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61.
We consider studies of cohorts of individuals after a critical event, such as an injury, with the following characteristics. First, the studies are designed to measure "input" variables, which describe the period before the critical event, and to characterize the distribution of the input variables in the cohort. Second, the studies are designed to measure "output" variables, primarily mortality after the critical event, and to characterize the predictive (conditional) distribution of mortality given the input variables in the cohort. Such studies often possess the complication that the input data are missing for those who die shortly after the critical event because the data collection takes place after the event. Standard methods of dealing with the missing inputs, such as imputation or weighting methods based on an assumption of ignorable missingness, are known to be generally invalid when the missingness of inputs is nonignorable, that is, when the distribution of the inputs is different between those who die and those who live. To address this issue, we propose a novel design that obtains and uses information on an additional key variable-a treatment or externally controlled variable, which if set at its "effective" level, could have prevented the death of those who died. We show that the new design can be used to draw valid inferences for the marginal distribution of inputs in the entire cohort, and for the conditional distribution of mortality given the inputs, also in the entire cohort, even under nonignorable missingness. The crucial framework that we use is principal stratification based on the potential outcomes, here mortality under both levels of treatment. We also show using illustrative preliminary injury data that our approach can reveal results that are more reasonable than the results of standard methods, in relatively dramatic ways. Thus, our approach suggests that the routine collection of data on variables that could be used as possible treatments in such studies of inputs and mortality should become common. 相似文献
62.
Constantine G. Boojamra Jay P. Parrish David Sperandio Ying Gao Oleg V. Petrakovsky Sharon K. Lee David Y. Markevitch Jennifer E. Vela Genevieve Laflamme James M. Chen Adrian S. Ray Abraham C. Barron Mark L. Sparacino Manoj C. Desai Choung U. Kim Tomas Cihlar Richard L. Mackman 《Bioorganic & medicinal chemistry》2009,17(4):1739-1746
63.
Hong Wang Liping Hu Knut Dalen Heidi Dorward Amy Marcinkiewicz Deanna Russell Dawei Gong Constantine Londos Tomohiro Yamaguchi Cecilia Holm Mark A. Rizzo Dawn Brasaemle Carole Sztalryd 《The Journal of biological chemistry》2009,284(46):32116-32125
Lipolysis is an important metabolic pathway controlling energy homeostasis through degradation of triglycerides stored in lipid droplets and release of fatty acids. Lipid droplets of mammalian cells are coated with one or more members of the PAT protein family, which serve important functions in regulating lipolysis. In this study, we investigate the mechanisms by which PAT family members, perilipin A, adipose differentiation-related protein (ADFP), and LSDP5, control lipolysis catalyzed by hormone-sensitive lipase (HSL), a major lipase in adipocytes and several non-adipose cells. We applied fluorescence microscopic tools to analyze proteins in situ in cultured Chinese hamster ovary cells using fluorescence recovery after photobleaching and anisotropy Forster resonance energy transfer. Fluorescence recovery after photobleaching data show that ADFP and LSDP5 exchange between lipid droplet and cytoplasmic pools, whereas perilipin A does not. Differences in protein mobility do not correlate with PAT protein-mediated control of lipolysis catalyzed by HSL or endogenous lipases. Forster resonance energy transfer and co-immunoprecipitation experiments reveal that each of the three PAT proteins bind HSL through interaction of the lipase with amino acids within the highly conserved amino-terminal PAT-1 domain. ADFP and LSDP5 bind HSL under basal conditions, whereas phosphorylation of serine residues within three amino-terminal protein kinase A consensus sequences of perilipin A is required for HSL binding and maximal lipolysis. Finally, protein kinase A-mediated phosphorylation of HSL increases lipolysis in cells expressing ADFP or LSDP5; in contrast, phosphorylation of perilipin A exerts the major control over HSL-mediated lipolysis when perilipin is the main lipid droplet protein. 相似文献
64.
