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1,422 results on '"Hughes, Daniel"'

6. Predicting programmed death-ligand 1 (PD-L1) expression with fluorine-18 fluorodeoxyglucose ([18F]FDG) positron emission tomography/computed tomography (PET/CT) metabolic parameters in resectable non-small cell lung cancer

Author

Hughes, Daniel Johnathan, Josephides, Eleni, O’Shea, Robert, Manickavasagar, Thubeena, Horst, Carolyn, Hunter, Sarah, Tanière, Philippe, Nonaka, Daisuke, Van Hemelrijck, Mieke, Spicer, James, Goh, Vicky, Bille, Andrea, Karapanagiotou, Eleni, and Cook, Gary J. R.

Published
2024
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8. [Problem] Cerberus: Minimalistic Multi-shard Byzantine-resilient Transaction Processing

Author

Hellings, Jelle, Hughes, Daniel P., Primero, Joshua, and Sadoghi, Mohammad

Abstract

To enable scalable resilient blockchain systems, several powerful general-purpose approaches toward sharding such systems have been demonstrated. Unfortunately, these approaches all come with substantial costs for ordering andexecution of multi-shard transactions.In this work, we ask whether one can achieve significantcost reductions for processing multi-shard transactions by limiting the type of workloads supported. To initiate the study of this problem, we propose CERBERUS, a family of minimalistic primitives for processing single-shard and multi-shard UTXO-like transactions. The first CERBERUS variant we propose is core-CERBERUS (CCERBERUS). CCERBERUS uses strict UTXO-based environmental requirements to enable powerful multi-shard transaction processing with an absolute minimum amount of coordination between shards. In the environment we designed CCERBERUS for, CCERBERUS will operate perfectly with respect to all transactions proposed and approved by well-behaved clients, but does not provide any other guarantees.To illustrate that CCERBERUS -like protocols can also be of use in environments with faulty clients, we also demonstrate two generalizations of CCERBERUS, optimistic-CERBERUS and resilient-CERBERUS, that make different tradeoffs in complexity and costs when dealing with faulty behavior and attacks. Finally, we compare these three protocols and show their potential scalability and performance benefits over state-of-the-art general-purpose systems. These results underline the importance of the study of specialized approaches toward sharding in resilient systems.

Published
2023

10. Five-year recurrence/survival after pancreatoduodenectomy for pancreatic adenocarcinoma: does pre-existing diabetes matter? Results from the Recurrence After Whipple's (RAW) study

Author

Lead Unit, Aroori, Somaiah, Labib, Peter L., Russell, Thomas B., Streeter, Adam, Denson, Jemimah, Puckett, Mark, Zhou, Shang-Ming, Browning, Matthew, Collaborating Units, Ausania, Fabio, Gonzalez-Abos, Carolina, Pando, Elizabeth, Fernandes, Nair, Moller, Elsa G., Taboada, Cristina D., Roberts, Keith, Pande, Rupaly, Alfarah, Jameel, Kausar, Ambareen, Bandyopadhyay, Samik, Abdelrahim, Ahmed, Khan, Ayesha, Mavroeidis, Vasileios K., Jordan, Caitlin, Rees, Jonathan R.E., Marangoni, Gabriele, Blege, Harry, Thomasset, Sarah, Cambridge, William, White, Olga, Frampton, Adam, Blacker, Sarah, Blackburn, Jessie, Sweeney, Casie, Lykoudis, Pavlos, Field, Daniel, Gouda, Mohammed, Maglione, Manuel, Bellotti, Ruben, Alhaboob, Nassir, Hamid, Hytham K.S., Bari, Hassaan, Ahmed, Hassan, Smith, Andrew, Moriarty, Catherine, White, Louise, Priestley, Mark, Bode, Kerry, Sharp, Judith, Wragg, Rosie, Jackson, Beverley, Craven, Samuel, Spalding, Duncan, Fehervari, Matyas, Pai, Madhava, Alghazawi, Laith, Onifade, Anjola, Srinivasan, Parthi, Ribaud, Julliette, Nair, Ashitha, Mariathasan, Michael, Grayson, Niamh, Davidson, Brian, Pericleous, Stephanos, Patel, Krishna, Shaw, Conrad, Morare, Nolitha, Zaban, Mohamad K., Bhogal, Ricky, Doyle, Joseph, Croagh, Daniel, Rajagopalan, Ashray, Dominguez, Ismael, Guerrero, Alan, Moguel, Andre, Chan, Carlos, Thakkar, Rohan, Jones, Michael, Buckley, Edward, Akter, Nasreen, Treherne, Kyle, Gomez, Dhanny, Gordon, Gregory, Silva, Michael, Hughes, Daniel, Urbonas, Tomas, Lapolla, Pierfrancesco, Mingoli, Andrea, Brachini, Gioia, Caronna, Roberto, Chirletti, Piero, Porcu, Alberto, Perra, Teresa, Shah, Nehal S., Abd Kahar, Nurul N., Hall, Thomas, Nadeem, Nabeegh, Hamady, Zaed, Karar, Shoura, Arshad, Ali, Al-Sarrieh, Bilal, Yarwood, Adam, Hammoda, Mohammed, Serrablo, Alejandro, Artigas, Maria, Paterna-López, Sandra, Roberts, Keith J., Thomasset, Sarah C., Frampton, Adam E., Smith, Andrew M., Davidson, Brian R., Bhogal, Ricky H., Silva, Michael A., and Hamady, Zaed Z.R.

Published
2024
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12. Patterns, timing and predictors of recurrence following pancreaticoduodenectomy for distal cholangiocarcinoma: An international multicentre retrospective cohort study

Author

Browning, Matthew, Mownah, Omar, Gonzalez-Abos, Carolina, Fernandes, Nair, Moller, Elsa Garcia, Taboada, Cristina Dopazo, Pande, Rupaly, Alfarah, Jameel, Bandyopadhyay, Samik, Abdelrahim, Ahmed, Khan, Ayesha, Jordan, Caitlin, Rees, Jonathan RE., Doyle, Joseph, Blege, Harry, Cambridge, William, White, Olga, Blacker, Sarah, Blackburn, Jessie, Sweeney, Casie, Fehervari, Matyas, Pai, Madhava, Alghazawi, Laith, Onifade, Anjola, Field, Daniel, Gouda, Mohammed, Maglione, Manuel, Hamid, Hytham KS., Ribaud, Julliette, Nair, Ashitha, Mariathasan, Michael, Grayson, Niamh, Ahmed, Hassan, Moriarty, Catherine, White, Louise, Priestley, Mark, Bode, Kerry, Sharp, Judith, Wragg, Rosie, Jackson, Beverley, Craven, Samuel, Guerrero, Alan, Moguel, Andre, Chan, Carlos, Jones, Michael, Buckley, Edward, Akter, Nasreen, Treherne, Kyle, Gordon, Gregory, Hughes, Daniel, Urbonas, Tomas, Brachini, Gioia, Caronna, Roberto, Chirletti, Piero, Pericleous, Stephanos, Patel, Krishna, Shaw, Conrad, Morare, Nolitha, Zaban, Mohamad K., Perra, Teresa, Abd Kahar, Nurul Nadhirah, Hall, Thomas, Nadeem, Nabeegh, Karar, Shoura, Arshad, Ali, Yarwood, Adam, Hammoda, Mohammed, Artigas, Maria Consuelo, Paterna-López, Sandra, Labib, Peter LZ., Russell, Thomas B., Denson, Jemimah L., Puckett, Mark A., Ausania, Fabio, Pando, Elizabeth, Roberts, Keith J., Kausar, Ambareen, Mavroeidis, Vasileios K., Bhogal, Ricky H., Marangoni, Gabriele, Thomasset, Sarah C., Frampton, Adam E., Spalding, Duncan R., Lykoudis, Pavlos, Bellotti, Ruben, Alhaboob, Nassir, Srinivasan, Parthi, Bari, Hassaan, Smith, Andrew, Dominguez-Rosado, Ismael, Croagh, Daniel, Thakkar, Rohan G., Gomez, Dhanny, Silva, Michael A., Lapolla, Pierfrancesco, Mingoli, Andrea, Davidson, Brian R., Porcu, Alberto, Shah, Nehal S., Hamady, Zaed Z., Al-Sarireh, Bilal A., Serrablo, Alejandro, and Aroori, Somaiah

