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630 results on '"Jackson, Adam"'

1. A fast approximate method for variable-width broadening of spectra

Author

Farmer, Jessica and Jackson, Adam J.

Subjects
Condensed Matter - Materials Science, Physics - Computational Physics
Abstract

Spectral data is routinely broadened in order to improve appearance, approximate a higher sampling level or model experimental measurement effects. While there has been extensive work in the signal processing field to develop efficient methods for the application of fixed-width broadening functions, these are not suitable for all scientific applications -- for example, the instrumental resolution of inelastic neutron scattering measurements varies along the energy-transfer axis. Na\"ive application of a kernel to every point has $O(N \times M)$ complexity and scales poorly for a high-resolution spectrum over many data points. Here we present an approximate method with complexity $O(N + W\times M \log M)$, where $W$ scales with the range of required broadening widths; in practice the number and cost of mathematical operations is drastically reduced to $N$ polynomial evaluations and a modest number of discrete Fourier transforms. Applications are demonstrated for Gaussian interpolation of density-of-states data and to instrumental resolution functions. We anticipate that these performance improvements will assist application of resolution functions inside fitting procedures and interactive tools.

Published
2023

2. Lunapark deficiency leads to an autosomal recessive neurodevelopmental phenotype with a degenerative course, epilepsy and distinct brain anomalies

Author

Accogli, Andrea, Zaki, Maha S, Al-Owain, Mohammed, Otaif, Mansour Y, Jackson, Adam, Argilli, Emanuela, Chandler, Kate E, De Goede, Christian GEL, Cora, Tülün, Alvi, Javeria Raza, Eslahi, Atieh, Asl Mohajeri, Mahsa Sadat, Ashtiani, Setareh, Au, PY Billie, Scocchia, Alicia, Alakurtti, Kirsi, Pagnamenta, Alistair T, Toosi, Mehran Beiraghi, Ghayoor Karimiani, Ehsan, Mojarrad, Majid, Arab, Fatemeh, Duymuş, Fahrettin, Scantlebury, Morris H, Yeşil, Gözde, Rosenfeld, Jill Anne, Türkyılmaz, Ayberk, Sağer, Safiye Güneş, Sultan, Tipu, Ashrafzadeh, Farah, Zahra, Tatheer, Rahman, Fatima, Maqbool, Shazia, Abdel-Hamid, Mohamed S, Issa, Mahmoud, Efthymiou, Stephanie, Bauer, Peter, Zifarelli, Giovanni, Salpietro, Vincenzo, Al-Hassnan, Zuhair, Banka, Siddharth, Sherr, Elliot H, Gleeson, Joseph G, Striano, Pasquale, Houlden, Henry, Severino, Mariasavina, and Maroofian, Reza

Subjects
Pediatric, Neurosciences, Genetics, Neurodegenerative, Clinical Research, Congenital Structural Anomalies, Brain Disorders, Rare Diseases, Human Genome, Epilepsy, 2.1 Biological and endogenous factors, Aetiology, Mental health, Neurological, Clinical sciences, Biological psychology
Abstract

Abstract: LNPK encodes a conserved membrane protein that stabilizes the junctions of the tubular endoplasmic reticulum network playing crucial roles in diverse biological functions. Recently, homozygous variants in LNPK were shown to cause a neurodevelopmental disorder (OMIM#618090) in four patients displaying developmental delay, epilepsy, and non-specific brain malformations including corpus callosum hypoplasia and variable impairment of cerebellum. We sought to delineate the molecular and phenotypic spectrum of LNPK-related disorder. Exome or genome sequencing was carried out in eleven families. Thorough clinical and neuroradiological evaluation was performed for all the affected individuals, including review of previously reported patients. We identified twelve distinct homozygous loss-of-function variants in sixteen individuals presenting with moderate to profound developmental delay, cognitive impairment, regression, refractory epilepsy and a recognizable neuroimaging pattern consisting of corpus callosum hypoplasia and signal alterations of the forceps minor (“ear-of-the-lynx” sign), variably associated with substantia nigra signal alterations, mild brain atrophy, short midbrain, and cerebellar hypoplasia/atrophy. In summary, we define the core phenotype of LNPK-related disorder and expand the list of neurological disorders presenting with the “ear of the lynx” sign suggesting a possible common underlying mechanism related to endoplasmic reticulum-phagy dysfunction.

Published
2023

3. Null and missense mutations of ERI1 cause a recessive phenotypic dichotomy in humans.

Author

Guo, Long, Salian, Smrithi, Xue, Jing-Yi, Rath, Nicola, Rousseau, Justine, Kim, Hyunyun, Ehresmann, Sophie, Moosa, Shahida, Nakagawa, Norio, Kuroda, Hiroshi, Clayton-Smith, Jill, Wang, Juan, Wang, Zheng, Banka, Siddharth, Jackson, Adam, Zhang, Yan-Min, Wei, Zhen-Jie, Hüning, Irina, Brunet, Theresa, Ohashi, Hirofumi, Thomas, Molly, Bupp, Caleb, Miyake, Noriko, Matsumoto, Naomichi, Mendoza-Londono, Roberto, Costain, Gregory, Hahn, Gabriele, Di Donato, Nataliya, Yigit, Gökhan, Yamada, Takahiro, Nishimura, Gen, Ansel, Karl, Wollnik, Bernd, Hrabě de Angelis, Martin, Mégarbané, André, Rosenfeld, Jill, Heissmeyer, Vigo, Ikegawa, Shiro, and Campeau, Philippe

Subjects
ERI1, exoribonuclease, ribosomopathy, short stature, skeletal dysplasia, spondyloepimetaphyseal dysplasia, Humans, Exoribonucleases, Histones, Mutation, Missense, RNA, Ribosomal, 5.8S, RNA, RNA, Messenger
Abstract

ERI1 is a 3-to-5 exoribonuclease involved in RNA metabolic pathways including 5.8S rRNA processing and turnover of histone mRNAs. Its biological and medical significance remain unclear. Here, we uncover a phenotypic dichotomy associated with bi-allelic ERI1 variants by reporting eight affected individuals from seven unrelated families. A severe spondyloepimetaphyseal dysplasia (SEMD) was identified in five affected individuals with missense variants but not in those with bi-allelic null variants, who showed mild intellectual disability and digital anomalies. The ERI1 missense variants cause a loss of the exoribonuclease activity, leading to defective trimming of the 5.8S rRNA 3 end and a decreased degradation of replication-dependent histone mRNAs. Affected-individual-derived induced pluripotent stem cells (iPSCs) showed impaired in vitro chondrogenesis with downregulation of genes regulating skeletal patterning. Our study establishes an entity previously unreported in OMIM and provides a model showing a more severe effect of missense alleles than null alleles within recessive genotypes, suggesting a key role of ERI1-mediated RNA metabolism in human skeletal patterning and chondrogenesis.

Published
2023

4. Euphonic: inelastic neutron scattering simulations from force constants and visualisation tools for phonon properties

Author

Fair, Rebecca, Jackson, Adam, Voneshen, David, Jochym, Dominik, Le, Duc, Refson, Keith, and Perring, Toby

Subjects
Condensed Matter - Materials Science, Physics - Computational Physics
Abstract

Interpretation of vibrational inelastic neutron scattering spectra of complex systems is frequently reliant on accompanying simulations from theoretical models. Ab-initio codes can routinely generate force constants, but additional steps are required for direct comparison to experimental spectra. On modern spectrometers this is a computationally expensive task due to the large data volumes collected. In addition, workflows are frequently cumbersome as the simulation software and experimental data analysis software often do not easily interface to each other. Here a new package, Euphonic, is presented. Euphonic is a robust, easy to use and computationally efficient tool designed to be integrated into experimental software and able to interface directly with the force constant matrix output of ab-initio codes.

Published
2022

5. Gain and loss of function variants in EZH1 disrupt neurogenesis and cause dominant and recessive neurodevelopmental disorders

Author

Gracia-Diaz, Carolina, Zhou, Yijing, Yang, Qian, Maroofian, Reza, Espana-Bonilla, Paula, Lee, Chul-Hwan, Zhang, Shuo, Padilla, Natàlia, Fueyo, Raquel, Waxman, Elisa A., Lei, Sunyimeng, Otrimski, Garrett, Li, Dong, Sheppard, Sarah E., Mark, Paul, Harr, Margaret H., Hakonarson, Hakon, Rodan, Lance, Jackson, Adam, Vasudevan, Pradeep, Powel, Corrina, Mohammed, Shehla, Maddirevula, Sateesh, Alzaidan, Hamad, Faqeih, Eissa A., Efthymiou, Stephanie, Turchetti, Valentina, Rahman, Fatima, Maqbool, Shazia, Salpietro, Vincenzo, Ibrahim, Shahnaz H., di Rosa, Gabriella, Houlden, Henry, Alharbi, Maha Nasser, Al-Sannaa, Nouriya Abbas, Bauer, Peter, Zifarelli, Giovanni, Estaras, Conchi, Hurst, Anna C. E., Thompson, Michelle L., Chassevent, Anna, Smith-Hicks, Constance L., de la Cruz, Xavier, Holtz, Alexander M., Elloumi, Houda Zghal, Hajianpour, M J, Rieubland, Claudine, Braun, Dominique, Banka, Siddharth, French, Deborah L., Heller, Elizabeth A., Saade, Murielle, Song, Hongjun, Ming, Guo-li, Alkuraya, Fowzan S., Agrawal, Pankaj B., Reinberg, Danny, Bhoj, Elizabeth J., Martínez-Balbás, Marian A., and Akizu, Naiara

Published
2023
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6. The impact of inversions across 33,924 families with rare disease from a national genome sequencing project

Author

Pagnamenta, Alistair T., Yu, Jing, Walker, Susan, Noble, Alexandra J., Lord, Jenny, Dutta, Prasun, Hashim, Mona, Camps, Carme, Green, Hannah, Devaiah, Smrithi, Nashef, Lina, Parr, Jason, Fratter, Carl, Ibnouf Hussein, Rana, Lindsay, Sarah J., Lalloo, Fiona, Banos-Pinero, Benito, Evans, David, Mallin, Lucy, Waite, Adrian, Evans, Julie, Newman, Andrew, Allen, Zoe, Perez-Becerril, Cristina, Ryan, Gavin, Hart, Rachel, Taylor, John, Bedenham, Tina, Clement, Emma, Blair, Ed, Hay, Eleanor, Forzano, Francesca, Higgs, Jenny, Canham, Natalie, Majumdar, Anirban, McEntagart, Meriel, Lahiri, Nayana, Stewart, Helen, Smithson, Sarah, Calpena, Eduardo, Jackson, Adam, Banka, Siddharth, Titheradge, Hannah, McGowan, Ruth, Rankin, Julia, Shaw-Smith, Charles, Evans, D. Gareth, Burghel, George J., Smith, Miriam J., Anderson, Emily, Madhu, Rajesh, Firth, Helen, Ellard, Sian, Brennan, Paul, Anderson, Claire, Taupin, Doug, Rogers, Mark T., Cook, Jackie A., Durkie, Miranda, East, James E., Fowler, Darren, Wilson, Louise, Igbokwe, Rebecca, Gardham, Alice, Tomlinson, Ian, Baralle, Diana, Uhlig, Holm H., and Taylor, Jenny C.

Published
2024
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8. Variants in ZFX are associated with an X-linked neurodevelopmental disorder with recurrent facial gestalt

Author

Shepherdson, James L., Hutchison, Katie, Don, Dilan Wellalage, McGillivray, George, Choi, Tae-Ik, Allan, Carolyn A., Amor, David J., Banka, Siddharth, Basel, Donald G., Buch, Laura D., Carere, Deanna Alexis, Carroll, Renée, Clayton-Smith, Jill, Crawford, Ali, Dunø, Morten, Faivre, Laurence, Gilfillan, Christopher P., Gold, Nina B., Gripp, Karen W., Hobson, Emma, Holtz, Alexander M., Innes, A. Micheil, Isidor, Bertrand, Jackson, Adam, Katsonis, Panagiotis, Amel Riazat Kesh, Leila, Küry, Sébastien, Lecoquierre, François, Lockhart, Paul, Maraval, Julien, Matsumoto, Naomichi, McCarrier, Julie, McCarthy, Josephine, Miyake, Noriko, Moey, Lip Hen, Németh, Andrea H., Østergaard, Elsebet, Patel, Rushina, Pope, Kate, Posey, Jennifer E., Schnur, Rhonda E., Shaw, Marie, Stolerman, Elliot, Taylor, Julie P., Wadman, Erin, Wakeling, Emma, White, Susan M., Wong, Lawrence C., Lupski, James R., Lichtarge, Olivier, Corbett, Mark A., Gecz, Jozef, Nicolet, Charles M., Farnham, Peggy J., Kim, Cheol-Hee, and Shinawi, Marwan

Published
2024
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9. Genotype–phenotype correlations and novel molecular insights into the DHX30-associated neurodevelopmental disorders

Author

Mannucci, Ilaria, Dang, Nghi DP, Huber, Hannes, Murry, Jaclyn B, Abramson, Jeff, Althoff, Thorsten, Banka, Siddharth, Baynam, Gareth, Bearden, David, Beleza-Meireles, Ana, Benke, Paul J, Berland, Siren, Bierhals, Tatjana, Bilan, Frederic, Bindoff, Laurence A, Braathen, Geir Julius, Busk, Øyvind L, Chenbhanich, Jirat, Denecke, Jonas, Escobar, Luis F, Estes, Caroline, Fleischer, Julie, Groepper, Daniel, Haaxma, Charlotte A, Hempel, Maja, Holler-Managan, Yolanda, Houge, Gunnar, Jackson, Adam, Kellogg, Laura, Keren, Boris, Kiraly-Borri, Catherine, Kraus, Cornelia, Kubisch, Christian, Le Guyader, Gwenael, Ljungblad, Ulf W, Brenman, Leslie Manace, Martinez-Agosto, Julian A, Might, Matthew, Miller, David T, Minks, Kelly Q, Moghaddam, Billur, Nava, Caroline, Nelson, Stanley F, Parant, John M, Prescott, Trine, Rajabi, Farrah, Randrianaivo, Hanitra, Reiter, Simone F, Schuurs-Hoeijmakers, Janneke, Shieh, Perry B, Slavotinek, Anne, Smithson, Sarah, Stegmann, Alexander PA, Tomczak, Kinga, Tveten, Kristian, Wang, Jun, Whitlock, Jordan H, Zweier, Christiane, McWalter, Kirsty, Juusola, Jane, Quintero-Rivera, Fabiola, Fischer, Utz, Yeo, Nan Cher, Kreienkamp, Hans-Jürgen, and Lessel, Davor

