717 results on '"Farber, D."'
Search Results
2. Expanding the Scope of Transnational Environmental Law
- Author
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Etty, T, Heyvaert, V, Carlarne, C, Farber, D, Huber, B, and Van Zeben, J
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Law - Published
- 2017
3. The Maturing of Transnational Environmental Law
- Author
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Etty, T, Heyvaert, V, Carlarne, C, Farber, D, Huber, B, and Van Zeben, J
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Law - Published
- 2017
4. Disease Gradients of Late Blight of Potato from Infrared Images of Commercial Fields
- Author
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Farber, D. H., Kogan, C., and Johnson, D. A.
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- 2020
- Full Text
- View/download PDF
5. GAP-independent termination of photoreceptor light response by excess gamma subunit of the cGMP-phosphodiesterase
- Author
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Tsang, S H, Woodruff, M L, Chen, C K, Yamashita, C Y, Cilluffo, M C, Rao, A L, Farber, D B, and Fain, G L
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rod ,phototransduction ,retina ,phosphodiesterase ,G-protein ,RGS protein - Abstract
We have generated a mouse with rod photoreceptors overexpressing the gamma inhibitory subunit ( PDE6 gamma) of the photoreceptor G-protein effector cGMP phosphodiesterase ( PDE6). PDE6 gamma overexpression decreases the rate of rise of the rod response at dim intensities, indicating a reduction in the gain of transduction that may be the result of cytoplasmic PDE6 gamma binding to activated transducin alpha GTP (T-alpha-GTP) before the T-alpha-GTP binds to endogenous PDE6 gamma. Excess PDE6 gamma also produces a marked acceleration in the falling phase of the light response and more rapid recovery of sensitivity and circulating current after prolonged light exposure. These effects are not mediated by accelerating GTP hydrolysis through the GAP ( GTPase activating protein) complex, because the decay of the light response is also accelerated in rods that overexpress PDE6 gamma but lack RGS9. Our results show that the PDE6 gamma binding sites of PDE6 alpha and beta are accessible to excess (presumably cytoplasmic) PDE6 gamma in the light, once endogenous PDE6 has been displaced from its binding site by T-alpha-GTP. They also suggest that in the presence of T alpha-GTP, the PDE6 gamma remains attached to the rest of the PDE6 molecule, but after conversion of T-alpha-GTP to T-alpha-GDP, the PDE6 gamma may dissociate from the PDE6 and exchange with a cytoplasmic pool. This pool may exist even in wild- type rods and may explain the decay of rod photoresponses in the presence of nonhydrolyzable analogs of GTP.
- Published
- 2006
6. Cross-tissue immune cell analysis reveals tissue-specific features in humans
- Author
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Dominguez Conde, C, Xu, C, Jarvis, L, Rainbow, D, Wells, S, Gomes, T, Howlett, S, Suchanek, O, Polanski, K, King, H, Mamanova, L, Huang, N, Szabo, P, Richardson, L, Bolt, L, Fasouli, E, Mahbubani, K, Prete, M, Tuck, L, Richoz, N, Tuong, Z, Campos, L, Mousa, H, Needham, E, Pritchard, S, Li, T, Elmentaite, R, Park, J, Rahmani, E, Chen, D, Menon, D, Bayraktar, O, James, L, Meyer, K, Yosef, N, Clatworthy, M, Sims, P, Farber, D, Saeb-Parsy, K, Jones, J, Teichmann, S, Dominguez Conde C., Xu C., Jarvis L. B., Rainbow D. B., Wells S. B., Gomes T., Howlett S. K., Suchanek O., Polanski K., King H. W., Mamanova L., Huang N., Szabo P. A., Richardson L., Bolt L., Fasouli E. S., Mahbubani K. T., Prete M., Tuck L., Richoz N., Tuong Z. K., Campos L., Mousa H. S., Needham E. J., Pritchard S., Li T., Elmentaite R., Park J., Rahmani E., Chen D., Menon D. K., Bayraktar O. A., James L. K., Meyer K. B., Yosef N., Clatworthy M. R., Sims P. A., Farber D. L., Saeb-Parsy K., Jones J. L., Teichmann S. A., Dominguez Conde, C, Xu, C, Jarvis, L, Rainbow, D, Wells, S, Gomes, T, Howlett, S, Suchanek, O, Polanski, K, King, H, Mamanova, L, Huang, N, Szabo, P, Richardson, L, Bolt, L, Fasouli, E, Mahbubani, K, Prete, M, Tuck, L, Richoz, N, Tuong, Z, Campos, L, Mousa, H, Needham, E, Pritchard, S, Li, T, Elmentaite, R, Park, J, Rahmani, E, Chen, D, Menon, D, Bayraktar, O, James, L, Meyer, K, Yosef, N, Clatworthy, M, Sims, P, Farber, D, Saeb-Parsy, K, Jones, J, Teichmann, S, Dominguez Conde C., Xu C., Jarvis L. B., Rainbow D. B., Wells S. B., Gomes T., Howlett S. K., Suchanek O., Polanski K., King H. W., Mamanova L., Huang N., Szabo P. A., Richardson L., Bolt L., Fasouli E. S., Mahbubani K. T., Prete M., Tuck L., Richoz N., Tuong Z. K., Campos L., Mousa H. S., Needham E. J., Pritchard S., Li T., Elmentaite R., Park J., Rahmani E., Chen D., Menon D. K., Bayraktar O. A., James L. K., Meyer K. B., Yosef N., Clatworthy M. R., Sims P. A., Farber D. L., Saeb-Parsy K., Jones J. L., and Teichmann S. A.
- Abstract
Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the immune compartment of 16 tissues from 12 adult donors by single-cell RNA sequencing and VDJ sequencing generating a dataset of ~360,000 cells. To systematically resolve immune cell heterogeneity across tissues, we developed CellTypist, a machine learning tool for rapid and precise cell type annotation. Using this approach, combined with detailed curation, we determined the tissue distribution of finely phenotyped immune cell types, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. Our multitissue approach lays the foundation for identifying highly resolved immune cell types by leveraging a common reference dataset, tissue-integrated expression analysis, and antigen receptor sequencing.
- Published
- 2022
7. Retinoschisin, a photoreceptor-secreted protein, and its interaction with bipolar and muller cells
- Author
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Reid, SNM, Yamashita, C, and Farber, D B
- Subjects
photoreceptor ,glia ,neurodegenerative disease ,retinal disease ,retinal development ,neurodegeneration ,bipolar cell ,protein secretion ,cell interaction ,retinoschisis ,Muller cell - Abstract
Usually, photoreceptors interact with other retinal cells through the neurotransmitter glutamate. Here we describe a nonsynaptic interaction via a secreted protein, retinoschisin. Using in situ hybridization, we found that from early postnatal life retinoschisin mRNA is present only in the outer retina of the mouse, and with single-cell RT-PCR we demonstrated its localization in rod and cone photoreceptor cells but not in Muller cells. Western blot analyses of proteins from cultured ocular tissues and microdissected outer and inner retinas, as well as from the culture media of these samples, showed that retinoschisin is secreted from the photoreceptor cells. Immunostaining of permeabilized and nonpermeabilized dissociated retinal cells revealed that retinoschisin is mainly inside and outside the photoreceptors, outside bipolar cells, and associated with plasma membranes of Muller cells and inside their distal processes. Because we showed previously that retinoschisin is distributed all over the retina, our current data suggest that after synthesis and secretion by the photoreceptors, retinoschisin reaches the surface of retinal cells and mediates interactions/adhesion between photoreceptor, bipolar, and Muller cells, contributing to the maintenance of the cytoarchitectural integrity of the retina. These interactions may not occur when the gene encoding retinoschisin is mutated, as it occurs in X-linked juvenile retinoschisis, a disease that results in morphological and electrophysiological defects of the retina.
