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3,418 results on '"Jez, P."'

1. Online Disjoint Set Covers: Randomization is not Necessary

Author

Bienkowski, Marcin, Byrka, Jarosław, and Jeż, Łukasz

Subjects
Computer Science - Data Structures and Algorithms
Abstract

In the online disjoint set covers problem, the edges of a hypergraph are revealed online, and the goal is to partition them into a maximum number of disjoint set covers. That is, n nodes of a hypergraph are given at the beginning, and then a sequence of hyperedges (subsets of [n]) is presented to an algorithm. For each hyperedge, an online algorithm must assign a color (an integer). Once an input terminates, the gain of the algorithm is the number of colors that correspond to valid set covers (i.e., the union of hyperedges that have that color contains all n nodes). We present a deterministic online algorithm that is O(log^2 n)-competitive, exponentially improving on the previous bound of O(n) and matching the performance of the best randomized algorithm by Emek et al. [ESA 2019]. For color selection, our algorithm uses a novel potential function, which can be seen as an online counterpart of the derandomization method of conditional probabilities and pessimistic estimators. There are only a few cases where derandomization has been successfully used in the field of online algorithms. In contrast to previous approaches, our result extends to the following new challenges: (i) the potential function derandomizes not only the Chernoff bound, but also the coupon collector's problem, (ii) the value of OPT of the maximization problem is not bounded a priori, and (iii) we do not produce a fractional solution first, but work directly on the input.

Published
2024

2. Parikh's Theorem Made Symbolic

Author

Hague, Matthew, Jeż, Artur, and Lin, Anthony W.

Subjects
Computer Science - Formal Languages and Automata Theory, Computer Science - Logic in Computer Science
Abstract

Parikh's Theorem is a fundamental result in automata theory with numerous applications in computer science: software verification (e.g. infinite-state verification, string constraints, and theory of arrays), verification of cryptographic protocols (e.g. using Horn clauses modulo equational theories) and database querying (e.g. evaluating path-queries in graph databases). Parikh's Theorem states that the letter-counting abstraction of a language recognized by finite automata or context-free grammars is definable in Presburger Arithmetic. Unfortunately, real-world applications typically require large alphabets - which are well-known to be not amenable to explicit treatment of the alphabets. Symbolic automata have proven in the last decade to be an effective algorithmic framework for handling large finite or even infinite alphabets. A symbolic automaton employs an effective boolean algebra, which offers a symbolic representation of character sets and often lends itself to an exponentially more succinct representation of a language. Instead of letter-counting, Parikh's Theorem for symbolic automata amounts to counting the number of times different predicates are satisfied by an input sequence. Unfortunately, naively applying Parikh's Theorem from classical automata theory to symbolic automata yields existential Presburger formulas of exponential size. We provide a new construction for Parikh's Theorem for symbolic automata and grammars, which avoids this exponential blowup: our algorithm computes an existential formula in polynomial-time over (quantifier-free) Presburger and the base theory. In fact, our algorithm extends to the model of parametric symbolic grammars, which are one of the most expressive models of languages over infinite alphabets. We have implemented our algorithm and show it can be used to solve string constraints that are difficult to solve by existing solvers., Comment: Accepted tp POPL '24

Published
2023

3. A machine learning algorithm for the detection of paroxysmal nocturnal haemoglobinuria (PNH) in UK primary care electronic health records

Author

Amanda Worker, Hadley Mahon, Jack Sams, Freya Boardman-Pretty, Elena Marchini, Rand Dubis, Alan Warren, Jez Stockdale, Jyothika Kumar, Elizabeth Varones, Daniel Ollerenshaw, Calum Grant, Peter Fish, and Richard J. Kelly

Subjects
Paroxysmal Nocturnal Haemoglobinuria (PNH), Machine learning, Rare disease, UK electronic health records, Primary care, Medicine
Abstract

Abstract Background Paroxysmal Nocturnal Haemoglobinuria (PNH) is an ultra-rare, acquired disorder that is challenging to diagnose due to varied symptoms, heterogeneous patient presentations, and lack of awareness among healthcare professionals. This leads to frequent misdiagnosis and delays in diagnosis. This study evaluated the feasibility of a machine learning model to identify undiagnosed PNH patients using structured electronic health records. Methods The study used data from the Optimum Patient Care Research Database, which contains electronic health records from general practitioner (GP) practices across the United Kingdom. PNH patients were identified by the presence, and control patients by the absence of a PNH diagnosis code in their records. Clinical features (symptoms, diagnoses, healthcare utilisation) from 131 patients in the PNH group and 593,838 patients in the control group, were inputted to a tree-based XGBoost machine learning model to classify patients as either “positive” or “negative” for PNH suspicion. The algorithm was finalised after additional exclusions and inclusions applied. Performance was assessed using positive predictive value (PPV), recall and specificity. As the sample used to develop the algorithm was not representative of the true population prevalence, PPV was additionally adjusted to reflect performance in the wider population. Results Of all the patients in the PNH group, 27% were classified as positive (recall). 99.99% of the control group were classified as negative (specificity). Of all the patients classified as positive, 60.4% had a diagnosis of PNH in their record (PPV). The PPV adjusted for the population prevalence of PNH was 19.59 suggesting nearly 1 in 5 patients flagged may warrant further PNH investigation. The key clinical features in the model were aplastic anaemia, pancytopenia, haemolytic anaemia, myelodysplastic syndrome, and Budd-Chiari syndrome. Conclusion This is the first study to combine clinical understanding of PNH with machine learning, demonstrating the ability to discriminate between PNH and control patients in retrospective electronic health records. With further investigation and validation, this algorithm could be deployed on live health data, potentially leading to earlier diagnosis for patients who currently experience long diagnostic delays or remain undiagnosed.

Published
2024
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4. Building Equity into Transition Practice and Service Delivery: A Call for Systemic Changes in the Field of Transition

Author

Sinclair, James, Jez, Rebekka, Banks, Joy, and Kucharczyk, Suzanne

Abstract

There is a common narrative in the field of transition: students with disabilities continue to experience poorer post-school outcomes compared with their peers without disabilities. After decades of research and practice, scholars and practitioners have impacted countless numbers of students. However, disparate outcomes for diverse youth still exist. The Division on Career Development and Transition takes the position that if we are to begin reducing persistent differential outcomes for diverse youth, we must examine our current practices and apply anti-oppressive practices to transition planning to ensure we do not continue to perpetuate White cultural norms and ableist approaches to transition. We applied four equity frameworks to transition planning and provided recommendations for transition practice and service delivery.

Published
2023
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5. Decision Procedures for Sequence Theories (Technical Report)

Author

Jeż, Artur, Lin, Anthony W., Markgraf, Oliver, and Rümmer, Philipp

Subjects
Computer Science - Logic in Computer Science
Abstract

Sequence theories are an extension of theories of strings with an infinite alphabet of letters, together with a corresponding alphabet theory (e.g. linear integer arithmetic). Sequences are natural abstractions of extendable arrays, which permit a wealth of operations including append, map, split, and concatenation. In spite of the growing amount of tool support for theories of sequences by leading SMT-solvers, little is known about the decidability of sequence theories, which is in stark contrast to the state of the theories of strings. We show that the decidable theory of strings with concatenation and regular constraints can be extended to the world of sequences over an alphabet theory that forms a Boolean algebra, while preserving decidability. In particular, decidability holds when regular constraints are interpreted as parametric automata (which extend both symbolic automata and variable automata), but fails when interpreted as register automata (even over the alphabet theory of equality). When length constraints are added, the problem is Turing-equivalent to word equations with length (and regular) constraints. Similar investigations are conducted in the presence of symbolic transducers, which naturally model sequence functions like map, split, filter, etc. We have developed a new sequence solver, SeCo, based on parametric automata, and show its efficacy on two classes of benchmarks: (i) invariant checking on array-manipulating programs and parameterized systems, and (ii) benchmarks on symbolic register automata.

Published
2023

9. Integrating human endogenous retroviruses into transcriptome-wide association studies highlights novel risk factors for major psychiatric conditions

Author

Rodrigo R. R. Duarte, Oliver Pain, Matthew L. Bendall, Miguel de Mulder Rougvie, Jez L. Marston, Sashika Selvackadunco, Claire Troakes, Szi Kay Leung, Rosemary A. Bamford, Jonathan Mill, Paul F. O’Reilly, Deepak P. Srivastava, Douglas F. Nixon, and Timothy R. Powell

Subjects
Science
Abstract

Abstract Human endogenous retroviruses (HERVs) are repetitive elements previously implicated in major psychiatric conditions, but their role in aetiology remains unclear. Here, we perform specialised transcriptome-wide association studies that consider HERV expression quantified to precise genomic locations, using RNA sequencing and genetic data from 792 post-mortem brain samples. In Europeans, we identify 1238 HERVs with expression regulated in cis, of which 26 represent expression signals associated with psychiatric disorders, with ten being conditionally independent from neighbouring expression signals. Of these, five are additionally significant in fine-mapping analyses and thus are considered high confidence risk HERVs. These include two HERV expression signatures specific to schizophrenia risk, one shared between schizophrenia and bipolar disorder, and one specific to major depressive disorder. No robust signatures are identified for autism spectrum conditions or attention deficit hyperactivity disorder in Europeans, or for any psychiatric trait in other ancestries, although this is likely a result of relatively limited statistical power. Ultimately, our study highlights extensive HERV expression and regulation in the adult cortex, including in association with psychiatric disorder risk, therefore providing a rationale for exploring neurological HERV expression in complex neuropsychiatric traits.

Published
2024
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10. Transforming Educators in the United States and South Africa: An International Collaboration to Enhance Culturally Responsive Inclusive Practices

Author

Jez, Rebekka J., Hauth, Clara M., and Ramers, Lauren H.

Abstract

This qualitative exploratory case study addresses constructs of educational inequity on a global scale through an iterative analysis of the cultural experiences of 61 educators from South Africa and the United States. The project provided an online and in-person network for educators to discuss cross-cultural challenges, educational system assets, and inclusive strategies for supporting culturally and linguistically diverse learners. A shared professional development process, designed from an adapted Changemaking process, increased the knowledge, understanding, and application of innovative, culturally responsive inclusive practices of new teachers while also serving as an opportunity for veteran teachers to receive additional teacher training. Educators exchanged ideas on increasing positive classroom management, motivating learners using empathy, collaborating effectively, linking learning and postsecondary transition experiences, and improving partnership with families. This global and cultural exchange exposed them to unique and diverse educational perspectives, a critical aspect in supporting all learners within the K-12 educational system. Results of this project indicate that using the adapted Changemaking process increased educators' awareness of culturally responsive inclusive practices, allowed participants to make comparisons between global contexts, developed empathy, and inspired collaborative engagement and leadership within their individual educational settings.

Published
2022

11. Space-efficient conversions from SLPs

Author

Gagie, Travis, Goga, Adrián, Jeż, Artur, and Navarro, Gonzalo

Subjects
Computer Science - Data Structures and Algorithms
Abstract

We give algorithms that, given a straight-line program (SLP) with $g$ rules that generates (only) a text $T [1..n]$, builds within $O(g)$ space the Lempel-Ziv (LZ) parse of $T$ (of $z$ phrases) in time $O(n\log^2 n)$ or in time $O(gz\log^2(n/z))$. We also show how to build a locally consistent grammar (LCG) of optimal size $g_{lc} = O(\delta\log\frac{n}{\delta})$ from the SLP within $O(g+g_{lc})$ space and in $O(n\log g)$ time, where $\delta$ is the substring complexity measure of $T$. Finally, we show how to build the LZ parse of $T$ from such a LCG within $O(g_{lc})$ space and in time $O(z\log^2 n \log^2(n/z))$. All our results hold with high probability.