Subjects
Biological Sciences, Genetics, Pediatric, Clinical Research, Mental Health, Prevention, Aetiology, 4.1 Discovery and preclinical testing of markers and technologies, 2.1 Biological and endogenous factors, Detection, screening and diagnosis, Animals, Biomarkers, Gene Expression, Gene Knockdown Techniques, Genetic Association Studies, Genetic Predisposition to Disease, Germ-Line Mutation, HEK293 Cells, Humans, Immunohistochemistry, Mutation, Neurodevelopmental Disorders, Phenotype, RNA Helicases, Zebrafish, Clinical Sciences
Abstract

BackgroundWe aimed to define the clinical and variant spectrum and to provide novel molecular insights into the DHX30-associated neurodevelopmental disorder.MethodsClinical and genetic data from affected individuals were collected through Facebook-based family support group, GeneMatcher, and our network of collaborators. We investigated the impact of novel missense variants with respect to ATPase and helicase activity, stress granule (SG) formation, global translation, and their effect on embryonic development in zebrafish. SG formation was additionally analyzed in CRISPR/Cas9-mediated DHX30-deficient HEK293T and zebrafish models, along with in vivo behavioral assays.ResultsWe identified 25 previously unreported individuals, ten of whom carry novel variants, two of which are recurrent, and provide evidence of gonadal mosaicism in one family. All 19 individuals harboring heterozygous missense variants within helicase core motifs (HCMs) have global developmental delay, intellectual disability, severe speech impairment, and gait abnormalities. These variants impair the ATPase and helicase activity of DHX30, trigger SG formation, interfere with global translation, and cause developmental defects in a zebrafish model. Notably, 4 individuals harboring heterozygous variants resulting either in haploinsufficiency or truncated proteins presented with a milder clinical course, similar to an individual harboring a de novo mosaic HCM missense variant. Functionally, we established DHX30 as an ATP-dependent RNA helicase and as an evolutionary conserved factor in SG assembly. Based on the clinical course, the variant location, and type we establish two distinct clinical subtypes. DHX30 loss-of-function variants cause a milder phenotype whereas a severe phenotype is caused by HCM missense variants that, in addition to the loss of ATPase and helicase activity, lead to a detrimental gain-of-function with respect to SG formation. Behavioral characterization of dhx30-deficient zebrafish revealed altered sleep-wake activity and social interaction, partially resembling the human phenotype.ConclusionsOur study highlights the usefulness of social media to define novel Mendelian disorders and exemplifies how functional analyses accompanied by clinical and genetic findings can define clinically distinct subtypes for ultra-rare disorders. Such approaches require close interdisciplinary collaboration between families/legal representatives of the affected individuals, clinicians, molecular genetics diagnostic laboratories, and research laboratories.

Published
2021

10. AMFR dysfunction causes autosomal recessive spastic paraplegia in human that is amenable to statin treatment in a preclinical model

Author

Deng, Ruizhi, Medico-Salsench, Eva, Nikoncuk, Anita, Ramakrishnan, Reshmi, Lanko, Kristina, Kühn, Nikolas A., van der Linde, Herma C., Lor-Zade, Sarah, Albuainain, Fatimah, Shi, Yuwei, Yousefi, Soheil, Capo, Ivan, van den Herik, Evita Medici, van Slegtenhorst, Marjon, van Minkelen, Rick, Geeven, Geert, Mulder, Monique T., Ruijter, George J. G., Lütjohann, Dieter, Jacobs, Edwin H., Houlden, Henry, Pagnamenta, Alistair T., Metcalfe, Kay, Jackson, Adam, Banka, Siddharth, De Simone, Lenika, Schwaede, Abigail, Kuntz, Nancy, Palculict, Timothy Blake, Abbas, Safdar, Umair, Muhammad, AlMuhaizea, Mohammed, Colak, Dilek, AlQudairy, Hanan, Alsagob, Maysoon, Pereira, Catarina, Trunzo, Roberta, Karageorgou, Vasiliki, Bertoli-Avella, Aida M., Bauer, Peter, Bouman, Arjan, Hoefsloot, Lies H., van Ham, Tjakko J., Issa, Mahmoud, Zaki, Maha S., Gleeson, Joseph G., Willemsen, Rob, Kaya, Namik, Arold, Stefan T., Maroofian, Reza, Sanderson, Leslie E., and Barakat, Tahsin Stefan

Published
2023
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11. Biallelic CRELD1 variants cause a multisystem syndrome, including neurodevelopmental phenotypes, cardiac dysrhythmias, and frequent infections

Author

Borras, Silvia, Clark, Caroline, Dean, John, Miedzybrodzka, Zosia, Ross, Alison, Tennant, Stephen, Dabir, Tabib, Donnelly, Deirdre, Humphreys, Mervyn, Magee, Alex, McConnell, Vivienne, McKee, Shane, McNerlan, Susan, Morrison, Patrick J., Rea, Gillian, Stewart, Fiona, Cole, Trevor, Cooper, Nicola, Cooper-Charles, Lisa, Cox, Helen, Islam, Lily, Jarvis, Joanna, Keelagher, Rebecca, Lim, Derek, McMullan, Dominic, Morton, Jenny, Naik, Swati, O’Driscoll, Mary, Ong, Kai-Ren, Osio, Deborah, Ragge, Nicola, Turton, Sarah, Vogt, Julie, Williams, Denise, Bodek, Simon, Donaldson, Alan, Hills, Alison, Low, Karen, Newbury-Ecob, Ruth, Norman, Andrew M., Roberts, Eileen, Scurr, Ingrid, Smithson, Sarah, Tooley, Madeleine, Abbs, Steve, Armstrong, Ruth, Dunn, Carolyn, Holden, Simon, Park, Soo-Mi, Paterson, Joan, Raymond, Lucy, Reid, Evan, Sandford, Richard, Simonic, Ingrid, Tischkowitz, Marc, Woods, Geoff, Bradley, Lisa, Comerford, Joanne, Green, Andrew, Lynch, Sally, McQuaid, Shirley, Mullaney, Brendan, Berg, Jonathan, Goudie, David, Mavrak, Eleni, McLean, Joanne, McWilliam, Catherine, Reavey, Eleanor, Azam, Tara, Cleary, Elaine, Jackson, Andrew, Lam, Wayne, Lampe, Anne, Moore, David, Porteous, Mary, Baple, Emma, Baptista, Júlia, Brewer, Carole, Castle, Bruce, Kivuva, Emma, Owens, Martina, Rankin, Julia, Shaw-Smith, Charles, Turner, Claire, Turnpenny, Peter, Tysoe, Carolyn, Bradley, Therese, Davidson, Rosemarie, Gardiner, Carol, Joss, Shelagh, Kinning, Esther, Longman, Cheryl, McGowan, Ruth, Murday, Victoria, Pilz, Daniela, Tobias, Edward, Whiteford, Margo, Williams, Nicola, Barnicoat, Angela, Clement, Emma, Faravelli, Francesca, Hurst, Jane, Jenkins, Lucy, Jones, Wendy, Ajith Kumar, V.K., Lees, Melissa, Loughlin, Sam, Male, Alison, Morrogh, Deborah, Rosser, Elisabeth, Scott, Richard, Wilson, Louise, Beleza, Ana, Deshpande, Charu, Flinter, Frances, Holder, Muriel, Irving, Melita, Izatt, Louise, Josifova, Dragana, Mohammed, Shehla, Molenda, Aneta, Robert, Leema, Roworth, Wendy, Ruddy, Deborah, Ryten, Mina, Yau, Shu, Bennett, Christopher, Blyth, Moira, Campbell, Jennifer, Coates, Andrea, Dobbie, Angus, Hewitt, Sarah, Hobson, Emma, Jackson, Eilidh, Jewell, Rosalyn, Kraus, Alison, Prescott, Katrina, Sheridan, Eamonn, Thomson, Jenny, Bradshaw, Kirsty, Dixit, Abhijit, Eason, Jacqueline, Haines, Rebecca, Harrison, Rachel, Mutch, Stacey, Sarkar, Ajoy, Searle, Claire, Shannon, Nora, Sharif, Abid, Suri, Mohnish, Vasudevan, Pradeep, Canham, Natalie, Ellis, Ian, Greenhalgh, Lynn, Howard, Emma, Stinton, Victoria, Swale, Andrew, Weber, Astrid, Banka, Siddharth, Breen, Catherine, Briggs, Tracy, Burkitt-Wright, Emma, Chandler, Kate, Clayton-Smith, Jill, Donnai, Dian, Douzgou, Sofia, Gaunt, Lorraine, Jones, Elizabeth, Kerr, Bronwyn, Langley, Claire, Metcalfe, Kay, Smith, Audrey, Wright, Ronnie, Bourn, David, Burn, John, Fisher, Richard, Hellens, Steve, Henderson, Alex, Montgomery, Tara, Splitt, Miranda, Straub, Volker, Wright, Michael, Zwolinski, Simon, Allen, Zoe, Bernhard, Birgitta, Brady, Angela, Brooks, Claire, Busby, Louise, Clowes, Virginia, Ghali, Neeti, Holder, Susan, Ibitoye, Rita, Wakeling, Emma, Blair, Edward, Carmichael, Jenny, Cilliers, Deirdre, Clasper, Susan, Gibbons, Richard, Kini, Usha, Lester, Tracy, Nemeth, Andrea, Poulton, Joanna, Price, Sue, Shears, Debbie, Stewart, Helen, Wilkie, Andrew, Albaba, Shadi, Baker, Duncan, Balasubramanian, Meena, Johnson, Diana, Parker, Michael, Quarrell, Oliver, Stewart, Alison, Willoughby, Josh, Crosby, Charlene, Elmslie, Frances, Homfray, Tessa, Jin, Huilin, Lahiri, Nayana, Mansour, Sahar, Marks, Karen, McEntagart, Meriel, Saggar, Anand, Tatton-Brown, Kate, Butler, Rachel, Clarke, Angus, Corrin, Sian, Fry, Andrew, Kamath, Arveen, McCann, Emma, Mugalaasi, Hood, Pottinger, Caroline, Procter, Annie, Sampson, Julian, Sansbury, Francis, Varghese, Vinod, Baralle, Diana, Callaway, Alison, Cassidy, Emma J., Daniels, Stacey, Douglas, Andrew, Foulds, Nicola, Hunt, David, Kharbanda, Mira, Lachlan, Katherine, Mercer, Catherine, Side, Lucy, Temple, I. Karen, Wellesley, Diana, Ambrose, J.C., Arumugam, P., Baple, E.L., Bleda, M., Boardman-Pretty, F., Boissiere, J.M., Boustred, C.R., Caulfield, M.J., Chan, G.C., Craig, C.E.H., Daugherty, L.C., de Burca, A., Devereau, A., Elgar, G., Foulger, R.E., Fowler, T., FurióTarí, P., Hackett, J.M., Halai, D., Hamblin, A., Henderson, S., Holman, J.E., Hubbard, T.J.P., Ibáñez, K., Jackson, R., Jones, L.J., Kasperaviciute, D., Kayikci, M., Lahnstein, L., Lawson, K., Leigh, S.E.A., Leong, I.U.S., Lopez, F.J., MaleadyCrowe, F., Mason, J., McDonagh, E.M., Moutsianas, L., Mueller, M., Murugaesu, N., Need, A.C., Odhams, C.A., Patch, C., Perez-Gil, D., Polychronopoulos, D., Pullinger, J., Rahim, T., Rendon, A., Riesgo-Ferreiro, P., Rogers, T., Ryten, M., Savage, K., Sawant, K., Scott, R.H., Siddiq, A., Sieghart, A., Smedley, D., Smith, K.R., Sosinsky, A., Spooner, W., Stevens, H.E., Stuckey, A., Sultana, R., Thomas, E.R.A., Thompson, S.R., Tucci, A., Walsh, E., Watters, S.A., Welland, M.J., Williams, E., Witkowska, K., Acosta, Maria T., Adam, Margaret, Adams, David R., Agrawal, Pankaj B., Alejandro, Mercedes E., Alvey, Justin, Amendola, Laura, Andrews, Ashley, Ashley, Euan A., Azamian, Mahshid S., Bacino, Carlos A., Bademci, Guney, Baker, Eva, Balasubramanyam, Ashok, Baldridge, Dustin, Bale, Jim, Bamshad, Michael, Barbouth, Deborah, Bayrak-Toydemir, Pinar, Beck, Anita, Beggs, Alan H., Behrens, Edward, Bejerano, Gill, Bennet, Jimmy, Berg-Rood, Beverly, Bernstein, Jonathan A., Berry, Gerard T., Bican, Anna, Bivona, Stephanie, Blue, Elizabeth, Bohnsack, John, Bonnenmann, Carsten, Bonner, Devon, Botto, Lorenzo, Boyd, Brenna, Briere, Lauren C., Brokamp, Elly, Brown, Gabrielle, Burke, Elizabeth A., Burrage, Lindsay C., Butte, Manish J., Byers, Peter, Byrd, William E., Carey, John, Carrasquillo, Olveen, Peter Chang, Ta Chen, Chanprasert, Sirisak, Chao, Hsiao-Tuan, Clark, Gary D., Coakley, Terra R., Cobban, Laurel A., Cogan, Joy D., Coggins, Matthew, Cole, F. Sessions, Colley, Heather A., Cooper, Cynthia M., Craigen, William J., Crouse, Andrew B., Cunningham, Michael, D'Souza, Precilla, Dai, Hongzheng, Dasari, Surendra, Davids, Mariska, Dayal, Jyoti G., Deardorff, Matthew, Dell'Angelica, Esteban C., Dhar, Shweta U., Dipple, Katrina, Doherty, Daniel, Dorrani, Naghmeh, Douine, Emilie D., Draper, David D., Duncan, Laura, Earl, Dawn, Eckstein, David J., Emrick, Lisa T., Eng, Christine M., Esteves, Cecilia, Estwick, Tyra, Falk, Marni, Fernandez, Liliana, Ferreira, Carlos, Fieg, Elizabeth L., Findley, Laurie C., Fisher, Paul G., Fogel, Brent L., Forghani, Irman, Fresard, Laure, Gahl, William A., Glass, Ian, Godfrey, Rena A., Golden-Grant, Katie, Goldman, Alica M., Goldstein, David B., Grajewski, Alana, Groden, Catherine A., Gropman, Andrea L., Gutierrez, Irma, Hahn, Sihoun, Hamid, Rizwan, Hanchard, Neil A., Hassey, Kelly, Hayes, Nichole, High, Frances, Hing, Anne, Hisama, Fuki M., Holm, Ingrid A., Hom, Jason, Horike-Pyne, Martha, Huang, Alden, Huang, Yong, Isasi, Rosario, Jamal, Fariha, Jarvik, Gail P., Jarvik, Jeffrey, Jayadev, Suman, Johnston, Jean M., Karaviti, Lefkothea, Kelley, Emily G., Kennedy, Jennifer, Kiley, Dana, Kohane, Isaac S., Kohler, Jennefer N., Krakow, Deborah, Krasnewich, Donna M., Kravets, Elijah, Korrick, Susan, Koziura, Mary, Krier, Joel B., Lalani, Seema R., Lam, Byron, Lam, Christina, Lanpher, Brendan C., Lanza, Ian R., Lau, C. Christopher, LeBlanc, Kimberly, Lee, Brendan H., Lee, Hane, Levitt, Roy, Lewis, Richard A., Lincoln, Sharyn A., Liu, Pengfei, Liu, Xue Zhong, Longo, Nicola, Loo, Sandra K., Loscalzo, Joseph, Maas, Richard L., Macnamara, Ellen F., MacRae, Calum A., Maduro, Valerie V., Majcherska, Marta M., Mak, Bryan, Malicdan, May Christine V., Mamounas, Laura A., Manolio, Teri A., Mao, Rong, Maravilla, Kenneth, Markello, Thomas C., Marom, Ronit, Marth, Gabor, Martin, Beth A., Martin, Martin G., Martínez-Agosto, Julian A., Marwaha, Shruti, McCauley, Jacob, McCormack, Colleen E., McCray, Alexa T., McGee, Elisabeth, Mefford, Heather, Merritt, J. Lawrence, Might, Matthew, Mirzaa, Ghayda, Morava, Eva, Moretti, Paolo M., Morimoto, Marie, Mulvihill, John J., Murdock, David R., Nakano-Okuno, Mariko, Nath, Avi, Nelson, Stan F., Newman, John H., Nicholas, Sarah K., Nickerson, Deborah, Nieves-Rodriguez, Shirley, Novacic, Donna, Oglesbee, Devin, Orengo, James P., Pace, Laura, Pak, Stephen, Pallais, J. Carl, Papp, Jeanette C., Parker, Neil H., Phillips, John A., Posey, Jennifer E., Potocki, Lorraine, Pusey, Barbara N., Quinlan, Aaron, Raskind, Wendy, Raja, Archana N., Rao, Deepak A., Renteria, Genecee, Reuter, Chloe M., Rives, Lynette, Robertson, Amy K., Rodan, Lance H., Rosenfeld, Jill A., Rosenwasser, Natalie, Ruzhnikov, Maura, Sacco, Ralph, Sampson, Jacinda B., Samson, Susan L., Saporta, Mario, Scott, C. Ron, Schaechter, Judy, Schedl, Timothy, Scott, Daryl A., Sharma, Prashant, Shin, Jimann, Signer, Rebecca, Sillari, Catherine H., Silverman, Edwin K., Sinsheimer, Janet S., Sisco, Kathy, Smith, Edward C., Smith, Kevin S., Solem, Emily, Solnica-Krezel, Lilianna, Stoler, Joan M., Stong, Nicholas, Sullivan, Jennifer A., Sun, Angela, Sutton, Shirley, Sweetser, David A., Sybert, Virginia, Tabor, Holly K., Tamburro, Cecelia P., Tekin, Mustafa, Telischi, Fred, Thorson, Willa, Tifft, Cynthia J., Toro, Camilo, Tran, Alyssa A., Tucker, Brianna M., Urv, Tiina K., Vanderver, Adeline, Velinder, Matt, Viskochil, Dave, Vogel, Tiphanie P., Wahl, Colleen E., Wallace, Stephanie, Walley, Nicole M., Walsh, Chris A., Walker, Melissa, Wambach, Jennifer, Wan, Jijun, Wang, Lee-Kai, Wangler, Michael F., Ward, Patricia A., Wegner, Daniel, Wener, Mark, Wenger, Tara, Perry, Katherine Wesseling, Westerfield, Monte, Wheeler, Matthew T., Whitlock, Jordan, Wolfe, Lynne A., Woods, Jeremy D., Yamamoto, Shinya, Yang, John, Yu, Guoyun, Zastrow, Diane B., Zhao, Chunli, Zuchner, Stephan, Jeffries, Lauren, Mis, Emily K., McWalter, Kirsty, Donkervoort, Sandra, Brodsky, Nina N., Carpier, Jean-Marie, Ji, Weizhen, Ionita, Cristian, Roy, Bhaskar, Morrow, Jon S., Darbinyan, Armine, Iyer, Krishna, Aul, Ritu B., Chao, Katherine R., Cobbold, Laura, Cohen, Stacey, Custodio, Helena M., Drummond-Borg, Margaret, Finanger, Erika, Hainline, Bryan E., Helbig, Ingo, Hewson, Stacy, Hu, Ying, Jackson, Adam, Konstantino, Monica, Leach, Meganne E., McCormick, David, Nelson, Stanley, Nguyen, Joanne, Nugent, Kimberly, Ortega, Lucy, Goodkin, Howard P., Roeder, Elizabeth, Roy, Sani, Sapp, Katie, Saade, Dimah, Sisodiya, Sanjay M., Stals, Karen, Towner, Shelley, Wilson, William, Khokha, Mustafa K., Bönnemann, Carsten G., Lucas, Carrie L., and Lakhani, Saquib A.

