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38 results on '"National Research Foundation Singapore"'

1. Identification of constrained sequence elements across 239 primate genomes

Author: Natural Environment Research Council (UK), UK Research and Innovation, National Human Genome Research Institute (US), Fundación la Caixa, Vienna Science and Technology Fund, European Commission, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Fonds de la Recherche Scientifique (Fédération Wallonie-Bruxelles), Fundação de Amparo à Pesquisa do Estado do Amazonas, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), German Research Foundation, Ministry of Science and Technology of Vietnam, Agencia Estatal de Investigación (España), Generalitat de Catalunya, Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs, Wenner-Gren Foundation, Leakey Foundation, National Science Foundation (US), National Geographic Society, National Institute on Aging (US), Swedish Research Council, National Research Foundation Singapore, European Research Council, Ministerio de Ciencia e Innovación (España), Ministerio de Ciencia, Innovación y Universidades (España), Kuderna, Lukas F. K. [0000-0002-9992-9295], Kuhlwilm, Martin [0000-0002-0115-1797], Valenzuela, Alejandro [0000-0001-6120-6246], Juan, David [0000-0003-1912-9667], Lizano, Esther [0000-0003-3304-9807], Navarro, Arcadi [0000-0003-2162-8246], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Kuderna, Lukas F. K., Ulirsch, Jacob C., Rashid, Sabrina, Ameen, Mohamed, Sundaram, Laksshman, Hickey, Glenn, Cox, Anthony J., Gao, Hong, Kumar, Arvind, Aguet, Francois, Christmas, Matthew J., Clawson, Hiram, Haeussler, Maximilian, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, Vries, Dorien de, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., Melo, Fabiano R. de, Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, Silva, Maria N. F. da, Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M. D., Karakikes, Ioannis, Wang, Kevin C., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Siepel, Adam, Kundaje, Anshul, Paten, Benedict, Lindblad-Toh, Kerstin, Rogers, Jeffrey, Marqués-Bonet, Tomàs, Farh, Kyle Kai-How, Natural Environment Research Council (UK), UK Research and Innovation, National Human Genome Research Institute (US), Fundación la Caixa, Vienna Science and Technology Fund, European Commission, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Fonds de la Recherche Scientifique (Fédération Wallonie-Bruxelles), Fundação de Amparo à Pesquisa do Estado do Amazonas, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), German Research Foundation, Ministry of Science and Technology of Vietnam, Agencia Estatal de Investigación (España), Generalitat de Catalunya, Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs, Wenner-Gren Foundation, Leakey Foundation, National Science Foundation (US), National Geographic Society, National Institute on Aging (US), Swedish Research Council, National Research Foundation Singapore, European Research Council, Ministerio de Ciencia e Innovación (España), Ministerio de Ciencia, Innovación y Universidades (España), Kuderna, Lukas F. K. [0000-0002-9992-9295], Kuhlwilm, Martin [0000-0002-0115-1797], Valenzuela, Alejandro [0000-0001-6120-6246], Juan, David [0000-0003-1912-9667], Lizano, Esther [0000-0003-3304-9807], Navarro, Arcadi [0000-0003-2162-8246], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Kuderna, Lukas F. K., Ulirsch, Jacob C., Rashid, Sabrina, Ameen, Mohamed, Sundaram, Laksshman, Hickey, Glenn, Cox, Anthony J., Gao, Hong, Kumar, Arvind, Aguet, Francois, Christmas, Matthew J., Clawson, Hiram, Haeussler, Maximilian, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, Vries, Dorien de, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., Melo, Fabiano R. de, Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, Silva, Maria N. F. da, Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M. D., Karakikes, Ioannis, Wang, Kevin C., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Siepel, Adam, Kundaje, Anshul, Paten, Benedict, Lindblad-Toh, Kerstin, Rogers, Jeffrey, Marqués-Bonet, Tomàs, and Farh, Kyle Kai-How
Abstract: Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3,4,5,6,7,8,9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.
Published: 2024

2. Assigning the unassigned: A signature-based classification of rDNA metabarcodes reveals new deep-sea diversity

Author: Swiss National Science Foundation, Norwegian Offshore Directorate, National University of Singapore, National Research Foundation Singapore, Agencia Estatal de Investigación (España), Barrenechea, Inés, Nguyen, Ngoc-Loi, Greco, Mattia, Koh Siang, Tan, Pawlowski, Jan, Swiss National Science Foundation, Norwegian Offshore Directorate, National University of Singapore, National Research Foundation Singapore, Agencia Estatal de Investigación (España), Barrenechea, Inés, Nguyen, Ngoc-Loi, Greco, Mattia, Koh Siang, Tan, and Pawlowski, Jan
Abstract: Environmental DNA metabarcoding reveals a vast genetic diversity of marine eukaryotes. Yet, most of the metabarcoding data remain unassigned due to the paucity of reference databases. This is particularly true for the deep-sea meiofauna and eukaryotic microbiota, whose hidden diversity is largely unexplored. Here, we tackle this issue by using unique DNA signatures to classify unknown metabarcodes assigned to deep-sea foraminifera. We analyzed metabarcoding data obtained from 311 deep-sea sediment samples collected in the Clarion-Clipperton Fracture Zone, an area of potential polymetallic nodule exploitation in the Eastern Pacific Ocean. Using the signatures designed in the 37F hypervariable region of the 18S rRNA gene, we were able to classify 802 unassigned metabarcodes into 61 novel lineages, which have been placed in 27 phylogenetic clades. The comparison of new lineages with other foraminiferal datasets shows that most novel lineages are widely distributed in the deep sea. Five lineages are also present in the shallow-water datasets; however, phylogenetic analysis of these lineages separates deep-sea and shallow-water metabarcodes except in one case. While the signature-based classification does not solve the problem of gaps in reference databases, this taxonomy-free approach provides insight into the distribution and ecology of deep-sea species represented by unassigned metabarcodes, which could be useful in future applications of metabarcoding for environmental monitoring
Published: 2024

3. Self-testing of a single quantum system from theory to experiment

Author: Universidad de Sevilla. Departamento de Física Aplicada II, Universidad de Sevilla. FQM239: Fundamentos de Mecánica Cuántica, National Natural Science Foundation of China, Universidad de Sevilla, European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER), Ministerio de Economia, Industria y Competitividad (MINECO). España, Ministerio de Ciencia, Innovación y Universidades (MICINN). España, Ministry of Education, Singapore, National Research Foundation Singapore, Department of Energy. United States, Institute for Quantum Information and Matter, Belgian Fonds pour la Formation à la Recherche, Hu, Xiao-Min, Xie, Yi, Arora, Atul Singh, Ai, Ming-Zhong, Bharti, Kishor, Zhang, Jie, Wu, Wei, Chen, Ping Xing, Cui, Jin Ming, Liu, Bi-Heng, Huang, Yun-Feng, Li, Chuan-Feng, Guo, Guang-Can, Roland, Jérémie, Cabello Quintero, Adán, Kwek, Leong-Chuan, Universidad de Sevilla. Departamento de Física Aplicada II, Universidad de Sevilla. FQM239: Fundamentos de Mecánica Cuántica, National Natural Science Foundation of China, Universidad de Sevilla, European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER), Ministerio de Economia, Industria y Competitividad (MINECO). España, Ministerio de Ciencia, Innovación y Universidades (MICINN). España, Ministry of Education, Singapore, National Research Foundation Singapore, Department of Energy. United States, Institute for Quantum Information and Matter, Belgian Fonds pour la Formation à la Recherche, Hu, Xiao-Min, Xie, Yi, Arora, Atul Singh, Ai, Ming-Zhong, Bharti, Kishor, Zhang, Jie, Wu, Wei, Chen, Ping Xing, Cui, Jin Ming, Liu, Bi-Heng, Huang, Yun-Feng, Li, Chuan-Feng, Guo, Guang-Can, Roland, Jérémie, Cabello Quintero, Adán, and Kwek, Leong-Chuan
Abstract: Self-testing allows one to characterise quantum systems under minimal assumptions. However, existing schemes rely on quantum nonlocality and cannot be applied to systems that are not entangled. Here, we introduce a robust method that achieves self-testing of individual systems by taking advantage of contextuality. The scheme is based on the simplest contextuality witness for the simplest contextual quantum system—the Klyachko-Can-Binicioğlu-Shumovsky inequality for the qutrit. We establish a lower bound on the fidelity of the state and the measurements as a function of the value of the witness under a pragmatic assumption on the measurements. We apply the method in an experiment on a single trapped 40Ca+ using randomly chosen measurements and perfect detection efficiency. Using the observed statistics, we obtain an experimental demonstration of self-testing of a single quantum system.
Published: 2023

4. Self-testing of a single quantum system from theory to experiment

Author: Universidad de Sevilla. Departamento de Física Aplicada II, Universidad de Sevilla. FQM239: Fundamentos de Mecánica Cuántica, National Natural Science Foundation of China, Universidad de Sevilla, European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER), Ministerio de Economia, Industria y Competitividad (MINECO). España, Ministerio de Ciencia, Innovación y Universidades (MICINN). España, Ministry of Education, Singapore, National Research Foundation Singapore, Department of Energy. United States, Institute for Quantum Information and Matter, Belgian Fonds pour la Formation à la Recherche, Hu, Xiao-Min, Xie, Yi, Arora, Atul Singh, Ai, Ming-Zhong, Bharti, Kishor, Zhang, Jie, Wu, Wei, Chen, Ping Xing, Cui, Jin Ming, Liu, Bi-Heng, Huang, Yun-Feng, Li, Chuan-Feng, Guo, Guang-Can, Roland, Jérémie, Cabello Quintero, Adán, Kwek, Leong-Chuan, Universidad de Sevilla. Departamento de Física Aplicada II, Universidad de Sevilla. FQM239: Fundamentos de Mecánica Cuántica, National Natural Science Foundation of China, Universidad de Sevilla, European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER), Ministerio de Economia, Industria y Competitividad (MINECO). España, Ministerio de Ciencia, Innovación y Universidades (MICINN). España, Ministry of Education, Singapore, National Research Foundation Singapore, Department of Energy. United States, Institute for Quantum Information and Matter, Belgian Fonds pour la Formation à la Recherche, Hu, Xiao-Min, Xie, Yi, Arora, Atul Singh, Ai, Ming-Zhong, Bharti, Kishor, Zhang, Jie, Wu, Wei, Chen, Ping Xing, Cui, Jin Ming, Liu, Bi-Heng, Huang, Yun-Feng, Li, Chuan-Feng, Guo, Guang-Can, Roland, Jérémie, Cabello Quintero, Adán, and Kwek, Leong-Chuan
Abstract: Self-testing allows one to characterise quantum systems under minimal assumptions. However, existing schemes rely on quantum nonlocality and cannot be applied to systems that are not entangled. Here, we introduce a robust method that achieves self-testing of individual systems by taking advantage of contextuality. The scheme is based on the simplest contextuality witness for the simplest contextual quantum system—the Klyachko-Can-Binicioğlu-Shumovsky inequality for the qutrit. We establish a lower bound on the fidelity of the state and the measurements as a function of the value of the witness under a pragmatic assumption on the measurements. We apply the method in an experiment on a single trapped 40Ca+ using randomly chosen measurements and perfect detection efficiency. Using the observed statistics, we obtain an experimental demonstration of self-testing of a single quantum system.
Published: 2023