Published
2022

12. Stratified analyses refine association between TLR7 rare variants and severe COVID-19

Author

Jannik Boos, Caspar I. van der Made, Gayatri Ramakrishnan, Eamon Coughlan, Rosanna Asselta, Britt-Sabina Löscher, Luca V.C. Valenti, Rafael de Cid, Luis Bujanda, Antonio Julià, Erola Pairo-Castineira, J. Kenneth Baillie, Sandra May, Berina Zametica, Julia Heggemann, Agustín Albillos, Jesus M. Banales, Jordi Barretina, Natalia Blay, Paolo Bonfanti, Maria Buti, Javier Fernandez, Sara Marsal, Daniele Prati, Luisa Ronzoni, Nicoletta Sacchi, Joachim L. Schultze, Olaf Riess, Andre Franke, Konrad Rawlik, David Ellinghaus, Alexander Hoischen, Axel Schmidt, Kerstin U. Ludwig, Valeria Rimoldi, Elvezia M. Paraboschi, Alessandra Bandera, Flora Peyvandi, Giacomo Grasselli, Francesco Blasi, Francesco Malvestiti, Serena Pelusi, Cristiana Bianco, Lorenzo Miano, Angela Lombardi, Pietro Invernizzi, Alessio Gerussi, Giuseppe Citerio, Andrea Biondi, Maria Grazia Valsecchi, Marina Elena Cazzaniga, Giuseppe Foti, Ilaria Beretta, Mariella D'Angiò, Laura Rachele Bettini, Xavier Farré, Susana Iraola-Guzmán, Manolis Kogevinas, Gemma Castaño-Vinyals, Koldo Garcia-Etxebarria, Beatriz Nafria, Mauro D'Amato, Adriana Palom, Colin Begg, Sara Clohisey, Charles Hinds, Peter Horby, Julian Knight, Lowell Ling, David Maslove, Danny McAuley, Johnny Millar, Hugh Montgomery, Alistair Nichol, Peter J.M. Openshaw, Alexandre C. Pereira, Chris P. Ponting, Kathy Rowan, Malcolm G. Semple, Manu Shankar-Hari, Charlotte Summers, Timothy Walsh, Latha Aravindan, Ruth Armstrong, Heather Biggs, Ceilia Boz, Adam Brown, Richard Clark, Audrey Coutts, Judy Coyle, Louise Cullum, Sukamal Das, Nicky Day, Lorna Donnelly, Esther Duncan, Angie Fawkes, Paul Fineran, Max Head Fourman, Anita Furlong, James Furniss, Bernadette Gallagher, Tammy Gilchrist, Ailsa Golightly, Fiona Griffiths, Katarzyna Hafezi, Debbie Hamilton, Ross Hendry, Andy Law, Dawn Law, Rachel Law, Sarah Law, Rebecca Lidstone-Scott, Louise Macgillivray, Alan Maclean, Hanning Mal, Sarah McCafferty, Ellie Mcmaster, Jen Meikle, Shona C. Moore, Kirstie Morrice, Lee Murphy, Sheena Murphy, Mybaya Hellen, Wilna Oosthuyzen, Chenqing Zheng, Jiantao Chen, Nick Parkinson, Trevor Paterson, Katherine Schon, Andrew Stenhouse, Mihaela Das, Maaike Swets, Helen Szoor-McElhinney, Filip Taneski, Lance Turtle, Tony Wackett, Mairi Ward, Jane Weaver, Nicola Wrobel, Marie Zechner, Gill Arbane, Aneta Bociek, Sara Campos, Neus Grau, Tim Owen Jones, Rosario Lim, Martina Marotti, Marlies Ostermann, Christopher Whitton, Zoe Alldis, Raine Astin-Chamberlain, Fatima Bibi, Jack Biddle, Sarah Blow, Matthew Bolton, Catherine Borra, Ruth Bowles, Maudrian Burton, Yasmin Choudhury, David Collier, Amber Cox, Amy Easthope, Patrizia Ebano, Stavros Fotiadis, Jana Gurasashvili, Rosslyn Halls, Pippa Hartridge, Delordson Kallon, Jamila Kassam, Ivone Lancoma-Malcolm, Maninderpal Matharu, Peter May, Oliver Mitchelmore, Tabitha Newman, Mital Patel, Jane Pheby, Irene Pinzuti, Zoe Prime, Oleksandra Prysyazhna, Julian Shiel, Melanie Taylor, Carey Tierney, Suzanne Wood, Anne Zak, Olivier Zongo, Stephen Bonner, Keith Hugill, Jessica Jones, Steven Liggett, Evie Headlam, Nageswar Bandla, Minnie Gellamucho, Michelle Davies, Christopher Thompson, Marwa Abdelrazik, Dhanalakshmi Bakthavatsalam, Munzir Elhassan, Arunkumar Ganesan, Anne Haldeos, Jeronimo Moreno-Cuesta, Dharam Purohit, Rachel Vincent, Kugan Xavier, Kumar Rohit, Frater Alasdair, Malik Saleem, Carter David, Jenkins Samuel, Zoe Lamond, Wall Alanna, Jaime Fernandez-Roman, David O. Hamilton, Emily Johnson, Brian Johnston, Maria Lopez Martinez, Suleman Mulla, David Shaw, Alicia A.C. Waite, Victoria Waugh, Ingeborg D. Welters, Karen Williams, Anna Cavazza, Maeve Cockrell, Eleanor Corcoran, Maria Depante, Clare Finney, Ellen Jerome, Mark McPhail, Monalisa Nayak, Harriet Noble, Kevin O'Reilly, Evita Pappa, Rohit Saha, Sian Saha, John Smith, Abigail Knighton, David Antcliffe, Dorota Banach, Stephen Brett, Phoebe Coghlan, Ziortza Fernandez, Anthony Gordon, Roceld Rojo, Sonia Sousa Arias, Maie Templeton, Megan Meredith, Lucy Morris, Lucy Ryan, Amy Clark, Julia Sampson, Cecilia Peters, Martin Dent, Margaret Langley, Saima Ashraf, Shuying Wei, Angela Andrew, Archana Bashyal, Neil Davidson, Paula Hutton, Stuart McKechnie, Jean Wilson, David Baptista, Rebecca Crowe, Rita Fernandes, Rosaleen Herdman-Grant, Anna Joseph, Denise O'Connor, Meryem Allen, Adam Loveridge, India McKenley, Eriko Morino, Andres Naranjo, Richard Simms, Kathryn Sollesta, Andrew Swain, Harish Venkatesh, Jacyntha Khera, Jonathan Fox, Gillian Andrew, Lucy Barclay, Marie Callaghan, Rachael Campbell, Sarah Clark, Dave Hope, Lucy Marshall, Corrienne McCulloch, Kate Briton, Jo Singleton, Sohphie Birch, Lutece Brimfield, Zoe Daly, David Pogson, Steve Rose, Ceri Battle, Elaine Brinkworth, Rachel Harford, Carl Murphy, Luke Newey, Tabitha Rees, Marie Williams, Sophie Arnold, Petra Polgarova, Katerina Stroud, Eoghan Meaney, Megan Jones, Anthony Ng, Shruti Agrawal, Nazima Pathan, Deborah White, Esther Daubney, Kay Elston, Lina Grauslyte, Musarat Hussain, Mandeep Phull, Tatiana Pogreban, Lace Rosaroso, Erika Salciute, George Franke, Joanna Wong, Aparna George, Laura Ortiz-Ruiz de Gordoa, Emily Peasgood, Claire Phillips, Michelle Bates, Jo Dasgin, Jaspret Gill, Annette Nilsson, James Scriven, Carlos Castro Delgado, Deborah Dawson, Lijun Ding, Georgia Durrant, Obiageri Ezeobu, Sarah Farnell-Ward, Abiola Harrison, Rebecca Kanu, Susannah Leaver, Elena Maccacari, Soumendu Manna, Romina Pepermans Saluzzio, Joana Queiroz, Tinashe Samakomva, Christine Sicat, Joana Texeira, Edna Fernandes Da Gloria, Ana Lisboa, John Rawlins, Jisha Mathew, Ashley Kinch, William James Hurt, Nirav Shah, Victoria Clark, Maria Thanasi, Nikki Yun, Kamal Patel, Sara Bennett, Emma Goodwin, Matthew Jackson, Alissa Kent, Clare Tibke, Wiesia Woodyatt, Ahmed Zaki, Azmerelda Abraheem, Peter Bamford, Kathryn Cawley, Charlie Dunmore, Maria Faulkner, Rumanah Girach, Helen Jeffrey, Rhianna Jones, Emily London, Imrun Nagra, Farah Nasir, Hannah Sainsbury, Clare Smedley, Tahera Patel, Matthew Smith, Srikanth Chukkambotla, Aayesha Kazi, Janice Hartley, Joseph Dykes, Muhammad Hijazi, Sarah Keith, Meherunnisa Khan, Janet Ryan-Smith, Philippa Springle, Jacqueline Thomas, Nick Truman, Samuel Saad, Dabheoc Coleman, Christopher Fine, Roseanna Matt, Bethan Gay, Jack Dalziel, Syamlan Ali, Drew Goodchild, Rhiannan Harling, Ravi Bhatterjee, Wendy Goddard, Chloe Davison, Stephen Duberly, Jeanette Hargreaves, Rachel Bolton, Miriam Davey, David Golden, Rebecca Seaman, Shiney Cherian, Sean Cutler, Anne Emma Heron, Anna Roynon-Reed, Tamas Szakmany, Gemma Williams, Owen Richards, Yusuf Cheema, Hollie Brooke, Sarah Buckley, Jose Cebrian Suarez, Ruth Charlesworth, Karen Hansson, John Norris, Alice Poole, Alastair Rose, Rajdeep Sandhu, Brendan Sloan, Elizabeth Smithson, Muthu Thirumaran, Veronica Wagstaff, Alexandra Metcalfe, Mark Brunton, Jess Caterson, Holly Coles, Matthew Frise, Sabi Gurung Rai, Nicola Jacques, Liza Keating, Emma Tilney, Shauna Bartley, Parminder Bhuie, Sian Gibson, Amanda Lyle, Fiona McNeela, Jayachandran Radhakrishnan, Alistair Hughes, Bryan Yates, Jessica Reynolds, Helen Campbell, Maria Thompsom, Steve Dodds, Stacey Duffy, Sandra Greer, Karen Shuker, Ascanio Tridente, Reena Khade, Ashok Sundar, George Tsinaslanidis, Isobel Birkinshaw, Joseph Carter, Kate Howard, Joanne Ingham, Rosie Joy, Harriet Pearson, Samantha Roche, Zoe Scott, Hollie Bancroft, Mary Bellamy, Margaret Carmody, Jacqueline Daglish, Faye Moore, Joanne Rhodes, Mirriam Sangombe, Salma Kadiri, Maria Croft, Ian White, Victoria Frost, Maia Aquino, Rajeev Jha, Vinodh Krishnamurthy, Lai Lim, Li Lim, Edward Combes, Teishel Joefield, Sonja Monnery, Valerie Beech, Sallyanne Trotman, Christine Almaden-Boyle, Pauline Austin, Louise Cabrelli, Stephen Cole, Matt Casey, Susan Chapman, Clare Whyte, Yolanda Baird, Aaron Butler, Indra Chadbourn, Linda Folkes, Heather Fox, Amy Gardner, Raquel Gomez, Gillian Hobden, Luke Hodgson, Kirsten King, Michael Margarson, Tim Martindale, Emma Meadows, Dana Raynard, Yvette Thirlwall, David Helm, Jordi Margalef, Kristine Criste, Rebecca Cusack, Kim Golder, Hannah Golding, Oliver Jones, Samantha Leggett, Michelle Male, Martyna Marani, Kirsty Prager, Toran Williams, Belinda Roberts, Karen Salmon, Peter Anderson, Katie Archer, Karen Austin, Caroline Davis, Alison Durie, Olivia Kelsall, Jessica Thrush, Charlie Vigurs, Laura Wild, Hannah-Louise Wood, Helen Tranter, Alison Harrison, Nicholas Cowley, Michael McAlindon, Andrew Burtenshaw, Stephen Digby, Emma Low, Aled Morgan, Naiara Cother, Tobias Rankin, Sarah Clayton, Alex McCurdy, Cecilia Ahmed, Balvinder Baines, Sarah Clamp, Julie Colley, Risna Haq, Anne Hayes, Jonathan Hulme, Samia Hussain, Sibet Joseph, Rita Kumar, Zahira Maqsood, Manjit Purewal, Leonie Benham, Zena Bradshaw, Joanna Brown, Melanie Caswell, Jason Cupitt, Sarah Melling, Stephen Preston, Nicola Slawson, Emma Stoddard, Scott Warden, Bethan Deacon, Ceri Lynch, Carla Pothecary, Lisa Roche, Gwenllian Sera Howe, Jayaprakash Singh, Keri Turner, Hannah Ellis, Natalie Stroud, Jodie Hunt, Joy Dearden, Emma Dobson, Andy Drummond, Michelle Mulcahy, Sheila Munt, Grainne O'Connor, Jennifer Philbin, Chloe Rishton, Redmond Tully, Sarah Winnard, Susanne Cathcart, Katharine Duffy, Alex Puxty, Kathryn Puxty, Lynne Turner, Jane Ireland, Gary Semple, Kate Long, Simon Whiteley, Elizabeth Wilby, Bethan Ogg, Amanda Cowton, Andrea Kay, Melanie Kent, Kathryn Potts, Ami Wilkinson, Suzanne Campbell, Ellen Brown, Julie Melville, Jay Naisbitt, Rosane Joseph, Maria Lazo, Olivia Walton, Alan Neal, Peter Alexander, Schvearn Allen, Joanne Bradley-Potts, Craig Brantwood, Jasmine Egan, Timothy Felton, Grace Padden, Luke Ward, Stuart Moss, Susannah Glasgow, Lynn Abel, Michael Brett, Brian Digby, Lisa Gemmell, James Hornsby, Patrick MacGoey, Pauline O'Neil, Richard Price, Natalie Rodden, Kevin Rooney, Radha Sundaram, Nicola Thomson, Bridget Hopkins, Laura Thrasyvoulou, Heather Willis, Martyn Clark, Martina Coulding, Edward Jude, Jacqueline McCormick, Oliver Mercer, Darsh Potla, Hafiz Rehman, Heather Savill, Victoria Turner, Charlotte Downes, Kathleen Holding, Katie Riches, Mary Hilton, Mel Hayman, Deepak Subramanian, Priya Daniel, Oluronke Adanini, Nikhil Bhatia, Maines Msiska, Rebecca Collins, Ian Clement, Bijal Patel, A. Gulati, Carole Hays, K. Webster, Anne Hudson, Andrea Webster, Elaine Stephenson, Louise McCormack, Victoria Slater, Rachel Nixon, Helen Hanson, Maggie Fearby, Sinead Kelly, Victoria Bridgett, Philip Robinson, Julie Camsooksai, Charlotte Humphrey, Sarah Jenkins, Henrik Reschreiter, Beverley Wadams, Yasmin Death, Victoria Bastion, Daphene Clarke, Beena David, Harriet Kent, Rachel Lorusso, Gamu Lubimbi, Sophie Murdoch, Melchizedek Penacerrada, Alastair Thomas, Jennifer Valentine, Ana Vochin, Retno Wulandari, Brice Djeugam, Gillian Bell, Katy English, Amro Katary, Louise Wilcox, Michelle Bruce, Karen Connolly, Tracy Duncan, Helen T-Michael, Gabriella Lindergard, Samuel Hey, Claire Fox, Jordan Alfonso, Laura Jayne Durrans, Jacinta Guerin, Bethan Blackledge, Jade Harris, Martin Hruska, Ayaa Eltayeb, Thomas Lamb, Tracey Hodgkiss, Lisa Cooper, Joanne Rothwell, Angela Allan, Felicity Anderson, Callum Kaye, Jade Liew, Jasmine Medhora, Teresa Scott, Erin Trumper, Adriana Botello, Liana Lankester, Nikitas Nikitas, Colin Wells, Bethan Stowe, Kayleigh Spencer, Craig Brandwood, Lara Smith, Katie Birchall, Laurel Kolakaluri, Deborah Baines, Anila Sukumaran, Elena Apetri, Cathrine Basikolo, Laura Catlow, Bethan Charles, Paul Dark, Reece Doonan, Alice Harvey, Daniel Horner, Karen Knowles, Stephanie Lee, Diane Lomas, Chloe Lyons, Tracy Marsden, Danielle McLaughlan, Liam McMorrow, Jessica Pendlebury, Jane Perez, Maria Poulaka, Nicola Proudfoot, Melanie Slaughter, Kathryn Slevin, Vicky Thomas, Danielle Walker, Angiy Michael, Matthew Collis, Tracey Cosier, Gemma Millen, Neil Richardson, Natasha Schumacher, Heather Weston, James Rand, Nicola Baxter, Steven Henderson, Sophie Kennedy-Hay, Christopher McParland, Laura Rooney, Malcolm Sim, Gordan McCreath, Louise Akeroyd, Shereen Bano, Matt Bromley, Lucy Gurr, Tom Lawton, James Morgan, Kirsten Sellick, Deborah Warren, Brian Wilkinson, Janet McGowan, Camilla Ledgard, Amelia Stacey, Kate Pye, Ruth Bellwood, Michael Bentley, Jeremy Bewley, Zoe Garland, Lisa Grimmer, Bethany Gumbrill, Rebekah