Author: "G. Underwood" - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"G. Underwood"' showing total 1,313 results

Start Over Author "G. Underwood"

1,313 results on '"G. Underwood"'

1. Strangeness production in s NN $$ \sqrt{s_{\textrm{NN}}} $$ = 3 GeV Au+Au collisions at RHIC

Author: The STAR collaboration, M. I. Abdulhamid, B. E. Aboona, J. Adam, L. Adamczyk, J. R. Adams, I. Aggarwal, M. M. Aggarwal, Z. Ahammed, E. C. Aschenauer, S. Aslam, J. Atchison, V. Bairathi, J. G. Ball Cap, K. Barish, R. Bellwied, P. Bhagat, A. Bhasin, S. Bhatta, S. R. Bhosale, J. Bielcik, J. Bielcikova, J. D. Brandenburg, C. Broodo, X. Z. Cai, H. Caines, M. Calderón de la Barca Sánchez, D. Cebra, J. Ceska, I. Chakaberia, P. Chaloupka, B. K. Chan, Z. Chang, A. Chatterjee, D. Chen, J. Chen, J. H. Chen, Z. Chen, J. Cheng, Y. Cheng, W. Christie, X. Chu, H. J. Crawford, M. Csanád, G. Dale-Gau, A. Das, I. M. Deppner, A. Dhamija, P. Dixit, X. Dong, J. L. Drachenberg, E. Duckworth, J. C. Dunlop, J. Engelage, G. Eppley, S. Esumi, O. Evdokimov, O. Eyser, R. Fatemi, S. Fazio, C. J. Feng, Y. Feng, E. Finch, Y. Fisyak, F. A. Flor, C. Fu, C. A. Gagliardi, T. Galatyuk, T. Gao, F. Geurts, N. Ghimire, A. Gibson, K. Gopal, X. Gou, D. Grosnick, A. Gupta, W. Guryn, A. Hamed, Y. Han, S. Harabasz, M. D. Harasty, J. W. Harris, H. Harrison-Smith, W. He, X. H. He, Y. He, N. Herrmann, L. Holub, C. Hu, Q. Hu, Y. Hu, H. Huang, H. Z. Huang, S. L. Huang, T. Huang, Y. Huang, T. J. Humanic, M. Isshiki, W. W. Jacobs, A. Jalotra, C. Jena, A. Jentsch, Y. Ji, J. Jia, C. Jin, X. Ju, E. G. Judd, S. Kabana, D. Kalinkin, K. Kang, D. Kapukchyan, K. Kauder, D. Keane, A. Khanal, Y. V. Khyzhniak, D. P. Kikoła, D. Kincses, I. Kisel, A. Kiselev, A. G. Knospe, H. S. Ko, J. Kołaś, L. K. Kosarzewski, L. Kumar, M. C. Labonte, R. Lacey, J. M. Landgraf, J. Lauret, A. Lebedev, J. H. Lee, Y. H. Leung, C. Li, D. Li, H-S. Li, H. Li, W. Li, X. Li, Y. Li, Z. Li, X. Liang, Y. Liang, R. Licenik, T. Lin, Y. Lin, M. A. Lisa, C. Liu, G. Liu, H. Liu, L. Liu, T. Liu, X. Liu, Y. Liu, Z. Liu, T. Ljubicic, O. Lomicky, R. S. Longacre, E. M. Loyd, T. Lu, J. Luo, X. F. Luo, L. Ma, R. Ma, Y. G. Ma, N. Magdy, D. Mallick, R. Manikandhan, S. Margetis, C. Markert, O. Matonoha, G. McNamara, O. Mezhanska, K. Mi, S. Mioduszewski, B. Mohanty, B. Mondal, M. M. Mondal, I. Mooney, J. Mrazkova, M. I. Nagy, A. S. Nain, J. D. Nam, M. Nasim, D. Neff, J. M. Nelson, M. Nie, G. Nigmatkulov, T. Niida, T. Nonaka, G. Odyniec, A. Ogawa, S. Oh, K. Okubo, B. S. Page, S. Pal, A. Pandav, A. Panday, A. K. Pandey, T. Pani, A. Paul, B. Pawlik, D. Pawlowska, C. Perkins, J. Pluta, B. R. Pokhrel, M. Posik, T. L. Protzman, V. Prozorova, N. K. Pruthi, M. Przybycien, J. Putschke, Z. Qin, H. Qiu, C. Racz, S. K. Radhakrishnan, A. Rana, R. L. Ray, R. Reed, C. W. Robertson, M. Robotkova, M. A. Rosales Aguilar, D. Roy, P. Roy Chowdhury, L. Ruan, A. K. Sahoo, N. R. Sahoo, H. Sako, S. Salur, S. Sato, B. C. Schaefer, W. B. Schmidke, N. Schmitz, F-J. Seck, J. Seger, R. Seto, P. Seyboth, N. Shah, P. V. Shanmuganathan, T. Shao, M. Sharma, N. Sharma, R. Sharma, S. R. Sharma, A. I. Sheikh, D. Shen, D. Y. Shen, K. Shen, S. S. Shi, Y. Shi, Q. Y. Shou, F. Si, J. Singh, S. Singha, P. Sinha, M. J. Skoby, N. Smirnov, Y. Söhngen, Y. Song, B. Srivastava, T. D. S. Stanislaus, M. Stefaniak, D. J. Stewart, Y. Su, M. Sumbera, C. Sun, X. Sun, Y. Sun, B. Surrow, M. Svoboda, Z. W. Sweger, A. C. Tamis, A. H. Tang, Z. Tang, T. Tarnowsky, J. H. Thomas, A. R. Timmins, D. Tlusty, T. Todoroki, S. Trentalange, P. Tribedy, S. K. Tripathy, T. Truhlar, B. A. Trzeciak, O. D. Tsai, C. Y. Tsang, Z. Tu, J. Tyler, T. Ullrich, D. G. Underwood, I. Upsal, G. Van Buren, J. Vanek, I. Vassiliev, V. Verkest, F. Videbæk, S. A. Voloshin, G. Wang, J. S. Wang, J. Wang, K. Wang, X. Wang, Y. Wang, Z. Wang, J. C. Webb, P. C. Weidenkaff, G. D. Westfall, D. Wielanek, H. Wieman, G. Wilks, S. W. Wissink, R. Witt, J. Wu, X. Wu, B. Xi, Z. G. Xiao, G. Xie, W. Xie, H. Xu, N. Xu, Q. H. Xu, Y. Xu, Z. Xu, G. Yan, Z. Yan, C. Yang, Q. Yang, S. Yang, Y. Yang, Z. Ye, L. Yi, Y. Yu, H. Zbroszczyk, W. Zha, C. Zhang, D. Zhang, J. Zhang, S. Zhang, W. Zhang, X. Zhang, Y. Zhang, Z. J. Zhang, Z. Zhang, F. Zhao, J. Zhao, M. Zhao, S. Zhou, Y. Zhou, X. Zhu, M. Zurek, and M. Zyzak
Subjects: Fixed Target Experiments, Relativistic Heavy Ion Physics, Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Abstract: Abstract We report multi-differential measurements of strange hadron production ranging from mid- to target-rapidity in Au+Au collisions at a center-of-momentum energy per nucleon pair of s NN $$ \sqrt{s_{\textrm{NN}}} $$ = 3 GeV with the STAR experiment at RHIC. K S 0 $$ {K}_S^0 $$ meson and Λ hyperon yields are measured via their weak decay channels. Collision centrality and rapidity dependences of the transverse momentum spectra and particle ratios are presented. Particle mass and centrality dependence of the average transverse momenta of Λ and K S 0 $$ {K}_S^0 $$ are compared with other strange particles, providing evidence of the development of hadronic rescattering in such collisions. The 4π yields of each of these strange hadrons show a consistent centrality dependence. Discussions on radial flow, the strange hadron production mechanism, and properties of the medium created in such collisions are presented together with results from hadronic transport and thermal model calculations.
Published: 2024
Full Text: View/download PDF

2. Risk of physical health comorbidities in autistic adults: clinical nested cross-sectional study

Author: Megan Hunt, Jack F. G. Underwood, Leon Hubbard, and Jeremy Hall
Subjects: Autism, physical health, co-occurring conditions, Psychiatry, RC435-571
Abstract: Background Physical health conditions are more common in individuals with autism. Some, like epilepsy, have considerable evidence supporting their increased prevalence, but many diseases lack literature to make strong conclusions. Aims To investigate the prevalence of physical health comorbidities in autism. Method We undertook a nested cross-sectional study, using a sample from the National Centre for Mental Health database. It included participants from England and Wales who reported a clinician-made diagnosis of autism (n = 813), and a control sample without autism or mental illness (n = 2781). Participants had provided a medical history at enrolment. Analysis was carried out by binomial logistic regressions controlling for age, gender, smoking status, and antipsychotic and mood stabiliser use. A subanalysis of individuals with concurrent intellectual disability (n = 86) used binomial logistic regression with the same control variables. Results Many physical health conditions were significantly more common in autism. Sixteen out of 28 conditions showed increased odds, with the highest odds ratios observed for liver disease, chronic obstructive pulmonary disease, kidney disease, osteoporosis and rheumatoid arthritis. A subanalysis demonstrated a similar pattern of physical health in individuals with autism with and without concurrent intellectual disability. Some conditions, including osteoporosis, hyperthyroidism, head injury and liver disease, had larger odds ratios in individuals with concurrent intellectual disability. Conclusions Physical health conditions occur more commonly in individuals with autism, and certain conditions are further increased in those with concurrent intellectual disability. Our findings contribute to prior evidence, including novel associations, and suggest that people with autism are at greater risk of physical health problems throughout adulthood.
Published: 2024
Full Text: View/download PDF

3. Upper limit on the chiral magnetic effect in isobar collisions at the Relativistic Heavy-Ion Collider

Author: M. I. Abdulhamid, B. E. Aboona, J. Adam, J. R. Adams, G. Agakishiev, I. Aggarwal, M. M. Aggarwal, Z. Ahammed, A. Aitbaev, I. Alekseev, E. Alpatov, A. Aparin, S. Aslam, J. Atchison, G. S. Averichev, V. Bairathi, J. G. Ball Cap, K. Barish, P. Bhagat, A. Bhasin, S. Bhatta, S. R. Bhosale, I. G. Bordyuzhin, J. D. Brandenburg, A. V. Brandin, C. Broodo, X. Z. Cai, H. Caines, M. Calderón de la Barca Sánchez, D. Cebra, J. Ceska, I. Chakaberia, B. K. Chan, Z. Chang, A. Chatterjee, D. Chen, J. Chen, J. H. Chen, Z. Chen, J. Cheng, Y. Cheng, S. Choudhury, W. Christie, X. Chu, H. J. Crawford, G. Dale-Gau, A. Das, T. G. Dedovich, I. M. Deppner, A. A. Derevschikov, A. Dhamija, P. Dixit, X. Dong, J. L. Drachenberg, E. Duckworth, J. C. Dunlop, J. Engelage, G. Eppley, S. Esumi, O. Evdokimov, O. Eyser, R. Fatemi, S. Fazio, C. J. Feng, Y. Feng, E. Finch, Y. Fisyak, F. A. Flor, C. Fu, T. Gao, F. Geurts, N. Ghimire, A. Gibson, K. Gopal, X. Gou, D. Grosnick, A. Gupta, A. Hamed, Y. Han, M. D. Harasty, J. W. Harris, H. Harrison-Smith, W. He, X. H. He, Y. He, C. Hu, Q. Hu, Y. Hu, H. Huang, H. Z. Huang, S. L. Huang, T. Huang, X. Huang, Y. Huang, T. J. Humanic, M. Isshiki, W. W. Jacobs, A. Jalotra, C. Jena, Y. Ji, J. Jia, C. Jin, X. Ju, E. G. Judd, S. Kabana, D. Kalinkin, K. Kang, D. Kapukchyan, K. Kauder, D. Keane, A. Kechechyan, A. Khanal, A. Kiselev, A. G. Knospe, H. S. Ko, L. Kochenda, A. A. Korobitsin, A. Yu. Kraeva, P. Kravtsov, L. Kumar, M. C. Labonte, R. Lacey, J. M. Landgraf, A. Lebedev, R. Lednicky, J. H. Lee, Y. H. Leung, N. Lewis, C. Li, D. Li, H-S. Li, H. Li, W. Li, X. Li, Y. Li, Z. Li, X. Liang, Y. Liang, T. Lin, Y. Lin, C. Liu, G. Liu, H. Liu, L. Liu, T. Liu, X. Liu, Y. Liu, Z. Liu, T. Ljubicic, O. Lomicky, R. S. Longacre, E. M. Loyd, T. Lu, J. Luo, X. F. Luo, V. B. Luong, L. Ma, R. Ma, Y. G. Ma, N. Magdy, R. Manikandhan, S. Margetis, H. S. Matis, G. McNamara, O. Mezhanska, K. Mi, N. G. Minaev, B. Mohanty, M. M. Mondal, I. Mooney, D. A. Morozov, A. Mudrokh, M. I. Nagy, A. S. Nain, J. D. Nam, M. Nasim, E. Nedorezov, D. Neff, J. M. Nelson, D. B. Nemes, M. Nie, G. Nigmatkulov, T. Niida, L. V. Nogach, T. Nonaka, G. Odyniec, A. Ogawa, S. Oh, V. A. Okorokov, K. Okubo, B. S. Page, R. Pak, S. Pal, A. Pandav, A. K. Pandey, Y. Panebratsev, T. Pani, P. Parfenov, A. Paul, C. Perkins, B. R. Pokhrel, M. Posik, A. Povarov, T. Protzman, N. K. Pruthi, J. Putschke, Z. Qin, H. Qiu, C. Racz, S. K. Radhakrishnan, A. Rana, R. L. Ray, H. G. Ritter, C. W. Robertson, O. V. Rogachevsky, M. A. Rosales Aguilar, D. Roy, L. Ruan, A. K. Sahoo, N. R. Sahoo, H. Sako, S. Salur, E. Samigullin, S. Sato, B. C. Schaefer, W. B. Schmidke, N. Schmitz, J. Seger, R. Seto, P. Seyboth, N. Shah, E. Shahaliev, P. V. Shanmuganathan, T. Shao, M. Sharma, N. Sharma, R. Sharma, S. R. Sharma, A. I. Sheikh, D. Shen, D. Y. Shen, K. Shen, S. S. Shi, Y. Shi, Q. Y. Shou, F. Si, J. Singh, S. Singha, P. Sinha, M. J. Skoby, Y. Söhngen, Y. Song, B. Srivastava, T. D. S. Stanislaus, D. J. Stewart, M. Strikhanov, B. Stringfellow, Y. Su, C. Sun, X. Sun, Y. Sun, B. Surrow, D. N. Svirida, Z. W. Sweger, A. C. Tamis, A. H. Tang, Z. Tang, A. Taranenko, T. Tarnowsky, J. H. Thomas, D. Tlusty, T. Todoroki, M. V. Tokarev, S. Trentalange, P. Tribedy, O. D. Tsai, C. Y. Tsang, Z. Tu, J. Tyler, T. Ullrich, D. G. Underwood, I. Upsal, G. Van Buren, A. N. Vasiliev, V. Verkest, F. Videbæk, S. Vokal, S. A. Voloshin, F. Wang, G. Wang, J. S. Wang, J. Wang, K. Wang, X. Wang, Y. Wang, Z. Wang, J. C. Webb, P. C. Weidenkaff, G. D. Westfall, H. Wieman, G. Wilks, S. W. Wissink, J. Wu, X. Wu, Wu X., B. Xi, Z. G. Xiao, G. Xie, W. Xie, H. Xu, N. Xu, Q. H. Xu, Y. Xu, Z. Xu, G. Yan, Z. Yan, C. Yang, Q. Yang, S. Yang, Y. Yang, Z. Ye, L. Yi, K. Yip, Y. Yu, W. Zha, C. Zhang, D. Zhang, J. Zhang, S. Zhang, W. Zhang, X. Zhang, Y. Zhang, Z. J. Zhang, Z. Zhang, F. Zhao, J. Zhao, M. Zhao, J. Zhou, S. Zhou, Y. Zhou, X. Zhu, M. Zurek, and M. Zyzak
Subjects: Physics, QC1-999
Abstract: The chiral magnetic effect (CME) is a phenomenon that arises from the QCD anomaly in the presence of an external magnetic field. The experimental search for its evidence has been one of the key goals of the physics program of the Relativistic Heavy-Ion Collider. The STAR Collaboration has previously presented the results of a blind analysis of isobar collisions (_{44}^{96}Ru+_{44}^{96}Ru, _{40}^{96}Zr+_{40}^{96}Zr) in the search for the CME. The isobar ratio (Y) of CME-sensitive observable, charge separation scaled by elliptic anisotropy, is close to but systematically larger than the inverse multiplicity ratio, the naive background baseline. This indicates the potential existence of a CME signal and the presence of remaining nonflow background due to two- and three-particle correlations, which are different between the isobars. In this postblind analysis, we estimate the contributions from those nonflow correlations as a background baseline to Y, utilizing the isobar data as well as Heavy Ion Jet Interaction Generator simulations. This baseline is found consistent with the isobar ratio measurement, and an upper limit of 10% at 95% confidence level is extracted for the CME fraction in the charge separation measurement in isobar collisions at sqrt[s_{NN}]=200 GeV.
Published: 2024
Full Text: View/download PDF