Published
2024
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16. Ex vivo human pancreatic cancer avatars : an in-line personalised therapeutic response assessment platform

Author

Hughes, Daniel Llwyd, O'Neill, Eric, Mukherjee, Somnath, and Soonawalla, Zahir

Subjects
Oncology, Cancer
Abstract

A paradigm shift in long-term survival rates for patients with Pancreatic Ductal Adenocarcinoma (PDAC) has yet to be witnessed. Long-term survival is only achieved in a small minority of patients. Systemic control of the disease can be secured with chemotherapy, however PDAC harbours high rates of chemotherapeutic resistance. Within current clinical practice, chemotherapeutic treatment strategies for PDAC are dictated by the patients' level of fitness. There is no assessment of the individual's tumour biology or acknowledgement of the significant heterogeneity that exists across tumours. Precision therapy incorporates individual tumour phenotype and biological characteristics and utilises this information to guide future management. Such an approach may improve the outcome for patients with PDAC. Whilst several different models for precision therapies have been reported, they all possess weaknesses that limit their use within a clinical setting. Within this thesis, I present the creation of patient derived cancer avatars as a method for delivering precision therapy for patients with PDAC. This approach allows for the creation of individual and miniature versions of a patient's tumour for detailed cellular profiling in addition to an opportunity to perform a therapeutic drug screen. This approach overcomes several of the limitations of other models of precision therapy notably the preservation of the cellular diversity of the primary tumour and can be implemented within a clinically meaningful time frame. I further investigated as to whether long-term ex vivo culture of patient avatars can be achieved through utilising novel perfusion culture. To date, we are the first group to describe the use of perfusion culture of PDAC tissue slices. We demonstrated that perfusion culture is associated with a physiological benefit as we were able to maintain both glucose and lactate levels at a constant level during 12 days of ex vivo culture (p < 0.001 and p<0.0001 respectively). Native functional biological processes within the avatars were preserved ex vivo through the use of perfusion culture. Avatars that were cultured with perfusion culture ex vivo maintained a significantly higher proliferation rate (p < 0.01) and demonstrated reduced rates of cell death as per cleaved caspase 3 activation (p < 0.01). The metabolic activity of the avatars (mTOR) was preserved with perfusion culture (p < 0.01). Our model system also preserved native immune cells present within the tumour during ex vivo culture. Our initial experience with ex vivo chemotherapy treatment of avatars demonstrated a correlation with the patients' clinical response to adjuvant therapy. Therefore, the avatar response to treatment may provide a unique opportunity and a window of insight into the future response of the patient to systemic treatment. This information can be harnessed and utilised to create individual, personalised treatment regimes for each patient. This in turn would change the historic approach to systemic therapy for PDAC, evolving from a generic, standardised treatment approach for all patients to establishing an individual, customisable regime for an individual tumour for each patient. Such an approach may finally translate into prolonging survival for patients with this lethal disease.

Published
2022

18. Impact of Interventional Policies Including Vaccine on Covid-19 Propagation and Socio-Economic Factors

Author

Wu, Haonan, Banerjee, Rajarshi, Venkatachalam, Indhumathi, Percy-Hughes, Daniel, and Chougale, Praveen

Subjects
Computer Science - Machine Learning, Statistics - Applications
Abstract

A novel coronavirus disease has emerged (later named COVID-19) and caused the world to enter a new reality, with many direct and indirect factors influencing it. Some are human-controllable (e.g. interventional policies, mobility and the vaccine); some are not (e.g. the weather). We have sought to test how a change in these human-controllable factors might influence two measures: the number of daily cases against economic impact. If applied at the right level and with up-to-date data to measure, policymakers would be able to make targeted interventions and measure their cost. This study aims to provide a predictive analytics framework to model, predict and simulate COVID-19 propagation and the socio-economic impact of interventions intended to reduce the spread of the disease such as policy and/or vaccine. It allows policymakers, government representatives and business leaders to make better-informed decisions about the potential effect of various interventions with forward-looking views via scenario planning. We have leveraged a recently launched open-source COVID-19 big data platform and used published research to find potentially relevant variables (features) and leveraged in-depth data quality checks and analytics for feature selection and predictions. An advanced machine learning pipeline has been developed armed with a self-evolving model, deployed on a modern machine learning architecture. It has high accuracy for trend prediction (back-tested with r-squared) and is augmented with interpretability for deeper insights.

Published
2021

19. New technology for Force XXI artillery

Author

Clancy, John and Hughes, Daniel P., Maj

Subjects
ARTILLERY - Army - United States, FIRE DIRECTION SYSTEMS, WAR AND TECHNOLOGY
Abstract

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Published
1996

20. Cerberus: Minimalistic Multi-shard Byzantine-resilient Transaction Processing

Author

Hellings, Jelle, Hughes, Daniel P., Primero, Joshua, and Sadoghi, Mohammad

Subjects
Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science - Databases
Abstract

To enable high-performance and scalable blockchains, we need to step away from traditional consensus-based fully-replicated designs. One direction is to explore the usage of sharding in which we partition the managed dataset over many shards that independently operate as blockchains. Sharding requires an efficient fault-tolerant primitive for the ordering and execution of multi-shard transactions, however. In this work, we seek to design such a primitive suitable for distributed ledger networks with high transaction throughput. To do so, we propose Cerberus, a set of minimalistic primitives for processing single-shard and multi-shard UTXO-like transactions. Cerberus aims at maximizing parallel processing at shards while minimizing coordination within and between shards. First, we propose Core-Cerberus, that uses strict environmental requirements to enable simple yet powerful multi-shard transaction processing. In our intended UTXO-environment, Core-Cerberus will operate perfectly with respect to all transactions proposed and approved by well-behaved clients, but does not provide any guarantees for other transactions. To also support more general-purpose environments, we propose two generalizations of Core-Cerberus: we propose Optimistic-Cerberus, a protocol that does not require any additional coordination phases in the well-behaved optimistic case, while requiring intricate coordination when recovering from attacks; and we propose Pessimistic-Cerberus, a protocol that adds sufficient coordination to the well-behaved case of Core-Cerberus, allowing it to operate in a general-purpose fault-tolerant environments without significant costs to recover from attacks. Finally, we compare the three protocols, showing their potential scalability and high transaction throughput in practical environments.