Johnson, Katie Sweet, Denise Webster, Georgia Efford, Karen Convery, Deirdre Fottrell-Gould, Lisa Hudig, Jocelyn Keshet-Price, Georgina Randell, Katie Stammers, Maria Bokhari, Vanessa Linnett, Rachael Lucas, Wendy McCormick, Jenny Ritzema, Amanda Sanderson, Helen Wild, Anthony Rostron, Alistair Roy, Lindsey Woods, Sarah Cornell, Fiona Wakinshaw, Kimberley Rogerson, Jordan Jarmain, Robert Parker, Amie Reddy, Ian Turner-Bone, Laura Wilding, Peter Harding, Caroline Abernathy, Louise Foster, Andrew Gratrix, Vicky Martinson, Priyai Parkinson, Elizabeth Stones, Llucia Carbral-Ortega, Georgia Bercades, David Brealey, Ingrid Hass, Niall MacCallum, Gladys Martir, Eamon Raith, Anna Reyes, Deborah Smyth, Letizia Zitter, Sarah Benyon, Suzie Marriott, Linda Park, Samantha Keenan, Elizabeth Gordon, Helen Quinn, Kizzy Baines, Lenka Cagova, Adama Fofano, Lucie Garner, Helen Holcombe, Sue Mepham, Alice Michael Mitchell, Lucy Mwaura, Krithivasan Praman, Alain Vuylsteke, Julie Zamikula, Bally Purewal, Vanessa Rivers, Stephanie Bell, Hayley Blakemore, Borislava Borislavova, Beverley Faulkner, Emma Gendall, Elizabeth Goff, Kati Hayes, Matt Thomas, Ruth Worner, Kerry Smith, Deanna Stephens, Louise Mew, Esther Mwaura, Richard Stewart, Felicity Williams, Lynn Wren, Sara-Beth Sutherland, Emily Bevan, Jane Martin, Dawn Trodd, Geoff Watson, Caroline Wrey Brown, Amy Collins, Waqas Khaliq, Estefania Treus Gude, Olugbenga Akinkugbe, Alasdair Bamford, Emily Beech, Holly Belfield, Michael Bell, Charlene Davies, Gareth A.L. Jones, Tara McHugh, Hamza Meghari, Lauran O'Neill, Mark J. Peters, Samiran Ray, Ana Luisa Tomas, Iona Burn, Geraldine Hambrook, Katarina Manso, Ruth Penn, Pradeep Shanmugasundaram, Julie Tebbutt, Danielle Thornton, Jade Cole, Rhys Davies, Donna Duffin, Helen Hill, Ben Player, Emma Thomas, Angharad Williams, Denise Griffin, Nycola Muchenje, Mcdonald Mupudzi, Richard Partridge, Jo-Anna Conyngham, Rachel Thomas, Mary Wright, Maria Alvarez Corral, Reni Jacob, Cathy Jones, Craig Denmade, Sarah Beavis, Katie Dale, Rachel Gascoyne, Joanne Hawes, Kelly Pritchard, Lesley Stevenson, Amanda Whileman, Patricia Doble, Joanne Hutter, Corinne Pawley, Charmaine Shovelton, Marius Vaida, Deborah Butcher, Susie O'Sullivan, Nicola Butterworth-Cowin, Norfaizan Ahmad, Joann Barker, Kris Bauchmuller, Sarah Bird, Kay Cawthron, Kate Harrington, Yvonne Jackson, Faith Kibutu, Becky Lenagh, Shamiso Masuko, Gary H. Mills, Ajay Raithatha, Matthew Wiles, Jayne Willson, Helen Newell, Alison Lye, Lorenza Nwafor, Claire Jarman, Sarah Rowland-Jones, David Foote, Joby Cole, Roger Thompson, James Watson, Lisa Hesseldon, Irene Macharia, Luke Chetam, Jacqui Smith, Amber Ford, Samantha Anderson, Kathryn Birchall, Kay Housley, Sara Walker, Leanne Milner, Helena Hanratty, Helen Trower, Patrick Phillips, Simon Oxspring, Ben Donne, Catherine Jardine, Dewi Williams, Alasdair Hay, Rebecca Flanagan, Gareth Hughes, Scott Latham, Emma McKenna, Jennifer Anderson, Robert Hull, Kat Rhead, Carina Cruz, Natalie Pattison, Rob Charnock, Denise McFarland, Denise Cosgrove, Ashar Ahmed, Anna Morris, Srinivas Jakkula, Asifa Ali, Megan Brady, Sam Dale, Annalisa Dance, Lisa Gledhill, Jill Greig, Kathryn Hanson, Kelly Holdroyd, Marie Home, Diane Kelly, Ross Kitson, Lear Matapure, Deborah Melia, Samantha Mellor, Tonicha Nortcliffe, Jez Pinnell, Matthew Robinson, Lisa Shaw, Ryan Shaw, Lesley Thomis, Alison Wilson, Tracy Wood, Lee-Ann Bayo, Ekta Merwaha, Tahira Ishaq, Sarah Hanley, Meg Hibbert, Dariusz Tetla, Chrsitopher Woodford, Latha Durga, Gareth Kennard-Holden, Debbie Branney, Jordan Frankham, Sally Pitts, Nigel White, Shondipon Laha, Mark Verlander, Alexandra Williams, Abdelhakim Altabaibeh, Ana Alvaro, Kayleigh Gilbert, Louise Ma, Loreta Mostoles, Chetan Parmar, Kathryn Simpson, Champa Jetha, Lauren Booker, Anezka Pratley, Colene Adams, Anita Agasou, Tracie Arden, Amy Bowes, Pauline Boyle, Mandy Beekes, Heather Button, Nigel Capps, Mandy Carnahan, Anne Carter, Danielle Childs, Denise Donaldson, Kelly Hard, Fran Hurford, Yasmin Hussain, Ayesha Javaid, James Jones, Sanal Jose, Michael Leigh, Terry Martin, Helen Millward, Nichola Motherwell, Rachel Rikunenko, Jo Stickley, Julie Summers, Louise Ting, Helen Tivenan, Louise Tonks, Rebecca Wilcox, Maureen Holland, Natalie Keenan, Marc Lyons, Helen Wassall, Chris Marsh, Mervin Mahenthran, Emma Carter, Thomas Kong, Helen Blackman, Ben Creagh-Brown, Sinead Donlon, Natalia Michalak-Glinska, Sheila Mtuwa, Veronika Pristopan, Armorel Salberg, Eleanor Smith, Sarah Stone, Charles Piercy, Jerik Verula, Dorota Burda, Rugia Montaser, Lesley Harden, Irving Mayangao, Cheryl Marriott, Paul Bradley, Celia Harris, Susan Anderson, Eleanor Andrews, Janine Birch, Emma Collins, Kate Hammerton, Ryan O'Leary, Michele Clark, Sarah Purvis, Russell Barber, Claire Hewitt, Annette Hilldrith, Karen Jackson-Lawrence, Sarah Shepardson, Maryanne Wills, Susan Butler, Silvia Tavares, Amy Cunningham, Julia Hindale, Sarwat Arif, Sarah Bean, Karen Burt, Michael Spivey, Carrie Demetriou, Charlotte Eckbad, Sarah Hierons, Lucy Howie, Sarah Mitchard, Lidia Ramos, Alfredo Serrano-Ruiz, Katie White, Fiona Kelly, Daniele Cristiano, Natalie Dormand, Zohreh Farzad, Mahitha Gummadi, Kamal Liyanage, Brijesh Patel, Sara Salmi, Geraldine Sloane, Vicky Thwaites, Mathew Varghese, Anelise C. Zborowski, John Allan, Tim Geary, Gordon Houston, Alistair Meikle, Peter O'Brien, Miranda Forsey, Agilan Kaliappan, Anne Nicholson, Joanne Riches, Mark Vertue, Elizabeth Allan, Kate Darlington, Ffyon Davies, Jack Easton, Sumit Kumar, Richard Lean, Daniel Menzies, Richard Pugh, Xinyi Qiu, Llinos Davies, Hannah Williams, Jeremy Scanlon, Gwyneth Davies, Callum Mackay, Joannne Lewis, Stephanie Rees, Metod Oblak, Monica Popescu, Mini Thankachen, Andrew Higham, Kerry Simpson, Jayne Craig, Rosie Baruah, Sheila Morris, Susie Ferguson, Amy Shepherd, Luke Stephen Prockter Moore, Marcela Paola Vizcaychipi, Laura Gomes de Almeida Martins, Jaime Carungcong, Inthakab Ali Mohamed Ali, Karen Beaumont, Mark Blunt, Zoe Coton, Hollie Curgenven, Mohamed Elsaadany, Kay Fernandes, Sameena Mohamed Ally, Harini Rangarajan, Varun Sarathy, Sivarupan Selvanayagam, Dave Vedage, Matthew White, Mandy Gill, Paul Paul, Valli Ratnam, Sarah Shelton, Inez Wynter, Siobhain Carmody, Valerie Joan Page, Claire Marie Beith, Karen Black, Suzanne Clements, Alan Morrison, Dominic Strachan, Margaret Taylor, Michelle Clarkson, Stuart D'Sylva, Kathryn Norman, Fiona Auld, Joanne Donnachie, Ian Edmond, Lynn Prentice, Nikole Runciman, Dario Salutous, Lesley Symon, Anne Todd, Patricia Turner, Abigail Short, Laura Sweeney, Euan Murdoch, Dhaneesha Senaratne, Michaela Hill, Thogulava Kannan, Wild Laura, Rikki Crawley, Abigail Crew, Mishell Cunningham, Allison Daniels, Laura Harrison, Susan Hope, Ken Inweregbu, Sian Jones, Nicola Lancaster, Jamie Matthews, Alice Nicholson, Gemma Wray, Helen Langton, Rachel Prout, Malcolm Watters, Catherine Novis, Anthony Barron, Ciara Collins, Sundeep Kaul, Heather Passmore, Claire Prendergast, Anna Reed, Paula Rogers, Rajvinder Shokkar, Meriel Woodruff, Hayley Middleton, Oliver Polgar, Claire Nolan, Kanta Mahay, Dawn Collier, Anil Hormis, Victoria Maynard, Cheryl Graham, Rachel Walker, Ellen Knights, Alicia Price, Alice Thomas, Chris Thorpe, Teresa Behan, Caroline Burnett, Jonathan Hatton, Elaine Heeney, Atideb Mitra, Maria Newton, Rachel Pollard, Rachael Stead, Vishal Amin, Elena Anastasescu, Vikram Anumakonda, Komala Karthik, Rizwana Kausar, Karen Reid, Jacqueline Smith, Janet Imeson-Wood, Denise Skinner, Jane Gaylard, Dee Mullan, Julie Newman, Alison Brown, Vikki Crickmore, Gabor Debreceni, Joy Wilkins, Liz Nicol, Rosie Reece-Anthony, Mark Birt, Alison Ghosh, Emma Williams, Louise Allen, Eva Beranova, Nikki Crisp, Joanne Deery, Tracy Hazelton, Alicia Knight, Carly Price, Sorrell Tilbey, Salah Turki, Sharon Turney, Joshua Cooper, Cheryl Finch, Sarah Liderth, Alison Quinn, Natalia Waddington, Tina Coventry, Susan Fowler, Michael MacMahon, Amanda McGregor, Anne Cowley, Judith Highgate, Jane Gregory, Susan O'Connell, Tim Smith, Luigi Barberis, Shameer Gopal, Nichola Harris, Victoria Lake, Stella Metherell, Elizabeth Radford, Amelia Daniel, Joanne Finn, Rajnish Saha, Nikki White, Phil Donnison, Fiona Trim, Beena Eapen, Jenny Birch, Laura Bough, Josie Goodsell, Rebecca Tutton, Patricia Williams, Sarah Williams, Barbara Winter-Goodwin, Ailstair Nichol, Kathy Brickell, Michelle Smyth, Lorna Murphy, Samantha Coetzee, Alistair Gales, Igor Otahal, Meena Raj, Craig Sell, Paula Hilltout, Jayne Evitts, Amanda Tyler, Joanne Waldron, Kate Beesley, Sarah Board, Agnieszka Kubisz-Pudelko, Alison Lewis, Jess Perry, Lucy Pippard, Di Wood, Clare Buckley, Peter Barry, Neil Flint, Patel Rekha, Dawn Hales, Lara Bunni, Claire Jennings, Monica Latif, Rebecca Marshall, Gayathri Subramanian, Peter J. McGuigan, Christopher Wasson, Stephanie Finn, Jackie Green, Erin Collins, Bernadette King, Andy Campbell, Sara Smuts, Joseph Duffield, Oliver Smith, Lewis Mallon, Watkins Claire, Liam Botfield, Joanna Butler, Catherine Dexter, Jo Fletcher, Atul Garg, Aditya Kuravi, Poonam Ranga, Emma Virgilio, Zakaula Belagodu, Bridget Fuller, Anca Gherman, Olumide Olufuwa, Remi Paramsothy, Carmel Stuart, Naomi Oakley, Charlotte Kamundi, David Tyl, Katy Collins, Pedro Silva, June Taylor, Laura King, Charlotte Coates, Maria Crowley, Phillipa Wakefield, Jane Beadle, Laura Johnson, Janet Sargeant, Madeleine Anderson, Ailbhe Brady, Rebekah Chan, Jeff Little, Shane McIvor, Helena Prady, Helen Whittle, Bijoy Mathew, Ben Attwood, Penny Parsons, Geraldine Ward, Pamela Bremmer, West Joe, Baird Tracy, Ruddy Jim, Ellie Davies, Sonia Sathe, Catherine Dennis, Alastair McGregor, Victoria Parris, Sinduya Srikaran, Anisha Sukha, Noreen Clarke, Jonathan Whiteside, Mairi Mascarenhas, Avril Donaldson, Joanna Matheson, Fiona Barrett, Marianne O'Hara, Laura Okeefe, Clare Bradley, Christine Eastgate-Jackson, Helder Filipe, Daniel Martin, Amitaa Maharajh, Sara Mingo Garcia, Glykeria Pakou, Mark De Neef, Kathy Dent, Elizabeth Horsley, Muhmmad Nauman Akhtar, Sandra Pearson, Dorota Potoczna, Sue Spencer, Melanie Clapham, Rosemary Harper, Una Poultney, Polly Rice, Rachel Mutch, Lisa Armstrong, Hayley Bates, Emma Dooks, Fiona Farquhar, Brigid Hairsine, Chantal McParland, Sophie Packham, Rehana Bi, Barney Scholefield, Lydia Ashton, Linsha George, Sophie Twiss, David Wright, Manish Chablani, Amy Kirkby, Kimberley Netherton, Kim Davies, Linda O'Brien, Zohra Omar, Emma Perkins, Tracy Lewis, Isobel Sutherland, Karen Burns, Dr Ben Chandler, Kerry Elliott, Janine Mallinson, Alison Turnbull, Prisca Gondo, Bernard Hadebe, Abdul Kayani, Bridgett Masunda, Taya Anderson, Dan Hawcutt, Laura O'Malley, Laura Rad, Naomi Rogers, Paula Saunderson, Kathryn Sian Allison, Deborah Afolabi, Jennifer Whitbread, Dawn Jones, Rachael Dore, Matthew Halkes, Pauline Mercer, Lorraine Thornton, Joy Dawson, Sweyn Garrioch, Melanie Tolson, Jonathan Aldridge, Ritoo Kapoor, David Loader, Karen Castle, Sally Humphreys, Ruth Tampsett, Katherine Mackintosh, Amanda Ayers, Wendy Harrison, Julie North, Suzanne Allibone, Roman Genetu, Vidya Kasipandian, Amit Patel, Ainhi Mac, Anthony Murphy, Parisa Mahjoob, Roonak Nazari, Lucy Worsley, Andrew Fagan, Thomas Bemand, Ethel Black, Arnold Dela Rosa, Ryan Howle, Shaman Jhanji, Ravishankar Rao Baikady, Kate Colette Tatham, Benjamin Thomas, Dina Bell, Rosalind Boyle, Katie Douglas, Lynn Glass, Emma Lee, Liz Lennon, Austin Rattray, Abigail Taylor, Rachel Anne Hughes, Helen Thomas, Alun Rees, Michaela Duskova, Janet Phipps, Suzanne Brooks, Michelle Edwards, Sheena Quaid, Ekaterina Watson, Adam Brayne, Emma Fisher, Jane Hunt, Peter Jackson, Duncan Kaye, Nicholas Love, Juliet Parkin, Victoria Tuckey, Lynne Van Koutrik, Sasha Carter, Benedict Andrew, Louise Findlay, Katie Adams, Jen Service, Alison Williams, Claire Cheyne, Anne Saunderson, Sam Moultrie, Miranda Odam, Kathryn Hall, Isheunesu Mapfunde, Charlotte Willis, Alex Lyon, Chunda Sri-Chandana, Joslan Scherewode, Lorraine Stephenson, Sarah Marsh, John Hardy, Henry Houlden, Eleanor Moncur, Ambreen Tariq, Arianna Tucci, Maria Hobrok, Ronda Loosley, Heather McGuinness, Helen Tench, Rebecca Wolf-Roberts, Val Irvine, Benjamin Shelley, Claire Gorman, Abhinav Gupta, Elizabeth Timlick, Rebecca Brady, Barry Milligan, Arianna Bellini, Jade Bryant, Anton Mayer, Amy Pickard, Nicholas Roe, Jason Sowter, Alex Howlett, Katy Fidler, Emma Tagliavini, and Kevin Donnelly