4. Measurement of electrons from open heavy-flavor hadron decays in Au+Au collisions at s NN $$ \sqrt{s_{\textrm{NN}}} $$ = 200 GeV with the STAR detector

Author: The STAR collaboration, M. I. Abdulhamid, B. E. Aboona, J. Adam, L. Adamczyk, J. R. Adams, I. Aggarwal, M. M. Aggarwal, Z. Ahammed, D. M. Anderson, E. C. Aschenauer, S. Aslam, J. Atchison, V. Bairathi, W. Baker, J. G. Ball Cap, K. Barish, R. Bellwied, P. Bhagat, A. Bhasin, S. Bhatta, J. Bielcik, J. Bielcikova, J. D. Brandenburg, X. Z. Cai, H. Caines, M. Calderón de la Barca Sánchez, D. Cebra, J. Ceska, I. Chakaberia, P. Chaloupka, B. K. Chan, Z. Chang, A. Chatterjee, D. Chen, J. Chen, J. H. Chen, Z. Chen, J. Cheng, Y. Cheng, S. Choudhury, W. Christie, X. Chu, H. J. Crawford, M. Csanád, G. Dale-Gau, A. Das, M. Daugherity, I. M. Deppner, A. Dhamija, L. Di Carlo, L. Didenko, P. Dixit, X. Dong, J. L. Drachenberg, E. Duckworth, J. C. Dunlop, J. Engelage, G. Eppley, S. Esumi, O. Evdokimov, A. Ewigleben, O. Eyser, R. Fatemi, S. Fazio, C. J. Feng, Y. Feng, E. Finch, Y. Fisyak, F. A. Flor, C. Fu, C. A. Gagliardi, T. Galatyuk, F. Geurts, N. Ghimire, A. Gibson, K. Gopal, X. Gou, D. Grosnick, A. Gupta, W. Guryn, A. Hamed, Y. Han, S. Harabasz, M. D. Harasty, J. W. Harris, H. Harrison-Smith, W. He, X. H. He, Y. He, N. Herrmann, L. Holub, C. Hu, Q. Hu, Y. Hu, H. Huang, H. Z. Huang, S. L. Huang, T. Huang, X. Huang, Y. Huang, T. J. Humanic, D. Isenhower, M. Isshiki, W. W. Jacobs, A. Jalotra, C. Jena, A. Jentsch, Y. Ji, J. Jia, C. Jin, X. Ju, E. G. Judd, S. Kabana, M. L. Kabir, S. Kagamaster, D. Kalinkin, K. Kang, D. Kapukchyan, D. Keane, M. Kelsey, Y. V. Khyzhniak, D. P. Kikoła, B. Kimelman, D. Kincses, I. Kisel, A. Kiselev, A. G. Knospe, H. S. Ko, L. K. Kosarzewski, L. Kramarik, L. Kumar, S. Kumar, R. Kunnawalkam Elayavalli, R. Lacey, J. M. Landgraf, J. Lauret, A. Lebedev, J. H. Lee, Y. H. Leung, N. Lewis, C. Li, W. Li, X. Li, Y. Li, Z. Li, X. Liang, Y. Liang, R. Licenik, T. Lin, M. A. Lisa, C. Liu, F. Liu, G. Liu, H. Liu, L. Liu, T. Liu, X. Liu, Y. Liu, Z. Liu, T. Ljubicic, W. J. Llope, O. Lomicky, R. S. Longacre, E. M. Loyd, T. Lu, N. S. Lukow, X. F. Luo, L. Ma, R. Ma, Y. G. Ma, N. Magdy, D. Mallick, S. Margetis, C. Markert, H. S. Matis, J. A. Mazer, G. McNamara, K. Mi, S. Mioduszewski, B. Mohanty, M. M. Mondal, I. Mooney, A. Mukherjee, M. I. Nagy, A. S. Nain, J. D. Nam, M. Nasim, D. Neff, J. M. Nelson, D. B. Nemes, M. Nie, T. Niida, R. Nishitani, T. Nonaka, G. Odyniec, A. Ogawa, S. Oh, K. Okubo, B. S. Page, R. Pak, J. Pan, A. Pandav, A. K. Pandey, T. Pani, A. Paul, B. Pawlik, D. Pawlowska, C. Perkins, J. Pluta, B. R. Pokhrel, M. Posik, T. Protzman, V. Prozorova, N. K. Pruthi, M. Przybycien, J. Putschke, Z. Qin, H. Qiu, A. Quintero, C. Racz, S. K. Radhakrishnan, N. Raha, R. L. Ray, R. Reed, H. G. Ritter, C. W. Robertson, M. Robotkova, M. A. Rosales Aguilar, D. Roy, P. Roy Chowdhury, L. Ruan, A. K. Sahoo, N. R. Sahoo, H. Sako, S. Salur, S. Sato, W. B. Schmidke, N. Schmitz, F-J. Seck, J. Seger, R. Seto, P. Seyboth, N. Shah, P. V. Shanmuganathan, T. Shao, M. Sharma, N. Sharma, R. Sharma, S. R. Sharma, A. I. Sheikh, D. Y. Shen, K. Shen, S. S. Shi, Y. Shi, Q. Y. Shou, F. Si, J. Singh, S. Singha, P. Sinha, M. J. Skoby, N. Smirnov, Y. Söhngen, Y. Song, B. Srivastava, T. D. S. Stanislaus, M. Stefaniak, D. J. Stewart, B. Stringfellow, Y. Su, A. A. P. Suaide, M. Sumbera, C. Sun, X. Sun, Y. Sun, B. Surrow, Z. W. Sweger, P. Szymanski, A. Tamis, A. H. Tang, Z. Tang, T. Tarnowsky, J. H. Thomas, A. R. Timmins, D. Tlusty, T. Todoroki, C. A. Tomkiel, S. Trentalange, R. E. Tribble, P. Tribedy, T. Truhlar, B. A. Trzeciak, O. D. Tsai, C. Y. Tsang, Z. Tu, J. Tyler, T. Ullrich, D. G. Underwood, I. Upsal, G. Van Buren, J. Vanek, I. Vassiliev, V. Verkest, F. Videbæk, S. A. Voloshin, F. Wang, G. Wang, J. S. Wang, X. Wang, Y. Wang, Z. Wang, J. C. Webb, P. C. Weidenkaff, G. D. Westfall, D. Wielanek, H. Wieman, G. Wilks, S. W. Wissink, R. Witt, J. Wu, X. Wu, Y. Wu, B. Xi, Z. G. Xiao, G. Xie, W. Xie, H. Xu, N. Xu, Q. H. Xu, Y. Xu, Z. Xu, G. Yan, Z. Yan, C. Yang, Q. Yang, S. Yang, Y. Yang, Z. Ye, L. Yi, K. Yip, Y. Yu, H. Zbroszczyk, W. Zha, C. Zhang, D. Zhang, J. Zhang, S. Zhang, W. Zhang, X. Zhang, Y. Zhang, Z. J. Zhang, Z. Zhang, F. Zhao, J. Zhao, M. Zhao, C. Zhou, J. Zhou, S. Zhou, Y. Zhou, X. Zhu, M. Zurek, and M. Zyzak
Subjects: Heavy Ion Experiments, Heavy Quark Production, Heavy-Ion Collision, Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Abstract: Abstract We report a new measurement of the production of electrons from open heavy-flavor hadron decays (HFEs) at mid-rapidity (|y| < 0.7) in Au+Au collisions at s NN $$ \sqrt{s_{\textrm{NN}}} $$ = 200 GeV. Invariant yields of HFEs are measured for the transverse momentum range of 3.5 < p T < 9 GeV/c in various configurations of the collision geometry. The HFE yields in head-on Au+Au collisions are suppressed by approximately a factor of 2 compared to that in p + p collisions scaled by the average number of binary collisions, indicating strong interactions between heavy quarks and the hot and dense medium created in heavy-ion collisions. Comparison of these results with models provides additional tests of theoretical calculations of heavy quark energy loss in the quark-gluon plasma.
Published: 2023
Full Text: View/download PDF

5. Erratum to: Evidence of Mass Ordering of Charm and Bottom Quark Energy Loss in Au+Au Collisions at RHIC

Author: M. S. Abdallah, B. E. Aboona, J. Adam, L. Adamczyk, J. R. Adams, J. K. Adkins, I. Aggarwal, M. M. Aggarwal, Z. Ahammed, D. M. Anderson, E. C. Aschenauer, J. Atchison, X. Bai, V. Bairathi, W. Baker, J. G. Ball Cap, K. Barish, R. Bellwied, P. Bhagat, A. Bhasin, S. Bhatta, J. Bielcik, J. Bielcikova, J. D. Brandenburg, X. Z. Cai, H. Caines, M. Calderón de la Barca Sánchez, D. Cebra, I. Chakaberia, P. Chaloupka, B. K. Chan, Z. Chang, A. Chatterjee, S. Chattopadhyay, D. Chen, J. Chen, J. H. Chen, X. Chen, Z. Chen, J. Cheng, Y. Cheng, S. Choudhury, W. Christie, X. Chu, H. J. Crawford, M. Csanád, M. Daugherity, I. M. Deppner, A. Dhamija, L. Di Carlo, L. Didenko, P. Dixit, X. Dong, J. L. Drachenberg, E. Duckworth, J. C. Dunlop, J. Engelage, G. Eppley, S. Esumi, O. Evdokimov, A. Ewigleben, O. Eyser, R. Fatemi, F. M. Fawzi, S. Fazio, C. J. Feng, Y. Feng, E. Finch, Y. Fisyak, A. Francisco, C. Fu, C. A. Gagliardi, T. Galatyuk, F. Geurts, N. Ghimire, A. Gibson, K. Gopal, X. Gou, D. Grosnick, A. Gupta, W. Guryn, A. Hamed, Y. Han, S. Harabasz, M. D. Harasty, J. W. Harris, H. Harrison, S. He, W. He, X. H. He, Y. He, S. Heppelmann, N. Herrmann, E. Hoffman, L. Holub, C. Hu, Q. Hu, Y. Hu, H. Huang, H. Z. Huang, S. L. Huang, T. Huang, X. Huang, Y. Huang, T. J. Humanic, D. Isenhower, M. Isshiki, W. W. Jacobs, C. Jena, A. Jentsch, Y. Ji, J. Jia, K. Jiang, C. Jin, X. Ju, E. G. Judd, S. Kabana, M. L. Kabir, S. Kagamaster, D. Kalinkin, K. Kang, D. Kapukchyan, K. Kauder, H. W. Ke, D. Keane, M. Kelsey, Y. V. Khyzhniak, D. P. Kikoła, B. Kimelman, D. Kincses, I. Kisel, A. Kiselev, A. G. Knospe, H. S. Ko, L. K. Kosarzewski, L. Kramarik, L. Kumar, S. Kumar, R. Kunnawalkam Elayavalli, J. H. Kwasizur, R. Lacey, S. Lan, J. M. Landgraf, J. Lauret, A. Lebedev, J. H. Lee, Y. H. Leung, N. Lewis, C. Li, W. Li, X. Li, Y. Li, Z. Li, X. Liang, Y. Liang, R. Licenik, T. Lin, Y. Lin, M. A. Lisa, F. Liu, H. Liu, T. Liu, X. Liu, Y. Liu, T. Ljubicic, W. J. Llope, R. S. Longacre, E. Loyd, T. Lu, N. S. Lukow, X. F. Luo, L. Ma, R. Ma, Y. G. Ma, N. Magdy, D. Mallick, S. Margetis, C. Markert, H. S. Matis, J. A. Mazer, G. McNamara, S. Mioduszewski, B. Mohanty, M. M. Mondal, I. Mooney, A. Mukherjee, M. I. Nagy, A. S. Nain, J. D. Nam, Md. Nasim, K. Nayak, D. Neff, J. M. Nelson, D. B. Nemes, M. Nie, T. Niida, R. Nishitani, T. Nonaka, A. S. Nunes, G. Odyniec, A. Ogawa, S. Oh, K. Okubo, B. S. Page, R. Pak, J. Pan, A. Pandav, A. K. Pandey, T. Pani, A. Paul, B. Pawlik, D. Pawlowska, C. Perkins, J. Pluta, B. R. Pokhrel, J. Porter, M. Posik, T. Protzman, V. Prozorova, N. K. Pruthi, M. Przybycien, J. Putschke, Z. Qin, H. Qiu, A. Quintero, C. Racz, S. K. Radhakrishnan, N. Raha, R. L. Ray, R. Reed, H. G. Ritter, M. Robotkova, J. L. Romero, D. Roy, P. Roy Chowdhury, L. Ruan, A. K. Sahoo, N. R. Sahoo, H. Sako, S. Salur, S. Sato, W. B. Schmidke, N. Schmitz, F.-J. Seck, J. Seger, R. Seto, P. Seyboth, N. Shah, P. V. Shanmuganathan, M. Shao, T. Shao, R. Sharma, A. I. Sheikh, D. Y. Shen, K. Shen, S. S. Shi, Y. Shi, Q. Y. Shou, E. P. Sichtermann, R. Sikora, J. Singh, S. Singha, P. Sinha, M. J. Skoby, N. Smirnov, Y. Söhngen, W. Solyst, Y. Song, B. Srivastava, T. D. S. Stanislaus, D. J. Stewart, B. Stringfellow, A. A. P. Suaide, M. Sumbera, C. Sun, X. M. Sun, X. Sun, Y. Sun, B. Surrow, Z. W. Sweger, P. Szymanski, A. H. Tang, Z. Tang, T. Tarnowsky, J. H. Thomas, A. R. Timmins, D. Tlusty, T. Todoroki, C. A. Tomkiel, S. Trentalange, R. E. Tribble, P. Tribedy, S. K. Tripathy, T. Truhlar, B. A. Trzeciak, O. D. Tsai, C. Y. Tsang, Z. Tu, T. Ullrich, D. G. Underwood, I. Upsal, G. Van Buren, J. Vanek, I. Vassiliev, V. Verkest, F. Videbæk, S. A. Voloshin, F. Wang, G. Wang, J. S. Wang, P. Wang, X. Wang, Y. Wang, Z. Wang, J. C. Webb, P. C. Weidenkaff, G. D. Westfall, D. Wielanek, H. Wieman, S. W. Wissink, R. Witt, J. Wu, X. Wu, Y. Wu, B. Xi, Z. G. Xiao, G. Xie, W. Xie, H. Xu, N. Xu, Q. H. Xu, Y. Xu, Z. Xu, G. Yan, Z. Yan, C. Yang, Q. Yang, S. Yang, Y. Yang, Z. Ye, L. Yi, K. Yip, Y. Yu, H. Zbroszczyk, W. Zha, C. Zhang, D. Zhang, J. Zhang, S. Zhang, Y. Zhang, Z. J. Zhang, Z. Zhang, F. Zhao, J. Zhao, M. Zhao, C. Zhou, J. Zhou, Y. Zhou, X. Zhu, M. Zurek, M. Zyzak, and STAR Collaboration
Subjects: Astrophysics, QB460-466, Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Published: 2023
Full Text: View/download PDF