Published
2020

21. Evaluating the evidence for a liver shrinkage diet for obese patients prior to laparoscopic cholecystectomy: A systematic review and meta-analysis

Author

Hughes, Daniel, Elmasry, Mohamed, Wilson, Iain, and Kafsi, JihèNe El

Subjects
Laparoscopy, Laparoscopic surgery, Patient compliance, Liver, Type 2 diabetes, Health
Abstract

Byline: Daniel. Hughes, Mohamed. Elmasry, Iain. Wilson, Jihène. El Kafsi Patients and Methods: A systematic review and meta-analysis was performed (PROSPERO ID CRD42022374610). The primary outcome was to determine the [...]

Published
2024

22. Serious complications of pancreatoduodenectomy correlate with lower rates of adjuvant chemotherapy: Results from the recurrence after Whipple's (RAW) study

Author

Labib, Peter L., Russell, Thomas B., Streeter, Adam, Denson, Jemimah, Puckett, Mark, Zhou, Shang-Ming, Browning, Matthew, Aroori, Somaiah, Ausania, Fabio, Pando, Elizabeth, Roberts, Keith, Kausar, Ambareen, Mavroeidis, Vasileios K., Marangoni, Gabriele, Thomasset, Sarah, Frampton, Adam, Lykoudis, Pavlos, Maglione, Manuel, Alhaboob, Nassir, Bari, Hassaan, Smith, Andrew, Spalding, Duncan, Srinivasan, Parthi, Davidson, Brian, Bhogal, Ricky, Croagh, Daniel, Dominguez, Ismael, Thakkar, Rohan, Gomez, Dhanny, Silva, Michael, Lapolla, Pierfrancesco, Mingoli, Andrea, Porcu, Alberto, Shah, Nehal Sureshkumar, Hamady, Zaed, Al-Sarrieh, Bilal, Serrablo, Alejandro, Gonzalez-Abos, Carolina, Fernandes, Nair, Moller, Elsa Garcia, Taboada, Cristina Dopazo, Pande, Rupaly, Alfarah, Jameel, Bandyopadhyay, Samik, Abdelrahim, Ahmed, Khan, Ayesha, Jordan, Caitlin, Rees, Jonathan R.E., Blege, Harry, Cambridge, William, White, Olga, Blacker, Sarah, Blackburn, Jessie, Sweeney, Casie, Field, Daniel, Gouda, Mohammed, Bellotti, Ruben, Hamid, Hytham K.S., Ahmed, Hassan, Moriarty, Catherine, White, Louise, Priestley, Mark, Bode, Kerry, Sharp, Judith, Wragg, Rosie, Jackson, Beverley, Craven, Samuel, Fehervari, Matyas, Pai, Madhava, Alghazawi, Laith, Onifade, Anjola, Ribaud, Julliette, Nair, Ashitha, Mariathasan, Michael, Grayson, Niamh, Pericleous, Stephanos, Patel, Krishna, Shaw, Conrad, Morare, Nolitha, Zaban, Mohamad Khish, Doyle, Joseph, Guerrero, Alan, Moguel, Andre, Chan, Carlos, Jones, Michael, Buckley, Edward, Akter, Nasreen, Treherne, Kyle, Gordon, Gregory, Hughes, Daniel, Urbonas, Tomas, Brachini, Gioia, Caronna, Roberto, Chirletti, Piero, Perra, Teresa, Abd Kahar, Nurul Nadhirah, Hall, Thomas, Nadeem, Nabeegh, Karar, Shoura, Arshad, Ali, Yarwood, Adam, Hammoda, Mohammed, Artigas, Maria, Paterna-López, Sandra, Roberts, Keith J., Thomasset, Sarah C., Frampton, Adam E., Smith, Andrew M., Davidson, Brian R., Bhogal, Ricky H., Silva, Michael A., Shah, Nehal S., and Hamady, Zaed Z.R.

Published
2023
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23. Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest

Author

Sparks, Michael E, Bansal, Raman, Benoit, Joshua B, Blackburn, Michael B, Chao, Hsu, Chen, Mengyao, Cheng, Sammy, Childers, Christopher, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dugan, Shannon, Elpidina, Elena N, Farrow, David W, Friedrich, Markus, Gibbs, Richard A, Hall, Brantley, Han, Yi, Hardy, Richard W, Holmes, Christopher J, Hughes, Daniel ST, Ioannidis, Panagiotis, Cheatle Jarvela, Alys M, Johnston, J Spencer, Jones, Jeffery W, Kronmiller, Brent A, Kung, Faith, Lee, Sandra L, Martynov, Alexander G, Masterson, Patrick, Maumus, Florian, Munoz-Torres, Monica, Murali, Shwetha C, Murphy, Terence D, Muzny, Donna M, Nelson, David R, Oppert, Brenda, Panfilio, Kristen A, Paula, Débora Pires, Pick, Leslie, Poelchau, Monica F, Qu, Jiaxin, Reding, Katie, Rhoades, Joshua H, Rhodes, Adelaide, Richards, Stephen, Richter, Rose, Robertson, Hugh M, Rosendale, Andrew J, Tu, Zhijian Jake, Velamuri, Arun S, Waterhouse, Robert M, Weirauch, Matthew T, Wells, Jackson T, Werren, John H, Worley, Kim C, Zdobnov, Evgeny M, and Gundersen-Rindal, Dawn E

Subjects
Genetics, Biotechnology, Human Genome, Animals, Ecosystem, Gene Transfer, Horizontal, Genome Size, Heteroptera, Insect Proteins, Insecticide Resistance, Introduced Species, Phylogeny, Whole Genome Sequencing, Brown marmorated stink bug genome, Pentatomid genomics, polyphagy, chemoreceptors, odorant binding proteins, opsins, cathepsins, xenobiotic detoxification, invasive species, Biological Sciences, Information and Computing Sciences, Medical and Health Sciences, Bioinformatics
Abstract

BackgroundHalyomorpha halys (Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in human-made structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species' feeding and habitat traits, defining potential targets for pest management strategies.ResultsAnalysis of the 1.15-Gb draft genome assembly has identified a wide variety of genetic elements underpinning the biological characteristics of this formidable pest species, encompassing the roles of sensory functions, digestion, immunity, detoxification and development, all of which likely support H. halys' capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications.ConclusionsAvailability of the H. halys genome sequence will be useful for the development of environmentally friendly biomolecular pesticides to be applied in concert with more traditional, synthetic chemical-based controls.

