772 results on '"James R Anderson"'
Search Results
2. La non-réciprocité d’un tiers induit la méfiance chez les singes capucins
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James R Anderson, Benoit Bucher, Margaux Levasseur, and Kazuo Fujita
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capuchin monkeys ,distrust ,exchange ,reciprocity ,social evaluation ,trust ,Science ,Zoology ,QL1-991 - Abstract
Recent studies have established that some species of primates are able to detect reciprocity and non-reciprocity in the context of exchanges of objects between third parties. For example, we have shown that capuchin monkeys discriminate between a human actor who exchanges equitably with a third party and an actor who does not respect reciprocity of exchange. More specifically, monkeys were significantly less willing to accept food from the non-reciprocator. In other words, the monkeys took a binary decision to engage preferentially with one actor at the expense of the other. In a new study, we asked whether monkeys would differentially trust two actors depending on the degree of reciprocity shown by the latter. Following a fair or an unfair exchange, one of the two actors started to transfer pieces of food to within reach of the monkey. In this situation of delay of gratification, the monkey can start to eat the food whenever it desires, but doing so stops the transfer; thus to maximize the amount of food obtained the monkey should wait and let the number of food items accumulate. Results showed that the monkeys were less likely to show delay of gratification when the food was transferred by an actor who behaved non-reciprocally in the exchange with a third party. This tendency towards “impulsive” responding was especially evident when the total quantity of food potentially available was unknown to the monkey, in other words, in a situation of uncertainty. We conclude from these data that non-reciprocity in a third-party exchange can induce a reaction of distrust in capuchin monkeys.
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- 2016
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3. La mort naturelle d'une femelle chimpanzé âgée au sein de son groupe
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James R Anderson
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chimpanzé ,comportement ,vieillissement mort naturelle ,Science ,Zoology ,QL1-991 - Abstract
A l'exception des jeunes bébés malades ou tués par d'autres individus, le moment de la mort chez les grands singes anthropoïdes reste un événement rarement observé dans la nature. Deux cas rapportés chez les chimpanzés ont révélé des réponses très agitées et diverses chez les autres membres du groupe. Ces deux cas concernent une mort accidentelle et une attaque fatale par un prédateur. Je décrirai le cas d'une vieille femelle chimpanzé qui est morte pacifiquement, de causes naturelles, entourée des membres de son groupe, en captivité. Au contraire des réactions décrites pour les cas de mort soudaine, les membres du groupe sont restés calmes et silencieux suite au décès de la vieille femelle. Immédiatement avant son décès, la femelle mourante recevait des contacts physiques affiliatifs de la part des autres membres du groupe. Ces derniers regardaient le visage de la mourante de très près, et ils ont doucement secoué la tête et les épaules de la femelle, avant de l'abandonner après sa mort. Après que le corps de la vieille femelle ait été retiré, le lieu où elle s'est éteinte a été évité par les autres, qui sont restés silencieux et sombres pendant plusieurs jours. J'en conclus que les comportements des chimpanzés ont des implications pour notre compréhension et nos rituels concernant la mort au sein des sociétés humaines.
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- 2015
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4. A high-resolution morphological and ultrastructural map of anterior sensory cilia and glia in Caenorhabditis elegans
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David B Doroquez, Cristina Berciu, James R Anderson, Piali Sengupta, and Daniela Nicastro
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cilia ,electron microscopy ,electron tomography ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Many primary sensory cilia exhibit unique architectures that are critical for transduction of specific sensory stimuli. Although basic ciliogenic mechanisms are well described, how complex ciliary structures are generated remains unclear. Seminal work performed several decades ago provided an initial but incomplete description of diverse sensory cilia morphologies in C. elegans. To begin to explore the mechanisms that generate these remarkably complex structures, we have taken advantage of advances in electron microscopy and tomography, and reconstructed three-dimensional structures of fifty of sixty sensory cilia in the C. elegans adult hermaphrodite at high resolution. We characterize novel axonemal microtubule organization patterns, clarify structural features at the ciliary base, describe new aspects of cilia–glia interactions, and identify structures suggesting novel mechanisms of ciliary protein trafficking. This complete ultrastructural description of diverse cilia in C. elegans provides the foundation for investigations into underlying ciliogenic pathways, as well as contributions of defined ciliary structures to specific neuronal functions.
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- 2014
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5. TP53 mutational status is a potential marker for risk stratification in Wilms tumour with diffuse anaplasia.
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Mariana Maschietto, Richard D Williams, Tasnim Chagtai, Sergey D Popov, Neil J Sebire, Gordan Vujanic, Elizabeth Perlman, James R Anderson, Paul Grundy, Jeffrey S Dome, and Kathy Pritchard-Jones
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Medicine ,Science - Abstract
The presence of diffuse anaplasia in Wilms tumours (DAWT) is associated with TP53 mutations and poor outcome. As patients receive intensified treatment, we sought to identify whether TP53 mutational status confers additional prognostic information.We studied 40 patients with DAWT with anaplasia in the tissue from which DNA was extracted and analysed for TP53 mutations and 17p loss. The majority of cases were profiled by copy number (n = 32) and gene expression (n = 36) arrays. TP53 mutational status was correlated with patient event-free and overall survival, genomic copy number instability and gene expression profiling.From the 40 cases, 22 (55%) had TP53 mutations (2 detected only after deep-sequencing), 20 of which also had 17p loss (91%); 18 (45%) cases had no detectable mutation but three had 17p loss. Tumours with TP53 mutations and/or 17p loss (n = 25) had an increased risk of recurrence as a first event (p = 0.03, hazard ratio (HR), 3.89; 95% confidence interval (CI), 1.26-16.0) and death (p = 0.04, HR, 4.95; 95% CI, 1.36-31.7) compared to tumours lacking TP53 abnormalities. DAWT carrying TP53 mutations showed increased copy number alterations compared to those with wild-type, suggesting a more unstable genome (p = 0.03). These tumours showed deregulation of genes associated with cell cycle and DNA repair biological processes.This study provides evidence that TP53 mutational analysis improves risk stratification in DAWT. This requires validation in an independent cohort before clinical use as a biomarker.
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- 2014
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6. Which primates recognize themselves in mirrors?
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James R Anderson and Gordon G Gallup
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Biology (General) ,QH301-705.5 - Published
- 2011
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7. A computational framework for ultrastructural mapping of neural circuitry.
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James R Anderson, Bryan W Jones, Jia-Hui Yang, Marguerite V Shaw, Carl B Watt, Pavel Koshevoy, Joel Spaltenstein, Elizabeth Jurrus, Kannan U V, Ross T Whitaker, David Mastronarde, Tolga Tasdizen, and Robert E Marc
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Biology (General) ,QH301-705.5 - Abstract
Circuitry mapping of metazoan neural systems is difficult because canonical neural regions (regions containing one or more copies of all components) are large, regional borders are uncertain, neuronal diversity is high, and potential network topologies so numerous that only anatomical ground truth can resolve them. Complete mapping of a specific network requires synaptic resolution, canonical region coverage, and robust neuronal classification. Though transmission electron microscopy (TEM) remains the optimal tool for network mapping, the process of building large serial section TEM (ssTEM) image volumes is rendered difficult by the need to precisely mosaic distorted image tiles and register distorted mosaics. Moreover, most molecular neuronal class markers are poorly compatible with optimal TEM imaging. Our objective was to build a complete framework for ultrastructural circuitry mapping. This framework combines strong TEM-compliant small molecule profiling with automated image tile mosaicking, automated slice-to-slice image registration, and gigabyte-scale image browsing for volume annotation. Specifically we show how ultrathin molecular profiling datasets and their resultant classification maps can be embedded into ssTEM datasets and how scripted acquisition tools (SerialEM), mosaicking and registration (ir-tools), and large slice viewers (MosaicBuilder, Viking) can be used to manage terabyte-scale volumes. These methods enable large-scale connectivity analyses of new and legacy data. In well-posed tasks (e.g., complete network mapping in retina), terabyte-scale image volumes that previously would require decades of assembly can now be completed in months. Perhaps more importantly, the fusion of molecular profiling, image acquisition by SerialEM, ir-tools volume assembly, and data viewers/annotators also allow ssTEM to be used as a prospective tool for discovery in nonneural systems and a practical screening methodology for neurogenetics. Finally, this framework provides a mechanism for parallelization of ssTEM imaging, volume assembly, and data analysis across an international user base, enhancing the productivity of a large cohort of electron microscopists.
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- 2009
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8. Chimpanzees share forbidden fruit.
