611 research outputs found
SEARCHING FOR GENETIC DETERMINANTS FOR SODIUM LITHIUM COUNTERTRANSPORT, AN INTERMEDIATE TRAIT FOR ESSENTIAL HYPERTENSION
Essential hypertension (EH) is a major risk factor for cardiovascular disorders, the leading cause of death in the United States. Given its great public health impact, it is crucial to understand the genetic basis of EH. EH is highly heterogeneous and to use an intermediate phenotype of EH, sodium lithium countertransport (SLC), will provide substantial advantage for disease genes discovery. We proposed two approaches to explore the genes for SLC.The first study examined the relationship between SLC and a positional candidate gene, SLC34A2, which is linked to SLC in baboon. We sequenced gene SLC34A2 in baboon and human. Strong homology was established in exonic organization and sequence between human and baboon SLC34A2 genes and extensive variation in both species was identified. Association studies between SLC and SLC34A2 were carried out in 1856 RFHS phase II individuals and 634 baboons. Significant association of SLC with human SNP rs3775909 (p=0.03) in SLC34A2 and haplotype block 2 (p<0.005) were observed. Strong evidence for association of SLC with SLC34A2 was found for baboon SNP Asn136Asn (p=0.0001). Consistent findings in two different species implied that SLC34A2 may be one of the genes involved in SLC. However, linkage analyses conditional on genotypes of baboon Asn136Asn suggest that Asn136Asn is not the primarily functional site for SLC. We conclude that SLC34A2 is associated with SLC, though it may not be the major effect gene.In second study, we integrated gene expression micrarray with linkage analysis to search for genes for SLC. Two independent microarrays (U133A and U133_plus_2.0) were used to identify the differentially expressed genes in high verse low SLC groups. Five genes, IER3, ARHGAP15, CD47, CDKAL1 and PRKRA, were among top 1% of differentially expressed genes in both arrays and also mapped to linkage region for SLC in RFHS Phase II population. A follow-up association study for IER3 shows that SNP rs8512 is significantly associated with SBP (p=0.002) and DBP (p=0.0008), and SNP rs2284174 has marginal association with SLC (p=0.055) and SBP (p=0.085). In conclusion, we identified some interesting susceptible genes for SLC by combining gene expression profiling and linkage study
Probing the Diffuse Lyman-alpha Emission on Cosmological Scales: Ly{\alpha} Emission Intensity Mapping Using the Complete SDSS-IV eBOSS Survey
Based on the Sloan Digital Sky Survey Data Release 16, we have detected the
large-scale structure of Ly emission in the Universe at redshifts --3.5 by cross-correlating quasar positions and Ly emission imprinted
in the residual spectra of luminous red galaxies. We apply an analytical model
to fit the corresponding Ly surface brightness profile and multipoles
of the redshift-space quasar-Ly emission cross-correlation function.
The model suggests an average cosmic Ly luminosity density of
, a detection with a median value about 8--9 times those estimated from
deep narrowband surveys of Ly emitters at similar redshifts. Although
the low signal-to-noise ratio prevents us from a significant detection of the
Ly forest-Ly emission cross-correlation, the measurement is
consistent with the prediction of our best-fit model from quasar-Ly
emission cross-correlation within current uncertainties. We rule out the
scenario that these Ly photons mainly originate from quasars. We find
that Ly emission from star-forming galaxies, including contributions
from that concentrated around the galaxy centers and that in the diffuse
Ly emitting halos, is able to explain the bulk of the the Ly
luminosity density inferred from our measurements. Ongoing and future surveys
can further improve the measurements and advance our understanding of the
cosmic Ly emission field.Comment: Accepted for Publication in ApJS; 21 pages, 15 figures, 2 table
A multiple-time-step integration algorithm for particle-resolved simulation with physical collision time
In this paper, we present a multiple-time-step integration algorithm (MTSA)
for particle collisions in particle-resolved simulations. Since the time step
required for resolving a collision process is much smaller than that for a
fluid flow, the computational cost of the traditional soft-sphere model by
reducing the time step is quite high in particle-resolved simulations. In one
state-of-the-art methodology, collision time is stretched to several times the
flow solver time step for the fluid to adapt to the sudden change in particle
motion. However, the stretched collision time is not physical, the hydrodynamic
force may be severely underestimated during a stretched collision, and the
simulation of sediment transport may be sensitive to the stretched collision
time. The proposed MTSA adopts different time steps to resolve fluid flow,
fluid-particle interaction, and particle collision. We assessed the MTSA for
particle-wall collisions as well as particle-particle collisions, determined
the optimal iteration number in the algorithm, and obtained excellent
agreements with experimental measurements and reference simulations. The
computational cost of the MTSA can be reduced to about one order of magnitude
less than that using the traditional soft-sphere model with almost the same
accuracy. The MTSA was then implemented in a particle-resolved simulation of
sediment transport with thousands of particles. {By comparing the results
obtained using the MTSA and a version of the stretching collision time
algorithm similar to Costa et al.(2015), we found that stretching the collision
time reduced particle stiffness, weakened particle entrainment, and affected
some turbulence and particle statistics
Statistical Methods and Analysis for Human Genetic Copy Number Variation and Homozygosity Mapping
Single nucleotide polymorphism (SNP) arrays are used primarily for genetic association studies, with data being analyzed in most cases one SNP at a time. Several other applications of SNP arrays, however, involve integration of data over multiple markers for a single individual. Two such applications of SNP arrays are studies of copy number variants (CNVs) and regions of homozygosity or identity by descent. Hidden Markov models are a common approach to both of these problems, but other methods have been used as well. In this dissertation I address several methodological issues related to these two types of analysis, and also apply the methods to several datasets.