5. Mechanistic insights into the regulation of cell wall hydrolysis by FtsEX and EnvC at the bacterial division site

Author: National University of Singapore, National Research Foundation Singapore, Ministerio de Ciencia e Innovación (España), Swiss National Science Foundation, Howard Hughes Medical Institute, National Institutes of Health (US), Xu, Xin, Li, Jianwei, Chua, Wan-Zhen, Alcorlo, Martín, Shi, Jian, Hermoso, Juan A., Bernhardt, Thomas, Sham, Lok-To, Luo, Min, National University of Singapore, National Research Foundation Singapore, Ministerio de Ciencia e Innovación (España), Swiss National Science Foundation, Howard Hughes Medical Institute, National Institutes of Health (US), Xu, Xin, Li, Jianwei, Chua, Wan-Zhen, Alcorlo, Martín, Shi, Jian, Hermoso, Juan A., Bernhardt, Thomas, Sham, Lok-To, and Luo, Min
Abstract: The peptidoglycan (PG) cell wall produced by the bacterial division machinery is initially shared between the daughters and must be split to promote cell separation and complete division. In gram-negative bacteria, enzymes that cleave PG called amidases play major roles in the separation process. To prevent spurious cell wall cleavage that can lead to cell lysis, amidases like AmiB are autoinhibited by a regulatory helix. Autoinhibition is relieved at the division site by the activator EnvC, which is in turn regulated by the ATP-binding cassette (ABC) transporter-like complex called FtsEX. EnvC is also known to be autoinhibited by a regulatory helix (RH), but how its activity is modulated by FtsEX and the mechanism by which it activates the amidases have remained unclear. Here, we investigated this regulation by determining the structure of Pseudomonas aeruginosa FtsEX alone with or without bound ATP, in complex with EnvC, and in a FtsEX-EnvC-AmiB supercomplex. In combination with biochemical studies, the structures reveal that ATP binding is likely to activate FtsEX-EnvC and promote its association with AmiB. Furthermore, the AmiB activation mechanism is shown to involve a RH rearrangement. In the activated state of the complex, the inhibitory helix of EnvC is released, freeing it to associate with the RH of AmiB, which liberates its active site for PG cleavage. These regulatory helices are found in many EnvC proteins and amidases throughout gram-negative bacteria, suggesting that the activation mechanism is broadly conserved and a potential target for lysis-inducing antibiotics that misregulate the complex.
Published: 2023

6. JNK signaling in pioneer neurons organizes ventral nerve cord architecture in Drosophila embryos

Author: Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Fundación Ramón Areces, National Research Foundation Singapore, University of Warwick, Karkali, Katerina, Saunders, Timothy E., Panayotou, George, Martín-Blanco, Enrique, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Fundación Ramón Areces, National Research Foundation Singapore, University of Warwick, Karkali, Katerina, Saunders, Timothy E., Panayotou, George, and Martín-Blanco, Enrique
Abstract: Morphogenesis of the Central Nervous System (CNS) is a complex process that obeys precise architectural rules. Yet, the mechanisms dictating these rules remain unknown. Analyzing morphogenesis of the Drosophila embryo Ventral Nerve Cord (VNC), we observe that a tight control of JNK signaling is essential for attaining the final VNC architecture. JNK signaling in a specific subset of pioneer neurons autonomously regulates the expression of Fasciclin 2 (Fas 2) and Neurexin IV (Nrx IV) adhesion molecules, probably via the transcription factor zfh1. Interfering at any step in this cascade affects fasciculation along pioneer axons, leading to secondary cumulative scaffolding defects during the structural organization of the axonal network. The global disorder of architectural landmarks ultimately influences nervous system condensation. In summary, our data point to JNK signaling in a subset of pioneer neurons as a key element underpinning VNC architecture, revealing critical milestones on the mechanism of control of its structural organization.
Published: 2023

7. The landscape of tolerated genetic variation in humans and primates

Author: EMBO, National Institutes of Health (US), Fundación la Caixa, Vienna Science and Technology Fund, European Commission, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), International Primatological Society, Rufford Foundation, Margot Marsh Biodiversity Foundation, Primate Conservation, Mamirauá Institute for Sustainable Development, Gordon and Betty Moore Foundation, Fundação de Amparo à Pesquisa do Estado do Amazonas, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), German Research Foundation, National Science Foundation (US), Ministry of Science and Technology of Vietnam, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs, Illumina, Natural Environment Research Council (UK), San Diego Zoo Wildlife Alliance, Wenner-Gren Foundation, Leakey Foundation, National Geographic Society, National Institute on Aging (US), National Research Foundation Singapore, Swedish Research Council, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad (España), Juan, David [0000-0003-1912-9667], Valenzuela, Alejandro [0000-0001-6120-6246], Lizano, Esther [0000-0003-3304-9807], Navarro, Arcadi [0000-0003-2162-8246], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Gao, Hong, Hamp, Tobias, Ede, Jeffrey, Schraiber, Joshua G., McRae, Jeremy, Singer-Berk, Moriel, Yang, Yanshen, Dietrich, Anastasia S. D., Fiziev, Petko P., Kuderna, Lukas F. K., Sundaram, Laksshman, Wu, Yibing, Adhikari, Aashish, Field, Yair, Chen, Chen, Batzoglou, Serafim, Aguet, Francois, Lemire, Gabrielle, Reimers, Rebecca, Balick, Daniel, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, Vries, Dorien de, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Melo, Fabiano R. de, Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Amaral, João Valsecchi do, Messias, Mariluce, Silva, Maria N. F. da, Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Bataillon, Thomas, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda, Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M. D., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Lek, Monkol, Sunyaev, Shamil, O’Donnell-Luria, Anne, Rehm, Heidi L., Xu, Jinbo, Rogers, Jeffrey, Marqués-Bonet, Tomàs, Farh, Kyle Kai-How, EMBO, National Institutes of Health (US), Fundación la Caixa, Vienna Science and Technology Fund, European Commission, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), International Primatological Society, Rufford Foundation, Margot Marsh Biodiversity Foundation, Primate Conservation, Mamirauá Institute for Sustainable Development, Gordon and Betty Moore Foundation, Fundação de Amparo à Pesquisa do Estado do Amazonas, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), German Research Foundation, National Science Foundation (US), Ministry of Science and Technology of Vietnam, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs, Illumina, Natural Environment Research Council (UK), San Diego Zoo Wildlife Alliance, Wenner-Gren Foundation, Leakey Foundation, National Geographic Society, National Institute on Aging (US), National Research Foundation Singapore, Swedish Research Council, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad (España), Juan, David [0000-0003-1912-9667], Valenzuela, Alejandro [0000-0001-6120-6246], Lizano, Esther [0000-0003-3304-9807], Navarro, Arcadi [0000-0003-2162-8246], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Gao, Hong, Hamp, Tobias, Ede, Jeffrey, Schraiber, Joshua G., McRae, Jeremy, Singer-Berk, Moriel, Yang, Yanshen, Dietrich, Anastasia S. D., Fiziev, Petko P., Kuderna, Lukas F. K., Sundaram, Laksshman, Wu, Yibing, Adhikari, Aashish, Field, Yair, Chen, Chen, Batzoglou, Serafim, Aguet, Francois, Lemire, Gabrielle, Reimers, Rebecca, Balick, Daniel, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, Vries, Dorien de, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Melo, Fabiano R. de, Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Amaral, João Valsecchi do, Messias, Mariluce, Silva, Maria N. F. da, Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Bataillon, Thomas, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda, Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M. D., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Lek, Monkol, Sunyaev, Shamil, O’Donnell-Luria, Anne, Rehm, Heidi L., Xu, Jinbo, Rogers, Jeffrey, Marqués-Bonet, Tomàs, and Farh, Kyle Kai-How
Abstract: [INTRODUCTION] Millions of people have received genome and exome sequencing to date, a collective effort that has illuminated for the first time the vast catalog of small genetic differences that distinguish us as individuals within our species. However, the effects of most of these genetic variants remain unknown, limiting their clinical utility and actionability. New approaches that can accurately discern disease-causing from benign mutations and interpret genetic variants on a genome-wide scale would constitute a meaningful initial step towards realizing the potential of personalized genomic medicine., [RATIONALE] As a result of the short evolutionary distance between humans and nonhuman primates, our proteins share near-perfect amino acid sequence identity. Hence, the effects of a protein-altering mutation found in one species are likely to be concordant in the other species. By systematically cataloging common variants of nonhuman primates, we aimed to annotate these variants as being unlikely to cause human disease as they are tolerated by natural selection in a closely related species. Once collected, the resulting resource may be applied to infer the effects of unobserved variants across the genome using machine learning., [RESULTS] Following the strategy outlined above we obtained whole-genome sequencing data for 809 individuals from 233 primate species and cataloged 4.3 million common missense variants. We confirmed that human missense variants seen in at least one nonhuman primate species were annotated as benign in the ClinVar clinical variant database in 99% of cases. By contrast, common variants from mammals and vertebrates outside the primate lineage were substantially less likely to be benign in the ClinVar database (71 to 87% benign), restricting this strategy to nonhuman primates. Overall, we reclassified more than 4 million human missense variants of previously unknown consequence as likely benign, resulting in a greater than 50-fold increase in the number of annotated missense variants compared to existing clinical databases. To infer the pathogenicity of the remaining missense variants in the human genome, we constructed PrimateAI-3D, a semisupervised 3D-convolutional neural network that operates on voxelized protein structures. We trained PrimateAI-3D to separate common primate variants from matched control variants in 3D space as a semisupervised learning task. We evaluated the trained PrimateAI-3D model alongside 15 other published machine learning methods on their ability to distinguish between benign and pathogenic variants in six different clinical benchmarks and demonstrated that PrimateAI-3D outperformed all other classifiers in each of the tasks., [CONCLUSION] Our study addresses one of the key challenges in the variant interpretation field, namely, the lack of sufficient labeled data to effectively train large machine learning models. By generating the most comprehensive primate sequencing dataset to date and pairing this resource with a deep learning architecture that leverages 3D protein structures, we were able to achieve meaningful improvements in variant effect prediction across multiple clinical benchmarks.
Published: 2023

8. A global catalog of whole-genome diversity from 233 primate species

Author: Fundación la Caixa, Vienna Science and Technology Fund, European Commission, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), International Primatological Society, Rufford Foundation, Margot Marsh Biodiversity Foundation, Primate Conservation, Fundação de Amparo à Pesquisa do Estado do Amazonas, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), German Research Foundation, National Science Foundation (US), Ministry of Science and Technology of Vietnam, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs, European Research Council, Natural Environment Research Council (UK), UK Research and Innovation, Department of Biotechnology (India), San Diego Zoo Wildlife Alliance, Wenner-Gren Foundation, Leakey Foundation, National Geographic Society, National Institute on Aging (US), National Institutes of Health (US), Swedish Research Council, National Research Foundation Singapore, Government of Singapore, Kuderna, Lukas F. K. [0000-0002-9992-9295], Kuhlwilm, Martin [0000-0002-0115-1797], Orkin, Joseph D. [0000-0001-6922-2072], Valenzuela, Alejandro [0000-0001-6120-6246], Juan, David [0000-0003-1912-9667], Lizano, Esther [0000-0003-3304-9807], Navarro, Arcadi [0000-0003-2162-8246], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Kuderna, Lukas F. K., Gao, Hong, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, Vries, Dorien de, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idrissa S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., Melo, Fabiano R. de, Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, Silva, Maria N. F. da, Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M. D., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Rogers, Jeffrey, Farh, Kyle Kai-How, Marqués-Bonet, Tomàs, Fundación la Caixa, Vienna Science and Technology Fund, European Commission, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), International Primatological Society, Rufford Foundation, Margot Marsh Biodiversity Foundation, Primate Conservation, Fundação de Amparo à Pesquisa do Estado do Amazonas, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), German Research Foundation, National Science Foundation (US), Ministry of Science and Technology of Vietnam, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs, European Research Council, Natural Environment Research Council (UK), UK Research and Innovation, Department of Biotechnology (India), San Diego Zoo Wildlife Alliance, Wenner-Gren Foundation, Leakey Foundation, National Geographic Society, National Institute on Aging (US), National Institutes of Health (US), Swedish Research Council, National Research Foundation Singapore, Government of Singapore, Kuderna, Lukas F. K. [0000-0002-9992-9295], Kuhlwilm, Martin [0000-0002-0115-1797], Orkin, Joseph D. [0000-0001-6922-2072], Valenzuela, Alejandro [0000-0001-6120-6246], Juan, David [0000-0003-1912-9667], Lizano, Esther [0000-0003-3304-9807], Navarro, Arcadi [0000-0003-2162-8246], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Kuderna, Lukas F. K., Gao, Hong, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, Vries, Dorien de, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idrissa S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., Melo, Fabiano R. de, Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, Silva, Maria N. F. da, Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M. D., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Rogers, Jeffrey, Farh, Kyle Kai-How, and Marqués-Bonet, Tomàs
Abstract: The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.
Published: 2023