Pingzhao Hu Sarath Chandra Janga Mohan Babu J. Javier Díaz-Mejía Gareth Butland Wenhong Yang Oxana Pogoutse Xinghua Guo Sadhna Phanse Peter Wong Shamanta Chandran Constantine Christopoulos Anaies Nazarians-Armavil Negin Karimi Nasseri Gabriel Musso Mehrab Ali Nazila Nazemof Veronika Eroukova Ashkan Golshani Alberto Paccanaro Jack F Greenblatt Gabriel Moreno-Hagelsieb Andrew Emili 《PLoS biology》2009,7(4)
One-third of the 4,225 protein-coding genes of Escherichia coli K-12 remain functionally unannotated (orphans). Many map to distant clades such as Archaea, suggesting involvement in basic prokaryotic traits, whereas others appear restricted to E. coli, including pathogenic strains. To elucidate the orphans' biological roles, we performed an extensive proteomic survey using affinity-tagged E. coli strains and generated comprehensive genomic context inferences to derive a high-confidence compendium for virtually the entire proteome consisting of 5,993 putative physical interactions and 74,776 putative functional associations, most of which are novel. Clustering of the respective probabilistic networks revealed putative orphan membership in discrete multiprotein complexes and functional modules together with annotated gene products, whereas a machine-learning strategy based on network integration implicated the orphans in specific biological processes. We provide additional experimental evidence supporting orphan participation in protein synthesis, amino acid metabolism, biofilm formation, motility, and assembly of the bacterial cell envelope. This resource provides a “systems-wide” functional blueprint of a model microbe, with insights into the biological and evolutionary significance of previously uncharacterized proteins. 相似文献
65.
Sztalryd C Bell M Lu X Mertz P Hickenbottom S Chang BH Chan L Kimmel AR Londos C 《The Journal of biological chemistry》2006,281(45):34341-34348
Ectopic accumulation of lipid droplets in non-adipose tissues correlates with the degree of insulin resistance in these tissues. Emerging evidence indicates that lipid droplets are specialized organelles that participate in lipid metabolism and intracellular trafficking. These properties are thought to derive from the lipid droplet-associated PAT protein family (perilipin, ADFP, and Tip47). The functions of the ubiquitously distributed adipose differentiation-related protein (ADFP) and Tip47 remain unknown. To evaluate the roles of ADFP and Tip47 in lipid biogenesis and metabolism, ADFP null and wild type (wt) clonal cell lines were established from ADFP null and wt mice, respectively. In ADFP null cells, Tip47 was identified as the sole lipid droplet-associated protein from the PAT family by mass spectroscopy, which was further confirmed by immunoblotting and immunocytochemistry. Following incubation with oleic acid, ADFP null cells were able to form lipid droplets to the same extent as wt cells. No statistical differences between the two cell types were observed in NEFA uptake or lipolysis. Small interference RNAs (siRNAs) against Tip47 were found to down-regulate protein levels for Tip47 by 85%. ADFP null cells treated with Tip47 siRNA retained the ability to form lipid droplets but to a lesser extent and shunted the utilization of exogenously added NEFA from triglycerides to phospholipids. These data support the hypothesis that Tip47 plays an important role in lipid metabolism. Tip47 and ADFP in peripheral tissues may play a critical role in regulating the formation and turnover, and hence metabolic consequences, of ectopic fat. 相似文献
66.
Anqi Qiu Kenichi Oishi Michael I. Miller Constantine G. Lyketsos Susumu Mori Marilyn Albert 《PloS one》2010,5(3)
Background
White matter disruption has been suggested as one of anatomical features associated with Alzheimer''s disease (AD). Diffusion tensor imaging (DTI), which has been widely used in AD studies, obtains new insights into the white matter structure.Methods
We introduced surface-based geometric models of the deep white matter tracts extracted from DTI, allowing the characterization of their shape variations relative to an atlas as well as fractional anisotropy (FA) variations on the atlas surface through large deformation diffeomorphic metric mapping (LDDMM). We applied it to assess local shapes and FA variations of twenty-three deep white matter tracts in 13 patients with AD and 19 healthy control subjects.Results
Our results showed regionally-specific shape abnormalities and FA reduction in the cingulum tract and the sagittal stratum tract in AD, suggesting that disruption in the white matter tracts near the temporal lobe may represent the secondary consequence of the medial temporal lobe pathology in AD. Moreover, the regionally-specific patterns of FA and shape of the white matter tracts were shown to be of sufficient sensitivity to robustly differentiate patients with AD from healthy comparison controls when compared with the mean FA and volumes within the regions of the white matter tracts. Finally, greater FA or deformation abnormalities of the white matter tracts were associated with lower MMSE scores.Conclusion
The regionally-specific shape and FA patterns could be potential imaging markers for differentiating AD from normal aging. 相似文献67.