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Kimberley J Hockings, Tatyana Humle, James R Anderson, Dora Biro, Claudia Sousa, Gaku Ohashi, and Tetsuro Matsuzawa
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Medicine ,Science - Abstract
The sharing of wild plant foods is infrequent in chimpanzees, but in chimpanzee communities that engage in hunting, meat is frequently used as a 'social tool' for nurturing alliances and social bonds. Here we report the only recorded example of regular sharing of plant foods by unrelated, non-provisioned wild chimpanzees, and the contexts in which these sharing behaviours occur. From direct observations, adult chimpanzees at Bossou (Republic of Guinea, West Africa) very rarely transferred wild plant foods. In contrast, they shared cultivated plant foods much more frequently (58 out of 59 food sharing events). Sharing primarily consists of adult males allowing reproductively cycling females to take food that they possess. We propose that hypotheses focussing on 'food-for-sex and -grooming' and 'showing-off' strategies plausibly account for observed sharing behaviours. A changing human-dominated landscape presents chimpanzees with fresh challenges, and our observations suggest that crop-raiding provides adult male chimpanzees at Bossou with highly desirable food commodities that may be traded for other currencies.
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- 2007
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9. Male aggressive behaviors as an indicator in primate tourism management assessment
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Bin Yang, James R. Anderson, Meng-Ya Han, Xin-Yu Meng, Jun Luo, Kang-Sheng Jia, Yong-Feng Chen, Wen-Yong Tian, Bing-Bo Qiao, Chao Zhang, Han-Qing Jing, Pei-Yuan Zhou, and Bao-Guo Li
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Sichuan snub-nosed monkeys ,Ecotourism ,Aggressive behaviors ,Tourism risk assessment ,Ecology ,QH540-549.5 - Abstract
Primate tourism brings many benefits, but also some problems. How to better evaluate primate tourism is of significance for formulating tourism management strategies. In this study, we compared the aggressive behavior of three Sichuan snub-nosed monkey groups that encounter ecotourists and found that male aggressive behavior is a useful indicator for assessing ecotourism of these and, by inference, other groups. In high-risk tourism groups multiple monkeys direct aggression towards tourists, whereas low-risk tourism groups are characterized by low rates of such aggression. We found that tourists touching or attempting to touch the monkeys can trigger aggressive behaviors in all groups, while carrying food and eating have different effects across groups. In well-managed groups, tourist-directed aggressive behaviors are milder than in less well-managed groups. We propose that male monkey aggressive behavior elicited by tourists’ behavior is a useful indicator in assessing primate tourism, and can help guide further improvements in tourism management.
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- 2024
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10. Maternal caretaking behavior towards a dead juvenile in a wild, multi-level primate society
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Bin Yang, James R. Anderson, Min Mao, Kaifeng Wang, and Baoguo Li
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Medicine ,Science - Abstract
Abstract Maternal caretaking and transport of dead infants are widespread among nonhuman primates, having been reported in numerous species of monkeys and apes. By contrast, accounts of such behaviors toward dead juveniles are scarce. Here, we describe responses by the mother and other group members to the death of a juvenile in a wild, multi-level group of Sichuan snub-nosed monkeys (Rhinopithecus roxellana). Following the juvenile’s fatal accident, his mother transported and cared for the corpse for four days. Immature monkeys belonging to the same one-male unit, and some individuals from other social units also showed interest in and tended the corpse. Comparisons of this case with those involving the deaths of infants and an adult female in the same population highlight possible effects of physiological, psychological and emotional factors in primate thanatological responses, and provide an additional perspective on the origin and evolution of compassionate acts.
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- 2022
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11. Mitochondrial Inorganic Polyphosphate (polyP) Is a Potent Regulator of Mammalian Bioenergetics in SH-SY5Y Cells: A Proteomics and Metabolomics Study
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Mariona Guitart-Mampel, Pedro Urquiza, Fausto Carnevale Neto, James R. Anderson, Vedangi Hambardikar, Ernest R. Scoma, Gennifer E. Merrihew, Lu Wang, Michael J. MacCoss, Daniel Raftery, Mandy J. Peffers, and Maria E. Solesio
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mitochondria ,bioenergetics ,mitochondrial metabolism ,OXPHOS ,inorganic polyphosphate ,metabolomics ,Biology (General) ,QH301-705.5 - Abstract
Inorganic polyphosphate (polyP) is an ancient, ubiquitous, and well-conserved polymer which is present in all the studied organisms. It is formed by individual subunits of orthophosphate which are linked by structurally similar bonds and isoenergetic to those found in ATP. While the metabolism and the physiological roles of polyP have already been described in some organisms, including bacteria and yeast, the exact role of this polymer in mammalian physiology still remains poorly understood. In these organisms, polyP shows a co-localization with mitochondria, and its role as a key regulator of the stress responses, including the maintenance of appropriate bioenergetics, has already been demonstrated by our group and others. Here, using Wild-type (Wt) and MitoPPX (cells enzymatically depleted of mitochondrial polyP) SH-SY5Y cells, we have conducted a comprehensive study of the status of cellular physiology, using proteomics and metabolomics approaches. Our results suggest a clear dysregulation of mitochondrial physiology, especially of bioenergetics, in MitoPPX cells when compared with Wt cells. Moreover, the effects induced by the enzymatic depletion of polyP are similar to those present in the mitochondrial dysfunction that is observed in neurodegenerative disorders and in neuronal aging. Based on our findings, the metabolism of mitochondrial polyP could be a valid and innovative pharmacological target in these conditions.
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- 2022
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12. Mouse microRNA signatures in joint ageing and post-traumatic osteoarthritis
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Catarina I.G.D. Castanheira, James R. Anderson, Yongxiang Fang, Peter I. Milner, Katarzyna Goljanek-Whysall, Louise House, Peter D. Clegg, and Mandy J. Peffers
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Osteoarthritis ,Joint ageing ,microRNA ,Biomarkers ,Diseases of the musculoskeletal system ,RC925-935 - Abstract
Objective: This study investigated mice serum and joint microRNA expression profiles in ageing and osteoarthritis to elucidate the role of microRNAs in the development and progression of disease, and provide biomarkers for ageing and osteoarthritis. Design: Whole joints and serum samples were collected from C57BL6/J male mice and subjected to small RNA sequencing. Groups used included; surgically-induced post-traumatic osteoarthritis, (DMM; 24 months-old); sham surgery (24 months-old); old mice (18 months-old); and young mice (8 months-old). Differentially expressed microRNAs between the four groups were identified and validated using real-time quantitative PCR. MicroRNA differential expression data was used for target prediction and pathway analysis. Results: In joint tissues, miR-140–5p, miR-205–5p, miR-682, miR-208b-3p, miR-499–5p, miR-455–3p and miR-6238 were differentially expressed between young and old groups; miR-146a-5p, miR-3474, miR-615–3p and miR-151–5p were differentially expressed between DMM and Sham groups; and miR-652–3p, miR-23b-3p, miR-708–5p, miR-5099, miR-23a-3p, miR-214–3p, miR-6238 and miR-148–3p between the old and DMM groups. The number of differentially expressed microRNAs in serum was higher, some in common with joint tissues including miR-140–5p and miR-455–3p between young and old groups; and miR-23b-3p, miR-5099 and miR-6238 between old and DMM groups.We confirmed miR-140–5p, miR-499–5p and miR-455–3p expression to be decreased in old mouse joints compared to young, suggesting their potential use as biomarkers of joint ageing in mice. Conclusions: MiR-140–5p, miR-499–5p and miR-455–3p could be used as joint ageing biomarkers in mice. Further research into these specific molecules in human tissues is now warranted to check their potential suitability as human biomarkers of ageing.
