type on carbon and chlorine isotopic signals observed during reductive dechlorination of chloroform by the RDase CfrA. Microcosm experiments with two subcultures of a Dehalobacter‐containing culture expressing CfrA—one with exogenous cobamide (Vitamin B12, B12+) and one without (to drive native cobamide production)—resulted in a markedly smaller carbon isotope enrichment factor (εC, bulk) for B12− (−22.1 ± 1.9‰) compared to B12+ (−26.8 ± 3.2‰). Both cultures exhibited significant chlorine isotope fractionation, and although a lower εCl, bulk was observed for B12− (−6.17 ± 0.72‰) compared to B12+ (−6.86 ± 0.77‰) cultures, these values are not statistically different. Importantly, dual‐isotope plots produced identical slopes of ΛCl/C (ΛCl/C, B12+ = 3.41 ± 0.15, ΛCl/C, B12− = 3.39 ± 0.15), suggesting the same reaction mechanism is involved in both experiments, independent of the lower cobamide bases. A nonisotopically fractionating masking effect may explain the smaller fractionations observed for the B12− containing culture.
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- 2024
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18. Beyond CREA: Evolutionary patterns of non‐allometric shape variation and divergence in a highly allometric clade of murine rodents
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Ariel E. Marcy, D. Rex Mitchell, Thomas Guillerme, Matthew J. Phillips, and Vera Weisbecker
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allometry ,CREA ,geometric morphometrics ,integration ,modularity ,Muridae ,Ecology ,QH540-549.5 - Abstract
Abstract The shared functions of the skull are thought to result in common evolutionary patterns in mammalian cranial shape. Craniofacial evolutionary allometry (CREA) is a particularly prominent pattern where larger species display proportionally elongate facial skeletons and smaller braincases. It was recently proposed that CREA arises from biomechanical effects of cranial scaling when diets are similar. Thus, deviations from CREA should occur with changes in cranial biomechanics, for example due to dietary change. Here, we test this using 3D geometric morphometric analysis in a dataset of Australian murine crania, which are highly allometric. We contrast allometric and non‐allometric variation in the cranium by comparing evolutionary mode, allometry, ordinations, as well as allometry, integration, and modularity in functional modules. We found evidence of stabilising selection in allometry‐containing and size‐free shape, and substantial non‐allometric variation aligned with dietary specialisation in parallel with CREA. Integration among cranial modules was higher, and modularity lower, with size included, but integration between rostrum and cranial vault, which are involved in the CREA pattern, dropped dramatically after size removal. Our results thus support the hypothesis that CREA is a composite arising from selection on cranial function, with substantial non‐allometric shape variation occurring alongside CREA where dietary specialisation impacts selection on gnawing function. This emphasises the need to research mammalian cranial evolution in the context of allometric and non‐allometric selection on biomechanical function.
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- 2024
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19. Sustained predation pressure may prevent the loss of anti‐predator traits from havened populations
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Natasha D. Harrison, Ben L. Phillips, Adrian F. Wayne, and Nicola J. Mitchell
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agitation ,Bettongia penicillata ogilbyi ,escape behaviour ,foraging ,giving‐up density ,prey naivete ,Ecology ,QH540-549.5 - Abstract
Abstract Conservation havens free of invasive predators are increasingly relied upon for fauna conservation, although havened populations can lose anti‐predator traits, likely making them less suitable for life ‘beyond the fence’. Sustaining low levels of mammalian predator pressure inside havens may prevent the loss of anti‐predator traits from havened populations. We opportunistically compared behavioural and morphological anti‐predator traits between four woylie (Bettongia penicillata ogilbyi) populations– one haven isolated from all mammalian predators, one haven containing a native mammalian predator (chuditch; Dasyurus geoffroii), and their respective non‐havened counterparts (each containing both chuditch and invasive predators). Havened woylies existing without mammalian predators were smaller (shorter hindfeet, smaller body weight) and less reactive (consumed more food from fox‐treated and control feeding stations, less agitated during human handling) than a non‐havened reference population. However, in the haven containing chuditch, we found no difference in behaviour or morphology compared to the adjacent non‐havened population. Across populations, anti‐predator responses tended to appear stronger at sites with higher predator activity, suggestive of an adaptive response across a gradient of predation pressure. Our findings suggest that maintaining mammalian predation pressure in conservation havens could be effective for preventing or slowing the loss of anti‐predator traits from these populations.
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- 2024
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20. Motor and sensory impairment in survivors of childhood central nervous system (CNS) tumors in the St. Jude Lifetime Cohort (SJLIFE)
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Rozalyn L. Rodwin, Fang Wang, Lu Lu, Zhenghong Li, Deo Kumar Srivastava, Nicholas S. Phillips, Raja B. Khan, Tara M. Brinkman, Kevin R. Krull, Frederick A. Boop, Gregory T. Armstrong, Thomas E. Merchant, Amar Gajjar, Leslie L. Robison, Melissa M. Hudson, Nina S. Kadan‐Lottick, and Kirsten K. Ness
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central nervous system tumor ,childhood cancer ,cranial radiation ,etoposide ,motor impairment ,peripheral neuropathy ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Background Survivors of childhood central nervous system (CNS) tumors can develop motor and sensory impairment from their cancer and treatment history. We estimated the prevalence of motor and sensory impairment in survivors compared with controls through clinical assessment and identified associated treatment exposures and functional, quality of life (QOL), and social outcomes. Methods Survivors of childhood CNS tumors from the St. Jude Lifetime Cohort (n = 378, median [range] age 24.0 [18.0–53.0] years, 43.4% female) ≥5 years from diagnosis and controls (n = 445, median [range] age 34.0 [18.0–70.0] years, 55.7% female) completed in‐person evaluation for motor and sensory impairment using the modified Total Neuropathy Score. Impairment was graded by modified Common Terminology Criteria for Adverse Events. Multivariable models estimated associations between grade ≥2 motor/sensory impairment, individual/treatment characteristics, and secondary outcomes (function by Physical Performance Test, fitness by physiologic cost index, QOL by Medical Outcomes Survey Short Form‐36 physical/mental summary scores, social attainment). Results Grade ≥2 motor or sensory impairment was more prevalent in survivors (24.1%, 95% Confidence Interval [CI] 19.8%–29.4%) than controls (2.9%, CI 1.4–4.5%). Among survivors, in multivariable models, motor impairment was associated with vinca exposure 2036 mg/m2 versus none (OR 12.61, CI 2.19–72.72). Sensory impairment was associated with older age at diagnosis (OR 1.09, CI 1.01–1.16) and craniospinal irradiation versus none (OR 4.39, CI 1.68–11.50). There were lower odds of motor/sensory impairment in survivors treated in the year 2000 or later versus before 1990 (Motor: OR 0.29, CI 0.10–0.84, Sensory: OR 0.35, CI 0.13–0.96). Motor impairment was associated with impaired physical QOL (OR 2.64, CI 1.22–5.72). Conclusions In survivors of childhood CNS tumors, motor and sensory impairment is prevalent by clinical assessment, especially after exposure to etoposide, vinca, or craniospinal radiation. Treating motor impairment may improve survivors' QOL.