Subjects
SARS-CoV-2, host genetics, toll-like receptor 7, targeted sequencing, rare variants, variant collapsing analysis, Genetics, QH426-470
Abstract

Summary: Despite extensive global research into genetic predisposition for severe COVID-19, knowledge on the role of rare host genetic variants and their relation to other risk factors remains limited. Here, 52 genes with prior etiological evidence were sequenced in 1,772 severe COVID-19 cases and 5,347 population-based controls from Spain/Italy. Rare deleterious TLR7 variants were present in 2.4% of young (

Published
2024
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13. Northern Gannet foraging trip length increases with colony size and decreases with latitude

Author

Bethany L. Clark, Freydís Vigfúsdóttir, Sarah Wanless, Keith C. Hamer, Thomas W. Bodey, Stuart Bearhop, Ashley Bennison, Jez Blackburn, Sam L. Cox, Kyle J. N. d’Entremont, Stefan Garthe, David Grémillet, Mark Jessopp, Jude Lane, Amélie Lescroël, William A. Montevecchi, David J. Pascall, Pascal Provost, Ewan D. Wakefield, Victoria Warwick‐Evans, Saskia Wischnewski, Lucy J. Wright, and Stephen C. Votier

Subjects
central place foraging, coloniality, species distributions, bio-logging, predator–prey, seabird, Science
Abstract

Density-dependent competition for food influences the foraging behaviour and demography of colonial animals, but how this influence varies across a species’ latitudinal range is poorly understood. Here we used satellite tracking from 21 Northern Gannet Morus bassanus colonies (39% of colonies worldwide, supporting 73% of the global population) during chick-rearing to test how foraging trip characteristics (distance and duration) covary with colony size (138–60 953 breeding pairs) and latitude across 89% of their latitudinal range (46.81–71.23° N). Tracking data for 1118 individuals showed that foraging trip duration and maximum distance both increased with square-root colony size. Foraging effort also varied between years for the same colony, consistent with a link to environmental variability. Trip duration and maximum distance also decreased with latitude, after controlling for colony size. Our results are consistent with density-dependent reduction in prey availability influencing colony size and reveal reduced competition at the poleward range margin. This provides a mechanism for rapid population growth at northern colonies and, therefore, a poleward shift in response to environmental change. Further work is required to understand when and how colonial animals deplete nearby prey, along with the positive and negative effects of social foraging behaviour.

Published
2024
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14. Investigating the biosynthesis and roles of the auxin phenylacetic acid during Pseudomonas syringae-Arabidopsis thaliana pathogenesis

Author

Chia-Yun Lee, Christopher P. Harper, Soon Goo Lee, Yunci Qi, Taylor Clay, Yuki Aoi, Joseph M. Jez, Hiroyuki Kasahara, Joshua A. V. Blodgett, and Barbara N. Kunkel

Subjects
auxin, Indole-3-acetaldehyde dehydrogenase, indole-3-acetic acid, phenylacetic acid, Pseudomonas syringae, Plant culture, SB1-1110
Abstract

Several plant-associated microbes synthesize the auxinic plant growth regulator phenylacetic acid (PAA) in culture; however, the role of PAA in plant-pathogen interactions is not well understood. In this study, we investigated the role of PAA during interactions between the phytopathogenic bacterium Pseudomonas syringae strain PtoDC3000 (PtoDC3000) and the model plant host, Arabidopsis thaliana. Previous work demonstrated that indole-3-acetaldehyde dehydrogenase A (AldA) of PtoDC3000 converts indole-3-acetaldehyde (IAAld) to the auxin indole-3-acetic acid (IAA). Here, we further demonstrated the biochemical versatility of AldA by conducting substrate screening and steady-state kinetic analyses, and showed that AldA can use both IAAld and phenylacetaldehyde as substrates to produce IAA and PAA, respectively. Quantification of auxin in infected plant tissue showed that AldA-dependent synthesis of either IAA or PAA by PtoDC3000 does not contribute significantly to the increase in auxin levels in infected A. thaliana leaves. Using available arogenate dehydratase (adt) mutant lines of A. thaliana compromised for PAA synthesis, we observed that a reduction in PAA-Asp and PAA-Glu is correlated with elevated levels of IAA and increased susceptibility. These results provide evidence that PAA/IAA homeostasis in A. thaliana influences the outcome of plant-microbial interactions.

Published
2024
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15. As Catholic Schools Become More Diverse, How Should We Prepare New Catholic School Educators for Inclusive Schools? An Analysis of Research on University and Diocesan Teacher Training

Author

Jez, Rebekka J., Cantillon, Julie C., Ramers, Lauren H., and Burgess, Melissa M.

Abstract

Educators can improve the academic and socioemotional wellbeing of their students if they are equipped with strategies and skills to support learners and families from diverse backgrounds and experiences--such as culturally and linguistically diverse students, students with differing abilities, and those who may experience trauma and/or socioeconomic challenges. To learn more about this topic, a Catholic university and local diocese partnered to examine the literature on the impact of Catholic teachers in under-resourced schools; practices for training Catholic educators with skills to meet the needs of all learners; and the structures needed to ensure that diocesan and university supervisors are able to effectively support the development of new teachers. The literature review was organized using the three pillars of the University Consortium of Catholic Education: service through teaching, community connections, and spiritual development. The review resulted in the following recommendations: train teachers in culturally responsive practices, incentivize educator collaboration, train supervisors in inclusive practices with purposeful faith-based integration, and mentor principals in effective methods of coaching and support for teachers.

Published
2021

16. Chemical inhibition of the auxin inactivation pathway uncovers the roles of metabolic turnover in auxin homeostasis

Author

Fukui, Kosuke, Arai, Kazushi, Tanaka, Yuka, Aoi, Yuki, Kukshal, Vandna, Jez, Joseph M, Kubes, Martin F, Napier, Richard, Zhao, Yunde, Kasahara, Hiroyuki, and Hayashi, Ken-ichiro

Subjects
Arabidopsis, Homeostasis, Indoleacetic Acids, Plant Growth Regulators, auxin, plant hormone, chemical biology
Abstract

The phytohormone auxin, indole-3-acetic acid (IAA), plays a prominent role in plant development. Auxin homeostasis is coordinately regulated by auxin synthesis, transport, and inactivation; however, the physiological contribution of auxin inactivation to auxin homeostasis has not been determined. The GH3 IAA-amino acid conjugating enzymes play a central role in auxin inactivation. Chemical inhibition of GH3 proteins in planta is challenging because the inhibition of these enzymes leads to IAA overaccumulation that rapidly induces GH3 expression. Here, we report the characterization of a potent GH3 inhibitor, kakeimide, that selectively targets IAA-conjugating GH3 proteins. Chemical knockdown of the auxin inactivation pathway demonstrates that auxin turnover is very rapid (about 10 min) and indicates that both auxin biosynthesis and inactivation dynamically regulate auxin homeostasis.

Published
2022

17. Ribosomal profiling of human endogenous retroviruses in healthy tissues

Author

Nicholas Dopkins, Bhavya Singh, Stephanie Michael, Panpan Zhang, Jez L. Marston, Tongyi Fei, Manvendra Singh, Cedric Feschotte, Nicholas Collins, Matthew L. Bendall, and Douglas F. Nixon

Subjects
Human endogenous retrovirus (HERV), Ribosomal profiling (RiboSeq), Protein translation, Dark genome, Endoretrotranslatome (ERT), Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Human endogenous retroviruses (HERVs) are the germline embedded proviral fragments of ancient retroviral infections that make up roughly 8% of the human genome. Our understanding of HERVs in physiology primarily surrounds their non-coding functions, while their protein coding capacity remains virtually uncharacterized. Therefore, we applied the bioinformatic pipeline “hervQuant” to high-resolution ribosomal profiling of healthy tissues to provide a comprehensive overview of translationally active HERVs. We find that HERVs account for 0.1–0.4% of all translation in distinct tissue-specific profiles. Collectively, our study further supports claims that HERVs are actively translated throughout healthy tissues to provide sequences of retroviral origin to the human proteome.

Published
2024
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18. Lower bounds on the performance of online algorithms for relaxed packing problems

Author

Balogh, János, Dósa, György, Epstein, Leah, and Jeż, Łukasz

Subjects
Computer Science - Data Structures and Algorithms, Computer Science - Discrete Mathematics, Mathematics - Combinatorics, Mathematics - Optimization and Control
Abstract

We prove new lower bounds for suitable competitive ratio measures of two relaxed online packing problems: online removable multiple knapsack, and a recently introduced online minimum peak appointment scheduling problem. The high level objective in both problems is to pack arriving items of sizes at most 1 into bins of capacity 1 as efficiently as possible, but the exact formalizations differ. In the appointment scheduling problem, every item has to be assigned to a position, which can be seen as a time interval during a workday of length 1. That is, items are not assigned to bins, but only once all the items are processed, the optimal number of bins subject to chosen positions is determined, and this is the cost of the online algorithm. On the other hand, in the removable knapsack problem there is a fixed number of bins, and the goal of packing items, which consists in choosing a particular bin for every packed item (and nothing else), is to pack as valuable a subset as possible. In this last problem it is possible to reject items, that is, deliberately not pack them, as well as to remove packed items at any later point in time, which adds flexibility to the problem.

Published
2022

19. Application of Electrical Protection on Subsea Electrically Trace Heated Pipe-in-Pipe Line

Author

Radoslaw Jez, Michal Lazarczyk, Jakub Ejma-Multanski, Ryszard Kowalik, Marcin Januszewski, Karol Kurek, Lukasz Nogal, Radosław Szreder, and Marcin Szewczyk

Subjects
power protection, ETH-PiP, trace heating, subsea pipeline, power system simulation, Technology
Abstract

The deployment of Electrically Trace Heated Pipe-in-Pipe (ETH-PiP) brings the challenges of reliable protection selection and setting. This paper presents a study of relays and protection function optimization for ETH-PiP systems. The study is based on the developed simulation model of a typical ETH-PiP system. The paper presents simulation studies of physical phenomena occurring during electrical disturbances in the ETH-PiP system and offers detailed analyses applicable to system protection, including detection of disturbances, location, and elimination.

Published
2024
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20. Examining Equitable Practices within Teacher Praparation

Author

Jez, Rebekka J.

Abstract

The articles within this issue of "Teacher Education Quarterly" examined the role and impact of equity within teacher preparation. Each author described a commitment to preparing teachers with equitable, social justice minded practices to meet the needs of the diverse learners in U.S. classrooms, yet, demonstrated a need for a closer look at how teacher education programs are preparing educators for this work. This article poses the question: How are teacher education programs that identify as social justice leaders providing preservice teachers with opportunities to move theory into practice with integrity?