6. Evidence of Mass Ordering of Charm and Bottom Quark Energy Loss in Au+Au Collisions at RHIC

Author: M. S. Abdallah, B. E. Aboona, J. Adam, L. Adamczyk, J. R. Adams, J. K. Adkins, I. Aggarwal, M. M. Aggarwal, Z. Ahammed, D. M. Anderson, E. C. Aschenauer, J. Atchison, X. Bai, V. Bairathi, W. Baker, J. G. Ball Cap, K. Barish, R. Bellwied, P. Bhagat, A. Bhasin, S. Bhatta, J. Bielcik, J. Bielcikova, J. D. Brandenburg, X. Z. Cai, H. Caines, M. Calderón de la Barca Sánchez, D. Cebra, I. Chakaberia, P. Chaloupka, B. K. Chan, Z. Chang, A. Chatterjee, S. Chattopadhyay, D. Chen, J. Chen, J. H. Chen, X. Chen, Z. Chen, J. Cheng, Y. Cheng, S. Choudhury, W. Christie, X. Chu, H. J. Crawford, M. Csanád, M. Daugherity, I. M. Deppner, A. Dhamija, L. Di Carlo, L. Didenko, P. Dixit, X. Dong, J. L. Drachenberg, E. Duckworth, J. C. Dunlop, J. Engelage, G. Eppley, S. Esumi, O. Evdokimov, A. Ewigleben, O. Eyser, R. Fatemi, F. M. Fawzi, S. Fazio, C. J. Feng, Y. Feng, E. Finch, Y. Fisyak, A. Francisco, C. Fu, C. A. Gagliardi, T. Galatyuk, F. Geurts, N. Ghimire, A. Gibson, K. Gopal, X. Gou, D. Grosnick, A. Gupta, W. Guryn, A. Hamed, Y. Han, S. Harabasz, M. D. Harasty, J. W. Harris, H. Harrison, S. He, W. He, X. H. He, Y. He, S. Heppelmann, N. Herrmann, E. Hoffman, L. Holub, C. Hu, Q. Hu, Y. Hu, H. Huang, H. Z. Huang, S. L. Huang, T. Huang, X. Huang, Y. Huang, T. J. Humanic, D. Isenhower, M. Isshiki, W. W. Jacobs, C. Jena, A. Jentsch, Y. Ji, J. Jia, K. Jiang, C. Jin, X. Ju, E. G. Judd, S. Kabana, M. L. Kabir, S. Kagamaster, D. Kalinkin, K. Kang, D. Kapukchyan, K. Kauder, H. W. Ke, D. Keane, M. Kelsey, Y. V. Khyzhniak, D. P. Kikoła, B. Kimelman, D. Kincses, I. Kisel, A. Kiselev, A. G. Knospe, H. S. Ko, L. K. Kosarzewski, L. Kramarik, L. Kumar, S. Kumar, R. Kunnawalkam Elayavalli, J. H. Kwasizur, R. Lacey, S. Lan, J. M. Landgraf, J. Lauret, A. Lebedev, J. H. Lee, Y. H. Leung, N. Lewis, C. Li, W. Li, X. Li, Y. Li, Z. Li, X. Liang, Y. Liang, R. Licenik, T. Lin, Y. Lin, M. A. Lisa, F. Liu, H. Liu, T. Liu, X. Liu, Y. Liu, T. Ljubicic, W. J. Llope, R. S. Longacre, E. Loyd, T. Lu, N. S. Lukow, X. F. Luo, L. Ma, R. Ma, Y. G. Ma, N. Magdy, D. Mallick, S. Margetis, C. Markert, H. S. Matis, J. A. Mazer, G. McNamara, S. Mioduszewski, B. Mohanty, M. M. Mondal, I. Mooney, A. Mukherjee, M. I. Nagy, A. S. Nain, J. D. Nam, Md. Nasim, K. Nayak, D. Neff, J. M. Nelson, D. B. Nemes, M. Nie, T. Niida, R. Nishitani, T. Nonaka, A. S. Nunes, G. Odyniec, A. Ogawa, S. Oh, K. Okubo, B. S. Page, R. Pak, J. Pan, A. Pandav, A. K. Pandey, T. Pani, A. Paul, B. Pawlik, D. Pawlowska, C. Perkins, J. Pluta, B. R. Pokhrel, J. Porter, M. Posik, T. Protzman, V. Prozorova, N. K. Pruthi, M. Przybycien, J. Putschke, Z. Qin, H. Qiu, A. Quintero, C. Racz, S. K. Radhakrishnan, N. Raha, R. L. Ray, R. Reed, H. G. Ritter, M. Robotkova, J. L. Romero, D. Roy, P. Roy Chowdhury, L. Ruan, A. K. Sahoo, N. R. Sahoo, H. Sako, S. Salur, S. Sato, W. B. Schmidke, N. Schmitz, F-J. Seck, J. Seger, R. Seto, P. Seyboth, N. Shah, P. V. Shanmuganathan, M. Shao, T. Shao, R. Sharma, A. I. Sheikh, D. Y. Shen, K. Shen, S. S. Shi, Y. Shi, Q. Y. Shou, E. P. Sichtermann, R. Sikora, J. Singh, S. Singha, P. Sinha, M. J. Skoby, N. Smirnov, Y. Söhngen, W. Solyst, Y. Song, B. Srivastava, T. D. S. Stanislaus, D. J. Stewart, B. Stringfellow, A. A. P. Suaide, M. Sumbera, C. Sun, X. M. Sun, X. Sun, Y. Sun, B. Surrow, Z. W. Sweger, P. Szymanski, A. H. Tang, Z. Tang, T. Tarnowsky, J. H. Thomas, A. R. Timmins, D. Tlusty, T. Todoroki, C. A. Tomkiel, S. Trentalange, R. E. Tribble, P. Tribedy, S. K. Tripathy, T. Truhlar, B. A. Trzeciak, O. D. Tsai, C. Y. Tsang, Z. Tu, T. Ullrich, D. G. Underwood, I. Upsal, G. Van Buren, J. Vanek, I. Vassiliev, V. Verkest, F. Videbæk, S. A. Voloshin, F. Wang, G. Wang, J. S. Wang, P. Wang, X. Wang, Y. Wang, Z. Wang, J. C. Webb, P. C. Weidenkaff, G. D. Westfall, D. Wielanek, H. Wieman, S. W. Wissink, R. Witt, J. Wu, X. Wu, Y. Wu, B. Xi, Z. G. Xiao, G. Xie, W. Xie, H. Xu, N. Xu, Q. H. Xu, Y. Xu, Z. Xu, G. Yan, Z. Yan, C. Yang, Q. Yang, S. Yang, Y. Yang, Z. Ye, L. Yi, K. Yip, Y. Yu, H. Zbroszczyk, W. Zha, C. Zhang, D. Zhang, J. Zhang, S. Zhang, Y. Zhang, Z. J. Zhang, Z. Zhang, F. Zhao, J. Zhao, M. Zhao, C. Zhou, J. Zhou, Y. Zhou, X. Zhu, M. Zurek, M. Zyzak, and STAR Collaboration
Subjects: Astrophysics, QB460-466, Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Abstract: Abstract Partons traversing the strongly interacting medium produced in heavy-ion collisions are expected to lose energy depending on their color charge and mass. We measure the nuclear modification factors for charm- and bottom-decay electrons, defined as the ratio of yields, divided by the number of binary nucleon–nucleon collisions, in $$\sqrt{s_{\textrm{NN}}}=200$$ s NN = 200 GeV Au+Au collisions to p+p collisions ( $$R_{\textrm{AA}}$$ R AA ), or in central to peripheral Au+Au collisions ( $$R_{\textrm{CP}}$$ R CP ). We find the bottom-decay electron $$R_{\textrm{AA}}$$ R AA and $$R_{\textrm{CP}}$$ R CP to be significantly higher than those of charm-decay electrons. Model calculations including mass-dependent parton energy loss in a strongly coupled medium are consistent with the measured data. These observations provide evidence of mass ordering of charm and bottom quark energy loss when traversing through the strongly coupled medium created in heavy-ion collisions.
Published: 2022
Full Text: View/download PDF

7. Observation of the Electromagnetic Field Effect via Charge-Dependent Directed Flow in Heavy-Ion Collisions at the Relativistic Heavy Ion Collider