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- 2021
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13. Impact of Retinal Degeneration on Response of ON and OFF Cone Bipolar Cells to Electrical Stimulation
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Shayan Farzad, Pragya Kosta, Ege Iseri, Steven T. Walston, Jean-Marie C. Bouteiller, Rebecca L. Pfeiffer, Crystal L. Sigulinsky, Jia-Hui Yang, Jessica C. Garcia, James R. Anderson, Bryan W. Jones, and Gianluca Lazzi
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General Neuroscience ,Rehabilitation ,Biomedical Engineering ,Internal Medicine - Published
- 2023
14. Dominants, subordinates, enigmatic intermediates
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James R. Anderson
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Animal Science and Zoology - Published
- 2022
15. Supplementary Figure S7 from Comprehensive Genomic Analysis of Rhabdomyosarcoma Reveals a Landscape of Alterations Affecting a Common Genetic Axis in Fusion-Positive and Fusion-Negative Tumors
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Javed Khan, Douglas S. Hawkins, Matthew Meyerson, Frederic G. Barr, Stephen X. Skapek, James R. Anderson, Jaume Mora, Gad Getz, Thomas Badgett, Daniel Catchpoole, Sivasish Sindiri, Andrew S. Brohl, Dominik Bogen, Shile Zhang, Hongling Liao, Laura Hurd, Catherine Tolman, Young K. Song, Jianjun Wang, Daniel Auclair, Lauren Ambrogio, Mara Rosenberg, Rajesh Patidar, Jun S. Wei, Juliann Chmielecki, Li Chen, and Jack F. Shern
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PDF file 186K, Loss of heterozygosity on Chromosome 11p15.5
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- 2023
16. Supplementary Legends from Comprehensive Genomic Analysis of Rhabdomyosarcoma Reveals a Landscape of Alterations Affecting a Common Genetic Axis in Fusion-Positive and Fusion-Negative Tumors
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Javed Khan, Douglas S. Hawkins, Matthew Meyerson, Frederic G. Barr, Stephen X. Skapek, James R. Anderson, Jaume Mora, Gad Getz, Thomas Badgett, Daniel Catchpoole, Sivasish Sindiri, Andrew S. Brohl, Dominik Bogen, Shile Zhang, Hongling Liao, Laura Hurd, Catherine Tolman, Young K. Song, Jianjun Wang, Daniel Auclair, Lauren Ambrogio, Mara Rosenberg, Rajesh Patidar, Jun S. Wei, Juliann Chmielecki, Li Chen, and Jack F. Shern
- Abstract
PDF file 92K, Supplementary Legends
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- 2023
17. Supplementary Tables S1-S10 from Comprehensive Genomic Analysis of Rhabdomyosarcoma Reveals a Landscape of Alterations Affecting a Common Genetic Axis in Fusion-Positive and Fusion-Negative Tumors
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Javed Khan, Douglas S. Hawkins, Matthew Meyerson, Frederic G. Barr, Stephen X. Skapek, James R. Anderson, Jaume Mora, Gad Getz, Thomas Badgett, Daniel Catchpoole, Sivasish Sindiri, Andrew S. Brohl, Dominik Bogen, Shile Zhang, Hongling Liao, Laura Hurd, Catherine Tolman, Young K. Song, Jianjun Wang, Daniel Auclair, Lauren Ambrogio, Mara Rosenberg, Rajesh Patidar, Jun S. Wei, Juliann Chmielecki, Li Chen, and Jack F. Shern
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XLSX file 2844K, Supplementary Tables S1-S10
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- 2023
18. Supplementary Figure 3 from Clinical Application of Prognostic Gene Expression Signature in Fusion Gene–Negative Rhabdomyosarcoma: A Report from the Children's Oncology Group
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Stephen X. Skapek, Douglas S. Hawkins, Michele Wing, Julie Gastier-Foster, Mauro Delorenzi, Timothy J. Triche, James R. Anderson, Janet Shipley, Edoardo Missiaglia, and Pooja Hingorani
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Box-and-whisker plot of MG5 score split by specific clinic-pathological variables, including patient gender and age, tumor histology, size, location, stage and risk group. Correlations were tested by Wilcoxon or Kruskal−Wallis rank sum tests.
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- 2023
19. Data from Clinical Application of Prognostic Gene Expression Signature in Fusion Gene–Negative Rhabdomyosarcoma: A Report from the Children's Oncology Group
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Stephen X. Skapek, Douglas S. Hawkins, Michele Wing, Julie Gastier-Foster, Mauro Delorenzi, Timothy J. Triche, James R. Anderson, Janet Shipley, Edoardo Missiaglia, and Pooja Hingorani
- Abstract
Purpose: Pediatric rhabdomyosarcoma (RMS) has two common histologic subtypes: embryonal (ERMS) and alveolar (ARMS). PAX–FOXO1 fusion gene status is a more reliable prognostic marker than alveolar histology, whereas fusion gene–negative (FN) ARMS patients are clinically similar to ERMS patients. A five-gene expression signature (MG5) previously identified two diverse risk groups within the fusion gene–negative RMS (FN-RMS) patients, but this has not been independently validated. The goal of this study was to test whether expression of the MG5 metagene, measured using a technical platform that can be applied to routine pathology material, would correlate with outcome in a new cohort of patients with FN-RMS.Experimental Design: Cases were taken from the Children's Oncology Group (COG) D9803 study of children with intermediate-risk RMS, and gene expression profiling for the MG5 genes was performed using the nCounter assay. The MG5 score was correlated with clinical and pathologic characteristics as well as overall and event-free survival.Results: MG5 standardized score showed no significant association with any of the available clinicopathologic variables. The MG5 signature score showed a significant correlation with overall (N = 57; HR, 7.3; 95% CI, 1.9–27.0; P = 0.003) and failure-free survival (N = 57; HR, 6.1; 95% CI, 1.9–19.7; P = 0.002).Conclusions: This represents the first, validated molecular prognostic signature for children with FN-RMS who otherwise have intermediate-risk disease. The capacity to measure the expression of a small number of genes in routine pathology material and apply a simple mathematical formula to calculate the MG5 metagene score provides a clear path toward better risk stratification in future prospective clinical trials. Clin Cancer Res; 21(20); 4733–9. ©2015 AACR.
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- 2023
20. Supplemental Table and Figure Legends from Clinical Application of Prognostic Gene Expression Signature in Fusion Gene–Negative Rhabdomyosarcoma: A Report from the Children's Oncology Group
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Stephen X. Skapek, Douglas S. Hawkins, Michele Wing, Julie Gastier-Foster, Mauro Delorenzi, Timothy J. Triche, James R. Anderson, Janet Shipley, Edoardo Missiaglia, and Pooja Hingorani
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Contains Supplemental Table 1 showing the target sequences used for the 5 genes and Supplementary Figure Legends
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- 2023
21. Suplpementary Figure 1 from Clinical Application of Prognostic Gene Expression Signature in Fusion Gene–Negative Rhabdomyosarcoma: A Report from the Children's Oncology Group
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Stephen X. Skapek, Douglas S. Hawkins, Michele Wing, Julie Gastier-Foster, Mauro Delorenzi, Timothy J. Triche, James R. Anderson, Janet Shipley, Edoardo Missiaglia, and Pooja Hingorani
- Abstract
Plot of the mean expression versus the standard deviation (SD) of all the genes included in (A) ITCC/CIT dataset (Affy HGU133plus2 platform) or (B) COG/IRSG dataset (Affy HGU133a platform). Genes included in the nCounter assay were colored in blue or in red (if their SD was below 0.6). C) Plot of the mean expression of the selected genes in the two datasets. Excluding NDUFS4, the other genes showed similar level of expression across datasets.
- Published
- 2023
22. Supplementary Figure 2 from Clinical Application of Prognostic Gene Expression Signature in Fusion Gene–Negative Rhabdomyosarcoma: A Report from the Children's Oncology Group
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Stephen X. Skapek, Douglas S. Hawkins, Michele Wing, Julie Gastier-Foster, Mauro Delorenzi, Timothy J. Triche, James R. Anderson, Janet Shipley, Edoardo Missiaglia, and Pooja Hingorani
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Box-and-whisker plot of the raw endogenous genes log intensities (A), positive and negative controls (B), Invariant Endogenous Control (C), normalized endogenous genes (D) and normalized Invariant Endogenous Control (E). (F) We also compared the log raw median gene expression versus the log upper-lower quartile range gene expression after normalization. Based on the distribution, we set a threshold at 7.6 for IQR (horizontal dotted line).
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- 2023
23. Data from A Novel Algorithm for Simplification of Complex Gene Classifiers in Cancer
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Samuel L. Volchenboum, Stephen X. Skapek, James R. Anderson, Douglas S. Hawkins, Frederic G. Barr, Julie M. Gastier-Foster, Michele R. Wing, Timothy J. Triche, David M. Parham, Aliya N. Husain, Mei Lin Z. Bissonnette, Karen M. Bachmeyer, Ling Teng, and Raphael A. Wilson
- Abstract
The clinical application of complex molecular classifiers as diagnostic or prognostic tools has been limited by the time and cost needed to apply them to patients. Using an existing 50-gene expression signature known to separate two molecular subtypes of the pediatric cancer rhabdomyosarcoma, we show that an exhaustive iterative search algorithm can distill this complex classifier down to two or three features with equal discrimination. We validated the two-gene signatures using three separate and distinct datasets, including one that uses degraded RNA extracted from formalin-fixed, paraffin-embedded material. Finally, to show the generalizability of our algorithm, we applied it to a lung cancer dataset to find minimal gene signatures that can distinguish survival. Our approach can easily be generalized and coupled to existing technical platforms to facilitate the discovery of simplified signatures that are ready for routine clinical use. Cancer Res; 73(18); 5625–32. ©2013 AACR.