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- 2024
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21. Variant calling in polyploids for population and quantitative genetics
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Alyssa R. Phillips
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mixed ploidy ,polyploidy ,population genetics ,quantitative genetics ,variant calling ,whole genome sequence ,Biology (General) ,QH301-705.5 ,Botany ,QK1-989 - Abstract
Abstract Advancements in genome assembly and sequencing technology have made whole genome sequence (WGS) data and reference genomes accessible to study polyploid species. Compared to popular reduced‐representation sequencing approaches, the genome‐wide coverage and greater marker density provided by WGS data can greatly improve our understanding of polyploid species and polyploid biology. However, biological features that make polyploid species interesting also pose challenges in read mapping, variant identification, and genotype estimation. Accounting for characteristics in variant calling like allelic dosage uncertainty, homology between subgenomes, and variance in chromosome inheritance mode can reduce errors. Here, I discuss the challenges of variant calling in polyploid WGS data and discuss where potential solutions can be integrated into a standard variant calling pipeline.
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- 2024
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22. Invertebrate diversity in groundwater‐filled lava caves is influenced by both neutral‐ and niche‐based processes
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Bjarni K. Kristjánsson, Doriane Combot, Anett Reilent, Joseph S. Phillips, and Camille A.‐L. Leblanc
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benthic ,Cladocera ,epibenthic ,isolation ,small populations ,Ecology ,QH540-549.5 - Abstract
Abstract Understanding which factors shape and maintain biodiversity is essential to understand how ecosystems respond to crises. Biodiversity observed in ecological communities is a result of the interaction of various factors which can be classified as either neutral‐ or niche‐based. The importance of these processes has been debated, but many scientists believe that both processes are important. Here, we use unique ecosystems in groundwater‐filled lava caves near Lake Mývatn, to examine the importance of neutral‐ versus niche‐based factors for shaping invertebrate communities. We studied diversity in benthic and epibenthic invertebrate communities and related them to ecological variables. We hypothesized that if neutral processes are the main drivers of community structure we would not see any clear relationship between the structure of community within caves and ecological factors. If niche‐based processes are important we should see clear relationships between community structure and variation in ecological variables across caves. Both communities were species poor, with low densities of invertebrates, showing the resource limited and oligotrophic nature of these systems. Unusually for Icelandic freshwater ecosystems, the benthic communities were not dominated by Chironomidae (Diptera) larvae, but rather by crustaceans, mainly Cladocera. The epibenthic communities were not shaped by environmental variables, suggesting that they may have been structured primarily by neutral processes. The benthic communities were shaped by the availability of energy, and to some extent pH, suggesting that niche‐based processes were important drivers of community structure, although neutral processes may still be relevant. The results suggest that both processes are important for invertebrate communities in freshwater, and research should focus on understanding both of these processes. The ponds we studied are representative of a number of freshwater ecosystems that are extremely vulnerable for human disturbance, making it even more important to understand how their biodiversity is shaped and maintained.
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- 2024
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23. Characterization of low‐grade epilepsy‐associated tumor from implanted stereoelectroencephalography electrodes
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Taylor A. Gatesman, Jasmine L. Hect, H. Westley Phillips, Brenden J. Johnson, Abigail I. Wald, Colleen McClung, Marina N. Nikiforova, John M. Skaugen, Ian F. Pollack, Taylor J. Abel, and Sameer Agnihotri
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LEATs ,methylation ,mutation ,sEEG ,Neurology. Diseases of the nervous system ,RC346-429 - Abstract
Abstract Low‐grade epilepsy‐associated tumors (LEATs) are a common cause of drug‐resistant epilepsy in children. Herein, we demonstrate the feasibility of using tumor tissue derived from stereoelectroencephalography (sEEG) electrodes upon removal to molecularly characterize tumors and aid in diagnosis. An 18‐year‐old male with focal epilepsy and MRI suggestive of a dysembryoplastic neuroepithelial tumor (DNET) in the left posterior temporal lobe underwent implantation of seven peri‐tumoral sEEG electrodes for peri‐operative language mapping and demarcation of the peri‐tumoral ictal zone prior to DNET resection. Using electrodes that passed through tumor tissue, we show successful isolation of tumor DNA and subsequent analysis using standard methods for tumor classification by DNA, including Glioseq targeted sequencing and DNA methylation array analysis. This study provides preliminary evidence for the feasibility of molecular diagnosis of LEATs or other lesions using a minimally invasive method with microscopic tissue volumes. The implications of sEEG electrodes in tumor characterization are broad but would aid in diagnosis and subsequent targeted therapeutic strategies.
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- 2024
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24. Comparison of magnetic resonance‐guided laser interstitial thermal therapy corpus callosum ablation to open microsurgical corpus callosotomy: A single‐center retrospective cohort study
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H. Westley Phillips, Jasmine L. Hect, Emily Harford, Evelyn Pan, and Taylor J. Abel
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atonic seizures ,laser ablation ,pediatric drug‐resistant epilepsy ,seizure outcomes ,Neurology. Diseases of the nervous system ,RC346-429 - Abstract
Abstract Objective Corpus callosotomy (CC) is an important treatment for atonic seizures in patients with generalized or multifocal drug‐resistant epilepsy (DRE). Traditionally, CC is performed via an open microsurgical approach, but more recently, MR‐guided stereotactic laser interstitial thermal therapy (LITT) corpus callosum ablation (CCA) has been developed to leverage the safety and minimally invasive nature of LITT. Given the recent adoption of CCA at select centers, how CCA compares to CC is unknown. We aim to compare the clinical seizure outcomes of CCA and CC after extended follow‐up. Methods We performed a retrospective cohort study to compare the effectiveness and safety of CC to CCA from 1994 to 2022. The primary outcome was a 50% reduction in target seizure. Secondary outcome measures were postoperative length of stay, adverse events, and other effectiveness metrics. Comparative statistics were executed using Stata. Normality for continuous variables was assessed, and parametric statistics were utilized as needed. Frequency was compared with chi‐squared or Fischer's exact tests, when applicable. Results Data from 47 operations performed on 36 patients were included in this study, of which 13 (36%) patients underwent 17 CCA. Patients who received CCA had similar rates of meaningful reduction (>50%) of atonic seizures as their CC counterparts (55% vs 70% P = 0.15). Patients undergoing CCA had significantly shorter hospitalizations than those receiving CC (2.5 vs 6.0 days P
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- 2024
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25. Birds are not the only ones impacted by guidance to cease bird feeding
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Ashley A. Dayer, P. Christy Pototsky, Richard J. Hall, Dana M. Hawley, Tina B. Phillips, David N. Bonter, Alia M. Dietsch, Emma Greig, and Wesley M. Hochachka
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avian disease ,bird feeding ,fish and wildlife agency ,human–wildlife interaction ,mental well‐being ,social–ecological systems ,Human ecology. Anthropogeography ,GF1-900 ,Ecology ,QH540-549.5 - Abstract
Abstract Humans have a particularly strong connection with birds, driving the enormous popularity of residential bird feeding in much of the world. We conducted a web search to document US state wildlife management agency responses to two recent avian disease outbreaks, finding that 23 agencies made recommendations to cease feeding wild birds in 2021–2022. The psychological benefits of bird feeding for humans are well‐documented but often overlooked in management decisions in response to avian disease outbreaks. Likewise, ecological evidence does not necessarily support ceasing bird feeding to reduce the spread of every avian disease. Ecological and social science need to be applied in tandem to ensure that well‐intended guidance to cease feeding of birds does not have unintended consequences.