9. Regulation of the cell division hydrolase RipC by the FtsEX system in Mycobacterium tuberculosis

Author: National University of Singapore, National Research Foundation Singapore, Ministry of Education (Singapore), Ministerio de Ciencia e Innovación (España), Swiss National Science Foundation, Li, Jianwei [0000-0001-9181-4760], Hermoso, Juan A. [0000-0002-1862-8950], Sham, Lok-To [0000-0001-9047-0310], Luo, Min [0000-0002-3493-2282], Li, Jianwei, Xu, Xin, Shi, Jian, Hermoso, Juan A., Sham, Lok-To, Luo, Min, National University of Singapore, National Research Foundation Singapore, Ministry of Education (Singapore), Ministerio de Ciencia e Innovación (España), Swiss National Science Foundation, Li, Jianwei [0000-0001-9181-4760], Hermoso, Juan A. [0000-0002-1862-8950], Sham, Lok-To [0000-0001-9047-0310], Luo, Min [0000-0002-3493-2282], Li, Jianwei, Xu, Xin, Shi, Jian, Hermoso, Juan A., Sham, Lok-To, and Luo, Min
Abstract: The FtsEX complex regulates, directly or via a protein mediator depending on bacterial genera, peptidoglycan degradation for cell division. In mycobacteria and Gram-positive bacteria, the FtsEX system directly activates peptidoglycan-hydrolases by a mechanism that remains unclear. Here we report our investigation of Mycobacterium tuberculosis FtsEX as a non-canonical regulator with high basal ATPase activity. The cryo-EM structures of the FtsEX system alone and in complex with RipC, as well as the ATP-activated state, unveil detailed information on the signal transduction mechanism, leading to the activation of RipC. Our findings indicate that RipC is recognized through a "Match and Fit" mechanism, resulting in an asymmetric rearrangement of the extracellular domains of FtsX and a unique inclined binding mode of RipC. This study provides insights into the molecular mechanisms of FtsEX and RipC regulation in the context of a critical human pathogen, guiding the design of drugs targeting peptidoglycan remodeling.
Published: 2023

10. Jordan in The Church of The Higher Hilbert Space: Entanglement and Thermal Fluctuations

Author: National Research Foundation, Singapore, Ministry of Education, Singapore, Wolfson College, University of Oxford, United Kingdom, Vedral, Vlatko, National Research Foundation, Singapore, Ministry of Education, Singapore, Wolfson College, University of Oxford, United Kingdom, and Vedral, Vlatko
Abstract: I revisit Jordan's derivation of Einstein's formula for energy fluctuations in the black body in thermal equilibrium. This formula is usually taken to represent the unification of the wave and the particle aspects of the electromagnetic field since the fluctuations can be shown to be the sum of wave-like and particle-like contributions. However, in Jordan's treatment there is no mention of the Planck distribution and all averages are performed with respect to pure number states of radiation (mixed states had not yet been discovered!). The chief reason why Jordan does reproduce Einstein's result despite not using thermal states of radiation is that he focuses on fluctuations in a small (compared to the whole) volume of the black body. The state of radiation in a small volume is highly entangled to the rest of the black body which leads to the correct fluctuations even though the overall state might, in fact, be assumed to be pure (i.e. at zero temperature). I present a simple derivation of the fluctuations formula as an instance of mixed states being reductions of higher level pure states, a representation that is affectionately known as "Church of the Higher Hilbert Space". According to this view of mixed states, temperature is nothing but the amount of entanglement between the system and its environment.Quanta 2022; 11: 1–4.
Published: 2022

11. The absence of the queuosine tRNA modification leads to pleiotropic phenotypes revealing perturbations of metal and oxidative stress homeostasis in Escherichia coli K12

Author: National Institute of General Medical Sciences (US), National Science Foundation (US), National Research Foundation Singapore, Singapore-MIT Alliance for Research and Technology, Pollo-Oliveira, Leticia, Davis, Nick K., Hossain, Intekhab, Ho, Peiying, Yuan, Yifeng, Salguero, Pedro, Pereira, Cécile, Byrne, Shane R., Leng, Jiapeng, Sze, Melody, Blaby-Haas, Crysten E., Sekowska, Agnieszka, Montoya, Alvaro, Begley, Thomas, Danchin, Antoine, Aalberts, Daniel P., Angerhofer, Alexander, Hunt, John, Conesa, Ana, Dedon, Peter C., Crécy-lagard, Valérie de, National Institute of General Medical Sciences (US), National Science Foundation (US), National Research Foundation Singapore, Singapore-MIT Alliance for Research and Technology, Pollo-Oliveira, Leticia, Davis, Nick K., Hossain, Intekhab, Ho, Peiying, Yuan, Yifeng, Salguero, Pedro, Pereira, Cécile, Byrne, Shane R., Leng, Jiapeng, Sze, Melody, Blaby-Haas, Crysten E., Sekowska, Agnieszka, Montoya, Alvaro, Begley, Thomas, Danchin, Antoine, Aalberts, Daniel P., Angerhofer, Alexander, Hunt, John, Conesa, Ana, Dedon, Peter C., and Crécy-lagard, Valérie de
Abstract: Queuosine (Q) is a conserved hypermodification of the wobble base of tRNA containing GUN anticodons but the physiological consequences of Q deficiency are poorly understood in bacteria. This work combines transcriptomic, proteomic and physiological studies to characterize a Q-deficient Escherichia coli K12 MG1655 mutant. The absence of Q led to an increased resistance to nickel and cobalt, and to an increased sensitivity to cadmium, compared to the wild-type (WT) strain. Transcriptomic analysis of the WT and Q-deficient strains, grown in the presence and absence of nickel, revealed that the nickel transporter genes (nikABCDE) are downregulated in the Q- mutant, even when nickel is not added. This mutant is therefore primed to resist to high nickel levels. Downstream analysis of the transcriptomic data suggested that the absence of Q triggers an atypical oxidative stress response, confirmed by the detection of slightly elevated reactive oxygen species (ROS) levels in the mutant, increased sensitivity to hydrogen peroxide and paraquat, and a subtle growth phenotype in a strain prone to accumulation of ROS.
Published: 2022

12. Ultralarge free-standing imine-based covalent organic framework membranes fabricated via compression

Author: Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, National Research Foundation Singapore, Ministry of Education (Singapore), Martín-Illán, Jesús Á., Suárez, José Antonio, Gómez-Herrero, Julio, Ares, Pablo, Gallego-Fuente, Daniel, Cheng, Youdong, Zhao, Dan, Maspoch, Daniel, Zamora, Félix, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, National Research Foundation Singapore, Ministry of Education (Singapore), Martín-Illán, Jesús Á., Suárez, José Antonio, Gómez-Herrero, Julio, Ares, Pablo, Gallego-Fuente, Daniel, Cheng, Youdong, Zhao, Dan, Maspoch, Daniel, and Zamora, Félix
Abstract: Demand continues for processing methods to shape covalent organic frameworks (COFs) into macroscopic objects that are needed for their practical applications. Herein, a simple compression method to prepare large-scale, free-standing homogeneous and porous imine-based COF-membranes with dimensions in the centimeter range and excellent mechanical properties is reported. This method entails the compression of imine-based COF-aerogels, which undergo a morphological change from an elastic to plastic material. The COF-membranes fabricated upon compression show good performances for the separation of gas mixtures of industrial interest, N2/CO2 and CH4/CO2. It is believed that the new procedure paves the way to a broader range of COF-membranes.
Published: 2022

13. Condensation of the Drosophila nerve cord is oscillatory and depends on coordinated mechanical interactions

Author: Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Fundación Ramón Areces, National Research Foundation Singapore, University of Warwick, European Commission, Generalitat de Catalunya, Karkali, Katerina, Tiwari, Prabhat, Singh, Anand, Tlili, Sham, Jorba, Ignasi, Navajas, Daniel, Muñoz, José J., Saunders, Timothy E., Martín-Blanco, Enrique, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Fundación Ramón Areces, National Research Foundation Singapore, University of Warwick, European Commission, Generalitat de Catalunya, Karkali, Katerina, Tiwari, Prabhat, Singh, Anand, Tlili, Sham, Jorba, Ignasi, Navajas, Daniel, Muñoz, José J., Saunders, Timothy E., and Martín-Blanco, Enrique
Abstract: During development, organs reach precise shapes and sizes. Organ morphology is not always obtained through growth; a classic counterexample is the condensation of the nervous system during Drosophila embryogenesis. The mechanics underlying such condensation remain poorly understood. Here, we characterize the condensation of the embryonic ventral nerve cord (VNC) at both subcellular and tissue scales. This analysis reveals that condensation is not a unidirectional continuous process but instead occurs through oscillatory contractions. The VNC mechanical properties spatially and temporally vary, and forces along its longitudinal axis are spatially heterogeneous. We demonstrate that the process of VNC condensation is dependent on the coordinated mechanical activities of neurons and glia. These outcomes are consistent with a viscoelastic model of condensation, which incorporates time delays and effective frictional interactions. In summary, we have defined the progressive mechanics driving VNC condensation, providing insights into how a highly viscous tissue can autonomously change shape and size.
Published: 2022

14. Two-dimensional materials prospects for non-volatile spintronic memories

Author: European Commission, Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), National Research Foundation Singapore, Agence Nationale de la Recherche (France), Yang, Hyun-Soo, Valenzuela, Sergio O., Chshiev, Mairbek, Couet, Sébastien, Dieny, Bernard, Dlubak, Bruno, Fert, A., Garello, Kevin, Jamet, Matthieu, Jeong, Dae-Eun, Lee, Kangho, Lee, Taeyoung, Martin, Marie-Blandine, Kar, Gouri Sankar, Seneor, Pierre, Shin, Hyeon-Jin, Roche, Stephan, European Commission, Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), National Research Foundation Singapore, Agence Nationale de la Recherche (France), Yang, Hyun-Soo, Valenzuela, Sergio O., Chshiev, Mairbek, Couet, Sébastien, Dieny, Bernard, Dlubak, Bruno, Fert, A., Garello, Kevin, Jamet, Matthieu, Jeong, Dae-Eun, Lee, Kangho, Lee, Taeyoung, Martin, Marie-Blandine, Kar, Gouri Sankar, Seneor, Pierre, Shin, Hyeon-Jin, and Roche, Stephan
Abstract: Non-volatile magnetic random-access memories (MRAMs), such as spin-transfer torque MRAM and next-generation spin–orbit torque MRAM, are emerging as key to enabling low-power technologies, which are expected to spread over large markets from embedded memories to the Internet of Things. Concurrently, the development and performances of devices based on two-dimensional van der Waals heterostructures bring ultracompact multilayer compounds with unprecedented material-engineering capabilities. Here we provide an overview of the current developments and challenges in regard to MRAM, and then outline the opportunities that can arise by incorporating two-dimensional material technologies. We highlight the fundamental properties of atomically smooth interfaces, the reduced material intermixing, the crystal symmetries and the proximity effects as the key drivers for possible disruptive improvements for MRAM at advanced technology nodes.
Published: 2022