Published
2024
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12. Discovery of DNA methylation signature in the peripheral blood of individuals with history of antenatal exposure to valproic acid

Author

Haghshenas, Sadegheh, Putoux, Audrey, Reilly, Jack, Levy, Michael A., Relator, Raissa, Ghosh, Sourav, Kerkhof, Jennifer, McConkey, Haley, Edery, Patrick, Lesca, Gaetan, Besson, Alicia, Coubes, Christine, Willems, Marjolaine, Ruiz-Pallares, Nathalie, Barat-Houari, Mouna, Tizzano, Eduardo F., Valenzuela, Irene, Sabbagh, Quentin, Clayton-Smith, Jill, Jackson, Adam, O’Sullivan, James, Bromley, Rebecca, Banka, Siddharth, Genevieve, David, and Sadikovic, Bekim

Published
2024
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13. Bi-allelic loss-of-function variants in BCAS3 cause a syndromic neurodevelopmental disorder

Author

Hengel, Holger, Hannan, Shabab B, Dyack, Sarah, MacKay, Sara B, Schatz, Ulrich, Fleger, Martin, Kurringer, Andreas, Balousha, Ghassan, Ghanim, Zaid, Alkuraya, Fowzan S, Alzaidan, Hamad, Alsaif, Hessa S, Mitani, Tadahiro, Bozdogan, Sevcan, Pehlivan, Davut, Lupski, James R, Gleeson, Joseph J, Dehghani, Mohammadreza, Mehrjardi, Mohammad YV, Sherr, Elliott H, Parks, Kendall C, Argilli, Emanuela, Begtrup, Amber, Galehdari, Hamid, Balousha, Osama, Shariati, Gholamreza, Mazaheri, Neda, Malamiri, Reza A, Pagnamenta, Alistair T, Kingston, Helen, Banka, Siddharth, Jackson, Adam, Osmond, Mathew, Consortium, Care4Rare Canada, Consortium, Genomics England Research, Rieß, Angelika, Haack, Tobias B, Nägele, Thomas, Schuster, Stefanie, Hauser, Stefan, Admard, Jakob, Casadei, Nicolas, Velic, Ana, Macek, Boris, Ossowski, Stephan, Houlden, Henry, Maroofian, Reza, and Schöls, Ludger

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Human Genome, Brain Disorders, Congenital Structural Anomalies, Pediatric, Aetiology, 2.1 Biological and endogenous factors, Adolescent, Adult, Animals, Cell Movement, Child, Child, Preschool, Drosophila, Female, Fibroblasts, Humans, Infant, Loss of Function Mutation, Loss of Heterozygosity, Male, Mice, Mice, Knockout, Neoplasm Proteins, Neurodevelopmental Disorders, Pedigree, Proteome, Young Adult, Care4Rare Canada Consortium, Genomics England Research Consortium, BCAS3, UAS-Gal4, fibroblasts, global developmental delay, microcephaly, neurodevelopmental disorder, proteomics, pyramidal tract involvement, thin corpus callosum, transcriptomics, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

BCAS3 microtubule-associated cell migration factor (BCAS3) is a large, highly conserved cytoskeletal protein previously proposed to be critical in angiogenesis and implicated in human embryogenesis and tumorigenesis. Here, we established BCAS3 loss-of-function variants as causative for a neurodevelopmental disorder. We report 15 individuals from eight unrelated families with germline bi-allelic loss-of-function variants in BCAS3. All probands share a global developmental delay accompanied by pyramidal tract involvement, microcephaly, short stature, strabismus, dysmorphic facial features, and seizures. The human phenotype is less severe compared with the Bcas3 knockout mouse model and cannot be explained by angiogenic defects alone. Consistent with being loss-of-function alleles, we observed absence of BCAS3 in probands' primary fibroblasts. By comparing the transcriptomic and proteomic data based on probands' fibroblasts with those of the knockout mouse model, we identified similar dysregulated pathways resulting from over-representation analysis, while the dysregulation of some proposed key interactors could not be confirmed. Together with the results from a tissue-specific Drosophila loss-of-function model, we demonstrate a vital role for BCAS3 in neural tissue development.

Published
2021

16. Mutation-specific pathophysiological mechanisms define different neurodevelopmental disorders associated with SATB1 dysfunction.

Author

den Hoed, Joery, de Boer, Elke, Voisin, Norine, Dingemans, Alexander, Guex, Nicolas, Wiel, Laurens, Nellaker, Christoffer, Amudhavalli, Shivarajan, Banka, Siddharth, Bena, Frederique, Ben-Zeev, Bruria, Bonagura, Vincent, Bruel, Ange-Line, Brunet, Theresa, Brunner, Han, Chew, Hui, Chrast, Jacqueline, Cimbalistienė, Loreta, Coon, Hilary, Délot, Emmanuèlle, Démurger, Florence, Denommé-Pichon, Anne-Sophie, Depienne, Christel, Donnai, Dian, Dyment, David, Elpeleg, Orly, Faivre, Laurence, Gilissen, Christian, Granger, Leslie, Haber, Benjamin, Hachiya, Yasuo, Abedi, Yasmin, Hanebeck, Jennifer, Hehir-Kwa, Jayne, Horist, Brooke, Itai, Toshiyuki, Jackson, Adam, Jewell, Rosalyn, Jones, Kelly, Joss, Shelagh, Kashii, Hirofumi, Kato, Mitsuhiro, Kattentidt-Mouravieva, Anja, Kok, Fernando, Kotzaeridou, Urania, Krishnamurthy, Vidya, Kučinskas, Vaidutis, Kuechler, Alma, Lavillaureix, Alinoë, Liu, Pengfei, Manwaring, Linda, Matsumoto, Naomichi, Mazel, Benoît, McWalter, Kirsty, Meiner, Vardiella, Mikati, Mohamad, Miyatake, Satoko, Mizuguchi, Takeshi, Moey, Lip, Mohammed, Shehla, Mor-Shaked, Hagar, Mountford, Hayley, Newbury-Ecob, Ruth, Odent, Sylvie, Orec, Laura, Osmond, Matthew, Palculict, Timothy, Parker, Michael, Petersen, Andrea, Pfundt, Rolph, Preikšaitienė, Eglė, Radtke, Kelly, Ranza, Emmanuelle, Rosenfeld, Jill, Santiago-Sim, Teresa, Schwager, Caitlin, Sinnema, Margje, Snijders Blok, Lot, Spillmann, Rebecca, Stegmann, Alexander, Thiffault, Isabelle, Tran, Linh, Vaknin-Dembinsky, Adi, Vedovato-Dos-Santos, Juliana, Schrier Vergano, Samantha, Vilain, Eric, Vitobello, Antonio, Wagner, Matias, Waheeb, Androu, Willing, Marcia, Zuccarelli, Britton, Kini, Usha, Newbury, Dianne, Kleefstra, Tjitske, Reymond, Alexandre, Fisher, Simon, and Vissers, Lisenka

Subjects
HPO-based analysis, SATB1, cell-based functional assays, de novo variants, intellectual disability, neurodevelopmental disorders, seizures, teeth abnormalities, Chromatin, Female, Genetic Association Studies, Haploinsufficiency, Humans, Male, Matrix Attachment Region Binding Proteins, Models, Molecular, Mutation, Mutation, Missense, Neurodevelopmental Disorders, Protein Binding, Protein Domains, Transcription, Genetic
Abstract

Whereas large-scale statistical analyses can robustly identify disease-gene relationships, they do not accurately capture genotype-phenotype correlations or disease mechanisms. We use multiple lines of independent evidence to show that different variant types in a single gene, SATB1, cause clinically overlapping but distinct neurodevelopmental disorders. Clinical evaluation of 42 individuals carrying SATB1 variants identified overt genotype-phenotype relationships, associated with different pathophysiological mechanisms, established by functional assays. Missense variants in the CUT1 and CUT2 DNA-binding domains result in stronger chromatin binding, increased transcriptional repression, and a severe phenotype. In contrast, variants predicted to result in haploinsufficiency are associated with a milder clinical presentation. A similarly mild phenotype is observed for individuals with premature protein truncating variants that escape nonsense-mediated decay, which are transcriptionally active but mislocalized in the cell. Our results suggest that in-depth mutation-specific genotype-phenotype studies are essential to capture full disease complexity and to explain phenotypic variability.

