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1.
Identifying common prognostic factors in genomic cancer studies: A novel index for censored outcomes
Background
With the growing number of public repositories for high-throughput genomic data, it is of great interest to combine the results produced by independent research groups. Such a combination allows the identification of common genomic factors across multiple cancer types and provides new insights into the disease process. In the framework of the proportional hazards model, classical procedures, which consist of ranking genes according to the estimated hazard ratio or the p-value obtained from a test statistic of no association between survival and gene expression level, are not suitable for gene selection across multiple genomic datasets with different sample sizes. We propose a novel index for identifying genes with a common effect across heterogeneous genomic studies designed to remain stable whatever the sample size and which has a straightforward interpretation in terms of the percentage of separability between patients according to their survival times and gene expression measurements. 相似文献2.
L J Petterborg M K Vaughan L Y Johnson T H Champney R J Reiter 《Comparative biochemistry and physiology. A, Comparative physiology》1984,78(1):31-34
Exposure of male Syrian hamsters (Mesocricetus auratus) for 10 weeks to short photoperiod (SP) providing 10 hr light: 14 hr darkness (10:14 LD) produced a significant reduction in the weights of the reproductive organs, plasma thyroxine (T4) levels and free T4 index (FT4I) compared to the values of animals exposed to long photoperiod (LP, 14:10 LD). C57bl male house mice (Mus musculus) kept in SP (10:14 LD) had reproductive organ weights equivalent to those of mice kept in long days (14:10 LD) and lower T3 uptake (T3U) values. Male gerbils (Meriones unguiculatus) exposed to 13 weeks of SP (10:14 LD) had lower body weights, testes and seminal vesicle weights and higher T3U values compared to LP (14:10 LD) controls. However, no effect was seen on plasma T4 and triiodothyronine (T3) values nor the FT4I and free T3 index (FT3I). White-footed male mice (Peromyscus leucopus) exposed to SP (8:16 LD) had significantly lower testes and seminal vesicle weights while plasma T4 and T3 levels were unaffected. Snell strain house mice (Mus musculus) exposed to SP (8:16 LD) had normal reproductive organ weights compared to the values of LP-exposed (16:8 LD) control animals. However, there was a significant depression in T3 and in the FT3I in the SP animals. 相似文献
3.
Plant somatic cells have the capability to switch their cell fates from differentiated to undifferentiated status under proper
culture conditions, which is designated as totipotency. As a result, plant cells can easily regenerate new tissues or organs
from a wide variety of explants. However, the mechanism by which plant cells have such remarkable regeneration ability is
still largely unknown. In this study, we used a set of meristem-specific marker genes to analyze the patterns of stem cell
differentiation in the processes of somatic embryogenesis as well as shoot or root organogenesis in vitro. Our studies furnish preliminary and important information on the patterns of the de novo stem cell differentiation during various types of in vitro organogenesis. 相似文献
4.
Claudia Raedig Carsten F. Dormann Anke Hildebrandt Sven Lautenbach 《Biodiversity and Conservation》2010,19(6):1523-1546
Monographic data rely on specimens deposited in herbaria and museums, which have been thoroughly revised by experts. However,
monographic data have been rarely used to map species richness at large scale, mainly because of the difficulties caused by
spatially heterogeneous sampling effort. In this paper we estimate patterns of species richness and narrow endemism, based
on monographic data of 4,055 Neotropical angiosperm species. We propose a geometric interpolation method to derive species
ranges at a 1° grid resolution. To this we apply an inverse distance-weighted summation scheme to derive maps of species richness
and endemism. In the latter we also adjust for heterogeneous sampling effort. Finally, we test the robustness of the interpolated
species ranges and derived species richness by applying the same method but using a leave-one-out-cross-validation (LOOCV).
The derived map shows four distinct regions of elevated species richness: (1) Central America, (2) the Northern Andes, (3)
Amazonia and (4) the Brazilian Atlantic coast (‘Mata Atlantica’). The region with the highest estimated species richness is
Amazonia, with Central America following closely behind. Centers of narrow endemism are located over the entire Neotropics,
several of them coinciding with regions of elevated species richness. Sampling effort has a minor influence on the interpolation
of overall species richness, but it substantially influences the estimation of regions of narrow endemism. Thus, in order
to improve maps of narrow endemism and resulting conservation efforts, more collection and identification activity is required. 相似文献
5.