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- 2024
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26. Urinary comprehensive genomic profiling predicts urothelial carcinoma recurrence and identifies responders to intravesical therapy
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Goran Rac, Hiten D. Patel, Christopher James, Shalin Desai, Vincent M. Caruso, Daniel S. Fischer, Peter S. Lentz, Ceressa T. Ward, Brian C. Mazzarella, Kevin G. Phillips, Chirag Doshi, Vincent T. Bicocca, Trevor G. Levin, Alan J. Wolfe, and Gopal N. Gupta
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Bacillus Calmette‐Guérin ,bladder cancer ,genomics ,intravesical instillation ,personalized medicine ,risk assessment ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Intravesical therapy (IVT) is the standard of care to decrease risk of recurrence and progression for high‐grade nonmuscle‐invasive bladder cancer. However, post‐IVT recurrence remains common and the ability to risk‐stratify patients before or after IVT is limited. In this prospectively designed and accrued cohort study, we examine the utility of urinary comprehensive genomic profiling (uCGP) for predicting recurrence risk following transurethral resection of bladder tumor (TURBT) and evaluating longitudinal IVT response. Urine was collected before and after IVT instillation and uCGP testing was done using the UroAmp™ platform. Baseline uCGP following TURBT identified patients with high (61%) and low (39%) recurrence risk. At 24 months, recurrence‐free survival (RFS) was 100% for low‐risk and 45% for high‐risk patients with a hazard ratio (HR) of 9.3. Longitudinal uCGP classified patients as minimal residual disease (MRD) Negative, IVT Responder, or IVT Refractory with 24‐month RFS of 100%, 50%, and 32%, respectively. Compared with MRD Negative patients, IVT Refractory patients had a HR of 10.5. Collectively, uCGP enables noninvasive risk assessment of patients following TURBT and induction IVT. uCGP could inform surveillance cystoscopy schedules and identify high‐risk patients in need of additional therapy.
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- 2024
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27. Exploring the utility of bedside tests for predicting cardiorespiratory fitness in older adults
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Laura Carrick, Brett Doleman, Joshua Wall, Amanda Gates, Jon N. Lund, John P. Williams, and Bethan E. Phillips
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aging ,function ,muscle ,strength ,ultrasound ,Geriatrics ,RC952-954.6 - Abstract
Abstract Objectives Cardiorespiratory fitness (CRF) declines with advancing and has also, independent of age, been shown to be predictive of all‐cause mortality, morbidity, and poor clinical outcomes. In relation to the older patient, there is a particular wealth of evidence highlighting the relationship between low CRF and poor surgical outcomes. Cardiopulmonary exercise testing (CPET) is accepted as the gold‐standard measure of CRF. However, this form of assessment has significant personnel and equipment demands and is not feasible for those with certain age‐associated physical limitations, including joint and cardiovascular comorbidities. As such, alternative ways to assess the CRF of older patients are very much needed. Methods Sixty‐four participants (45% female) with a median age of 74 (65–90) years were recruited to this study via community‐based advertisements. All participants completed three tests of physical function: (1) a step‐box test; (2) handgrip strength dynamometry; and (3) a CPET on a cycle ergometer; and also had their muscle architecture (vastus lateralis) assessed by B‐mode ultrasonography to provide measures of muscle thickness, pennation angle, and fascicle length. Multivariate linear regression was then used to ascertain bedside predictors of CPET parameters from the alternative measures of physical function and demographic (age, gender, body mass index (BMI)) data. Results There was no significant association between ultrasound‐assessed parameters of muscle architecture and measures of CRF. VO2peak was predicted to some extent from fast step time during the step‐box test, gender, and BMI, leading to a model that achieved an R2 of 0.40 (p
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- 2024
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28. Evaluating the impact of generative adversarial models on the performance of anomaly intrusion detection
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Mohammad Arafah, Iain Phillips, and Asma Adnane
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computer network security ,data mining ,feature selection ,learning (artificial intelligence) ,pattern classification ,Telecommunication ,TK5101-6720 - Abstract
Abstract With the increasing rate and types of cyber attacks against information systems and communication infrastructures, many tools are needed to detect and mitigate against such attacks, for example, Intrusion Detection Systems (IDSs). Unfortunately, traditional Signature‐based IDSs (SIDSs) perform poorly against previously unseen adversarial attacks. Anomaly‐based IDSs (AIDSs) use Machine Learning (ML) and Deep Learning (DL) approaches to overcome these limitations. However, AIDS performance can be poor when trained on imbalanced datasets. To address the challenge of AIDS performance caused by these unbalanced training datasets, generative adversarial models are proposed to obtain adversarial attacks from one side and analyse their quality from another. According to extensive usage and reliability criteria for generative adversarial models in different disciplines, Generative Adversarial Networks (GANs), Bidirectional GAN (BiGAN), and Wasserstein GAN (WGAN) are employed to serve AIDS. The authors have extensively assessed their abilities and robustness to deliver high‐quality attacks for AIDS. AIDSs are constructed, trained, and tuned based on these models to measure their impacts. The authors have employed two datasets: NSL‐KDD and CICIDS‐2017 for generalisation purposes, where ML and DL approaches are utilised to implement AIDSs. Their results show that the WGAN model outperformed GANs and BiGAN models in binary and multiclass classifications for both datasets.
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- 2024
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29. The presence of busulfan metabolites and pharmacometabolomics in plasma drawn immediately before allograft infusion in hematopoietic cell transplant recipients
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Jeannine S. McCune, Sandi L. Navarro, Linda J. Risler, Brian R. Phillips, Suping Ren, H. Gary Schoch, and K. Scott Baker
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Therapeutics. Pharmacology ,RM1-950 ,Public aspects of medicine ,RA1-1270 - Abstract
Abstract Busulfan is hepatically metabolized through glutathione (GSH) conjugation; in vitro, this process depletes hepatocyte GSH stores and generates the cytotoxic metabolite γ‐glutamyldehydroalanylglycine, which is too unstable to be quantitated in vivo. We sought to evaluate if pre‐graft (i.e., immediately before allograft infusion) concentrations of busulfan metabolites' and of endogenous metabolomic compounds (EMCs) representing the glutathione pathway were associated with clinical outcomes in hematopoietic cell transplant (HCT) recipients receiving busulfan. The clinical outcomes evaluated were relapse, acute graft versus host disease (GVHD), chronic GVHD, non‐relapse mortality, and neutrophil nadir. In pre‐graft samples obtained from patients immediately before allograft infusion, our objectives were to evaluate for: (1) the presence of busulfan and its metabolites tetrahydrothiophenium ion (THT+), tetrahydrothiophene 1‐oxide, sulfolane, and 3‐hydroxysulfolane (N = 124); (2) EMCs using a global metabolomics assay (N = 77); and (3) the association of the busulfan metabolites and the EMCs with clinical outcomes. In the pre‐graft samples, busulfan and THT+ could not be detected. THT 1‐oxide, sulfolane, and 3‐hydroxysulfolane were quantitated in 9.6%, 26%, and 58% of pre‐graft samples; their concentrations were not associated with clinical outcomes. Four pre‐graft EMCs were statistically significantly associated with the neutrophil nadir. The pre‐graft EMCs were not associated with the other clinical outcomes. In conclusion, busulfan's metabolites are present in patients' plasma immediately before allograft infusion; the neutrophil nadir is associated with pre‐graft EMCs. Future research should investigate the association of clinical outcomes with the concentrations of busulfan's metabolites and EMCs in the pre‐graft plasma from allogeneic HCT recipients.
