Victoria L. Bland  Jennifer W. Bea  Scott B. Going  Hanieh Yaghootkar  Amit Arora  Ferris Ramadan  Janet L. Funk  Zhao Chen  Yann C. Klimentidis 《Obesity (Silver Spring, Md.)》2023,31(1):267-278

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Denis Rustand  Janet van Niekerk  Håvard Rue  Christophe Tournigand  Virginie Rondeau  Laurent Briollais 《Biometrical journal. Biometrische Zeitschrift》2023,65(4):2100322

Two-part joint models for a longitudinal semicontinuous biomarker and a terminal event have been recently introduced based on frequentist estimation. The biomarker distribution is decomposed into a probability of positive value and the expected value among positive values. Shared random effects can represent the association structure between the biomarker and the terminal event. The computational burden increases compared to standard joint models with a single regression model for the biomarker. In this context, the frequentist estimation implemented in the R package frailtypack can be challenging for complex models (i.e., a large number of parameters and dimension of the random effects). As an alternative, we propose a Bayesian estimation of two-part joint models based on the Integrated Nested Laplace Approximation (INLA) algorithm to alleviate the computational burden and fit more complex models. Our simulation studies confirm that INLA provides accurate approximation of posterior estimates and to reduced computation time and variability of estimates compared to frailtypack in the situations considered. We contrast the Bayesian and frequentist approaches in the analysis of two randomized cancer clinical trials (GERCOR and PRIME studies), where INLA has a reduced variability for the association between the biomarker and the risk of event. Moreover, the Bayesian approach was able to characterize subgroups of patients associated with different responses to treatment in the PRIME study. Our study suggests that the Bayesian approach using the INLA algorithm enables to fit complex joint models that might be of interest in a wide range of clinical applications.  相似文献   

    

Nicholas H. Farina  Stephanie Scalia  Caroline E. Adams  Deli Hong  Andrew J. Fritz  Terri L. Messier  Veronica Balatti  Dario Veneziano  Jane B. Lian  Carlo M. Croce  Gary S. Stein  Janet L. Stein 《Journal of cellular physiology》2020,235(6):5318-5327

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Daniel Moena  Paola Merino  Jane B. Lian  Gary S. Stein  Janet L. Stein  Martin Montecino 《Journal of cellular physiology》2020,235(6):5328-5339

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Darren W. Stevens  Matthew R. Dunn  Matthew H. Pinkerton  Janet M. Bradford-Grieve 《Journal of fish biology》2020,96(1):217-229

Feeding habits of six deep-sea demersal trawl-caught macrourids on Chatham Rise, New Zealand, were examined from stomach contents during the austral summer. Three species were predominantly benthic foragers: smallbanded rattail Coelorinchus parvifasciatus on small epifaunal crustaceans, twosaddle rattail Coelorinchus biclinozonalis on epifaunal decapods and humpback rattail Coryphaenoides dossenus on benthic fishes and epifaunal decapods. Three species were predominantly benthopelagic foragers: banded rattail Coelorinchus fasciatus on hyperiid and gammarid amphipods and calanoid copepods, blackspot rattail Lucigadus nigromaculatus on small epifaunal crustaceans and suprabenthic mysids and Mahia rattail Coelorinchus matamua on epifaunal decapods and calanoid copepods. The most important predictors of diet variability were identified using distance-based linear models and included areal predictors in C. parvifasciatus, L. nigromaculatus and C. dossenus, fish size in C. dossenus, C. biclinozonalis and C. matamua, sample year in C. biclinozonalis and C. fasciatus and depth in C. matamua. Results are compared with previously published data for four other macrourid species from the same study area. The 10 grenadier species comprise benthic, benthopelagic and mesopelagic foraging guilds. This study brings the number of grenadier species for which diet on Chatham Rise has been described in detail to 12.  相似文献   

    

Deli Hong  Andrew J. Fritz  Jonathan A. Gordon  Coralee E. Tye  Joseph R. Boyd  Kirsten M. Tracy  Seth E. Frietze  Frances E. Carr  Jeffrey A. Nickerson  Andre J. Van Wijnen  Anthony N. Imbalzano  Sayyed K. Zaidi  Jane B. Lian  Janet L. Stein  Gary S. Stein 《Journal of cellular physiology》2019,234(6):8597-8609

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Dánae Cabrera-Toledo  Jorge González-Astorga  Andrew P. Vovides  Alejandro Casas  Ofelia Vargas-Ponce  Pablo Carrillo-Reyes  Janet Nolasco-Soto  Ernesto Vega 《Population Ecology》2019,61(1):62-73