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- 2003
8. Macrochimerism in Intestinal Transplantation: Association With Lower Rejection Rates and Multivisceral Transplants, Without GVHD
- Author
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Zuber, J., Rosen, S., Shonts, B., Sprangers, B., Savage, T.M., Richman, S., Yang, S., Lau, S.P., DeWolf, S., Farber, D., Vlad, G., Zorn, E., Wong, W., Emond, J., Levin, B., Martinez, M., Kato, T., and Sykes, M.
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- 2015
- Full Text
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9. Human immunology studies using organ donors: Impact of clinical variations on immune parameters in tissues and circulation
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Carpenter, D. J., Granot, T., Matsuoka, N., Senda, T., Kumar, B. V., Thome, J. J. C., Gordon, C. L., Miron, M., Weiner, J., Connors, T., Lerner, H., Friedman, A., Kato, T., Griesemer, A. D., and Farber, D. L.
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- 2018
- Full Text
- View/download PDF
10. Functional Organization of the Brain during Preparation for Recognition of Image Fragments
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Farber, D. A., Machinskaya, R. I., Kurganskii, A. V., and Petrenko, N. E.
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- 2015
- Full Text
- View/download PDF
11. Brain organization of the preparation to visual recognition in preadolescent children
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Farber, D. A., Kurganskii, A. V., and Petrenko, N. E.
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- 2015
- Full Text
- View/download PDF
12. Cross-tissue immune cell analysis reveals tissue-specific features in humans
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Domínguez Conde, C., primary, Xu, C., additional, Jarvis, L. B., additional, Rainbow, D. B., additional, Wells, S. B., additional, Gomes, T., additional, Howlett, S. K., additional, Suchanek, O., additional, Polanski, K., additional, King, H. W., additional, Mamanova, L., additional, Huang, N., additional, Szabo, P. A., additional, Richardson, L., additional, Bolt, L., additional, Fasouli, E. S., additional, Mahbubani, K. T., additional, Prete, M., additional, Tuck, L., additional, Richoz, N., additional, Tuong, Z. K., additional, Campos, L., additional, Mousa, H. S., additional, Needham, E. J., additional, Pritchard, S., additional, Li, T., additional, Elmentaite, R., additional, Park, J., additional, Rahmani, E., additional, Chen, D., additional, Menon, D. K., additional, Bayraktar, O. A., additional, James, L. K., additional, Meyer, K. B., additional, Yosef, N., additional, Clatworthy, M. R., additional, Sims, P. A., additional, Farber, D. L., additional, Saeb-Parsy, K., additional, Jones, J. L., additional, and Teichmann, S. A., additional
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- 2022
- Full Text
- View/download PDF
13. Phonons of the anomalous element cerium
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Krisch, Michael, Farber, D. L., Xu, R., Antonangeli, Daniele, Aracne, C. M., Beraud, Alexandre, Chiang, Tai-Chang, Zarestky, J., Kim, Duck Young, Isaev, Eyvaz I., Ahuja, Rajeev, and Johansson, Börje
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- 2011
14. Functional organization of the brain in the period of preparation for recognizing fragmented images in seven- to eight-year-old children and adults
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Farber, D. A., Machinskaya, R. I., Kurgansky, A. V., and Petrenko, N. E.
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- 2014
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15. Large expert-curated database for benchmarking document similarity detection in biomedical literature search
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Brown, P, Zhou, Y, Tan, A, El-Esawi, M, Liehr, T, Blanck, O, Gladue, D, Almeida, G, Cernava, T, Sorzano, C, Yeung, A, Engel, M, Chandrasekaran, A, Muth, T, Staege, M, Daulatabad, S, Widera, D, Zhang, J, Meule, A, Honjo, K, Pourret, O, Yin, C, Zhang, Z, Cascella, M, Flegel, W, Goodyear, C, van Raaij, M, Bukowy-Bieryllo, Z, Campana, L, Kurniawan, N, Lalaouna, D, Huttner, F, Ammerman, B, Ehret, F, Cobine, P, Tan, E, Han, H, Xia, W, Mccrum, C, Dings, R, Marinello, F, Nilsson, H, Nixon, B, Voskarides, K, Yang, L, Costa, V, Bengtsson-Palme, J, Bradshaw, W, Grimm, D, Kumar, N, Martis, E, Prieto, D, Sabnis, S, Amer, S, Liew, A, Perco, P, Rahimi, F, Riva, G, Zhang, C, Devkota, H, Ogami, K, Basharat, Z, Fierz, W, Siebers, R, Tan, K, Boehme, K, Brenneisen, P, Brown, J, Dalrymple, B, Harvey, D, Ng, G, Werten, S, Bleackley, M, Dai, Z, Dhariwal, R, Gelfer, Y, Hartmann, M, Miotla, P, Tamaian, R, Govender, P, Gurney-Champion, O, Kauppila, J, Zhang, X, Echeverria, N, Subhash, S, Sallmon, H, Tofani, M, Bae, T, Bosch, O, Cuiv, P, Danchin, A, Diouf, B, Eerola, T, Evangelou, E, Filipp, F, Klump, H, Kurgan, L, Smith, S, Terrier, O, Tuttle, N, Ascher, D, Janga, S, Schulte, L, Becker, D, Browngardt, C, Bush, S, Gaullier, G, Ide, K, Meseko, C, Werner, G, Zaucha, J, Al-Farha, A, Greenwald, N, Popoola, S, Rahman, S, Xu, J, Yang, S, Hiroi, N, Alper, O, Baker, C, Bitzer, M, Chacko, G, Debrabant, B, Dixon, R, Forano, E, Gilliham, M, Kelly, S, Klempnauer, K, Lidbury, B, Lin, M, Lynch, I, Ma, W, Maibach, E, Mather, D, Nandakumar, K, Ohgami, R, Parchi, P, Tressoldi, P, Xue, Y, Armitage, C, Barraud, P, Chatzitheochari, S, Coelho, L, Diao, J, Doxey, A, Gobet, A, Hu, P, Kaiser, S, Mitchell, K, Salama, M, Shabalin, I, Song, H, Stevanovic, D, Yadollahpour, A, Zeng, E, Zinke, K, Alimba, C, Beyene, T, Cao, Z, Chan, S, Gatchell, M, Kleppe, A, Piotrowski, M, Torga, G, Woldesemayat, A, Cosacak, M, Haston, S, Ross, S, Williams, R, Wong, A, Abramowitz, M, Effiong, A, Lee, S, Abid, M, Agarabi, C, Alaux, C, Albrecht, D, Atkins, G, Beck, C, Bonvin, A, Bourke, E, Brand, T, Braun, R, Bull, J, Cardoso, P, Carter, D, Delahay, R, Ducommun, B, Duijf, P, Epp, T, Eskelinen, E, Fallah, M, Farber, D, Fernandez-Triana, J, Feyerabend, F, Florio, T, Friebe, M, Furuta, S, Gabrielsen, M, Gruber, J, Grybos, M, Han, Q, Heinrich, M, Helantera, H, Huber, M, Jeltsch, A, Jiang, F, Josse, C, Jurman, G, Kamiya, H, de Keersmaecker, K, Kristiansson, E, de Leeuw, F, Li, J, Liang, S, Lopez-Escamez, J, Lopez-Ruiz, F, Marchbank, K, Marschalek, R, Martin, C, Miele, A, Montagutelli, X, Morcillo, E, Nicoletti, R, Niehof, M, O'Toole, R, Ohtomo, T, Oster, H, Palma, J, Paterson, R, Peifer, M, Portilla, M, Portillo, M, Pritchard, A, Pusch, S, Raghava, G, Roberts, N, Ross, K, Schuele, B, Sergeant, K, Shen, J, Stella, A, Sukocheva, O, Uversky, V, Vanneste, S, Villet, M, Viveiros, M, Vorholt, J, Weinstock, C, Yamato, M, Zabetakis, I, Zhao, X, Ziegler, A, Aizat, W, Atlas, L, Bridges, K, Chakraborty, S, Deschodt, M, Domingues, H, Esfahlani, S, Falk, S, Guisado, J, Kane, N, Kueberuwa, G, Lau, C, Liang, D, Liu, E, Luu, A, Ma, C, Ma, L, Moyer, R, Norris, A, Panthee, S, Parsons, J, Peng, Y, Pinto, I, Reschke, C, Sillanpaa, E, Stewart, C, Uhle, F, Yang, H, Zhou, K, Zhu, S, Ashry, M, Bergsland, N, Berthold, M, Chen, C, Colella, V, Cuypers, M, Eskew, E, Fan, X, Gajda, M, Gonzalezlez-Prendes, R, Goodin, A, Graham, E, Groen, E, Gutierrez-Sacristan, A, Habes, M, Heffler, E, Higginbottom, D, Janzen, T, Jayaraman, J, Jibb, L, Jongen, S, Kinyanjui, T, Koleva-Kolarova, R, Li, Z, Liu, Y, Lund, B, Lussier, A, Mier, P, Moore, M, Nagler, K, Orme, M, Pearson, J, Prajapati, A, Saito, Y, Troder, S, Uchendu, F, Verloh, N, Voutchkova, D, Abu-Zaid, A, Bakkach, J, Baumert, P, Dono, M, Hanson, J, Herbelet, S, Hobbs, E, Kulkarni, A, Liu, S, Loft, N, Reddan, T, Senghore, T, Vindin, H, Xu, H, Bannon, R, Chen, B, Cheung, J, Cooper, J, Esnakula, A, Feghali, K, Ghelardi, E, Gnasso, A, Horbar, J, Lai, H, Ma, R, Pan, Z, Peres, M, Pranata, R, Seow, E, Sydes, M, Testoni, I, Westermair, A, Yang, Y, Afnan, M, Albiol, J, Albuquerque, L, Amir, S, Amiya, E, Amorim, R, An, Q, Andersen, S, Aplin, J, Argyropoulos, C, Asmann, Y, Assaeed, A, Atanasov, A, Atchison, D, Avery, S, Avillach, P, Baade, P, Backman, L, Badie, C, Baldi, A, Ball, E, Bardot, O, Barnett, A, Basner, M, Batra, J, Bazanova, O, Beale, A, Beddoe, T, Bell, M, Berezikov, E, Berners-Price, S, Bernhardt, P, Berry, E, Bessa, T, Billington, C, Birch, J, Blakely, R, Blaskovich, M, Blum, R, Boelaert, M, Bogdanos, D, Bosch, C, Bourgoin, T, Bouvard, D, Boykin, L, Bradley, G, Braun, D, Brownlie, J, Bruhl, A, Burt, A, Butler, L, Byrareddy, S, Byrne, H, Cabantous, S, Calatayud, S, Candal, E, Carlson, K, Casillas, S, Castelvetro, V, Caswell, P, Cavalli, G, Cerovsky, V, Chagoyen, M, Chen, D, Chen, H, Chen, J, Chen, Y, Cheng, C, Cheng, J, Chinapaw, M, Chinopoulos, C, Cho, W, Chong, L, Chowdhury, D, Chwalibog, A, Ciresi, A, Cockcroft, S, Conesa, A, Cook, P, Cooper, D, Coqueret, O, Corea, E, Costa, A, Costa, E, Coupland, C, Crawford, S, Cruz, A, Cui, H, Cui, Q, Culver, D, D'Angiulli, A, Dahms, T, Daigle, F, Dalgleish, R, Danielsen, H, Darras, S, Davidson, S, Day, D, Degirmenci, V, Demaison, L, Devriendt, K, Ding, J, Dogan, Y, Dong, X, Donner, C, Dressick, W, Drevon, C, Duan, H, Ducho, C, Dumaz, N, Dwarakanath, B, Ebell, M, Eisenhardt, S, Elkum, N, Engel, N, Erickson, T, Fairhead, M, Faville, M, Fejzo, M, Festa, F, Feteira, A, Flood-Page, P, Forsayeth, J, Fox, S, Franks, S, Frentiu, F, Frilander, M, Fu, X, Fujita, S, Galea, I, Galluzzi, L, Gani, F, Ganpule, A, Garcia-Alix, A, Gedye, K, Giordano, M, Giunta, C, Gleeson, P, Goarant, C, Gong, H, Gora, D, Gough, M, Goyal, R, Graham, K, Grande-Perez, A, Graves, P, Greidanus, H, Grice, D, Grunau, C, Gumulya, Y, Guo, Y, Gurevich, V, Gusev, O, Hacker, E, Hage, S, Hagen, G, Hahn, S, Haller, D, Hammerschmidt, S, Han, J, Han, R, Handfield, M, Hapuarachchi, H, Harder, T, Hardingham, J, Heck, M, Heers, M, Hew, K, Higuchi, Y, Hilaire, C, Hilton, R, Hodzic, E, Hone, A, Hongoh, Y, Hu, G, Huber, H, Hueso, L, Huirne, J, Hurt, L, Idborg, H, Ikeo, K, Ingley, E, Jakeman, P, Jensen, A, Jia, H, Jia, S, Jiang, J, Jiang, X, Jin, Y, Jo, D, Johnson, A, Johnston, M, Jonscher, K, Jorens, P, Jorgensen, J, Joubert, J, Jung, S, Junior, A, Kahan, T, Kamboj, S, Kang, Y, Karamanos, Y, Karp, N, Kelly, R, Kenna, R, Kennedy, J, Kersten, B, Khalaf, R, Khalid, J, Khatlani, T, Khider, T, Kijanka, G, King, S, Kluz, T, Knox, P, Kobayashi, T, Koch, K, Kohonen-Corish, M, Kong, X, Konkle-Parker, D, Korpela, K, Kostrikis, L, Kraiczy, P, Kratz, H, Krause, G, Krebsbach, P, Kristensen, S, Kumari, P, Kunimatsu, A, Kurdak, H, Kwon, Y, Lachat, C, Lagisz, M, Laky, B, Lammerding, J, Lange, M, Larrosa, M, Laslett, A, Laverman, G, Leclair, E, Lee, K, Lee, M, Li, G, Lieb, K, Lim, Y, Lindsey, M, Line, P, Liu, D, Liu, F, Liu, H, Lloyd, V, Lo, T, Locci, E, Loidl, J, Lorenzen, J, Lorkowski, S, Lovell, N, Lu, H, Lu, W, Lu, Z, Luengo, G, Lundh, L, Lysy, P, Mabb, A, Mack, H, Mackey, D, Mahdavi, S, Maher, P, Maher, T, Maity, S, Malgrange, B, Mamoulakis, C, Mangoni, A, Manke, T, Manstead, A, Mantalaris, A, Marsal, J, Marschall, H, Martin, F, Martinez-Raga, J, Martinez-Salas, E, Mathieu, D, Matsui, Y, Maza, E, Mccutcheon, J, Mckay, G, Mcmillan, B, Mcmillan, N, Meads, C, Medina, L, Merrick, B, Metzger, D, Meunier, F, Michaelis, M, Micheau, O, Mihara, H, Mintz, E, Mizukami, T, Moalic, Y, Mohapatra, D, Monteiro, A, Montes, M, Moran, J, Morozov, S, Mort, M, Murai, N, Murphy, D, Murphy, S, Murray, S, Naganawa, S, Nammi, S, Nasios, G, Natoli, R, Nguyen, F, Nicol, C, van Nieuwerburgh, F, Nilsen, E, Nobile, C, O'Mahony, M, Ohlsson, S, Olatunbosun, O, Olofsson, P, Ortiz, A, Ostrikov, K, Otto, S, Outeiro, T, Ouyang, S, Paganoni, S, Page, A, Palm, C, Paradies, Y, Parsons, M, Parsons, N, Pascal, P, Paul, E, Peckham, M, Pedemonte, N, Pellizzon, M, Petrelli, M, Pichugin, A, Pinto, C, Plevris, J, Pollesello, P, Polz, M, Ponti, G, Porcelli, P, Prince, M, Quinn, G, Quinn, T, Ramula, S, Rappsilber, J, Rehfeldt, F, Reiling, J, Remacle, C, Rezaei, M, Riddick, E, Ritter, U, Roach, N, Roberts, D, Robles, G, Rodrigues, T, Rodriguez, C, Roislien, J, Roobol, M, Rowe, A, Ruepp, A, van Ruitenbeek, J, Rust, P, Saad, S, Sack, G, Santos, M, Saudemont, A, Sava, G, Schrading, S, Schramm, A, Schreiber, M, Schuler, S, Schymkowitz, J, Sczyrba, A, Seib, K, Shi, H, Shimada, T, Shin, J, Shortt, C, Silveyra, P, Skinner, D, Small, I, Smeets, P, So, P, Solano, F, Sonenshine, D, Song, J, Southall, T, Speakman, J, Srinivasan, M, Stabile, L, Stasiak, A, Steadman, K, Stein, N, Stephens, A, Stewart, D, Stine, K, Storlazzi, C, Stoynova, N, Strzalka, W, Suarez, O, Sultana, T, Sumant, A, Summers, M, Sun, G, Tacon, P, Tanaka, K, Tang, H, Tanino, Y, Targett-Adams, P, Tayebi, M, Tayyem, R, Tebbe, C, Telfer, E, Tempel, W, Teodorczyk-Injeyan, J, Thijs, G, Thorne, S, Thrift, A, Tiffon, C, Tinnefeld, P, Tjahjono, D, Tolle, F, Toth, E, Del Tredici, A, Tsapas, A, Tsirigotis, 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- Abstract
Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical science.
- Published
- 2019
16. Brain organization of the recognition of fragmented images in subjects who show different levels of task performance success
- Author
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Petrenko, N. E. and Farber, D. A.
- Published
- 2013
- Full Text
- View/download PDF
17. Development of a function to recognize angry facial expressions in 5- to 11-year-old children
- Author
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Kostandov, E. A., Farber, D. A., Petrenko, N. E., and Cheremushkin, E. A.
- Published
- 2012
- Full Text
- View/download PDF
18. Development of mechanisms of recognition of fragmented images differing in the degree of fragmentation in children of preschool and primary school ages
- Author
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Farber, D. A. and Petrenko, N. E.
- Published
- 2012
- Full Text
- View/download PDF
19. Neurophysiological mechanisms of recognition fragmented images by five- to six-year-old children
- Author
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Farber, D. A. and Petrenko, N. E.
- Published
- 2011
- Full Text
- View/download PDF
20. Spatial synchronization of the θ and α band cortical electrical oscillations in the formation of a set to an angry face expression in 5- to 11-year-old children
- Author
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Kostandov, E. A., Farber, D. A., Cheremushkin, E. A., Petrenko, N. E., and Ashkinazi, M. L.
- Published
- 2011
- Full Text
- View/download PDF
21. Cognitive control in recognition of an emotionally negative face in five- to ten-year-old children
- Author
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Kostandov, E. A., Farber, D. A., Cheremushkin, E. A., Petrenko, N. E., and Ashkinazi, M. L.
- Published
- 2011
- Full Text
- View/download PDF
22. Spatial Synchronization of Cortical Electrical Activity at Different Stages of a Visual Set in 8-Year-Old Children with Different Levels of Development of the Frontothalamic Selective Attention System
- Author
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Kostandov, E. A., Farber, D. A., Machinskaya, R. I., Cheremushkin, E. A., Petrenko, N. E., and Ashkinazi, M. L.
- Published
- 2011
- Full Text
- View/download PDF
23. Development of the brain’s organization of working memory in young schoolchildren
- Author
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Farber, D. A. and Beteleva, T. G.
- Published
- 2011
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- View/download PDF
24. Age-related specificity of the processing of visual information in the system of working memory
- Author
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Beteleva, T. G., Sinitsyn, S. V., and Farber, D. A.
- Published
- 2009
- Full Text
- View/download PDF
25. Structural and functional organization of a developing brain and formation of cognitive functions in child ontogeny
- Author
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Bezrukikh, M. M., Machinskaya, R. I., and Farber, D. A.