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- 2023
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30. Evolutionary predictions for a parasite metapopulation: Modelling salmon louse resistance to pest controls in aquaculture
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Andrew Coates, Nicholas A. Robinson, Tim Dempster, Ingrid Johnsen, and Ben L. Phillips
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evolution model ,integrated pest management ,meta‐population ,pesticide resistance ,sea lice ,Evolution ,QH359-425 - Abstract
Abstract Pests often evolve resistance to pest controls used in agriculture and aquaculture. The rate of pest adaptation is influenced by the type of control, the selective pressure it imposes, and the gene flow between farms. By understanding how these factors influence evolution at the metapopulation level, pest management strategies that prevent resistance from evolving can be developed. We developed a model for the metapopulation and evolutionary dynamics of the salmon louse (Lepeophtheirus salmonis), which is a major parasite affecting salmon aquaculture. Different management scenarios were simulated across a network of salmon farms covering half of Norway, and their effects on louse epidemiology and evolution were investigated. We compared louse controls that differed in how they were deployed through time (discrete vs. continuous), how they impacted the louse life cycle, and in their overall efficacy. We adjusted the strength of selection imposed by treatments, the dominance effect of the resistant allele, and the geographic location at which resistance originated. Continuously acting strategies (e.g., louse‐resistant salmon) were generally more effective than discrete strategies at controlling lice, especially when they increased louse mortality during early developmental stages. However, effective strategies also risked imposing frequent and/or strong selection on lice, thus driving rapid adaptation. Resistant alleles were more likely to be lost through genetic drift when they were recessive, had a low‐fitness advantage, or originated in low‐farm‐density areas. The north‐flowing current along the Norwegian coastline dispersed resistant genes from south to north, and limited gene flow in the opposite direction. We demonstrate how evolutionary models can produce quantitative predictions over large spatial and temporal scales and for a range of pest control scenarios. Quantitative outputs can be translated into practical management decisions applied at a regional level to minimise the risk of resistance developing.
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- 2023
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31. Bisphosphonates attenuate age‐related muscle decline in Caenorhabditis elegans
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Luke Slade, Shelby E. Bollen, Joseph J. Bass, Bethan E. Phillips, Kenneth Smith, Daniel J. Wilkinson, Nathaniel J. Szewczyk, Philip J. Atherton, and Timothy Etheridge
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Healthspan ,Lifespan ,Muscle ,Sarcopenia ,Zoledronic acid ,Diseases of the musculoskeletal system ,RC925-935 ,Human anatomy ,QM1-695 - Abstract
Abstract Background Age‐related muscle decline (sarcopenia) associates with numerous health risk factors and poor quality of life. Drugs that counter sarcopenia without harmful side effects are lacking, and repurposing existing pharmaceuticals could expedite realistic clinical options. Recent studies suggest bisphosphonates promote muscle health; however, the efficacy of bisphosphonates as an anti‐sarcopenic therapy is currently unclear. Methods Using Caenorhabditis elegans as a sarcopenia model, we treated animals with 100 nM, 1, 10, 100 and 500 μM zoledronic acid (ZA) and assessed lifespan and healthspan (movement rates) using a microfluidic chip device. The effects of ZA on sarcopenia were examined using GFP‐tagged myofibres or mitochondria at days 0, 4 and 6 post‐adulthood. Mechanisms of ZA‐mediated healthspan extension were determined using combined ZA and targeted RNAi gene knockdown across the life‐course. Results We found 100 nM and 1 μM ZA increased lifespan (P 0.05), whereas 100 and 500 μM ZA were larval lethal. ZA (1 μM) significantly improved myofibrillar structure on days 4 and 6 post‐adulthood (83 and 71% well‐organized myofibres, respectively, vs. 56 and 34% controls, P 0.05). Life/healthspan was extended through knockdown of igdb‐1/FNDC5 (635 ± 10 vs. 523 ± 10% population activity AUC in gene knockdown vs. untreated controls, P 0.05]. Conversely, let‐756/FGF21 and sir‐2.2/SIRT‐4 were dispensable for ZA‐induced healthspan [630 ± 6 vs. 523 ± 10% population activity AUC in knockdown + 1 μM ZA vs. untreated controls, P
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- 2023
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32. 2024 Solar Eclipse For Dummies
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Cynthia Phillips, Shana Priwer
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- 2024
33. Astrophysics For Dummies
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Cynthia Phillips, Shana Priwer
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- 2024
34. Flow depth estimates and avulsion behaviour in alluvial stratigraphy (Willwood Formation, Bighorn Basin, Wyoming, USA)
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Brady Z. Foreman, Grace M. Sutherland, Delaney J. Todd, Kristopher D. Phillips, and Anthony Semeraro
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avulsion ,fluvial ,Laramide ,Palaeogene ,Western Interior ,Geology ,QE1-996.5 - Abstract
Abstract The size and geometry of river channels play a central role in sediment transport and the character of deposition within alluvial basins across spatiotemporal scales spanning the initiation of grain movement to the filling of accommodation generated by subsidence. This study compares several different approaches to estimating palaeoflow depths from fluvial deposits in the early Palaeogene Willwood Formation of north‐west Wyoming, USA. Fluvial story heights (n = 60) and mud plug thicknesses (n = 13) are statistically indistinguishable from one another and yield palaeoflow depth estimates of 4 to 6 m. The vertical relief on bar clinoforms (n = 112) yields smaller flow depths, by a factor of ca 0.3, with the exception that the largest bar clinoforms match story heights and mud plug estimates. This observation is consistent with modern river data sets that indicate unit bar clinoforms do not capture the reach‐mean bank‐full flow depths except in rare circumstances. Future studies should use story heights (i.e. compound bar deposits) and mud plugs to estimate bank‐full flow depths in alluvial strata. Additionally, the thickness of multi‐storied fluvial sandbodies (n = 102) and overbank cycles composed of paired crevasse splay and palaeosol deposits (n = 45) were compared. The two depositional units display statistically indistinguishable mean and median values. Building upon previous depositional models, these observations suggest basin rivers aggraded approximately one flow depth prior to major avulsion. This avulsion process generated widespread crevasse splay deposition across the floodplain. Once the main river channel stem was reestablished, overbank flooding and palaeosol development dominated floodplain settings. The depositional model implies river aggradation autogenically generated topography in the basin that was effectively filled during the subsequent avulsion. This constitutes a meso‐timescale (103–104 years) compensational pattern driven by morphodynamics that may account for the high completeness of fossil and palaeoclimate records recovered from the basin.
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- 2023
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35. Presumptive phenobarbital‐induced systemic lupus erythematosus in a domestic dog
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Erin Phillips, Matthew Kornya, Allison Collier, Maureen Barry, Katherine Morrison, and Felipe Reggeti
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autoimmunity ,CNS disorders ,drug reaction ,epilepsy ,immunology ,lupus ,Veterinary medicine ,SF600-1100 - Abstract
Abstract Case Description We describe a case of presumptive acquired systemic lupus erythematosus secondary to phenobarbital administration in a dog, which resolved with withdrawal of the drug. Clinical Findings A 3.5 year‐old poodle presented to a veterinary teaching hospital for Tier 1 idiopathic epilepsy and was treated with phenobarbital. The dog experienced fever, multiple cytopenias, and proteinuria in conjunction with a positive antinuclear antibody (ANA) titer. Diagnostics Serial CBCs, urine protein : creatinine ratios, and sternal bone marrow aspirates were performed to evaluate improvement. Treatment and Outcome Phenobarbital was withdrawn and levetiracetam initiated. All abnormalities resolved with supportive care, without initiation of immunosuppressive drugs. All cytopenias and proteinuria resolved and ANA test results became negative within 3 months. The patient recovered and did well clinically. Clinical Relevance Systemic lupus erythematosus is a disease of multiple autoimmune syndromes occurring concurrently or sequentially in conjunction with the presence of circulating ANA. It has been well described in dogs as an idiopathic condition, but in human medicine may occur secondary to drug reactions (drug‐associated lupus) including as a reaction to phenobarbital. The findings in our case are consistent with the criteria for drug‐induced lupus in humans and we suggest it as the first report of phenobarbital‐induced lupus in a dog.
