Single Parameter Inference of Non-sparse Logistic Regression Models

This paper infers a single parameter in non-sparse logistic regression models. By transforming the null hypothesis into a moment condition, we construct the test statistic and obtain the asymptotic null distribution. Numerical experiments show that our method performs well

MEASUREMENT OF IN SITU EXPRESSION OF PROTEORHODOPSIN GENES AT THE NORTH PACIFIC CENTRAL GYRE STATION ALOHA

A novel approach was developed for the measurement of microbial gene expression in the oceans, and used to test the hypothesis that Proteorhodopsin (PR) gene expression is regulated at the transcriptional level. Chapter 1 describes the optimization of total nucleic-acid extraction that allows "quasi-absolute" quantification of PR mRNAs and coding genes, and the subsequent use of mRNA to gene ratio as a measure of PR gene transcription. In Chapter 2, I describe the construction of a PR cDNA clone library using an RNA sample collected from the North Pacific Central Gyre Station ALOHA, from which diverse PR gene sequences were retrieved and subjected to phylogenetic analyses based on the amino acid sequences. Chapter 3 describes the measurement of in situ PR gene transcription during three diel cycles. Light availability and physical processes such as advection were both found to affect measured PR gene transcription at 25 m at station ALOHA

Mildly Suppressed Star Formation in Central Regions of MaNGA Seyfert Galaxies

Negative feedback from accretion onto super-massive black holes (SMBHs), that is to remove gas and suppress star formation in galaxies, has been widely suggested. However, for Seyfert galaxies which harbor less active, moderately accreting SMBHs in the local universe, the feedback capability of their black hole activity is elusive. We present spatially-resolved H$\alpha$ measurements to trace ongoing star formation in Seyfert galaxies and compare their specific star formation rate with a sample of star-forming galaxies whose global galaxy properties are controlled to be the same as the Seyferts. From the comparison we find that the star formation rates within central kpc of Seyfert galaxies are mildly suppressed as compared to the matched normal star forming galaxies. This suggests that the feedback of moderate SMBH accretion could, to some extent, regulate the ongoing star formation in these intermediate to late type galaxies under secular evolution.Comment: 12 pages, 7 figures, accepted by MNRA

Sub-percentage measure of distances to redshift of 0.1 by a new cosmic ruler

Distance-redshift diagrams probe expansion history of the Universe. We show that the stellar mass-binding energy (massE) relation of galaxies proposed in our previous study offers a new distance ruler at cosmic scales. By using elliptical galaxies in the main galaxy sample of the Sloan Digital Sky Survey Data Release 7, we construct a distance-redshift diagram over the redshift range from 0.05 to 0.2 with the massE ruler. The best-fit dark energy density is 0.675+-0.079 for flat Lambda-CDM, consistent with those by other probes. At the median redshift of 0.11, the median distance is estimated to have a fractional error of 0.34%, much lower than those by supernova (SN) Ia and baryonic acoustic oscillation (BAO) and even exceeding their future capability at this redshift. The above low-z measurement is useful for probing dark energy that dominates at the late Universe. For a flat dark energy equation of state model (flat wCDM), the massE alone constrains w to an error that is only a factor of 2.2, 1.7 and 1.3 times larger than those by BAO, SN Ia, and cosmic microwave background (CMB), respectively.Comment: 8 pages, 5 figures, MNRAS in press. The cosmoSIS modules for the massE ruler is at https://astronomy.nju.edu.cn/DFS//file/2022/07/02/20220702161632756vbde28.zi

Microbial metatranscriptomics : towards understanding microbial gene expression and regulation in natural habitats

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2011.Cataloged from PDF version of thesis.Includes bibliographical references (p. 195-212).Metagenomic research has paved the way for a comprehensive understanding of the microbial gene parts list in nature, but a full understanding of microbial gene expression, regulation, and ecology remains a challenge. In this thesis, I present the methodological foundations and applications of deep sequencing-based metatranscriptomics, for profiling community transcriptomes on spatial and temporal scales. Several findings and relevant hypotheses have emerged from this work. I show that transcripts of house-keeping genes necessary for the maintenance of basic cellular machinery are abundant and readily detectable. Habitat-specific transcripts are also discernible when comparing community transcriptomes along distinct geochemical conditions. Normalization of detected transcripts to their corresponding gene abundance suggests that numerically less abundant microorganisms may nevertheless contribute actively to ecologically relevant processes. Along the same lines, it is a recurrent observation that many transcripts are of unknown function or phylogenetic origin, and have not been detected in genomic/metagenomic data sets. These novel sequences may be derived from less abundant species or variable genomic regions that are not represented in sequenced genomes. Furthermore, I applied metatranscriptomics in a microcosm experiment, where a deep water mixing event was simulated and community transcriptomes were monitored over the course of 27 hours. Relative to the control, the treatment sample showed signals of stimulated photosynthesis and carbon fixation by phytoplankton cells, enhanced chemotactic, motility, and growth responses of heterotrophic bacteria, as well as possibly altered phage-host interactions. Such experimental metatranscriptomic studies are well suited to reveal how microorganisms respond during the early stages of environmental perturbations. Finally, I show that metatranscriptomic data sets contain a wealth of highly expressed small RNAs (sRNAs), transcripts that are not translated to proteins but instead function as regulators. I propose a bioinformatics pipeline for identifying these sRNA elements, characterizing their structures and genomic contexts, and predicting possible regulatory targets. The extraordinary abundance of some of the identified sRNAs raises questions about their ecological function, which warrants further biochemical and genetic studies. Overall, this work has extended our knowledge of functional potentials and in situ gene expression of natural microbial communities.by Yanmei Shi.Ph.D

What drives the velocity dispersion of ionized gas in star-forming galaxies?

We analyze the intrinsic velocity dispersion properties of 648 star-forming galaxies observed by the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, to explore the relation of intrinsic gas velocity dispersions with star formation rates (SFRs), SFR surface densities ($\rm{\Sigma_{SFR}}$), stellar masses and stellar mass surface densities ($\rm{\Sigma_{*}}$). By combining with high z galaxies, we found that there is a good correlation between the velocity dispersion and the SFR as well as $\rm{\Sigma_{SFR}}$. But the correlation between the velocity dispersion and the stellar mass as well as $\rm{\Sigma_{*}}$ is moderate. By comparing our results with predictions of theoretical models, we found that the energy feedback from star formation processes alone and the gravitational instability alone can not fully explain simultaneously the observed velocity-dispersion/SFR and velocity-dispersion/$\rm{\Sigma_{SFR}}$ relationships.Comment: 11 pages, 11 figures. Accepted for publication in MNRA

SDSS-IV MaNGA : star-formation-driven biconical outflows in the local universe

We present a sample of 48 nearby galaxies with central, biconical outflows identified by the Mapping Nearby Galaxies at APO survey. All considered galaxies have star-formation-driven biconical (SFB) central outflows, with no signs of an active galactic nucleus. We find that the SFB outflows require high central concentration of the star formation rate. This increases the gas velocity dispersion over the equilibrium limit and helps maintain the gas outflows. The central starbursts increase the metallicity, extinction, and the [α/Fe] ratio in the gas. A significant amount of young stellar population at the centers suggests that the SFBs are associated with the formation of young bulges in galaxies. More than 70% of SFB galaxies are group members or have companions with no prominent interaction, or show asymmetry of external isophotes. In 15% of SFB cases, stars and gas rotate in the opposite directions, which points at the gas infall from satellites as the primary reason for triggering the SFB phenomena