The Fis protein: it''s not just for DNA inversion anymore 总被引:36,自引:0,他引:36
6.
Hostile intercommunity relations, including attacking and killing extra-community infants of both sexes have occurred at most
wild chimpanzee sites. We describe three recent cases of intercommunity attacks on infants committed by members of the Ngogo
chimpanzee community in Kibale National Park, Uganda. Two of the attacks resulted in confirmed infanticides while a third
attack probably resulted in the infant's death. In common with previous accounts of chimpanzee infanticides, the attacks described
here occurred during boundary patrols outside the Ngogo community's usual range, adult and adolescent males were the main
participants, one infant was cannibalized after being killed, and the victims’ mothers did not accompany the attacking party
back to the Ngogo range. However, the patrol parties during each infanticide were larger than before and included females
from the Ngogo community. Our observations indirectly support both the range expansion and imbalance of power hypotheses,
which address why and under which conditions chimpanzee intercommunity encounters lead to aggression. These cases of intercommunity
infanticide add to the growing database of the phenomenon in wild chimpanzees. 相似文献
7.
(Z)- and (E)-4-amino-2-(trifluoromethyl)-2-butenoic acid (4 and 5, respectively) were synthesized and investigated as potential mechanism-based inactivators of gamma-aminobutyric acid aminotransferase (GABA-AT) in a continuing effort to map the active site of this enzyme. The core alpha-trifluoromethyl-alpha,beta-unsaturated ester moiety was prepared via a Reformatsky/reductive elimination coupling of the key intermediates tert-butyl 2,2-dichloro-3,3,3-trifluoropropionate and N,N-bis(tert-butoxy-carbonyl)glycinal. Both 4 and 5 inhibited GABA-AT in a time-dependent manner, but displayed non-pseudo-first-order inactivation kinetics; initially, the inactivation rate increased with time. Further investigation demonstrated that the actual inactivator is generated enzymatically from 4 or 5. This inactivating species is released from the active site prior to inactivation, and as a result, 4 and 5 cannot be defined as mechanism-based inactivators. Furthermore, 4 and 5 are alternate substrates for GABA-AT, transaminated by the enzyme with Km values of 0.74 and 20.5 mM, respectively. Transamination occurs approximately 276 and 305 times per inactivation event for 4 and 5, respectively. The enzyme also catalyzes the elimination of the fluoride ion from 4 and 5. A mechanism to account for these observations is proposed. 相似文献
8.
9.
Lincoln D Stein 《Genome biology》2010,11(5):207
With DNA sequencing now getting cheaper more quickly than data storage or computation, the time may have come for genome informatics
to migrate to the cloud. 相似文献
10.
Scott P. Lawrence Nicholas A. Bright J. Paul Luzio Katherine Bowers 《Molecular biology of the cell》2010,21(20):3540-3551
The pH and lumenal environment of intracellular organelles is considered essential for protein sorting and trafficking through the cell. We provide the first evidence that a mammalian NHE sodium (potassium)/proton exchanger, NHE8, plays a key role in the control of protein trafficking and endosome morphology. At steady state, the majority of epitope-tagged NHE8 was found in the trans-Golgi network of HeLa M-cells, but a proportion was also localized to multivesicular bodies (MVBs). Depletion of NHE8 in HeLa M-cells with siRNA resulted in the perturbation of MVB protein sorting, as shown by an increase in epidermal growth factor degradation. Additionally, NHE8-depleted cells displayed striking perinuclear clustering of endosomes and lysosomes, and there was a ninefold increase in the cellular volume taken up by LAMP1/LBPA-positive, dense MVBs. Our data points to a role for the ion exchange activity of NHE8 being required to maintain endosome morphology, as overexpression of a nonfunctional point mutant protein (NHE8 E225Q) resulted in phenotypes similar to those seen after siRNA depletion of endogenous NHE8. Interestingly, we found that depletion of NHE8, despite its function as a sodium (potassium)/proton antiporter, did not affect the overall pH inside dense MVBs. 相似文献