Published
2021

17. A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Author

Abbott, Kristin M., Banka, Siddharth, de Boer, Elke, Ciolfi, Andrea, Clayton-Smith, Jill, Dallapiccola, Bruno, Denommé-Pichon, Anne-Sophie, Faivre, Laurence, Gilissen, Christian, Haack, Tobias B., Havlovicova, Marketa, Hoischen, Alexander, Jackson, Adam, Kerstjens, Mieke, Kleefstra, Tjitske, Martín, Estrella López, Macek, Milan, Jr., Matalonga, Leslie, Maystadt, Isabelle, Morleo, Manuela, Nigro, Vicenzo, Pinelli, Michele, Pizzi, Simone, Posada, Manuel, Radio, Francesca C., Renieri, Alessandra, Riess, Olaf, Rooryck, Caroline, Ryba, Lukas, Agathe, Jean-Madeleine de Sainte, Santen, Gijs W.E., Schwarz, Martin, Tartaglia, Marco, Thauvin, Christel, Torella, Annalaura, Trimouille, Aurélien, Verloes, Alain, Vissers, Lisenka, Vitobello, Antonio, Votypka, Pavel, Zguro, Kristina, Boer, Elke de, Cohen, Enzo, Danis, Daniel, Gao, Fei, Horvath, Rita, Johari, Mridul, Johanson, Lennart, Li, Shuang, Morsy, Heba, Nelson, Isabelle, Paramonov, Ida, te Paske, Iris B.A.W., Robinson, Peter, Savarese, Marco, Steyaert, Wouter, Töpf, Ana, van der Velde, Joeri K., Vandrovcova, Jana, Graessner, Holm, Zurek, Birte, Ellwanger, Kornelia, Ossowski, Stephan, Demidov, German, Sturm, Marc, Schulze-Hentrich, Julia M., Schüle, Rebecca, Xu, Jishu, Kessler, Christoph, Wayand, Melanie, Synofzik, Matthis, Wilke, Carlo, Traschütz, Andreas, Schöls, Ludger, Hengel, Holger, Lerche, Holger, Kegele, Josua, Heutink, Peter, Brunner, Han, Scheffer, Hans, Hoogerbrugge, Nicoline, ‘t Hoen, Peter A.C., Vissers, Lisenka E.L.M., Sablauskas, Karolis, de Voer, Richarda M., Kamsteeg, Erik-Jan, van de Warrenburg, Bart, van Os, Nienke, Paske, Iris te, Janssen, Erik, Steehouwer, Marloes, Yaldiz, Burcu, Brookes, Anthony J., Veal, Colin, Gibson, Spencer, Maddi, Vatsalya, Mehtarizadeh, Mehdi, Riaz, Umar, Warren, Greg, Dizjikan, Farid Yavari, Shorter, Thomas, Straub, Volker, Bettolo, Chiara Marini, Manera, Jordi Diaz, Hambleton, Sophie, Engelhardt, Karin, Alexander, Elizabeth, Duffourd, Yannis, Bruel, Ange-Line, Peyron, Christine, Pélissier, Aurore, Beltran, Sergi, Gut, Ivo Glynne, Laurie, Steven, Piscia, Davide, Papakonstantinou, Anastasios, Bullich, Gemma, Corvo, Alberto, Fernandez-Callejo, Marcos, Hernández, Carles, Picó, Daniel, Lochmüller, Hanns, Gumus, Gulcin, Bros-Facer, Virginie, Rath, Ana, Hanauer, Marc, Lagorce, David, Hongnat, Oscar, Chahdil, Maroua, Lebreton, Emeline, Stevanin, Giovanni, Durr, Alexandra, Davoine, Claire-Sophie, Guillot-Noel, Léna, Heinzmann, Anna, Coarelli, Giulia, Bonne, Gisèle, Evangelista, Teresinha, Allamand, Valérie, Ben Yaou, Rabah, Metay, Corinne, Eymard, Bruno, Atalaia, Antonio, Stojkovic, Tanya, Turnovec, Marek, Thomasová, Dana, Kremliková, Radka Pourová, Franková, Vera, Havlovicová, Markéta, Lišková, Petra, Doležalová, Pavla, Parkinson, Helen, Keane, Thomas, Freeberg, Mallory, Thomas, Coline, Spalding, Dylan, Robert, Glenn, Costa, Alessia, Patch, Christine, Hanna, Mike, Houlden, Henry, Reilly, Mary, Efthymiou, Stephanie, Cali, Elisa, Magrinelli, Francesca, Sisodiya, Sanjay M., Rohrer, Jonathan, Muntoni, Francesco, Zaharieva, Irina, Sarkozy, Anna, Timmerman, Vincent, Baets, Jonathan, de Vries, Geert, De Winter, Jonathan, Beijer, Danique, de Jonghe, Peter, Van de Vondel, Liedewei, De Ridder, Willem, Weckhuysen, Sarah, Nigro, Vincenzo, Mutarelli, Margherita, Varavallo, Alessandra, Banfi, Sandro, Musacchia, Francesco, Piluso, Giulio, Ferlini, Alessandra, Selvatici, Rita, Gualandi, Francesca, Bigoni, Stefania, Rossi, Rachele, Neri, Marcella, Aretz, Stefan, Spier, Isabel, Sommer, Anna Katharina, Peters, Sophia, Oliveira, Carla, Pelaez, Jose Garcia, Matos, Ana Rita, José, Celina São, Ferreira, Marta, Gullo, Irene, Fernandes, Susana, Garrido, Luzia, Ferreira, Pedro, Carneiro, Fátima, Swertz, Morris A., Johansson, Lennart, van der Vries, Gerben, Neerincx, Pieter B., Ruvolo, David, Kerstjens Frederikse, Wilhemina S., Zonneveld-Huijssoon, Eveline, Roelofs-Prins, Dieuwke, van Gijn, Marielle, Köhler, Sebastian, Metcalfe, Alison, Drunat, Séverine, Heron, Delphine, Mignot, Cyril, Keren, Boris, Lacombe, Didier, Trimouille, Aurelien, Capella, Gabriel, Valle, Laura, Holinski-Feder, Elke, Laner, Andreas, Steinke-Lange, Verena, Cilio, Maria-Roberta, Carpancea, Evelina, Depondt, Chantal, Lederer, Damien, Sznajer, Yves, Duerinckx, Sarah, Mary, Sandrine, Macaya, Alfons, Cazurro-Gutiérrez, Ana, Pérez-Dueñas, Belén, Munell, Francina, Jarava, Clara Franco, Masó, Laura Batlle, Marcé-Grau, Anna, Colobran, Roger, Hackman, Peter, Udd, Bjarne, Hemelsoet, Dimitri, Dermaut, Bart, Schuermans, Nika, Poppe, Bruce, Verdin, Hannah, Osorio, Andrés Nascimento, Depienne, Christel, Roos, Andreas, Cordts, Isabell, Deschauer, Marcus, Striano, Pasquale, Zara, Federico, Riva, Antonella, Iacomino, Michele, Uva, Paolo, Scala, Marcello, Scudieri, Paolo, Başak, Ayşe Nazlı, Claeys, Kristl, Boztug, Kaan, Haimel, Matthias, W.E, Gijs, Ruivenkamp, Claudia A.L., Natera de Benito, Daniel, Thompson, Rachel, Polavarapu, Kiran, Grimbacher, Bodo, Zaganas, Ioannis, Kokosali, Evgenia, Lambros, Mathioudakis, Evangeliou, Athanasios, Spilioti, Martha, Kapaki, Elisabeth, Bourbouli, Mara, Radio, Francesca Clementina, Balicza, Peter, Molnar, Maria Judit, De la Paz, Manuel Posada, Sánchez, Eva Bermejo, Delgado, Beatriz Martínez, Alonso García de la Rosa, F. Javier, Schröck, Evelin, Rump, Andreas, Mei, Davide, Vetro, Annalisa, Balestrini, Simona, Guerrini, Renzo, Chinnery, Patrick F., Ratnaike, Thiloka, Schon, Katherine, Maver, Ales, Peterlin, Borut, Münchau, Alexander, Lohmann, Katja, Herzog, Rebecca, Pauly, Martje, May, Patrick, Beeson, David, Cossins, Judith, Furini, Simone, Fallerini, Chiara, Benetti, Elisa, Afenjar, Alexandra, Goldenberg, Alice, Masurel, Alice, Phan, Alice, Dieux-Coeslier, Anne, Fargeot, Anne, Guerrot, Anne-Marie, Toutain, Annick, Molin, Arnaud, Sorlin, Arthur, Putoux, Audrey, Jouret, Béatrice, Laudier, Béatrice, Demeer, Bénédicte, Doray, Bérénice, Bonniaud, Bertille, Isidor, Bertrand, Gilbert-Dussardier, Brigitte, Leheup, Bruno, Reversade, Bruno, Paul, Carle, Vincent-Delorme, Catherine, Neiva, Cecilia, Poirsier, Céline, Quélin, Chloé, Chiaverini, Christine, Coubes, Christine, Francannet, Christine, Colson, Cindy, Desplantes, Claire, Wells, Constance, Goizet, Cyril, Sanlaville, Damien, Amram, Daniel, Lehalle, Daphné, Geneviève, David, Gaillard, Dominique, Zivi, Einat, Sarrazin, Elisabeth, Steichen, Elisabeth, Schaefer, Élise, Lacaze, Elodie, Jacquemin, Emmanuel, Bongers, Ernie, Kilic, Esra, Colin, Estelle, Giuliano, Fabienne, Prieur, Fabienne, Laffargue, Fanny, Morice-Picard, Fanny, Petit, Florence, Cartault, François, Feillet, François, Baujat, Geneviève, Morin, Gilles, Diene, Gwenaëlle, Journel, Hubert, Perthus, Isabelle, Lespinasse, James, Alessandri, Jean-Luc, Amiel, Jeanne, Martinovic, Jelena, Delanne, Julian, Albuisson, Juliette, Lambert, Laëtitia, Perrin, Laurence, Ousager, Lilian Bomme, Van Maldergem, Lionel, Pinson, Lucile, Ruaud, Lyse, Samimi, Mahtab, Bournez, Marie, Bonnet-Dupeyron, Marie Noëlle, Vincent, Marie, Jacquemont, Marie-Line, Cordier-Alex, Marie-Pierre, Gérard-Blanluet, Marion, Willems, Marjolaine, Spodenkiewicz, Marta, Doco-Fenzy, Martine, Rossi, Massimiliano, Renaud, Mathilde, Fradin, Mélanie, Mathieu, Michèle, Holder-Espinasse, Muriel H., Houcinat, Nada, Hanna, Nadine, Leperrier, Nathalie, Chassaing, Nicolas, Philip, Nicole, Boute, Odile, Van Kien, Philippe Khau, Parent, Philippe, Bitoun, Pierre, Sarda, Pierre, Vabres, Pierre, Jouk, Pierre-Simon, Touraine, Renaud, El Chehadeh, Salima, Whalen, Sandra, Marlin, Sandrine, Passemard, Sandrine, Grotto, Sarah, Bellanger, Séverine Audebert, Blesson, Sophie, Nambot, Sophie, Naudion, Sophie, Lyonnet, Stanislas, Odent, Sylvie, Attie-Bitach, Tania, Busa, Tiffany, Drouin-Garraud, Valérie, Layet, Valérie, Bizaoui, Varoona, Cusin, Véronica, Capri, Yline, Alembik, Yves, Jean-Marçais, Nolwenn, López-Martín, Estrella, Macek, Milan, Mencarelli, Maria Antonietta, Moutton, Sébastien, Pfundt, Rolph, Safraou, Hana, Thauvin-Robinet, Christel, Thevenon, Julien, Tran Mau-Them, Frédéric, de Vries, Bert B.A., Willemsen, Marjolein H., and Philippe, Christophe

Published
2023
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19. Imbalance of flight–freeze responses and their cellular correlates in the Nlgn3−/y rat model of autism

Author

Anstey, Natasha J., Kapgal, Vijayakumar, Tiwari, Shashank, Watson, Thomas C., Toft, Anna K. H., Dando, Owen R., Inkpen, Felicity H., Baxter, Paul S., Kozić, Zrinko, Jackson, Adam D., He, Xin, Nawaz, Mohammad Sarfaraz, Kayenaat, Aiman, Bhattacharya, Aditi, Wyllie, David J. A., Chattarji, Sumantra, Wood, Emma R., Hardt, Oliver, and Kind, Peter C.

Published
2022
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21. Genome-wide variant calling in reanalysis of exome sequencing data uncovered a pathogenic TUBB3 variant

Author

Boer, Elke de, Cohen, Enzo, Cuesta, Isabel, Danis, Daniel, Denommé-Pichon, Anne-Sophie, Gao, Fei, Gilissen, Christian, Horvath, Rita, Johari, Mridul, Johanson, Lennart, Li, Shuang, Matalonga, Leslie, Morsy, Heba, Nelson, Isabelle, Paramonov, Ida, Paske, Iris B.A.W. te, Robinson, Peter, Savarese, Marco, Steyaert, Wouter, Töpf, Ana, Trimouille, Aurélien, van der Velde, Joeri K., Vandrovcova, Jana, Vitobello, Antonio, Zurek, Birte, Abbot, Kristin M., Banka, Siddharth, Benetti, Elisa, de Boer, Elke, Casari, Giorgio, Ciolfi, Andrea, Clayton-Smith, Jill, Dallapiccola, Bruno, Ellwanger, Kornelia, Faivre, Laurence, Graessner, Holm, Haack, Tobias B., Hammarsjö, Anna, Havlovicova, Marketa, Hoischen, Alexander, Hugon, Anne, Jackson, Adam, Kerstjens, Mieke, Kleefstra, Tjitske, Lindstrand, Anna, Martín, Estrella López, Macek, Milan, Jr., Maystadt, Isabelle, Morleo, Manuela, Nigro, Vicenzo, Nordgren, Ann, Pettersson, Maria, Pinelli, Michele, Pizzi, Simone, Posada, Manuel, Radio, Francesca C., Renieri, Alessandra, Rooryck, Caroline, Ryba, Lukas, Santen, Gijs W.E., Schwarz, Martin, Tartaglia, Marco, Thauvin, Christel, Torella, Annalaura, Verloes, Alain, Vissers, Lisenka, Votypka, Pavel, Vyshka, Klea, Zguro, Kristina, Yaldiz, Burcu, Laurie, Steve, de Reuver, Rick, Kwint, Michael, Pfundt, Rolph, Willemsen, Michèl A.A.P., Vries, Bert B.A. de, Vitobello, A., and Vissers, Lisenka E.L.M.