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- 2023
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36. Long‐term outcomes of second‐line versus later‐line zanubrutinib treatment in patients with relapsed/refractory mantle cell lymphoma: An updated pooled analysis
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Yuqin Song, Keshu Zhou, Dehui Zou, Dengju Li, Jianda Hu, Haiyan Yang, Huilai Zhang, Jie Ji, Wei Xu, Jie Jin, Fangfang Lv, Ru Feng, Sujun Gao, Daobin Zhou, Constantine S. Tam, David Simpson, Michael Wang, Tycel J. Phillips, Stephen Opat, Cheng Fang, Shaohui Sun, and Jun Zhu
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mantle cell lymphoma ,overall survival ,pooled analysis ,second‐line therapy ,zanubrutinib ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Background We previously reported results of a pooled analysis of two zanubrutinib studies in relapsed or refractory (R/R) MCL showing better survival outcomes when zanubrutinib is used in second‐line versus later‐line. Here, we present an updated pooled analysis with a longer follow‐up of 35.2 months. Methods Data were pooled from two studies—BGB‐3111‐AU‐003 (NCT02343120) and BGB‐3111‐206 (NCT03206970) of zanubrutinib in R/R MCL. The patients were divided into two groups based on the treatment line of zanubrutinib: the second‐line and the later‐line group. The inverse propensity score weighting method was used to balance the baseline covariates between the groups. The primary outcome was overall survival (OS). Secondary outcomes included progression‐free survival (PFS), PFS, and OS rates, objective response rate (ORR), duration of response (DOR), and safety. Results Among 112 pooled patients, 41 (36.6%) patients received zanubrutinib as second‐line and 71 (63.4%) patients as later‐line therapy. After weighting, OS was significantly improved in the second‐line versus later‐line group (HR, 0.459 [95% CI: 0.215, 0.98]; p = 0.044) with median OS not estimable in both groups. The PFS was similar between the two groups (HR, 0.78 [95% CI: 0.443, 1.373]; p = 0.389) but with numerically longer median PFS in the second‐line versus later‐line group (27.8 vs. 22.1 months). ORR was numerically higher in the second‐line versus later‐line (88.6% vs. 85.7%), and DOR was similar between the two groups (25.2 vs. 25.1 months). Zanubrutinib showed a similar safety profile in both groups. Conclusion Zanubrutinib in second‐line treatment was associated with significantly improved OS compared with later‐line treatment of R/R MCL.
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- 2023
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37. Translation, cultural adaptation and validation of the Swahili Pain Catastrophizing Scale among refugees who survived torture and/or war trauma in Kenya: An observational study
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Jepkemoi J. Kibet, Joliana S. Phillips, Mariem C. Latrous, Hanan Khalil, and Linzette D. Morris
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cross‐cultural adaptation/validation ,Kenya ,pain catastrophization scale ,refugees ,survivors of torture ,Medicine - Abstract
Abstract Background and Aims Accurate assessment of any patient relies on the use of appropriate measurements which are culturally‐ and linguistically‐applicable and valid. The following study aimed to translate, cross‐culturally adapt and test the nomological validity, structural validity, internal consistency, test‐retest reliability, sensitivity‐to‐change and feasibility of the Swahili version of the Pain Catastrophizing Scale (Swa‐PCS) among refugees who survived torture/war trauma living with chronic pain in Kenya. Methods An observational study was conducted. Translation and cultural adaptation of the original PCS for the Swahili‐speaking refugee population in Kenya, who survived torture or war trauma was undertaken. Following this process, a validation study was conducted on the newly‐adapted instrument, to ascertain the psychometric properties (nomological validity, structural validity, internal consistency, test‐retest reliability, sensitivity‐to change, and ceiling and floor effects). Results Fifty participants were included in this study. Correlations between pain catastrophization and fear‐avoidance behavior measures were significant (r = 0.538, p
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- 2024
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38. Gene expression, evolution, and the genetics of electrosensing in the smalltooth sawfish, Pristis pectinata
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Taiya M. Jarva, Nicole M. Phillips, Cory Von Eiff, Gregg R. Poulakis, Gavin Naylor, Kevin A. Feldheim, and Alex S. Flynt
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conservation ,electrosensing ,evolution ,sawfish ,transcriptome ,Ecology ,QH540-549.5 - Abstract
Abstract Sawfishes (Pristidae) are large, highly threatened rays named for their tooth‐studded rostrum, which is used for prey sensing and capture. Of all five species, the smalltooth sawfish, Pristis pectinata, has experienced the greatest decline in range, currently found in only ~20% of its historic range. To better understand the genetic underpinnings of these taxonomically and morphologically unique animals, we collected transcriptomic data from several tissue types, mapped them to the recently completed reference genome, and contrasted the patterns observed with comparable data from other elasmobranchs. Evidence of positive selection was detected in 79 genes in P. pectinata, several of which are involved in growth factor/receptor tyrosine kinase signaling and body symmetry and may be related to the unique morphology of sawfishes. Changes in these genes may impact cellular responses to environmental conditions such as temperature, dissolved oxygen, and salinity. Data acquired also allow for examination of the molecular components of P. pectinata electrosensory systems, which are highly developed in sawfishes and have likely been influential in their evolutionary success.
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- 2024
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39. Assessing wild turkey productivity before and after a 14‐day delay in the start date of the spring hunting season in Tennessee
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Joseph O. Quehl, Lindsey M. Phillips, Vincent M. Johnson, Craig A. Harper, Joseph D. Clark, Roger D. Shields, and David A. Buehler
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hunting‐season framework ,Meleagris gallopavo ,regulation changes ,reproduction ,southeastern U.S. ,telemetry ,Ecology ,QH540-549.5 - Abstract
Abstract Ten state wildlife management agencies in the United States, including six within the Southeast, have delayed their spring wild turkey (Meleagris gallopavo) hunting seasons since 2017 by five or more days to address concerns related to the potential effects of hunting on wild turkey seasonal productivity. One hypothesis posits that if the spring hunting season is too early, there may be insufficient time for males to breed hens before being harvested, thus leading to reduced seasonal productivity. We conducted an experiment to determine whether delaying the wild turkey hunting season by 2 weeks in south‐middle Tennessee would affect various reproductive rates. In 2021 and 2022, the Tennessee Fish and Wildlife Commission experimentally delayed the spring hunting season to open 14 days later than the traditional date (the Saturday closest to 1 April) in Giles, Lawrence, and Wayne counties. We monitored reproductive rates from 2017 to 2022 in these three counties as well as two adjacent counties, Bedford and Maury, that were not delayed. We used a Before‐After‐Control‐Impact design to analyze the proportion of hens nesting, clutch size, hatchability, nest success, poult survival and hen survival with linear mixed‐effect models and AIC model selection to detect relationships between the 14‐day delay and reproductive parameters. We detected no relationship (p > .05) between the 14‐day delay and any individual reproductive parameter. In addition, recruitment (hen poults per hen that survived until the next breeding season) was very low (
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- 2024
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40. Effects of stocking density during simulated transport on physiology and behavior of largemouth bass (Micropterus salmoides)
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Yifei Yang, Edward Narayan, Sonia Rey Planellas, Clive J. C. Phillips, Lu Zheng, Bingying Xu, Lei Wang, Yuechong Liu, Yuxiao Sun, Gladstone Sagada, Hao‐Yu Shih, Qingjun Shao, and Kris Descovich
- Subjects
behavior ,fish welfare ,largemouth bass ,physiology ,simulated transport ,skin mucus cortisol ,Aquaculture. Fisheries. Angling ,SH1-691 - Abstract
Abstract The live transport of farmed fish is an important practice in Chinese aquaculture due to consumer preferences in its domestic market. However, live transport can be stressful for fish and may cause many welfare issues. This study aimed to examine the effects of transport density on the welfare of largemouth bass (Micropterus salmoides). Adult fish were allocated to four experimental treatments in a two‐factor design (N = 5 groups per treatment). Factor one was stocking density of either 39 (low density) or 78 (high density) g L−1. Factor two was transport, with half of the fish groups exposed to simulated transport stress for 3 h using a motion platform, and the other half kept in static tanks for the same length of time. Baseline behavior and physiology were determined from a subset of fish after acclimation but before selection into groups and application of transport. To determine the effects of transport, stocking density, and their interaction on the experimental groups, physiological sampling and behavioral recording were carried out immediately after simulated transport, and water quality was measured both before and after transport. Changes in water quality were observed between two timepoints, with decreased dissolved oxygen levels and increased water temperature. Total ammonia nitrogen levels significantly increased in all treatments over time, particularly in the high‐density groups. Fish ventilation rates were significantly elevated in the groups kept at a high stocking density regardless of whether they also experienced transport stress. Fish transported at a high stocking density also showed more fear‐related behaviors such as freezing and thigmotaxis than non‐transported groups. Serum cortisol, catalase, and aspartate transaminase levels were significantly higher in the transported treatment groups compared to the baseline fish, but no difference was found for serum glucose, lactate, and glutathione peroxidase. We concluded that 3 h of simulated transport was stressful to largemouth bass kept at 78 g L−1, as evidenced by altered fish physiological and behavioral indicators of stress, as well as deteriorated water quality. Additionally, we identified a positive correlation between serum and skin mucus samples for cortisol, glucose, and lactate in transported fish, providing important information for developing less invasive methods for the welfare assessment of largemouth bass.