- Published
- 2009
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- View/download PDF
26. Specificity of recognition of fragmented images in seven- to eight-year-old children: Analysis of event-related potentials
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Farber, D. A. and Petrenko, N. E.
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- 2009
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27. Functional organization of working memory in seven- to eight-year-old children
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Farber, D. A. and Sinitsyn, S. V.
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- 2009
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28. Spatial organization of cortical electrical activity at different stages of a visual set in preschool and early school age
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Kostandov, É. A., Farber, D. A., Cheremushkin, E. A., Machinskaya, R. I., Petrenko, N. E., and Ashkinazi, M. L.
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- 2009
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29. POS0956 MEDITERRANEAN DIET IN AXIAL SPONDYLOARTHRITIS: A NUTRITIONAL INTERVENTION STUDY
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Ometto, F., primary, Farber, D. M., additional, Lorenzin, M., additional, Ortolan, A., additional, Dellamaria, G., additional, Felicetti, M., additional, Favero, M., additional, Valentini, R., additional, Doria, A., additional, and Ramonda, R., additional
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- 2021
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30. Recognition of fragmented images and mechanisms of memory
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Farber, D. A. and Petrenko, N. E.
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- 2008
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31. Influence of neuroendocrine shifts in the pubertal period on the working memory operation in adolescents
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Farber, D. A. and Ignat’eva, I. S.
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- 2006
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32. Formation of the System of Visual Perception in Ontogeny
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Farber, D. A. and Beteleva, T. G.
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- 2005
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- View/download PDF
33. Functional Organization of the Brain during the Operation of Working Memory
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Farber, D. A., Beteleva, T. G., and Ignat'eva, I. S.
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- 2004
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34. Role of the Frontal Cortical Areas in the Analysis of Visual Stimuli at Conscious and Unconscious Levels
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Beteleva, T. G. and Farber, D. A.
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- 2002
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35. Methodological Aspects of Studies of the Physiology of Child Development
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Farber, D. A. and Bezrukikh, M. M.
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- 2001
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36. Functional organization of the cortex of the large hemispheres during voluntary movement performance: Age aspect
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Farber, D. A. and Anisimova, I. O.
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- 2000
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37. The founder mutation MSH2*1906G [right arrow] C is an important cause of hereditary nonpolyposis colorectal cancer in the Ashkenazi Jewish population
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Foulkes, W.D., Thiffault, I., Gruber, S.B., Horwitz, M., Hamel, N., Lee, C., Shia, J., Markowitz, A., Figer, A., Friedman, E., Farber, D., Greenwood, C.M. T., Bonner, J.D., Nafa, K., Walsh, T., Marcus, V., Tomsho, L., Gebert, J., Macrae, F.A., Gaff, C.L., Bressac-de Paillerets, B., Gregersen, P.K., Weitzel, J.N., Gordon, P.H., MacNamara, E., King, M.-C., Hampel, H., de la Chapelle, A., Boyd, J., Offit, K., Rennert, G., Chong, G., and Ellis, N.A.
- Subjects
Colorectal cancer -- Genetic aspects ,Genetic disorders -- Research ,Familial diseases -- Research ,Gene mutations -- Health aspects ,Ashkenazim -- Genetic aspects ,Ashkenazim -- Diseases ,Biological sciences - Published
- 2002
38. Endogenous Expansion of Regulatory T Cells Leads to Long-Term Islet Graft Survival in Diabetic NOD Mice
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Shi, Q., Lees, J. R., Scott, D. W., Farber, D. L., and Bartlett, S. T.
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- 2012
- Full Text
- View/download PDF
39. The Use of Organ Donor Tissue for Steady-State Evaluation of Human Immune Responses in Lymphoid and Mucosal Compartments.: Abstract# 1475 Poster Board #-Session: P37-IV
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Kubota, M., Sathaliyawala, T., Kato, Y., Kato, T., and Farber, D.
- Published
- 2012
40. Tissue Specific Compartmentalization of Human T Cells.: Abstract# 1468 Poster Board #-Session: P30-IV
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Sathaliyawala, T., Kubota, M., Turner, D., and Farber, D.
- Published
- 2012
41. Memory T-Cell Predominance Following T-Cell Depletional Therapy Derives from Homeostatic Expansion of Naive T Cells
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Sener, A., Tang, A. L., and Farber, D. L.
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- 2009
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42. Removal of phosphorylation sites of γ subunit of phosphodiesterase 6 alters rod light response
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Tsang, S. H., Woodruff, M. L., Janisch, Kerstin M., Cilluffo, M. C., Farber, D. B., and Fain, G. L.
- Published
- 2007
43. Generation and Functional Capacity of Polyclonal Alloantigen-Specific Memory CD4 T Cells
- Author
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Tang, A. L., Bingaman, A. W., Kadavil, E. A., Leeser, D. B., and Farber, D. L.
- Published
- 2006
44. Cyclic AMP modulation of ion transport across frog retinal pigment epithelium. Measurements in the short-circuit state.
- Author
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Miller, S and Farber, D
- Subjects
Medical Physiology ,Biomedical and Clinical Sciences ,Neurosciences ,Eye Disease and Disorders of Vision ,Animals ,Biological Transport ,Cell Membrane ,Chlorides ,Cyclic AMP ,Electric Conductivity ,Pigment Epithelium of Eye ,Potassium ,Rana catesbeiana ,Sodium ,Physiology ,Biochemistry and cell biology ,Zoology ,Medical physiology - Abstract
In the frog retinal pigment epithelium (RPE), the cellular levels of cyclic AMP (cAMP) were measured in control conditions and after treatment with substances that are known to inhibit phosphodiesterase (PDE) activity (isobutyl-1-methylxanthine, SQ65442) or stimulate adenylate cyclase activity (forskolin). The cAMP levels were elevated by a factor of 5-7 compared with the controls in PDE-treated tissues and by a factor of 18 in forskolin-treated tissues. The exogenous application of cAMP (1 mM), PDE inhibitors (0.5 mM), or forskolin (0.1 mM) all produced similar changes in epithelial electrical parameters, such as transepithelial potential (TEP) and resistance (Rt), as well as changes in active ion transport. Adding 1 mM cAMP to the solution bathing the apical membrane transiently increased the short-circuit current (SCC) and the TEP (apical side positive) and decreased Rt. Microelectrode experiments showed that the elevation in TEP is due mainly to a depolarization of the basal membrane followed by, and perhaps also accompanied by, a smaller hyperpolarization of the apical membrane. The ratio of the apical to the basolateral membrane resistance increased in the presence of cAMP, and this increase, coupled with the decrease in Rt and the basolateral membrane depolarization, is consistent with a conductance increase at the basolateral membrane. Radioactive tracer experiments showed that cAMP increased the active secretion of Na (choroid to retina) and the active absorption of K (retina to choroid). Cyclic AMP also abolished the active absorption of Cl across the RPE. In sum, elevated cellular levels of cAMP affect active and passive transport mechanisms at the apical and basolateral membranes of the bullfrog RPE.
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- 1984
45. Large expert-curated database for benchmarking document similarity detection in biomedical literature search
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Brown, P., Zhou, Y., Tan, A. -C., El-Esawi, M. A., Liehr, T., Blanck, O., Gladue, D. P., Almeida, G. M. F., Cernava, T., Sorzano, C. O., Yeung, A. W. K., Engel, M. S., Chandrasekaran, A. R., Muth, T., Staege, M. S., Daulatabad, S. V., Widera, D., Zhang, J., Meule, A., Honjo, K., Pourret, O., Yin, C. -C., Zhang, Z., Cascella, M., Flegel, W. A., Goodyear, C. S., van Raaij, M. J., Bukowy-Bieryllo, Z., Campana, L. G., Kurniawan, N. A., Lalaouna, D., Huttner, F. J., Ammerman, B. A., Ehret, F., Cobine, P. A., Tan, E. -C., Han, H., Xia, W., Mccrum, C., Dings, R. P. M., Marinello, F., Nilsson, H., Nixon, B., Voskarides, K., Yang, L., Costa, V. D., Bengtsson-Palme, J., Bradshaw, W., Grimm, D. G., Kumar, N., Martis, E., Prieto, D., Sabnis, S. C., Amer, S. E. D. R., Liew, A. W. C., Perco, P., Rahimi, F., Riva, G., Zhang, C., Devkota, H. P., Ogami, K., Basharat, Z., Fierz, W., Siebers, R., Tan, K. H., Boehme, K. A., Brenneisen, P., Brown, J. A. L., Dalrymple, B. P., Harvey, D. J., Ng, G., Werten, S., Bleackley, M., Dai, Z., Dhariwal, R., Gelfer, Y., Hartmann, M. D., Miotla, P., Tamaian, R., Govender, P., Gurney-Champion, O. J., Kauppila, J. H., Zhang, X., Echeverria, N., Subhash, S., Sallmon, H., Tofani, M., Bae, T., Bosch, O., Cuiv, P. O., Danchin, A., Diouf, B., Eerola, T., Evangelou, E., Filipp, F., Klump, H., Kurgan, L., Smith, S. S., Terrier, O., Tuttle, N., Ascher, D. B., Janga, S. C., Schulte, L. N., Becker, D., Browngardt, C., Bush, S. J., Gaullier, G., Ide, K., Meseko, C., Werner, G. D. A., Zaucha, J., Al-Farha, A. A., Greenwald, N. F., Popoola, S. I., Rahman, S., Xu, J., Yang, S. Y., Hiroi, N., Alper, O. M., Baker, C. I., Bitzer, M., Chacko, G., Debrabant, B., Dixon, R., Forano, E., Gilliham, M., Kelly, S., Klempnauer, K. -H., Lidbury, B. A., Lin, M. Z., Lynch, I., Ma, W., Maibach, E. W., Mather, D. E., Nandakumar, K. S., Ohgami, R. S., Parchi, P., Tressoldi, P., Xue, Y., Armitage, C., Barraud, P., Chatzitheochari, S., Coelho, L. P., Diao, J., Doxey, A. C., Gobet, A., Hu, P., Kaiser, S., Mitchell, K. M., Salama, M. F., Shabalin, I. G., Song, H., Stevanovic, D., Yadollahpour, A., Zeng, E., Zinke, K., Alimba, C. G., Beyene, T. J., Cao, Z., Chan, S. S., Gatchell, M., Kleppe, A., Piotrowski, M., Torga, G., Woldesemayat, A. A., Cosacak, M. I., Haston, S., Ross, S. A., Williams, R., Wong, A., Abramowitz, M. K., Effiong, A., Lee, S., Abid, M. B., Agarabi, C., Alaux, C., Albrecht, D. R., Atkins, G. J., Beck, C. R., Bonvin, A. M. J. J., Bourke, E., Brand, T., Braun, R. J., Bull, J. A., Cardoso, P., Carter, D., Delahay, R. M., Ducommun, B., Duijf, P. H. G., Epp, T., Eskelinen, E. -L., Fallah, M., Farber, D. B., Fernandez-Triana, J., Feyerabend, F., Florio, T., Friebe, M., Furuta, S., Gabrielsen, M., Gruber, J., Grybos, M., Han, Q., Heinrich, M., Helantera, H., Huber, M., Jeltsch, A., Jiang, F., Josse, C., Jurman, G., Kamiya, H., de Keersmaecker, K., Kristiansson, E., de Leeuw, F. -E., Li, J., Liang, S., Lopez-Escamez, J. A., Lopez-Ruiz, F. J., Marchbank, K. J., Marschalek, R., Martin, C. S., Miele, A. E., Montagutelli, X., Morcillo, E., Nicoletti, R., Niehof, M., O'Toole, R., Ohtomo, T., Oster, H., Palma, J. -A., Paterson, R., Peifer, M., Portilla, M., Portillo, M. C., Pritchard, A. L., Pusch, S., Raghava, G. P. S., Roberts, N. J., Ross, K., Schuele, B., Sergeant, K., Shen, J., Stella, A., Sukocheva, O., Uversky, V. N., Vanneste, S., Villet, M. H., Viveiros, M., Vorholt, J. A., Weinstock, C., Yamato, M., Zabetakis, I., Zhao, X., Ziegler, A., Aizat, W. M., Atlas, L., Bridges, K. M., Chakraborty, S., Deschodt, M., Domingues, H. S., Esfahlani, S. S., Falk, S., Guisado, J. L., Kane, N. C., Kueberuwa, G., Lau, C. L., Liang, D., Liu, E., Luu, A. M., Ma, C., Ma, L., Moyer, R., Norris, A. D., Panthee, S., Parsons, J. R., Peng, Y., Pinto, I. M., Reschke, C. R., Sillanpaa, E., Stewart, C. J., Uhle, F., Yang, H., Zhou, K., Zhu, S., Ashry, M., Bergsland, N., Berthold, M., Chen, C. -E., Colella, V., Cuypers, M., Eskew, E. A., Fan, X., Gajda, M., Gonzalezlez-Prendes, R., Goodin, A., Graham, E. B., Groen, E. J. N., Gutierrez-Sacristan, A., Habes, M., Heffler, E., Higginbottom, D. B., Janzen, T., Jayaraman, J., Jibb, L. A., Jongen, S., Kinyanjui, T., Koleva-Kolarova, R. G., Li, Z., Liu, Y. -P., Lund, B. A., Lussier, A. A., Mier, P., Moore, M. D., Nagler, K., Orme, M. W., Pearson, J. A., Prajapati, A. S., Saito, Y., Troder, S. E., Uchendu, F., Verloh, N., Voutchkova, D. D., Abu-Zaid, A., Bakkach, J., Baumert, P., Dono, M., Hanson, J., Herbelet, S., Hobbs, E., Kulkarni, A., Liu, S., Loft, N. D., Reddan, T., Senghore, T., Vindin, H., Xu, H., Bannon, R., Chen, B., Cheung, J. T. K., Cooper, J., Esnakula, A. K., Feghali, K. A., Ghelardi, E., Gnasso, A., Horbar, J., Lai, H. M., Ma, R., Pan, Z., Peres, M. A., Pranata, R., Seow, E., Sydes, M., Testoni, I., Westermair, A. L., Yang, Y., Afnan, M., Albiol, J., Albuquerque, L. G., Amir, S., Amiya, E., Amorim, R. M., An, Q., Andersen, S. U., Aplin, J. D., Argyropoulos, C., Asmann, Y. W., Assaeed, A. M., Atanasov, A. G., Atchison, D. A., Avery, S. V., Avillach, P., Baade, P. D., Backman, L., Badie, C., Baldi, A., Ball, E., Bardot, O., Barnett, A. G., Basner, M., Batra, J., Bazanova, O. M., Beale, A., Beddoe, T., Bell, M. L., Berezikov, E., Berners-Price, S., Bernhardt, P., Berry, E., Bessa, T. B., Billington, C., Birch, J., Blakely, R. D., Blaskovich, M. A. T., Blum, R., Boelaert, M., Bogdanos, D., Bosch, C., Bourgoin, T., Bouvard, D., Boykin, L. M., Bradley, G., Braun, D., Brownlie, J., Bruhl, A., Burt, A., Butler, L. M., Byrareddy, S. N., Byrne, H. J., Cabantous, S., Calatayud, S., Candal, E., Carlson, K., Casillas, S., Castelvetro, V., Caswell, P. T., Cavalli, G., Cerovsky, V., Chagoyen, M., Chen, C. -S., Chen, D. F., Chen, H., Chen, J. -T., Chen, Y., Cheng, C., Cheng, J., Chinapaw, M., Chinopoulos, C., Cho, W. C. S., Chong, L., Chowdhury, D., Chwalibog, A., Ciresi, A., Cockcroft, S., Conesa, A., Cook, P. A., Cooper, D. N., Coqueret, O., Corea, E. M., Costa, A., Costa, E., Coupland, C., Crawford, S. Y., Cruz, A. D., Cui, H., Cui, Q., Culver, D. C., D'Angiulli, A., Dahms, T. E. S., Daigle, F., Dalgleish, R., Danielsen, H. E., Darras, S., Davidson, S. M., Day, D. A., Degirmenci, V., Demaison, L., Devriendt, K., Ding, J., Dogan, Y., Dong, X. C., Donner, C. F., Dressick, W., Drevon, C. A., Duan, H., Ducho, C., Dumaz, N., Dwarakanath, B. S., Ebell, M. H., Eisenhardt, S., Elkum, N., Engel, N., Erickson, T. B., Fairhead, M., Faville, M. J., Fejzo, M. S., Festa, F., Feteira, A., Flood-Page, P., Forsayeth, J., Fox, S. A., Franks, S. J., Frentiu, F. D., Frilander, M. J., Fu, X., Fujita, S., Galea, I., Galluzzi, L., Gani, F., Ganpule, A. P., Garcia-Alix, A., Gedye, K., Giordano, M., Giunta, C., Gleeson, P. A., Goarant, C., Gong, H., Gora, D., Gough, M. J., Goyal, R., Graham, K. E., Grande-Perez, A., Graves, P. M., Greidanus, H., Grice, D., Grunau, C., Gumulya, Y., Guo, Y., Gurevich, V. V., Gusev, O., Hacker, E., Hage, S. R., Hagen, G., Hahn, S., Haller, D. M., Hammerschmidt, S., Han, J., Han, R., Handfield, M., Hapuarachchi, H. C., Harder, T., Hardingham, J. E., Heck, M., Heers, M., Hew, K. F., Higuchi, Y., Hilaire, C. St., Hilton, R., Hodzic, E., Hone, A., Hongoh, Y., Hu, G., Huber, H. P., Hueso, L. E., Huirne, J., Hurt, L., Idborg, H., Ikeo, K., Ingley, E., Jakeman, P. M., Jensen, A., Jia, H., Jia, S., Jiang, J., Jiang, X., Jin, Y., Jo, D., Johnson, A. M., Johnston, M., Jonscher, K. R., Jorens, P. G., Jorgensen, J. O. L., Joubert, J. W., Jung, S. -H., Junior, A. M., Kahan, T., Kamboj, S. K., Kang, Y. -K., Karamanos, Y., Karp, N. A., Kelly, R., Kenna, R., Kennedy, J., Kersten, B., Khalaf, R. A., Khalid, J. M., Khatlani, T., Khider, T., Kijanka, G. S., King, S. R. B., Kluz, T., Knox, P., Kobayashi, T., Koch, K. -W., Kohonen-Corish, M. R. J., Kong, X., Konkle-Parker, D., Korpela, K. M., Kostrikis, L. G., Kraiczy, P., Kratz, H., Krause, G., Krebsbach, P. H., Kristensen, S. R., Kumari, P., Kunimatsu, A., Kurdak, H., Kwon, Y. D., Lachat, C., Lagisz, M., Laky, B., Lammerding, J., Lange, M., Larrosa, M., Laslett, A. L., Laverman, G. D., Leclair, E. E., Lee, K. -W., Lee, M. -Y., Lee, M. -S., Li, G., Lieb, K., Lim, Y. Y., Lindsey, M. L., Line, P. -D., Liu, D., Liu, F., Liu, H., Lloyd, V. K., Lo, T. -W., Locci, E., Loidl, J., Lorenzen, J., Lorkowski, S., Lovell, N. H., Lu, H., Lu, W., Lu, Z., Luengo, G. S., Lundh, L. -G., Lysy, P. A., Mabb, A., Mack, H. G., Mackey, D. A., Mahdavi, S. R., Maher, P., Maher, T., Maity, S. N., Malgrange, B., Mamoulakis, C., Mangoni, A. A., Manke, T., Manstead, A. S. R., Mantalaris, A., Marsal, J., Marschall, H. -U., Martin, F. L., Martinez-Raga, J., Martinez-Salas, E., Mathieu, D., Matsui, Y., Maza, E., Mccutcheon, J. E., Mckay, G. J., Mcmillan, B., Mcmillan, N., Meads, C., Medina, L., Merrick, B. A., Metzger, D. W., Meunier, F. A., Michaelis, M., Micheau, O., Mihara, H., Mintz, E. M., Mizukami, T., Moalic, Y., Mohapatra, D. P., Monteiro, A., Montes, M., Moran, J. V., Morozov, S. Y., Mort, M., Murai, N., Murphy, D. J., Murphy, S. K., Murray, S. A., Naganawa, S., Nammi, S., Nasios, G., Natoli, R. M., Nguyen, F., Nicol, C., van Nieuwerburgh, F., Nilsen, E. B., Nobile, C. J., O'Mahony, M., Ohlsson, S., Olatunbosun, O., Olofsson, P., Ortiz, A., Ostrikov, K., Otto, S., Outeiro, T. F., Ouyang, S., Paganoni, S., Page, A., Palm, C., Paradies, Y., Parsons, M. H., Parsons, N., Pascal, P., Paul, E., Peckham, M., Pedemonte, N., Pellizzon, M. A., Petrelli, M., Pichugin, A., Pinto, C. J. C., Plevris, J. N., Pollesello, P., Polz, M., Ponti, G., Porcelli, P., Prince, M., Quinn, G. P., Quinn, T. J., Ramula, S., Rappsilber, J., Rehfeldt, F., Reiling, J. H., Remacle, C., Rezaei, M., Riddick, E. W., Ritter, U., Roach, N. W., Roberts, D. D., Robles, G., Rodrigues, T., Rodriguez, C., Roislien, J., Roobol, M. J., Rowe, A., Ruepp, A., van