15. Jordan in The Church of The Higher Hilbert Space: Entanglement and Thermal Fluctuations

Author: National Research Foundation, Singapore, Ministry of Education, Singapore, Wolfson College, University of Oxford, United Kingdom, Vedral, Vlatko, National Research Foundation, Singapore, Ministry of Education, Singapore, Wolfson College, University of Oxford, United Kingdom, and Vedral, Vlatko
Abstract: I revisit Jordan's derivation of Einstein's formula for energy fluctuations in the black body in thermal equilibrium. This formula is usually taken to represent the unification of the wave and the particle aspects of the electromagnetic field since the fluctuations can be shown to be the sum of wave-like and particle-like contributions. However, in Jordan's treatment there is no mention of the Planck distribution and all averages are performed with respect to pure number states of radiation (mixed states had not yet been discovered!). The chief reason why Jordan does reproduce Einstein's result despite not using thermal states of radiation is that he focuses on fluctuations in a small (compared to the whole) volume of the black body. The state of radiation in a small volume is highly entangled to the rest of the black body which leads to the correct fluctuations even though the overall state might, in fact, be assumed to be pure (i.e. at zero temperature). I present a simple derivation of the fluctuations formula as an instance of mixed states being reductions of higher level pure states, a representation that is affectionately known as "Church of the Higher Hilbert Space". According to this view of mixed states, temperature is nothing but the amount of entanglement between the system and its environment.Quanta 2022; 11: 1–4.
Published: 2022

16. Jordan in The Church of The Higher Hilbert Space: Entanglement and Thermal Fluctuations

Author: National Research Foundation, Singapore, Ministry of Education, Singapore, Wolfson College, University of Oxford, United Kingdom, Vedral, Vlatko, National Research Foundation, Singapore, Ministry of Education, Singapore, Wolfson College, University of Oxford, United Kingdom, and Vedral, Vlatko
Abstract: I revisit Jordan's derivation of Einstein's formula for energy fluctuations in the black body in thermal equilibrium. This formula is usually taken to represent the unification of the wave and the particle aspects of the electromagnetic field since the fluctuations can be shown to be the sum of wave-like and particle-like contributions. However, in Jordan's treatment there is no mention of the Planck distribution and all averages are performed with respect to pure number states of radiation (mixed states had not yet been discovered!). The chief reason why Jordan does reproduce Einstein's result despite not using thermal states of radiation is that he focuses on fluctuations in a small (compared to the whole) volume of the black body. The state of radiation in a small volume is highly entangled to the rest of the black body which leads to the correct fluctuations even though the overall state might, in fact, be assumed to be pure (i.e. at zero temperature). I present a simple derivation of the fluctuations formula as an instance of mixed states being reductions of higher level pure states, a representation that is affectionately known as "Church of the Higher Hilbert Space". According to this view of mixed states, temperature is nothing but the amount of entanglement between the system and its environment.Quanta 2022; 11: 1–4.
Published: 2022

17. Amorphizing noble metal chalcogenide catalysts at the single-layer limit towards hydrogen production

Author: National Research Foundation Singapore, National Key Research and Development Program (China), Generalitat de Catalunya, Ministerio de Ciencia e Innovación (España), European Commission, He, Yongmin, Liu, Liren, Zhu, Chao, Guo, Shasha, Golani, Prafful, Koo, Bonhyeong, Tang, Peng-Yi, Zhao, Zhiqiang, Xu, Manzhang, Yu, Peng, Zhou, Xin, Gao, Caitian, Wang, Xuewen, Shi, Zude, Zheng, Lu, Yang, Jiefu, Shin, Byungha, Arbiol, Jordi, Duan, Huigao, Du, Yonghua, Heggen, Marc, Dunin-Borkowski, Rafal E., Guo, Wanlin, Wang, Qi Jie, Zhang, Zhuahua, Liu, Zheng, National Research Foundation Singapore, National Key Research and Development Program (China), Generalitat de Catalunya, Ministerio de Ciencia e Innovación (España), European Commission, He, Yongmin, Liu, Liren, Zhu, Chao, Guo, Shasha, Golani, Prafful, Koo, Bonhyeong, Tang, Peng-Yi, Zhao, Zhiqiang, Xu, Manzhang, Yu, Peng, Zhou, Xin, Gao, Caitian, Wang, Xuewen, Shi, Zude, Zheng, Lu, Yang, Jiefu, Shin, Byungha, Arbiol, Jordi, Duan, Huigao, Du, Yonghua, Heggen, Marc, Dunin-Borkowski, Rafal E., Guo, Wanlin, Wang, Qi Jie, Zhang, Zhuahua, and Liu, Zheng
Abstract: Rational design of noble metal catalysts with the potential to leverage efficiency is vital for industrial applications. Such an ultimate atom-utilization efficiency can be achieved when all noble metal atoms exclusively contribute to catalysis. Here, we demonstrate the fabrication of a wafer-size amorphous PtSe film on a SiO substate via a low-temperature amorphization strategy, which offers single-atom-layer Pt catalysts with high atom-utilization efficiency (~26 wt%). This amorphous PtSe (1.2 < x < 1.3) behaves as a fully activated surface, accessible to catalytic reactions, and features a nearly 100% current density relative to a pure Pt surface and reliable production of sustained high-flux hydrogen over a 2 inch wafer as a proof-of-concept. Furthermore, an electrolyser is demonstrated to generate a high current density of 1,000 mA cm. Such an amorphization strategy is potentially extendable to other noble metals, including the Pd, Ir, Os, Rh and Ru elements, demonstrating the universality of single-atom-layer catalysts. [Figure not available: see fulltext.]
Published: 2022

18. Canted persistent spin texture and quantum spin hall effect in WTe2

Author: Fundación la Caixa, National University of Singapore, Agence Nationale de la Recherche (France), European Commission, Generalitat de Catalunya, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), National Research Foundation Singapore, Garcia, Jose H., Vila, Marc, Hsu, Chuang-Han, Waintal, X., Pereira, Vitor M., Roche, Stephan, Fundación la Caixa, National University of Singapore, Agence Nationale de la Recherche (France), European Commission, Generalitat de Catalunya, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), National Research Foundation Singapore, Garcia, Jose H., Vila, Marc, Hsu, Chuang-Han, Waintal, X., Pereira, Vitor M., and Roche, Stephan
Abstract: We report an unconventional quantum spin Hall phase in the monolayer WTe2, which exhibits hitherto unknown features in other topological materials. The low symmetry of the structure induces a canted spin texture in the yz plane, which dictates the spin polarization of topologically protected boundary states. Additionally, the spin Hall conductivity gets quantized (2e2/h) with a spin quantization axis parallel to the canting direction. These findings are based on large-scale quantum simulations of the spin Hall conductivity tensor and nonlocal resistances in multiprobe geometries using a realistic tight-binding model elaborated from first-principle methods. The observation of this canted quantum spin Hall effect, related to the formation of topological edge states with nontrivial spin polarization, demands for specific experimental design and suggests interesting alternatives for manipulating spin information in topological materials.
Published: 2020

19. Understanding the nature of the passivation layer enabling reversible calcium plating

Author: European Research Council, European Commission, Ministerio de Economía, Industria y Competitividad (España), National Research Foundation Singapore, Forero Saboya, Juan, Davoisne, Carine, Dedryvère, Rémi, Yousef, Ibraheem, Canepa, Pieremanuele, Ponrouch, Alexandre, European Research Council, European Commission, Ministerio de Economía, Industria y Competitividad (España), National Research Foundation Singapore, Forero Saboya, Juan, Davoisne, Carine, Dedryvère, Rémi, Yousef, Ibraheem, Canepa, Pieremanuele, and Ponrouch, Alexandre
Abstract: As for other multivalent systems, the interface between the calcium (Ca) metal anode and the electrolyte is of paramount importance for reversible plating/stripping. Here, we combined experimental and theoretical approaches to unveil the potential solid electrolyte interphase (SEI) components enabling facile Ca plating. Borates compounds, in the form of cross-linked polymers are suggested as divalent conducting component. A pre-passivation protocol with such SEI is demonstrated and allows to broaden the possibility for electrolyte formulation. We also demonstrated a 10-fold increase in Ca plating kinetics by tuning the cation solvation structure in the electrolyte limiting the degree of contact ion pair.
Published: 2020

20. System-wide molecular dynamics of endothelial dysfunction in Gram-negative sepsis

Author: National Research Foundation Singapore, Ministry of Education (Singapore), Comunidad de Madrid, Ministerio de Economía y Competitividad (España), European Commission, Gallart-Palau, Xavier, Serra, Aida, Sze, Siu Kwan, National Research Foundation Singapore, Ministry of Education (Singapore), Comunidad de Madrid, Ministerio de Economía y Competitividad (España), European Commission, Gallart-Palau, Xavier, Serra, Aida, and Sze, Siu Kwan
Abstract: [Background]: Inflammation affecting whole organism vascular networks plays a central role in the progression and establishment of several human diseases, including Gram-negative sepsis. Although the molecular mechanisms that control inflammation of specific vascular beds have been partially defined, knowledge lacks on the impact of these on the molecular dynamics of whole organism vascular beds. In this study, we have generated an in vivo model by coupling administration of lipopolysaccharide with stable isotope labeling in mammals to mimic vascular beds inflammation in Gram-negative sepsis and to evaluate its effects on the proteome molecular dynamics. Proteome molecular dynamics of individual vascular layers (glycocalyx (GC), endothelial cells (EC), and smooth muscle cells (SMC)) were then evaluated by coupling differential systemic decellularization in vivo with unbiased systems biology proteomics., [Results]: Our data confirmed the presence of sepsis-induced disruption of the glycocalyx, and we show for the first time the downregulation of essential molecular maintenance processes in endothelial cells affecting this apical vascular coating. Similarly, a novel catabolic phenotype was identified in the newly synthesized EC proteomes that involved the impairment of protein synthesis, which affected multiple cellular mechanisms, including oxidative stress, the immune system, and exacerbated EC-specific protein turnover. In addition, several endogenous molecular protective mechanisms involving the synthesis of novel antithrombotic and anti-inflammatory proteins were also identified as active in EC. The molecular dynamics of smooth muscle cells in whole organism vascular beds revealed similar patterns of impairment as those identified in EC, although this was observed to a lesser extent. Furthermore, the dynamics of protein posttranslational modifications showed disease-specific phosphorylation sites in the EC proteomes., [Conclusions]: Together, the novel findings reported here provide a broader picture of the molecular dynamics that take place in whole organism vascular beds in Gram-negative sepsis inflammation. Similarly, the obtained data can pave the way for future therapeutic strategies aimed at intervening in specific protein synthesis mechanisms of the vascular unit during acute inflammatory processes.
Published: 2020