Published
2022
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23. Mercury Levels in the Crab Grapsus grapsus across the Galápagos Archipelago.

Author

Jackson, George D., Jackson, Christine H., Brandao, Maura, Jackson, Adam K., Espinoza, Eduardo, and Soria-Carvajal, Monica

Subjects
ARCHIPELAGOES, CRABS, MERCURY, LEG muscles, GOVERNMENT agencies, BARNACLES
Abstract

The levels of mercury (Hg) were examined in the leg muscle of the crab Grapsus grapsus from five sites on four islands within the Galápagos archipelago. Mercury values obtained using a Milestone DMA 80 evo direct mercury analyzer varied both within and among sites. Total mercury concentrations (mg kg−1 dry weight) ranged from the lowest at a protected location at Isabela Island (0.06 ± 0.02) to the highest at the San Cristóbal urban location (2.04 ± 0.069). Crabs from South Plaza Island also had surprisingly high levels of mercury with a mean of 1.2 ± 0.6. Values from urban sites at Isabela Island and Academy Bay, Santa Cruz, had intermediate values. When converted to wet weight, crabs from both San Cristóbal and South Plaza were within or above the levels (0.3–0.5 mg kg−1 wet weight set by various government agencies) considered potentially harmful to human health if ingested. A lesser number of both oysters and barnacles were also analyzed for mercury at South Plaza and Academy Bay, and while the values were lower compared to the crabs, they followed the same pattern of elevated levels at South Plaza compared to Academy Bay. It is unclear as to whether the mercury comes from natural sources, such as volcanism, or anthropogenic causes. [ABSTRACT FROM AUTHOR]

Published
2024
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24. Haploinsufficiency of ARFGEF1 is associated with developmental delay, intellectual disability, and epilepsy with variable expressivity

Author

Thomas, Quentin, Gautier, Thierry, Marafi, Dana, Besnard, Thomas, Willems, Marjolaine, Moutton, Sébastien, Isidor, Bertand, Cogné, Benjamin, Conrad, Solène, Tenconi, Romano, Iascone, Maria, Sorlin, Arthur, Masurel, Alice, Dabir, Tabib, Jackson, Adam, Banka, Siddharth, Delanne, Julian, Lupski, James R., Saadi, Nebal Waill, Alkuraya, Fowzan S., Zahrani, Fatema Al, Agrawal, Pankaj B., England, Eleina, Madden, Jill A., Posey, Jennifer E., Burglen, Lydie, Rodriguez, Diana, Chevarin, Martin, Nguyen, Sylvie, Mau-Them, Frédéric Tran, Duffourd, Yannis, Garret, Philippine, Bruel, Ange-Line, Callier, Patrick, Marle, Nathalie, Denomme-Pichon, Anne-Sophie, Duplomb, Laurence, Philippe, Christophe, Thauvin-Robinet, Christel, Govin, Jérôme, Faivre, Laurence, and Vitobello, Antonio

Published
2021
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28. Cellular and synaptic pathophysiology in a rat model of Fragile X syndrome

Author

Jackson, Adam, Kind, Peter, and Wyllie, David

Subjects
616.85, fragile X syndrome, autism, synaptic plasticity
Abstract

Fragile X syndrome (FXS) is the most commonly inherited form of intellectual disability as well as a leading genetic cause of autism spectrum disorder. It is typically the result of a trinucleotide repeat expansion in the Fmr1 gene which leads to loss of the encoded protein, fragile X mental retardation protein (FMRP). Animal model studies over the past twenty years, mainly focusing on the Fmr1 knockout (KO) mouse, have uncovered several cellular and behavioural phenotypes associated with the loss of FMRP. Seminal work using the Fmr1 KO mouse found that metabotropic glutamate receptor mediated long-term depression (mGluR-LTD) in the hippocampus is both exaggerated (Huber et al., 2002) and independent of new protein synthesis (Nosyreva & Huber, 2006). These findings, together with studies focusing on other brain regions including the prefrontal cortex (Zhao et al., 2005) and amygdala (Suvrathan et al., 2010), have contributed to the ‘mGluR theory of FXS’ (Bear et al., 2004) which suggests that group 1 metabotropic receptor function is exaggerated in FXS. The development of genetically modified rats allows the modelling of FXS in an animal model with more complex cognitive and social behaviours than has been previously available. It also provides an opportunity for comparison of phenotypes across mammalian species that result from FMRP deletion. While the study of Fmr1 rats can significantly contribute to our understanding of FXS, we must first confirm the assumption that cellular phenotypes are conserved across mouse and rat models. In this thesis, we first aimed to test if the key cellular and synaptic phenotypes that contribute to the ‘mGluR theory of FXS’ are conserved in both the hippocampus and amygdala of Fmr1 KO rats. In agreement with mouse studies, we found mGluR-LTD was both enhanced and independent of new protein synthesis in Fmr1 KO rats. Similarly, group 1 mGluR long-term potentiation (LTP) was significantly decreased at both cortical and thalamic inputs to the lateral amygdala. Secondly, we investigated mPFC intrinsic excitability and synaptic plasticity in Fmr1 KO rats. The mPFC plays a key role in several of the cognitive functions that are affected in fragile X patients including attention, cognitive flexibility and anxiety (Goto et al., 2010). The regulation of mPFC plasticity and intrinsic excitability has also been associated with mGluR signalling. Here we found that intralaminar LTP in the mPFC showed an age-dependent deficit in Fmr1 KO rats. The mPFC also provides top down control of several cortical and subcortical regions through long-range connectivity. One pathway of interest in the study of FXS is mPFC-amygdala connectivity which is associated with fear learning and anxiety behaviours (Burgos- Robles et al., 2009). Using retrograde tracing, we showed layer 5 pyramidal neurons that provide long-range connections to the basal amygdala were intrinsically hypoexcitable in Fmr1 KO rats. This phenotype could possibly be explained through homeostatic changes in the axon initial segment which regulates neuronal excitability. This work provides the first evidence for conservation of cellular phenotypes associated with the loss of FMRP in mice and rats which will be key in the interpretation of future studies using Fmr1 KO rats. We also provide evidence of deficits in mPFC long-range connectivity to the basal amygdala, a pathway that is associated with FXS relevant behaviours. Together this highlights how study of the rat model of FXS can complement existing studies of Fmr1 KO mice as well as provide new insights into the pathophysiology resulting from the loss of FMRP. Some of this work was published in Till et al., 2015.

Published
2017

29. Suppression of lattice thermal conductivity by mass-conserving cation mutation in multi-component semiconductors

Author

Shibuya, Taizo, Skelton, Jonathan M., Jackson, Adam J., Yasuoka, Kenju, Togo, Atsushi, Tanaka, Isao, and Walsh, Aron

Subjects
Condensed Matter - Materials Science
Abstract

In semiconductors almost all heat is conducted by phonons (lattice vibrations), which is limited by their quasi-particle lifetimes. Phonon-phonon interactions represent scattering mechanisms that produce thermal resistance. In thermoelectric materials, this resistance due to anharmonicity should be maximised for optimal performance. We use a first-principles lattice-dynamics approach to explore the changes in lattice dynamics across an isostructural series where the average atomic mass is conserved: ZnS to CuGaS$_2$ to Cu$_2$ZnGeS$_4$. Our results demonstrate an enhancement of phonon interactions in the multernary materials, and confirm that lattice thermal conductivity can be controlled independently of the average mass and local coordination environments., Comment: 13 pages, 4 figures

Published
2016
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30. A universal chemical potential for sulfur vapours

Author

Jackson, Adam J., Tiana, Davide, and Walsh, Aron

Subjects
Condensed Matter - Materials Science
Abstract

The unusual chemistry of sulfur is illustrated by the tendency for catenation. Sulfur forms a range of open and closed S$_n$ species in the gas phase, which has led to speculation on the composition of sulfur vapours as a function of temperature and pressure for over a century. Unlike elemental gases such as O$_2$ and N$_2$, there is no widely accepted thermodynamic potential for sulfur. Here we combine a first-principles global structure search for the low energy clusters from S$_2$ to S$_8$ with a thermodynamic model for the mixed-allotrope system, including the Gibbs free energy for all gas-phase sulfur on an atomic basis. A strongly pressure-dependent transition from a mixture dominant in S$_2$ to S$_8$ is identified. A universal chemical potential function, $\mu_{\mathrm{S}}(T,P)$, is proposed with wide utility in modelling sulfurisation processes including the formation of metal chalcogenide semiconductors., Comment: 12 pages, 9 figures. Supporting code and data is available at https://github.com/WMD-Bath/sulfur-model [snapshot DOI: 10.5281/zenodo.28536]. Further data will be available from DOI:10.6084/m9.figshare.1513736 and DOI:10.6084/m9.figshare.1513833 following peer-review

Published
2015
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31. Crystal structure optimisation using an auxiliary equation of state

Author

Jackson, Adam J., Skelton, Jonathan M., Hendon, Christopher H., Butler, Keith T., and Walsh, Aron

Subjects
Condensed Matter - Materials Science
Abstract

Standard procedures for local crystal-structure optimisation involve numerous energy and force calculations. It is common to calculate an energy-volume curve, fitting an equation of state around the equilibrium cell volume. This is a computationally intensive process, in particular for low-symmetry crystal structures where each isochoric optimisation involves energy minimisation over many degrees of freedom. Such procedures can be prohibitive for non-local exchange-correlation functionals or other 'beyond' density functional theory electronic structure techniques, particularly where analytical gradients are not available. We present a simple approach for efficient optimisation of crystal structures based on a known equation of state. The equilibrium volume can be predicted from one single-point calculation, and refined with successive calculations if required. The approach is validated for PbS, PbTe, ZnS and ZnTe using nine density functionals, and applied to the quaternary semiconductor Cu$_{2}$ZnSnS$_{4}$ and the magnetic metal-organic framework HKUST-1.

Published
2015
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32. Lattice dynamics and vibrational spectra of the orthorhombic, tetragonal and cubic phases of methylammonium lead iodide

Author

Brivio, Federico, Frost, Jarvist M., Skelton, Jonathan M., Jackson, Adam J., Weber, Oliver J., Weller, Mark T., Goni, Alejandro R., Leguy, Aurelien M. A., Barnes, Piers R. F., and Walsh, Aron

Subjects
Condensed Matter - Materials Science
Abstract

The hybrid halide perovskite CH3NH3PbI3 exhibits a complex structural behaviour, with successive transitions between orthorhombic, tetragonal and cubic polymorphs at ca. 165 K and 327 K. Herein we report first-principles lattice dynamics (phonon spectrum) for each phase of CH3NH3PbI3. The equilibrium structures compare well to solutions of temperature-dependent powder neutron diffraction. By following the normal modes we calculate infrared and Raman intensities of the vibrations, and compare them to the measurement of a single crystal where the Raman laser is controlled to avoid degradation of the sample. Despite a clear separation in energy between low frequency modes associated with the inorganic PbI3 network and high-frequency modes of the organic CH3NH3+ cation, significant coupling between them is found, which emphasises the interplay between molecular orientation and the corner-sharing octahedral networks in the structural transformations. Soft modes are found at the boundary of the Brillouin zone of the cubic phase, consistent with displacive instabilities and anharmonicity involving tilting of the PbI6 octahedra around room temperature., Comment: 9 pages, 4 figures

Published
2015
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33. Thermodynamics for practical kesterite photovoltaics

Author

Jackson, Adam, Walsh, Aron, Patterson, Darrell, and Peter, Laurence

Subjects
621.31
Abstract

Copper zinc tin sulfide (CZTS) is a photovoltaic absorber material used in thin-film devices. Research into the kesterite absorbers Cu2ZnSn(S1-xSex )4 has been particularly active in the last decade: this is motivated by the abundance of the constituent elements, which presents a long-term advantage over existing thin-film technologies including CIGS and CdTe. However, the efficiency of CZTS-based devices has been lower than expected and among other factors this is attributed to is the presence of secondary phases. In this thesis, a novel thermochemical model is developed for the mixed sulfur vapour phase that is present during the annealing of CZTS films. Temperature and pressure-dependent phase diagrams are then constructed for the Cu-Zn-Sn-S system from first-principles calculations within density-functional theory. While research-grade CZTS is produced in both low and high-pressure processes, it is found that the phase diagram is similar in both regimes except for the oxidation state of tin sulfide. The dominant ternary phase, of those modelled, is a monoclinic phase of Cu2 SnS3 . A small temperature/pressure envelope appears to exist in which this phase is unstable relative to CZTS and the binary phases. This potentially offers a route to copper-rich CZTS without the presence of ternary phases. Rapid, high-temperature annealing for industrial deployment appears to be feasible without decomposition of the kesterite, provided that an adequately high system pressure is maintained. This work demonstrates that with high-performance computing it is possible to explore the thermodynamic space around a quaternary compound before traditional thermochemical data has been obtained. The methodology developed here is applicable to other multi-component systems.

Published
2016

34. Metagames : the evolution of game-changing traits

Author

Jackson, Adam and Watson, Richard

Subjects
794.8
Abstract

Cooperative social behaviours are ubiquitous in nature and essential to biological theory, yet they present an apparent paradox since cooperators benefit others while potentially incurring a fitness cost. The standard resolution is that cooperation is evolutionarily stable if cooperative behaviours are positively assorted, so their benefits are directed at other cooperators, shifting the problem to explaining the presence of positive assortment. If we view individuals as playing an evolutionary game, then the evolution of assorting traits changes the rules of the game to allow for greater cooperation. This is one of many ways that individuals can evolve game-changing traits that modify their social niche, since social interactions occur in social environments that are in part the product of evolved traits. We investigate this by introducing a game-theoretic model of metagames where the evolution of individual strategies changes the social game. Because of mathematical equivalences between game-changing mechanisms and pay off matrix transformations, we can use metagames as a common framework to model the coevolution of social games and social conditions. Instead of simply identifying the conditions under which cooperation evolves, metagames explain how these conditions arise by identifying the circumstances under which the conditions for cooperation evolve. While positive assortment on social traits is necessary for cooperation to be stable, we show that alone it will only allow game-changing traits promoting cooperation to evolve when cooperation is already favoured. This is insuffi?cient to explain the evolution of assortment in the Prisoner's Dilemma. We find that much as assortment on social traits is crucial to the evolution of cooperation, assortment on game-changing traits is crucial to the evolution of social assortment. Because assortment on social and game-changing traits are connected, this assortment has been hidden in existing accounts. We are able to characterise the relationship between the two types of assortment, and show how assortment on game-changing traits can enable the evolution of social assortment. We can therefore explain the evolution of the conditions assumed necessary for the evolution of cooperation.