Ruitenbeek, J., Rust, P., Saad, S., Sack, G. H., Santos, M., Saudemont, A., Sava, G., Schrading, S., Schramm, A., Schreiber, M., Schuler, S., Schymkowitz, J., Sczyrba, A., Seib, K. L., Shi, H. -P., Shimada, T., Shin, J. -S., Shortt, C., Silveyra, P., Skinner, D., Small, I., Smeets, P. A. M., So, P. -W., Solano, F., Sonenshine, D. E., Song, J., Southall, T., Speakman, J. R., Srinivasan, M. V., Stabile, L. P., Stasiak, A., Steadman, K. J., Stein, N., Stephens, A. W., Stewart, D. I., Stine, K., Storlazzi, C., Stoynova, N. V., Strzalka, W., Suarez, O. M., Sultana, T., Sumant, A. V., Summers, M. J., Sun, G., Tacon, P., Tanaka, K., Tang, H., Tanino, Y., Targett-Adams, P., Tayebi, M., Tayyem, R., Tebbe, C. C., Telfer, E. E., Tempel, W., Teodorczyk-Injeyan, J. A., Thijs, G., Thorne, S., Thrift, A. G., Tiffon, C., Tinnefeld, P., Tjahjono, D. H., Tolle, F., Toth, E., Del Tredici, A. L., Tsapas, A., Tsirigotis, K., Turak, A., Tzotzos, G., Udo, E. E., Utsumi, T., Vaidyanathan, S., Vaillant, M., Valsesia, A., Vandenbroucke, R. E., Veiga, F. H., Vendrell, M., Vesk, P. A., Vickers, P., Victor, V. M., Villemur, R., Vohl, M. -C., Voolstra, C. R., Vuillemin, A., Wakelin, S., Waldron, L., Walsh, L. J., Wang, A. Y., Wang, F., Wang, Y., Watanabe, Y., Weigert, A., Wen, J. -C., Wham, C., White, E. P., Wiener, J., Wilharm, G., Wilkinson, S., Willmann, R., Wilson, C., Wirth, B., Wojan, T. R., Wolff, M., Wong, B. M., Wu, T. -W., Wuerbel, H., Xiao, X., Xu, D., Xu, J. W., Xue, B., Yalcin, S., Yan, H., Yang, E. -C., Yang, S., Yang, W., Ye, Y., Ye, Z. -Q., Yli-Kauhaluoma, J., Yoneyama, H., Yu, Y., Yuan, G. -C., Yuh, C. -H., Zaccolo, M., Zeng, C., Zevnik, B., Zhang, L., Zhang, Y., Zhang, Z. -Y., Zhao, Y., Zhou, M., Zuberbier, T., Aanei, C. M., Ahmad, R., Al-Lawama, M., Alanio, A., Allardyce, J., Alonso-Caneiro, D., Atack, J. M., Baier, D., Bansal, A., Benezeth, Y., Berbesque, C., Berrevoet, F., Biedermann, P. H. W., Bijleveld, E., Bittner, F., Blombach, F., van den Bos, W., Boudreau, S. A., Bramoweth, A. D., Braubach, O., Cai, Y., Campbell, M., Catry, T., Chen, X., Cheng, S., Chung, H. -J., Chavez-Fumagalli, M. A., Conway, A., Costa, B. M., Cyr, N., Dean, L. T., Denzel, M. S., Dlamini, S. V., Dudley, K. J., Dufies, M., Ecke, T., Eckweiler, D., Eixarch, E., El-Adawy, H., Emmrich, J. V., Eustace, A. J., Falter-Wagner, C. M., Farhoudi, R., Fuss, J., Gao, J., Gill, M. R., Gloyn, L., Goggs, R., Govinden, U., Greene, G., Greiff, V., Grundle, D. 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- Abstract
Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical science.
- Published
- 2019
46. Putative common origin of two MLH1 mutations in Italian-Quebec hereditary non-polyposis colorectal cancer families
- Author
-
Thiffault, I, Foulkes, W D, Marcus, V A, Farber, D, Kasprzak, L, MacNamara, E, Wong, N, Hutter, P, Radice, P, Bertario, L, and Chong, G
- Published
- 2004
47. Remembrance of Antigens Past: New Insights into Memory T Cells
- Author
-
Farber, D. L.
- Published
- 2003
48. An MLH1 haplotype is over-represented on chromosomes carrying an HNPCC predisposing mutation in MLH1
- Author
-
Hutter, P, Wijnen, J, Rey-Berthod, C, Thiffault, I, Verkuijlen, P, Farber, D, Hamel, N, Bapat, B, Thibodeau, S N, Burn, J, Wu, J, MacNamara, E, Heinimann, K, Chong, G, and Foulkes, W D
- Published
- 2002
49. Response and Recovery After Hurricane Maria: Lessons for Disaster Law and Policy
- Author
-
Farber, D
- Subjects
disaster,s, Hurricane Maria, disaster response, FEMA, environmental justice - Abstract
Hurricane Maria had a devastating impact on Puerto Rico. The federal response to Maria was slow, leaving much of the population without basic necessities for extended periods. Lives were lost as a result. The federal government failed to rise to the challenges posed by logistic difficulties and strained agency resources due to preceding disasters. The response was hindered by unrealistic planning, by Puerto Rico’s lack of political power in Washington, and by presidential indifference. In the end, despite its much greater needs, Puerto Rico received assistance much more slowly than Houston. This article analyzes the reasons for the flawed response and proposes improvements in future disaster policy. Like Katrina, Maria is a story of how systems failed just when they were most needed by our most vulnerable citizens.
- Published
- 2018
50. CD103+Lung Tissue Resident Memory T Cells (TRM) Represent an Airway Centered, Clonally Expanded Subset of TRM with ZNF683 (Hobit) Expression Differentiating CD4+and CD8+CD103+TRM
- Author
-
Snyder, M.E., primary, Cvetkovski, F., additional, Dogra, P., additional, Szabo, P., additional, Miron, M., additional, Carpenter, D., additional, Senda, T., additional, and Farber, D., additional
- Published
- 2019
- Full Text
- View/download PDF
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