Published
2020

24. Gene content evolution in the arthropods

Author

Thomas, Gregg WC, Dohmen, Elias, Hughes, Daniel ST, Murali, Shwetha C, Poelchau, Monica, Glastad, Karl, Anstead, Clare A, Ayoub, Nadia A, Batterham, Phillip, Bellair, Michelle, Binford, Greta J, Chao, Hsu, Chen, Yolanda H, Childers, Christopher, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Duan, Jian J, Dugan, Shannon, Esposito, Lauren A, Friedrich, Markus, Garb, Jessica, Gasser, Robin B, Goodisman, Michael AD, Gundersen-Rindal, Dawn E, Han, Yi, Handler, Alfred M, Hatakeyama, Masatsugu, Hering, Lars, Hunter, Wayne B, Ioannidis, Panagiotis, Jayaseelan, Joy C, Kalra, Divya, Khila, Abderrahman, Korhonen, Pasi K, Lee, Carol Eunmi, Lee, Sandra L, Li, Yiyuan, Lindsey, Amelia RI, Mayer, Georg, McGregor, Alistair P, McKenna, Duane D, Misof, Bernhard, Munidasa, Mala, Munoz-Torres, Monica, Muzny, Donna M, Niehuis, Oliver, Osuji-Lacy, Nkechinyere, Palli, Subba R, Panfilio, Kristen A, Pechmann, Matthias, Perry, Trent, Peters, Ralph S, Poynton, Helen C, Prpic, Nikola-Michael, Qu, Jiaxin, Rotenberg, Dorith, Schal, Coby, Schoville, Sean D, Scully, Erin D, Skinner, Evette, Sloan, Daniel B, Stouthamer, Richard, Strand, Michael R, Szucsich, Nikolaus U, Wijeratne, Asela, Young, Neil D, Zattara, Eduardo E, Benoit, Joshua B, Zdobnov, Evgeny M, Pfrender, Michael E, Hackett, Kevin J, Werren, John H, Worley, Kim C, Gibbs, Richard A, Chipman, Ariel D, Waterhouse, Robert M, Bornberg-Bauer, Erich, Hahn, Matthew W, and Richards, Stephen

Subjects
Human Genome, Genetics, Biotechnology, Generic health relevance, Animals, Arthropods, DNA Methylation, Evolution, Molecular, Genetic Speciation, Genetic Variation, Phylogeny, Genome assembly, Genomics, Protein domains, Gene content, Evolution, DNA methylation, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundArthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods.ResultsUsing 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception.ConclusionsThese analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity.

Published
2020

25. Correction to: Genome-enabled insights into the biology of thrips as crop pests

Author

Rotenberg, Dorith, Baumann, Aaron A, Ben-Mahmoud, Sulley, Christiaens, Olivier, Dermauw, Wannes, Ioannidis, Panagiotis, Jacobs, Chris GC, Vargas Jentzsch, Iris M, Oliver, Jonathan E, Poelchau, Monica F, Rajarapu, Swapna Priya, Schneweis, Derek J, Snoeck, Simon, Taning, Clauvis NT, Wei, Dong, Widana Gamage, Shirani MK, Hughes, Daniel ST, Murali, Shwetha C, Bailey, Samuel T, Bejerman, Nicolas E, Holmes, Christopher J, Jennings, Emily C, Rosendale, Andrew J, Rosselot, Andrew, Hervey, Kaylee, Schneweis, Brandi A, Cheng, Sammy, Childers, Christopher, Simão, Felipe A, Dietzgen, Ralf G, Chao, Hsu, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dugan, Shannon, Han, Yi, Lee, Sandra L, Muzny, Donna M, Qu, Jiaxin, Worley, Kim C, Benoit, Joshua B, Friedrich, Markus, Jones, Jeffery W, Panfilio, Kristen A, Park, Yoonseong, Robertson, Hugh M, Smagghe, Guy, Ullman, Diane E, van der Zee, Maurijn, Van Leeuwen, Thomas, Veenstra, Jan A, Waterhouse, Robert M, Weirauch, Matthew T, Werren, John H, Whitfield, Anna E, Zdobnov, Evgeny M, Gibbs, Richard A, and Richards, Stephen

Subjects
Biological Sciences, Developmental Biology, Biological sciences
Abstract

An amendment to this paper has been published and can be accessed via the original article.

Published
2020

26. Genome-enabled insights into the biology of thrips as crop pests

Author

Rotenberg, Dorith, Baumann, Aaron A, Ben-Mahmoud, Sulley, Christiaens, Olivier, Dermauw, Wannes, Ioannidis, Panagiotis, Jacobs, Chris GC, Vargas Jentzsch, Iris M, Oliver, Jonathan E, Poelchau, Monica F, Rajarapu, Swapna Priya, Schneweis, Derek J, Snoeck, Simon, Taning, Clauvis NT, Wei, Dong, Widana Gamage, Shirani MK, Hughes, Daniel ST, Murali, Shwetha C, Bailey, Samuel T, Bejerman, Nicolas E, Holmes, Christopher J, Jennings, Emily C, Rosendale, Andrew J, Rosselot, Andrew, Hervey, Kaylee, Schneweis, Brandi A, Cheng, Sammy, Childers, Christopher, Simão, Felipe A, Dietzgen, Ralf G, Chao, Hsu, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dugan, Shannon, Han, Yi, Lee, Sandra L, Muzny, Donna M, Qu, Jiaxin, Worley, Kim C, Benoit, Joshua B, Friedrich, Markus, Jones, Jeffery W, Panfilio, Kristen A, Park, Yoonseong, Robertson, Hugh M, Smagghe, Guy, Ullman, Diane E, van der Zee, Maurijn, Van Leeuwen, Thomas, Veenstra, Jan A, Waterhouse, Robert M, Weirauch, Matthew T, Werren, John H, Whitfield, Anna E, Zdobnov, Evgeny M, Gibbs, Richard A, and Richards, Stephen

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Animals, Crops, Agricultural, Feeding Behavior, Food Chain, Genome, Insect, Immunity, Innate, Life History Traits, Perception, Phylogeny, Reproduction, Thysanoptera, Transcriptome, Western flower thrips, Hemipteroid assemblage, Insect genomics, Tospovirus, Salivary glands, Chemosensory receptors, Opsins, Detoxification, Innate immunity, Developmental Biology, Biological sciences
Abstract

BackgroundThe western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set.ResultsWe report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta.ConclusionsAnalysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species.

Published
2020

27. A scoring system for predicting malignancy in intraductal papillary mucinous neoplasms of the pancreas: a multicenter EUROPEAN validation

Author

Manuel-Vázquez, Alba, Balakrishnan, Anita, Agami, Paul, Andersson, Bodil, Berrevoet, Frederik, Besselink, Marc G., Boggi, Ugo, Caputo, Damiano, Carabias, Alberto, Carrion-Alvarez, Lucia, Franco, Carmen Cepeda, Coppola, Alessandro, Dasari, Bobby V. M., Diaz-Mercedes, Sherley, Feretis, Michail, Fondevila, Constantino, Fusai, Giuseppe Kito, Garcea, Giuseppe, Gonzabay, Victor, Bravo, Miguel Ángel Gómez, Gorris, Myrte, Hendrikx, Bart, Hidalgo-Salinas, Camila, Kadam, Prashant, Karavias, Dimitrios, Kauffmann, Emanuele, Kourdouli, Amar, La Vaccara, Vincenzo, van Laarhoven, Stijn, Leighton, James, Liem, Mike S. L., Machairas, Nikolaos, Magouliotis, Dimitris, Mahmoud, Adel, Marino, Marco V., Massani, Marco, Requena, Paola Melgar, Mentor, Keno, Napoli, Niccolò, Nijhuis, Jorieke H. T., Nikov, Andrej, Nistri, Cristina, Nunes, Victor, Ruiz, Eduardo Ortiz, Pandanaboyana, Sanjay, Saborido, Baltasar Pérez, Pohnán, Radek, Popa, Mariuca, Pérez, Belinda Sánchez, Bueno, Francisco Sánchez, Serrablo, Alejandro, Serradilla-Martín, Mario, Skipworth, James R. A., Soreide, Kjetil, Symeonidis, Dimitris, Zacharoulis, Dimitris, Zelga, Piotr, Aliseda, Daniel, Santiago, María Jesús Castro, Mancilla, Carlos Fernández, Fragua, Raquel Latorre, Hughes, Daniel Llwyd, Llorente, Carmen Payá, Lesurtel, Mickaël, Gallagher, Tom, and Ramia, José Manuel

