Forecast dataset associated with “From Random Forests to Flood Forecasts: A Research to Operations Success Story”

Gridded forecasts from the Colorado State University-Machine Learning Probabilities (CSU-MLP) system for excessive rainfall prediction over the continental United States. The dataset includes probabilistic forecasts for days 1, 2, and 3 from the 2017, 2019, and 2020 versions of the CSU-MLP forecast system. For the day 2 and 3 forecasts, daily forecasts are included from 19 June 2018 through 15 October 2020; for day-1 forecasts a period from 15 March 2019 through 15 October 2020 is used.Because excessive rainfall is poorly defined and difficult to forecast, there is a need for tools for Weather Prediction Center (WPC) forecasters to use when generating Excessive Rainfall Outlooks (EROs), which are issued for the contiguous United States at lead times of 1--3 days. To address this need, a probabilistic forecast system for excessive rainfall, known as the Colorado State University-Machine Learning Probabilities (CSU-MLP) system, was developed based on ensemble reforecasts, precipitation observations, and machine learning algorithms, specifically random forests. The CSU-MLP forecasts were designed to emulate the EROs, with the goal being a tool that forecasters can use as a ``first guess'' in the ERO forecast process. Resulting from close collaboration between CSU and WPC and evaluation at the Flash Flood and Intense Rainfall experiment, iterative improvements were made to the forecast system and it was transitioned into operational use at WPC. Quantitative evaluation shows that the CSU-MLP forecasts are skillful and reliable, and they are now being used as a part of the WPC forecast process. This project represents an example of a successful research-to-operations transition, and highlights the potential for machine learning and other post-processing techniques to improve operational predictions.This research and operational transition was supported by NOAA Joint Technology Transfer Initiative grants NA16OAR4590238 and NA18OAR4590378

Experimental Realization of A Two Bit Phase Damping Quantum Code

Using nuclear magnetic resonance techniques, we experimentally investigated the effects of applying a two bit phase error detection code to preserve quantum information in nuclear spin systems. Input states were stored with and without coding, and the resulting output states were compared with the originals and with each other. The theoretically expected result, net reduction of distortion and conditional error probabilities to second order, was indeed observed, despite imperfect coding operations which increased the error probabilities by approximately 5%. Systematic study of the deviations from the ideal behavior provided quantitative measures of different sources of error, and good agreement was found with a numerical model. Theoretical questions in quantum error correction in bulk nuclear spin systems including fidelity measures, signal strength and syndrome measurements are discussed.Comment: 21 pages, 17 figures, mypsfig2, revtex. Minor changes made to appear in PR

Analysis of Hurricanes Using Long-Range Lightning Detection Networks

The new GOES-R satellite will be equipped with the Geostationary Lightning Mapper (GLM) that will provide unprecedented total lightning data with the potential to improve hurricane intensity forecasts. Past studies have provided conflicting interpretations of the role that lightning plays in forecasting tropical cyclone (TC) intensity changes. With the goal of improving the usefulness of total lightning, detailed case studies were conducted of five TCs that underwent rapid intensification (RI) within the domains of two unique ground-based long-range lightning detection networks, the World Wide Lightning Location Network (WWLLN) and Earth Networks Total Lightning Network (ENTLN). This analysis will provide greater details of the distribution of lightning within predefined storm features to highlight specific phenomena that large statistical studies cannot resolve.Both WWLLN and ENTLN datasets showed similar spatial and temporal patterns in lightning that validates the independent use of either network for analysis. For the cases examined, a maxima in eyewall lightning was located downshear and in the front-right quadrants relative to storm motion. Results show that RI follows a burst of lightning in the eyewall when coinciding with a period of little environmental vertical shear. Eyewall lightning would cycle with greater frequency during intensification compared to weakening. Bursts of lightning were observed in the eyewall just prior to eye formation in both the infrared and microwave imagery. Eyewall lightning bursts in low shear environments could be used to indicate intensification and improve forecasts.University Libraries Undergraduate Research Awardundergraduat

Intercellular calcium signaling in a gap junction-coupled cell network establishes asymmetric neuronal fates in C. elegans

The C. elegans left and right AWC olfactory neurons specify asymmetric subtypes, one default AWC(OFF) and one induced AWC(ON), through a stochastic, coordinated cell signaling event. Intercellular communication between AWCs and non-AWC neurons via a NSY-5 gap junction network coordinates AWC asymmetry. However, the nature of intercellular signaling across the network and how individual non-AWC cells in the network influence AWC asymmetry is not known. Here, we demonstrate that intercellular calcium signaling through the NSY-5 gap junction neural network coordinates a precise 1AWC(ON)/1AWC(OFF) decision. We show that NSY-5 gap junctions in C. elegans cells mediate small molecule passage. We expressed vertebrate calcium-buffer proteins in groups of cells in the network to reduce intracellular calcium levels, thereby disrupting intercellular communication. We find that calcium in non-AWC cells of the network promotes the AWC(ON) fate, in contrast to the autonomous role of calcium in AWCs to promote the AWC(OFF) fate. In addition, calcium in specific non-AWCs promotes AWC(ON) side biases through NSY-5 gap junctions. Our results suggest a novel model in which calcium has dual roles within the NSY-5 network: autonomously promoting AWC(OFF) and non-autonomously promoting AWC(ON)