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- 2024
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41. ART history prior to conception: trends and association with postpartum disengagement from HIV care in Khayelitsha, South Africa (2013–2019): a retrospective cohort study
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Tamsin Kate Phillips, Reshma Kassanjee, Nicola Maxwell, Kim Anderson, Leigh Johnson, Haroon Moolla, Landon Myer, Benjamin H. Chi, Jonathan Euvrard, Andrew Boulle, Mary‐Ann Davies, Morna Cornell, and Renee deWaal
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disengagement from care ,return to care ,retention ,antiretroviral therapy ,postpartum ,South Africa ,Immunologic diseases. Allergy ,RC581-607 - Abstract
Abstract Introduction In recent years, the expansion of HIV treatment eligibility has resulted in an increase in people with antiretroviral therapy (ART) experience prior to pregnancy but little is known about postpartum engagement in care in this population. We examined differences in disengagement from HIV care after delivery by maternal ART history before conception. Methods We analysed data from people living with HIV (aged 15–49) in Khayelitsha, South Africa, with ≥1 live birth between April 2013 and March 2019. We described trends over time in ART history prior to estimated conception, classifying ART history groups as: (A) on ART with no disengagement (>270 days with no evidence of HIV care); (B) returned before pregnancy following disengagement; (C) restarted ART in pregnancy after disengagement; and (D) ART new start in pregnancy. We used Kaplan–Meier curves and proportional‐hazards models (adjusted for maternal age, number of pregnancy records and year of delivery) to examine the time to disengagement from delivery to 2 years postpartum. Results Among 7309 pregnancies (in 6680 individuals), the proportion on ART (A) increased from 19% in 2013 to 41% in 2019. The proportions of those who returned (B) and restarted (C) increased from 2% to 13% and from 2% to 10%, respectively. There was a corresponding decline in the proportion of new starts (D) from 77% in 2013 to 36% in 2019. In the first recorded pregnancy per person in the study period, 26% (95% CI 25–27%) had disengaged from care by 1 year and 34% (95% CI 33–36%) by 2 years postpartum. Individuals who returned (B: aHR 2.10, 95% CI 1.70–2.60), restarted (C: aHR 3.32, 95% CI 2.70–4.09) and newly started ART (D: aHR 2.41, 95% CI 2.12–2.74) had increased hazards of postpartum disengagement compared to those on ART (A). Conclusions There is a growing population of people with ART experience prior to conception and postpartum disengagement varies substantially by ART history. Antenatal care presents an important opportunity to understand prior ART experiences and an entry into interventions for strengthened engagement in HIV care.
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- 2024
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42. Non‐Linear Climate Change Impacts on Crop Yields May Mislead Stakeholders
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Alex C. Ruane, Meridel Phillips, Jonas Jägermeyr, and Christoph Müller
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global warming levels ,food security ,adaptation ,crop productivity ,climate impacts ,climate sensitivity ,Environmental sciences ,GE1-350 ,Ecology ,QH540-549.5 - Abstract
Abstract We utilize a global warming level (GWL) lens to evaluate global and regional patterns of agricultural impacts as global surface temperature increases, providing a unique perspective on the experience of stakeholders with continued warming in the 21st century. We analyze crop productivity outputs from 11 crop models simulating 5 climate models under 3 emissions scenarios across 4 crops within the AgMIP/ISIMIP Phase 3 ensemble. We categorize regional productivity changes (without adaptation) into 9 characteristic climate change response patterns, identifying consistent increases and decreases as well as non‐linear (peak or dip) responses indicative of inflection points reversing trends as GWLs increase. Many maize regions and pockets of wheat, rice and soybean show peak decrease patterns where initial increases may lull stakeholders into complacency or maladaptation before productivity shifts to losses at higher GWLs. Although the GWL perspective has proven useful in connecting diverse climate models and emissions scenarios, we identify multiple pitfalls that recommend proceeding with caution when applying this approach to climate impacts. Chief among these is that carbon dioxide (CO2) concentrations at any GWL depend on a climate model's transient climate response (TCR). Higher CO2 concentrations generally benefit crop productivity, so this leads to more pessimistic agricultural projections for so‐called “hot” models and can skew multi‐model ensemble results as models with high TCR are disproportionately likely to reach higher GWLs. While there are strong connections between many climatic impact‐drivers and GWLs, vulnerability and exposure components of food system risk are strongly dependent on development pathways.
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- 2024
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43. Design and use of an ex vivo peripheral simulating bioreactor system for pharmacokinetic analysis of a drug coated stent
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Danyi Chen, Colin Krinsky, Mollie Phillips, Catherine Allred, Ava Khan, Linda B. Liu, Uwe Christians, and Saami K. Yazdani
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bioreactor ,drug delivery ,ex vivo ,paclitaxel ,peripheral arterial disease ,pharmacokinetics ,Chemical engineering ,TP155-156 ,Biotechnology ,TP248.13-248.65 ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Abstract Currently, there are no ex vivo systems that can model the motion of peripheral arteries and allow for the evaluation of pharmacokinetics (PK) of endovascular devices. The objective of this study was to develop a novel peripheral simulating bioreactor system to evaluate drug pharmacokinetics of stents. We utilized 3D‐printed and off‐the‐shelf components to construct a peripheral‐simulating bioreactor system capable of mimicking the motion of peripheral arteries. Servo motors were primarily used to shorten/elongate, twist, and bend explanted porcine carotid arteries. To evaluate the pharmacokinetics in the bioreactor, drug‐eluting stents were deployed within explanted arteries and subjected to vascular motion along with pulsatile flow conditions. Following 30 min and 24 h, the arteries were removed, and paclitaxel levels were measured. Scanning electron microscopy was also performed to evaluate the stent surface. Arterial paclitaxel levels of the stent‐treated arteries were found to be higher at 30 min than at 24 h following pulsatile and no vascular motion and even higher at 24 h following pulsatile flow and vascular motion. The residual drug on the stent significantly decreased from 30 min to 24 h. Scanning electron microscopy confirmed the loss of paclitaxel coating at 24 h and greater disturbance in stents under peripheral motion versus pulsatile only. This system represents the first ex vivo system to determine the PK of drug‐eluting stents under physiological flow and vascular motion conditions. This work provides a novel system for a quick and inexpensive preclinical tool to study acute drug tissue concentration kinetics of drug‐releasing interventional vascular devices designed for peripheral applications.