Published
2022
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29. Predictors of actual five-year survival and recurrence after pancreatoduodenectomy for ampullary adenocarcinoma: results from an international multicentre retrospective cohort study

Author

Aroori, Somaiah, Labib, Peter L., Russell, Thomas B., Streeter, Adam, Denson, Jemimah, Puckett, Mark, Browning, Matthew G., Ausania, Fabio, González-Abós, Carolina, Pando, Elizabeth, Fernandes, Nair, Moller, Elsa G., Taboada, Cristina D., Roberts, Keith J., Pande, Rupaly, Alfarah, Jameel, Kausar, Ambareen, Bandyopadhyay, Samik, Abdelrahim, Ahmed, Khan, Ayesha, Mavroeidis, Vasileios K., Jordan, Caitlin, Rees, Jonathan R.E., Marangoni, Gabriele, Blege, Collaborator: Harry, Thomasset, Sarah, Cambridge, William, White, Olga, Frampton, Adam, Blacker, Sarah, Blackburn, Jessie, Sweeney, Casie, Lykoudis, Pavlos, Field, Daniel, Gouda, Mohammed, Maglione, Manuel, Bellotti, Ruben, Alhaboob, Nassir, Hamid, Hytham K.S., Bari, Hassaan, Ahmed, Hassan, Smith, Andrew, Moriarty, Catherine, White, Louise, Priestley, Mark, Bode, Kerry, Sharp, Judith, Wragg, Rosie, Jackson, Beverley, Craven, Samuel, Spalding, Duncan, Fehervari, Matyas, Pai, Madhava, Alghazawi, Laith, Onifade, Anjola, Srinivasan, Parthi, Ribaud, Julliette, Nair, Ashitha, Mariathasan, Michael, Grayson, Niamh, Davidson, Brian, Pericleous, Stephanos, Krishna Patel, Shaw, Conrad, Morare, Nolitha, Zaban, Mohamad K., Bhogal, Ricky, Doyle, Joseph, Croagh, Daniel, Dominguez, Ismael, Guerrero, Alan, Moguel, Andre, Chan, Carlos, Thakkar, Rohan, Jones, Michael, Buckley, Edward, Akter, Nasreen, Treherne, Kyle, Gomez, Dhanny, Gordon, Gregory, Silva, Michael, Hughes, Daniel, Urbonas, Tomas, Lapolla, Pierfrancesco, Mingoli, Andrea, Brachini, Gioia, Caronna, Roberto, Chirletti, Piero, Porcu, Alberto, Perra, Teresa, Shah, Nehal S., Abd Kahar, Nurul N., Hall, Thomas, Nadeem, Nabeegh, Hamady, Zaed, Karar, Shoura, Arshad, Ali, Al-Sarrieh, Bilal, Yarwood, Adam, Hammoda, Mohammed, Serrablo, Alejandro, Artigas, Maria, Paterna-López, Sandra, Thomasset, Sarah C., Frampton, Adam E., Smith, Andrew M., Davidson, Brian R., Bhogal, Ricky H., Silva, Michael A., and Hamady, Zaed Z.R.

Published
2023
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30. Surgical outcomes of gallbladder cancer: the OMEGA retrospective, multicentre, international cohort study

