The reprogramming of human somatic cells to primed or naive induced pluripotent stem cells recapitulates the stages of early embryonic development
. The molecular mechanism that underpins these ...reprogramming processes remains largely unexplored, which impedes our understanding and limits rational improvements to reprogramming protocols. Here, to address these issues, we reconstruct molecular reprogramming trajectories of human dermal fibroblasts using single-cell transcriptomics. This revealed that reprogramming into primed and naive pluripotency follows diverging and distinct trajectories. Moreover, genome-wide analyses of accessible chromatin showed key changes in the regulatory elements of core pluripotency genes, and orchestrated global changes in chromatin accessibility over time. Integrated analysis of these datasets revealed a role for transcription factors associated with the trophectoderm lineage, and the existence of a subpopulation of cells that enter a trophectoderm-like state during reprogramming. Furthermore, this trophectoderm-like state could be captured, which enabled the derivation of induced trophoblast stem cells. Induced trophoblast stem cells are molecularly and functionally similar to trophoblast stem cells derived from human blastocysts or first-trimester placentas
. Our results provide a high-resolution roadmap for the transcription-factor-mediated reprogramming of human somatic cells, indicate a role for the trophectoderm-lineage-specific regulatory program during this process, and facilitate the direct reprogramming of somatic cells into induced trophoblast stem cells.
ABSTRACT Faraday rotation measures (RMs) and more general Faraday structures are key parameters for studying cosmic magnetism and are also sensitive probes of faint ionized thermal gas. A definition ...of which derived quantities are required for various scientific studies is needed, as well as addressing the challenges in determining Faraday structures. A wide variety of algorithms has been proposed to reconstruct these structures. In preparation for the Polarization Sky Survey of the Universe's Magnetism (POSSUM) to be conducted with the Australian Square Kilometre Array Pathfinder and the ongoing Galactic Arecibo L-band Feeds Array Continuum Transit Survey (GALFACTS), we run a Faraday structure determination data challenge to benchmark the currently available algorithms, including Faraday synthesis (previously called RM synthesis in the literature), wavelet, compressive sampling, and QU-fitting. The input models include sources with one Faraday thin component, two Faraday thin components, and one Faraday thick component. The frequency set is similar to POSSUM/GALFACTS with a 300 MHz bandwidth from 1.1 to 1.4 GHz. We define three figures of merit motivated by the underlying science: (1) an average RM weighted by polarized intensity, , (2) the separation of two Faraday components, and (3) the reduced chi-squared . Based on the current test data with a signal-to-noise ratio of about 32, we find the following. (1) When only one Faraday thin component is present, most methods perform as expected, with occasional failures where two components are incorrectly found. (2) For two Faraday thin components, QU-fitting routines perform the best, with errors close to the theoretical ones for but with significantly higher errors for . All other methods, including standard Faraday synthesis, frequently identify only one component when is below or near the width of the Faraday point-spread function. (3) No methods as currently implemented work well for Faraday thick components due to the narrow bandwidth. (4) There exist combinations of two Faraday components that produce a large range of acceptable fits and hence large uncertainties in the derived single RMs; in these cases, different RMs lead to the same behavior, so no method can recover a unique input model. Further exploration of all these issues is required before upcoming surveys will be able to provide reliable results on Faraday structures.
Although lipid profiles tend to worsen with age, it is not fully known if such age-related changes are influenced primarily by body composition and lifestyle or by other aspects of aging.
We ...investigated the extent to which the fat and fat-free components of body mass index (BMI) and lifestyle factors influence patterns of change in lipids independent of age.
Serial data were analyzed using sex-specific longitudinal models. These models use serial data from individuals to assume a general pattern of change over time, while allowing baseline age and the rate of change to vary among individuals.
Serial data were obtained from 940 examinations of 269 healthy white participants (126 men, 143 women), aged 40-60 years, in the Fels Longitudinal Study.
Measurements included age, the fat (FMI) and fat-free mass (FFMI) components of BMI, high-density lipoprotein (HDL-C), low-density lipoprotein (LDL-C), triglycerides (TG), total cholesterol (TC), fasting glucose and insulin, physical activity, alcohol use and smoking, and women's menopausal status and estrogen use.
In both sexes, increased FMI was significantly associated with increased LDL-C, TG and TC, and decreased HDL-C. Increased FFMI was significantly related to decreased HDL-C and increased TG. Independent age effects remained significant only for LDL-C and TC in men and TC in women. Increased insulin was significantly related to increased TG in women. Moderate alcohol consumption was associated with higher HDL-C in men. Physical activity lowered male LDL-C and TC levels, and increased female HDL-C levels. Menopause was associated with increases in LDL-C. Premenopausal women not using estrogen had significantly lower HDL-C, TG, and TC than postmenopausal women taking estrogen.
(1) Age is an important independent predictor for LDL-C and TC in men, and TC in women, but it is not as influential as body composition and lifestyle on HDL-C and TG in men and women, and LDL-C in women. (2) Increasing FMI is the major contributor to elevated TC, LDL-C and TG levels, and decreased HDL-C levels in men and women. (3) FFMI significantly influences HDL and TG levels in both sexes. (4) Maintaining a lower BMI via a reduced fat component may be more beneficial in lowering CVD risks than other factors.