The purpose of my studies in CNVs is to better detect and analyze CNVs. A major concern for all copy number variation (CNV) calling algorithms is their reliability and repeatability. I use family data as a verification standard to evaluate CNV calling strategies and methods. I make recommendations for how CNV calls can be used in genome-wide association studies. I then apply them to analyze CNVs in studies of psychiatric disorders and birth outcomes. Results from these studies have the potential for great public health significance, because they can lead to better understanding of the genetic etiology and eventually to better markers for disease screening and diagnosis.
Homozygosity mapping is a powerful method to map genes for rare recessive disorders. However, current methods are not ideal, especially when using high density SNP array data from consanguineous families. This study develops improved methods for homozygosity mapping using dense SNP data, and thus will improve the ability of geneticists to find genetic causes of rare recessive diseases. Many of these rare disorders are life-threatening; identification of the disease genes may help with early diagnosis and treatment
The growth of non-c-axis-oriented ferroelectric BLT thin films on silicon using ZnO buffer layer
Lanthanum-doped bismuth titanate (BLT) thin films were grown on buffered Si substrates using a RF magnetron sputtering system. Electrically conducting ZnO layers were used as an effective buffer layer to facilitate the growth of the ferroelectric thin films. X-ray diffraction data shows the Aurivilius phase structure with the highest diffraction peak (1 1 7), indicating non-c-axis-oriented microstructure. Random oriented plate-like grains were observed using scanning electron microscopy. The ferroelectric nature of the film was proved by ferroelectric domain switching under an electrical field
Constraining the Halo Mass of Damped Ly Absorption Systems (DLAs) at using the Quasar-CMB Lensing Cross-correlation
We study the cross correlation of damped Ly systems (DLAs) and their
background quasars, using the most updated DLA catalog and the Planck 2018 CMB
lensing convergence field. Our measurement suggests that the DLA bias is smaller than , corresponding to
at a confidence of . These constraints are broadly consistent with Alonso
et al. (2018) and previous measurements by cross-correlation between DLAs and
the Ly forest (e.g. Font-Ribera et al. 2012; Perez-Rafols et al. 2018).
Further, our results demonstrate the potential of obtaining a more precise
measurement of the halo mass of high-redshift sources using next generation CMB
experiments with a higher angular resolution. The python-based codes and data
products of our analysis are available at
https://github.com/LittleLin1999/CMB-lensingxDLA.Comment: Accepted for Publication in ApJ; 16 pages, 9 figure
Target Selection and Annotation for the Structural Genomics of the Amidohydrolase and Enolase Superfamilies
To study the substrate specificity of enzymes, we use the amidohydrolase and enolase superfamilies as model systems; members of these superfamilies share a common TIM barrel fold and catalyze a wide range of chemical reactions. Here, we describe a collaboration between the Enzyme Specificity Consortium (ENSPEC) and the New York SGX Research Center for Structural Genomics (NYSGXRC) that aims to maximize the structural coverage of the amidohydrolase and enolase superfamilies. Using sequence- and structure-based protein comparisons, we first selected 535 target proteins from a variety of genomes for high-throughput structure determination by X-ray crystallography; 63 of these targets were not previously annotated as superfamily members. To date, 20 unique amidohydrolase and 41 unique enolase structures have been determined, increasing the fraction of sequences in the two superfamilies that can be modeled based on at least 30% sequence identity from 45% to 73%. We present case studies of proteins related to uronate isomerase (an amidohydrolase superfamily member) and mandelate racemase (an enolase superfamily member), to illustrate how this structure-focused approach can be used to generate hypotheses about sequence-structure-function relationships
An H{\alpha} Impression of Ly{\alpha} Galaxies at with Deep JWST/NIRCam Imaging
We present a study of seven spectroscopically confirmed Ly{\alpha} emitting
galaxies at redshift using the James Webb Space Telescope (JWST)
NIRCam images. These galaxies, with a wide range of Ly{\alpha} luminosities,
were recently observed in a series of NIRCam broad- and medium-bands. We
measure the continuum and H{\alpha} line properties of the galaxies using the
combination of the NIRCam photometry and archival Hubble Space Telescope
imaging data. We find that galaxies with bluer UV continuum slopes likely have
higher escape fractions of Ly{\alpha} photons. We also find that galaxies with
higher Ly{\alpha} line emission tend to produce ionizing photons more
efficiently. The most Ly{\alpha}-luminous galaxy in the sample has a high
ionizing photon production efficiency of log (Hz
erg) > 26. Our results support that Ly{\alpha} galaxies may have served
as an important contributor to the cosmic reionization. Blue and bright
Ly{\alpha} galaxies are also excellent targets for JWST follow-up spectroscopic
observations.Comment: 10 pages, 4 figures, 2 tables, submitted to ApJ
Vibration characteristics and environmental responses of different vehicle-track-ballast coupling systems in subway operation
The vibration characteristics of two ballast beds are analyzed in this study from five aspects including the amplitude-frequency characteristic curve of foundation reaction. This study also shows that the maximum ground Z vibration level caused by a normal monolithic ballast bed structure is 75 dB. The range of its vibration influence during daytime is approximately 30 m. The maximum ground Z vibration level caused by a rubber floating slab track structure is 52 dB, whereas that caused by a steel spring floating slab track structure is 57 dB. The maximum damping amount in horizontal speed of a rubber floating slab track structure is 74 %, whereas the reduction of vertical ground vibration speed and acceleration is 92 % and 93 %, respectively. The reduction in Z level is 37 %. The horizontal speed reduction in a steel spring floating slab track structure is 71 %, whereas the reduction of ground vertical vibration speed and acceleration is 83 % and 84 %, respectively. The reduction in Z level is 29 %
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