Soil moisture and hydrological drought in the Colorado River basin

This dissertation investigates the interannual variability of soil moisture as related to large-scale climate variability, and oceanic-atmospheric patterns. Firstly, a three-layer hydrological model VIC-3L (Variable Infiltration Capacity Model - 3 layers) was used in the Upper Colorado River basin at a daily time step and a 1/8 spatial resolution over a 50-year (1950 to 2000) period. Using wavelet analysis, deep soil moisture was compared to the Palmer Drought Severity Index (PDSI), precipitation, and streamflow to determine whether deep soil moisture is an indicator of climate extremes; Secondly, this research evaluates the spatial and temporal variability of soil moisture by using map analysis and t-test statistical method. The soil moisture in drought years was significantly different from the soil moisture in normal and wet years. An extended temporal soil moisture evaluation was performed in pre-drought, drought, and post-drought periods. The results show that soil moisture may be a potential drought indicator, which could improve drought predictability. Finally, the correlation between soil moisture and oceanic-atmospheric patterns, such as Sea Surface Temperatures (SSTs), El Nino-Southern Oscillation (ENSO), the Pacific Decadal Oscillation (PDO), and the Atlantic Multidecadal Oscillation (AMO) were evaluated. Singular Variable Decomposition (SVD) was used in evaluating the relation between soil moisture and Pacific Ocean SSTs; The current research resulted in several significant contributions: The main contributions of this research are: (a) the development of a 1/8 spatial resolution and a temporal daily time step soil moisture dataset for the Upper Colorado River basin, (b) the evaluation of the soil moisture as a drought indicator, (c) improving the comprehensive understanding of how spatial and temporal variability of soil moisture varies during drought periods, and (d) the coupling of oceanic-atmospheric/patterns with soil moisture to improve long-term drought forecasts

Soil Moisture as an Indicator of Weather Extremes

In this paper, we investigate floods and droughts in the Upper Mississippi basin over a 50-year period (1950–1999) using a hydrological model (Variable Infiltration Capacity Model – 3 Layer). Simulations have been carried out between January 1950 and December 1999 at daily time-step and 1/8° spatial resolution for the water budget and at hourly time-step and 1° spatial resolution for the energy balance. This paper will provide valuable insights to the slow response components of the hydrological cycle and its diagnostic/predictive value in the case of floods and droughts. The paper compares the use of the Palmer Drought Severity Index against the anomalies of the third layer soil moisture for characterizing droughts and floods. Wavelet and coherency analysis is performed on the soil moisture, river discharge, precipitation and PDSI time series confirm our hypothesis of a strong relationship between droughts and the third layer soil moisture

Relating surface backscatter response from TRMM precipitation radar to soil moisture: Results over a semi-arid region

The Tropical Rainfall Measuring Mission (TRMM) carries aboard the Precipitation Radar (TRMMPR) that measures the backscatter (σº) of the surface. σº is sensitive to surface soil moisture and vegetation conditions. Due to sparse vegetation in arid and semi-arid regions, TRMMPR σº primarily depends on the soil water content. In this study we relate TRMMPR σº measurements to soil water content (m(s)) in the Lower Colorado River Basin (LCRB). σº dependence on ms is studied for different vegetation greenness values determined through Normalized Difference Vegetation Index (NDVI). A new model of σº that couples incidence angle, m(s), and NDVI is used to derive parameters and retrieve soil water content. The calibration and validation of this model are performed using simulated and measured ms data. Simulated m(s) is estimated using the Variable Infiltration Capacity (VIC) model and measured m(s) is acquired from ground measuring stations in Walnut Gulch Experimental Watershed (WGEW). σº model is calibrated using VIC and WGEW m(s) data during 1998 and the calibrated model is used to derive m(s) during later years. The temporal trends of derived ms are consistent with VIC and WGEW ms data with a correlation coefficient (R) of 0.89 and 0.74, respectively. Derived ms is also consistent with the measured precipitation data with R=0.76. The gridded VIC data is used to calibrate the model at each grid point in LCRB and spatial maps of the model parameters are prepared. The model parameters are spatially coherent with the general regional topography in LCRB. TRMMPR σº derived soil moisture maps during May (dry) and August (wet) 1999 are spatially similar to VIC estimates with correlation 0.67 and 0.76, respectively. This research provides new insights into Ku-band σº dependence on soil water content in the arid regions

SegmentAnything helps microscopy images based automatic and quantitative organoid detection and analysis