Author: M. I. Abdulhamid, B. E. Aboona, J. Adam, J. R. Adams, G. Agakishiev, I. Aggarwal, M. M. Aggarwal, Z. Ahammed, A. Aitbaev, I. Alekseev, E. Alpatov, A. Aparin, S. Aslam, J. Atchison, G. S. Averichev, V. Bairathi, J. G. Ball Cap, K. Barish, P. Bhagat, A. Bhasin, S. Bhatta, S. R. Bhosale, I. G. Bordyuzhin, J. D. Brandenburg, A. V. Brandin, X. Z. Cai, H. Caines, M. Calderón de la Barca Sánchez, D. Cebra, J. Ceska, I. Chakaberia, B. K. Chan, Z. Chang, A. Chatterjee, D. Chen, J. Chen, J. H. Chen, Z. Chen, J. Cheng, Y. Cheng, S. Choudhury, W. Christie, X. Chu, H. J. Crawford, G. Dale-Gau, A. Das, A. P. Dash, M. Daugherity, T. G. Dedovich, I. M. Deppner, A. A. Derevschikov, A. Dhamija, P. Dixit, X. Dong, J. L. Drachenberg, E. Duckworth, J. C. Dunlop, J. Engelage, G. Eppley, S. Esumi, O. Evdokimov, O. Eyser, R. Fatemi, S. Fazio, C. J. Feng, Y. Feng, E. Finch, Y. Fisyak, F. A. Flor, C. Fu, T. Gao, F. Geurts, N. Ghimire, A. Gibson, K. Gopal, X. Gou, D. Grosnick, A. Gupta, A. Hamed, Y. Han, M. D. Harasty, J. W. Harris, H. Harrison-Smith, W. He, X. H. He, Y. He, C. Hu, Q. Hu, Y. Hu, H. Huang, H. Z. Huang, S. L. Huang, T. Huang, X. Huang, Y. Huang, T. J. Humanic, D. Isenhower, M. Isshiki, W. W. Jacobs, A. Jalotra, C. Jena, Y. Ji, J. Jia, C. Jin, X. Ju, E. G. Judd, S. Kabana, D. Kalinkin, K. Kang, D. Kapukchyan, K. Kauder, D. Keane, A. Kechechyan, A. Kiselev, A. G. Knospe, H. S. Ko, L. Kochenda, A. A. Korobitsin, A. Yu. Kraeva, P. Kravtsov, L. Kumar, M. C. Labonte, R. Lacey, J. M. Landgraf, A. Lebedev, R. Lednicky, J. H. Lee, Y. H. Leung, N. Lewis, C. Li, H-S. Li, W. Li, X. Li, Y. Li, Z. Li, X. Liang, Y. Liang, T. Lin, Y. Lin, C. Liu, F. Liu, G. Liu, H. Liu, L. Liu, T. Liu, X. Liu, Y. Liu, Z. Liu, T. Ljubicic, O. Lomicky, R. S. Longacre, E. M. Loyd, T. Lu, N. S. Lukow, X. F. Luo, V. B. Luong, L. Ma, R. Ma, Y. G. Ma, N. Magdy, D. Mallick, S. Margetis, H. S. Matis, G. McNamara, K. Mi, N. G. Minaev, B. Mohanty, M. M. Mondal, I. Mooney, D. A. Morozov, A. Mudrokh, M. I. Nagy, A. S. Nain, J. D. Nam, M. Nasim, E. Nedorezov, D. Neff, J. M. Nelson, D. B. Nemes, M. Nie, G. Nigmatkulov, T. Niida, L. V. Nogach, T. Nonaka, G. Odyniec, A. Ogawa, S. Oh, V. A. Okorokov, K. Okubo, B. S. Page, R. Pak, A. Pandav, Y. Panebratsev, T. Pani, P. Parfenov, A. Paul, C. Perkins, B. R. Pokhrel, M. Posik, A. Povarov, T. Protzman, N. K. Pruthi, J. Putschke, Z. Qin, H. Qiu, A. Quintero, C. Racz, S. K. Radhakrishnan, A. Rana, R. L. Ray, H. G. Ritter, C. W. Robertson, O. V. Rogachevsky, M. A. Rosales Aguilar, D. Roy, L. Ruan, A. K. Sahoo, N. R. Sahoo, H. Sako, S. Salur, E. Samigullin, S. Sato, B. C. Schaefer, W. B. Schmidke, N. Schmitz, J. Seger, R. Seto, P. Seyboth, N. Shah, E. Shahaliev, P. V. Shanmuganathan, T. Shao, M. Sharma, N. Sharma, R. Sharma, S. R. Sharma, A. I. Sheikh, D. Shen, D. Y. Shen, K. Shen, S. S. Shi, Y. Shi, Q. Y. Shou, F. Si, J. Singh, S. Singha, P. Sinha, M. J. Skoby, Y. Söhngen, Y. Song, B. Srivastava, T. D. S. Stanislaus, D. J. Stewart, M. Strikhanov, B. Stringfellow, Y. Su, C. Sun, X. Sun, Y. Sun, B. Surrow, D. N. Svirida, Z. W. Sweger, A. C. Tamis, A. H. Tang, Z. Tang, A. Taranenko, T. Tarnowsky, J. H. Thomas, D. Tlusty, T. Todoroki, M. V. Tokarev, S. Trentalange, P. Tribedy, S. K. Tripathy, O. D. Tsai, C. Y. Tsang, Z. Tu, J. Tyler, T. Ullrich, D. G. Underwood, I. Upsal, G. Van Buren, A. N. Vasiliev, V. Verkest, F. Videbæk, S. Vokal, S. A. Voloshin, F. Wang, G. Wang, J. S. Wang, J. Wang, X. Wang, Y. Wang, Z. Wang, J. C. Webb, P. C. Weidenkaff, G. D. Westfall, H. Wieman, G. Wilks, S. W. Wissink, J. Wu, X. Wu, B. Xi, Z. G. Xiao, G. Xie, W. Xie, H. Xu, N. Xu, Q. H. Xu, Y. Xu, Z. Xu, G. Yan, Z. Yan, C. Yang, Q. Yang, S. Yang, Y. Yang, Z. Ye, L. Yi, K. Yip, Y. Yu, W. Zha, C. Zhang, D. Zhang, J. Zhang, S. Zhang, W. Zhang, X. Zhang, Y. Zhang, Z. J. Zhang, Z. Zhang, F. Zhao, J. Zhao, M. Zhao, C. Zhou, J. Zhou, S. Zhou, Y. Zhou, X. Zhu, M. Zurek, and M. Zyzak
Subjects: Physics, QC1-999
Abstract: The deconfined quark-gluon plasma (QGP) created in relativistic heavy-ion collisions enables the exploration of the fundamental properties of matter under extreme conditions. Noncentral collisions can produce strong magnetic fields on the order of 10^{18} G, which offers a probe into the electrical conductivity of the QGP. In particular, quarks and antiquarks carry opposite charges and receive contrary electromagnetic forces that alter their momenta. This phenomenon can be manifested in the collective motion of final-state particles, specifically in the rapidity-odd directed flow, denoted as v_{1}(y). Here, we present the charge-dependent measurements of dv_{1}/dy near midrapidities for π^{±}, K^{±}, and p(p[over ¯]) in Au+Au and isobar (_{44}^{96}Ru+_{44}^{96}Ru and _{40}^{96}Zr+_{40}^{96}Zr) collisions at sqrt[s_{NN}]=200 GeV, and in Au+Au collisions at 27 GeV, recorded by the STAR detector at the Relativistic Heavy Ion Collider. The combined dependence of the v_{1} signal on collision system, particle species, and collision centrality can be qualitatively and semiquantitatively understood as several effects on constituent quarks. While the results in central events can be explained by the u and d quarks transported from initial-state nuclei, those in peripheral events reveal the impacts of the electromagnetic field on the QGP. Our data put valuable constraints on the electrical conductivity of the QGP in theoretical calculations.
Published: 2024
Full Text: View/download PDF

8. DRAGON-Data: a platform and protocol for integrating genomic and phenotypic data across large psychiatric cohorts

Author: Amy J. Lynham, Sarah Knott, Jack F. G. Underwood, Leon Hubbard, Sharifah S. Agha, Jonathan I. Bisson, Marianne B. M. van den Bree, Samuel J. R. A. Chawner, Nicholas Craddock, Michael O'Donovan, Ian R. Jones, George Kirov, Kate Langley, Joanna Martin, Frances Rice, Neil P. Roberts, Anita Thapar, Richard Anney, Michael J. Owen, Jeremy Hall, Antonio F. Pardiñas, and James T. R. Walters
Subjects: Genetics, schizophrenia, developmental disorders, bipolar affective disorders, attention-deficit hyperactivity disorders, Psychiatry, RC435-571
Abstract: Background Current psychiatric diagnoses, although heritable, have not been clearly mapped onto distinct underlying pathogenic processes. The same symptoms often occur in multiple disorders, and a substantial proportion of both genetic and environmental risk factors are shared across disorders. However, the relationship between shared symptoms and shared genetic liability is still poorly understood. Aims Well-characterised, cross-disorder samples are needed to investigate this matter, but few currently exist. Our aim is to develop procedures to purposely curate and aggregate genotypic and phenotypic data in psychiatric research. Method As part of the Cardiff MRC Mental Health Data Pathfinder initiative, we have curated and harmonised phenotypic and genetic information from 15 studies to create a new data repository, DRAGON-Data. To date, DRAGON-Data includes over 45 000 individuals: adults and children with neurodevelopmental or psychiatric diagnoses, affected probands within collected families and individuals who carry a known neurodevelopmental risk copy number variant. Results We have processed the available phenotype information to derive core variables that can be reliably analysed across groups. In addition, all data-sets with genotype information have undergone rigorous quality control, imputation, copy number variant calling and polygenic score generation. Conclusions DRAGON-Data combines genetic and non-genetic information, and is available as a resource for research across traditional psychiatric diagnostic categories. Algorithms and pipelines used for data harmonisation are currently publicly available for the scientific community, and an appropriate data-sharing protocol will be developed as part of ongoing projects (DATAMIND) in partnership with Health Data Research UK.
Published: 2023
Full Text: View/download PDF

9. Evidence for opposing selective forces operating on human-specific duplicated TCAF genes in Neanderthals and humans

Author: PingHsun Hsieh, Vy Dang, Mitchell R. Vollger, Yafei Mao, Tzu-Hsueh Huang, Philip C. Dishuck, Carl Baker, Stuart Cantsilieris, Alexandra P. Lewis, Katherine M. Munson, Melanie Sorensen, AnneMarie E. Welch, Jason G. Underwood, and Evan E. Eichler
Subjects: Science
Abstract: Duplications of gene segments can allow novel physiological adaptations to evolve. A detailed analysis of the TCAF gene family in primates and archaic humans suggest rapid duplication and diversification in this gene family is associated with cold or dietary adaptations.
Published: 2021
Full Text: View/download PDF

10. Motif-based spectral clustering of weighted directed networks

Author: William G. Underwood, Andrew Elliott, and Mihai Cucuringu
Subjects: Motif, Spectral clustering, Weighted network, Directed network, Community detection, Graph Laplacian, Applied mathematics. Quantitative methods, T57-57.97
Abstract: Abstract Clustering is an essential technique for network analysis, with applications in a diverse range of fields. Although spectral clustering is a popular and effective method, it fails to consider higher-order structure and can perform poorly on directed networks. One approach is to capture and cluster higher-order structures using motif adjacency matrices. However, current formulations fail to take edge weights into account, and thus are somewhat limited when weight is a key component of the network under study.We address these shortcomings by exploring motif-based weighted spectral clustering methods. We present new and computationally useful matrix formulae for motif adjacency matrices on weighted networks, which can be used to construct efficient algorithms for any anchored or non-anchored motif on three nodes. In a very sparse regime, our proposed method can handle graphs with a million nodes and tens of millions of edges. We further use our framework to construct a motif-based approach for clustering bipartite networks.We provide comprehensive experimental results, demonstrating (i) the scalability of our approach, (ii) advantages of higher-order clustering on synthetic examples, and (iii) the effectiveness of our techniques on a variety of real world data sets; and compare against several techniques from the literature. We conclude that motif-based spectral clustering is a valuable tool for analysis of directed and bipartite weighted networks, which is also scalable and easy to implement.
Published: 2020
Full Text: View/download PDF

11. An evolutionary driver of interspersed segmental duplications in primates

Author: Stuart Cantsilieris, Susan M. Sunkin, Matthew E. Johnson, Fabio Anaclerio, John Huddleston, Carl Baker, Max L. Dougherty, Jason G. Underwood, Arvis Sulovari, PingHsun Hsieh, Yafei Mao, Claudia Rita Catacchio, Maika Malig, AnneMarie E. Welch, Melanie Sorensen, Katherine M. Munson, Weihong Jiang, Santhosh Girirajan, Mario Ventura, Bruce T. Lamb, Ronald A. Conlon, and Evan E. Eichler
Subjects: Segmental duplication, Nuclear pore interacting protein, LCR16a, Gene fusion, Genomic instability, Biology (General), QH301-705.5, Genetics, QH426-470
Abstract: Abstract Background The complex interspersed pattern of segmental duplications in humans is responsible for rearrangements associated with neurodevelopmental disease, including the emergence of novel genes important in human brain evolution. We investigate the evolution of LCR16a, a putative driver of this phenomenon that encodes one of the most rapidly evolving human–ape gene families, nuclear pore interacting protein (NPIP). Results Comparative analysis shows that LCR16a has independently expanded in five primate lineages over the last 35 million years of primate evolution. The expansions are associated with independent lineage-specific segmental duplications flanking LCR16a leading to the emergence of large interspersed duplication blocks at non-orthologous chromosomal locations in each primate lineage. The intron-exon structure of the NPIP gene family has changed dramatically throughout primate evolution with different branches showing characteristic gene models yet maintaining an open reading frame. In the African ape lineage, we detect signatures of positive selection that occurred after a transition to more ubiquitous expression among great ape tissues when compared to Old World and New World monkeys. Mouse transgenic experiments from baboon and human genomic loci confirm these expression differences and suggest that the broader ape expression pattern arose due to mutational changes that emerged in cis. Conclusions LCR16a promotes serial interspersed duplications and creates hotspots of genomic instability that appear to be an ancient property of primate genomes. Dramatic changes to NPIP gene structure and altered tissue expression preceded major bouts of positive selection in the African ape lineage, suggestive of a gene undergoing strong adaptive evolution.
Published: 2020
Full Text: View/download PDF

12. Measurement of the central exclusive production of charged particle pairs in proton-proton collisions at s $$ \sqrt{s} $$ = 200 GeV with the STAR detector at RHIC