Transcription factors Sp1 and Sp4 regulate TRPV1 gene expression in rat sensory neurons

<p>Abstract</p> <p>Background</p> <p>The capsaicin receptor, transient receptor potential vanilloid type -1 (TRPV1) directs complex roles in signal transduction including the detection of noxious stimuli arising from cellular injury and inflammation. Under pathophysiologic conditions, TRPV1 mRNA and receptor protein expression are elevated in dorsal root ganglion (DRG) neurons for weeks to months and is associated with hyperalgesia. Building on our previous isolation of a promoter system for the rat TRPV1 gene, we investigated the proximal TRPV1 P2-promoter by first identifying candidate Sp1-like transcription factors bound <it>in vivo </it>to the P2-promoter using chromatin immunoprecipitation (ChIP) assay. We then performed deletion analysis of GC-box binding sites, and quantified promoter activity under conditions of Sp1 / Sp4 over-expression versus inhibition/knockdown. mRNA encoding Sp1, Sp4 and TRPV1 were quantified by qRT-PCR under conditions of Sp1/Sp4 over-expression or siRNA mediated knockdown in cultured DRG neurons.</p> <p>Results</p> <p>Using ChIP analysis of DRG tissue, we demonstrated that Sp1 and Sp4 are bound to the candidate GC-box site region within the endogenous TRPV1 P2-promoter. Deletion of GC-box "a" or "a + b" within the P2- promoter resulted in a complete loss of transcriptional activity indicating that GC-box "a" was the critical site for promoter activation. Co-transfection of Sp1 increased P2-promoter activity in cultured DRG neurons whereas mithramycin-a, an inhibitor of Sp1-like function, dose dependently blocked NGF and Sp1-dependent promoter activity in PC12 cells. Co-transfection of siRNA directed against Sp1 or Sp4 decreased promoter activity in DRG neurons and NGF treated PC12 cells. Finally, electroporation of Sp1 or Sp4 cDNA into cultures of DRG neurons directed an increase in Sp1/Sp4 mRNA and importantly an increase in TRPV1 mRNA. Conversely, combined si-RNA directed knockdown of Sp1/Sp4 resulted in a decrease in TRPV1 mRNA.</p> <p>Conclusion</p> <p>Based on these studies, we now propose a model of TRPV1 expression that is dependent on Sp1-like transcription factors with Sp4 playing a predominant role in activating TRPV1 RNA transcription in DRG neurons. Given that increases of TRPV1 expression have been implicated in a wide range of pathophysiologic states including persistent painful conditions, blockade of Sp1-like transcription factors represents a novel direction in therapeutic strategies.</p

Late presentation of a mucinous ovarian adenocarcinoma which was initially diagnosed as a primary pancreatic carcinoma: a case report and review of the literature

<p>Abstract</p> <p>Introduction</p> <p>Adenocarcinoma of the ovary is an aggressive neoplasm which often metastasizes to the lung or liver. Metastases rarely occur to the pancreas, but a tissue diagnosis is required to confirm this event. Although most tumors of the pancreas are primary pancreatic neoplasms, metastatic lesions have been reported most commonly as arising from renal cell carcinoma.</p> <p>Case presentation</p> <p>We report the case of a 51-year-old Caucasian woman with ovarian mucinous adenocarcinoma with metastasis to the head of the pancreas that was originally misdiagnosed as a pancreatic primary tumor.</p> <p>Conclusion</p> <p>Mucinous ovarian adenocarcinomas rarely metastasize to the pancreas. New pancreatic lesions should be investigated through tissue biopsy and tumor markers, while keeping an open-minded differential diagnosis to avoid a misdiagnosis or a delay in treatment.</p