Published
2016

35. Medical marijuana firms left warming the bench; The companies entered the market first with eyes on recreational sales, but now they're last in line

Author

Jackson, Adam

Subjects
Medical marijuana -- Laws, regulations and rules, Chief executive officers -- Beliefs, opinions and attitudes, Marijuana industry -- Licensing, certification and accreditation, Consulting services -- Officials and employees, Government regulation, Business, Business, regional, New York. Marijuana Regulation and Taxation Act of 2021
Abstract

Byline: ADAM JACKSON When New York gave the sale and use of medical marijuana the green light, officially permitting it in 2014, the firms that vied for a spot as [...]

Published
2023

36. Biallelic CRELD1 variants cause a multisystem syndrome including neurodevelopmental phenotypes, cardiac dysrhythmias, and frequent infections.

Author

Jeffries, Lauren, primary, Mis, Emily K., additional, McWalter, Kirsty, additional, Donkervoort, Sandra, additional, Brodsky, Nina N., additional, Carpier, Jean-Marie, additional, Ji, Weizhen, additional, Ionita, Cristian, additional, Roy, Bhaskar, additional, Morrow, Jon S., additional, Darbinyan, Armine, additional, Iyer, Krishna, additional, Aul, Ritu B., additional, Banka, Siddharth, additional, Chao, Katherine R., additional, Cobbold, Laura, additional, Cohen, Stacey, additional, Custodio, Helena M., additional, Drummond-Borg, Margaret, additional, Elmslie, Frances, additional, Finanger, Erika, additional, Hainline, Bryan E., additional, Helbig, Ingo, additional, Hewson, Stacy, additional, Hu, Ying, additional, Jackson, Adam, additional, Josifova, Dragana, additional, Konstantino, Monica, additional, Leach, Meganne E., additional, Mak, Bryan, additional, McCormick, David, additional, McGee, Elisabeth, additional, Nelson, Stanley, additional, Nguyen, Joanne, additional, Nugent, Kimberly, additional, Ortega, Lucy, additional, Goodkin, Howard P., additional, Roeder, Elizabeth, additional, Roy, Sani, additional, Sapp, Katie, additional, Saade, Dimah, additional, Sisodiya, Sanjay M., additional, Stals, Karen, additional, Towner, Shelley, additional, Wilson, William, additional, Khokha, Mustafa K., additional, Bönnemann, Carsten G., additional, Lucas, Carrie L., additional, Lakhani, Saquib A., additional, Acosta, Maria T., additional, Adam, Margaret, additional, Adams, David R., additional, Agrawal, Pankaj B., additional, Alejandro, Mercedes E., additional, Alvey, Justin, additional, Amendola, Laura, additional, Andrews, Ashley, additional, Ashley, Euan A., additional, Azamian, Mahshid S., additional, Bacino, Carlos A., additional, Bademci, Guney, additional, Baker, Eva, additional, Balasubramanyam, Ashok, additional, Baldridge, Dustin, additional, Bale, Jim, additional, Bamshad, Michael, additional, Barbouth, Deborah, additional, Bayrak-Toydemir, Pinar, additional, Beck, Anita, additional, Beggs, Alan H., additional, Behrens, Edward, additional, Bejerano, Gill, additional, Bennet, Jimmy, additional, Berg-Rood, Beverly, additional, Bernstein, Jonathan A., additional, Berry, Gerard T., additional, Bican, Anna, additional, Bivona, Stephanie, additional, Blue, Elizabeth, additional, Bohnsack, John, additional, Bonnenmann, Carsten, additional, Bonner, Devon, additional, Botto, Lorenzo, additional, Boyd, Brenna, additional, Briere, Lauren C., additional, Brokamp, Elly, additional, Brown, Gabrielle, additional, Burke, Elizabeth A., additional, Burrage, Lindsay C., additional, Butte, Manish J., additional, Byers, Peter, additional, Byrd, William E., additional, Carey, John, additional, Carrasquillo, Olveen, additional, Peter Chang, Ta Chen, additional, Chanprasert, Sirisak, additional, Chao, Hsiao-Tuan, additional, Clark, Gary D., additional, Coakley, Terra R., additional, Cobban, Laurel A., additional, Cogan, Joy D., additional, Coggins, Matthew, additional, Cole, F Sessions, additional, Colley, Heather A., additional, Cooper, Cynthia M., additional, Craigen, William J., additional, Crouse, Andrew B., additional, Cunningham, Michael, additional, D'Souza, Precilla, additional, Dai, Hongzheng, additional, Dasari, Surendra, additional, Davids, Mariska, additional, Dayal, Jyoti G., additional, Deardorff, Matthew, additional, Dell'Angelica, Esteban C., additional, Dhar, Shweta U., additional, Dipple, Katrina, additional, Doherty, Daniel, additional, Dorrani, Naghmeh, additional, Douine, Emilie D., additional, Draper, David D., additional, Duncan, Laura, additional, Earl, Dawn, additional, Eckstein, David J., additional, Emrick, Lisa T., additional, Eng, Christine M., additional, Esteves, Cecilia, additional, Estwick, Tyra, additional, Falk, Marni, additional, Fernandez, Liliana, additional, Ferreira, Carlos, additional, Fieg, Elizabeth L., additional, Findley, Laurie C., additional, Fisher, Paul G., additional, Fogel, Brent L., additional, Forghani, Irman, additional, Fresard, Laure, additional, Gahl, William A., additional, Glass, Ian, additional, Godfrey, Rena A., additional, Golden-Grant, Katie, additional, Goldman, Alica M., additional, Goldstein, David B., additional, Grajewski, Alana, additional, Groden, Catherine A., additional, Gropman, Andrea L., additional, Gutierrez, Irma, additional, Hahn, Sihoun, additional, Hamid, Rizwan, additional, Hanchard, Neil A., additional, Hassey, Kelly, additional, Hayes, Nichole, additional, High, Frances, additional, Hing, Anne, additional, Hisama, Fuki M., additional, Holm, Ingrid A., additional, Hom, Jason, additional, Horike-Pyne, Martha, additional, Huang, Alden, additional, Huang, Yong, additional, Isasi, Rosario, additional, Jamal, Fariha, additional, Jarvik, Gail P., additional, Jarvik, Jeffrey, additional, Jayadev, Suman, additional, Johnston, Jean M., additional, Karaviti, Lefkothea, additional, Kelley, Emily G., additional, Kennedy, Jennifer, additional, Kiley, Dana, additional, Kohane, Isaac S., additional, Kohler, Jennefer N., additional, Krakow, Deborah, additional, Krasnewich, Donna M., additional, Kravets, Elijah, additional, Korrick, Susan, additional, Koziura, Mary, additional, Krier, Joel B., additional, Lalani, Seema R., additional, Lam, Byron, additional, Lam, Christina, additional, Lanpher, Brendan C., additional, Lanza, Ian R., additional, Lau, C Christopher, additional, LeBlanc, Kimberly, additional, Lee, Brendan H., additional, Lee, Hane, additional, Levitt, Roy, additional, Lewis, Richard A., additional, Lincoln, Sharyn A., additional, Liu, Pengfei, additional, Liu, Xue Zhong, additional, Longo, Nicola, additional, Loo, Sandra K., additional, Loscalzo, Joseph, additional, Maas, Richard L., additional, Macnamara, Ellen F., additional, MacRae, Calum A., additional, Maduro, Valerie V., additional, Majcherska, Marta M., additional, Christine V Malicdan, May, additional, Mamounas, Laura A., additional, Manolio, Teri A., additional, Mao, Rong, additional, Maravilla, Kenneth, additional, Markello, Thomas C., additional, Marom, Ronit, additional, Marth, Gabor, additional, Martin, Beth A., additional, Martin, Martin G., additional, Martínez-Agosto, Julian A., additional, Marwaha, Shruti, additional, McCauley, Jacob, additional, McCormack, Colleen E., additional, McCray, Alexa T., additional, Mefford, Heather, additional, Merritt, J Lawrence, additional, Might, Matthew, additional, Mirzaa, Ghayda, additional, Morava, Eva, additional, Moretti, Paolo M., additional, Morimoto, Marie, additional, Mulvihill, John J., additional, Murdock, David R., additional, Nakano-Okuno, Mariko, additional, Nath, Avi, additional, Nelson, Stan F., additional, Newman, John H., additional, Nicholas, Sarah K., additional, Nickerson, Deborah, additional, Nieves-Rodriguez, Shirley, additional, Novacic, Donna, additional, Oglesbee, Devin, additional, Orengo, James P., additional, Pace, Laura, additional, Pak, Stephen, additional, Pallais, J Carl, additional, Papp, Jeanette C., additional, Parker, Neil H., additional, Phillips, John A., additional, Posey, Jennifer E., additional, Potocki, Lorraine, additional, Pusey, Barbara N., additional, Quinlan, Aaron, additional, Raskind, Wendy, additional, Raja, Archana N., additional, Rao, Deepak A., additional, Renteria, Genecee, additional, Reuter, Chloe M., additional, Rives, Lynette, additional, Robertson, Amy K., additional, Rodan, Lance H., additional, Rosenfeld, Jill A., additional, Rosenwasser, Natalie, additional, Ruzhnikov, Maura, additional, Sacco, Ralph, additional, Sampson, Jacinda B., additional, Samson, Susan L., additional, Saporta, Mario, additional, Scott, C Ron, additional, Schaechter, Judy, additional, Schedl, Timothy, additional, Scott, Daryl A., additional, Sharma, Prashant, additional, Shin, Jimann, additional, Signer, Rebecca, additional, Sillari, Catherine H., additional, Silverman, Edwin K., additional, Sinsheimer, Janet S., additional, Sisco, Kathy, additional, Smith, Edward C., additional, Smith, Kevin S., additional, Solem, Emily, additional, Solnica-Krezel, Lilianna, additional, Stoler, Joan M., additional, Stong, Nicholas, additional, Sullivan, Jennifer A., additional, Sun, Angela, additional, Sutton, Shirley, additional, Sweetser, David A., additional, Sybert, Virginia, additional, Tabor, Holly K., additional, Tamburro, Cecelia P., additional, Tekin, Mustafa, additional, Telischi, Fred, additional, Thorson, Willa, additional, Tifft, Cynthia J., additional, Toro, Camilo, additional, Tran, Alyssa A., additional, Tucker, Brianna M., additional, Urv, Tiina K., additional, Vanderver, Adeline, additional, Velinder, Matt, additional, Viskochil, Dave, additional, Vogel, Tiphanie P., additional, Wahl, Colleen E., additional, Wallace, Stephanie, additional, Walley, Nicole M., additional, Walsh, Chris A., additional, Walker, Melissa, additional, Wambach, Jennifer, additional, Wan, Jijun, additional, Wang, Lee-Kai, additional, Wangler, Michael F., additional, Ward, Patricia A., additional, Wegner, Daniel, additional, Wener, Mark, additional, Wenger, Tara, additional, Perry, Katherine Wesseling, additional, Westerfield, Monte, additional, Wheeler, Matthew T., additional, Whitlock, Jordan, additional, Wolfe, Lynne A., additional, Woods, Jeremy D., additional, Yamamoto, Shinya, additional, Yang, John, additional, Yu, Guoyun, additional, Zastrow, Diane B., additional, Zhao, Chunli, additional, Zuchner, Stephan, additional, Ambrose, J.C., additional, Arumugam, P., additional, Baple, E.L., additional, Bleda, M., additional, Boardman-Pretty, F., additional, Boissiere, J.M., additional, Boustred, C.R., additional, Caulfield, M.J., additional, Chan, G.C., additional, Craig, C.E.H., additional, Daugherty, L.C., additional, de Burca, A., additional, Devereau, A., additional, Elgar, G., additional, Foulger, R.E., additional, Fowler, T., additional, FurióTarí, P., additional, Hackett, J.M., additional, Halai, D., additional, Hamblin, A., additional, Henderson, S., additional, Holman, J.E., additional, Hubbard, T.J.P., additional, Ibáñez, K., additional, Jackson, R., additional, Jones, L.J., additional, Kasperaviciute, D., additional, Kayikci, M., additional, Lahnstein, L., additional, Lawson, K., additional, Leigh, S.E.A., additional, Leong, I.U.S., additional, Lopez, F.J., additional, MaleadyCrowe, F., additional, Mason, J., additional, McDonagh, E.M., additional, Moutsianas, L., additional, Mueller, M., additional, Murugaesu, N., additional, Need, A.C., additional, Odhams, C.A., additional, Patch, C., additional, Perez-Gil, D., additional, Polychronopoulos, D., additional, Pullinger, J., additional, Rahim, T., additional, Rendon, A., additional, Riesgo-Ferreiro, P., additional, Rogers, T., additional, Ryten, M., additional, Savage, K., additional, Sawant, K., additional, Scott, R.H., additional, Siddiq, A., additional, Sieghart, A., additional, Smedley, D., additional, Smith, K.R., additional, Sosinsky, A., additional, Spooner, W., additional, Stevens, H.E., additional, Stuckey, A., additional, Sultana, R., additional, Thomas, E.R.A., additional, Thompson, S.R., additional, Tucci, A., additional, Walsh, E., additional, Watters, S.A., additional, Welland, M.J., additional, Williams, E., additional, and Witkowska, K., additional

Published
2023
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39. Ab initio thermodynamic model of Cu$_2$ZnSnS$_4$

Author

Jackson, Adam J. and Walsh, Aron

Subjects
Condensed Matter - Materials Science
Abstract

Thin-film solar cells based on the semiconductor Cu$_2$ZnSnS$_4$ (CZTS) are a promising candidate for Terawatt-scale renewable energy generation. While CZTS is composed of earth abundant and non-toxic elements, arranged in the kesterite crystal structure, there is a synthetic challenge to produce high-quality stoichiometric materials over large areas. We calculate the thermodynamic potentials of CZTS and its elemental and binary components based on energetic and vibrational data computed using density functional theory. These chemical potentials are combined to produce a thermodynamic model for the stability of CZTS under arbitrary temperatures and pressures, which provide insights into the materials chemistry. CZTS was shown to be thermodynamically stable with respect to its component elements and their major binary phases binaries under modest partial pressure of sulfur and temperatures below 1100K. Under near-vacuum conditions with sulfur partial pressures below 1 Pa decomposition into binaries including solid SnS becomes favourable, with a strongly temperature-dependent stability window., Comment: Thermodynamic model programs and supporting data are available at https://github.com/WMD-Bath/CZTS-model

Published
2014
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40. Oxidation of GaN: An ab initio thermodynamic approach

Author

Jackson, Adam J. and Walsh, Aron

Subjects
Condensed Matter - Materials Science
Abstract

GaN is a wide-bandgap semiconductor used in high-efficiency LEDs and solar cells. The solid is produced industrially at high chemical purities by deposition from a vapour phase, and oxygen may be included at this stage. Oxidation represents a potential path for tuning its properties without introducing more exotic elements or extreme processing conditions. In this work, ab initio computational methods are used to examine the energy potentials and electronic properties of different extents of oxidation in GaN. Solid-state vibrational properties of Ga, GaN, Ga2O3 and a single substitutional oxygen defect have been studied using the harmonic approximation with supercells. A thermodynamic model is outlined which combines the results of ab initio calculations with data from experimental literature. This model allows free energies to be predicted for arbitrary reaction conditions within a wide process envelope. It is shown that complete oxidation is favourable for all industrially-relevant conditions, while the formation of defects can be opposed by the use of high temperatures and a high N2:O2 ratio.

Published
2013
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41. Clinical, genetic, epidemiologic, evolutionary, and functional delineation of TSPEAR-related autosomal recessive ectodermal dysplasia 14

Author

Jackson, Adam, primary, Lin, Sheng-Jia, additional, Jones, Elizabeth A., additional, Chandler, Kate E., additional, Orr, David, additional, Moss, Celia, additional, Haider, Zahra, additional, Ryan, Gavin, additional, Holden, Simon, additional, Harrison, Mike, additional, Burrows, Nigel, additional, Jones, Wendy D., additional, Loveless, Mary, additional, Petree, Cassidy, additional, Stewart, Helen, additional, Low, Karen, additional, Donnelly, Deirdre, additional, Lovell, Simon, additional, Drosou, Konstantina, additional, Varshney, Gaurav K., additional, Banka, Siddharth, additional, Ambrose, J.C., additional, Arumugam, P., additional, Bevers, R., additional, Bleda, M., additional, Boardman-Pretty, F., additional, Boustred, C.R., additional, Brittain, H., additional, Brown, M.A., additional, Caulfield, M.J., additional, Chan, G.C., additional, Giess, A., additional, Griffin, J.N., additional, Hamblin, A., additional, Henderson, S., additional, Hubbard, T.J.P., additional, Jackson, R., additional, Jones, L.J., additional, Kasperaviciute, D., additional, Kayikci, M., additional, Kousathanas, A., additional, Lahnstein, L., additional, Lakey, A., additional, Leigh, S.E.A., additional, Leong, I.U.S., additional, Lopez, F.J., additional, Maleady-Crowe, F., additional, McEntagart, M., additional, Minneci, F., additional, Mitchell, J., additional, Moutsianas, L., additional, Mueller, M., additional, Murugaesu, N., additional, Need, A.C., additional, O‘Donovan, P., additional, Odhams, C.A., additional, Patch, C., additional, Perez-Gil, D., additional, Pereira, M.B., additional, Pullinger, J., additional, Rahim, T., additional, Rendon, A., additional, Rogers, T., additional, Savage, K., additional, Sawant, K., additional, Scott, R.H., additional, Siddiq, A., additional, Sieghart, A., additional, Smith, S.C., additional, Sosinsky, A., additional, Stuckey, A., additional, Tanguy, M., additional, Taylor Tavares, A.L., additional, Thomas, E.R.A., additional, Thompson, S.R., additional, Tucci, A., additional, Welland, M.J., additional, Williams, E., additional, Witkowska, K., additional, Wood, S.M., additional, Zarowiecki, M., additional, Riess, Olaf, additional, Haack, Tobias B., additional, Graessner, Holm, additional, Zurek, Birte, additional, Ellwanger, Kornelia, additional, Ossowski, Stephan, additional, Demidov, German, additional, Sturm, Marc, additional, Schulze-Hentrich, Julia M., additional, Schüle, Rebecca, additional, Kessler, Christoph, additional, Wayand, Melanie, additional, Synofzik, Matthis, additional, Wilke, Carlo, additional, Traschütz, Andreas, additional, Schöls, Ludger, additional, Hengel, Holger, additional, Heutink, Peter, additional, Brunner, Han, additional, Scheffer, Hans, additional, Hoogerbrugge, Nicoline, additional, Hoischen, Alexander, additional, ’t Hoen, Peter A.C., additional, Vissers, Lisenka E.L.M., additional, Gilissen, Christian, additional, Steyaert, Wouter, additional, Sablauskas, Karolis, additional, de Voer, Richarda M., additional, Kamsteeg, Erik-Jan, additional, van de Warrenburg, Bart, additional, van Os, Nienke, additional, Paske, Iris te, additional, Janssen, Erik, additional, de Boer, Elke, additional, Steehouwer, Marloes, additional, Yaldiz, Burcu, additional, Kleefstra, Tjitske, additional, Brookes, Anthony J., additional, Veal, Colin, additional, Gibson, Spencer, additional, Wadsley, Marc, additional, Mehtarizadeh, Mehdi, additional, Riaz, Umar, additional, Warren, Greg, additional, Dizjikan, Farid Yavari, additional, Shorter, Thomas, additional, Töpf, Ana, additional, Straub, Volker, additional, Bettolo, Chiara Marini, additional, Specht, Sabine, additional, Clayton-Smith, Jill, additional, Alexander, Elizabeth, additional, Jackson, Adam, additional, Faivre, Laurence, additional, Thauvin, Christel, additional, Vitobello, Antonio, additional, Denommé-Pichon, Anne-Sophie, additional, Duffourd, Yannis, additional, Tisserant, Emilie, additional, Bruel, Ange-Line, additional, Peyron, Christine, additional, Pélissier, Aurore, additional, Beltran, Sergi, additional, Gut, Ivo Glynne, additional, Laurie, Steven, additional, Piscia, Davide, additional, Matalonga, Leslie, additional, Papakonstantinou, Anastasios, additional, Bullich, Gemma, additional, Corvo, Alberto, additional, Garcia, Carles, additional, Fernandez-Callejo, Marcos, additional, Hernández, Carles, additional, Picó, Daniel, additional, Paramonov, Ida, additional, Lochmüller, Hanns, additional, Gumus, Gulcin, additional, Bros-Facer, Virginie, additional, Rath, Ana, additional, Hanauer, Marc, additional, Olry, Annie, additional, Lagorce, David, additional, Havrylenko, Svitlana, additional, Izem, Katia, additional, Rigour, Fanny, additional, Stevanin, Giovanni, additional, Durr, Alexandra, additional, Davoine, Claire-Sophie, additional, Guillot-Noel, Léna, additional, Heinzmann, Anna, additional, Coarelli, Giulia, additional, Bonne, Gisèle, additional, Evangelista, Teresinha, additional, Allamand, Valérie, additional, Nelson, Isabelle, additional, Ben Yaou, Rabah, additional, Metay, Corinne, additional, Eymard, Bruno, additional, Cohen, Enzo, additional, Atalaia, Antonio, additional, Stojkovic, Tanya, additional, Macek, Milan, additional, Turnovec, Marek, additional, Thomasová, Dana, additional, Kremliková, Radka Pourová, additional, Franková, Vera, additional, Havlovicová, Markéta, additional, Kremlik, Vlastimil, additional, Parkinson, Helen, additional, Keane, Thomas, additional, Spalding, Dylan, additional, Senf, Alexander, additional, Robinson, Peter, additional, Danis, Daniel, additional, Robert, Glenn, additional, Costa, Alessia, additional, Patch, Christine, additional, Hanna, Mike, additional, Houlden, Henry, additional, Reilly, Mary, additional, Vandrovcova, Jana, additional, Muntoni, Francesco, additional, Zaharieva, Irina, additional, Sarkozy, Anna, additional, Timmerman, Vincent, additional, Baets, Jonathan, additional, Van de Vondel, Liedewei, additional, Beijer, Danique, additional, de Jonghe, Peter, additional, Nigro, Vincenzo, additional, Banfi, Sandro, additional, Torella, Annalaura, additional, Musacchia, Francesco, additional, Piluso, Giulio, additional, Ferlini, Alessandra, additional, Selvatici, Rita, additional, Rossi, Rachele, additional, Neri, Marcella, additional, Aretz, Stefan, additional, Spier, Isabel, additional, Sommer, Anna Katharina, additional, Peters, Sophia, additional, Oliveira, Carla, additional, Pelaez, Jose Garcia, additional, Matos, Ana Rita, additional, José, Celina São, additional, Ferreira, Marta, additional, Gullo, Irene, additional, Fernandes, Susana, additional, Garrido, Luzia, additional, Ferreira, Pedro, additional, Carneiro, Fátima, additional, Swertz, Morris A., additional, Johansson, Lennart, additional, van der Velde, Joeri K., additional, van der Vries, Gerben, additional, Neerincx, Pieter B., additional, Roelofs-Prins, Dieuwke, additional, Köhler, Sebastian, additional, Metcalfe, Alison, additional, Verloes, Alain, additional, Drunat, Séverine, additional, Rooryck, Caroline, additional, Trimouille, Aurelien, additional, Castello, Raffaele, additional, Morleo, Manuela, additional, Pinelli, Michele, additional, Varavallo, Alessandra, additional, De la Paz, Manuel Posada, additional, Sánchez, Eva Bermejo, additional, Martín, Estrella López, additional, Delgado, Beatriz Martínez, additional, Alonso García de la Rosa, F. Javier, additional, Ciolfi, Andrea, additional, Dallapiccola, Bruno, additional, Pizzi, Simone, additional, Radio, Francesca Clementina, additional, Tartaglia, Marco, additional, Renieri, Alessandra, additional, Benetti, Elisa, additional, Balicza, Peter, additional, Molnar, Maria Judit, additional, Maver, Ales, additional, Peterlin, Borut, additional, Münchau, Alexander, additional, Lohmann, Katja, additional, Herzog, Rebecca, additional, Pauly, Martje, additional, Macaya, Alfons, additional, Marcé-Grau, Anna, additional, Osorio, Andres Nascimiento, additional, Natera de Benito, Daniel, additional, Thompson, Rachel, additional, Polavarapu, Kiran, additional, Beeson, David, additional, Cossins, Judith, additional, Rodriguez Cruz, Pedro M., additional, Hackman, Peter, additional, Johari, Mridul, additional, Savarese, Marco, additional, Udd, Bjarne, additional, Horvath, Rita, additional, Capella, Gabriel, additional, Valle, Laura, additional, Holinski-Feder, Elke, additional, Laner, Andreas, additional, Steinke-Lange, Verena, additional, Schröck, Evelin, additional, and Rump, Andreas, additional

Published
2023
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44. The clinical and molecular spectrum of the KDM6B-related neurodevelopmental disorder

Author

Rots, Dmitrijs, primary, Jakub, Taryn E., additional, Keung, Crystal, additional, Jackson, Adam, additional, Banka, Siddharth, additional, Pfundt, Rolph, additional, de Vries, Bert B.A., additional, van Jaarsveld, Richard H., additional, Hopman, Saskia M.J., additional, van Binsbergen, Ellen, additional, Valenzuela, Irene, additional, Hempel, Maja, additional, Bierhals, Tatjana, additional, Kortüm, Fanny, additional, Lecoquierre, Francois, additional, Goldenberg, Alice, additional, Hertz, Jens Michael, additional, Andersen, Charlotte Brasch, additional, Kibæk, Maria, additional, Prijoles, Eloise J., additional, Stevenson, Roger E., additional, Everman, David B., additional, Patterson, Wesley G., additional, Meng, Linyan, additional, Gijavanekar, Charul, additional, De Dios, Karl, additional, Lakhani, Shenela, additional, Levy, Tess, additional, Wagner, Matias, additional, Wieczorek, Dagmar, additional, Benke, Paul J., additional, Lopez Garcia, María Soledad, additional, Perrier, Renee, additional, Sousa, Sergio B., additional, Almeida, Pedro M., additional, Simões, Maria José, additional, Isidor, Bertrand, additional, Deb, Wallid, additional, Schmanski, Andrew A., additional, Abdul-Rahman, Omar, additional, Philippe, Christophe, additional, Bruel, Ange-Line, additional, Faivre, Laurence, additional, Vitobello, Antonio, additional, Thauvin, Christel, additional, Smits, Jeroen J., additional, Garavelli, Livia, additional, Caraffi, Stefano G., additional, Peluso, Francesca, additional, Davis-Keppen, Laura, additional, Platt, Dylan, additional, Royer, Erin, additional, Leeuwen, Lisette, additional, Sinnema, Margje, additional, Stegmann, Alexander P.A., additional, Stumpel, Constance T.R.M., additional, Tiller, George E., additional, Bosch, Daniëlle G.M., additional, Potgieter, Stephanus T., additional, Joss, Shelagh, additional, Splitt, Miranda, additional, Holden, Simon, additional, Prapa, Matina, additional, Foulds, Nicola, additional, Douzgou, Sofia, additional, Puura, Kaija, additional, Waltes, Regina, additional, Chiocchetti, Andreas G., additional, Freitag, Christine M., additional, Satterstrom, F. Kyle, additional, De Rubeis, Silvia, additional, Buxbaum, Joseph, additional, Gelb, Bruce D., additional, Branko, Aleksic, additional, Kushima, Itaru, additional, Howe, Jennifer, additional, Scherer, Stephen W., additional, Arado, Alessia, additional, Baldo, Chiara, additional, Patat, Olivier, additional, Bénédicte, Demeer, additional, Lopergolo, Diego, additional, Santorelli, Filippo M., additional, Haack, Tobias B., additional, Dufke, Andreas, additional, Bertrand, Miriam, additional, Falb, Ruth J., additional, Rieß, Angelika, additional, Krieg, Peter, additional, Spranger, Stephanie, additional, Bedeschi, Maria Francesca, additional, Iascone, Maria, additional, Josephi-Taylor, Sarah, additional, Roscioli, Tony, additional, Buckley, Michael F., additional, Liebelt, Jan, additional, Dagli, Aditi I., additional, Aten, Emmelien, additional, Hurst, Anna C.E., additional, Hicks, Alesha, additional, Suri, Mohnish, additional, Aliu, Ermal, additional, Naik, Sunil, additional, Sidlow, Richard, additional, Coursimault, Juliette, additional, Nicolas, Gaël, additional, Küpper, Hanna, additional, Petit, Florence, additional, Ibrahim, Veyan, additional, Top, Deniz, additional, Di Cara, Francesca, additional, Louie, Raymond J., additional, Stolerman, Elliot, additional, Brunner, Han G., additional, Vissers, Lisenka E.L.M., additional, Kramer, Jamie M., additional, and Kleefstra, Tjitske, additional

Published
2023
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45. Blade tip heat transfer measurements in a shroudless, transonic, high pressure turbine

Author

Jackson, Adam James

Subjects
621.406015367
Abstract

To improve the performance of aero-engines manufacturers strive to increase the inlet temperature to the high pressure turbine. The components that are exposed to the hot gas - particularly the over-tip casing and blade tips of shroud less turbines - are vulnerable to heat damage. A previous investigation using the Oxford Rotor Facility demonstrated that a backwards facing casing step - located 20 % of high pressure blade axial chord upstream of the leading edge of the rotor - could mitigate the significant convective heat loads that the over-tip casing must withstand. This thesis describes an investigation into the effect ofthe aforementioned casing step on blade tip heat transfer rates. A second investigation, to determine the effect of the tip gap size on blade tip heat transfer rates, is also reported. These investigations necessitated the acquisition of two sets of experimental measurements. In both instances the casing step was present. The time resolved heat transfer rate data was obtained using thirty- five thin film gauges distributed over three blade tips. A small number of blade relative aerodynamic measurements were also performed. The aerodynamic measurements were valuable in helping to elucidate the mechanisms responsible for the measured changes of heat transfer rate. In order to investigate the effect of the tip gap size it was necessary to modify the over-tip casing before the second set of measurements were made. Detailed measurements of the over-tip casing were made before and after the modifications. It was shown that the mod- ifications reduced the mean tip gap to approximately two thirds ofthe baseline size. Computational fluid dynamics calculations were performed to complement the predomi- nantlyexperimental investigations. The predictive work was undertaken in order to obtain further insight into the mechanisms underpinning the changes of heat transfer rate that were observed in the experiments.

Published
2011

46. Effect of helicases on the instability of CTG・CAG trinucleotide repeat arrays in the escherichia coli chromosome

Author

Jackson, Adam and Leach, David

Subjects
572.8, trinucleotide repeat, TNR, genetic instability, pseudo-hairpins, genetic assay, UvrD, arrested replication fork, helicase
Abstract

A trinucleotide repeat (TNR) is a 3 base pair (bp) DNA sequence tandemly repeated in an array. In humans, TNR sequences have been found to be associated with at least 14 severe neurological diseases including Huntington disease, myotonic dystrophy and several of the spinocerebellar ataxias. Such diseases are caused by an expansion of the repeat sequence beyond a threshold length and are characterized by non-Mendelian patterns of inheritance which lead to genetic anticipation. Although the mechanism of the genetic instability in these arrays is not yet fully understood, various models have been suggested based on the in vitro observation that TNR sequences can form secondary structures such as pseudo-hairpins. In order to investigate the mechanisms responsible for instability of TNR sequences, a study was carried out on Escherichia coli cells in which TNR arrays had been integrated into the chromosomal lacZ gene. This genetic assay was used to identify proteins and pathways involved in deletion and/or expansion instability. Deletion instability was clearly dependent on orientation of the TNR sequence relative to the origin of replication. Interestingly, it was found that expansion instability is not dependent on the orientation of the repeat array relative to the origin of replication. The replication fork reversal pathway and the RecFOR mediated gap repair pathway were found to have no statistically significant influence on the instability of TNR arrays. However, the protein UvrD was found to affect the deletion instability of TNR sequences. The roles of key helicase genes were investigated for their effects on instability of chromosomal CTG•CAG repeats. Mutation of the rep gene increased deletion in the CTG leading-strand orientation of the repeat array, and expansion in both orientations - destabilizing the TNR array. RecQ helicase was found to have a significant effect on TNR instability in the orientation in which CAG repeats were present on the leading-strand relative to the origin of replication. Mutation of the recQ gene severely limited the number of expansion events in this orientation, whilst having no effect on deletions. This dependence of expansions on RecQ was lost in a rep mutant strain. In a rep mutant expansions were shown to be partially dependent on the DinG helicase. All together, these results suggest a model of TNR instability in which expansions are due to events occurring at either the leading or lagging strand of an arrested replication fork, facilitated by helicase action. The identity of the helicase implicated is determined by the nature of the arrest.

Published
2010

47. Bi-allelic genetic variants in the translational GTPases GTPBP1 and GTPBP2 cause a distinct identical neurodevelopmental syndrome

Author

Hannah, Michael G., Bugiardini, Enrico, Bertini, Enrico, Kriouile, Yamna, El-Khorassani, Mohamed, Aguennouz, Mhammed, Groppa, Stanislav, Karashova, Blagovesta M., Goraya, Jatinder S., Sultan, Tipu, Avdjieva, Daniela, Kathom, Hadil, Tincheva, Radka, Banu, Selina, Veggiotti, Pierangelo, Verrotti, Alberto, Lanari, Marcello, Savasta, Salvatore, Macaya, Alfons, Garavaglia, Barbara, Borgione, Eugenia, Papacostas, Savvas, Vikelis, Michail, Chelban, Viorica, Kaiyrzhanov, Rauan, Cortese, Andrea, Sullivan, Roisin, Papanicolaou, Eleni Z., Dardiotis, Efthymios, Maqbool, Shazia, Ibrahim, Shahnaz, Kirmani, Salman, Rana, Nuzhat N., Atawneh, Osama, Lim, Shen-Yang, Zuccotti, Gian V., Marseglia, Gian L., Esposito, Susanna, Shaikh, Farooq, Cogo, Paola, Corsello, Giovanni, Mangano, Salvatore, Nardello, Rosaria, Mangano, Donato, Scardamaglia, Annarita, Koutsis, George, Scuderi, Carmela, Ferrara, Pietro, Morello, Giovanna, Zollo, Massimo, Berni-Canani, Roberto, Terracciano, Luigi M., Sisto, Antonio, Di Fabio, Sandra, Strano, Federica, Scorrano, Giovanna, Di Bella, Saverio, Di Francesco, Ludovica, Manizha, Ganieva, Isrofilov, Maksud, Guliyeva, Ulviyya, Salayev, Kamran, Khachatryan, Samson, Xiromerisiou, Georgia, Spanaki, Cleanthe, Fiorillo, Chiara, Iacomino, Michele, Gaudio, Eugenio, Munell, Francina, Gagliano, Antonella, Jan, Farida, Chimenz, Roberto, Gitto, Eloisa, Iughetti, Lorenzo, Di Rosa, Gabriella, Maghnie, Mohamad, Pettoello-Mantovani, Massimo, Gupta, Neerja, Kabra, Madhulika, Benrhouma, Hanene, Tazir, Meriem, Bottone, Gabriella, Farello, Giovanni, Delvecchio, Maurizio, Di-Donato, Giulio, Obeid, Makram, Bakhtadze, Sophia, Saadi, Nebal W., Miraglia-Del-Giudice, Michele, Maccarone, Rita, Zaki, Maha S., Triki, Chahnez C., Kara, Majdi, Karimiani, Ehsan G., Salih, Ahmed M., Ramenghi, Luca A., Seri, Marco, Di-Falco, Giovanna, Mandarà, Luana, Barrano, Giuseppe, Elisa, Maurizio, Cherubini, Enrico, Operto, Francesca F., Valenzise, Mariella, Cattaneo, Antonino, Zazzeroni, Francesca, Alesse, Edoardo, Matricardi, Sara, Zafar, Faisal, Ullah, Ehsan, Afzal, Erum, Rahman, Fatima, Ahmed, Muhammad M., Parisi, Pasquale, Spalice, Alberto, De Filippo, Maria, Licari, Amelia, Trebbi, Edoardo, Romano, Ferdinando, Heimer, Gali, Al-Khawaja, Issam, Al-Mutairi, Fuad, Alkuraya, Fowzan S., Rizig, Mie, Shashkin, Chingiz, Zharkynbekova, Nazira, Koneyev, Kairgali, Salpietro, Vincenzo, Maroofian, Reza, Wangen, Jamie, Ciolfi, Andrea, Barresi, Sabina, Efthymiou, Stephanie, Lamaze, Angelique, Aughey, Gabriel N., Al Mutairi, Fuad, Rad, Aboulfazl, Rocca, Clarissa, Calì, Elisa, Accogli, Andrea, Zara, Federico, Striano, Pasquale, Mojarrad, Majid, Tariq, Huma, Giacopuzzi, Edoardo, Taylor, Jenny C., Oprea, Gabriela, Skrahina, Volha, Rehman, Khalil Ur, Abd Elmaksoud, Marwa, Bassiony, Mahmoud, El Said, Huda G., Abdel-Hamid, Mohamed S., Al Shalan, Maha, Seo, Gohun, Kim, Sohyun, Lee, Hane, Khang, Rin, Issa, Mahmoud Y., Elbendary, Hasnaa M., Rafat, Karima, Marinakis, Nikolaos M., Traeger-Synodinos, Joanne, Ververi, Athina, Sourmpi, Mara, Eslahi, Atieh, Khadivi Zand, Farhad, Beiraghi Toosi, Mehran, Babaei, Meisam, Jackson, Adam, Bertoli-Avella, Aida, Pagnamenta, Alistair T., Niceta, Marcello, Battini, Roberta, Corsello, Antonio, Leoni, Chiara, Chiarelli, Francesco, Dallapiccola, Bruno, Faqeih, Eissa Ali, Tallur, Krishnaraya K., Alfadhel, Majid, Alobeid, Eman, Maddirevula, Sateesh, Mankad, Kshitij, Banka, Siddharth, Ghayoor-Karimiani, Ehsan, Tartaglia, Marco, Chung, Wendy K., Green, Rachel, Jepson, James E.C., and Houlden, Henry

Published
2024
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49. Rare EIF4A2 variants are associated with a neurodevelopmental disorder characterized by intellectual disability, hypotonia, and epilepsy

Author

Paul, Maimuna S., primary, Duncan, Anna R., additional, Genetti, Casie A., additional, Pan, Hongling, additional, Jackson, Adam, additional, Grant, Patricia E., additional, Shi, Jiahai, additional, Pinelli, Michele, additional, Brunetti-Pierri, Nicola, additional, Garza-Flores, Alexandra, additional, Shahani, Dave, additional, Saneto, Russell P., additional, Zampino, Giuseppe, additional, Leoni, Chiara, additional, Agolini, Emanuele, additional, Novelli, Antonio, additional, Blümlein Tobias B. Haack, Ulrike, additional, Heinritz, Wolfram, additional, Matzker, Eva, additional, Alhaddad, Bader, additional, Jamra, Rami Abou, additional, Bartolomaeus, Tobias, additional, AlHamdan, Saber, additional, Carapito, Raphael, additional, Isidor, Bertrand, additional, Bahram, Seiamak, additional, Ritter, Alyssa, additional, Izumi, Kosuke, additional, Shakked, Ben Pode, additional, Barel, Ortal, additional, Ben Zeev, Bruria, additional, Begtrup, Amber, additional, Carere, Deanna Alexis, additional, Mullegama, Sureni V., additional, Palculict, Timothy Blake, additional, Calame, Daniel G., additional, Schwan, Katharina, additional, Aycinena, Alicia R.P., additional, Traberg, Rasa, additional, Douzgou, Sofia, additional, Pirt, Harrison, additional, Ismayilova, Naila, additional, Banka, Siddharth, additional, Chao, Hsiao-Tuan, additional, and Agrawal, Pankaj B., additional

Published
2023
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50. Interpreting artefactual deposition in East Mediterranean and Near Eastern archaeology

Author

Jackson, Adam

Subjects
930.1
Abstract

This thesis is the outcome of a realisation that, within the East Mediterranean and Near East region, archaeological reconstructions of past societies and of major socio-political and economic transformations are often seriously limited by theoretical and practical shortcomings in the collection, analysis and interpretation of settlement data. In particular, there is a marked failure to account for site formation processes in the interpretation of artefacts and contexts, which is exacerbated by a failure to appreciate the limitations of the functionalism that is intrinsic to archaeological classifications and approaches. Chapter 2 begins with a review of the history of site formation research and a discussion of some of the biases in this research. The discussion includes a critique of the functionalist tenor of much of the extant work that employs modern values in the estimation of the utility and value of artefacts and materials. This is followed in Chapter 3 by a further critique of past and current theoretical frameworks that have informed archaeological approaches to the use and abandonment of space. Special emphasis is placed in the meanings and associations attached to artefacts and to their treatment on deposition. Chapter 4 outlines a method for the contextual analysis of artefactual deposition. Chapters 5, 6 and 7 comprise analyses of three case study sites that are used to illustrate the contention that archaeological interpretations of settlement space, which are founded on the assumption of in situ deposition and of function, are suspect. It is argued that the examination of the differential treatment of artefacts and of contexts at their abandonment is a more fruitful avenue of investigation. Each of the study sites, while being unique, is considered as representative of other archaeological situations involving burnt open settlements, circumscribed dense built environments and eroded ephemeral occupations. In Chapter 8, discussion focuses on the implications of this study for wider archaeological understandings of cultures and socio-cultural change. A series of well-known sites and studies from the East Mediterranean and Near East region are briefly considered in the light of the conclusion that the operation of formation processes has a profound effect on the character of the settlement record and, consequently, on archaeological reconstructions of past societies.

Published
2003

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