Author: The STAR collaboration, J. Adam, L. Adamczyk, J. R. Adams, J. K. Adkins, G. Agakishiev, M. M. Aggarwal, Z. Ahammed, I. Alekseev, D. M. Anderson, A. Aparin, E. C. Aschenauer, M. U. Ashraf, F. G. Atetalla, A. Attri, G. S. Averichev, V. Bairathi, K. Barish, A. Behera, R. Bellwied, A. Bhasin, J. Bielcik, J. Bielcikova, L. C. Bland, I. G. Bordyuzhin, J. D. Brandenburg, A. V. Brandin, J. Butterworth, H. Caines, M. Calderón de la Barca Sánchez, D. Cebra, I. Chakaberia, P. Chaloupka, B. K. Chan, F-H. Chang, Z. Chang, N. Chankova-Bunzarova, A. Chatterjee, D. Chen, J. H. Chen, X. Chen, Z. Chen, J. Cheng, M. Cherney, M. Chevalier, S. Choudhury, W. Christie, X. Chu, H. J. Crawford, M. Csanád, M. Daugherity, T. G. Dedovich, I. M. Deppner, A. A. Derevschikov, L. Didenko, X. Dong, J. L. Drachenberg, J. C. Dunlop, T. Edmonds, N. Elsey, J. Engelage, G. Eppley, R. Esha, S. Esumi, O. Evdokimov, A. Ewigleben, O. Eyser, R. Fatemi, S. Fazio, P. Federic, J. Fedorisin, C. J. Feng, Y. Feng, P. Filip, E. Finch, Y. Fisyak, A. Francisco, L. Fulek, C. A. Gagliardi, T. Galatyuk, F. Geurts, A. Gibson, K. Gopal, D. Grosnick, W. Guryn, A. I. Hamad, A. Hamed, S. Harabasz, J. W. Harris, S. He, W. He, X. H. He, S. Heppelmann, N. Herrmann, E. Hoffman, L. Holub, Y. Hong, S. Horvat, Y. Hu, H. Z. Huang, S. L. Huang, T. Huang, X. Huang, T. J. Humanic, P. Huo, G. Igo, D. Isenhower, W. W. Jacobs, C. Jena, A. Jentsch, Y. JI, J. Jia, K. Jiang, S. Jowzaee, X. Ju, E. G. Judd, S. Kabana, M. L. Kabir, S. Kagamaster, D. Kalinkin, K. Kang, D. Kapukchyan, K. Kauder, H. W. Ke, D. Keane, A. Kechechyan, M. Kelsey, Y. V. Khyzhniak, D. P. Kikoła, C. Kim, B. Kimelman, D. Kincses, T. A. Kinghorn, I. Kisel, A. Kiselev, A. Kisiel, M. Kocan, L. Kochenda, L. K. Kosarzewski, L. Kramarik, P. Kravtsov, K. Krueger, N. Kulathunga Mudiyanselage, L. Kumar, R. Kunnawalkam Elayavalli, J. H. Kwasizur, R. Lacey, S. Lan, J. M. Landgraf, J. Lauret, A. Lebedev, R. Lednicky, J. H. Lee, Y. H. Leung, C. Li, W. Li, X. Li, Y. Li, Y. Liang, R. Licenik, T. Lin, Y. Lin, M. A. Lisa, F. Liu, H. Liu, P. Liu, T. Liu, X. Liu, Y. Liu, Z. Liu, T. Ljubicic, W. J. Llope, R. S. Longacre, N. S. Lukow, S. Luo, X. Luo, G. L. Ma, L. Ma, R. Ma, Y. G. Ma, N. Magdy, R. Majka, D. Mallick, S. Margetis, C. Markert, H. S. Matis, J. A. Mazer, N. G. Minaev, S. Mioduszewski, B. Mohanty, M. M. Mondal, I. Mooney, Z. Moravcova, D. A. Morozov, M. Nagy, J. D. Nam, Md. Nasim, K. Nayak, D. Neff, J. M. Nelson, D. B. Nemes, M. Nie, G. Nigmatkulov, T. Niida, L. V. Nogach, T. Nonaka, A. S. Nunes, G. Odyniec, A. Ogawa, S. Oh, V. A. Okorokov, B. S. Page, R. Pak, A. Pandav, Y. Panebratsev, B. Pawlik, D. Pawlowska, H. Pei, C. Perkins, L. Pinsky, R. L. Pintér, J. Pluta, J. Porter, M. Posik, N. K. Pruthi, M. Przybycien, J. Putschke, H. Qiu, A. Quintero, S. K. Radhakrishnan, S. Ramachandran, R. L. Ray, R. Reed, H. G. Ritter, J. B. Roberts, O. V. Rogachevskiy, J. L. Romero, L. Ruan, J. Rusnak, N. R. Sahoo, H. Sako, S. Salur, J. Sandweiss, S. Sato, W. B. Schmidke, N. Schmitz, B. R. Schweid, F. Seck, J. Seger, M. Sergeeva, R. Seto, P. Seyboth, N. Shah, E. Shahaliev, P. V. Shanmuganathan, M. Shao, F. Shen, W. Q. Shen, S. S. Shi, Q. Y. Shou, E. P. Sichtermann, R. Sikora, M. Simko, J. Singh, S. Singha, N. Smirnov, W. Solyst, P. Sorensen, H. M. Spinka, B. Srivastava, T. D. S. Stanislaus, M. Stefaniak, D. J. Stewart, M. Strikhanov, B. Stringfellow, A. A. P. Suaide, M. Sumbera, B. Summa, X. M. Sun, X. Sun, Y. Sun, B. Surrow, D. N. Svirida, P. Szymanski, A. H. Tang, Z. Tang, A. Taranenko, T. Tarnowsky, J. H. Thomas, A. R. Timmins, D. Tlusty, M. Tokarev, C. A. Tomkiel, S. Trentalange, R. E. Tribble, P. Tribedy, S. K. Tripathy, O. D. Tsai, Z. Tu, T. Ullrich, D. G. Underwood, I. Upsal, G. Van Buren, J. Vanek, A. N. Vasiliev, I. Vassiliev, F. Videbæk, S. Vokal, S. A. Voloshin, F. Wang, G. Wang, J. S. Wang, P. Wang, Y. Wang, Z. Wang, J. C. Webb, P. C. Weidenkaff, L. Wen, G. D. Westfall, H. Wieman, S. W. Wissink, R. Witt, Y. Wu, Z. G. Xiao, G. Xie, W. Xie, H. Xu, N. Xu, Q. H. Xu, Y. F. Xu, Y. Xu, Z. Xu, C. Yang, Q. Yang, S. Yang, Y. Yang, Z. Yang, Z. Ye, L. Yi, K. Yip, H. Zbroszczyk, W. Zha, D. Zhang, S. Zhang, X. P. Zhang, Y. Zhang, Z. J. Zhang, Z. Zhang, J. Zhao, C. Zhong, C. Zhou, X. Zhu, Z. Zhu, M. Zurek, and M. Zyzak
Subjects: Diffraction, Forward physics, Hadron-Hadron scattering (experiments), Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Abstract: Abstract We report on the measurement of the Central Exclusive Production of charged particle pairs h + h − (h = π, K, p) with the STAR detector at RHIC in proton-proton collisions at s $$ \sqrt{s} $$ = 200 GeV. The charged particle pairs produced in the reaction pp → p′ + h + h − + p′ are reconstructed from the tracks in the central detector and identified using the specific energy loss and the time of flight method, while the forward-scattered protons are measured in the Roman Pot system. Exclusivity of the event is guaranteed by requiring the transverse momentum balance of all four final-state particles. Differential cross sections are measured as functions of observables related to the central hadronic final state and to the forward-scattered protons. They are measured in a fiducial region corresponding to the acceptance of the STAR detector and determined by the central particles’ transverse momenta and pseudorapidities as well as by the forward-scattered protons’ momenta. This fiducial region roughly corresponds to the square of the four-momentum transfers at the proton vertices in the range 0.04 GeV2 < −t 1 , −t 2 < 0.2 GeV2, invariant masses of the charged particle pairs up to a few GeV and pseudorapidities of the centrally-produced hadrons in the range |η| < 0.7. The measured cross sections are compared to phenomenological predictions based on the Double Pomeron Exchange (DPE) model. Structures observed in the mass spectra of π + π − and K + K − pairs are consistent with the DPE model, while angular distributions of pions suggest a dominant spin-0 contribution to π + π − production. For π + π − production, the fiducial cross section is extrapolated to the Lorentz-invariant region, which allows decomposition of the invariant mass spectrum into continuum and resonant contributions. The extrapolated cross section is well described by the continuum production and at least three resonances, the f 0(980), f 2(1270) and f 0(1500), with a possible small contribution from the f 0(1370). Fits to the extrapolated differential cross section as a function of t 1 and t 2 enable extraction of the exponential slope parameters in several bins of the invariant mass of π + π − pairs. These parameters are sensitive to the size of the interaction region.
Published: 2020
Full Text: View/download PDF

13. ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms

Author: Gloria M. Sheynkman, Katharine S. Tuttle, Florent Laval, Elizabeth Tseng, Jason G. Underwood, Liang Yu, Da Dong, Melissa L. Smith, Robert Sebra, Luc Willems, Tong Hao, Michael A. Calderwood, David E. Hill, and Marc Vidal
Subjects: Science
Abstract: Most human protein-coding genes are expressed as multiple isoforms. Here the authors present ORF Capture-seq that uses cloned ORFs as probes to capture and sequence full length transcript sequences. This enables highly sensitive characterization of eukaryotic transcriptomes.
Published: 2020
Full Text: View/download PDF

14. R|S Atlas: Identifying existing cohort study data resources to accelerate epidemiological research on the influence of religion and spirituality on human health

Author: M Austin Argentieri, Bobak Seddighzadeh, Laura Mandel, Lynn G Underwood, Anna Boonin Schachter, Oluwaseyi O Isehunwa, Blake Victor Kent, Philip Trevvett, Michael McDuffie, Kenneth I Pargament, Alexa T McCray, and Alexandra E Shields
Subjects: Medicine
Abstract: Objective Many studies have documented significant associations between religion and spirituality (R/S) and health, but relatively few prospective analyses exist that can support causal inferences. To date, there has been no systematic analysis of R/S survey items collected in US cohort studies. We conducted a systematic content analysis of all surveys ever fielded in 20 diverse US cohort studies funded by the National Institutes of Health (NIH) to identify all R/S-related items collected from each cohort’s baseline survey through 2014.Design An R|S Ontology was developed from our systematic content analysis to categorise all R/S survey items identified into key conceptual categories. A systematic literature review was completed for each R/S item to identify any cohort publications involving these items through 2018.Results Our content analysis identified 319 R/S survey items, reflecting 213 unique R/S constructs and 50 R|S Ontology categories. 193 of the 319 extant R/S survey items had been analysed in at least one published paper. Using these data, we created the R|S Atlas (https://atlas.mgh.harvard.edu/), a publicly available, online relational database that allows investigators to identify R/S survey items that have been collected by US cohorts, and to further refine searches by other key data available in cohorts that may be necessary for a given study (eg, race/ethnicity, availability of DNA or geocoded data).Conclusions R|S Atlas not only allows researchers to identify available sources of R/S data in cohort studies but will also assist in identifying novel research questions that have yet to be explored within the context of US cohort studies.
Published: 2021
Full Text: View/download PDF

15. Pharmacological-assisted Psychotherapy for Post Traumatic Stress Disorder: a systematic review and meta-analysis

Author: Mathew D. Hoskins, Robert Sinnerton, Anna Nakamura, Jack F. G. Underwood, Alan Slater, Catrin Lewis, Neil P. Roberts, Jonathan I. Bisson, Matthew Lee, and Liam Clarke
Subjects: ptsd, pharmacological therapy, drug-assisted therapy, mdma, d-cycloserine, ssri, snri, Psychiatry, RC435-571
Abstract: Background: Pharmacological-assisted psychotherapies, using conventional and novel drug agents, are increasingly being used both in clinical and experimental research settings, respectively. Objective: To determine the efficacy of conventional and novel pharmacological-assisted psychotherapies in reducing PTSD symptom severity. Method: A systematic review and meta-analysis of randomised-controlled trials were undertaken; 21 studies were included. Results: MDMA-assisted therapy was found to statistically superior to active and inactive placebo-assisted therapy in reduction of PTSD symptoms (standardised mean difference −1.09, 95% CI −1.60 to −0.58). There was no evidence of superiority over placebo for any other intervention. Conclusions: MDMA-assisted therapy demonstrated an impressive effect size; however, it is difficult to have confidence at this stage in this intervention due to the small numbers of participants included, and more research in this area is needed. There was no evidence to support the efficacy of any other drug-assisted interventions.
Published: 2021
Full Text: View/download PDF

16. Pharmacological therapy for post-traumatic stress disorder: a systematic review and meta-analysis of monotherapy, augmentation and head-to-head approaches

Author: Mathew D. Hoskins, Jack Bridges, Robert Sinnerton, Anna Nakamura, Jack F. G. Underwood, Alan Slater, Matthew R. D. Lee, Liam Clarke, Catrin Lewis, Neil P. Roberts, and Jonathan I. Bisson
Subjects: ptsd, pharmacological therapy, medication, systematic review, meta-analysis, Psychiatry, RC435-571
Abstract: Background: Pharmacological approaches are widely used for post-traumatic stress disorder (PTSD) despite uncertainty over efficacy. Objectives: To determine the efficacy of all pharmacological approaches, including monotherapy, augmentation and head-to-head approaches (drug versus drug, drug versus psychotherapy), in reducing PTSD symptom severity. Method: A systematic review and meta-analysis of randomised controlled trials were undertaken; 115 studies were included. Results: Selective serotonin reuptake inhibitors (SSRIs) were found to be statistically superior to placebo in reduction of PTSD symptoms but the effect size was small (standardised mean difference −0.28, 95% CI −0.39 to −0.17). For individual monotherapy agents compared to placebo in two or more studies, we found small statistically significant evidence for the antidepressants fluoxetine, paroxetine, sertraline, venlafaxine and the antipsychotic quetiapine. For pharmacological augmentation, we found small statistically significant evidence for prazosin and risperidone. Conclusions: Some medications have a small positive effect on reducing PTSD symptom severity and can be considered as potential monotherapy treatments; these include fluoxetine, paroxetine, sertraline, venlafaxine and quetiapine. Two medications, prazosin and risperidone, also have a small positive effect when used to augment pharmacological monotherapy. There was no evidence of superiority for one intervention over another in the small number of head-to-head comparison studies.
Published: 2021
Full Text: View/download PDF

17. Space planning in libraries: For students, by students.

Author: Michelle Kahn and Peter G. Underwood
Published: 2018
Full Text: View/download PDF

18. Massively multiplex single-molecule oligonucleosome footprinting

Author: Nour J Abdulhay, Colin P McNally, Laura J Hsieh, Sivakanthan Kasinathan, Aidan Keith, Laurel S Estes, Mehran Karimzadeh, Jason G Underwood, Hani Goodarzi, Geeta J Narlikar, and Vijay Ramani
Subjects: chromatin, high-throughput sequencing, nucleosomes, Medicine, Science, Biology (General), QH301-705.5
Abstract: Our understanding of the beads-on-a-string arrangement of nucleosomes has been built largely on high-resolution sequence-agnostic imaging methods and sequence-resolved bulk biochemical techniques. To bridge the divide between these approaches, we present the single-molecule adenine methylated oligonucleosome sequencing assay (SAMOSA). SAMOSA is a high-throughput single-molecule sequencing method that combines adenine methyltransferase footprinting and single-molecule real-time DNA sequencing to natively and nondestructively measure nucleosome positions on individual chromatin fibres. SAMOSA data allows unbiased classification of single-molecular 'states' of nucleosome occupancy on individual chromatin fibres. We leverage this to estimate nucleosome regularity and spacing on single chromatin fibres genome-wide, at predicted transcription factor binding motifs, and across human epigenomic domains. Our analyses suggest that chromatin is comprised of both regular and irregular single-molecular oligonucleosome patterns that differ subtly in their relative abundance across epigenomic domains. This irregularity is particularly striking in constitutive heterochromatin, which has typically been viewed as a conformationally static entity. Our proof-of-concept study provides a powerful new methodology for studying nucleosome organization at a previously intractable resolution and offers up new avenues for modeling and visualizing higher order chromatin structure.
Published: 2020
Full Text: View/download PDF

19. Factors promoting the recolonization of Oahu, Hawaii, by Bristle-thighed Curlews

Author: T. Lee Tibbitts, Daniel R. Ruthrauff, Jared G. Underwood, and Vijay P. Patil
Subjects: Ecology, QH540-549.5
Abstract: Suitable habitat for Arctic-breeding migratory shorebirds is decreasing at their traditional wintering islands and atolls in the Central Pacific Flyway (i.e., Oceania) due to habitat degradation, reclamation, and sea-level rise. To maintain the size and resiliency of their populations, migratory shorebirds will need to expand their winter ranges by either colonizing new sites or recolonizing old sites from which they were extirpated. Bristle-thighed Curlews (Numenius tahitiensis) are long-distance migratory shorebirds that breed only in Alaska and winter across a vast region of the Central Pacific, typically on remote, unpopulated islands and atolls. Historically, Bristle-thighed Curlews were considered uncommon transients on the main Hawaiian Islands, but in the mid-1990s, curlews became regular visitors to Oahu and subsequently began wintering at the James Campbell National Wildlife Refuge on Oahu Island in Hawaii. Curlew numbers at this site grew steadily from
Published: 2020
Full Text: View/download PDF

20. The Daily Spiritual Experience Scale: Empirical Relationships to Resiliency-Related Outcomes, Addictions, and Interventions