21. Conserving evolutionary history does notresult in greater diversity over geologicaltime scales

Author: German Centre for Integrative Biodiversity Research, Canadian Institute for Ecology and Evolution, Natural Sciences and Engineering Research Council of Canada, National Research Foundation Singapore, Alexander von Humboldt Foundation, German Research Foundation, Comunidad de Madrid, Cantalapiedra, Juan L., Aze, T., Cadotte, Marc W., Dalla Riva, G.V., Huang, Danwei, Mazel, F., Pennell, M.W., Ríos, M., Mooers, A.Ø., German Centre for Integrative Biodiversity Research, Canadian Institute for Ecology and Evolution, Natural Sciences and Engineering Research Council of Canada, National Research Foundation Singapore, Alexander von Humboldt Foundation, German Research Foundation, Comunidad de Madrid, Cantalapiedra, Juan L., Aze, T., Cadotte, Marc W., Dalla Riva, G.V., Huang, Danwei, Mazel, F., Pennell, M.W., Ríos, M., and Mooers, A.Ø.
Abstract: Alternative prioritization strategies have been proposed to safeguard biodiversity over macroevolutionary time scales. The first prioritizes the most distantly related species-maximizing phylogenetic diversity (PD)-in the hopes of capturing at least some lineages that will successfully diversify into the future. The second prioritizes lineages that are currently speciating, in the hopes that successful lineages will continue to generate species into the future. These contrasting schemes also map onto contrasting predictions about the role of slow diversifiers in the production of biodiversity over palaeontological time scales. We consider the performance of the two schemes across 10 dated species-level palaeo-phylogenetic trees ranging from Foraminifera to dinosaurs. We find that prioritizing PD for conservation generally led to fewer subsequent lineages, while prioritizing diversifiers led to modestly more subsequent diversity, compared with random sets of lineages. Importantly for conservation, the tree shape when decisions are made cannot predict which scheme will be most successful. These patterns are inconsistent with the notion that long-lived lineages are the source of new species. While there may be sound reasons for prioritizing PD for conservation, long-term species production might not be one of them.
Published: 2019

22. Mutational spectrum in a worldwide study of 29,700 families with BRCA1 or BRCA2 mutations

Author: Fundações de Amparo à Pesquisa (Brasil), Research Foundation - Flanders, University of Helsinki, Sigrid Juselius Foundation, Dutch Cancer Society, Netherlands Organization for Scientific Research, Asociación Española Contra el Cáncer, Generalitat de Catalunya, Ministero della Salute, Istituto Oncologico Veneto, University of Tasmania, Australian Cancer Research Foundation, Ministry of Health and Welfare (South Korea), Charles University (Czech Republic), National Research Foundation Singapore, Russian Foundation for Basic Research, Istituto Toscano Tumori, Israel Cancer Association USA, Swedish Cancer Society, Foundation for Women's Cancer, University of Pittsburgh, Cancer Australia, American Cancer Society, The Ohio State University, National Institutes of Health (US), Cancer Research UK, European Commission, Canadian Institutes of Health Research, Department of Trade and Industry (UK), Susan G. Komen Foundation, Breast Cancer Research Foundation, Genome Canada, National Cancer Institute (US), Research Council of Lithuania, Cancer Association of South Africa, Consejo Nacional de Investigaciones Científicas y Técnicas (Argentina), Instituto de Salud Carlos III, Ministerio de Economía y Competitividad (España), Ministerio de Sanidad y Política Social (España), Associazione Italiana per la Ricerca sul Cancro, Fondazione Italiana per la Ricerca sul Cancro, Ministero dell'Istruzione, dell'Università e della Ricerca, Institut Pasteur, Fondazione Cenci Bolognetti, Greek Government, Pontificia Universidad Javeriana, Royal Marsden NHS Foundation Trust, Kansas State University, Fundación Mutua Madrileña, Ligue Nationale contre le Cancer (France), Georgetown University, Rebbeck, Timothy R., Friebel, Tara M., Friedman, Eitan, Hamann, Ute, Huo, Dezheng, Kwong, Ava, Olah, Edith, Olopade, Olufunmilayo I., Solano, Angela R., Teo, Soo-Hwamg, Thomassen, Mads, Mebirouk, Noura, Meijers-Heijboer, Hanne, Meindl, Alfons, Mensenkamp, Arjen R., Kruse, Torben A., Benitez, Javier, Mickys, Ugnius, Greene, Mark H., Miller, Austin, thomas, Abigail, Cook, Jackie, Montagna, Marco, Moysich, Kirsten B., Mulligan, Anna Marie, Musinsky, Jacob, Neuhausen, Susan L., Nevanlinna, Heli, Ngeow, Joanne, Berger, Andreas, Nguyen, Huu Phuc, Palmero, Edenir Inêz, Davidson, Rosemarie, Bonadona, Valérie, Schmutzler, Rita Katharina, Niederacher, Dieter, Nielsen, Henriette Roed, Nielsen, Finn Cilius, Nussbaum, Robert L., Offit, Kenneth, Öfverholm, Anna, Ong, Kai-ren, Berger, Raanan, Hoya, Miguel de la, Osorio, Ana, Konstantopoulou, Irene, Papi, Laura, Papp, Janos, Senter, Leigha, Kyung Park, Sue, Pasini, Barbara, Pedersen, Inge Sokilde, Peixoto, Ana, Peruga, Nina, Leeneer, Kim de, Peterlongo, Paolo, Blanco, Amie M., Thull, Darcy L., Pohl, Esther, Pradhan, Nisha, Prajzendanc, Karolina, Prieur, Fabienne, Shah, Payal D., Pujol, Pascal, Torres, Diana, Pauw, Antoine de, Radice, Paolo, Sharma, Priyanka, Side, Lucy E., Tischkowitz, Marc, Blazer, Kathleen R., Simard, Jacques, Singer, Christian F., Skytte, Anne-Bine, Slavin, Thomas P., Snape, Katie, Rashid, Muhammad Usman, Gronwald, Jacek, McGuffog, Lesley, Sobol, Hagay, Southey, Melissa, Tognazzo, Silvia, Steele, Linda, Blok, Marinus J., Steinemann, Doris, Toland, Amanda Ewart, Topka, Sabine, Delnatte, Capucine, Trainer, Alison H., Tung, Nadine, Hahnen, Eric, Asperen, Christi J. van, Hout, Annemieke H. van der, Korach, Jacob, Hogervorst, Frans B. L., Leslie, Goska, Kolk, Lizet E. van der, Luijt, Rob B. van der, Weitzel, Jeffrey N., Heetvelde, Mattias van, Varesco, Liliana, Varon-Mateeva, Raymonda, Vega, Ana, Villarreal-Garza, Cynthia, Hauke, Jan, Laitman, Yael, Wachenfeldt, Anna von, Ramus, Susan J., Walker, Lisa, Díez, Orland, Wang-Gohrke, Shan, Aalfs, Cora M., Wappenschmidt, Barbara, Weber, Bernhard H. F., Yannoukakos, Drakoulis, Yoon, Sook-Yee, Zanzottera, Cristina, Lasa, Adrian, Zidan, Jamal, HEBON, Lee, Min Hyuk, Bonanni, Bernardo, Zorn, Kristin K., Selkirk, Christina G. Hutten, Hulick, Peter J., Chenevix-Trench, Georgia, Abugattas, Julio, Spurdle, Amanda B., Antoniou, Antonis C., Lasset, Christine, Nathanson, Katherine L., Sukiennicki, Grzegorz, Adlard, Julian, Agata, Simona, Bradbury, Angela R., Henderson, Alex, Aittomäki, Kristiina, Andrews, Lesley, Andrulis, Irene L., Arason, Adalgeir, Arnold, Norbert, Couch, Fergus J., Ding, Yuan Chun, Arun, Branu K., Asseryanis, Ella, Auerbach, Leo, Azzollini, Jacopo, Brewer, Carole, Balmaña, Judith, Hentschel, Julia, Barile, Monica, Buecher, Bruno, Buys, Saundra S., Ditsch, Nina, Lázaro, Conxi, Caldés, Trinidad, Caliebe, Almuth, Caligo, Maria A., Campbell, Ian, Caputo, Sandrine M., Rantala, Johanna, Honisch, Ellen, Chiquette, Jocelyne, Chung, Wendy K., Domchek, Susan M., Claes, Kathleen B., Lee, Annette T., Collée, J. Margriet, Evans, D. Gareth, Dorfling, Cecilia M., Velázquez Pérez, Carolina, Dworniczak, Bernd, Eason, Jacqueline, Rhiem, Kerstin, Easton, Douglas F., Eeles, Ros, Sutter, Christian, Schmidt, Ane Y., Imyanitov, Evgeny N., Ehrencrona, Hans, Ejlertsen, Bent, EMBRACE, Engel, Christoph, Engert, Stefanie, Faivre, Laurence, Feliubadaló, Lidia, Robson, Mark, szabo, Csilla I., Tan, Yen Y., Fert Ferrer, Sandra, Barkardottir, Rosa B., Foretova, Lenka, Fowler, Jeffrey, Isaacs, Claudine, Frost, Debra, Galvão, Henrique C. R., Ganz, Patricia A., Garber, Judy, Gauthier-Villars, Marion, Teixeira, Manuel R., Gehrig, Andrea, Rodriguez, Gustavo C., Lester, Jenny, GEMO Study Collaborators, Gerdes, Anne-Marie, Gesta, Paul, Giannini, Giuseppe, Izat, Louise, Giraud, Sophie, Glendon, Gord, Terry, Mary Beth, Godwin, Andrew K., Izquierdo, Angel, Jakubowska, Anna, Lesueur, Fabienne, Rogers, Mark T., James, Paul, Janavicius, Ramunas, Jensen, Uffe Birk, John, Esther M., Vijai, Joseph, Gutierrez-Barrera, Angelica, Chan, T. L., Kaczmarek, Katarzyna, Karlan, Beth Y., Kast, Karin, Liljegren, Annelie, KConFab Investigators, Rudaitis, Vilius, Kim, Sung-Won, Lindor, Noralane M., Longy, Michel, Teulé, Alex, Loud, Jennifer T., Lu, Karen H., Goldgar, David E., Lubinski, Jan, Machackova, Eva, Barrowdale, Daniel, Rensburg, Elizabeth J. van, Manoukian, Siranoush, Mari, Véronique, Martínez-Bouzaz, Cristina, Parsons, Michael T., Matrai, Zoltan, Fundações de Amparo à Pesquisa (Brasil), Research Foundation - Flanders, University of Helsinki, Sigrid Juselius Foundation, Dutch Cancer Society, Netherlands Organization for Scientific Research, Asociación Española Contra el Cáncer, Generalitat de Catalunya, Ministero della Salute, Istituto Oncologico Veneto, University of Tasmania, Australian Cancer Research Foundation, Ministry of Health and Welfare (South Korea), Charles University (Czech Republic), National Research Foundation Singapore, Russian Foundation for Basic Research, Istituto Toscano Tumori, Israel Cancer Association USA, Swedish Cancer Society, Foundation for Women's Cancer, University of Pittsburgh, Cancer Australia, American Cancer Society, The Ohio State University, National Institutes of Health (US), Cancer Research UK, European Commission, Canadian Institutes of Health Research, Department of Trade and Industry (UK), Susan G. Komen Foundation, Breast Cancer Research Foundation, Genome Canada, National Cancer Institute (US), Research Council of Lithuania, Cancer Association of South Africa, Consejo Nacional de Investigaciones Científicas y Técnicas (Argentina), Instituto de Salud Carlos III, Ministerio de Economía y Competitividad (España), Ministerio de Sanidad y Política Social (España), Associazione Italiana per la Ricerca sul Cancro, Fondazione Italiana per la Ricerca sul Cancro, Ministero dell'Istruzione, dell'Università e della Ricerca, Institut Pasteur, Fondazione Cenci Bolognetti, Greek Government, Pontificia Universidad Javeriana, Royal Marsden NHS Foundation Trust, Kansas State University, Fundación Mutua Madrileña, Ligue Nationale contre le Cancer (France), Georgetown University, Rebbeck, Timothy R., Friebel, Tara M., Friedman, Eitan, Hamann, Ute, Huo, Dezheng, Kwong, Ava, Olah, Edith, Olopade, Olufunmilayo I., Solano, Angela R., Teo, Soo-Hwamg, Thomassen, Mads, Mebirouk, Noura, Meijers-Heijboer, Hanne, Meindl, Alfons, Mensenkamp, Arjen R., Kruse, Torben A., Benitez, Javier, Mickys, Ugnius, Greene, Mark H., Miller, Austin, thomas, Abigail, Cook, Jackie, Montagna, Marco, Moysich, Kirsten B., Mulligan, Anna Marie, Musinsky, Jacob, Neuhausen, Susan L., Nevanlinna, Heli, Ngeow, Joanne, Berger, Andreas, Nguyen, Huu Phuc, Palmero, Edenir Inêz, Davidson, Rosemarie, Bonadona, Valérie, Schmutzler, Rita Katharina, Niederacher, Dieter, Nielsen, Henriette Roed, Nielsen, Finn Cilius, Nussbaum, Robert L., Offit, Kenneth, Öfverholm, Anna, Ong, Kai-ren, Berger, Raanan, Hoya, Miguel de la, Osorio, Ana, Konstantopoulou, Irene, Papi, Laura, Papp, Janos, Senter, Leigha, Kyung Park, Sue, Pasini, Barbara, Pedersen, Inge Sokilde, Peixoto, Ana, Peruga, Nina, Leeneer, Kim de, Peterlongo, Paolo, Blanco, Amie M., Thull, Darcy L., Pohl, Esther, Pradhan, Nisha, Prajzendanc, Karolina, Prieur, Fabienne, Shah, Payal D., Pujol, Pascal, Torres, Diana, Pauw, Antoine de, Radice, Paolo, Sharma, Priyanka, Side, Lucy E., Tischkowitz, Marc, Blazer, Kathleen R., Simard, Jacques, Singer, Christian F., Skytte, Anne-Bine, Slavin, Thomas P., Snape, Katie, Rashid, Muhammad Usman, Gronwald, Jacek, McGuffog, Lesley, Sobol, Hagay, Southey, Melissa, Tognazzo, Silvia, Steele, Linda, Blok, Marinus J., Steinemann, Doris, Toland, Amanda Ewart, Topka, Sabine, Delnatte, Capucine, Trainer, Alison H., Tung, Nadine, Hahnen, Eric, Asperen, Christi J. van, Hout, Annemieke H. van der, Korach, Jacob, Hogervorst, Frans B. L., Leslie, Goska, Kolk, Lizet E. van der, Luijt, Rob B. van der, Weitzel, Jeffrey N., Heetvelde, Mattias van, Varesco, Liliana, Varon-Mateeva, Raymonda, Vega, Ana, Villarreal-Garza, Cynthia, Hauke, Jan, Laitman, Yael, Wachenfeldt, Anna von, Ramus, Susan J., Walker, Lisa, Díez, Orland, Wang-Gohrke, Shan, Aalfs, Cora M., Wappenschmidt, Barbara, Weber, Bernhard H. F., Yannoukakos, Drakoulis, Yoon, Sook-Yee, Zanzottera, Cristina, Lasa, Adrian, Zidan, Jamal, HEBON, Lee, Min Hyuk, Bonanni, Bernardo, Zorn, Kristin K., Selkirk, Christina G. Hutten, Hulick, Peter J., Chenevix-Trench, Georgia, Abugattas, Julio, Spurdle, Amanda B., Antoniou, Antonis C., Lasset, Christine, Nathanson, Katherine L., Sukiennicki, Grzegorz, Adlard, Julian, Agata, Simona, Bradbury, Angela R., Henderson, Alex, Aittomäki, Kristiina, Andrews, Lesley, Andrulis, Irene L., Arason, Adalgeir, Arnold, Norbert, Couch, Fergus J., Ding, Yuan Chun, Arun, Branu K., Asseryanis, Ella, Auerbach, Leo, Azzollini, Jacopo, Brewer, Carole, Balmaña, Judith, Hentschel, Julia, Barile, Monica, Buecher, Bruno, Buys, Saundra S., Ditsch, Nina, Lázaro, Conxi, Caldés, Trinidad, Caliebe, Almuth, Caligo, Maria A., Campbell, Ian, Caputo, Sandrine M., Rantala, Johanna, Honisch, Ellen, Chiquette, Jocelyne, Chung, Wendy K., Domchek, Susan M., Claes, Kathleen B., Lee, Annette T., Collée, J. Margriet, Evans, D. Gareth, Dorfling, Cecilia M., Velázquez Pérez, Carolina, Dworniczak, Bernd, Eason, Jacqueline, Rhiem, Kerstin, Easton, Douglas F., Eeles, Ros, Sutter, Christian, Schmidt, Ane Y., Imyanitov, Evgeny N., Ehrencrona, Hans, Ejlertsen, Bent, EMBRACE, Engel, Christoph, Engert, Stefanie, Faivre, Laurence, Feliubadaló, Lidia, Robson, Mark, szabo, Csilla I., Tan, Yen Y., Fert Ferrer, Sandra, Barkardottir, Rosa B., Foretova, Lenka, Fowler, Jeffrey, Isaacs, Claudine, Frost, Debra, Galvão, Henrique C. R., Ganz, Patricia A., Garber, Judy, Gauthier-Villars, Marion, Teixeira, Manuel R., Gehrig, Andrea, Rodriguez, Gustavo C., Lester, Jenny, GEMO Study Collaborators, Gerdes, Anne-Marie, Gesta, Paul, Giannini, Giuseppe, Izat, Louise, Giraud, Sophie, Glendon, Gord, Terry, Mary Beth, Godwin, Andrew K., Izquierdo, Angel, Jakubowska, Anna, Lesueur, Fabienne, Rogers, Mark T., James, Paul, Janavicius, Ramunas, Jensen, Uffe Birk, John, Esther M., Vijai, Joseph, Gutierrez-Barrera, Angelica, Chan, T. L., Kaczmarek, Katarzyna, Karlan, Beth Y., Kast, Karin, Liljegren, Annelie, KConFab Investigators, Rudaitis, Vilius, Kim, Sung-Won, Lindor, Noralane M., Longy, Michel, Teulé, Alex, Loud, Jennifer T., Lu, Karen H., Goldgar, David E., Lubinski, Jan, Machackova, Eva, Barrowdale, Daniel, Rensburg, Elizabeth J. van, Manoukian, Siranoush, Mari, Véronique, Martínez-Bouzaz, Cristina, Parsons, Michael T., and Matrai, Zoltan
Abstract: The prevalence and spectrum of germline mutations in BRCA1 and BRCA2 have been reported in single populations, with the majority of reports focused on White in Europe and North America. The Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA) has assembled data on 18,435 families with BRCA1 mutations and 11,351 families with BRCA2 mutations ascertained from 69 centers in 49 countries on six continents. This study comprehensively describes the characteristics of the 1,650 unique BRCA1 and 1,731 unique BRCA2 deleterious (disease-associated) mutations identified in the CIMBA database. We observed substantial variation in mutation type and frequency by geographical region and race/ethnicity. In addition to known founder mutations, mutations of relatively high frequency were identified in specific racial/ethnic or geographic groups that may reflect founder mutations and which could be used in targeted (panel) first pass genotyping for specific populations. Knowledge of the population-specific mutational spectrum in BRCA1 and BRCA2 could inform efficient strategies for genetic testing and may justify a more broad-based oncogenetic testing in some populations.
Published: 2018