Published
2020

21. Earthquake-enhanced dissolved carbon cycles in ultra-deep ocean sediments

Author

Chu, Mengfan, Bao, Rui, Strasser, Michael, Ikehara, Ken, Everest, Jez, Maeda, Lena, Hochmuth, Katharina, Xu, Li, McNichol, Ann, Bellanova, Piero, Rasbury, Troy, Kölling, Martin, Riedinger, Natascha, Johnson, Joel, Luo, Min, März, Christian, Straub, Susanne, Jitsuno, Kana, Brunet, Morgane, Cai, Zhirong, Cattaneo, Antonio, Hsiung, Kanhsi, Ishizawa, Takashi, Itaki, Takuya, Kanamatsu, Toshiya, Keep, Myra, Kioka, Arata, McHugh, Cecilia, Micallef, Aaron, Pandey, Dhananjai, Proust, Jean Noël, Satoguchi, Yasufumi, Sawyer, Derek, Seibert, Chloé, Silver, Maxwell, Virtasalo, Joonas, Wang, Yonghong, Wu, Ting-Wei, and Zellers, Sarah

Published
2023
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23. Preclinical evaluation of two phylogenetically distant arenavirus vectors for the development of novel immunotherapeutic combination strategies for cancer treatment

Author

Pedro Berraondo, Catarina Pinto, Sarah Schmidt, Henning Lauterbach, Timo Schippers, Josipa Raguz, Theresa Pölzlbauer, Mohamed Habbeddine, Sandra Rosskopf, Judith Strauß, Valentin Just, Katell Bidet Huang, Felix Stemeseder, Ethan Stewart, Jakub Jez, and Klaus K. Orlinger

Subjects
Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Background Engineered arenavirus vectors have recently been developed to leverage the body’s immune system in the fight against chronic viral infections and cancer. Vectors based on Pichinde virus (artPICV) and lymphocytic choriomeningitis virus (artLCMV) encoding a non-oncogenic fusion protein of human papillomavirus (HPV)16 E6 and E7 are currently being tested in patients with HPV16+ cancer, showing a favorable safety and tolerability profile and unprecedented expansion of tumor-specific CD8+ T cells. Although the strong antigen-specific immune response elicited by artLCMV vectors has been demonstrated in several preclinical models, PICV-based vectors are much less characterized.Methods To advance our understanding of the immunobiology of these two vectors, we analyzed and compared their individual properties in preclinical in vivo and in vitro systems. Immunogenicity and antitumor effect of intratumoral or intravenous administration of both vectors, as well as combination with NKG2A blockade, were evaluated in naïve or TC-1 mouse tumor models. Flow cytometry, Nanostring, and histology analysis were performed to characterize the tumor microenvironment (TME) and T-cell infiltrate following treatment.Results Despite being phylogenetically distant, both vectors shared many properties, including preferential infection and activation of professional antigen-presenting cells, and induction of potent tumor-specific CD8+ T-cell responses. Systemic as well as localized treatment induced a proinflammatory shift in the TME, promoting the infiltration of inducible T cell costimulator (ICOS)+CD8+ T cells capable of mediating tumor regression and prolonging survival in a TC-1 mouse tumor model. Still, there was evidence of immunosuppression built-up over time, and increased expression of H2-T23 (ligand for NKG2A T cell inhibitory receptor) following treatment was identified as a potential contributing factor. NKG2A blockade improved the antitumor efficacy of artARENA vectors, suggesting a promising new combination approach. This demonstrates how detailed characterization of arenavirus vector-induced immune responses and TME modulation can inform novel combination therapies.Conclusions The artARENA platform represents a strong therapeutic vaccine approach for the treatment of cancer. The induced antitumor immune response builds the backbone for novel combination therapies, which warrant further investigation.

Published
2024
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24. Superiority and cost-effectiveness of Individual Placement and Support versus standard employment support for people with alcohol and drug dependence: a pragmatic, parallel-group, open-label, multicentre, randomised, controlled, phase 3 trialResearch in context

Author

John Marsden, Paul Anders, Claire Shaw, Chioma Amasiatu, Winnie Collate, Brian Eastwood, Patrick Horgan, Meetal Khetani, Jonathan Knight, Sandy Knight, Alexandra Melaugh, Helen Clark, and Jez Stannard

Subjects
Individual placement and support, Employment support, Alcohol use disorder, Opioid use disorder, Drug use disorder, Medicine (General), R5-920
Abstract

Summary: Background: Individual Placement and Support (IPS) is a specialist intervention to help people attain employment in the open competitive labour market. IPS has been developed in severe mental illness and other disabilities, but it is of unknown effectiveness for people with alcohol and drug dependence. The Individual Placement and Support—Alcohol and Drug (IPS-AD) is the first superiority trial to evaluate effectiveness and cost-effectiveness. Methods: IPS-AD was a pragmatic, parallel-group, multi-centre, randomised, controlled, phase 3 trial of standard employment support (treatment-as-usual [TAU]) versus IPS. IPS was offered as a single episode for up to 13 months. The study was done at seven community treatment centres for alcohol and drug dependence in England. Study participants were adults (18–65 years), who had been enrolled for at least 14 days in treatment for alcohol use disorder (AUD), opioid use disorder (OUD), or another drug use disorder (DUD; mostly cannabis and stimulants); were unemployed or economically inactive for at least six months; and wished to attain employment in the open competitive labour market. After random allocation to study interventions, the primary outcome was employment during 18-months of follow-up, analysed by mixed-effects logistic regression, using multiple imputation for the management of missing outcome data. There were two cost-effectiveness outcomes: a health outcome expressed as a quality adjusted life year (QALY) using £30,000 and £70,000 willingness-to-pay [WTP] thresholds; and additional days of employment, with a WTP threshold of £200 per day worked. The study was registered with ISRCTN (ISRCTN24159790) and is completed. Findings: Between 8 May 2018 and 30 September 2019, 2781 potentially eligible patients were identified. 812 were excluded before screening, and 1720 participants were randomly allocated to TAU or IPS. In error, nine participants were randomised to study interventions on two occasions—so data for their first randomisation was analysed (modified intention-to-treat). A further 24 participants withdrew consent for all data to be used (full-analysis set therefore 1687 participants [70.1% male; mean age 40.8 years]; TAU, n = 844; IPS, n = 843 [AUD, n = 610; OUD, n = 837; DUD, n = 240]). Standard employment support was received by 559 [66.2%] of 844 participants in the TAU group. IPS was received by 804 [95.37%] of 843 participants in the IPS group. IPS was associated with an increase in attainment of employment compared with TAU (adjusted odds ratio [OR] 1.29; 95% CI 1.02–1.64; p-value 0.036). IPS was effective for the AUD and DUD groups (OR 1.48; 95% CI 1.14–1.92; p-value 0.004; OR 1.45, 95% CI 1.03–2.04, p-value 0.031, respectively), but not the OUD group. IPS returned an incremental QALY outcome gain of 0.01 (range 0.003–0.02) per participant with no evidence of cost-effectiveness at either WTP threshold—but QALY gains were cost-effective for the AUD and DUD groups at the £70,000 WTP threshold (probability 0.52 and 0.97, respectively). IPS was cost-effective for additional days of employment (probability 0.61), with effectiveness relating to the AUD group only (probability >0.99). Serious Adverse Events were reported by 39 participants (13 [1.5%] of 844 participants in the TAU group and 23 [2.7%] of 43 participants in the IPS group). There was a total of 25 deaths (1.5%; 9 in the TAU group and 16 in the IPS group)—none judged related to study interventions. Interpretation: In this first superiority randomised controlled trial of IPS in alcohol and drug dependence, IPS helped more people attain employment in the open competitive labour market than standard employment support. IPS was cost-effective for a QALY health outcome (£70,000 WTP threshold) for the AUD and DUD groups, and for additional days of employment for the AUD group (£200 per day worked WTP threshold). Funding: UK government Work and Health Unit.

Published
2024
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25. Microtubules promote the non-cell autonomous action of microRNAs by inhibiting their cytoplasmic loading onto ARGONAUTE1 in Arabidopsis

Author

Fan, Lusheng, Zhang, Cui, Gao, Bin, Zhang, Yong, Stewart, Ethan, Jez, Jakub, Nakajima, Keiji, and Chen, Xuemei

Subjects
Biochemistry and Cell Biology, Biological Sciences, Biotechnology, Genetics, Arabidopsis, Arabidopsis Proteins, Argonaute Proteins, Gene Expression Regulation, Plant, Katanin, MicroRNAs, Microtubules, Plants, Genetically Modified, AGO1 loading, MOR1, cell-to-cell movement, miR165/6, microRNA, microtubule, non-cell autonomy, systemic movement, Medical and Health Sciences, Developmental Biology, Biochemistry and cell biology
Abstract

Mobile microRNAs (miRNAs) serve as local and long-distance signals in the developmental patterning and stress responses in plants. However, mechanisms governing the non-cell autonomous activities of miRNAs remain elusive. Here, we show that mutations that disrupt microtubule dynamics are specifically defective for the non-cell autonomous actions of mobile miRNAs, including miR165/6 that is produced in the endodermis and moves to the vasculature to pattern xylem cell fates in Arabidopsis roots. We show that KTN1, a subunit of a microtubule-severing enzyme, is required in source cells to inhibit the loading of miR165/6 into ARGONUATE1 (AGO1), which is cell autonomous, to enable the miRNA to exit the cell. Microtubule disruption enhances the association of miR165/6 with AGO1 in the cytoplasm. These findings suggest that although cell-autonomous miRNAs load onto AGO1 in the nucleus, the cytoplasmic AGO1 loading of mobile miRNAs is a key step regulated by microtubules to promote the range of miRNA cell-to-cell movement.

Published
2022

26. Earthquake-enhanced dissolved carbon cycles in ultra-deep ocean sediments

Author

Mengfan Chu, Rui Bao, Michael Strasser, Ken Ikehara, Jez Everest, Lena Maeda, Katharina Hochmuth, Li Xu, Ann McNichol, Piero Bellanova, Troy Rasbury, Martin Kölling, Natascha Riedinger, Joel Johnson, Min Luo, Christian März, Susanne Straub, Kana Jitsuno, Morgane Brunet, Zhirong Cai, Antonio Cattaneo, Kanhsi Hsiung, Takashi Ishizawa, Takuya Itaki, Toshiya Kanamatsu, Myra Keep, Arata Kioka, Cecilia McHugh, Aaron Micallef, Dhananjai Pandey, Jean Noël Proust, Yasufumi Satoguchi, Derek Sawyer, Chloé Seibert, Maxwell Silver, Joonas Virtasalo, Yonghong Wang, Ting-Wei Wu, and Sarah Zellers

Subjects
Science
Abstract

Abstract Hadal trenches are unique geological and ecological systems located along subduction zones. Earthquake-triggered turbidites act as efficient transport pathways of organic carbon (OC), yet remineralization and transformation of OC in these systems are not comprehensively understood. Here we measure concentrations and stable- and radiocarbon isotope signatures of dissolved organic and inorganic carbon (DOC, DIC) in the subsurface sediment interstitial water along the Japan Trench axis collected during the IODP Expedition 386. We find accumulation and aging of DOC and DIC in the subsurface sediments, which we interpret as enhanced production of labile dissolved carbon owing to earthquake-triggered turbidites, which supports intensive microbial methanogenesis in the trench sediments. The residual dissolved carbon accumulates in deep subsurface sediments and may continue to fuel the deep biosphere. Tectonic events can therefore enhance carbon accumulation and stimulate carbon transformation in plate convergent trench systems, which may accelerate carbon export into the subduction zones.

Published
2023
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27. Solving one variable word equations in the free group in cubic time

Author

Ferens, Robert and Jeż, Artur

Subjects
Mathematics - Group Theory, Computer Science - Discrete Mathematics, Computer Science - Data Structures and Algorithms, Computer Science - Formal Languages and Automata Theory
Abstract

A word equation with one variable in a free group is given as $U = V$, where both $U$ and $V$ are words over the alphabet of generators of the free group and $X, X^{-1}$, for a fixed variable $X$. An element of the free group is a solution when substituting it for $X$ yields a true equality (interpreted in the free group) of left- and right-hand sides. It is known that the set of all solutions of a given word equation with one variable is a finite union of sets of the form $\{\alpha w^i \beta \: : \: i \in \mathbb Z \}$, where $\alpha, w, \beta$ are reduced words over the alphabet of generators, and a polynomial-time algorithm (of a high degree) computing this set is known. We provide a cubic time algorithm for this problem, which also shows that the set of solutions consists of at most a quadratic number of the above-mentioned sets. The algorithm uses only simple tools of word combinatorics and group theory and is simple to state. Its analysis is involved and focuses on the combinatorics of occurrences of powers of a word within a larger word., Comment: 52 pages, accepted to STACS 2021

Published
2021

28. Mouse embryonic stem cell-derived blood–brain barrier model: applicability to studying antibody triggered receptor mediated transcytosis

Author

Anna Jezierski, Jez Huang, Arsalan S. Haqqani, Julie Haukenfrers, Ziying Liu, Ewa Baumann, Caroline Sodja, Claudie Charlebois, Christie E. Delaney, Alexandra T. Star, Qing Liu, and Danica B. Stanimirovic

Subjects
Blood brain barrier, Mouse brain endothelial cells, Receptor mediated transcytosis, Antibodies, Apparent permeability, Embryonic stem cells, Neurology. Diseases of the nervous system, RC346-429
Abstract

Abstract Blood brain barrier (BBB) models in vitro are an important tool to aid in the pre-clinical evaluation and selection of BBB-crossing therapeutics. Stem cell derived BBB models have recently demonstrated a substantial advantage over primary and immortalized brain endothelial cells (BECs) for BBB modeling. Coupled with recent discoveries highlighting significant species differences in the expression and function of key BBB transporters, the field is in need of robust, species-specific BBB models for improved translational predictability. We have developed a mouse BBB model, composed of mouse embryonic stem cell (mESC-D3)-derived brain endothelial-like cells (mBECs), employing a directed monolayer differentiation strategy. Although the mBECs showed a mixed endothelial-epithelial phenotype, they exhibited high transendothelial electrical resistance, inducible by retinoic acid treatment up to 400 Ω cm2. This tight cell barrier resulted in restricted sodium fluorescein permeability (1.7 × 10–5 cm/min), significantly lower than that of bEnd.3 cells (1.02 × 10–3 cm/min) and comparable to human induced pluripotent stem cell (iPSC)-derived BECs (2.0 × 10–5 cm/min). The mBECs expressed tight junction proteins, polarized and functional P-gp efflux transporter and receptor mediated transcytosis (RMT) receptors; collectively important criteria for studying barrier regulation and drug delivery applications in the CNS. In this study, we compared transport of a panel of antibodies binding species selective or cross-reactive epitopes on BBB RMT receptors in both the mBEC and human iPSC-derived BEC model, to demonstrate discrimination of species-specific BBB transport mechanisms.

Published
2023
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30. Unbounded lower bound for k-server against weak adversaries

Author

Bienkowski, Marcin, Byrka, Jarosław, Coester, Christian, and Jeż, Łukasz

Subjects
Computer Science - Data Structures and Algorithms
Abstract

We study the resource augmented version of the $k$-server problem, also known as the $k$-server problem against weak adversaries or the $(h,k)$-server problem. In this setting, an online algorithm using $k$ servers is compared to an offline algorithm using $h$ servers, where $h\le k$. For uniform metrics, it has been known since the seminal work of Sleator and Tarjan (1985) that for any $\epsilon>0$, the competitive ratio drops to a constant if $k=(1+\epsilon) \cdot h$. This result was later generalized to weighted stars (Young 1994) and trees of bounded depth (Bansal et al. 2017). The main open problem for this setting is whether a similar phenomenon occurs on general metrics. We resolve this question negatively. With a simple recursive construction, we show that the competitive ratio is at least $\Omega(\log \log h)$, even as $k\to\infty$. Our lower bound holds for both deterministic and randomized algorithms. It also disproves the existence of a competitive algorithm for the infinite server problem on general metrics., Comment: To appear in STOC 2020

Published
2019

31. From Nouns to Verbs: Exploring Educators' Learnings, Beliefs, Actions, and Growth

Author

Jez, Rebekka J.