Author: Lynn G. Underwood and Kaitlyn M. Vagnini
Subjects: Daily Spiritual Experience Scale, spiritual experiences, spirituality, resilience, post-traumatic growth, addictions, Religions. Mythology. Rationalism, BL1-2790
Abstract: The Daily Spiritual Experience Scale (DSES) is a 16-item self-report measure designed to assess a set of experiences that may occur in the context of daily life for many different kinds of people. These include awe, a merciful attitude, giving other-centered love, deep inner peace, finding strength, guidance, or consolation from a transcendent source, among others. The DSES includes theistic and non-theistic language and alternatives, and has proven useful for those from many religions and for the unaffiliated. Since its original publication, it has been translated into over 40 languages, used in hundreds of published studies, and adopted for use in many practical settings. Empirically, the DSES predicts greater resilience, stress buffering, post-traumatic growth, and a sense of meaning in the face of illness, trauma, and daily stressors, as well as less substance abuse and burnout. Intervention studies using the DSES show that a variety of interventions can increase the frequency of these experiences. In this article, we will provide a brief overview of the scale and review its use in the empirical literature with respect to resilience and related outcomes. Findings suggest that the experiences measured by the DSES may serve as a resource for those experiencing distress of various kinds.
Published: 2022
Full Text: View/download PDF

21. Landscape genetics identifies streams and drainage infrastructure as dispersal corridors for an endangered wetland bird

Author: Charles B. vanRees, J. Michael Reed, Robert E. Wilson, Jared G. Underwood, and Sarah A. Sonsthagen
Subjects: connectivity, Hawaii, landscape resistance, metapopulation, Moorhen, Waterbird, Ecology, QH540-549.5
Abstract: Abstract Anthropogenic alterations to landscape structure and composition can have significant impacts on biodiversity, potentially leading to species extinctions. Population‐level impacts of landscape change are mediated by animal behaviors, in particular dispersal behavior. Little is known about the dispersal habits of rails (Rallidae) due to their cryptic behavior and tendency to occupy densely vegetated habitats. The effects of landscape structure on the movement behavior of waterbirds in general are poorly studied due to their reputation for having high dispersal abilities. We used a landscape genetic approach to test hypotheses of landscape effects on dispersal behavior of the Hawaiian gallinule (Gallinula galeata sandvicensis), an endangered subspecies endemic to the Hawaiian Islands. We created a suite of alternative resistance surfaces representing biologically plausible a priori hypotheses of how gallinules might navigate the landscape matrix and ranked these surfaces by their ability to explain observed patterns in genetic distance among 12 populations on the island of O`ahu. We modeled effective distance among wetland locations on all surfaces using both cumulative least‐cost‐path and resistance‐distance approaches and evaluated relative model performance using Mantel tests, a causal modeling approach, and the mixed‐model maximum‐likelihood population‐effects framework. Across all genetic markers, simulation methods, and model comparison metrics, surfaces that treated linear water features like streams, ditches, and canals as corridors for gallinule movement outperformed all other models. This is the first landscape genetic study on the movement behavior of any waterbird species to our knowledge. Our results indicate that lotic water features, including drainage infrastructure previously thought to be of minimal habitat value, contribute to habitat connectivity in this listed subspecies.
Published: 2018
Full Text: View/download PDF

22. Book review: Paul Levay and Jenny Craven (eds), Systematic searching: Practical ideas for improving results.

Author: Peter G. Underwood
Published: 2020
Full Text: View/download PDF

23. Massively parallel digital transcriptional profiling of single cells

Author: Grace X. Y. Zheng, Jessica M. Terry, Phillip Belgrader, Paul Ryvkin, Zachary W. Bent, Ryan Wilson, Solongo B. Ziraldo, Tobias D. Wheeler, Geoff P. McDermott, Junjie Zhu, Mark T. Gregory, Joe Shuga, Luz Montesclaros, Jason G. Underwood, Donald A. Masquelier, Stefanie Y. Nishimura, Michael Schnall-Levin, Paul W. Wyatt, Christopher M. Hindson, Rajiv Bharadwaj, Alexander Wong, Kevin D. Ness, Lan W. Beppu, H. Joachim Deeg, Christopher McFarland, Keith R. Loeb, William J. Valente, Nolan G. Ericson, Emily A. Stevens, Jerald P. Radich, Tarjei S. Mikkelsen, Benjamin J. Hindson, and Jason H. Bielas
Subjects: Science
Abstract: Single-cell gene expression analysis is challenging. This work describes a new droplet-based single cell RNA-seq platform capable of processing tens of thousands of cells across 8 independent samples in minutes, and demonstrates cellular subtypes and host–donor chimerism in transplant patients.
Published: 2017
Full Text: View/download PDF

24. Hawaiian waterbird movement across a developed landscape

Author: Eben H. Paxton, Kristina L. Paxton, Martha T. Kawasaki, P. Marcos Gorresen, Charles B. van Rees, and Jared G. Underwood
Subjects: Ecology, General Earth and Planetary Sciences, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation, General Environmental Science
Published: 2022
Full Text: View/download PDF

25. Neurological and psychiatric disorders among autistic adults: a population healthcare record study

Author: Jack F. G. Underwood, Marcos DelPozo-Banos, Aura Frizzati, Dheeraj Rai, Ann John, and Jeremy Hall
Subjects: Psychiatry and Mental health, Applied Psychology
Abstract: Background Co-occurring psychiatric disorders are common in autism, with previous studies suggesting 54–94% of autistic individuals develop a mental health condition in their lifetime. Most studies have looked at clinically-recruited cohorts, or paediatric cohorts followed into adulthood, with less known about the autistic community at a population level. We therefore studied the prevalence of co-occurring psychiatric and neurological conditions in autistic individuals in a national sample. Methods This retrospective case-control study utilised the SAIL Databank to examine anonymised whole population electronic health record data from 2001 to 2016 in Wales, UK (N = 3.6 million). We investigated the prevalence of co-occurring psychiatric and selected neurological diagnoses in autistic adults' records during the study period using International Classification of Diseases-10 and Read v2 clinical codes compared to general population controls matched for age, sex and deprivation Results All psychiatric conditions examined were more common amongst adults with autism after adjusting for age, sex and deprivation. Prevalence of attention-deficit hyperactivity disorder (7.00%), bipolar disorder (2.50%), obsessive-compulsive disorder (3.02%), psychosis (18.30%) and schizophrenia (5.20%) were markedly elevated in those with autism, with corresponding odds ratios 8.24–10.74 times the general population. Depression (25.90%) and anxiety (22.40%) were also more prevalent, with epilepsy 9.21 times more common in autism. Conclusions We found that a range of psychiatric conditions were more frequently recorded in autistic individuals. We add to understanding of under-reporting and diagnostic overshadowing in autism. With increasing awareness of autism, services should be cognisant of the psychiatric conditions that frequently co-occur in this population.
Published: 2022
Full Text: View/download PDF

26. A Class of Automatic Sequences.

Author: Robert G. Underwood
Published: 2017

27. Information literacy-related practices in the legal workplace: The applicability of Kuhlthau's model to the legal profession.

Author: Vicki Lawal, Christine Stilwell, Rosemary Kuhn, and Peter G. Underwood
Published: 2014
Full Text: View/download PDF

28. Fundamentals of Modern Algebra: A Global Perspective

Author: Robert G Underwood
Published: 2015

29. Fallacy of the Unique Genome: Sequence Diversity within Single Helicobacter pylori Strains

Author: Jenny L. Draper, Lori M. Hansen, David L. Bernick, Samar Abedrabbo, Jason G. Underwood, Nguyet Kong, Bihua C. Huang, Allison M. Weis, Bart C. Weimer, Arnoud H. M. van Vliet, Nader Pourmand, Jay V. Solnick, Kevin Karplus, and Karen M. Ottemann
Subjects: Microbiology, QR1-502
Abstract: ABSTRACT Many bacterial genomes are highly variable but nonetheless are typically published as a single assembled genome. Experiments tracking bacterial genome evolution have not looked at the variation present at a given point in time. Here, we analyzed the mouse-passaged Helicobacter pylori strain SS1 and its parent PMSS1 to assess intra- and intergenomic variability. Using high sequence coverage depth and experimental validation, we detected extensive genome plasticity within these H. pylori isolates, including movement of the transposable element IS607, large and small inversions, multiple single nucleotide polymorphisms, and variation in cagA copy number. The cagA gene was found as 1 to 4 tandem copies located off the cag island in both SS1 and PMSS1; this copy number variation correlated with protein expression. To gain insight into the changes that occurred during mouse adaptation, we also compared SS1 and PMSS1 and observed 46 differences that were distinct from the within-genome variation. The most substantial was an insertion in cagY, which encodes a protein required for a type IV secretion system function. We detected modifications in genes coding for two proteins known to affect mouse colonization, the HpaA neuraminyllactose-binding protein and the FutB α-1,3 lipopolysaccharide (LPS) fucosyltransferase, as well as genes predicted to modulate diverse properties. In sum, our work suggests that data from consensus genome assemblies from single colonies may be misleading by failing to represent the variability present. Furthermore, we show that high-depth genomic sequencing data of a population can be analyzed to gain insight into the normal variation within bacterial strains. IMPORTANCE Although it is well known that many bacterial genomes are highly variable, it is nonetheless traditional to refer to, analyze, and publish “the genome” of a bacterial strain. Variability is usually reduced (“only sequence from a single colony”), ignored (“just publish the consensus”), or placed in the “too-hard” basket (“analysis of raw read data is more robust”). Now that whole-genome sequences are regularly used to assess virulence and track outbreaks, a better understanding of the baseline genomic variation present within single strains is needed. Here, we describe the variability seen in typical working stocks and colonies of pathogen Helicobacter pylori model strains SS1 and PMSS1 as revealed by use of high-coverage mate pair next-generation sequencing (NGS) and confirmed by traditional laboratory techniques. This work demonstrates that reliance on a consensus assembly as “the genome” of a bacterial strain may be misleading.
Published: 2017
Full Text: View/download PDF

30. A Cross-Sectional Study of the Neuropsychiatric Phenotype of CACNA1C-Related Disorder

Author: Rebecca J. Levy, Katherine W. Timothy, Jack F. G. Underwood, Jeremy Hall, Jonathan A. Bernstein, and Sergiu P. Paşca
Subjects: Developmental Neuroscience, Neurology, Pediatrics, Perinatology and Child Health, Neurology (clinical)
Abstract: CACNA1C encodes the voltage gated L-type calcium channel CaV1.2. A specific gain of function pathogenic variant in CACNA1C causes Timothy syndrome type 1 (TS1) with cardiac long QT syndrome, syndactyly, and neuropsychiatric symptoms. Recent case series highlighted a broader spectrum of CACNA1C-related disorder (CRD) that includes isolated cardiac disease, isolated neurologic deficits, and TS, but it is unknown how the clinical presentation of other CRD variants relate to neural defects. We surveyed individuals with CRD to define the neuropsychiatric and developmental phenotype in an effort to guide future research into the role of calcium channels in neural development. Among 24 participants the most common neuropsychiatric symptoms and/or diagnoses were developmental delay in 92%, incoordination in 71%, hypotonia in 67%, autism spectrum disorder in 50% (autistic features in 92%), seizures in 38%, and attention deficit hyperactivity disorder in 21% of participants. There were no significant differences in symptoms between participants with and without long QT syndrome. These findings indicate the key role of CaV1.2 in brain development and the clinical importance of screening and therapeutically addressing neuropsychiatric symptoms in all individuals with CRD.
Published: 2022

31. Quantitative and qualitative analysis of exception reporting at a district general hospital

Author: Alexander B Gibson, Qamrunnisa U Yunus, and Charlotte G Underwood
Subjects: medicine.medical_specialty, Attitude of Health Personnel, business.industry, media_common.quotation_subject, Workload, General Medicine, 030204 cardiovascular system & hematology, Hospitals, District, Hospitals, General, 03 medical and health sciences, 0302 clinical medicine, Qualitative analysis, Work (electrical), Physicians, Family medicine, Medical Staff, Hospital, Humans, Medicine, 030212 general & internal medicine, General hospital, business, Function (engineering), media_common
Abstract: Background/aims Exception reporting is a function by which junior doctors report when their work has varied from expected. This study analysed the reporting at the authors' hospital. Methods The authors analysed 204 reports submitted across 12 months to investigate the nature and pattern of the exception reports. Results The majority of reports (86%) were for ‘hours and rest’, 5% for education and 9% for both. On average doctors reported an additional 1.32 hours of work per report. The most common response was time off in lieu, but 13% of reports were never responded to. Qualitative analysis showed the most common reasons for reporting were ‘work outside of rostered hours’, ‘workload’ and ‘staffing issues’. Over 10% of the reports discussed an educational issue. Conclusions The data were not specific and there was fewer than one report per junior doctor in the period analysed. It is therefore unlikely that the reports submitted represent the additional work done by junior doctors at the hospital. Guardians should investigate local attitudes to exception reporting and educate both seniors and juniors on the importance of submitting accurate exception reports.
Published: 2021
Full Text: View/download PDF

32. A high-quality bonobo genome refines the analysis of hominid evolution

Author: Melanie Sorensen, Yafei Mao, Sofie R. Salama, Claudia Rita Catacchio, Andy Wing Chun Pang, Françoise Thibaud-Nissen, Carl Baker, LaDeana W. Hillier, Ruiyang Li, Arvis Sulovari, Philip C. Dishuck, PingHsun Hsieh, Katherine M. Munson, Ludovica Mercuri, Jason D Fernandes, Jessica M. Storer, Joyce V. Lee, Benedict Paten, Mark A. Batzer, Peter A. Audano, David Porubsky, Tzu-Hsueh Huang, Jason G. Underwood, Evan E. Eichler, Jinna Hoffman, William T. Harvey, Kendra Hoekzema, Jerilyn A. Walker, Ian T. Fiddes, David Gordon, Marina Haukness, Alex Hastie, Alexandra P. Lewis, Francesca Antonacci, Mario Ventura, Shwetha C. Murali, Francesco Montinaro, Ilaria Piccolo, and Mark Diekhans
Subjects: Pan troglodytes, Sequence assembly, Genomics, Biology, Genome informatics, Genome, Article, Evolutionary genetics, Coalescent theory, Evolution, Molecular, 03 medical and health sciences, Segmental Duplications, Genomic, 0302 clinical medicine, Animals, Sequencing, Phylogeny, 030304 developmental biology, Segmental duplication, 0303 health sciences, Gorilla gorilla, Multidisciplinary, Bonobo, Pongo, Molecular Sequence Annotation, Sequence Analysis, DNA, Pan paniscus, biology.organism_classification, Genome evolution, Genes, Evolutionary biology, Eukaryotic Initiation Factor-4A, Female, Human genome, Mobile genetic elements, 030217 neurology & neurosurgery
Abstract: The divergence of chimpanzee and bonobo provides one of the few examples of recent hominid speciation1,2. Here we describe a fully annotated, high-quality bonobo genome assembly, which was constructed without guidance from reference genomes by applying a multiplatform genomics approach. We generate a bonobo genome assembly in which more than 98% of genes are completely annotated and 99% of the gaps are closed, including the resolution of about half of the segmental duplications and almost all of the full-length mobile elements. We compare the bonobo genome to those of other great apes1,3–5 and identify more than 5,569 fixed structural variants that specifically distinguish the bonobo and chimpanzee lineages. We focus on genes that have been lost, changed in structure or expanded in the last few million years of bonobo evolution. We produce a high-resolution map of incomplete lineage sorting and estimate that around 5.1% of the human genome is genetically closer to chimpanzee or bonobo and that more than 36.5% of the genome shows incomplete lineage sorting if we consider a deeper phylogeny including gorilla and orangutan. We also show that 26% of the segments of incomplete lineage sorting between human and chimpanzee or human and bonobo are non-randomly distributed and that genes within these clustered segments show significant excess of amino acid replacement compared to the rest of the genome., A high-quality bonobo genome assembly provides insights into incomplete lineage sorting in hominids and its relevance to gene evolution and the genetic relationship among living hominids.
Published: 2021
Full Text: View/download PDF

33. Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes

Author: Pratibha Jagannatha, Kevin D. Dong, Eric Kofman, Ryan J. Marina, Assael A. Madrigal, Jason G. Underwood, Isaac A. Chaim, Brian A. Yee, Gene W. Yeo, Daniel A. Lorenz, and Kristopher W. Brannan
Subjects: endocrine system, RNA-binding protein, Computational biology, Biochemistry, Ribosome, Article, 03 medical and health sciences, Gene expression, Animals, Humans, Molecular Biology, Gene, 030304 developmental biology, 0303 health sciences, Binding Sites, Sequence Analysis, RNA, Chemistry, Gene Expression Profiling, RNA-Binding Proteins, RNA, Cell Biology, Ribosomal RNA, Gene expression profiling, Nanopore Sequencing, HEK293 Cells, RNA editing, Single-Cell Analysis, Transcriptome, Biotechnology
Abstract: RNA-binding proteins (RBPs) are critical regulators of gene expression and RNA processing that are required for gene function. Yet the dynamics of RBP regulation in single cells is unknown. To address this gap in understanding, we developed STAMP (Surveying Targets by APOBEC-Mediated Profiling), which efficiently detects RBP–RNA interactions. STAMP does not rely on ultraviolet cross-linking or immunoprecipitation and, when coupled with single-cell capture, can identify RBP-specific and cell-type–specific RNA–protein interactions for multiple RBPs and cell types in single, pooled experiments. Pairing STAMP with long-read sequencing yields RBP target sites in an isoform-specific manner. Finally, Ribo-STAMP leverages small ribosomal subunits to measure transcriptome-wide ribosome association in single cells. STAMP enables the study of RBP–RNA interactomes and translational landscapes with unprecedented cellular resolution. Surveying targets by APOBEC-mediated profiling identifies binding sites of RBPs by C-to-U RNA editing. STAMP is isoform specific, can be multiplexed and enables detection of ribosome association in single cells.
Published: 2021
Full Text: View/download PDF

34. Intelligent libraries and apomediators: Distinguishing between Library 3.0 and Library 2.0.

Author: Tom Kwanya, Christine Stilwell, and Peter G. Underwood
Published: 2013
Full Text: View/download PDF

35. On the Content Bound for Real Quadratic Field Extensions.

Author: Robert G. Underwood
Published: 2013
Full Text: View/download PDF

36. Library 2.0 versus other library service models: A critical analysis.

Author: Tom Kwanya, Christine Stilwell, and Peter G. Underwood
Published: 2012
Full Text: View/download PDF

37. Quasitriangular Structure of Myhill-Nerode Bialgebras.

Author: Robert G. Underwood
Published: 2012
Full Text: View/download PDF

38. Book review: Martin De Saulles, Information 2.0: New Models of Information Production, Distribution and Consumption.

Author: Peter G. Underwood
Published: 2017
Full Text: View/download PDF

39. Algebraic Myhill-Nerode Theorems.

Author: Warren D. Nichols and Robert G. Underwood
Published: 2011
Full Text: View/download PDF

40. Owston’s civet Chrotogale owstoni : a priority for conservation breeding

Author: O. Taylor, Nguyen Van Thai, G. Underwood, J. Jimerson, and D. Willcox
Subjects: Geography, biology, Civet, Chrotogale owstoni, Zoology, biology.organism_classification, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation
Published: 2020
Full Text: View/download PDF

41. Medical and neurobehavioural phenotypes in male and female carriers of Xp22.31 duplications in the UK Biobank

Author: Jack F. G. Underwood, William Davies, Xavier Caseras, Lucija Brcic, Kimberley Kendall, George Kirov, and Samuel J A Gubb
Subjects: AcademicSubjects/SCI01140, Male, Heterozygote, Ichthyosis, X-Linked, Population, Physiology, Disease, Biology, 03 medical and health sciences, 0302 clinical medicine, Cognition, Gene duplication, Chromosome Duplication, Genetics, Steroid sulfatase, medicine, Humans, Bipolar disorder, education, Molecular Biology, Genetics (clinical), 030304 developmental biology, Aged, Biological Specimen Banks, 0303 health sciences, education.field_of_study, Chromosomes, Human, X, Comparative Genomic Hybridization, Ichthyosis, Genetic Diseases, X-Linked, General Medicine, Middle Aged, medicine.disease, United Kingdom, Neuroanatomy, Mental Health, Mood disorders, Female, Steryl-Sulfatase, General Article, medicine.symptom, Mania, 030217 neurology & neurosurgery
Abstract: Deletions spanning the STS (steroid sulfatase) gene at Xp22.31 are associated with X-linked ichthyosis, corneal opacities, testicular maldescent, cardiac arrhythmia, and higher rates of developmental and mood disorders/traits, possibly related to the smaller volume of some basal ganglia structures. The consequences of duplication of the same genomic region have not been systematically assessed in large or adult samples, although evidence from case reports/series has indicated high rates of developmental phenotypes. We compared multiple measures of physical and mental health, cognition and neuroanatomy in male (n = 414) and female (n = 938) carriers of 0.8–2.5 Mb duplications spanning STS, and non-carrier male (n = 192, 826) and female (n = 227, 235) controls from the UK Biobank (recruited aged 40–69 from the UK general population). Clinical and self-reported diagnoses indicated a higher prevalence of inguinal hernia and mania/bipolar disorder respectively in male duplication carriers, and a higher prevalence of gastro-oesophageal reflux disease and blistering/desquamating skin disorder respectively in female duplication carriers; duplication carriers also exhibited reductions in several depression-related measures, and greater happiness. Cognitive function and academic achievement did not differ between comparison groups. Neuroanatomical analysis suggested greater lateral ventricle and putamen volume in duplication carriers. In conclusion, Xp22.31 duplications appear largely benign, but could slightly increase the likelihood of specific phenotypes (although results were only nominally-significant). In contrast to deletions, duplications might protect against depressive symptoms, possibly via higher STS expression/activity (resulting in elevated endogenous free steroid levels), and through contributing towards an enlarged putamen volume. These results should enable better genetic counselling of individuals with Xp22.31 microduplications.
Published: 2020

42. ICT proficiency: perspectives of Tangaza University College librarians in Kenya

Author: Stanislaus L. Agava and Peter G. Underwood
Subjects: Engineering, business.industry, Information and Communications Technology, 05 social sciences, 0202 electrical engineering, electronic engineering, information engineering, Library science, Information technology, 020201 artificial intelligence & image processing, 02 engineering and technology, 0509 other social sciences, Library and Information Sciences, 050904 information & library sciences, business
Abstract: PurposeThis study aims to assess the information and communications technology (ICT) proficiency of library and information science (LIS) professionals working in Tangaza University College (TUC) Library, Kenya.Design/methodology/approachA qualitative research design using a single case study was adopted in the study, which gathered data through a census. Data were collected using a structured interview.FindingsThe study findings indicated that the majority of TUC librarians have very high ICT competence in basic ICT and some Web technologies; however, they lack technical ICT skills. Furthermore, though ICT courses are offered during LIS professional training, TUC librarians lack opportunities to implement some of their advanced ICT skills. Lack of funding, time, practical lessons, personal interest, training opportunities and ICT obsolescence were highlighted as challenges librarians encounter in their pursuit of acquiring ICT skills.Practical implicationsThe study recommends that regular ICT-related training programmes be conducted for librarians and be offered in the form of workshops, seminars and conferences. Furthermore, there is a need for an academic curriculum in LIS schools to have more practical ICT-related components. Library staff should be encouraged to develop a personal interest in pursuing ICT skills, and librarians should also make use of ICT training opportunities that are freely available online for personal development.Originality/valueThe study is beneficial to those concerned with developing training programmes for librarians to strengthen areas deemed to have shortcomings.
Published: 2020
Full Text: View/download PDF

43. ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms

Author: Melissa Smith, Elizabeth Tseng, Michael A. Calderwood, David E. Hill, Luc Willems, Tong Hao, Da Dong, Katharine Tuttle, Jason G. Underwood, Liang Yu, Florent Laval, Marc Vidal, Robert Sebra, and Gloria M. Sheynkman
Subjects: 0301 basic medicine, Gene isoform, RNA splicing, Science, General Physics and Astronomy, Genomics, Computational biology, Biology, Article, General Biochemistry, Genetics and Molecular Biology, DNA sequencing, Open Reading Frames, 03 medical and health sciences, 0302 clinical medicine, Humans, Protein Isoforms, RNA, Messenger, ORFS, lcsh:Science, Gene, Multidisciplinary, Sequence Analysis, RNA, RNA sequencing, General Chemistry, Reference Standards, Open reading frame, 030104 developmental biology, Proteome, lcsh:Q, 030217 neurology & neurosurgery, Transcription Factors
Abstract: Most human protein-coding genes are expressed as multiple isoforms, which greatly expands the functional repertoire of the encoded proteome. While at least one reliable open reading frame (ORF) model has been assigned for every coding gene, the majority of alternative isoforms remains uncharacterized due to (i) vast differences of overall levels between different isoforms expressed from common genes, and (ii) the difficulty of obtaining full-length transcript sequences. Here, we present ORF Capture-Seq (OCS), a flexible method that addresses both challenges for targeted full-length isoform sequencing applications using collections of cloned ORFs as probes. As a proof-of-concept, we show that an OCS pipeline focused on genes coding for transcription factors increases isoform detection by an order of magnitude when compared to unenriched samples. In short, OCS enables rapid discovery of isoforms from custom-selected genes and will accelerate mapping of the human transcriptome., Most human protein-coding genes are expressed as multiple isoforms. Here the authors present ORF Capture-seq that uses cloned ORFs as probes to capture and sequence full length transcript sequences. This enables highly sensitive characterization of eukaryotic transcriptomes.
Published: 2020

44. Medical and neurobehavioural phenotypes in carriers of X-linked ichthyosis-associated genetic deletions in the UK Biobank

Author: Kimberley Kendall, George Kirov, Xavier Caseras, William Davies, Lucija Brcic, and Jack F. G. Underwood
Subjects: 0301 basic medicine, Male, Physiology, 0302 clinical medicine, Surveys and Questionnaires, Genetics (clinical), Biological Specimen Banks, Skin, education.field_of_study, Ichthyosis, Mental Disorders, Genotype-Phenotype Correlations, Middle Aged, psychiatry, 3. Good health, dermatology, Phenotype, Female, medicine.symptom, arrhythmias, Adult, Heterozygote, Ichthyosis, X-Linked, Genetic counseling, Population, Irritability, 03 medical and health sciences, Genetics, medicine, Steroid sulfatase, copy-number, Humans, Genetic Predisposition to Disease, education, Genetic Association Studies, Aged, X-linked ichthyosis, business.industry, neurosciences, Arrhythmias, Cardiac, medicine.disease, United Kingdom, 030104 developmental biology, Mood disorders, Steryl-Sulfatase, business, Neurocognitive, 030217 neurology & neurosurgery, Gene Deletion
Abstract: BackgroundX-linked ichthyosis (XLI) is an uncommon dermatological condition resulting from a deficiency of the enzyme steroid sulfatase (STS), often caused by X-linked deletions spanning STS. Some medical comorbidities have been identified in XLI cases, but small samples of relatively young patients has limited this. STS is highly expressed in subcortical brain structures, and males with XLI and female deletion carriers appear at increased risk of developmental/mood disorders and associated traits; the neurocognitive basis of these findings has not been examined.MethodsUsing the UK Biobank resource, comprising participants aged 40–69 years recruited from the general UK population, we compared multiple medical/neurobehavioural phenotypes in males (n=86) and females (n=312) carrying genetic deletions spanning STS (0.8–2.5 Mb) (cases) to male (n=190 577) and female (n=227 862) non-carrier controls.ResultsWe identified an elevated rate of atrial fibrillation/flutter in male deletion carriers (10.5% vs 2.7% in male controls, Benjamini-Hochberg corrected p=0.009), and increased rates of mental distress (p=0.003), irritability (pConclusionAdult males with XLI disease-causing deletions are apparently at increased risk of cardiac arrhythmias and self-reported mood problems; altered basal ganglia structure may underlie altered function and XLI-associated psychiatric/behavioural phenotypes. These results provide information for genetic counselling of deletion-carrying individuals and reinforce the need for multidisciplinary medical care.
Published: 2020

45. A transcriptional roadblock protects yeast centromeres

Author: Sabrine Hedouin, Glennis A Logsdon, Jason G Underwood, and Sue Biggins
Subjects: Saccharomyces cerevisiae Proteins, Transcription, Genetic, Basic Helix-Loop-Helix Leucine Zipper Transcription Factors, Chromosome Segregation, Centromere, Genetics, Saccharomyces cerevisiae, Transcription Factors
Abstract: Centromeres are the chromosomal loci essential for faithful chromosome segregation during cell division. Although centromeres are transcribed and produce non-coding RNAs (cenRNAs) that affect centromere function, we still lack a mechanistic understanding of how centromere transcription is regulated. Here, using a targeted RNA isoform sequencing approach, we identified the transcriptional landscape at and surrounding all centromeres in budding yeast. Overall, cenRNAs are derived from transcription readthrough of pericentromeric regions but rarely span the entire centromere and are a complex mixture of molecules that are heterogeneous in abundance, orientation, and sequence. While most pericentromeres are transcribed throughout the cell cycle, centromere accessibility to the transcription machinery is restricted to S-phase. This temporal restriction is dependent on Cbf1, a centromere-binding transcription factor, that we demonstrate acts locally as a transcriptional roadblock. Cbf1 deletion leads to an accumulation of cenRNAs at all phases of the cell cycle which correlates with increased chromosome mis-segregation that is partially rescued when the roadblock activity is restored. We propose that a Cbf1-mediated transcriptional roadblock protects yeast centromeres from untimely transcription to ensure genomic stability.Centromeres are essential chromosomal regions that do not encode gene products and instead ensure the accurate partitioning of chromosomes during cell division. Despite the lack of genes, transcription has been detected at centromeres. It has not been clear where this centromeric RNA comes from and how it is regulated. In this study, the authors identified all of the centromeric RNAs at and around budding yeast centromeres during the cell cycle. Unlike RNAs that encode for proteins, centromeric RNAs are a complex mixture of transcripts that result from adjacent RNAs that continue into the centromere. The authors found that most transcription is blocked at the centromere border by a protein called Cbf1. This mechanism shields the centromere from untimely transcription to ensure genome stability.
Published: 2022