- Published
- 2023
24. Supplementary Figures 1 - 5, Tables 1 - 9 from A Novel Algorithm for Simplification of Complex Gene Classifiers in Cancer
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Samuel L. Volchenboum, Stephen X. Skapek, James R. Anderson, Douglas S. Hawkins, Frederic G. Barr, Julie M. Gastier-Foster, Michele R. Wing, Timothy J. Triche, David M. Parham, Aliya N. Husain, Mei Lin Z. Bissonnette, Karen M. Bachmeyer, Ling Teng, and Raphael A. Wilson
- Abstract
PDF file - 714K, Supplementary Figure 1 Two-gene combinations from the 50-gene F1/F2 classifier with >98% classification efficiency in the Williamson data set. Supplementary Figure 2 Thirteen two-gene combinations with >99% classification efficiency, identified from exhaustive analysis of top 2000 genes. Supplementary Figure 3 Gene dyads with classification efficiency >95% identified through exhaustive search of all possible combinations. Supplementary Figure 4 Detection of gene expression is comparable for fresh-frozen and paraformaldehyde-fixed material with nCounter. Supplementary Figure 5 Gene expression detected in each case with the Williamson F1/F2 metagene nCounter Code set. Supplementary Table 1 Four-gene combinations with ≥ 99% accuracy. Supplementary Table 2 Dyad classifiers from T-test ranking of Williamson data set with ≥ 98% accuracy, applied to Davicioni data. Supplementary Table 3 T-test dyad classifier genes found in F1/F2 metagenes (L) and F1/F2 metagene probes excluded from dyad pairs (R). Supplementary Table 4 Top-scoring classifiers from exhaustive search of 1.5 billion gene pairs from Williamson data set, also applied to Davicioni and Exon data. Supplementary Table 5 Tumor sample characteristics. Supplementary Table 6 Genes in nCounter set. Supplementary Table 7 PCA Scores by tumor sample for nCounter Data. Supplementary Table 8 CA Loadings for nCounter Data. Supplementary Table 9 Top-scoring nCounter dyad classifiers. Supplementary Table 10 Top gene combinations - Lung cancer data
- Published
- 2023
25. Mirror self-recognition in gorillas (Gorilla gorilla gorilla): a review and evaluation of mark test replications and variants
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Lindsay E. Murray, James R. Anderson, and Gordon G. Gallup
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Gorilla gorilla ,Behavior, Animal ,Animals ,Humans ,Experimental and Cognitive Psychology ,Ecology, Evolution, Behavior and Systematics - Abstract
Mirror self-recognition (MSR), widely regarded as an indicator of self-awareness, has not been demonstrated consistently in gorillas. We aimed to examine this issue by setting out a method to evaluate gorilla self-recognition studies that is objective, quantifiable, and easy to replicate. Using Suarez and Gallup’s (J Hum Evol 10:175–183, 1981) study as a reference point, we drew up a list of 15 methodological criteria and assigned scores to all published studies of gorilla MSR for both methodology and outcomes. Key features of studies finding both mark-directed and spontaneous self-directed responses included visually inaccessible marks, controls for tactile and olfactory cues, subjects who were at least 5 years old, and clearly distinguishing between responses in front of versus away from the mirror. Additional important criteria include videotaping the tests, having more than one subject, subjects with adequate social rearing, reporting post-marking observations with mirror absent, and giving mirror exposure in a social versus individual setting. Our prediction that MSR studies would obtain progressively higher scores as procedures and behavioural coding practices improved over time was supported for methods, but not for outcomes. These findings illustrate that methodological rigour does not guarantee stronger evidence of self-recognition in gorillas; methodological differences alone do not explain the inconsistent evidence for MSR in gorillas. By implication, it might be suggested that, in general, gorillas do not show compelling evidence of MSR. We advocate that future MSR studies incorporate the same criteria to optimize the quality of attempts to clarify the self-recognition abilities of gorillas as well as other species.
- Published
- 2022
26. Randomized, Double-Blind, Placebo-Controlled, Global Phase III Trial of Talimogene Laherparepvec Combined With Pembrolizumab for Advanced Melanoma
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Jason A. Chesney, Antoni Ribas, Georgina V. Long, John M. Kirkwood, Reinhard Dummer, Igor Puzanov, Christoph Hoeller, Thomas F. Gajewski, Ralf Gutzmer, Piotr Rutkowski, Lev Demidov, Petr Arenberger, Sang Joon Shin, Pier Francesco Ferrucci, Andrew Haydon, John Hyngstrom, Johannes V. van Thienen, Sebastian Haferkamp, Josep Malvehy Guilera, Bernardo Leon Rapoport, Ari VanderWalde, Scott J. Diede, James R. Anderson, Sheryl Treichel, Edward L. Chan, Sumita Bhatta, Jennifer Gansert, Frank Stephen Hodi, and Helen Gogas
- Subjects
Oncolytic Virotherapy ,Cancer Research ,Herpesvirus 1 ,Clinical Trials and Supportive Activities ,Clinical Sciences ,Oncology and Carcinogenesis ,Evaluation of treatments and therapeutic interventions ,Oncology ,Double-Blind Method ,Clinical Research ,6.1 Pharmaceuticals ,Humans ,Patient Safety ,Oncology & Carcinogenesis ,Melanoma ,Human ,Cancer - Abstract
PURPOSE The combination of talimogene laherparepvec (T-VEC) and pembrolizumab previously demonstrated an acceptable safety profile and an encouraging complete response rate (CRR) in patients with advanced melanoma in a phase Ib study. We report the efficacy and safety from a phase III, randomized, double-blind, multicenter, international study of T-VEC plus pembrolizumab (T-VEC-pembrolizumab) versus placebo plus pembrolizumab (placebo-pembrolizumab) in patients with advanced melanoma. METHODS Patients with stage IIIB-IVM1c unresectable melanoma, naïve to antiprogrammed cell death protein-1, were randomly assigned 1:1 to T-VEC-pembrolizumab or placebo-pembrolizumab. T-VEC was administered at ≤ 4 × 106 plaque-forming unit (PFU) followed by ≤ 4 × 108 PFU 3 weeks later and once every 2 weeks until dose 5 and once every 3 weeks thereafter. Pembrolizumab was administered intravenously 200 mg once every 3 weeks. The dual primary end points were progression-free survival (PFS) per modified RECIST 1.1 by blinded independent central review and overall survival (OS). Secondary end points included objective response rate per mRECIST, CRR, and safety. Here, we report the primary analysis for PFS, the second preplanned interim analysis for OS, and the final analysis. RESULTS Overall, 692 patients were randomly assigned (346 T-VEC-pembrolizumab and 346 placebo-pembrolizumab). T-VEC-pembrolizumab did not significantly improve PFS (hazard ratio, 0.86; 95% CI, 0.71 to 1.04; P = .13) or OS (hazard ratio, 0.96; 95% CI, 0.76 to 1.22; P = .74) compared with placebo-pembrolizumab. The objective response rate was 48.6% for T-VEC-pembrolizumab (CRR 17.9%) and 41.3% for placebo-pembrolizumab (CRR 11.6%); the durable response rate was 42.2% and 34.1% for the arms, respectively. Grade ≥ 3 treatment-related adverse events occurred in 20.7% of patients in the T-VEC-pembrolizumab arm and in 19.5% of patients in the placebo-pembrolizumab arm. CONCLUSION T-VEC-pembrolizumab did not significantly improve PFS or OS compared with placebo-pembrolizumab. Safety results of the T-VEC-pembrolizumab combination were consistent with the safety profiles of each agent alone.
- Published
- 2023
27. Lumber from World War I research at the Forest Products Laboratory helps repair the U.S. Capitol building
- Author
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R. Bruce Allison, James R. Anderson, Amy L. Androff, Robert J. Ross, C. Adam Senalik, Jeffrey Hagen, Mary L. Oehrlein, Nathan Kamprath, and Keith York
- Published
- 2022
28. Optical photothermal infrared spectroscopy can differentiate equine osteoarthritic plasma extracellular vesicles from healthy controls
- Author
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Emily J. Clarke, Cassio Lima, James R. Anderson, Catarina Castanheira, Alison Beckett, Victoria James, Jacob Hyett, Royston Goodacre, and Mandy J. Peffers
- Subjects
Extracellular Vesicles ,Spectroscopy, Near-Infrared ,General Chemical Engineering ,Nucleic Acids ,Osteoarthritis ,General Engineering ,Animals ,Humans ,Horses ,Lipids ,Analytical Chemistry - Abstract
Equine osteoarthritis is a chronic degenerative disease of the articular joint, characterised by cartilage degradation resulting in pain and reduced mobility and thus is a prominent equine welfare concern. Diagnosis is usually at a late stage through clinical examination and radiographic imaging, whilst treatment is symptomatic not curative. Extracellular vesicles are nanoparticles that are involved in intercellular communication. The objective of this study was to investigate the feasibility of Raman and Optical Photothermal Infrared Spectroscopies to detect osteoarthritis using plasma-derived extracellular vesicles, specifically differentiating extracellular vesicles in diseased and healthy controls within the parameters of the techniques used. Plasma samples were derived from thoroughbred racehorses. A total of 14 samples were selected (control; n = 6 and diseased; n = 8). Extracellular vesicles were isolated using differential ultracentrifugation and characterised using nanoparticle tracking analysis, transmission electron microscopy, and human tetraspanin chips. Samples were then analysed using combined Raman and Optical Photothermal Infrared Spectroscopies. Infrared spectra were collected between 950–1800 cm−1. Raman spectra had bands between the wavelengths of 900–1800 cm−1 analysed. Spectral data for both Raman and Optical Photothermal Infrared Spectroscopy were used to generate clustering via principal components analysis and classification models were generated using partial least squared discriminant analysis in order to characterize the techniques' ability to distinguish diseased samples. Optical Photothermal Infrared Spectroscopy could differentiate osteoarthritic extracellular vesicles from healthy with good classification (93.4% correct classification rate) whereas Raman displayed poor classification (correct classification rate = −64.3%). Inspection of the infrared spectra indicated that plasma-derived extracellular vesicles from osteoarthritic horses contained increased signal for proteins, lipids and nucleic acids. For the first time we demonstrated the ability to use optical photothermal infrared spectroscopy combined with Raman spectroscopy to interrogate extracellular vesicles and osteoarthritis-related samples. Optical Photothermal Infrared Spectroscopy was superior to Raman in this study, and could distinguish osteoarthritis samples, suggestive of its potential use diagnostically to identify osteoarthritis in equine patients. This study demonstrates the potential of Raman and Optical Photothermal Infrared Spectroscopy to be used as a future diagnostic tool in clinical practice, with the capacity to detect changes in extracellular vesicles from clinically derived samples.