Abstract

Our education system promotes moving from theory to practice; however, this often ends up being performative and thus perpetuates the disenfranchisement of historically marginalized communities. Preservice and in-service teachers share dissatisfaction with the amount of time, training, resources, and support they are given. This response highlights how educators and educator preparation programs can move from nouns (mere words) to verbs (intentional action) as we work to reimagine our current education system. Within this issue, recommendations are made to eliminate deficit language, dismantle ableist practices, increase teachers' self-efficacy, amplify students' voices, and support the development of teachers' pedagogy

Published
2022

33. The smallest grammar problem revisited

Author

Bannai, Hideo, Hirayama, Momoko, Hucke, Danny, Inenaga, Shunsuke, Jez, Artur, Lohrey, Markus, and Reh, Carl Philipp

Subjects
Computer Science - Data Structures and Algorithms
Abstract

In a seminal paper of Charikar et al. on the smallest grammar problem, the authors derive upper and lower bounds on the approximation ratios for several grammar-based compressors, but in all cases there is a gap between the lower and upper bound. Here the gaps for $\mathsf{LZ78}$ and $\mathsf{BISECTION}$ are closed by showing that the approximation ratio of $\mathsf{LZ78}$ is $\Theta( (n/\log n)^{2/3})$, whereas the approximation ratio of $\mathsf{BISECTION}$ is $\Theta(\sqrt{n/\log n})$. In addition, the lower bound for $\mathsf{RePair}$ is improved from $\Omega(\sqrt{\log n})$ to $\Omega(\log n/\log\log n)$. Finally, results of Arpe and Reischuk relating grammar-based compression for arbitrary alphabets and binary alphabets are improved., Comment: A short version of this paper appeared in the Proceedings of SPIRE 2016. This work has been supported by the DFG research project LO 748/10-1 (QUANT-KOMP)

Published
2019

34. ARCHANGEL: Tamper-proofing Video Archives using Temporal Content Hashes on the Blockchain

Author

Bui, Tu, Cooper, Daniel, Collomosse, John, Bell, Mark, Green, Alex, Sheridan, John, Higgins, Jez, Das, Arindra, Keller, Jared, Thereaux, Olivier, and Brown, Alan

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Artificial Intelligence, Computer Science - Cryptography and Security, Computer Science - Distributed, Parallel, and Cluster Computing
Abstract

We present ARCHANGEL; a novel distributed ledger based system for assuring the long-term integrity of digital video archives. First, we describe a novel deep network architecture for computing compact temporal content hashes (TCHs) from audio-visual streams with durations of minutes or hours. Our TCHs are sensitive to accidental or malicious content modification (tampering) but invariant to the codec used to encode the video. This is necessary due to the curatorial requirement for archives to format shift video over time to ensure future accessibility. Second, we describe how the TCHs (and the models used to derive them) are secured via a proof-of-authority blockchain distributed across multiple independent archives. We report on the efficacy of ARCHANGEL within the context of a trial deployment in which the national government archives of the United Kingdom, Estonia and Norway participated., Comment: Accepted to CVPR Blockchain Workshop 2019

Published
2019

35. Balancing Straight-Line Programs

Author

Ganardi, Moses, Jeż, Artur, and Lohrey, Markus

Subjects
Computer Science - Data Structures and Algorithms, 68P05, 68W32
Abstract

It is shown that a context-free grammar of size $m$ that produces a single string $w$ (such a grammar is also called a string straight-line program) can be transformed in linear time into a context-free grammar for $w$ of size $\mathcal{O}(m)$, whose unique derivation tree has depth $\mathcal{O}(\log |w|)$. This solves an open problem in the area of grammar-based compression. Similar results are shown for two formalism for grammar-based tree compression: top dags and forest straight-line programs. These balancing results are all deduced from a single meta theorem stating that the depth of an algebraic circuit over an algebra with a certain finite base property can be reduced to $\mathcal{O}(\log n)$ with the cost of a constant multiplicative size increase. Here, $n$ refers to the size of the unfolding (or unravelling) of the circuit., Comment: An extended abstract of this paper appears in the Proceedings of FOCS 2019

Published
2019

36. Better Bounds for Online Line Chasing

Author

Bienkowski, Marcin, Byrka, Jarosław, Chrobak, Marek, Coester, Christian, Jeż, Łukasz, and Koutsoupias, Elias

Subjects
Computer Science - Data Structures and Algorithms
Abstract

We study online competitive algorithms for the \emph{line chasing problem} in Euclidean spaces $\reals^d$, where the input consists of an initial point $P_0$ and a sequence of lines $X_1,X_2,...,X_m$, revealed one at a time. At each step $t$, when the line $X_t$ is revealed, the algorithm must determine a point $P_t\in X_t$. An online algorithm is called $c$-competitive if for any input sequence the path $P_0, P_1,...,P_m$ it computes has length at most $c$ times the optimum path. The line chasing problem is a variant of a more general convex body chasing problem, where the sets $X_t$ are arbitrary convex sets. To date, the best competitive ratio for the line chasing problem was $28.1$, even in the plane. We significantly improve this bound, by providing a~$3$-competitive algorithm for any dimension $d$. We also improve the lower bound on the competitive ratio, from $1.412$ to $1.5358$.