Author

Abe, Tomoyuki, Abu Hilal, Moh'd, Achalandabaso Boira, Maria del Mar, Adham, Mustapha, Adam, Mohamed, Ahmad, Maryam, Al-Sarireh, Bilal, Albiol, Maite, Alhaboob, Nassir, Alseidi, Adnan, Ammar, Houssem, Anand, Akshay, Andersson, Bodil, Antonakis, Pantelis, Araya, Veronica, Ashley, Stanley W., Atanasov, Georgi, Ausania, Fabio, Balestri, Ricardo, Banerjee, Abhirup, Banerjee, Sudeep, Banting, Simon, Barauskas, Giedrius, Bartsch, Fabian, Belli, Andrea, Beretta, Simona, Berrevoet, Frederik, Bhandari, Ramesh Singh, Blanco Fernandez, Gerardo, Bolm, Louisa, Bonal, Mathieu, Bozkurt, Emre, Braat, Andries E., Bradshaw, Luke, Bramis, Konstantinos, Branes, Alejandro, Burdine, Lyle, Byrne, Matthew, Caceres, Maria, Castro Santiago, Maria Jesus, Chan, Benjamin, Chong, Lynn, Çoker, Ahmet, Conde Rodriguez, Maria, Croagh, Daniel, Crutchley, Alyn, Cutolo, Carmen, D'Hondt, Mathieu, D'Souza, Daniel, Daams, Freek, Dalla Valle, Raffaele, Davide, José, de Bellis, Mario, de Boer, Marieke, de Meyere, Celine, de Reuver, Philip, Dixon, Matthew, Dorovinis, Panagiotis, Echeverría Bauer, Gabriela, Eduarda, Maria, Eker, Hasan, Erdmann, Joris, Erkan, Mert, Felekouras, Evangelos, Felli, Emanuele, Fernandes, Eduardo, Figueroa Rivera, Eduardo, Fulop, Andras, Galun, Daniel, Gerhards, Michael, Ghorbani, Poya, Giannone, Fabio, Gil, Luis, Giorgakis, Emmanouil, Giuffrida, Mario, Giuliante, Felice, Gkekas, Ioannis, Gomez Bravo, Miguel, Groot Koerkamp, Bas, Guevara, Oscar, Guglielmi, Alfredo, Gulla, Aiste, Gupta, Rahul, Gupta, Amit, Gutiérrez, Marta, Hafeez Bhatti, Abu Bakar, Hagendoorn, Jeroen, Hajee, Zain, Hakeem, Abdul Rahman, Hamid, Hytham, Hassen, Sayed, Heinrich, Stefan, Higuchi, Ryota, Hoffman, Daniel, Holroyd, David, Hughes, Daniel, Ivanecz, Arpad, Iype, Satheesh, Jaen Torrejimeno, Isabel, Joglekar, Shantanu, Jones, Robert, Kaczirek, Klaus, Kanhere, Harsh, Kausar, Ambareen, Kee, Zhanyi, Keilson, Jessica, Kleef, Jorg, Klose, Johannes, Knowles, Brett, Koong, Jun Kit, Kumar, Nagappan, Kunnuru, Supreeth, Lakhey, Paleswan Joshi, Laurenzi, Andrea, Lee, Yeong Sing, Leon, Felipe, Leow, Voon Meng, Lequeu, Jean-Baptiste, Lesurtel, Mickael, Lo, Elisabeth, Löb, Stefan, Lockie, Elizabeth, Lodge, Peter, López Garnica, Dolores, Lopez Lopez, Victor, Lundgren, Linda, Machairas, Nikolaos, Maharjan, Dhiresh, Malde, Deep, Martel, Guillaume, Martin, Julie, Mazzola, Michele, Mehrabi, Arianeb, Memeo, Ricardo, Milana, Flavio, Molina, George, Monette, Leah, Morgul, Haluk, Moris, Dimitrios, Morsi-Yeroyannis, Antonios, Mowbray, Nicholas, Mulita, Francesk, Muttillo, Edoardo Maria, Nandasena, Malith, Nashidengo, Pueya Rashid, Nickkholgh, Arash, Noel, Colin Byron, Ohtsuka, Masayuki, Ozolins, Arturs, Pandanaboyana, Sanjay, Pararas, Nikolaos, Parente, Alessandro, Peng, June, Perfecto Valero, Arkaitz, Perinel, Julie, Perivoliotis, Konstatinos, Perra, Teresa, Pessaux, Patrick, Petruch, Natalie, Piccolo, Gaetano, Piros, Laszlo, Porcu, Alberto, Prabakaran, Viswakumar, Prasad, Raj, Prieto Calvo, Mikel, Primavesi, Florian, Pueyo Periz, Eva Maria, Quaglia, Alberto, Ramia Angel, Jose M., Rammohan, Ashwin, Razionale, Francesco, Robles Campos, Ricardo, Roy, Manas, Rozwadowski, Sophie, Ruffolo, Luis, Ruiz, Natalia, Ruzzenante, Andrea, Saadat, Lily, Said, Mohamed Amine, Saladino, Edoardo, Saliba, Gabriel, Sandstrom, Per, Schena, Carlo Alberto, Scholer, Anthony, Schwarz, Christoph, Serafini, Lorenzo, Serrano, Pablo E., Sharma, Deepak, Sheen, Aali, Siddagangaiah, Vishwanath, Silva, Michael, Singh, Saurabh, Siriwardena, Ajith, Skalski, Michal, Smig, Mante, Soliman, Faris, Sonkar, Abhinav Arun, Sousa Silva, Donzília, Sparrelid, Ernesto, Srinivasan, Parthi, Sternby Eilard, Malin, Strobel, Oliver, Stupan, Urban, Suarez-Munoz, Miguel Angel, Subramaniam, Manisekar, Sugiura, Teiichi, Sutcliffe, Robert, Swank, Hilko, Taylor, Lillian, Thapa, Prabin Bikram, The, Catherine, Thepbunchonchai, Asara, Thieu, Caman, Tiwari, Navneet, Torzilli, Guido, Tovikkai, Chutwichai, Trotovsek, Blaz, Tsaramanidis, Savvas, Tsoulfas, Georgios, Uesaka, Katsuhiko, Umar, Garzali, Urbani, Lucio, Vailas, Michail, van Dam, Ronald, van de Boezem, Peter, van Laarhoven, Stijn, Vanagas, Tomas, Van Dooren, Mike, Viennet, Manon, Vigano, Luca, Vijayashanker, Aarathi, Villodre, Celia, Wakai, Toshifumi, Workneh, Aklile, Xu, Li, Yamamoto, Masakazu, Yang, Zhiying, Young, Robert, Zivanovic, Marko, Balakrishnan, Anita, Barmpounakis, Petros, Demiris, Nikolaos, Jah, Asif, Spiers, Harry V.M., Talukder, Shibojit, Martin, Jack L., Gibbs, Paul, Harper, Simon J.F., Huguet, Emmanuel L., Kosmoliaptsis, Vasilis, Liau, Siong S., Praseedom, Raaj K., Basu, Bristi, de Aretxabala, Xavier, Lendoire, Javier, Maithel, Shishir, Serrablo, Alejandro, and Adsay, Volkan

Published
2023
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33. Sawfly genomes reveal evolutionary acquisitions that fostered the mega-radiation of parasitoid and eusocial Hymenoptera

Author

Oeyen, Jan Philip, Baa-Puyoulet, Patrice, Benoit, Joshua B, Beukeboom, Leo W, Bornberg-Bauer, Erich, Buttstedt, Anja, Calevro, Federica, Cash, Elizabeth I, Chao, Hsu, Charles, Hubert, Chen, Mei-Ju May, Childers, Christopher, Cridge, Andrew G, Dearden, Peter, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dolan, Amanda, Donath, Alexander, Dowling, Daniel, Dugan, Shannon, Duncan, Elizabeth, Elpidina, Elena N, Friedrich, Markus, Geuverink, Elzemiek, Gibson, Joshua D, Grath, Sonja, Grimmelikhuijzen, Cornelis JP, Große-Wilde, Ewald, Gudobba, Cameron, Han, Yi, Hansson, Bill S, Hauser, Frank, Hughes, Daniel ST, Ioannidis, Panagiotis, Jacquin-Joly, Emmanuelle, Jennings, Emily C, Jones, Jeffery W, Klasberg, Steffen, Lee, Sandra L, Lesný, Peter, Lovegrove, Mackenzie, Martin, Sebastian, Martynov, Alexander G, Mayer, Christoph, Montagné, Nicolas, Moris, Victoria C, Munoz-Torres, Monica, Murali, Shwetha Canchi, Muzny, Donna M, Oppert, Brenda, Parisot, Nicolas, Pauli, Thomas, Peters, Ralph S, Petersen, Malte, Pick, Christian, Persyn, Emma, Podsiadlowski, Lars, Poelchau, Monica F, Provataris, Panagiotis, Qu, Jiaxin, Reijnders, Maarten JMF, von Reumont, Björn Marcus, Rosendale, Andrew J, Simao, Felipe A, Skelly, John, Sotiropoulos, Alexandros G, Stahl, Aaron L, Sumitani, Megumi, Szuter, Elise M, Tidswell, Olivia, Tsitlakidis, Evangelos, Vedder, Lucia, Waterhouse, Robert M, Werren, John H, Wilbrandt, Jeanne, Worley, Kim C, Yamamoto, Daisuke S, van de Zande, Louis, Zdobnov, Evgeny M, Ziesmann, Tanja, Gibbs, Richard A, Richards, Stephen, Hatakeyama, Masatsugu, Misof, Bernhard, and Niehuis, Oliver

Subjects
Human Genome, Genetics, Life Below Water, Amino Acid Sequence, Animals, Conserved Sequence, DNA Transposable Elements, Female, Gene Dosage, Genetic Speciation, Genome, Insect, Glycoproteins, Herbivory, Host-Parasite Interactions, Hymenoptera, Immunity, Insect Proteins, Male, Multigene Family, Receptors, Odorant, Social Behavior, Vision, Ocular, hexamerin, major royal jelly protein, microsynteny, odorant receptor, opsin, phytophagy, Biochemistry and Cell Biology, Evolutionary Biology, Developmental Biology
Abstract

The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO2 detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.