23. Dynamics of coherence, localization and excitation transfer in disordered nanorings

Author: National Natural Science Foundation of China, Consejo Superior de Investigaciones Científicas (España), Ministerio de Economía y Competitividad (España), National Research Foundation Singapore, Somoza, A. D., Sun, Ke-Wei, Molina, Rafael A., Zhao, Yang, National Natural Science Foundation of China, Consejo Superior de Investigaciones Científicas (España), Ministerio de Economía y Competitividad (España), National Research Foundation Singapore, Somoza, A. D., Sun, Ke-Wei, Molina, Rafael A., and Zhao, Yang
Abstract: Self-assembled supramolecular aggregates are excellent candidates for the design of efficient excitation transport devices. Both artificially prepared and natural photosynthetic aggregates in plants and bacteria present an important degree of disorder that is supposed to hinder excitation transport. Besides, molecular excitations couple to nuclear motion affecting excitation transport in a variety of ways. We present an exhaustive study of exciton dynamics in disordered nanorings with long-range interactions under the influence of a phonon bath taking the LH2 system of purple bacteria as a model. Nuclear motion is explicitly taken into account by employing the Davydov ansatz description of the polaron and quantum dynamics are obtained using a time-dependent variational method. We reveal an optimal exciton-phonon coupling that suppresses disorder-induced localization and facilitate excitation de-trapping. This excitation transfer enhancement, mediated by environmental phonons, is attributed to energy relaxation toward extended, low-energy excitons provided by the precise LH2 geometry with anti-parallel dipoles and long-range interactions. An analysis of localization and spectral statistics is followed by dynamic measures of coherence and localization, transfer efficiency and superradiance. Linear absorption, 2D photon-echo spectra and diffusion measures of the exciton are examined to monitor the diffusive behavior as a function of the strengths of disorder and exciton-phonon coupling.
Published: 2017

24. Heat-induced masculinization in domesticated zebrafish is family-specific and yields a set of different gonadal transcriptomes

Author: National Research Foundation Singapore, Prime Minister's Office Singapore, Agri-Food and Veterinary Authority of Singapore, Temasek Life Sciences Laboratory, Ministerio de Economía y Competitividad (España), Generalitat de Catalunya, Consejo Superior de Investigaciones Científicas (España), Ribas, Laia, Liew, Woei-Chang, Díaz, Noelia, Sreenivasan, Rajini, Orbán, László, Piferrer, Francesc, National Research Foundation Singapore, Prime Minister's Office Singapore, Agri-Food and Veterinary Authority of Singapore, Temasek Life Sciences Laboratory, Ministerio de Economía y Competitividad (España), Generalitat de Catalunya, Consejo Superior de Investigaciones Científicas (España), Ribas, Laia, Liew, Woei-Chang, Díaz, Noelia, Sreenivasan, Rajini, Orbán, László, and Piferrer, Francesc
Abstract: Understanding environmental influences on sex ratios is important for the study of the evolution of sex-determining mechanisms and for evaluating the effects of global warming and chemical pollution. Fishes exhibit sexual plasticity, but the underlying mechanisms of environmental effects on their reproduction are unclear even in the well-established teleost research model, the zebrafish. Here we established the conditions to study the effects of elevated temperature on zebrafish sex. We showed that sex ratio response to elevated temperature is family-specific and typically leads to masculinization (female-To-male sex reversal), resulting in neomales. These results uncovered genotype-by-environment interactions that support a polygenic sex determination system in domesticated (laboratory) zebrafish. We found that some heat-Treated fish had gene expression profiles similar to untreated controls of the same sex, indicating that they were resistant to thermal effects. Further, most neomales had gonadal transcriptomes similar to that of regular males. Strikingly, we discovered heat-Treated females that displayed a normal ovarian phenotype but with a >male-like> gonadal transcriptome. Such major transcriptomic reprogramming with preserved organ structure has never been reported. Juveniles were also found to have a male-like transcriptome shortly after exposure to heat. These findings were validated by analyzing the expression of genes and signaling pathways associated with sex differentiation. Our results revealed a lasting thermal effect on zebrafish gonads, suggesting new avenues for detection of functional consequences of elevated temperature in natural fish populations in a global warming scenario.
Published: 2017