Gene fusions created by somatic genomic rearrangements are known to play an important role in the onset and development of some cancers, such as lymphomas and sarcomas. RNA-Seq (whole transcriptome ...shotgun sequencing) is proving to be a useful tool for the discovery of novel gene fusions in cancer transcriptomes. However, algorithmic methods for the discovery of gene fusions using RNA-Seq data remain underdeveloped. We have developed deFuse, a novel computational method for fusion discovery in tumor RNA-Seq data. Unlike existing methods that use only unique best-hit alignments and consider only fusion boundaries at the ends of known exons, deFuse considers all alignments and all possible locations for fusion boundaries. As a result, deFuse is able to identify fusion sequences with demonstrably better sensitivity than previous approaches. To increase the specificity of our approach, we curated a list of 60 true positive and 61 true negative fusion sequences (as confirmed by RT-PCR), and have trained an adaboost classifier on 11 novel features of the sequence data. The resulting classifier has an estimated value of 0.91 for the area under the ROC curve. We have used deFuse to discover gene fusions in 40 ovarian tumor samples, one ovarian cancer cell line, and three sarcoma samples. We report herein the first gene fusions discovered in ovarian cancer. We conclude that gene fusions are not infrequent events in ovarian cancer and that these events have the potential to substantially alter the expression patterns of the genes involved; gene fusions should therefore be considered in efforts to comprehensively characterize the mutational profiles of ovarian cancer transcriptomes.
The presence of the nucleic acid of the spotted fever group (SPG) and typhus group (TG) rickettsiae was investigated in 200 serum specimens seropositive for SFG rickettsiae by multiplex-nested ...polymerase chain reaction with primers derived from the rickettsial outer membrane protein B gene. The DNA of SFG, TG, or both rickettsiae was amplified in the 24 serum specimens, and sequence analysis showed Rickettsia conorii, R. japonica, and R. felis in the specimens. R. conorii and R. typhi were found in 7 serum specimens, which indicated the possibility of dual infection in these patients. These findings suggest that several kinds of rickettsial diseases, including boutonneuse fever, rickettsialpox, R. felis infection, and Japanese spotted fever, as well as scrub typhus and murine typhus, are occurring in Korea.
With the severe spectrum shortage in conventional cellular bands, millimeter wave (mmW) frequencies between 30 and 300 GHz have been attracting growing attention as a possible candidate for ...next-generation micro- and picocellular wireless networks. The mmW bands offer orders of magnitude greater spectrum than current cellular allocations and enable very high-dimensional antenna arrays for further gains via beamforming and spatial multiplexing. This paper uses recent real-world measurements at 28 and 73 GHz in New York, NY, USA, to derive detailed spatial statistical models of the channels and uses these models to provide a realistic assessment of mmW micro- and picocellular networks in a dense urban deployment. Statistical models are derived for key channel parameters, including the path loss, number of spatial clusters, angular dispersion, and outage. It is found that, even in highly non-line-of-sight environments, strong signals can be detected 100-200 m from potential cell sites, potentially with multiple clusters to support spatial multiplexing. Moreover, a system simulation based on the models predicts that mmW systems can offer an order of magnitude increase in capacity over current state-of-the-art 4G cellular networks with no increase in cell density from current urban deployments.
The transfer of fresh embryos is generally preferred over the transfer of frozen embryos for in vitro fertilization (IVF), but some evidence suggests that frozen-embryo transfer may improve the ...live-birth rate and lower the rates of the ovarian hyperstimulation syndrome and pregnancy complications in women with the polycystic ovary syndrome.
In this multicenter trial, we randomly assigned 1508 infertile women with the polycystic ovary syndrome who were undergoing their first IVF cycle to undergo either fresh-embryo transfer or embryo cryopreservation followed by frozen-embryo transfer. After 3 days of embryo development, women underwent the transfer of up to two fresh or frozen embryos. The primary outcome was a live birth after the first embryo transfer.
Frozen-embryo transfer resulted in a higher frequency of live birth after the first transfer than did fresh-embryo transfer (49.3% vs. 42.0%), for a rate ratio of 1.17 (95% confidence interval CI, 1.05 to 1.31; P=0.004). Women who underwent frozen-embryo transfer also had a lower frequency of pregnancy loss (22.0% vs. 32.7%), for a rate ratio of 0.67 (95% CI, 0.54 to 0.83; P<0.001), and of the ovarian hyperstimulation syndrome (1.3% vs. 7.1%), for a rate ratio of 0.19 (95% CI, 0.10 to 0.37; P<0.001), but a higher frequency of preeclampsia (4.4% vs. 1.4%), for a rate ratio of 3.12 (95% CI, 1.26 to 7.73; P=0.009). There were no significant between-group differences in rates of other pregnancy and neonatal complications. There were five neonatal deaths in the frozen-embryo group and none in the fresh-embryo group (P=0.06).
Among infertile women with the polycystic ovary syndrome, frozen-embryo transfer was associated with a higher rate of live birth, a lower risk of the ovarian hyperstimulation syndrome, and a higher risk of preeclampsia after the first transfer than was fresh-embryo transfer. (Funded by the National Basic Research Program of China and others; ClinicalTrials.gov number, NCT01841528.).
PDF