Published
2020

34. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome

Author

Panfilio, Kristen A, Vargas Jentzsch, Iris M, Benoit, Joshua B, Erezyilmaz, Deniz, Suzuki, Yuichiro, Colella, Stefano, Robertson, Hugh M, Poelchau, Monica F, Waterhouse, Robert M, Ioannidis, Panagiotis, Weirauch, Matthew T, Hughes, Daniel ST, Murali, Shwetha C, Werren, John H, Jacobs, Chris GC, Duncan, Elizabeth J, Armisén, David, Vreede, Barbara MI, Baa-Puyoulet, Patrice, Berger, Chloé S, Chang, Chun-che, Chao, Hsu, Chen, Mei-Ju M, Chen, Yen-Ta, Childers, Christopher P, Chipman, Ariel D, Cridge, Andrew G, Crumière, Antonin JJ, Dearden, Peter K, Didion, Elise M, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dolan, Amanda, Dugan, Shannon, Extavour, Cassandra G, Febvay, Gérard, Friedrich, Markus, Ginzburg, Neta, Han, Yi, Heger, Peter, Holmes, Christopher J, Horn, Thorsten, Hsiao, Yi-min, Jennings, Emily C, Johnston, J Spencer, Jones, Tamsin E, Jones, Jeffery W, Khila, Abderrahman, Koelzer, Stefan, Kovacova, Viera, Leask, Megan, Lee, Sandra L, Lee, Chien-Yueh, Lovegrove, Mackenzie R, Lu, Hsiao-ling, Lu, Yong, Moore, Patricia J, Munoz-Torres, Monica C, Muzny, Donna M, Palli, Subba R, Parisot, Nicolas, Pick, Leslie, Porter, Megan L, Qu, Jiaxin, Refki, Peter N, Richter, Rose, Rivera-Pomar, Rolando, Rosendale, Andrew J, Roth, Siegfried, Sachs, Lena, Santos, M Emília, Seibert, Jan, Sghaier, Essia, Shukla, Jayendra N, Stancliffe, Richard J, Tidswell, Olivia, Traverso, Lucila, van der Zee, Maurijn, Viala, Séverine, Worley, Kim C, Zdobnov, Evgeny M, Gibbs, Richard A, and Richards, Stephen

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Underpinning research, 1.1 Normal biological development and functioning, Amino Acid Sequence, Animals, CYS2-HIS2 Zinc Fingers, Evolution, Molecular, Feeding Behavior, Gene Dosage, Gene Expression Profiling, Gene Transfer, Horizontal, Genes, Homeobox, Genome, Insect, Hemiptera, Pigmentation, Smell, Transcription Factors, Evolution of development, Gene family evolution, Gene structure, Lateral gene transfer, Phytophagy, RNAi, Transcription factors, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundThe Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae.ResultsThe 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding.ConclusionsWith the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.

Published
2019

37. High-quality read-based phasing of cystic fibrosis cohort informs genetic understanding of disease modification

Author

Mastromatteo, Scott, Chen, Angela, Gong, Jiafen, Lin, Fan, Thiruvahindrapuram, Bhooma, Sung, Wilson W.L., Whitney, Joe, Wang, Zhuozhi, Patel, Rohan V., Keenan, Katherine, Halevy, Anat, Panjwani, Naim, Avolio, Julie, Wang, Cheng, Côté-Maurais, Guillaume, Bégin, Stéphanie, Adam, Damien, Brochiero, Emmanuelle, Bjornson, Candice, Chilvers, Mark, Price, April, Parkins, Michael, van Wylick, Richard, Mateos-Corral, Dimas, Hughes, Daniel, Smith, Mary Jane, Morrison, Nancy, Tullis, Elizabeth, Stephenson, Anne L., Wilcox, Pearce, Quon, Bradley S., Leung, Winnie M., Solomon, Melinda, Sun, Lei, Ratjen, Felix, and Strug, Lisa J.

Published
2023
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41. 500 Single Best Answers for the Medical Oncology Specialty Certificate Exam

Author

Hughes, Daniel J, Olsson-Brown, Anna C, Cave, Judith, Earl, Helena, Hughes, Daniel J, Olsson-Brown, Anna C, Cave, Judith, Earl, Helena and Hughes, Daniel J, Olsson-Brown, Anna C, Cave, Judith, Earl, Helena, Hughes, Daniel J, Olsson-Brown, Anna C, Cave, Judith, Earl, Helena

Published
2022

44. The benefit of diagnostic whole genome sequencing in schizophrenia and other psychotic disorders

Author

Alkelai, Anna, Greenbaum, Lior, Docherty, Anna R., Shabalin, Andrey A., Povysil, Gundula, Malakar, Ayan, Hughes, Daniel, Delaney, Shannon L., Peabody, Emma P., McNamara, James, Gelfman, Sahar, Baugh, Evan H., Zoghbi, Anthony W., Harms, Matthew B., Hwang, Hann-Shyan, Grossman-Jonish, Anat, Aggarwal, Vimla, Heinzen, Erin L., Jobanputra, Vaidehi, Pulver, Ann E., Lerer, Bernard, and Goldstein, David B.

Published
2022
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45. Genetic evidence supports the development of SLC26A9 targeting therapies for the treatment of lung disease

Author

Gong, Jiafen, He, Gengming, Wang, Cheng, Bartlett, Claire, Panjwani, Naim, Mastromatteo, Scott, Lin, Fan, Keenan, Katherine, Avolio, Julie, Halevy, Anat, Shaw, Michelle, Esmaeili, Mohsen, Côté-Maurais, Guillaume, Adam, Damien, Bégin, Stéphanie, Bjornson, Candice, Chilvers, Mark, Reisman, Joe, Price, April, Parkins, Michael, van Wylick, Richard, Berthiaume, Yves, Bilodeau, Lara, Mateos-Corral, Dimas, Hughes, Daniel, Smith, Mary J., Morrison, Nancy, Brusky, Janna, Tullis, Elizabeth, Stephenson, Anne L., Quon, Bradley S., Wilcox, Pearce, Leung, Winnie M., Solomon, Melinda, Sun, Lei, Brochiero, Emmanuelle, Moraes, Theo J., Gonska, Tanja, Ratjen, Felix, Rommens, Johanna M., and Strug, Lisa J.

Published
2022
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47. Breaking up the traditional skyline : writing modernist Wales in English