Colorectal cancer linkage on chromosomes 4q21, 8q13, 12q24, and 15q22

A substantial proportion of familial colorectal cancer (CRC) is not a consequence of known susceptibility loci, such as mismatch repair (MMR) genes, supporting the existence of additional loci. To identify novel CRC loci, we conducted a genome-wide linkage scan in 356 white families with no evidence of defective MMR (i.e., no loss of tumor expression of MMR proteins, no microsatellite instability (MSI)-high tumors, or no evidence of linkage to MMR genes). Families were ascertained via the Colon Cancer Family Registry multi-site NCI-supported consortium (Colon CFR), the City of Hope Comprehensive Cancer Center, and Memorial University of Newfoundland. A total of 1,612 individuals (average 5.0 per family including 2.2 affected) were genotyped using genome-wide single nucleotide polymorphism linkage arrays; parametric and non-parametric linkage analysis used MERLIN in a priori-defined family groups. Five lod scores greater than 3.0 were observed assuming heterogeneity. The greatest were among families with mean age of diagnosis less than 50 years at 4q21.1 (dominant HLOD = 4.51, α = 0.84, 145.40 cM, rs10518142) and among all families at 12q24.32 (dominant HLOD = 3.60, α = 0.48, 285.15 cM, rs952093). Among families with four or more affected individuals and among clinic-based families, a common peak was observed at 15q22.31 (101.40 cM, rs1477798; dominant HLOD = 3.07, α = 0.29; dominant HLOD = 3.03, α = 0.32, respectively). Analysis of families with only two affected individuals yielded a peak at 8q13.2 (recessive HLOD = 3.02, α = 0.51, 132.52 cM, rs1319036). These previously unreported linkage peaks demonstrate the continued utility of family-based data in complex traits and suggest that new CRC risk alleles remain to be elucidated. © 2012 Cicek et al

Meta-analysis of 8q24 for seven cancers reveals a locus between NOV and ENPP2 associated with cancer development.

BACKGROUND: Human chromosomal region 8q24 contains several genes which could be functionally related to cancer, including the proto-oncogene c-MYC. However, the abundance of associations around 128 Mb on chromosome 8 could mask the appearance of a weaker, but important, association elsewhere on 8q24. METHODS: In this study, we completed a meta-analysis of results from nine genome-wide association studies for seven types of solid-tumor cancers (breast, prostate, pancreatic, lung, ovarian, colon, and glioma) to identify additional associations that were not apparent in any individual study. RESULTS: Fifteen SNPs in the 8q24 region had meta-analysis p-values < 1E-04. In particular, the region consisting of 120,576,000-120,627,000 bp contained 7 SNPs with p-values < 1.0E-4, including rs6993464 (p = 1.25E-07). This association lies in the region between two genes, NOV and ENPP2, which have been shown to play a role in tumor development and motility. An additional region consisting of 5 markers from 128,478,000 bp - 128,524,000 (around gene POU5F1B) had p-values < 1E-04, including rs6983267, which had the smallest p-value (p = 6.34E-08). This result replicates previous reports of association between rs6983267 and prostate and colon cancer. CONCLUSIONS: Further research in this area is warranted as these results demonstrate that the chromosomal region 8q24 may contain a locus that influences general cancer susceptibility between 120,576 and 120,630 kb.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Empirical Determination of Bang-Bang Operations

Strong and fast "bang-bang" (BB) pulses have been recently proposed as a means for reducing decoherence in a quantum system. So far theoretical analysis of the BB technique relied on model Hamiltonians. Here we introduce a method for empirically determining the set of required BB pulses, that relies on quantum process tomography. In this manner an experimenter may tailor his or her BB pulses to the quantum system at hand, without having to assume a model Hamiltonian.Comment: 14 pages, 2 eps figures, ReVTeX4 two-colum

A Systematic Mapping Approach of 16q12.2/FTO and BMI in More Than 20,000 African Americans Narrows in on the Underlying Functional Variation: Results from the Population Architecture using Genomics and Epidemiology (PAGE) Study

Genetic variants in intron 1 of the fat mass- and obesity-associated (FTO) gene have been consistently associated with body mass index (BMI) in Europeans. However, follow-up studies in African Americans (AA) have shown no support for some of the most consistently BMI-associated FTO index single nucleotide polymorphisms (SNPs). This is most likely explained by different race-specific linkage disequilibrium (LD) patterns and lower correlation overall in AA, which provides the opportunity to fine-map this region and narrow in on the functional variant. To comprehensively explore the 16q12.2/FTO locus and to search for second independent signals in the broader region, we fine-mapped a 646-kb region, encompassing the large FTO gene and the flanking gene RPGRIP1L by investigating a total of 3,756 variants (1,529 genotyped and 2,227 imputed variants) in 20,488 AAs across five studies. We observed associations between BMI and variants in the known FTO intron 1 locus: the SNP with the most significant p-value, rs56137030 (8.3×10-6) had not been highlighted in previous studies. While rs56137030was correlated at r2>0.5 with 103 SNPs in Europeans (including the GWAS index SNPs), this number was reduced to 28 SNPs in AA. Among rs56137030 and the 28 correlated SNPs, six were located within candidate intronic regulatory elements, including rs1421085, for which we predicted allele-specific binding affinity for the transcription factor CUX1, which has recently been implicated in the regulation of FTO. We did not find strong evidence for a second independent signal in the broader region. In summary, this large fine-mapping study in AA has substantially reduced the number of common alleles that are likely to be functional candidates of the known FTO locus. Importantly our study demonstrated that comprehensive fine-mapping in AA provides a powerful approach to narrow in on the functional candidate(s) underlying the initial GWAS findings in European populations