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- 2024
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44. A view of the pan‐genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.)
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Qihua Liang, María Muñoz‐Amatriaín, Shengqiang Shu, Sassoum Lo, Xinyi Wu, Joseph W. Carlson, Patrick Davidson, David M. Goodstein, Jeremy Phillips, Nadia M. Janis, Elaine J. Lee, Chenxi Liang, Peter L. Morrell, Andrew D. Farmer, Pei Xu, Timothy J. Close, and Stefano Lonardi
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Plant culture ,SB1-1110 ,Genetics ,QH426-470 - Abstract
Abstract Cowpea, Vigna unguiculata L. Walp., is a diploid warm‐season legume of critical importance as both food and fodder in sub‐Saharan Africa. This species is also grown in Northern Africa, Europe, Latin America, North America, and East to Southeast Asia. To capture the genomic diversity of domesticates of this important legume, de novo genome assemblies were produced for representatives of six subpopulations of cultivated cowpea identified previously from genotyping of several hundred diverse accessions. In the most complete assembly (IT97K‐499‐35), 26,026 core and 4963 noncore genes were identified, with 35,436 pan genes when considering all seven accessions. GO terms associated with response to stress and defense response were highly enriched among the noncore genes, while core genes were enriched in terms related to transcription factor activity, and transport and metabolic processes. Over 5 million single nucleotide polymorphisms (SNPs) relative to each assembly and over 40 structural variants >1 Mb in size were identified by comparing genomes. Vu10 was the chromosome with the highest frequency of SNPs, and Vu04 had the most structural variants. Noncore genes harbor a larger proportion of potentially disruptive variants than core genes, including missense, stop gain, and frameshift mutations; this suggests that noncore genes substantially contribute to diversity within domesticated cowpea.
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- 2024
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45. A conjoint experiment of three placebo rectal products used with receptive anal sex: results from MTN‐035
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José Bauermeister, Willey Lin, Ryan Tingler, Albert Liu, Suwat Chariyalertsak, Craig Hoesley, Pedro Gonzales, Ken Ho, Noel Kayange, Thesla Palanee Phillips, Sherri Johnson, Elizabeth Brown, Jillian Zemanek, Cindy E. Jacobson, Gustavo F. Doncel, Jeanna Piper, and the MTN‐035 Protocol Team for the Microbicide Trials Network
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acceptability ,HIV prevention ,men who have sex with men ,microbicides ,PrEP ,transgender ,Immunologic diseases. Allergy ,RC581-607 - Abstract
Abstract Introduction End‐user perspectives are vital to the design of new biomedical HIV prevention products. Conjoint analysis can support the integration of end‐user perspectives by examining their preferences of potential pre‐exposure prophylaxis (PrEP) products. The Microbicides Trial Network (MTN) 035 protocol examined three placebo rectal dosage forms (insert, enema and suppository) that could deliver PrEP prior to receptive anal sex (RAS). Methods Between April 2019 and July 2020, we enrolled 217 HIV‐negative, cisgender men who have sex with men (MSM; n = 172; 79.3%) and transgender people (n = 47; 20.7%) ages 18–35 into a randomized cross‐over trial across Malawi, Peru, South Africa, Thailand and the United States. Participants used each product prior to RAS over 4‐week periods. Participants completed a conjoint experiment where they selected between random profiles using seven features (dosage form, timing of use before sex, side effects, duration of protection, effectiveness, frequency of use and need for a prescription). Results Effectiveness was the strongest determinant of choice (30.4%), followed by modality (18.0%), potential side effects (17.2%), frequency of use (10.8%), duration of protection (10.4%), timing of use before sex (7.4%) and need for a prescription (5.9%). Relative utility scores indicated that the most desirable combination of attributes was a product with 95% efficacy, used 30 minutes before sex, offering a 3‐ to 5‐day protection window, used weekly, having no side effects, in the form of an enema and available over‐the‐counter. Conclusions Choice in next‐generation PrEP products is highly desired by MSM and transgender people, as no one‐size‐fits‐all approach satisfies all the preferences. MTN‐035 participants weighed product features differently, recognizing the need for diverse, behaviourally congruent biomedical options that fit the needs of intended end‐users.
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- 2024
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46. Young people's future thinking and mental health: The development and validation of the Adolescent Future Thinking Rating Scale
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Peiyao Tang, Edmund Sonuga‐Barke, Katarzyna Kostyrka‐Allchorne, and Jacqueline Phillips‐Owen
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depression ,future thinking ,generalised anxiety ,scale validation ,young people ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
Abstract Objectives We aimed to develop and validate a new scale of future thinking and adolescent mental health—the Adolescent Future Thinking Rating Scale (AFTRS). Methods A provisional AFTRS was developed from interviews with 19 adolescents. It was completed by three samples: exploratory (n = 161) aged 16–21 years, who also completed established measures of future thinking, cognitive risk factors, depression and anxiety; replication (n = 209) aged 16–25 years; and test‐retest (n = 102) aged 17–23 years. The reliability, convergent, predictive, and discriminant validity were examined. Results Exploratory factor analyses identified the AFTRS‐18 and AFTRS‐12. Both had three sub‐scales: (i) Concerns about Maladaptive Future Thinking, (ii) Future Positivity, and (iii) Ability to Visualise the Future. Established future thinking measures were combined into two factors: Negative Future Emotions (Cognitive Triad Inventory—View of Future and Beck's Hopelessness Scale) and Immediacy Preference (Consideration of Future Consequences and Quick Delay Questionnaire). The AFTRS‐18 and AFTRS‐12 were similarly associated with both factors and with depression/anxiety. Internal consistency and test‐retest reliability were high. Conclusions The AFTRS‐12 and AFTRS‐18 are reliable and valid measures of the three key dimensions of adolescent future thinking and mental health. The first subscale remained significant in predicting depression and anxiety after controlling for general cognitive risks.
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- 2024
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47. What is the risk of overcollecting for translocation? An opportunistic assessment of a wingless grasshopper
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Michael R. Kearney, Hiromi Yagui, Ary A. Hoffmann, and Ben L. Phillips
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Bayesian hierarchical model ,grasshopper ,invertebrate ,overcollection ,translocation ,General. Including nature conservation, geographical distribution ,QH1-199.5 - Abstract
Abstract Translocation is an increasingly used tool in conservation management, but there is a risk that source populations are overcollected. The risk depends critically on the detection probability and the source population size. We quantified this risk for a wingless grasshopper population in a patch of remnant habitat in suburban Melbourne that was condemned to be cleared for housing development. We collected ∼2000 grasshoppers in five samples spread over 1 month and used the results to estimate the initial population size (∼3400) with high confidence. Despite our perception of substantially depleting the population, we removed only an estimated 60%, and this relatively high fecundity (∼50 eggs per lifetime) annual species had recovered by the following year to near its original density. Wild‐to‐wild translocation is likely to be a low‐cost and effective strategy in the conservation of many invertebrates, and our findings highlight the feasibility of using natural source populations.