68.
Rebecca M. Hamner Rochelle Constantine Marc Oremus Martin Stanley Phillip Brown C. Scott Baker 《Marine Mammal Science》2014,30(1):139-153
For endangered populations with low genetic diversity, low levels of immigration could lead to genetic rescue, reducing the risk of inbreeding depression and enhancing chances of long‐term species survival. Our genetic monitoring of Maui's dolphins revealed the first contemporary dispersal of their sister subspecies, Hector's dolphin, from New Zealand's South Island into the Maui's dolphin distribution along ~300 km of the North Island's northwest coast. From 2010 to 2012, 44 individuals were sampled within the Maui's dolphin distribution, four of which were genetically identified as Hector's dolphins (two living females, one dead female, one dead male). We also report two Hector's dolphins (one dead female neonate, one living male) sampled along the North Island's southwest coast, outside the presumed range of either subspecies. Together, these records demonstrate long‐distance dispersal by Hector's dolphins (≥400 km) and the possibility of an unsampled Hector's dolphin population along the southwest coast of the North Island. Although two living Hector's dolphins were found in association with Maui's dolphins, there is currently no evidence of interbreeding between the subspecies. These results highlight the value of genetic monitoring for subspecies lacking distinctive physical appearances as such discoveries are not detected by other means, but have important conservation implications. 相似文献
69.
Stesha C. Joseph Brittany A. Blackman Megan L. Kelly Mariana Phillips Michael W. Beaury Ivonne Martinez Christopher J. Parronchi Constantine Bitsaktsis Allan D. Blake David Sabatino 《Journal of peptide science》2014,20(9):736-745
The solid‐phase synthesis, structural characterization, and biological evaluation of a small library of cancer‐targeting peptides have been determined in HepG2 hepatoblastoma cells. These peptides are based on the highly specific Pep42 motif, which has been shown to target the glucose‐regulated protein 78 receptors overexpressed and exclusively localized on the cell surface of tumors. In this study, Pep42 was designed to contain varying lengths (3–12) of poly(arginine) sequences to assess their influence on peptide structure and biology. Peptides were effectively synthesized by 9‐fluorenylmethoxycarbonyl‐based solid‐phase peptide synthesis, in which the use of a poly(ethylene glycol) resin provided good yields (14–46%) and crude purities >95% as analyzed by liquid chromatography–mass spectrometry. Peptide structure and biophysical properties were investigated using circular dichroism spectroscopy. Interestingly, peptides displayed secondary structures that were contingent on solvent and length of the poly(arginine) sequences. Peptides exhibited helical and turn conformations, while retaining significant thermal stability. Structure–activity relationship studies conducted by flow cytometry and confocal microscopy revealed that the poly(arginine) derived Pep42 sequences maintained glucose‐regulated protein 78 binding on HepG2 cells while exhibiting cell translocation activity that was contingent on the length of the poly(arginine) strand. In single dose (0.15 mM) and dose‐response (0–1.5 mM) cell viability assays, peptides were found to be nontoxic in human HepG2 liver cancer cells, illustrating their potential as safe cancer‐targeting delivery agents. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd. 相似文献
70.
Jose M. Martínez-Sánchez Montse Ballbè Marcela Fu Juan C. Martín-Sánchez Mark Gottlieb Esteve Saltó Constantine I. Vardavas Richard Daynard Gregory N. Connolly Esteve Fernández 《PloS one》2014,9(12)