Published
2018

37. Erratum to: Searches for long-lived charged particles in pp collisions at s $$ \sqrt{\textrm{s}} $$ = 7 and 8 TeV

Author

The CMS collaboration, S. Chatrchyan, V. Khachatryan, A. M. Sirunyan, A. Tumasyan, W. Adam, T. Bergauer, M. Dragicevic, J. Erö, C. Fabjan, M. Friedl, R. Frühwirth, V. M. Ghete, N. Hörmann, J. Hrubec, M. Jeitler, W. Kiesenhofer, V. Knünz, M. Krammer, I. Krätschmer, D. Liko, I. Mikulec, D. Rabady, B. Rahbaran, C. Rohringer, H. Rohringer, R. Schöfbeck, J. Strauss, A. Taurok, W. Treberer-Treberspurg, W. Waltenberger, C.-E. Wulz, V. Mossolov, N. Shumeiko, J. Suarez Gonzalez, S. Alderweireldt, M. Bansal, S. Bansal, T. Cornelis, E. A. De Wolf, X. Janssen, A. Knutsson, S. Luyckx, L. Mucibello, S. Ochesanu, B. Roland, R. Rougny, H. Van Haevermaet, P. Van Mechelen, N. Van Remortel, A. Van Spilbeeck, F. Blekman, S. Blyweert, J. D’Hondt, A. Kalogeropoulos, J. Keaveney, M. Maes, A. Olbrechts, S. Tavernier, W. Van Doninck, P. Van Mulders, G. P. Van Onsem, I. Villella, B. Clerbaux, G. De Lentdecker, L. Favart, A. P. R. Gay, T. Hreus, A. Léonard, P. E. Marage, A. Mohammadi, L. Perniè, T. Reis, T. Seva, L. Thomas, C. Vander Velde, P. Vanlaer, J. Wang, V. Adler, K. Beernaert, L. Benucci, A. Cimmino, S. Costantini, S. Dildick, G. Garcia, B. Klein, J. Lellouch, A. Marinov, J. Mccartin, A. A. Ocampo Rios, D. Ryckbosch, M. Sigamani, N. Strobbe, F. Thyssen, M. Tytgat, S. Walsh, E. Yazgan, N. Zaganidis, S. Basegmez, C. Beluffi, G. Bruno, R. Castello, A. Caudron, L. Ceard, C. Delaere, T. du Pree, D. Favart, L. Forthomme, A. Giammanco, J. Hollar, P. Jez, V. Lemaitre, J. Liao, O. Militaru, C. Nuttens, D. Pagano, A. Pin, K. Piotrzkowski, A. Popov, M. Selvaggi, J. M. Vizan Garcia, N. Beliy, T. Caebergs, E. Daubie, G. H. Hammad, G. A. Alves, M. Correa Martins Junior, T. Martins, M. E. Pol, M. H. G. Souza, W. L. Aldá Júnior, W. Carvalho, J. Chinellato, A. Custódio, E. M. Da Costa, D. De Jesus Damiao, C. De Oliveira Martins, S. Fonseca De Souza, H. Malbouisson, M. Malek, D. Matos Figueiredo, L. Mundim, H. Nogima, W. L. Prado Da Silva, A. Santoro, A. Sznajder, E. J. Tonelli Manganote, A. Vilela Pereira, C. A. Bernardes, F. A. Dias, T. R. Fernandez Perez Tomei, E. M. Gregores, C. Lagana, F. Marinho, P. G. Mercadante, S. F. Novaes, Sandra S. Padula, V. Genchev, P. Iaydjiev, S. Piperov, M. Rodozov, G. Sultanov, M. Vutova, A. Dimitrov, R. Hadjiiska, V. Kozhuharov, L. Litov, B. Pavlov, P. Petkov, J. G. Bian, G. M. Chen, H. S. Chen, C. H. Jiang, D. Liang, S. Liang, X. Meng, J. Tao, X. Wang, Z. Wang, H. Xiao, M. Xu, C. Asawatangtrakuldee, Y. Ban, Y. Guo, W. Li, S. Liu, Y. Mao, S. J. Qian, H. Teng, D. Wang, L. Zhang, W. Zou, C. Avila, C. A. Carrillo Montoya, J. P. Gomez, B. Gomez Moreno, J. C. Sanabria, N. Godinovic, D. Lelas, R. Plestina, D. Polic, I. Puljak, Z. Antunovic, M. Kovac, V. Brigljevic, S. Duric, K. Kadija, J. Luetic, D. Mekterovic, S. Morovic, L. Tikvica, A. Attikis, G. Mavromanolakis, J. Mousa, C. Nicolaou, F. Ptochos, P. A. Razis, M. Finger, Y. Assran, A. Ellithi Kamel, M. A. Mahmoud, A. Mahrous, A. Radi, M. Kadastik, M. Müntel, M. Murumaa, M. Raidal, L. Rebane, A. Tiko, P. Eerola, G. Fedi, M. Voutilainen, J. Härkönen, V. Karimäki, R. Kinnunen, M. J. Kortelainen, T. Lampén, K. Lassila-Perini, S. Lehti, T. Lindén, P. Luukka, T. Mäenpää, T. Peltola, E. Tuominen, J. Tuominiemi, E. Tuovinen, L. Wendland, A. Korpela, T. Tuuva, M. Besancon, S. Choudhury, F. Couderc, M. Dejardin, D. Denegri, B. Fabbro, J. L. Faure, F. Ferri, S. Ganjour, A. Givernaud, P. Gras, G. Hamel de Monchenault, P. Jarry, E. Locci, J. Malcles, L. Millischer, A. Nayak, J. Rander, A. Rosowsky, M. Titov, S. Baffioni, F. Beaudette, L. Benhabib, L. Bianchini, M. Bluj, P. Busson, C. Charlot, N. Daci, T. Dahms, M. Dalchenko, L. Dobrzynski, A. Florent, R. Granier de Cassagnac, M. Haguenauer, P. Miné, C. Mironov, I. N. Naranjo, M. Nguyen, C. Ochando, P. Paganini, D. Sabes, R. Salerno, Y. Sirois, C. Veelken, A. Zabi, J.-L. Agram, J. Andrea, D. Bloch, D. Bodin, J.-M. Brom, E. C. Chabert, C. Collard, E. Conte, F. Drouhin, J.-C. Fontaine, D. Gelé, U. Goerlach, C. Goetzmann, P. Juillot, A.-C. Le Bihan, P. Van Hove, S. Gadrat, S. Beauceron, N. Beaupere, G. Boudoul, S. Brochet, J. Chasserat, R. Chierici, D. Contardo, P. Depasse, H. El Mamouni, J. Fay, S. Gascon, M. Gouzevitch, B. Ille, T. Kurca, M. Lethuillier, L. Mirabito, S. Perries, L. Sgandurra, V. Sordini, Y. Tschudi, M. Vander Donckt, P. Verdier, S. Viret, Z. Tsamalaidze, C. Autermann, S. Beranek, B. Calpas, M. Edelhoff, L. Feld, N. Heracleous, O. Hindrichs, K. Klein, A. Ostapchuk, A. Perieanu, F. Raupach, J. Sammet, S. Schael, D. Sprenger, H. Weber, B. Wittmer, V. Zhukov, M. Ata, J. Caudron, E. Dietz-Laursonn, D. Duchardt, M. Erdmann, R. Fischer, A. Güth, T. Hebbeker, C. Heidemann, K. Hoepfner, D. Klingebiel, P. Kreuzer, M. Merschmeyer, A. Meyer, M. Olschewski, K. Padeken, P. Papacz, H. Pieta, H. Reithler, S. A. Schmitz, L. Sonnenschein, J. Steggemann, D. Teyssier, S. Thüer, M. Weber, V. Cherepanov, Y. Erdogan, G. Flügge, H. Geenen, M. Geisler, W. Haj Ahmad, F. Hoehle, B. Kargoll, T. Kress, Y. Kuessel, J. Lingemann, A. Nowack, I. M. Nugent, L. Perchalla, O. Pooth, A. Stahl, M. Aldaya Martin, I. Asin, N. Bartosik, J. Behr, W. Behrenhoff, U. Behrens, M. Bergholz, A. Bethani, K. Borras, A. Burgmeier, A. Cakir, L. Calligaris, A. Campbell, F. Costanza, C. Diez Pardos, S. Dooling, T. Dorland, G. Eckerlin, D. Eckstein, G. Flucke, A. Geiser, I. Glushkov, P. Gunnellini, S. Habib, J. Hauk, G. Hellwig, H. Jung, M. Kasemann, P. Katsas, C. Kleinwort, H. Kluge, M. Krämer, D. Krücker, E. Kuznetsova, W. Lange, J. Leonard, K. Lipka, W. Lohmann, B. Lutz, R. Mankel, I. Marfin, I.-A. Melzer-Pellmann, A. B. Meyer, J. Mnich, A. Mussgiller, S. Naumann-Emme, O. Novgorodova, F. Nowak, J. Olzem, H. Perrey, A. Petrukhin, D. Pitzl, R. Placakyte, A. Raspereza, P. M. Ribeiro Cipriano, C. Riedl, E. Ron, M. Ö. Sahin, J. Salfeld-Nebgen, R. Schmidt, T. Schoerner-Sadenius, N. Sen, M. Stein, R. Walsh, C. Wissing, V. Blobel, H. Enderle, J. Erfle, U. Gebbert, M. Görner, M. Gosselink, J. Haller, K. Heine, R. S. Höing, G. Kaussen, H. Kirschenmann, R. Klanner, R. Kogler, J. Lange, I. Marchesini, T. Peiffer, N. Pietsch, D. Rathjens, C. Sander, H. Schettler, P. Schleper, E. Schlieckau, A. Schmidt, M. Schröder, T. Schum, M. Seidel, J. Sibille, V. Sola, H. Stadie, G. Steinbrück, J. Thomsen, D. Troendle, L. Vanelderen, C. Barth, C. Baus, J. Berger, C. Böser, T. Chwalek, W. De Boer, A. Descroix, A. Dierlamm, M. Feindt, M. Guthoff, C. Hackstein, F. Hartmann, T. Hauth, M. Heinrich, H. Held, K. H. Hoffmann, U. Husemann, I. Katkov, J. R. Komaragiri, A. Kornmayer, P. Lobelle Pardo, D. Martschei, S. Mueller, Th. Müller, M. Niegel, A. Nürnberg, O. Oberst, J. Ott, G. Quast, K. Rabbertz, F. Ratnikov, S. Röcker, F.-P. Schilling, G. Schott, H. J. Simonis, F. M. Stober, R. Ulrich, J. Wagner-Kuhr, S. Wayand, T. Weiler, M. Zeise, G. Anagnostou, G. Daskalakis, T. Geralis, S. Kesisoglou, A. Kyriakis, D. Loukas, A. Markou, C. Markou, E. Ntomari, L. Gouskos, T. J. Mertzimekis, A. Panagiotou, N. Saoulidou, E. 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Petrucciani, M. Pieri, M. Sani, S. Simon, E. Sudano, M. Tadel, Y. Tu, A. Vartak, S. Wasserbaech, F. Würthwein, A. Yagil, J. Yoo, D. Barge, R. Bellan, C. Campagnari, M. D’Alfonso, T. Danielson, K. Flowers, P. Geffert, C. George, F. Golf, J. Incandela, C. Justus, P. Kalavase, D. Kovalskyi, V. Krutelyov, S. Lowette, R. Magaña Villalba, N. Mccoll, V. Pavlunin, J. Ribnik, J. Richman, R. Rossin, D. Stuart, W. To, C. West, A. Apresyan, A. Bornheim, J. Bunn, Y. Chen, E. Di Marco, J. Duarte, D. Kcira, Y. Ma, A. Mott, H. B. Newman, C. Rogan, M. Spiropulu, V. Timciuc, J. Veverka, R. Wilkinson, S. Xie, Y. Yang, R. Y. Zhu, V. Azzolini, A. Calamba, R. Carroll, T. Ferguson, Y. Iiyama, D. W. Jang, Y. F. Liu, M. Paulini, J. Russ, H. Vogel, I. Vorobiev, J. P. Cumalat, B. R. Drell, W. T. Ford, A. Gaz, E. Luiggi Lopez, U. Nauenberg, J. G. Smith, K. Stenson, K. A. Ulmer, S. R. Wagner, J. Alexander, A. Chatterjee, N. Eggert, L. K. Gibbons, W. Hopkins, A. Khukhunaishvili, B. Kreis, N. Mirman, G. Nicolas Kaufman, J. R. Patterson, A. Ryd, E. Salvati, W. Sun, W. D. Teo, J. Thom, J. Thompson, J. Tucker, Y. Weng, L. Winstrom, P. Wittich, D. Winn, S. Abdullin, M. Albrow, J. Anderson, G. Apollinari, L. A. T. Bauerdick, A. Beretvas, J. Berryhill, P. C. Bhat, K. Burkett, J. N. Butler, V. Chetluru, H. W. K. Cheung, F. Chlebana, S. Cihangir, V. D. Elvira, I. Fisk, J. Freeman, Y. Gao, E. Gottschalk, L. Gray, D. Green, O. Gutsche, D. Hare, R. M. Harris, J. Hirschauer, B. Hooberman, S. Jindariani, M. Johnson, U. Joshi, B. Klima, S. Kunori, S. Kwan, C. Leonidopoulos, J. Linacre, D. Lincoln, R. Lipton, J. Lykken, K. Maeshima, J. M. Marraffino, V. I. Martinez Outschoorn, S. Maruyama, D. Mason, P. McBride, K. Mishra, S. Mrenna, Y. Musienko, C. Newman-Holmes, V. O’Dell, O. Prokofyev, N. Ratnikova, E. Sexton-Kennedy, S. Sharma, W. J. Spalding, L. Spiegel, L. Taylor, S. Tkaczyk, N. V. Tran, L. Uplegger, E. W. Vaandering, R. Vidal, J. Whitmore, W. Wu, F. Yang, J. C. Yun, D. Acosta, P. Avery, D. Bourilkov, M. Chen, T. Cheng, S. Das, M. De Gruttola, G. P. Di Giovanni, D. Dobur, A. Drozdetskiy, R. D. Field, M. Fisher, Y. Fu, I. K. Furic, J. Hugon, B. Kim, J. Konigsberg, A. Korytov, A. Kropivnitskaya, T. Kypreos, J. F. Low, K. Matchev, P. Milenovic, G. Mitselmakher, L. Muniz, R. Remington, A. Rinkevicius, N. Skhirtladze, M. Snowball, J. Yelton, M. Zakaria, V. Gaultney, S. Hewamanage, L. M. Lebolo, S. Linn, P. Markowitz, G. Martinez, J. L. Rodriguez, T. Adams, A. Askew, J. Bochenek, J. Chen, B. Diamond, S. V. Gleyzer, J. Haas, S. Hagopian, V. Hagopian, K. F. Johnson, H. Prosper, V. Veeraraghavan, M. Weinberg, M. M. Baarmand, B. Dorney, M. Hohlmann, H. Kalakhety, F. Yumiceva, M. R. Adams, L. Apanasevich, V. E. Bazterra, R. R. Betts, I. Bucinskaite, J. Callner, R. Cavanaugh, O. Evdokimov, L. Gauthier, C. E. Gerber, D. J. Hofman, S. Khalatyan, P. Kurt, F. Lacroix, D. H. Moon, C. O’Brien, C. Silkworth, D. Strom, P. Turner, N. Varelas, U. Akgun, E. A. Albayrak, B. Bilki, W. Clarida, K. Dilsiz, F. Duru, S. Griffiths, J.-P. Merlo, H. Mermerkaya, A. Mestvirishvili, A. Moeller, J. Nachtman, C. R. Newsom, H. Ogul, Y. Onel, F. Ozok, S. Sen, P. Tan, E. Tiras, J. Wetzel, T. Yetkin, K. Yi, B. A. Barnett, B. Blumenfeld, S. Bolognesi, D. Fehling, G. Giurgiu, A. V. Gritsan, Z. J. Guo, G. Hu, P. Maksimovic, M. Swartz, A. Whitbeck, P. Baringer, A. Bean, G. Benelli, R. P. Kenny, M. Murray, D. Noonan, S. Sanders, R. Stringer, J. S. Wood, A. F. Barfuss, I. Chakaberia, A. Ivanov, S. Khalil, M. Makouski, Y. Maravin, S. Shrestha, I. Svintradze, J. Gronberg, D. Lange, F. Rebassoo, D. Wright, A. Baden, B. Calvert, S. C. Eno, J. A. Gomez, N. J. Hadley, R. G. Kellogg, T. Kolberg, Y. Lu, M. Marionneau, A. C. Mignerey, K. Pedro, A. Peterman, A. Skuja, J. Temple, M. B. Tonjes, S. C. Tonwar, A. Apyan, G. Bauer, W. Busza, E. Butz, I. A. Cali, M. Chan, V. Dutta, G. Gomez Ceballos, M. Goncharov, Y. Kim, M. Klute, Y. S. Lai, A. Levin, P. D. Luckey, T. Ma, S. Nahn, C. Paus, D. Ralph, C. Roland, G. Roland, G. S. F. Stephans, F. Stöckli, K. Sumorok, K. Sung, D. Velicanu, R. Wolf, B. Wyslouch, M. Yang, Y. Yilmaz, A. S. Yoon, M. Zanetti, V. Zhukova, B. Dahmes, A. De Benedetti, G. Franzoni, A. Gude, J. Haupt, S. C. Kao, K. Klapoetke, Y. Kubota, J. Mans, N. Pastika, R. Rusack, M. Sasseville, A. Singovsky, N. Tambe, J. Turkewitz, L. M. Cremaldi, R. Kroeger, L. Perera, R. Rahmat, D. A. Sanders, D. Summers, E. Avdeeva, K. Bloom, S. Bose, D. R. Claes, A. Dominguez, M. Eads, R. Gonzalez Suarez, J. Keller, I. Kravchenko, J. Lazo-Flores, S. Malik, F. Meier, G. R. Snow, J. Dolen, A. Godshalk, I. Iashvili, S. Jain, A. Kharchilava, A. Kumar, S. Rappoccio, Z. Wan, G. Alverson, E. Barberis, D. Baumgartel, M. Chasco, J. Haley, A. Massironi, D. Nash, T. Orimoto, D. Trocino, D. Wood, J. Zhang, A. Anastassov, K. A. Hahn, A. Kubik, L. Lusito, N. Mucia, N. Odell, B. Pollack, A. Pozdnyakov, M. Schmitt, S. Stoynev, M. Velasco, S. Won, D. Berry, A. Brinkerhoff, K. M. Chan, M. Hildreth, C. Jessop, D. J. Karmgard, J. Kolb, K. Lannon, W. Luo, S. Lynch, N. Marinelli, D. M. Morse, T. Pearson, M. Planer, R. Ruchti, J. Slaunwhite, N. Valls, M. Wayne, M. Wolf, L. Antonelli, B. Bylsma, L. S. Durkin, C. Hill, R. Hughes, K. Kotov, T. Y. Ling, D. Puigh, M. Rodenburg, G. Smith, C. Vuosalo, G. Williams, B. L. Winer, H. Wolfe, E. Berry, P. Elmer, V. Halyo, P. Hebda, J. Hegeman, A. Hunt, P. Jindal, S. A. Koay, D. Lopes Pegna, P. Lujan, D. Marlow, T. Medvedeva, M. Mooney, J. Olsen, P. Piroué, X. Quan, A. Raval, H. Saka, D. Stickland, C. Tully, J. S. Werner, S. C. Zenz, A. Zuranski, E. Brownson, A. Lopez, H. Mendez, J. E. Ramirez Vargas, E. Alagoz, D. Benedetti, G. Bolla, D. Bortoletto, M. De Mattia, A. Everett, Z. Hu, M. Jones, K. Jung, O. Koybasi, M. Kress, N. Leonardo, V. Maroussov, P. Merkel, D. H. Miller, N. Neumeister, I. Shipsey, D. Silvers, A. Svyatkovskiy, M. Vidal Marono, F. Wang, L. Xu, H. D. Yoo, J. Zablocki, Y. Zheng, S. Guragain, N. Parashar, A. Adair, B. Akgun, K. M. Ecklund, F. J. M. Geurts, B. P. Padley, R. Redjimi, J. Roberts, J. Zabel, B. Betchart, A. Bodek, R. Covarelli, P. de Barbaro, R. Demina, Y. Eshaq, T. Ferbel, A. Garcia-Bellido, P. Goldenzweig, J. Han, A. Harel, D. C. Miner, G. Petrillo, D. Vishnevskiy, M. Zielinski, A. Bhatti, R. Ciesielski, L. Demortier, K. Goulianos, G. Lungu, C. Mesropian, S. Arora, A. Barker, J. P. Chou, C. Contreras-Campana, E. Contreras-Campana, D. Duggan, D. Ferencek, Y. Gershtein, R. Gray, E. Halkiadakis, D. Hidas, A. Lath, S. Panwalkar, M. Park, R. Patel, V. Rekovic, J. Robles, K. Rose, S. Salur, S. Schnetzer, C. Seitz, S. Somalwar, R. Stone, S. Thomas, M. Walker, G. Cerizza, M. Hollingsworth, S. Spanier, Z. C. Yang, A. York, R. Eusebi, W. Flanagan, J. Gilmore, T. Kamon, V. Khotilovich, R. Montalvo, I. Osipenkov, Y. Pakhotin, A. Perloff, J. Roe, A. Safonov, T. Sakuma, I. Suarez, A. Tatarinov, D. Toback, N. Akchurin, J. Damgov, C. Dragoiu, P. R. Dudero, C. Jeong, K. Kovitanggoon, S. W. Lee, T. Libeiro, I. Volobouev, E. Appelt, A. G. Delannoy, S. Greene, A. Gurrola, W. Johns, C. Maguire, A. Melo, M. Sharma, P. Sheldon, B. Snook, S. Tuo, J. Velkovska, M. W. Arenton, S. Boutle, B. Cox, B. Francis, J. Goodell, R. Hirosky, A. Ledovskoy, C. Lin, C. Neu, J. Wood, S. Gollapinni, R. Harr, P. E. Karchin, C. Kottachchi Kankanamge Don, P. Lamichhane, A. Sakharov, M. Anderson, D. A. Belknap, L. Borrello, D. Carlsmith, M. Cepeda, S. Dasu, E. Friis, K. S. Grogg, M. Grothe, R. Hall-Wilton, M. Herndon, A. Hervé, K. Kaadze, P. Klabbers, J. Klukas, A. Lanaro, C. Lazaridis, R. Loveless, A. Mohapatra, M. U. Mozer, I. Ojalvo, G. A. Pierro, I. Ross, A. Savin, W. H. Smith, and J. Swanson

Subjects
Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Published
2022
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39. Efficacy and safety of novel temperature-controlled radiofrequency ablation system during pulmonary vein isolation in patients with paroxysmal atrial fibrillation: TRAC-AF study

Author

Starek, Zdenek, Lehar, Frantisek, Jez, Jiri, Pesl, Martin, Neuzil, Petr, Sediva, Lucie, Petru, Jan, Dujka, Libor, Funasako, Moritoshi, Kautzner, Josef, Peichl, Petr, Aldhoon, Bashar, Albenque, Jean-Paul, Combes, Stephane, Boveda, Serge, Dukkipati, Srinivas R., and Reddy, Vivek Y.