Organoids are self-organized 3D cell clusters that closely mimic the architecture and function of in vivo tissues and organs. Quantification of organoid morphology helps in studying organ development, drug discovery, and toxicity assessment. Recent microscopy techniques provide a potent tool to acquire organoid morphology features, but manual image analysis remains a labor and time-intensive process. Thus, this paper proposes a comprehensive pipeline for microscopy analysis that leverages the SegmentAnything to precisely demarcate individual organoids. Additionally, we introduce a set of morphological properties, including perimeter, area, radius, non-smoothness, and non-circularity, allowing researchers to analyze the organoid structures quantitatively and automatically. To validate the effectiveness of our approach, we conducted tests on bright-field images of human induced pluripotent stem cells (iPSCs) derived neural-epithelial (NE) organoids. The results obtained from our automatic pipeline closely align with manual organoid detection and measurement, showcasing the capability of our proposed method in accelerating organoids morphology analysis.Comment: submitted to SPIE: Medical Imaging 202

Effect of metabotropic glutamate receptor 3 genotype on N-acetylaspartate levels and neurocognition in non-smoking, active alcoholics

BACKGROUND: We studied the effects of single nucleotide polymorphisms (SNPs) in the metabotropic glutamate receptor 3 (GRM3) gene on brain N-acetylaspartate (NAA) concentrations and executive function (EF) skills in non-smoking, active alcoholics, and evaluated associations between these variables. METHODS: SNPs (rs6465084, rs1468412, and rs2299225) in GRM3 were genotyped in 49 male, non-smoking, alcohol-dependent patients and 45 healthy control subjects using ligase detection reactions. NAA/creatine (Cr) ratios in left prefrontal gray matter (GM) and white matter (WM), left parietal GM, left parietal WM, and cerebellar vermis regions were measured by Proton (1) H Magnetic resonance spectroscopy (MRS). EF was measured by the Wisconsin Card Sorting Test (WCST). RESULTS: Compared to controls, alcoholics had lower NAA/Cr ratios in prefrontal GM and WM regions and performed more poorly on all EF tests (P < 0.001). Alcoholics with the A/A genotype for SNP rs6465084 had lower NAA/Cr ratios in prefrontal GM and WM regions and had poorer EF skills than alcoholics who were G-carriers for this SNP (P < 0.01). Non-alcoholics with the A/A genotype for rs6465084 also had lower NAA/Cr levels in prefrontal GM and made more random errors in the WCST than G-carriers (P < 0.01). The A/A genotype group for SNP rs6465084 was significantly different from the G carriers for the variables of NAA/Cr ratios and WCST scores in both alcoholics and controls (P < 0.05). Alcoholics who were T-carriers for rs1468412 had lower NAA/Cr ratios in prefrontal GM and showed poorer EF skills (P < 0.05). No effects of rs2299225 genotype on NAA/Cr or executive skills were observed. NAA/Cr in left prefrontal regions correlated with certain parameters of EF testing in both alcoholics and controls (P < 0.05), but the significance of this correlation among alcoholics disappeared after adjustment for the effects of genotype. CONCLUSIONS: Our results provide evidence that glutamate system dysfunction may play a role in the prefrontal functional abnormalities seen in alcohol dependence. It is possible that certain GRM3 SNP genotypes (the A/A genotype of rs6465084 and the T allele of rs1468412) may further lower NAA/Cr levels and EF skills in addition to the effect of alcohol

Antibiotics in the offshore waters of the Bohai Sea and the Yellow Sea in China: Occurrence, distribution and ecological risks

The ocean is an important sink of land-based pollutants. Previous studies showed that serious antibiotic pollution occurred in the coastal waters, but limited studies focused on their presence in offshore waters. In this study, eleven antibiotics in three different categories were investigated in offshore waters of the Bohai Sea and the Yellow Sea in China. The results indicated that three antibiotics dehydration erythromycin, sulfamethoxazole and trimethoprim occurred throughout the offshore waters at concentrations of 0.10-16.6 ng L-1 and they decreased exponentially from the rivers to the coastal and offshore waters. The other antibiotics all presented very low detection rates (<10%) and concentrations (<0.51 ng L-1). Although the concentrations were very low, risk assessment based on the calculated risk quotients (RQs) showed that sulfamethoxazole, dehydration erythromycin and clarithromycin at most of sampling sites posed medium or low ecological risks (0.01 < RQ < 1) to some sensitive aquatic organisms, including Synechococcus leopoliensis and Pseudokirchneriella subcapitata. (C) 2012 Elsevier Ltd. All rights reserved.The ocean is an important sink of land-based pollutants. Previous studies showed that serious antibiotic pollution occurred in the coastal waters, but limited studies focused on their presence in offshore waters. In this study, eleven antibiotics in three different categories were investigated in offshore waters of the Bohai Sea and the Yellow Sea in China. The results indicated that three antibiotics dehydration erythromycin, sulfamethoxazole and trimethoprim occurred throughout the offshore waters at concentrations of 0.10-16.6 ng L-1 and they decreased exponentially from the rivers to the coastal and offshore waters. The other antibiotics all presented very low detection rates (<10%) and concentrations (<0.51 ng L-1). Although the concentrations were very low, risk assessment based on the calculated risk quotients (RQs) showed that sulfamethoxazole, dehydration erythromycin and clarithromycin at most of sampling sites posed medium or low ecological risks (0.01 < RQ < 1) to some sensitive aquatic organisms, including Synechococcus leopoliensis and Pseudokirchneriella subcapitata. (C) 2012 Elsevier Ltd. All rights reserved