Ecological and microevolutionary perspectives were used to investigate signs of background extinction in two endemic species. We studied relict populations of the cycad Dioon caputoi, contrasting its population structure and neighborhood size with those of Dioon planifolium as a demographically healthier reference population. Population dynamics analysis was performed on two populations of D. caputoi through Integral Projection Models and genetic neighborhoods compared between species through 172 Inter Simple Sequence Repeat loci performed in one population of each of the two study species. The D. caputoi populations mostly comprised adult plants, while D. planifolium presented mainly juvenile individuals. Dioon caputoi showed equilibrium in population growth (i.e., λ ≈ 1), with low recruitment, and its genetic neighborhood revealed highly related individuals in a unique distance class (r_ij = 0.407, 33 m). A contrasting pattern was found in D. planifolium, which showed higher relatedness in the first distance class (r_ij = 0.543, 5 m), gradually decreasing to 20 m. The discrepancies between the two species reflect different strategies of persistence. Dioon caputoi conserves a relict dynamics with signs of a multigenerational, attritional loss of reproductive fitness, while D. planifolium does not. This study furthers our understanding of the background extinction process and the information will thus contribute to the management and conservation of this endangered species.  相似文献   

    

Davide Sala  Yuanpeng Janet Huang  Casey A. Cole  David A. Snyder  Gaohua Liu  Yojiro Ishida  G.V.T. Swapna  Kelly P. Brock  Chris Sander  Krzysztof Fidelis  Andriy Kryshtafovych  Masayori Inouye  Roberto Tejero  Homayoun Valafar  Antonio Rosato  Gaetano T. Montelione 《Proteins》2019,87(12):1315-1332

CASP13 has investigated the impact of sparse NMR data on the accuracy of protein structure prediction. NOESY and ¹⁵N-¹H residual dipolar coupling data, typical of that obtained for ¹⁵N,¹³C-enriched, perdeuterated proteins up to about 40 kDa, were simulated for 11 CASP13 targets ranging in size from 80 to 326 residues. For several targets, two prediction groups generated models that are more accurate than those produced using baseline methods. Real NMR data collected for a de novo designed protein were also provided to predictors, including one data set in which only backbone resonance assignments were available. Some NMR-assisted prediction groups also did very well with these data. CASP13 also assessed whether incorporation of sparse NMR data improves the accuracy of protein structure prediction relative to nonassisted regular methods. In most cases, incorporation of sparse, noisy NMR data results in models with higher accuracy. The best NMR-assisted models were also compared with the best regular predictions of any CASP13 group for the same target. For six of 13 targets, the most accurate model provided by any NMR-assisted prediction group was more accurate than the most accurate model provided by any regular prediction group; however, for the remaining seven targets, one or more regular prediction method provided a more accurate model than even the best NMR-assisted model. These results suggest a novel approach for protein structure determination, in which advanced prediction methods are first used to generate structural models, and sparse NMR data is then used to validate and/or refine these models.  相似文献   

    

Ran Wei  Janet Pik Ching Wong  Peng Lyu  Xinping Xi  Olivia Tong  Shu‐Dong Zhang  Hiu Fung Yuen  Senji Shirasawa  Hang Fai Kwok 《Journal of cellular and molecular medicine》2018,22(9):4097-4105

Osteopontin (OPN) has been shown to promote colorectal cancer (CRC) progression; however, the mechanism of OPN‐induced CRC progression is largely unknown. In this study, we found that OPN overexpression led to enhanced anchorage‐independent growth, cell migration and invasion in KRAS gene mutant cells but to a lesser extent in KRAS wild‐type cells. OPN overexpression also induced PI3K signalling, expression of Snail and Matrix metallopeptidase 9 (MMP9), and suppressed the expression of E‐cadherin in KRAS mutant cells. In human CRC specimens, a high‐level expression of OPN significantly predicted poorer survival in CRC patients and OPN expression was positively correlated with MMP9 expression, and negatively correlated with E‐cadherin expression. Furthermore, we have found that 15 genes were co‐upregulated in OPN highly expression CRC and a list of candidate drugs that may have potential to reverse the secreted phosphoprotein 1 (SPP1) gene signature by connectivity mapping. In summary, OPN is a potential prognostic indicator and therapeutic target for colon cancer.  相似文献   

    

Teoman Taskesen  Janet Neerken  Johannes Schoneberg  Devendra Pareek  Vincent Steininger  Jürgen Parisi  Levent Gütay 《Liver Transplantation》2018,8(16)

Kesterite is an attractive material for absorber layers in thin film photovoltaics. Solar cells based on kesterite have shown a substantial progress over the last decade; nevertheless, further improvements in device efficiency are pending due to the open‐circuit voltage (V_oc) deficit (i.e., difference between the maximum V _oc that can be achieved according to Shockley–Queisser limit and actual V _oc from the device). In this study, the optoelectronic properties of the author's internal record Cu₂ZnSnSe₄ solar cell, which shows a power conversion efficiency of 11.4%, are presented. The device measurements reveal a V_oc deficit of 337 mV, which is one of the lowest V _oc deficits in the literature. Moreover, an unusual behavior for kesterite is observed: (i) photon energy of the photoluminescence emission and (ii) the extrapolated V _oc for 0 K are both matching the band gap region of the absorber. These results indicate a significant improvement in the recombination characteristics and absorber quality in comparison to other kesterite devices in literature.  相似文献