- Published
- 2022
29. Dead trees as an indicator in tourism risk monitoring at primate ecotourism sites
- Author
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Bin Yang, Bo Hong, James R Anderson, Wei-Wei Fu, Yi Ren, Ni-Na Gou, Jie-Na Shen, Kang-Sheng Jia, Ying-Hu Lei, Kai-Feng Wang, Min Mao, and Bao-Guo Li
- Subjects
Animal Science and Zoology - Published
- 2022
30. Synapse classification and localization in Electron Micrographs.
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Vignesh Jagadeesh, James R. Anderson 0002, Bryan W. Jones, Robert Marc, Steven K. Fisher, and B. S. Manjunath
- Published
- 2014
- Full Text
- View/download PDF
31. Putting the cart before the horse: claims for mirror self-recognition in horses are unfounded
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James R. Anderson and Gordon G. Gallup
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Cart ,Computer science ,Interpretation (philosophy) ,media_common.quotation_subject ,Assertion ,Experimental and Cognitive Psychology ,Scopa ,Ambiguity ,Terminology ,Control (linguistics) ,Ecology, Evolution, Behavior and Systematics ,Cognitive psychology ,media_common ,Coding (social sciences) - Abstract
The recent article by Baragli, Scopa, Maglieri, and Palagi (Anim Cogn https://doi.org/10.1007/s10071-021-01502-7 , 2021) that claims to demonstrate mirror self-recognition (MSR) in horses is not based on compelling evidence. We identify problems with their experimental procedures, data, and assertion about “demonstrating MSR at group level.” Examples of these problems include incomplete experimental design, absence of important control conditions, inappropriate terminology, suboptimal mark application procedures and coding of videos, ambiguity of videos presented as supporting evidence, and inconsistencies in data presentation and interpretation. It is not the case that their study “marks a turning point in the analytical technique of MSR exploration.”
- Published
- 2021
32. Cannula cricothyroidotomy in the impalpable neck: An observational study of simulated 'can't intubate, can't oxygenate' scenarios by teams following a cannula-first algorithm in live anaesthetised pigs
- Author
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Alexander S Wycherley, Edward M Debenham, Edmond O’Loughlin, James R Anderson, Faraz R Syed, and Anthea L Raisis
- Subjects
Anesthesiology and Pain Medicine ,Swine ,Intubation, Intratracheal ,Animals ,Cannula ,Humans ,Prospective Studies ,Airway Management ,Critical Care and Intensive Care Medicine ,Algorithms ,Catheterization - Abstract
Live animal models can be used to train anaesthetists to perform emergency front-of-neck-access. Cannula cricothyroidotomy success reported in previous wet lab studies contradicts human clinical data. This prospective, observational study reports success of a cannula-first ‘can't intubate, can't oxygenate’ algorithm for impalpable anatomy during high fidelity team simulations using live, anaesthetised pigs. Forty-two trained anaesthesia teams were instructed to follow the Royal Perth Hospital can't intubate, can't oxygenate algorithm to re-oxygenate a desaturating pig with impalpable neck anatomy (mean (standard deviation, SD) 16.2 (3.5) kg); mean (SD) tracheal internal diameter 11 (1.4) mm. Teams were informed that failure would prompt veterinary-led euthanasia. All teams performed percutaneous cannula cricothyroidotomy as the initial technique, with a median (interquartile range, IQR (range)) start time of 42 (35–50 (24–93)) s. First-pass percutaneous cannula success was 29% to both insufflate tracheal oxygen and re-oxygenate. Insufflation success improved with repeated percutaneous attempts (up to three), but prolonged hypoxia time increasingly necessitated euthanasia (insufflation 57%; re-oxygenation 48%). First, second and third percutaneous attempts achieved insufflation at median (IQR (range)) 74 (64–91 (46–110)) s, 111 (95–136 (79–150)) s and 141 (127–159 (122–179)) s, respectively. Eighteen teams failed with percutaneous cannulae and performed scalpel techniques, predominantly dissection cannulation ( n = 17) which achieved insufflation in all cases (insufflation 100%; re-oxygenation 47%). Scalpel attempts were started at median (IQR (range)) 142 (133–218 (97–293)) s and achieved insufflation at 232 (205–303 (152–344)) s. While percutaneous cannula cricothyroidotomy could rapidly re-oxygenate, the success rate was low and teams repeated attempts beyond the recommended 60 s time frame, delaying transition to the more successful dissection cannula technique. We recommend this ‘cannula-first’ can't intubate, can't oxygenate algorithm adopts a ‘single best effort’ strategy for percutaneous cannula, with failure prompting a scalpel technique.
- Published
- 2022
33. Synaptic inputs to broad thorny ganglion cells in macaque retina
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Judith Mosinger Ogilvie, James A. Kuchenbecker, Alice Z. Chuang, Diego Perez, Andrea S. Bordt, Rodrigo Gonzales-Rojas, Sara S. Patterson, James R. Anderson, Luke Tseng, Christian Puller, Ashley Roland, Rebecca J. Girresch, David W. Marshak, Charis Tang, Jay Neitz, and Marcus Mazzaferri
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Male ,Retinal Ganglion Cells ,0301 basic medicine ,Interneuron ,Inhibitory postsynaptic potential ,Macaque ,Retinal ganglion ,Retina ,Article ,03 medical and health sciences ,0302 clinical medicine ,biology.animal ,Connectome ,medicine ,Biological neural network ,Animals ,biology ,General Neuroscience ,Inner plexiform layer ,Amacrine Cells ,030104 developmental biology ,medicine.anatomical_structure ,Synapses ,Excitatory postsynaptic potential ,Macaca ,Macaca nemestrina ,Neuroscience ,030217 neurology & neurosurgery - Abstract
In primates, broad thorny retinal ganglion cells are highly sensitive to small, moving stimuli. They have tortuous, fine dendrites with many short, spine-like branches that occupy three contiguous strata in the middle of the inner plexiform layer. The neural circuits that generate their responses to moving stimuli are not well-understood, and that was the goal of this study. A connectome from central macaque retina was generated by serial block-face scanning electron microscopy, a broad thorny cell was reconstructed, and its synaptic inputs were analyzed. It received fewer than 2% of its inputs from both ON and OFF types of bipolar cells; the vast majority of its inputs were from amacrine cells. The presynaptic amacrine cells were reconstructed, and seven types were identified based on their characteristic morphology. Two types of narrow-field cells, knotty bistratified type 1 and wavy multistratified type 2, were identified. Two types of medium-field amacrine cells, ON starburst and spiny, were also presynaptic to the broad thorny cell. Three types of wide-field amacrine cells, wiry type 2, stellate wavy and semilunar type 2, also made synapses onto the broad thorny cell. Physiological experiments using a macaque retinal preparation in vitro confirmed that broad thorny cells received robust excitatory input from both the ON and the OFF pathways. Given the paucity of bipolar cell inputs, it is likely that amacrine cells provided much of the excitatory input, in addition to inhibitory input. This article is protected by copyright. All rights reserved.
- Published
- 2021
34. Cats (Felis catus) Show No Avoidance of People Who Behave Negatively to Their Owner
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Kazuo Fujita, Saho Takagi, Hika Kuroshima, Minori Arahori, Hitomi Chijiiwa, and James R. Anderson
- Subjects
CATS ,domesticated animals ,third-party interaction ,cats ,lcsh:Zoology ,Zoology ,General Medicine ,social cognition ,cat-human relationship ,lcsh:QL1-991 ,Psychology ,Felis catus ,social evaluation - Abstract
Humans evaluate others based on interactions between third parties, even when those interactions are of no direct relevance to the observer. Such social evaluation is not limited to humans. We previously showed that dogs avoided a person who behaved negatively to their owner (Chijiiwa et al., 2015). Here, we explored whether domestic cats, another common companion animal, similarly evaluate humans based on third-party interactions. We used the same procedure that we used with dogs: cats watched as their owner first tried unsuccessfully to open a transparent container to take out an object, and then requested help from a person sitting nearby. In the Helper condition, this second person (helper) helped the owner to open the container, whereas in the Non-Helper condition the actor refused to help, turning away instead. A third, passive (neutral) person sat on the other side of the owner in both conditions. After the interaction, the actor and the neutral person each offered a piece of food to the cat, and we recorded which person the cat took food from. Cats completed four trials and showed neither a preference for the helper nor avoidance of the non-helper. We consider that cats might not possess the same social evaluation abilities as dogs, at least in this situation, because unlike the latter, they have not been selected to cooperate with humans. However, further work on cats’ social evaluation capacities needs to consider ecological validity, notably with regard to the species’ sociality.
- Published
- 2021
35. Identification of tissue-dependent proteins in knee OA synovial fluid
- Author
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T.J. Welting, L.W. van Rhijn, A. Smagul, P.J. Emans, Holger Jahr, Mandy J. Peffers, Ufuk Tan Timur, James R Anderson, D.C. Green, RS: CAPHRI - R3 - Functioning, Participating and Rehabilitation, Orthopedie, MUMC+: MA AIOS Orthopedie (9), MUMC+: MA Orthopedie (9), MUMC+: MA Orthopedie (3), and MUMC+: Centrum voor Bewegen (3)
- Subjects
Cartilage, Articular ,Male ,Proteomics ,0301 basic medicine ,tissue-dependent ,Pathology ,medicine.medical_specialty ,Knee Joint ,Biomedical Engineering ,Osteoarthritis ,Meniscus (anatomy) ,Menisci, Tibial ,Fat pad ,03 medical and health sciences ,0302 clinical medicine ,Rheumatology ,Synovial Fluid ,medicine ,Humans ,Synovial fluid ,Orthopedics and Sports Medicine ,ddc:610 ,Aged ,Secretome ,030203 arthritis & rheumatology ,JOINT ,Chemistry ,Cartilage ,Synovial Membrane ,Biomarker ,Osteoarthritis, Knee ,musculoskeletal system ,medicine.disease ,stage ,osteoarthritis ,030104 developmental biology ,medicine.anatomical_structure ,Adipose Tissue ,Case-Control Studies ,Proteome ,Female - Abstract
Osteoarthritis and cartilage 29(1), 124-133 (2021). doi:10.1016/j.joca.2020.09.005, Published by Elsevier, [S.l.]
- Published
- 2021
36. LC-MS/MS-Based Serum Protein Profiling for Identification of Candidate Biomarkers in Pakistani Rheumatoid Arthritis Patients
- Author
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Sidrah Jahangir, Peter John, Attya Bhatti, Muhammad Muaaz Aslam, Javaid Mehmood Malik, James R. Anderson, and Mandy J. Peffers
- Subjects
Space and Planetary Science ,Paleontology ,rheumatoid arthritis ,serum ,proteomics ,biomarkers ,LC-MS ,General Biochemistry, Genetics and Molecular Biology ,Ecology, Evolution, Behavior and Systematics - Abstract
Rheumatoid arthritis is an autoimmune disorder of complex disease etiology. Currently available serological diagnostic markers lack in terms of sensitivity and specificity and thus additional biomarkers are warranted for early disease diagnosis and management. We aimed to screen and compare serum proteome profiles of rheumatoid arthritis serotypes with healthy controls in the Pakistani population for identification of potential disease biomarkers. Serum samples from rheumatoid arthritis patients and healthy controls were enriched for low abundance proteins using ProteoMinerTM columns. Rheumatoid arthritis patients were assigned to one of the four serotypes based on anti-citrullinated peptide antibodies and rheumatoid factor. Serum protein profiles were analyzed via liquid chromatography-tandem mass spectrometry. The changes in the protein abundances were determined using label-free quantification software ProgenesisQITM followed by pathway analysis. Findings were validated in an independent cohort of patients and healthy controls using an enzyme-linked immunosorbent assay. A total of 213 proteins were identified. Comparative analysis of all groups (false discovery rate < 0.05, >2-fold change, and identified with ≥2 unique peptides) identified ten proteins that were differentially expressed between rheumatoid arthritis serotypes and healthy controls including pregnancy zone protein, selenoprotein P, C4b-binding protein beta chain, apolipoprotein M, N-acetylmuramoyl-L-alanine amidase, catalytic chain, oncoprotein-induced transcript 3 protein, Carboxypeptidase N subunit 2, Apolipoprotein C-I and Apolipoprotein C-III. Pathway analysis predicted inhibition of liver X receptor/retinoid X receptor activation pathway and production of nitric oxide and reactive oxygen species pathway in macrophages in all serotypes. A catalogue of potential serum biomarkers for rheumatoid arthritis were identified. These biomarkers can be further evaluated in larger cohorts from different populations for their diagnostic and prognostic potential.
- Published
- 2022
- Full Text
- View/download PDF
37. Ultrastructural Mapping of Neural Circuitry: A Computational Framework.
- Author
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James R. Anderson 0002, Bryan W. Jones, Jia-Hui Yang, Maggie V. Shaw, Carl B. Watt, Paul Koshevoy, Joël Spaltenstein, Elizabeth Jurrus, Kannan Umadevi Venkataraju, Ross T. Whitaker, David N. Mastronarde, Tolga Tasdizen, and Robert Marc
- Published
- 2009
- Full Text
- View/download PDF
38. Detection of neuron membranes in electron microscopy images using a serial neural network architecture.
- Author
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Elizabeth Jurrus, António R. C. Paiva, Shigeki Watanabe, James R. Anderson 0002, Bryan W. Jones, Ross T. Whitaker, Erik M. Jorgensen, Robert Marc, and Tolga Tasdizen
- Published
- 2010
- Full Text
- View/download PDF
39. Tools and Approaches for Assembly, Review, and Analysis of Large-Scale Electron Microscopy
- Author
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Crystal Sigulinsky, James R. Anderson, Rebecca L. Pfeiffer, and Bryan W. Jones
- Subjects
Scale (ratio) ,Computer science ,law ,Nanotechnology ,Electron microscope ,Instrumentation ,law.invention - Published
- 2021
40. One thousand yawns
- Author
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James R. Anderson
- Subjects
Cognitive science ,Animal ecology ,Animal Science and Zoology ,Biology - Published
- 2020
41. Activity of Vincristine and Irinotecan in Diffuse Anaplastic Wilms Tumor and Therapy Outcomes of Stage II to IV Disease: Results of the Children’s Oncology Group AREN0321 Study
- Author
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Elizabeth Mullen, James R. Anderson, James I. Geller, Deborah A. Ward, Paul E. Grundy, Elizabeth J. Perlman, Anne B. Warwick, Arnold C. Paulino, Jeffrey S. Dome, Najat C. Daw, Eric J. Gratias, Yeonil Kim, Fredric A. Hoffer, John A. Kalapurakal, Peter F. Ehrlich, Yueh-Yun Chi, Conrad V. Fernandez, Brett Tornwall, and Geetika Khanna
- Subjects
Adult ,Male ,0301 basic medicine ,Oncology ,Cancer Research ,Vincristine ,medicine.medical_specialty ,Adolescent ,Disease ,Stage ii ,Irinotecan ,Pediatrics ,Wilms Tumor ,Young Adult ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Internal medicine ,Antineoplastic Combined Chemotherapy Protocols ,medicine ,Humans ,In patient ,Child ,Neoplasm Staging ,business.industry ,Wilms' tumor ,ORIGINAL REPORTS ,medicine.disease ,Carboplatin ,Regimen ,030104 developmental biology ,chemistry ,Child, Preschool ,030220 oncology & carcinogenesis ,Female ,business ,medicine.drug - Abstract
PURPOSE AREN0321 evaluated the activity of vincristine and irinotecan (VI) in patients with newly diagnosed diffuse anaplastic Wilms tumor (DAWT) and whether a regimen containing carboplatin (regimen UH1) in addition to regimen I agents used in the National Wilms Tumor Study 5 (NWTS-5; vincristine, doxorubicin, cyclophosphamide, and etoposide plus radiotherapy) would improve patient outcomes. PATIENTS AND METHODS Patients with stage II to IV DAWT without measurable disease received regimen UH1. Patients with stage IV measurable disease were eligible to receive VI (vincristine, 1.5 mg/m2 per day intravenously on days 1 and 8; irinotecan, 20 mg/m2 per day intravenously on days 1-5 and 8-12 of a 21-day cycle) in an upfront window; those with complete (CR) or partial response (PR) had VI incorporated into regimen UH1 (regimen UH2). The study was designed to detect improvement in outcomes of patients with stage II to IV DAWT compared with historical controls treated with regimen I. RESULTS Sixty-six eligible patients were enrolled. Of 14 patients with stage IV measurable disease who received VI, 11 (79%) achieved CR (n = 1) or PR (n = 10) after 2 cycles. Doses of doxorubicin, cyclophosphamide, and etoposide were reduced midstudy because of nonhematologic toxicity. Four patients (6%) died as a result of toxicity. Four-year event-free survival, relapse-free survival, and overall survival rates were 67.7% (95% CI, 55.9% to 79.4%), 72.9% (95% CI, 61.5% to 84.4%), and 73.7% (95% CI, 62.7% to 84.8%), respectively, compared with 57.5% (95% CI, 47.6% to 67.4%; P = .26), 57.5% (95% CI, 47.6% to 67.4%; P = .048), and 59.2% (95% CI, 49.4% to 69.0%; P = .08), respectively, in NWTS-5. CONCLUSION VI produced a high response rate in patients with metastatic DAWT. AREN0321 treatment seemed to improve outcomes for patients with stage II to IV DAWT compared with NWTS-5, but with increased toxicity. The UH2 regimen warrants further investigation with modifications to reduce toxicity.
- Published
- 2020
42. Investigating reactions of squirrel monkeys (Saimiri sciureus) towards unequal food distributions in a tray-pulling paradigm
- Author
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James R. Anderson, Benoit Bucher, Hika Kuroshima, Kazuo Fujita, and Maxime Bourgeois
- Subjects
Male ,Presence OR identity ,biology ,Squirrel monkey ,Saimiri sciureus ,biology.organism_classification ,Choice Behavior ,Reward ,Food ,Animal ecology ,Social relationship ,Animals ,Female ,Animal Science and Zoology ,Psychology ,Saimiri ,Demography ,Inequity aversion ,New World monkey - Abstract
The fact that squirrel monkeys do not routinely cooperate in the wild has been proposed to explain their failure to show disadvantageous inequity aversion (i.e., negative reactions when receiving less than a partner) in an experimental exchange. Here we assessed whether the use of a tray-pulling paradigm, allowing for a larger variety of unequal testing situations, would bring additional insights into inequity aversion in this species. Squirrel monkeys were tested in pairs in which only the donor could pull a tray baited with food to within reach of itself and a recipient. Using pairs with different social relationships, we examined donors' frequencies of pulling both in the presence and absence of a recipient, as well as across three different food distributions: equal, qualitative inequity (higher-value reward for the recipient), and quantitative inequity (no food reward for the donor). Results showed that female donors pulled the tray less often in the quantitative inequity condition with an out-group female recipient than when alone. However, such discrimination was not observed when females were with female in-group and male out-group recipients. By contrast, male donors did not adjust their pull frequencies according to the recipient's presence or identity (female and male out-group recipients). These results point towards possible disadvantageous inequity aversion in female squirrel monkeys. However, alternative hypotheses such as increased arousal caused by out-group female recipients cannot be ruled out. We discuss the data in line with major theories of inequity aversion and cooperation in primates.
- Published
- 2020
43. Responses to death and dying: primates and other mammals
- Author
-
James R. Anderson
- Subjects
Primates ,0106 biological sciences ,Value (ethics) ,Old World ,Adaptive value ,Behavior, Animal ,Elephants ,05 social sciences ,Behavioural sciences ,010603 evolutionary biology ,01 natural sciences ,Death ,Thanatology ,Animal ecology ,Animals ,0501 psychology and cognitive sciences ,Animal Science and Zoology ,Horses ,050102 behavioral science & comparative psychology ,Taxonomic rank ,Social Behavior ,Psychology ,Cognitive psychology - Abstract
Although some definitions of thanatology-broadly definable as the study of death and dying-exclude nonhumans as subjects, recognition of the scientific value of studying how other species respond to sick, injured, dying and dead conspecifics appears to be growing. And whereas earlier literature was largely characterized by anecdotal descriptions and sometimes fanciful interpretations, we now see more rigorous and often quantitative analysis of various behaviors displayed towards conspecifics (and sometimes heterospecifics) at various stages of incapacitation, including death. Studies of social insects in particular have revealed chemical cues that trigger corpse management behaviors, as well as the adaptive value of these behaviors. More recent research on other taxonomic groups (including aquatic and avian species, and mammals) has sought to better document these animals' responses to the dying and dead, to identify influencing factors and underlying mechanisms, and to better understand the physiological, emotional, social and psychological significance of the phenomena observed. This special issue presents original short reports, reviews, and full research articles relating to these topics in New World monkeys, Old World monkeys and apes, as well as equids and proboscids. The range of events, data, hypotheses and proposals presented will hopefully enrich the field and stimulate further developments in comparative evolutionary thanatology.
- Published
- 2020
44. KEYNOTE-716: Phase III study of adjuvant pembrolizumab versus placebo in resected high-risk stage II melanoma
- Author
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Piotr Rutkowski, Sama Ahsan, Jean-Jacques Grob, Matteo S. Carlino, James R. Anderson, Merrick I. Ross, John M. Kirkwood, Jeffrey E. Gershenwald, Caroline Robert, Jason J. Luke, Nageatte Ibrahim, Charles H. Yoon, Peter Mohr, Georgina V. Long, Alexander M.M. Eggermont, Axel Hauschild, Paolo A. Ascierto, Andrew Poklepovic, and Richard A. Scolyer
- Subjects
Adult ,Male ,Oncology ,Cancer Research ,medicine.medical_specialty ,Skin Neoplasms ,Adolescent ,medicine.medical_treatment ,Dermatologic Surgical Procedures ,Programmed Cell Death 1 Receptor ,Pembrolizumab ,Antibodies, Monoclonal, Humanized ,Placebo ,Disease-Free Survival ,Placebos ,Young Adult ,03 medical and health sciences ,Antineoplastic Agents, Immunological ,0302 clinical medicine ,Internal medicine ,medicine ,Adjuvant therapy ,Humans ,Multicenter Studies as Topic ,030212 general & internal medicine ,Young adult ,Child ,Melanoma ,Neoplasm Staging ,Randomized Controlled Trials as Topic ,Cross-Over Studies ,business.industry ,General Medicine ,medicine.disease ,Crossover study ,Clinical trial ,Clinical Trials, Phase III as Topic ,Chemotherapy, Adjuvant ,030220 oncology & carcinogenesis ,Female ,Neoplasm Recurrence, Local ,business ,Adjuvant - Abstract
Patients with high-risk stage II melanoma are at significant risk for recurrence after surgical resection. Adjuvant treatment options to lower the risk for distant metastases are limited. Although adjuvant IFN-α2b is associated with improved relapse-free survival in patients with high-risk melanoma, toxicity and limited overall survival benefits limit its use. Adjuvant treatment with the PD-1 inhibitor pembrolizumab significantly improved recurrence-free survival, compared with placebo, in patients with resected stage III melanoma in the Phase III KEYNOTE-054 trial; efficacy in patients with stage II disease has not been established. This article describes the design and rationale of KEYNOTE-716 (NCT03553836), a two-part, randomized, placebo-controlled, multicenter Phase III study of adjuvant pembrolizumab in patients with surgically resected high-risk stage II melanoma. Clinical trial registry & ID: ClinicalTrials.gov, NCT03553836
- Published
- 2020
45. Visual Self-Recognition
- Author
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David L. Butler and James R. Anderson
- Published
- 2022
46. Small non-coding RNA landscape of extracellular vesicles from a post-traumatic model of equine osteoarthritis
- Author
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James R. Anderson, Stine Jacobsen, Marie Walters, Louise Bundgaard, Andreas Diendorfer, Matthias Hackl, Emily J. Clarke, Victoria James, and Mandy J. Peffers
- Subjects
Veterinary Science, osteoarthritis, extracellular vesicles, small non-coding RNA, synovial fluid, plasma ,osteoarthritis ,synovial fluid ,General Veterinary ,extracellular vesicles ,plasma ,small non-coding RNA - Abstract
Extracellular vesicles comprise an as yet inadequately investigated intercellular communication pathway in the field of early osteoarthritis. We hypothesised that the small non-coding RNA expression pattern in synovial fluid and plasma would change during progression of experimental osteoarthritis. In this study, we conducted small RNA sequencing to provide a comprehensive overview of the temporal expression profiles of small non-coding transcripts carried by extracellular vesicles derived from plasma and synovial fluid for the first time in a posttraumatic model of equine osteoarthritis. Additionally, we characterised synovial fluid and plasma-derived extracellular vesicles with respect to quantity, size, and surface markers. The different temporal expressions of seven microRNAs in plasma and synovial fluid-derived extracellular vesicles, eca-miR-451, eca-miR-25, eca-miR-215, eca-miR-92a, eca-miR-let-7c, eca-miR-486-5p, and eca-miR-23a, and four snoRNAs, U3, snord15, snord46, and snord58, represent potential biomarkers for early osteoarthritis. Bioinformatics analysis of the differentially expressed microRNAs in synovial fluid highlighted that in early osteoarthritis these related to the inhibition of cell cycle, cell cycle progression, DNA damage and cell proliferation as well as increased cell viability and differentiation of stem cells. Plasma and synovial fluid-derived extracellular vesicle small non-coding signatures have been established for the first time in a temporal model of osteoarthritis. These could serve as novel biomarkers for evaluation of osteoarthritis progression or act as potential therapeutic targets.
- Published
- 2022
47. A Coarse-Grained FPGA Architecture for High-Performance FIR Filtering.
- Author
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James R. Anderson 0001, Siddharth Sheth, and Kaushik Roy 0001
- Published
- 1998
- Full Text
- View/download PDF
48. Wide‐field amacrine cell inputs to ON parasol ganglion cells in macaque retina
- Author
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Andrea S. Bordt, James R. Anderson, Conor M. Linehan, Luke Tseng, Nicole Barnes Harris, Judith Mosinger Ogilvie, David W. Marshak, Sriram Navuluri, James A. Kuchenbecker, Chaiss Matthews, Sara S. Patterson, Diego Perez, Eunice Yeo, Jay Neitz, Rebecca J. Girresch, Jacob Bauss, and Michael B. Manookin
- Subjects
Male ,Retinal Ganglion Cells ,0301 basic medicine ,Interneuron ,Biology ,Inhibitory postsynaptic potential ,Retinal ganglion ,Article ,Amacrine cell ,03 medical and health sciences ,0302 clinical medicine ,Connectome ,medicine ,Animals ,Retina ,General Neuroscience ,Inner plexiform layer ,Light intensity ,Amacrine Cells ,030104 developmental biology ,medicine.anatomical_structure ,Receptive field ,Synapses ,Macaca nemestrina ,Neuroscience ,030217 neurology & neurosurgery - Abstract
Parasol cells are one of the major types of primate retinal ganglion cells. The goal of this study was to describe the synaptic inputs that shape the light responses of the ON type of parasol cells, which are excited by increments in light intensity. A connectome from central macaque retina was generated by serial blockface scanning electron microscopy. Six neighboring ON parasol cells were reconstructed, and their synaptic inputs were analyzed. On average, they received 21% of their input from bipolar cells, excitatory local circuit neurons receiving input from cones. The majority of their input was from amacrine cells, local circuit neurons of the inner retina that are typically inhibitory. Their contributions to the neural circuit providing input to parasol cells are not well-understood, and the focus of this study was on the presynaptic wide-field amacrine cells, which provided 17% of the input to ON parasol cells. These are GABAergic amacrine cells with long, relatively straight dendrites, and sometimes also axons, that run in a single, narrow stratum of the inner plexiform layer. The presynaptic wide-field amacrine cells were reconstructed, and two types were identified based on their characteristic morphology. One presynaptic amacrine cell was identified as semilunar type 2, a polyaxonal cell that is electrically coupled to ON parasol cells. A second amacrine was identified as wiry type 2, a type known to be sensitive to motion. These inputs likely make ON parasol cells more sensitive to stimuli that are rapidly changing outside their classical receptive fields.
- Published
- 2019
49. Synovial Sarcoma in Children, Adolescents, and Young Adults: A Report From the Children's Oncology Group ARST0332 Study
- Author
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Wei Xue, Jennifer O. Black, Andrew Ostrenga, Simon C. Kao, Barry L. Shulkin, James R. Anderson, R. Lor Randall, Rajkumar Venkatramani, Suzanne L. Wolden, Dolores Lopez-Terrada, Alberto S. Pappo, and Sheri L. Spunt
- Subjects
Male ,Cancer Research ,Prospective Studies ,Young adult ,Child ,Cancer ,Pediatric ,screening and diagnosis ,Soft tissue sarcoma ,Soft tissue ,Sarcoma ,ORIGINAL REPORTS ,Prognosis ,Combined Modality Therapy ,Synovial sarcoma ,Neoadjuvant Therapy ,6.5 Radiotherapy and other non-invasive therapies ,Survival Rate ,Detection ,Oncology ,Child, Preschool ,Treatment strategy ,Female ,Patient Safety ,4.2 Evaluation of markers and technologies ,Adult ,medicine.medical_specialty ,Pediatric Research Initiative ,Adolescent ,Pediatric Cancer ,Clinical Trials and Supportive Activities ,Clinical Sciences ,Oncology and Carcinogenesis ,Sarcoma, Synovial ,Young Adult ,Rare Diseases ,Clinical Research ,Internal medicine ,medicine ,Humans ,Oncology & Carcinogenesis ,Preschool ,Synovial ,business.industry ,Infant ,Evaluation of treatments and therapeutic interventions ,medicine.disease ,Orphan Drug ,Early adolescents ,business ,Follow-Up Studies - Abstract
PURPOSE Synovial sarcoma (SS) is the second most common malignant soft tissue tumor in children. ARST0332 evaluated a risk-based treatment strategy for young patients with soft tissue sarcoma designed to limit therapy for low-risk (LR) disease and to test neoadjuvant chemoradiotherapy for unresected higher-risk disease. METHODS Newly diagnosed patients with SS age < 30 years were assigned to four treatment arms based on disease features: A (surgery only), B (55.8 Gy radiotherapy [RT]), C (ifosfamide and doxorubicin [ID] chemotherapy plus 55.8 Gy RT), and D (neoadjuvant ID and 45 Gy RT, then surgery and RT boost based on margins followed by adjuvant ID). Patients treated in Arms A and B were considered LR, arms C and D without metastases as intermediate-risk (IR), and those with metastases as high-risk (HR). RESULTS Of the 146 patients with SS enrolled, 138 were eligible and evaluable: LR (46), IR (71), and HR (21). Tumors were 80% extremity, 70% > 5 cm, 70% high-grade, 62% invasive, 95% deep, and 15% metastatic. Treatment was on arm A (29.7%), B (3.6%), C (16.7%), and D (50%). There were no toxic deaths and four unexpected grade 4 adverse events. By risk group, at a median follow-up of 6.8 years, estimated 5-year event-free survival was LR 82%, IR 70%, and HR 8%, and overall survival was LR 98%, IR 89%, and HR 13%. After accounting for the features that defined risk category, none of the other patient or disease characteristics (age, sex, tumor site, tumor invasiveness, and depth) improved the risk stratification model. CONCLUSION The risk-based treatment strategy used in ARST0332 produced favorable outcomes in patients with nonmetastatic SS relative to historical controls despite using RT less frequently and at lower doses. The outcome for metastatic SS remains unsatisfactory and new therapies are urgently needed.
- Published
- 2021
50. Mouse microRNA signatures in joint ageing and post-traumatic osteoarthritis
- Author
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Mandy J. Peffers, Katarzyna Goljanek-Whysall, Peter D. Clegg, Peter Milner, Catarina Castanheira, Louise House, James R Anderson, and Yongxiang Fang
- Subjects
Small RNA ,microRNA ,business.industry ,Post traumatic osteoarthritis ,Sham surgery ,Osteoarthritis ,Disease ,Diseases of the musculoskeletal system ,medicine.disease ,Article ,Joint ageing ,Andrology ,Real-time polymerase chain reaction ,RC925-935 ,Ageing ,Medicine ,business ,Biomarkers - Abstract
Objective This study investigated mice serum and joint microRNA expression profiles in ageing and osteoarthritis to elucidate the role of microRNAs in the development and progression of disease, and provide biomarkers for ageing and osteoarthritis. Design Whole joints and serum samples were collected from C57BL6/J male mice and subjected to small RNA sequencing. Groups used included; surgically-induced post-traumatic osteoarthritis, (DMM; 24 months-old); sham surgery (24 months-old); old mice (18 months-old); and young mice (8 months-old). Differentially expressed microRNAs between the four groups were identified and validated using real-time quantitative PCR. MicroRNA differential expression data was used for target prediction and pathway analysis. Results In joint tissues, miR-140–5p, miR-205–5p, miR-682, miR-208b-3p, miR-499–5p, miR-455–3p and miR-6238 were differentially expressed between young and old groups; miR-146a-5p, miR-3474, miR-615–3p and miR-151–5p were differentially expressed between DMM and Sham groups; and miR-652–3p, miR-23b-3p, miR-708–5p, miR-5099, miR-23a-3p, miR-214–3p, miR-6238 and miR-148–3p between the old and DMM groups. The number of differentially expressed microRNAs in serum was higher, some in common with joint tissues including miR-140–5p and miR-455–3p between young and old groups; and miR-23b-3p, miR-5099 and miR-6238 between old and DMM groups. We confirmed miR-140–5p, miR-499–5p and miR-455–3p expression to be decreased in old mouse joints compared to young, suggesting their potential use as biomarkers of joint ageing in mice. Conclusions MiR-140–5p, miR-499–5p and miR-455–3p could be used as joint ageing biomarkers in mice. Further research into these specific molecules in human tissues is now warranted to check their potential suitability as human biomarkers of ageing.
- Published
- 2021
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