Author

Hughes, Daniel and Brown, Anthony

Subjects
820
Abstract

Across the work of eleven key authors — Caradoc Evans, Gwyn Thomas, Glyn Jones, Nigel Heseltine, Dylan Thomas, Lynette Roberts, David Jones, Dorothy Edwards, Margiad Evans, Brenda Chamberlain, and Tony Conran — this thesis analyses the output of an Anglophone cultural formation of modernist writers in Wales, whose literature comprise a major — yet neglected — strand of European modernism. The introductory chapter engages with the history of the idea of ‘Modernism’, and the current state of modernist studies within and beyond Wales, arguing that conventional notions of ‘Modernism’ as a fixed, monolithic period confined to the major metropolitan areas of Europe and America are no longer sufficient in light of recent developments in the field. The second chapter examines the controversial writer Caradoc Evans, once considered the ‘father’ of what was commonly called ‘Anglo-Welsh’ literature, whose incendiary 1915 short story collection My People serves as the explosive genesis of Anglophone Welsh modernism. I compare Evans’s work with a later author, Gwyn Thomas, whose 1946 novella Oscar depicts a nihilistic void under the guise of a bleak South Walian valley. Across the following two chapters, I explore the work of writers connected to a cultural formation of Anglophone Welsh modernist writers, utilising the term ‘formation’ as conceptualised by Raymond Williams in Culture (1981). This ‘formation’ occupied the cultural space cleared by Caradoc Evans, used Wales as their social and literary nexus (the magazine was edited by their mutual friend, Keidrych Rhys) and included in their number key writers examined in the thesis, such as Glyn Jones, Nigel Heseltine, Dylan Thomas, Lynette Roberts, and David Jones. In the fifth chapter, I analyse the ‘Gothic Wastelands’ of two recently recovered women writers, Margiad Evans and Dorothy Edwards, who were tangentially connected to the formation. In the sixth chapter, the thesis explores the modernist life-writing of Brenda Chamberlain and Tony Conran, as well as their position as the last members of this particular cultural formation. Finally, the thesis concludes by asking a question which becomes increasingly obvious in the face of the strength, vitality and diversity of Welsh modernism as demonstrated by this thesis: what brings us here so late?

Published
2018

48. Gibbard-Satterthwaite Games for k-Approval Voting Rules

Author

Grandi, Umberto, Hughes, Daniel, Rossi, Francesca, and Slinko, Arkadii

Subjects
Computer Science - Computer Science and Game Theory
Abstract

The Gibbard-Satterthwaite theorem implies the existence of voters, called manipulators, who can change the election outcome in their favour by voting strategically. When a given preference profile admits several such manipulators, voting becomes a game played by these voters, who have to reason strategically about each others' actions. To complicate the game even further, counter-manipulators may then try to counteract the actions of manipulators. Our voters are boundedly rational and do not think beyond manipulating or countermanipulating. We call these games Gibbard--Satterthwaite Games. In this paper we look for conditions that guarantee the existence of a Nash equilibria in pure strategies.

Published
2017

49. Predicting programmed death-ligand 1 (PD-L1) expression with fluorine-18 fluorodeoxyglucose ([18F]FDG) positron emission tomography/computed tomography (PET/CT) metabolic parameters in resectable non-small cell lung cancer.

Author

Hughes, Daniel Johnathan, Josephides, Eleni, O'Shea, Robert, Manickavasagar, Thubeena, Horst, Carolyn, Hunter, Sarah, Tanière, Philippe, Nonaka, Daisuke, Van Hemelrijck, Mieke, Spicer, James, Goh, Vicky, Bille, Andrea, Karapanagiotou, Eleni, and Cook, Gary J. R.

Subjects
*PROGRAMMED death-ligand 1, *POSITRON emission tomography, *NON-small-cell lung carcinoma, *LEAN body mass, *COMPUTED tomography
Abstract

Background: Programmed death-ligand 1 (PD-L1) expression is a predictive biomarker for immunotherapy in non-small cell lung cancer (NSCLC). PD-L1 and glucose transporter 1 expression are closely associated, and studies demonstrate correlation of PD-L1 with glucose metabolism. Aim: The aim of this study was to investigate the association of fluorine-18 fluorodeoxyglucose positron emission tomography/computed tomography ([18F]FDG-PET/CT) metabolic parameters with PD-L1 expression in primary lung tumour and lymph node metastases in resected NSCLC. Methods: We conducted a retrospective analysis of 210 patients with node-positive resectable stage IIB–IIIB NSCLC. PD-L1 tumour proportion score (TPS) was determined using the DAKO 22C3 immunohistochemical assay. Semi-automated techniques were used to analyse pre-operative [18F]FDG-PET/CT images to determine primary and nodal metabolic parameter scores (including max, mean, peak and peak adjusted for lean body mass standardised uptake values (SUV), metabolic tumour volume (MTV), total lesional glycolysis (TLG) and SUV heterogeneity index (HISUV)). Results: Patients were predominantly male (57%), median age 70 years with non-squamous NSCLC (68%). A majority had negative primary tumour PD-L1 (TPS < 1%; 53%). Mean SUVmax, SUVmean, SUVpeak and SULpeak values were significantly higher (p < 0.05) in those with TPS ≥ 1% in primary tumour (n = 210) or lymph nodes (n = 91). However, ROC analysis demonstrated only moderate separability at the 1% PD-L1 TPS threshold (AUCs 0.58–0.73). There was no association of MTV, TLG and HISUV with PD-L1 TPS. Conclusion: This study demonstrated the association of SUV-based [18F]FDG-PET/CT metabolic parameters with PD-L1 expression in primary tumour or lymph node metastasis in resectable NSCLC, but with poor sensitivity and specificity for predicting PD-L1 positivity ≥ 1%. Clinical relevance statement: Whilst SUV-based fluorine-18 fluorodeoxyglucose positron emission tomography/computed tomography metabolic parameters may not predict programmed death-ligand 1 positivity ≥ 1% in the primary tumour and lymph nodes of resectable non-small cell lung cancer independently, there is a clear association which warrants further investigation in prospective studies. Trial registration: Non-applicable Key Points: • Programmed death-ligand 1 immunohistochemistry has a predictive role in non-small cell lung cancer immunotherapy; however, it is both heterogenous and dynamic. • SUV-based fluorine-18 fluorodeoxyglucose positron emission tomography/computed tomography ([18F]FDG-PET/CT) metabolic parameters were significantly higher in primary tumour or lymph node metastases with positive programmed death-ligand 1 expression. • These SUV-based parameters could potentially play an additive role along with other multi-modal biomarkers in selecting patients within a predictive nomogram. [ABSTRACT FROM AUTHOR]

Published
2024
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50. The Inverted Case Study Technique: changing the traditional case-study approach to prioritize physiological mechanisms over correct diagnosis and treatment.

Author

Brainard, Robert E., Paleville, Daniela G. L. Terson de, Long, Michael C., Hughes, Daniel G., Watson, Lewis J., and Anderson, Gary

Subjects
CRITICAL thinking studies, CRITICAL thinking, MEMORIZATION, PHYSIOLOGY, THERAPEUTICS, PHYSIOLOGY education
Abstract

The traditional case study has been used as a learning tool for the past 100 years, and in our program, graduate physiology students are presented with a real-world scenario and must determine the diagnosis and treatment of the patient. We found that students defaulted to memorization of disease with treatment and bypassed gaining an understanding of the mechanistic physiology behind disease and treatment. To adjust our student's approach, we developed a novel way to enhance student learning. To accomplish this shift from memorization to physiological mastery, we created the Inverted Case Study. This approach diverges from the traditional model in that students are given the diagnosis and treatment beforehand and are tasked with explaining the actual physiology of the case. In this way, students can no longer rely on the memorization of symptoms-disease-treatment but rather gain a solid understanding of the physiological mechanisms of the disease since that is the focus of the Inverted Case Study Technique. The Inverted Case Study approach is an effective approach to apply and hone critical thinking skills. NEW & NOTEWORTHY: This article presents a novel approach to century-old learning techniques that enhances students' self-reported learning and also their attitudes toward learning mechanistic physiology and increases their perception of preparedness for professional school. [ABSTRACT FROM AUTHOR]

Published
2024
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