25. Enhanced thermoelectric performance of solution-derived bismuth telluride based nanocomposites via liquid-phase Sintering

Author: Ministry of Education (Singapore), National Research Foundation Singapore, Nanyang Technological University, Ministerio de Economía y Competitividad (España), Agency for Science, Technology and Research A*STAR (Singapore), Generalitat de Catalunya, Zhang, Chaohua, Mata, Maria de la, Belarre, Francisco J., Arbiol, Jordi, Xiong, Qihua, Ministry of Education (Singapore), National Research Foundation Singapore, Nanyang Technological University, Ministerio de Economía y Competitividad (España), Agency for Science, Technology and Research A*STAR (Singapore), Generalitat de Catalunya, Zhang, Chaohua, Mata, Maria de la, Belarre, Francisco J., Arbiol, Jordi, and Xiong, Qihua
Abstract: Bismuth telluride based thermoelectric materials show great promise in electricity generation from waste heat and solid-state refrigeration, but improving their conversion efficiency with economical approaches for widespread use remains a challenge. An economical facile bottom-up approach has been developed to obtain nanostructured powders, which are used to build bulk thermoelectric materials. Using excess tellurium as sacrificial additive to enable liquid-phase sintering in the spark plasma sintering process, the lattice and bipolar contributions to the thermal conductivity are both greatly reduced without compromising too much the power factor, which leads to the achievement of high figure of merit (ZT) in both n-type and p-type bismuth telluride based nanocomposites. The ZT values are 1.59±0.16 for p-type BiSbTe and 0.98±0.07 for n-type BiTeSe at 370 K, which are significantly high for bottom-up approaches. These results demonstrate that solution-chemistry approaches as facile, scalable and low-energy-intensive ways to achieve nanopowders, combined with liquid-phase sintering process, can open up great possibilities in developing high-performance low-price thermoelectric bulk nanocomposites.
Published: 2016

26. Spin dynamics in bilayer graphene: Role of electron-hole puddles and Dyakonov-Perel mechanism

Author: European Commission, Ministerio de Economía y Competitividad (España), National Research Foundation Singapore, Tuan, Dinh van, Adam, Shaffique, Roche, Stephan, European Commission, Ministerio de Economía y Competitividad (España), National Research Foundation Singapore, Tuan, Dinh van, Adam, Shaffique, and Roche, Stephan
Abstract: We report on spin transport features which are unique to high quality bilayer graphene, in the absence of magnetic contaminants and strong intervalley mixing. The time-dependent spin polarization of a propagating wave packet is computed using an efficient quantum transport method. In the limit of vanishing effects of substrate and disorder, the energy dependence of the spin lifetime is similar to monolayer graphene with an M-shaped profile and minimum value at the charge neutrality point, but with an electron-hole asymmetry fingerprint. In sharp contrast, the incorporation of substrate-induced electron-hole puddles (characteristics of supported graphene either on SiO2 or hBN) surprisingly results in a large enhancement of the low-energy spin lifetime and a lowering of its high-energy values. Such a feature, unique to the bilayer, is explained in terms of a reinforced Dyakonov-Perel mechanism at the Dirac point, whereas spin relaxation at higher energies is driven by pure dephasing effects. This suggests further electrostatic control of the spin transport length scales in graphene devices.
Published: 2016

27. Superradiance at the localization-delocalization crossover in tubular chlorosomes

Author: National Research Foundation Singapore, Comunidad de Madrid, Ministerio de Economía y Competitividad (España), Consejo Superior de Investigaciones Científicas (España), Molina, Rafael A., Benito-Matías, E., Somoza, A. D., Chen, L., Zhao, Y., National Research Foundation Singapore, Comunidad de Madrid, Ministerio de Economía y Competitividad (España), Consejo Superior de Investigaciones Científicas (España), Molina, Rafael A., Benito-Matías, E., Somoza, A. D., Chen, L., and Zhao, Y.
Abstract: We study the effect of disorder on spectral properties of tubular chlorosomes in green sulfur bacteria Cf. aurantiacus. Employing a Frenkel-exciton Hamiltonian with diagonal and off-diagonal disorder consistent with spectral and structural studies, we analyze excitonic localization and spectral statistics of the chlorosomes. A size-dependent localization-delocalization crossover is found to occur as a function of the excitonic energy. The crossover energy region coincides with the more optically active states with maximized superradiance and is, consequently, more conducive for energy transfer. ©2016 American Physical Society
Published: 2016

28. Chemical control over the energy-level alignment in a two-terminal junction

Author: National Research Foundation Singapore, Consejo Superior de Investigaciones Científicas (España), European Commission, European Research Council, Ministerio de Economía y Competitividad (España), Generalitat de Catalunya, Centro de Investigación Biomédica en Red Bioingeniería, Biomateriales y Nanomedicina (España), Li, Yuan, Franco, Carlos, Crivillers, Núria, Mas Torrent, Marta, Liang, Cao, Suchand Sangeeth, C.S., Rovira, Concepció, Veciana, Jaume, Nijhuis, Christian A., National Research Foundation Singapore, Consejo Superior de Investigaciones Científicas (España), European Commission, European Research Council, Ministerio de Economía y Competitividad (España), Generalitat de Catalunya, Centro de Investigación Biomédica en Red Bioingeniería, Biomateriales y Nanomedicina (España), Li, Yuan, Franco, Carlos, Crivillers, Núria, Mas Torrent, Marta, Liang, Cao, Suchand Sangeeth, C.S., Rovira, Concepció, Veciana, Jaume, and Nijhuis, Christian A.
Abstract: The energy-level alignment of molecular transistors can be controlled by external gating to move molecular orbitals with respect to the Fermi levels of the source and drain electrodes. Two-terminal molecular tunnelling junctions, however, lack a gate electrode and suffer from Fermi-level pinning, making it difficult to control the energy-level alignment of the system. Here we report an enhancement of 2 orders of magnitude of the tunnelling current in a two-terminal junction via chemical molecular orbital control, changing chemically the molecular component between a stable radical and its non-radical form without altering the supramolecular structure of the junction. Our findings demonstrate that the energy-level alignment in self-assembled monolayer-based junctions can be regulated by purely chemical modifications, which seems an attractive alternative to control the electrical properties of two-terminal junctions.
Published: 2016

29. Endocrine remodelling of the adult intestine sustains reproduction in drosophila

Author: Wellcome Trust, European Research Council, Medical Research Council (UK), Generalitat Valenciana, Ministerio de Ciencia e Innovación (España), Ministerio de Economía y Competitividad (España), Fundación Botín, National Research Foundation Singapore, German Research Foundation, European Commission, EMBO, Reiff, Tobias, Jacobson, Jake, Cognigni, Paola, Antonello, Zeus A., Ballesta-Illan, Esther, Tan, Kah Junn, Yew, Joanne Y., Domínguez, María, Miguel-Aliaga, Irene, Wellcome Trust, European Research Council, Medical Research Council (UK), Generalitat Valenciana, Ministerio de Ciencia e Innovación (España), Ministerio de Economía y Competitividad (España), Fundación Botín, National Research Foundation Singapore, German Research Foundation, European Commission, EMBO, Reiff, Tobias, Jacobson, Jake, Cognigni, Paola, Antonello, Zeus A., Ballesta-Illan, Esther, Tan, Kah Junn, Yew, Joanne Y., Domínguez, María, and Miguel-Aliaga, Irene
Abstract: The production of offspring is energetically costly and relies on incompletely understood mechanisms that generate a positive energy balance. In mothers of many species, changes in key energy-associated internal organs are common yet poorly characterised functionally and mechanistically. In this study, we show that, in adult Drosophila females, the midgut is dramatically remodelled to enhance reproductive output. In contrast to extant models, organ remodelling does not occur in response to increased nutrient intake and/or offspring demands, but rather precedes them. With spatially and temporally directed manipulations, we identify juvenile hormone (JH) as an anticipatory endocrine signal released after mating. Acting through intestinal bHLH-PAS domain proteins Methoprene-tolerant (Met) and Germ cell-expressed (Gce), JH signals directly to intestinal progenitors to yield a larger organ, and adjusts gene expression and sterol regulatory element-binding protein (SREBP) activity in enterocytes to support increased lipid metabolism. Our findings identify a metabolically significant paradigm of adult somatic organ remodelling linking hormonal signals, epithelial plasticity, and reproductive output.
Published: 2015

30. Hunt for slow slip events along the Sumatran subduction zone in a decade of continuous GPS data

Author: National Research Foundation Singapore, Ministry of Education (Singapore), Feng, Lujia, Hill, Emma, Elosegui, Pedro, Qiu, Qiang, Hermawan, Iwan, Banerjee, Paramesh, Sieh, Kerry, National Research Foundation Singapore, Ministry of Education (Singapore), Feng, Lujia, Hill, Emma, Elosegui, Pedro, Qiu, Qiang, Hermawan, Iwan, Banerjee, Paramesh, and Sieh, Kerry
Abstract: Slow slip events (SSEs) have been observed in GPS time series for many subduction zones worldwide but not in decade-long GPS time series from the Sumatran GPS Array (SuGAr). An outstanding question has been whether SSEs have simply not occurred on the Sunda megathrust or whether they have been obscured by the prodigious number of earthquakes and their ensuing postseismic deformation within the time of geodetic observation. We remove all known tectonic signals from the time series to search for evidence of SSEs. The residuals are essentially flat at the centimeter scale. To search for signals at the millimeter scale we test various filtering and visualization techniques. Despite these efforts, we conclude that it is difficult to confirm that SSEs exist at this scale using the current data, although we do see a few suspicious signals. The lack of evidence for events may reflect SSEs occurring at a magnitude, location, or timescale that renders them undetectable with the current resolution of the SuGAr, that the properties of this megathrust are not conducive to SSEs, or because the megathrust is in an active period of the earthquake cycle
Published: 2015

31. High-yield synthesis and optical properties of g-C3N4

Author: National Research Foundation Singapore, Generalitat de Catalunya, Ministerio de Economía y Competitividad (España), European Commission, Ministry of Education (Singapore), German Academic Exchange Service, Yuan, Yanwen, Genç, Aziz, Dunin-Borkowski, Rafal E., Arbiol, Jordi, Xiong, Qihua, National Research Foundation Singapore, Generalitat de Catalunya, Ministerio de Economía y Competitividad (España), European Commission, Ministry of Education (Singapore), German Academic Exchange Service, Yuan, Yanwen, Genç, Aziz, Dunin-Borkowski, Rafal E., Arbiol, Jordi, and Xiong, Qihua
Abstract: Graphitic carbon nitride (g-C3N4), a metal-free semiconductor with a band gap of 2.7 eV, has received considerable attention owing to its fascinating photocatalytic performances under visible-light. g-C3N4 exhibits high thermal and chemical stability and non-toxicity such that it has been considered as the most promising photocatalyst for environmental improvement and energy conservation. Hence, it is of great importance to obtain high-quality g-C3N4 and gain a clear understanding of its optical properties. Herein, we report a high-yield synthesis of g-C3N4 products via heating of high vacuum-sealed melamine powder in an ampoule at temperatures between 450 and 650 °C. Using transmission electron microscopy (TEM), scanning transmission electron microscopy (STEM), electron energy loss spectroscopy (EELS), thermogravimetric analysis (TGA), X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS), the chemical composition and crystallization of the as-produced g-C3N4 are demonstrated. A systematic optical study of g-C3N4 is carried out with several approaches. The optical phonon behavior of g-C3N4 is revealed by infrared and Raman spectroscopy, and the emission properties of g-C3N4 are investigated using photoluminescence (PL) spectroscopy, while the photocatalytic properties are explored by the photodegradation experiment.
Published: 2015

32. Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants

Author: National Research Foundation Singapore, Agency for Science, Technology and Research A*STAR (Singapore), Centro Esther Koplowitz, European Foundation for the Study of Diabetes, Fundación Lilly, National University of Singapore, Junta de Andalucía, Wellcome Trust, Juvenile Diabetes Research Foundation International, European Commission, Ministerio de Economía y Competitividad (España), Tena, Juan J., Gómez-Marín, Carlos, Gómez-Skarmeta, José Luis, Ferrer, Jorge, National Research Foundation Singapore, Agency for Science, Technology and Research A*STAR (Singapore), Centro Esther Koplowitz, European Foundation for the Study of Diabetes, Fundación Lilly, National University of Singapore, Junta de Andalucía, Wellcome Trust, Juvenile Diabetes Research Foundation International, European Commission, Ministerio de Economía y Competitividad (España), Tena, Juan J., Gómez-Marín, Carlos, Gómez-Skarmeta, José Luis, and Ferrer, Jorge
Abstract: Type 2 diabetes affects over 300 million people, causing severe complications and premature death, yet the underlying molecular mechanisms are largely unknown. Pancreatic islet dysfunction is central in type 2 diabetes pathogenesis, and understanding islet genome regulation could therefore provide valuable mechanistic insights. We have now mapped and examined the function of human islet cis-regulatory networks. We identify genomic sequences that are targeted by islet transcription factors to drive islet-specific gene activity and show that most such sequences reside in clusters of enhancers that form physical three-dimensional chromatin domains. We find that sequence variants associated with type 2 diabetes and fasting glycemia are enriched in these clustered islet enhancers and identify trait-associated variants that disrupt DNA binding and islet enhancer activity. Our studies illustrate how islet transcription factors interact functionally with the epigenome and provide systematic evidence that the dysregulation of islet enhancers is relevant to the mechanisms underlying type 2 diabetes.
Published: 2014

33. Analytical model for polarization-dependent light propagation in waveguide arrays and applications

Author: Fondo Nacional de Desarrollo Científico y Tecnológico (Chile), Comisión Nacional de Investigación Científica y Tecnológica (Chile), Federal Ministry of Education and Research (Germany), Thuringian Ministry of Education, Science and Culture, National Research Foundation Singapore, German-Israeli Foundation for Scientific Research and Development, Ministry of Education (Singapore), Rojas-Rojas, Santiago, Naether, Uta, Fondo Nacional de Desarrollo Científico y Tecnológico (Chile), Comisión Nacional de Investigación Científica y Tecnológica (Chile), Federal Ministry of Education and Research (Germany), Thuringian Ministry of Education, Science and Culture, National Research Foundation Singapore, German-Israeli Foundation for Scientific Research and Development, Ministry of Education (Singapore), Rojas-Rojas, Santiago, and Naether, Uta
Abstract: We study the polarization properties of elliptical femtosecond-laser-written waveguide arrays. An analytical model is presented to explain the asymmetry of the spatial transverse profiles of linearly polarized modes in these waveguides. This asymmetry produces a polarization-dependent coupling coefficient, between adjacent waveguides, which strongly affects the propagation of light in a lattice. Our analysis explains how this effect can be exploited to tune the final intensity distribution of light propagated through the array and links the properties of a polarizing beam splitter in integrated optical circuits to the geometry of the waveguides.
Published: 2014

34. Bias induced transition from an ohmic to a non-ohmic interface in supramolecular tunneling junctions with Ga2O3/EGaIn top electrode

Author: National Research Foundation Singapore, Wimbush, Kim S., Fratila, Raluca M., Wang, Dandan, Qi, Dongchen, Liang, Cao, Yuan, Li, Yakovlev, Nikolai, Loh, Kian Ping, Reinhoudt, David N., Velders, Aldrik H., Nijhuis, Christian A., National Research Foundation Singapore, Wimbush, Kim S., Fratila, Raluca M., Wang, Dandan, Qi, Dongchen, Liang, Cao, Yuan, Li, Yakovlev, Nikolai, Loh, Kian Ping, Reinhoudt, David N., Velders, Aldrik H., and Nijhuis, Christian A.
Abstract: This study describes that the current rectification ratio, R ≡ |J|(−2.0 V)/|J|(+2.0 V) for supramolecular tunneling junctions with a top-electrode of eutectic gallium indium (EGaIn) that contains a conductive thin (0.7 nm) supporting outer oxide layer (Ga2O3), increases by up to four orders of magnitude under an applied bias of >+1.0 V up to +2.5 V; these junctions did not change their electrical characteristics when biased in the voltage range of ±1.0 V. The increase in R is caused by the presence of water and ions in the supramolecular assemblies which react with the Ga2O3/EGaIn layer and increase the thickness of the Ga2O3 layer. This increase in the oxide thickness from 0.7 nm to ∼2.0 nm changed the nature of the monolayer–top-electrode contact from an ohmic to a non-ohmic contact. These results unambiguously expose the experimental conditions that allow for a safe bias window of ±1.0 V (the range of biases studies of charge transport using this technique are normally conducted) to investigate molecular effects in molecular electronic junctions with Ga2O3/EGaIn top-electrodes where electrochemical reactions are not significant. Our findings also show that the interpretation of data in studies involving applied biases of >1.0 V may be complicated by electrochemical side reactions which can be recognized by changes of the electrical characteristics as a function voltage cycling or in current retention experiments.
Published: 2014

35. The growth of ultralong ZnTe micro/nanostructures: The influence of polarity and twin direction on the morphogenesis of nanobelts and nanosheets

Author: National Research Foundation Singapore, Ministry of Education (Singapore), Nanyang Technological University, Ministerio de Ciencia e Innovación (España), Generalitat de Catalunya, Utama, Muhammad Iqbal Bakti, Mata, María de la, Zhang, Qing, Magén, César, Arbiol, Jordi, Xiong, Qihua, National Research Foundation Singapore, Ministry of Education (Singapore), Nanyang Technological University, Ministerio de Ciencia e Innovación (España), Generalitat de Catalunya, Utama, Muhammad Iqbal Bakti, Mata, María de la, Zhang, Qing, Magén, César, Arbiol, Jordi, and Xiong, Qihua
Abstract: Although ZnTe nanobelts present an intriguing platform to study various optical properties and phenomena in semiconductors, there was very limited study regarding the crystalline structure and defects of ZnTe nanobelts. Here, we correlate the structural properties and features in the crystal of ZnTe nanobelts with the resulting as-synthesized morphology. Ultralong ZnTe nanobelts were synthesized to reach the subcentimeter length scale. Two types of nanobelts were identified according to whether tapering was present and discerned on the basis of crystallinity and polarity of the structure. We conclude that tapered sheetlike nanobelts have Te-terminated lateral facets that induced lateral growth, whereas untapered nanobelts have facets that are nonpolar and nonreactive. Axial and transversal twins were also observed, where the polarity was conserved across twinning boundaries. © 2013 American Chemical Society.
Published: 2013

36. Twinning-, polytypism-, and polarity-induced morphological modulation in nonplanar nanostructures with van der Waals Epitaxy

Author: National Research Foundation Singapore, Nanyang Technological University, Ministerio de Ciencia e Innovación (España), Generalitat de Catalunya, Utama, Muhammad Iqbal Bakti, Mata, María de la, Magen, Cesar, Arbiol, Jordi, Xiong, Qihua, National Research Foundation Singapore, Nanyang Technological University, Ministerio de Ciencia e Innovación (España), Generalitat de Catalunya, Utama, Muhammad Iqbal Bakti, Mata, María de la, Magen, Cesar, Arbiol, Jordi, and Xiong, Qihua
Abstract: Twinning, polytypism, and polarity are important aspects in nanostructural growth since their presence can affect various properties of the as-grown products. The morphology of nanostructures grown via van der Waals epitaxy is shown to be strongly influenced by the twinning density and the presence of polytypism within the nanostructures, while the growth direction is driven by the compound polarity. With ZnTe as the model material, vertically aligned nanorods are successfully produced with variable cross-section and branched crystals (tripods and tetrapods) on only a single type of substrate. Van der Waals epitaxy contributes by relaxing the lattice-mismatch requirements for epitaxial growth and by enabling a variety of crystal planes in the initial stages of the growth to be interfaced to the substrate, regardless of the polarity of the epitaxial material. These results may provide more flexibility in tuning rationally the morphology of epitaxial nanostructures into other shapes with higher complexity by routine adjustment of growth environment. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Published: 2013

37. Polarity assignment in ZnTe, GaAs, ZnO, and GaN-AlN nanowires from direct dumbbell analysis

Author: Ministerio de Ciencia e Innovación (España), Generalitat de Catalunya, European Research Council, National Centres of Competence in Research (Switzerland), National Research Foundation Singapore, Nanyang Technological University, European Commission, Mata, María de la, Magen, Cesar, Gazquez, Jaume, Utama, Muhammad Iqbal Bakti, Heiss, Martin, Lopatin, Sergei, Furtmayr, Florian, Fernández-Rojas, Carlos J, Peng, Bo, Morante, Joan Ramon, Rurali, Riccardo, Eickhoff, Martin, Fontcuberta i Morral, Anna, Xiong, Qihua, Arbiol, Jordi, Ministerio de Ciencia e Innovación (España), Generalitat de Catalunya, European Research Council, National Centres of Competence in Research (Switzerland), National Research Foundation Singapore, Nanyang Technological University, European Commission, Mata, María de la, Magen, Cesar, Gazquez, Jaume, Utama, Muhammad Iqbal Bakti, Heiss, Martin, Lopatin, Sergei, Furtmayr, Florian, Fernández-Rojas, Carlos J, Peng, Bo, Morante, Joan Ramon, Rurali, Riccardo, Eickhoff, Martin, Fontcuberta i Morral, Anna, Xiong, Qihua, and Arbiol, Jordi
Abstract: Aberration corrected scanning transmission electron microscopy (STEM) with high angle annular dark field (HAADF) imaging and the newly developed annular bright field (ABF) imaging are used to define a new guideline for the polarity determination of semiconductor nanowires (NWs) from binary compounds in two extreme cases: (i) when the dumbbell is formed with atoms of similar mass (GaAs) and (ii) in the case where one of the atoms is extremely light (N or O: ZnO and GaN/AlN). The theoretical fundaments of these procedures allow us to overcome the main challenge in the identification of dumbbell polarity. It resides in the separation and identification of the constituent atoms in the dumbbells. The proposed experimental via opens new routes for the fine characterization of nanostructures, e.g., in electronic and optoelectronic fields, where the polarity is crucial for the understanding of their physical properties (optical and electronic) as well as their growth mechanisms.
Published: 2012

38. Advancing techniques and insights in circulating tumor cell (CTC) research

Author: <p>National Research Foundation Singapore Mechanobiology Institute</p>, Khoo, Bee Luan, Chaudhuri, Parthiv Kant, Lim, Chwee Teck, Warkiani, Majid Ebrahimi, <p>National Research Foundation Singapore Mechanobiology Institute</p>, Khoo, Bee Luan, Chaudhuri, Parthiv Kant, Lim, Chwee Teck, and Warkiani, Majid Ebrahimi
Abstract: Khoo, B. L., Chaudhuri, P. K., Lim, C. T., & Warkiani, M. E. (2017). Advancing techniques and insights in circulating tumor cell (ctc) research. In A. R. Aref & D. Barbie (Eds.), Ex Vivo Engineering of the Tumor Microenvironment (pp. 71-94). Humana Press, Cham. https://doi.org/10.1007/978-3-319-45397-2_5

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