Rapid detection of porcine circovirus type 2 using a TaqMan-based real-time PCR

Porcine circovirus type 2 (PCV2) and the associated disease postweaning multisystemic wasting syndrome (PMWS) have caused heavy losses in global agriculture in recent decades. Rapid detection of PCV2 is very important for the effective prophylaxis and treatment of PMWS. To establish a sensitive, specific assay for the detection and quantitation of PCV2, we designed and synthesized specific primers and a probe in the open reading frame 2. The assay had a wide dynamic range with excellent linearity and reliable reproducibility, and detected between 102 and 1010 copies of the genomic DNA per reaction. The coefficient of variation for Ct values varied from 0.59% to 1.05% in the same assay and from 1.9% to 4.2% in 10 different assays. The assay did not cross-react with porcine circovirus type 1, porcine reproductive and respiratory, porcine epidemic diarrhea, transmissible gastroenteritis of pigs and rotavirus. The limits of detection and quantitation were 10 and 100 copies, respectively. Using the established real-time PCR system, 39 of the 40 samples we tested were detected as positive

DC-SCRIPT deficiency delays mouse mammary gland development and branching morphogenesis

Mammary glands are unique organs in which major adaptive changes occur in morphogenesis and development after birth. Breast cancer is the most common cancer and a major cause of mortality in females worldwide. We have previously identified the loss of expression of the transcription regulator DC-SCRIPT (Zfp366) as a prominent prognostic event in estrogen receptor positive breast cancer patients. DC-SCRIPT affects multiple transcriptional events in breast cancer cells, including estrogen and progesterone receptor-mediated transcription, and promotes CDKN2B-related cell cycle arrest. As loss of DC-SCRIPT expression appears an early event in breast cancer development, we here investigated the role of DC-SCRIPT in mammary gland development using wild-type and DC-SCRIPT knockout mice. Mice lacking DC-SCRIPT exhibited severe breeding problems and showed significant growth delay relative to littermate wild-type mice. Subsequent analysis revealed that DC-SCRIPT was expressed in mouse mammary epithelium and that DC-SCRIPT deficiency delayed mammary gland morphogenesis in vivo. Finally, analysis of 3D mammary gland organoid cultures confirmed that loss of DC-SCRIPT dramatically delayed mammary organoid branching in vitro. The study shows for the first time that DC-SCRIPT deficiency delays mammary gland morphogenesis in vivo and in vitro. These data define DC-SCRIPT as a novel modulator of mammary gland development

Joint analysis of three genome-wide association studies of esophageal squamous cell carcinoma in Chinese populations

We conducted a joint (pooled) analysis of three genome-wide association studies (GWAS) 1-3 of esophageal squamous cell carcinoma (ESCC) in ethnic Chinese (5,337 ESCC cases and 5,787 controls) with 9,654 ESCC cases and 10,058 controls for follow-up. In a logistic regression model adjusted for age, sex, study, and two eigenvectors, two new loci achieved genome-wide significance, marked by rs7447927 at 5q31.2 (per-allele odds ratio (OR) = 0.85, 95% CI 0.82-0.88; P=7.72x10−20) and rs1642764 at 17p13.1 (per-allele OR= 0.88, 95% CI 0.85-0.91; P=3.10x10−13). rs7447927 is a synonymous single nucleotide polymorphism (SNP) in TMEM173 and rs1642764 is an intronic SNP in ATP1B2, near TP53. Furthermore, a locus in the HLA class II region at 6p21.32 (rs35597309) achieved genome-wide significance in the two populations at highest risk for ESSC (OR=1.33, 95% CI 1.22-1.46; P=1.99x10−10). Our joint analysis identified new ESCC susceptibility loci overall as well as a new locus unique to the ESCC high risk Taihang Mountain region