Published
2022
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40. Changemakers share their why, collaborate as critical friends, and highlight leadership skills

Author

Rebekka J. Jez, Christopher Dennis, Michelle Coleman, Corné Conradie, Abongile Matyaleni, Diana Ramirez, Chanté Rezandt, Kayla Wilkins, and Cassie Herndon

Subjects
changemaker, education, leadership, sustainable change, collaboration, professional growth., Education
Abstract

Background: Changemakers are justice-minded individuals working toward implementing positive and sustainable change within their communities. Aim: The project created a space for Changemakers to connect, engage in critical dialogue, and leave with shared knowledge and skills to dismantle oppressive, deficit-based educational systems in the aftermath of COVID-19. Setting: From October 2021 to June 2022, 18 American and South African Changemakers from primary, secondary, and higher education institutions exchanged messages about their regional context and attended the Changemaker Symposium in South Africa. Method: This qualitative study examined how the Changemaker framework guided educators to frame [ubuntu], convene [masikhule], and ignite change [skep verandering]. They framed the strengths and challenges in their regions. Teams convened to address challenges using assets-based ideas that oppose deficit thinking and allow them to become leaders who ignite agency to ignite systemic change. The individual and group narratives were collected via open-ended questions, group discussions, and written artifacts. Results: They developed statements on: exploring reasons for teaching, collaborating with critical friends, and developing critical leadership skills. A phenomenological analysis of the narratives examined commonalities within each Changemakers’ lived experience. Conclusion: Findings indicate that this process allowed participants to collaborate and reimagine ways to inspire others while renewing their commitment to the responsibilities they face as educators affected by the pandemic. Contribution: From this project, educators have a framework to participate in global discourse that illuminates commonalities through critical friendships, decreases burnout, humanizes their experiences and increases the implementation of culturally responsive and sustaining inclusive practices.

Published
2023
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41. Slaying Hydrae: Improved Bounds for Generalized k-Server in Uniform Metrics

Author

Bienkowski, Marcin, Jeż, Łukasz, and Schmidt, Paweł

Subjects
Computer Science - Data Structures and Algorithms
Abstract

The generalized $k$-server problem is an extension of the weighted $k$-server problem, which in turn extends the classic $k$-server problem. In the generalized $k$-server problem, each of $k$ servers $s_1, \dots, s_k$ remains in its own metric space $M_i$. A request is a tuple $(r_1,\dots,r_k)$, where $r_i \in M_i$, and to service it, an algorithm needs to move at least one server $s_i$ to the point $r_i$. The objective is to minimize the total distance traveled by all servers. In this paper, we focus on the generalized $k$-server problem for the case where all $M_i$ are uniform metrics. We show an $O(k^2 \cdot \log k)$-competitive randomized algorithm improving over a recent result by Bansal et al. [SODA 2018], who gave an $O(k^3 \cdot \log k)$-competitive algorithm. To this end, we define an abstract online problem, called Hydra game, and we show that a randomized solution of low cost to this game implies a randomized algorithm to the generalized $k$-server problem with low competitive ratio. We also show that no randomized algorithm can achieve competitive ratio lower than $\Omega(k)$, thus improving the lower bound of $\Omega(k / \log^2 k)$ by Bansal et al.

Published
2018

42. A $\phi$-Competitive Algorithm for Scheduling Packets with Deadlines

Author

Veselý, Pavel, Chrobak, Marek, Jeż, Łukasz, and Sgall, Jiří

Subjects
Computer Science - Data Structures and Algorithms, 68W27, F.2.2
Abstract

In the online packet scheduling problem with deadlines (PacketSchD, for short), the goal is to schedule transmissions of packets that arrive over time in a network switch and need to be sent across a link. Each packet has a deadline, representing its urgency, and a non-negative weight, that represents its priority. Only one packet can be transmitted in any time slot, so if the system is overloaded, some packets will inevitably miss their deadlines and be dropped. In this scenario, the natural objective is to compute a transmission schedule that maximizes the total weight of packets that are successfully transmitted. The problem is inherently online, with the scheduling decisions made without the knowledge of future packet arrivals. The central problem concerning PacketSchD, that has been a subject of intensive study since 2001, is to determine the optimal competitive ratio of online algorithms, namely the worst-case ratio between the optimum total weight of a schedule (computed by an offline algorithm) and the weight of a schedule computed by a (deterministic) online algorithm. We solve this open problem by presenting a $\phi$-competitive online algorithm for PacketSchD (where $\phi\approx 1.618$ is the golden ratio), matching the previously established lower bound., Comment: Final version of the article, as it existed immediately prior to editing and production by SIAM and being published in SIAM Journal on Computing, published with SIAM's permission

Published
2018
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43. Scheduling under dynamic speed-scaling for minimizing weighted completion time and energy consumption

Author

Dürr, Christoph, Jeż, Łukasz, and Vásquez, Oscar C.

Subjects
Computer Science - Data Structures and Algorithms
Abstract

Since a few years there is an increasing interest in minimizing the energy consumption of computing systems. However in a shared computing system, users want to optimize their experienced quality of service, at the price of a high energy consumption. In this work, we address the problem of optimizing and designing mechanisms for a linear combination of weighted completion time and energy consumption on a single machine with dynamic speed-scaling. We show that minimizing linear combination reduces to a unit speed scheduling problem under a polynomial penalty function. In the mechanism design setting, we define a cost share mechanism and studied its properties, showing that it is truthful and the overcharging of total cost share is bounded by a constant.

Published
2018
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44. ARCHANGEL: Trusted Archives of Digital Public Documents

Author

Collomosse, John, Bui, Tu, Brown, Alan, Sheridan, John, Green, Alex, Bell, Mark, Fawcett, Jamie, Higgins, Jez, and Thereaux, Olivier

Subjects
Computer Science - Digital Libraries
Abstract

We present ARCHANGEL; a de-centralised platform for ensuring the long-term integrity of digital documents stored within public archives. Document integrity is fundamental to public trust in archives. Yet currently that trust is built upon institutional reputation --- trust at face value in a centralised authority, like a national government archive or University. ARCHANGEL proposes a shift to a technological underscoring of that trust, using distributed ledger technology (DLT) to cryptographically guarantee the provenance, immutability and so the integrity of archived documents. We describe the ARCHANGEL architecture, and report on a prototype of that architecture build over the Ethereum infrastructure. We report early evaluation and feedback of ARCHANGEL from stakeholders in the research data archives space., Comment: Submitted to ACM Document Engineering 2018

Published
2018

45. Improving Transfer in California: Trial and Error in Statewide Reform and Local Implementation

Author

Venezia, Andrea and Jez, Su Jin Gatlin

Subjects
higher education, transfer, student success, community college, state comprehensive university, education reform, state education policy
Abstract

California’s community colleges play a wide range of crucial roles in providing educational opportunities for state residents, including providing transfer for students to four-year universities. Transfer students represent about half of each entering class in the California State University System (CSU) and almost one-third in the University of California. In 2010, California enacted legislation to streamline transfer from community college to the state’s four-year universities by creating a new transfer degree. It was implemented in 2012. This study examined how students experience policies and practices related to transfer from community college to California State University in the context of the new degree. Key findings reveal that, although there are improvements, capacity within the CSU and other factors have kept transfer complex and confusing for most transfer students. Major implications are that the state and systems need to continue to simplify the transfer process and strengthen supports for students.

Published
2019

46. Application of blood brain barrier models in pre-clinical assessment of glioblastoma-targeting CAR-T based immunotherapies

Author

Jez Huang, Ying Betty Li, Claudie Charlebois, Tina Nguyen, Ziying Liu, Darin Bloemberg, Ahmed Zafer, Ewa Baumann, Caroline Sodja, Sonia Leclerc, Gwen Fewell, Qing Liu, Balabhaskar Prabhakarpandian, Scott McComb, Danica B. Stanimirovic, and Anna Jezierski

Subjects
Neurology. Diseases of the nervous system, RC346-429
Abstract

Abstract Human blood brain barrier (BBB) models derived from induced pluripotent stem cells (iPSCs) have become an important tool for the discovery and preclinical evaluation of central nervous system (CNS) targeting cell and gene-based therapies. Chimeric antigen receptor (CAR)-T cell therapy is a revolutionary form of gene-modified cell-based immunotherapy with potential for targeting solid tumors, such as glioblastomas. Crossing the BBB is an important step in the systemic application of CAR-T therapy for the treatment of glioblastomas and other CNS malignancies. In addition, even CAR-T therapies targeting non-CNS antigens, such as the well-known CD19-CAR-T therapies, are known to trigger CNS side-effects including brain swelling due to BBB disruption. In this study, we used iPSC-derived brain endothelial-like cell (iBEC) transwell co-culture model to assess BBB extravasation of CAR-T based immunotherapies targeting U87MG human glioblastoma (GBM) cells overexpressing the tumor-specific mutated protein EGFRvIII (U87vIII). Two types of anti-EGFRvIII targeting CAR-T cells, with varying tonic signaling profiles (CAR-F263 and CAR-F269), and control Mock T cells were applied on the luminal side of BBB model in vitro. CAR-F263 and CAR-F269 T cells triggered a decrease in transendothelial electrical resistance (TEER) and an increase in BBB permeability. CAR-T cell extravasation and U87vIII cytotoxicity were assessed from the abluminal compartment using flow cytometry and Incucyte real-time viability imaging, respectively. A significant decrease in U87vIII cell viability was observed over 48 h, with the most robust cytotoxicity response observed for the constitutively activated CAR-F263. CAR-F269 T cells showed a similar cytotoxic profile but were approximately four fold less efficient at killing the U87vIII cells compared to CAR-F263, despite similar transmigration rates. Visualization of CAR-T cell extravasation across the BBB was further confirmed using BBTB-on-CHIP models. The described BBB assay was able to discriminate the cytotoxic efficacies of different EGFRvIII-CARs and provide a measure of potential alterations to BBB integrity. Collectively, we illustrate how BBB models in vitro can be a valuable tool in deciphering the mechanisms of CAR-T–induced BBB disruption, accompanying toxicity and effector function on post-barrier target cells.

Published
2022
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47. Preventing male suicide through a psychosocial intervention that provides psychological support and tackles financial difficulties: a mixed method evaluation

Author

Joni Jackson, Michelle Farr, Kate Birnie, Philippa Davies, Loubaba Mamluk, Marina O’Brien, Jez Spencer, Rebecca Morgan, Christian Costello, John Smith, Jonathan Banks, and Maria Theresa Redaniel

Subjects
Evaluation, Intervention, Mixed-methods, Depression, Suicide, Financial advice, Psychiatry, RC435-571
Abstract

Abstract Background To help resolve high suicide rates in Bristol, North Somerset and South Gloucestershire, the charity Second Step was commissioned to roll-out the Hope service offering a psychosocial intervention for men, supporting them through acute distress and addressing financial difficulties. This study evaluated the impact of the Hope service on men at risk of suicide experiencing financial and other difficulties. Methods Mixed methods study using: (i) a prospective cohort study design to compare depression, suicidal ideation and financial self-efficacy scores of men aged 30–64, referred to the service between October 2018 and July 2020, at baseline and 6 months follow-up and between low and moderate to high-intensity service users; and (ii) a qualitative interview study to evaluate the acceptability and impact of the Hope service to Hope service users. Results There was a 49% reduction in depression score (mean reduction − 10.0, 95% CI − 11.7 to − 8.3) and in the proportion of service users with suicidal ideation (percent reduction − 52.5, 95% CI − 64.1% to − 40.9%) at 6 months follow-up compared to baseline. Financial self-efficacy scores increased by 26% (mean increase 2.9, 95% CI 1.8 to 3.9). Qualitative accounts illustrated how ‘Hope saved my life’ for several men interviewed; most respondents described being able to move forward and tackle challenges with more confidence following the Hope intervention. Professional advice to tackle financial and other difficulties such as housing helped to relieve anxiety and stress and enable practical issues to be resolved. Conclusions The Hope service offered practical and emotional support to men who have experienced suicidal feelings, redundancy, homelessness and poverty and occupies an important space between mental health and social care provision. Hope demonstrates the value of an intervention which cuts across traditional boundaries between psychiatric care and social advice agencies to provide, what is, in effect, an integrated care service.

Published
2022
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48. Endogenous Reverse Transcriptase Inhibition Attenuates TLR5-Mediated Inflammation

Author

Nicholas Dopkins, Bhavya Singh, Stephanie Michael, Morgan M. O’Mara, Jez L. Marston, Tongyi Fei, Matthew L. Bendall, and Douglas F. Nixon

Subjects
human endogenous retrovirus (HERV), long interspersed nuclear element (LINE), toll-like receptors (TLRs), innate immunity, flagella, Microbiology, QR1-502
Abstract

ABSTRACT Transposable elements (TEs) are mobile genomic sequences that encompass roughly 50% of the human genome. Class 1 TEs, or “retrotransposons,” mobilize through the production of an RNA intermediate that is then reverse transcribed to form complementary DNA (cDNA) molecules capable of genomic reinsertion. While TEs are traditionally silenced to maintain genomic integrity, the recognition of immunostimulatory cues, such as those provided by microorganisms, drastically alters host transcription to induce the differential expression of TEs. Emerging evidence demonstrates that the inducible production of TE cDNA is not an inert phenomenon but instead has been coopted by host immunity to facilitate cross talk between host and constituents of the microbiota by agonizing intrinsic antiviral receptors. Here, we demonstrate that immunostimulation of toll-like receptor 4 (TLR4) with lipopolysaccharide (LPS) and TLR5 with bacterial flagella (FLA) alters the expression of retrotransposons, such as human endogenous retroviruses (HERVs) and long interspersed nuclear elements (LINEs). Next, we demonstrate that reverse transcriptase inhibitor (RTi) delivery ameliorates the acute production of the proinflammatory cytokine “tumor necrosis factor alpha” (TNF-α) in response to FLA in a monocytic cell line (THP-1). Collectively, our findings demonstrate that TLR5-mediated cross talk between the host and microbiota is partially dependent on the reverse transcription (RT) of retrotransposons. IMPORTANCE The microbiota is a potent reservoir of immunostimulatory and immunosuppressive motifs that fundamentally shape host immunity. Despite broad associations between microbial composition and host immunity, the mechanisms underlying host microbiota-induced immunoregulation remain poorly defined. Here, we demonstrate a novel mechanism by which motifs overabundant during dysbiotic conditions influence host immunity through the upregulation of endogenous RT to produce motifs that agonize antiviral receptors.

Published
2023
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