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- 2024
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48. Association of the CHEK2 c.1100delC variant, radiotherapy, and systemic treatment with contralateral breast cancer risk and breast cancer‐specific survival
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Anna Morra, Maartje A. C. Schreurs, Irene L. Andrulis, Hoda Anton‐Culver, Annelie Augustinsson, Matthias W. Beckmann, Sabine Behrens, Stig E. Bojesen, Manjeet K. Bolla, Hiltrud Brauch, Annegien Broeks, Saundra S. Buys, Nicola J. Camp, Jose E. Castelao, Melissa H. Cessna, Jenny Chang‐Claude, Wendy K. Chung, NBCS Collaborators, Sarah V. Colonna, Fergus J. Couch, Angela Cox, Simon S. Cross, Kamila Czene, Mary B. Daly, Joe Dennis, Peter Devilee, Thilo Dörk, Alison M. Dunning, Miriam Dwek, Douglas F. Easton, Diana M. Eccles, Mikael Eriksson, D. Gareth Evans, Peter A. Fasching, Tanja N. Fehm, Jonine D. Figueroa, Henrik Flyger, Marike Gabrielson, Manuela Gago‐Dominguez, Montserrat García‐Closas, José A. García‐Sáenz, Jeanine Genkinger, Felix Grassmann, Melanie Gündert, Eric Hahnen, Christopher A. Haiman, Ute Hamann, Patricia A. Harrington, Jaana M. Hartikainen, Reiner Hoppe, John L. Hopper, Richard S. Houlston, Anthony Howell, ABCTB Investigators, kConFab Investigators, Anna Jakubowska, Wolfgang Janni, Helena Jernström, Esther M. John, Nichola Johnson, Michael E. Jones, Vessela N. Kristensen, Allison W. Kurian, Diether Lambrechts, Loic Le Marchand, Annika Lindblom, Jan Lubiński, Michael P. Lux, Arto Mannermaa, Dimitrios Mavroudis, Anna Marie Mulligan, Taru A. Muranen, Heli Nevanlinna, Ines Nevelsteen, Patrick Neven, William G. Newman, Nadia Obi, Kenneth Offit, Andrew F. Olshan, Tjoung‐Won Park‐Simon, Alpa V. Patel, Paolo Peterlongo, Kelly‐Anne Phillips, Dijana Plaseska‐Karanfilska, Eric C. Polley, Nadege Presneau, Katri Pylkäs, Brigitte Rack, Paolo Radice, Muhammad U. Rashid, Valerie Rhenius, Mark Robson, Atocha Romero, Emmanouil Saloustros, Elinor J. Sawyer, Rita K. Schmutzler, Sabine Schuetze, Christopher Scott, Mitul Shah, Snezhana Smichkoska, Melissa C. Southey, William J. Tapper, Lauren R. Teras, Rob A. E. M. Tollenaar, Katarzyna Tomczyk, Ian Tomlinson, Melissa A. Troester, Celine M. Vachon, Elke M. vanVeen, Qin Wang, Camilla Wendt, Hans Wildiers, Robert Winqvist, Argyrios Ziogas, Per Hall, Paul D. P. Pharoah, Muriel A. Adank, Antoinette Hollestelle, Marjanka K. Schmidt, and Maartje J. Hooning
- Subjects
CHEK2 c.1100delC germline genetic variant ,contralateral breast cancer risk ,radiotherapy ,survival ,systemic treatment ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Background Breast cancer (BC) patients with a germline CHEK2 c.1100delC variant have an increased risk of contralateral BC (CBC) and worse BC‐specific survival (BCSS) compared to non‐carriers. Aim To assessed the associations of CHEK2 c.1100delC, radiotherapy, and systemic treatment with CBC risk and BCSS. Methods Analyses were based on 82,701 women diagnosed with a first primary invasive BC including 963 CHEK2 c.1100delC carriers; median follow‐up was 9.1 years. Differential associations with treatment by CHEK2 c.1100delC status were tested by including interaction terms in a multivariable Cox regression model. A multi‐state model was used for further insight into the relation between CHEK2 c.1100delC status, treatment, CBC risk and death. Results There was no evidence for differential associations of therapy with CBC risk by CHEK2 c.1100delC status. The strongest association with reduced CBC risk was observed for the combination of chemotherapy and endocrine therapy [HR (95% CI): 0.66 (0.55–0.78)]. No association was observed with radiotherapy. Results from the multi‐state model showed shorter BCSS for CHEK2 c.1100delC carriers versus non‐carriers also after accounting for CBC occurrence [HR (95% CI): 1.30 (1.09–1.56)]. Conclusion Systemic therapy was associated with reduced CBC risk irrespective of CHEK2 c.1100delC status. Moreover, CHEK2 c.1100delC carriers had shorter BCSS, which appears not to be fully explained by their CBC risk.
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- 2023
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49. Acute adaptation of central and peripheral motor unit features to exercise‐induced fatigue differs with concentric and eccentric loading
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Eleanor J. Jones, Yuxiao Guo, Eduardo Martinez‐Valdes, Francesco Negro, Daniel W. Stashuk, Philip J. Atherton, Bethan E. Phillips, and Mathew Piasecki
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fatigue ,high density electromyography ,intramuscular electromyography ,motor unit ,Physiology ,QP1-981 - Abstract
Abstract Force output of muscle is partly mediated by the adjustment of motor unit (MU) firing rate (FR). Disparities in MU features in response to fatigue may be influenced by contraction type, as concentric (CON) and eccentric (ECC) contractions demand variable amounts of neural input, which alters the response to fatigue. This study aimed to determine the effects of fatigue following CON and ECC loading on MU features of the vastus lateralis (VL). High‐density surface (HD‐sEMG) and intramuscular (iEMG) electromyography were used to record MU potentials (MUPs) from bilateral VLs of 12 young volunteers (six females) during sustained isometric contractions at 25% and 40% of the maximum voluntary contraction (MVC), before and after completing CON and ECC weighted stepping exercise. Multi‐level mixed effects linear regression models were performed with significance assumed as P 0.1) but neuromuscular junction transmission instability increased in both legs (P
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- 2023
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50. Scalable purification of extracellular vesicles with high yield and purity using multimodal flowthrough chromatography
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Scott E. Bonner, Simonides I. van deWakker, William Phillips, Eduard Willms, Joost P. G. Sluijter, Andrew F. Hill, Matthew J. A. Wood, and Pieter Vader
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extracellular vesicles ,exosomes ,multimodal flowthrough chromatography ,purification ,size exclusion chromatography ,Cytology ,QH573-671 - Abstract
Abstract Extracellular vesicles (EVs) are cell derived membranous nanoparticles. EVs are important mediators of cell–cell communication via the transfer of bioactive content and as such they are being investigated for disease diagnostics as biomarkers and for potential therapeutic cargo delivery to recipient cells. However, existing methods for isolating EVs from biological samples suffer from challenges related to co‐isolation of unwanted materials such as proteins, nucleic acids, and lipoproteins. In the pursuit of improved EV isolation techniques, we introduce multimodal flowthrough chromatography (MFC) as a scalable alternative to size exclusion chromatography (SEC). The use of MFC offers significant advantages for purifying EVs, resulting in enhanced yields and increased purity with respect to protein and nucleic acid co‐isolates from conditioned 3D cell culture media. Compared to SEC, significantly higher EV yields with similar purity and preserved functionality were also obtained with MFC in 2D cell cultures. Additionally, MFC yielded EVs from serum with comparable purity to SEC and similar apolipoprotein B content. Overall, MFC presents an advancement in EV purification yielding EVs with high recovery, purity, and functionality, and offers an accessible improvement to researchers currently employing SEC.
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- 2024
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