46. DRAGON-Data: A platform and protocol for integrating genomic and phenotypic data across large psychiatric cohorts

Author: Leon Hubbard, Amy J. Lynham, Sarah Knott, Jack F. G. Underwood, Richard Anney, Jonathan I. Bisson, Marianne.B.M van den Bree, Nick Craddock, Michael O’Donovan, Ian Jones, George Kirov, Kate Langley, Joanna Martin, Frances Rice, Neil Roberts, Anita Thapar, Michael J. Owen, Jeremy Hall, Antonio F. Pardiñas, and James T.R. Walters
Abstract: IntroductionCurrent psychiatric diagnoses, although heritable, have not been clearly mapped onto distinct underlying pathogenic processes. The same symptoms often occur in multiple disorders, and a substantial proportion of both genetic and environmental risk factors are shared across disorders. However, the relationship between shared symptomatology and shared genetic liability is still poorly understood. Well-characterised, cross-disorder samples are needed to investigate this matter, but currently few exist, and severe mental disorders are poorly represented in existing biobanking efforts. Purposely curated and aggregated data from individual research groups can fulfil this unmet need, resulting in rich resources for psychiatric research.Methods and analysesAs part of the Cardiff MRC Mental Health Data Pathfinder, we have curated and harmonised phenotypic and genetic information from 15 studies within the MRC Centre for Neuropsychiatric Genetics and Genomics to create a new data repository, DRAGON-DATA. To date, DRAGON-DATA includes over 45,000 individuals: adults or children with psychiatric diagnoses, affected probands with family members and individuals who carry a known neurodevelopmental copy number variant (ND-CNV). We have processed the available phenotype information to derive core variables that can be reliably analysed across groups. In addition, all datasets with genotype information have undergone rigorous quality control, imputation, CNV calling and polygenic score generation.Ethics and DisseminationDRAGON-DATA combines genetic and non-genetic information and is available as a resource for research across traditional psychiatric diagnostic categories. Its structure and governance follow standard UK ethical requirements (at the level of participating studies and the project as a whole) and conforms to principles reflected in the EU data protection scheme (GDPR). Algorithms and pipelines used for data harmonisation are currently publicly available for the scientific community, and an appropriate data sharing protocol will be developed as part of ongoing projects (DATAMIND) in partnership with HDR UK.
Published: 2022
Full Text: View/download PDF

47. Evidence for Nonlinear Gluon Effects in QCD and Their Mass Number Dependence at STAR

Author: M S, Abdallah, B E, Aboona, J, Adam, L, Adamczyk, J R, Adams, J K, Adkins, G, Agakishiev, I, Aggarwal, M M, Aggarwal, Z, Ahammed, I, Alekseev, D M, Anderson, A, Aparin, E C, Aschenauer, M U, Ashraf, F G, Atetalla, A, Attri, G S, Averichev, V, Bairathi, W, Baker, J G, Ball Cap, K, Barish, A, Behera, R, Bellwied, P, Bhagat, A, Bhasin, J, Bielcik, J, Bielcikova, I G, Bordyuzhin, J D, Brandenburg, A V, Brandin, I, Bunzarov, X Z, Cai, H, Caines, M, Calderón de la Barca Sánchez, D, Cebra, I, Chakaberia, P, Chaloupka, B K, Chan, F-H, Chang, Z, Chang, N, Chankova-Bunzarova, A, Chatterjee, S, Chattopadhyay, D, Chen, J, Chen, J H, Chen, X, Chen, Z, Chen, J, Cheng, M, Chevalier, S, Choudhury, W, Christie, X, Chu, H J, Crawford, M, Csanád, M, Daugherity, T G, Dedovich, I M, Deppner, A A, Derevschikov, A, Dhamija, L, Di Carlo, L, Didenko, P, Dixit, X, Dong, J L, Drachenberg, E, Duckworth, J C, Dunlop, N, Elsey, J, Engelage, G, Eppley, S, Esumi, O, Evdokimov, A, Ewigleben, O, Eyser, R, Fatemi, F M, Fawzi, S, Fazio, P, Federic, J, Fedorisin, C J, Feng, Y, Feng, P, Filip, E, Finch, Y, Fisyak, A, Francisco, C, Fu, L, Fulek, C A, Gagliardi, T, Galatyuk, F, Geurts, N, Ghimire, A, Gibson, K, Gopal, X, Gou, D, Grosnick, A, Gupta, W, Guryn, A I, Hamad, A, Hamed, Y, Han, S, Harabasz, M D, Harasty, J W, Harris, H, Harrison, S, He, W, He, X H, He, Y, He, S, Heppelmann, N, Herrmann, E, Hoffman, L, Holub, Y, Hu, H, Huang, H Z, Huang, S L, Huang, T, Huang, X, Huang, Y, Huang, T J, Humanic, G, Igo, D, Isenhower, W W, Jacobs, C, Jena, A, Jentsch, Y, Ji, J, Jia, K, Jiang, X, Ju, E G, Judd, S, Kabana, M L, Kabir, S, Kagamaster, D, Kalinkin, K, Kang, D, Kapukchyan, K, Kauder, H W, Ke, D, Keane, A, Kechechyan, M, Kelsey, Y V, Khyzhniak, D P, Kikoła, C, Kim, B, Kimelman, D, Kincses, I, Kisel, A, Kiselev, A G, Knospe, H S, Ko, L, Kochenda, L K, Kosarzewski, L, Kramarik, P, Kravtsov, L, Kumar, S, Kumar, R, Kunnawalkam Elayavalli, J H, Kwasizur, R, Lacey, S, Lan, J M, Landgraf, J, Lauret, A, Lebedev, R, Lednicky, J H, Lee, Y H, Leung, N, Lewis, C, Li, W, Li, X, Li, Y, Li, X, Liang, Y, Liang, R, Licenik, T, Lin, Y, Lin, M A, Lisa, F, Liu, H, Liu, P, Liu, T, Liu, X, Liu, Y, Liu, Z, Liu, T, Ljubicic, W J, Llope, R S, Longacre, E, Loyd, N S, Lukow, X F, Luo, L, Ma, R, Ma, Y G, Ma, N, Magdy Abdelwahab Abdelrahman, D, Mallick, S, Margetis, C, Markert, H S, Matis, J A, Mazer, N G, Minaev, S, Mioduszewski, B, Mohanty, M M, Mondal, I, Mooney, D A, Morozov, A, Mukherjee, M, Nagy, J D, Nam, Md, Nasim, K, Nayak, D, Neff, J M, Nelson, D B, Nemes, M, Nie, G, Nigmatkulov, T, Niida, R, Nishitani, L V, Nogach, T, Nonaka, A S, Nunes, G, Odyniec, A, Ogawa, S, Oh, V A, Okorokov, B S, Page, R, Pak, J, Pan, A, Pandav, A K, Pandey, Y, Panebratsev, P, Parfenov, B, Pawlik, D, Pawlowska, C, Perkins, L, Pinsky, R L, Pintér, J, Pluta, B R, Pokhrel, G, Ponimatkin, J, Porter, M, Posik, V, Prozorova, N K, Pruthi, M, Przybycien, J, Putschke, H, Qiu, A, Quintero, C, Racz, S K, Radhakrishnan, N, Raha, R L, Ray, R, Reed, H G, Ritter, M, Robotkova, O V, Rogachevskiy, J L, Romero, D, Roy, L, Ruan, J, Rusnak, A K, Sahoo, N R, Sahoo, H, Sako, S, Salur, J, Sandweiss, S, Sato, W B, Schmidke, N, Schmitz, B R, Schweid, F, Seck, J, Seger, M, Sergeeva, R, Seto, P, Seyboth, N, Shah, E, Shahaliev, P V, Shanmuganathan, M, Shao, T, Shao, A I, Sheikh, D Y, Shen, S S, Shi, Y, Shi, Q Y, Shou, E P, Sichtermann, R, Sikora, M, Simko, J, Singh, S, Singha, M J, Skoby, N, Smirnov, Y, Söhngen, W, Solyst, P, Sorensen, H M, Spinka, B, Srivastava, T D S, Stanislaus, M, Stefaniak, D J, Stewart, M, Strikhanov, B, Stringfellow, A A P, Suaide, M, Sumbera, B, Summa, X M, Sun, X, Sun, Y, Sun, B, Surrow, D N, Svirida, Z W, Sweger, P, Szymanski, A H, Tang, Z, Tang, A, Taranenko, T, Tarnowsky, J H, Thomas, A R, Timmins, D, Tlusty, T, Todoroki, M, Tokarev, C A, Tomkiel, S, Trentalange, R E, Tribble, P, Tribedy, S K, Tripathy, T, Truhlar, B A, Trzeciak, O D, Tsai, Z, Tu, T, Ullrich, D G, Underwood, I, Upsal, G, Van Buren, J, Vanek, A N, Vasiliev, I, Vassiliev, V, Verkest, F, Videbæk, S, Vokal, S A, Voloshin, F, Wang, G, Wang, J S, Wang, P, Wang, X, Wang, Y, Wang, Z, Wang, J C, Webb, P C, Weidenkaff, L, Wen, G D, Westfall, H, Wieman, S W, Wissink, J, Wu, Y, Wu, B, Xi, Z G, Xiao, G, Xie, W, Xie, H, Xu, N, Xu, Q H, Xu, Y, Xu, Z, Xu, G, Yan, C, Yang, Q, Yang, S, Yang, Y, Yang, Z, Ye, L, Yi, K, Yip, Y, Yu, H, Zbroszczyk, W, Zha, C, Zhang, D, Zhang, J, Zhang, S, Zhang, X P, Zhang, Y, Zhang, Z J, Zhang, Z, Zhang, J, Zhao, C, Zhou, Y, Zhou, X, Zhu, M, Zurek, and M, Zyzak
Subjects: General Physics and Astronomy, CROMODINÂMICA QUÂNTICA
Abstract: The STAR Collaboration reports measurements of back-to-back azimuthal correlations of di-π^{0}s produced at forward pseudorapidities (2.6η4.0) in p+p, p+Al, and p+Au collisions at a center-of-mass energy of 200 GeV. We observe a clear suppression of the correlated yields of back-to-back π^{0} pairs in p+Al and p+Au collisions compared to the p+p data. The observed suppression of back-to-back pairs as a function of transverse momentum suggests nonlinear gluon dynamics arising at high parton densities. The larger suppression found in p+Au relative to p+Al collisions exhibits a dependence of the saturation scale Q_{s}^{2} on the mass number A. A linear scaling of the suppression with A^{1/3} is observed with a slope of -0.09±0.01.
Published: 2022

48. Elliptic Curves in Cryptography

Author: Robert G. Underwood
Published: 2022
Full Text: View/download PDF

49. Evidence of increasing recorded diagnosis of autism spectrum disorders in Wales, UK: An e-cohort study

Author: Ann John, Aura Frizzati, Jeremy Hall, Jack F. G. Underwood, and Marcos DelPozo-Banos
Subjects: Adult, medicine.medical_specialty, Autism Spectrum Disorder, Population, Prevalence, Cohort Studies, 03 medical and health sciences, Health services, 0302 clinical medicine, Health care, mental disorders, Developmental and Educational Psychology, medicine, Humans, 0501 psychology and cognitive sciences, Autistic Disorder, Psychiatry, education, Aged, education.field_of_study, Wales, business.industry, Incidence (epidemiology), 05 social sciences, medicine.disease, 030227 psychiatry, RC0321, Autism, Female, business, Psychology, 030217 neurology & neurosurgery, Demography, 050104 developmental & child psychology, Cohort study
Abstract: Estimates place the prevalence of autism spectrum disorders (autism) at around 1% in the population. New services for adult diagnosis have been set up in Wales, UK, at a time of rising awareness of the spectrum of autism experiences; however, no studies have examined adult autism prevalence in Wales. In this study, we used an anonymised e-cohort comprised of healthcare record data to produce all-age estimates of prevalence and incidence of recorded autism for the years 2001–2016. We found the overall prevalence rate of autism in healthcare records was 0.51%. The number of new-recorded cases of autism increased from 0.188 per 1000 person-years in 2001 to 0.644 per 1000 person-years in 2016. The estimate of 0.51% prevalence in the population is lower than suggested by population survey and cohort studies study methodologies, but comparable to other administrative record study estimates. Rates of new incident diagnoses of autism saw a >150% increase in the years 2008–2016, with a trend towards more diagnoses in those aged over 35 years and an eightfold increase in diagnoses in women from 2000 to 2016. This study suggests that while the number of people being diagnosed with autism is increasing, many are still unrecognised by healthcare services. Lay abstract Autism spectrum disorders (autism) are thought to be relatively common, with analyses estimating 1% in the population could meet diagnostic criteria. New services for adult diagnosis have been set up in Wales, UK; however, no studies have examined for the proportion of adults with autism in Wales. In this study, we take anonymised healthcare record data from more than 3.6 million people to produce a national estimate of recorded autism diagnoses. We found the overall prevalence rate of autism in healthcare records was 0.51%. The number of new-recorded cases of autism increased from 0.188 per 1000 person-years in 2001 to 0.644 per 1000 person-years in 2016. The estimate of 0.51% prevalence in the population is lower than suggested by population survey and cohort studies, but comparable to other administrative records. From 2001 to 2016, the number of autism services for adults has increased, and autism is more widely known in society, while concurrently in healthcare records, there was a >150% increase autism diagnoses in the years 2008–2016. An increasing number of diagnoses were among women and those aged over 35 years. This study suggests that while the number of people being diagnosed with autism is increasing, many are still unrecognised by healthcare services.
Published: 2022

50. Introduction to Probability

Author: Robert G. Underwood
Published: 2022
Full Text: View/download PDF

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Topic

Publication Year Range

Language

Category

Publication Type

Journal

Region

Database

Publisher

1,313 results on '"G. Underwood"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources