The Landscape of Long Non-Coding RNA Dysregulation and Clinical Relevance in Muscle Invasive Bladder Urothelial Carcinoma.

Bladder cancer is one of the most common cancers in the United States, but few advancements in treatment options have occurred in the past few decades. This study aims to identify the most clinically relevant long non-coding RNAs (lncRNAs) to serve as potential biomarkers and treatment targets for muscle invasive bladder cancer (MIBC). Using RNA-sequencing data from 406 patients in The Cancer Genome Atlas (TCGA) database, we identified differentially expressed lncRNAs in MIBC vs. normal tissues. We then associated lncRNA expression with patient survival, clinical variables, oncogenic signatures, cancer- and immune-associated pathways, and genomic alterations. We identified a panel of 20 key lncRNAs that were most implicated in MIBC prognosis after differential expression analysis and prognostic correlations. Almost all lncRNAs we identified are correlated significantly with oncogenic processes. In conclusion, we discovered previously undescribed lncRNAs strongly implicated in the MIBC disease course that may be leveraged for diagnostic and treatment purposes in the future. Functional analysis of these lncRNAs may also reveal distinct mechanisms of bladder cancer carcinogenesis

Pediatric cataracts of different etiologies contain insoluble, calcified particles

Our recent studies in mice suggest that a crucial event for the development of cataracts is the formation of calcium-containing deposits. To examine the generality of pathologic mineralization as a novel mechanism of cataract formation, we analyzed lens material from different human cataract surgeries. Human lens material was obtained from routine cataract surgeries performed on three patients with dense, white cataracts: a 10-month-old with congenital cataracts, a 9-year-old with a uveitic cataract, and a 17-year-old with a traumatic cataract. The aspirated material from the cataract surgeries contained insoluble material that could be isolated by centrifugation. Many particles within the insoluble fraction stained with Alizarin red, a dye that stains insoluble calcified material. The appearance of these human insoluble, Alizarin red-stained particles was similar to some of those detected in homogenates from cataractous mouse lenses. These results support the hypothesis that pathologic mineralization may have a mechanistic role in the formation of cataracts of different etiologies

Identification of RNase-Resistant RNAs in \u3cem\u3eSaccharomyces cerevisiae\u3c/em\u3e Extracts: Separation from Chromosomal DNA by Selective Precipitation

High-quality chromosomal DNA is a requirement for many biochemical and molecular biological techniques. To isolate cellular DNA, standard protocols typically lyse cells and separate nucleic acids from other biological molecules using a combination of chemical and physical methods. After a standard chemical-based protocol to isolate chromosomal DNA from Saccharomyces cerevisiae and then treatment with RNase A to degrade RNA, two RNase-resistant bands persisted when analyzed using gel electrophoresis. Interestingly, such resistant bands did not appear in preparations of Escherichia coli bacterial DNA after RNase treatment. Several enzymatic, chemical, and physical methods were employed in an effort to remove the resistant RNAs, including use of multiple RNases and alcohol precipitation, base hydrolysis, and chromatographic methods. These experiments resulted in the development of a new method for isolation of S. cerevisiae chromosomal DNA. This method utilizes selective precipitation of DNA in the presence of a potassium acetate/isopropanol mixture and produces high yields of chromosomal DNA without detectable contaminating RNAs

Accurate PCR detection of influenza A/B and respiratory syncytial viruses by use of Cepheid Xpert Flu+RSV Xpress Assay in point-of-care settings: Comparison to Prodesse ProFlu+

ABSTRACT The Xpert Flu+RSV Xpress Assay is a fast, automated in vitro diagnostic test for qualitative detection and differentiation of influenza A and B viruses and respiratory syncytial virus (RSV) performed on the Cepheid GeneXpert Xpress System. The objective of this study was to establish performance characteristics of the Xpert Flu+RSV Xpress Assay compared to those of the Prodesse ProFlu+ real-time reverse transcription-PCR (RT-PCR) assay (ProFlu+) for the detection of influenza A and B viruses as well as RSV in a Clinical Laboratory Improvement Amendments (CLIA)-waived (CW) setting. Overall, the assay, using fresh and frozen nasopharyngeal (NP) swabs, demonstrated high concordance with results of the ProFlu+ assay in the combined CW and non-CW settings with positive percent agreements (PPA) (100%, 100%, and 97.1%) and negative percent agreements (NPA) (95.2%, 99.5%, and 99.6%) for influenza A and B viruses and RSV, respectively. In conclusion, this multicenter study using the Cepheid Xpert Flu+RSV Xpress Assay demonstrated high sensitivities and specificities for influenza A and B viruses and RSV in ∼60 min for use at the point-of-care in the CW setting. </jats:p

Science with an ngVLA: Resolving the Radio Complexity of EXor and FUor-type Systems with the ngVLA

Episodic accretion may be a common occurrence in the evolution of young pre-main sequence stars and has important implications for our understanding of star and planet formation. Many fundamental aspects of what drives the accretion physics, however, are still unknown. The ngVLA will be a key tool in understanding the nature of these events. The high spatial resolution, broad spectral coverage, and unprecedented sensitivity will allow for the detailed analysis of outburst systems. The proposed frequency range of the ngVLA allows for observations of the gas, dust, and non-thermal emission from the star and disk.Comment: 8 pages, 1 figure, To be published in the ASP Monograph Series, "Science with a Next-Generation VLA", ed. E. J. Murphy (ASP, San Francisco, CA

Inverse electron demand Diels-Alder click chemistry for pretargeted PET imaging and radioimmunotherapy

This approach leverages the rapid, bio-orthogonal inverse electron demand Diels-Alder reaction between a radiolabeled tetrazine and a trans-cyclooctene-bearing antibody to enable pretargeted positron emission tomography imaging and endoradiotherapy in a murine model of cancer. Radiolabeled antibodies have shown promise as tools for both the nuclear imaging and endoradiotherapy of cancer, but the protracted circulation time of radioimmunoconjugates can lead to high radiation doses to healthy tissues. To circumvent this issue, we have developed an approach to positron emission tomography (PET) imaging and radioimmunotherapy (RIT) predicated on radiolabeling the antibody after it has reached its target within the body. This in vivo pretargeting strategy is based on the rapid and bio-orthogonal inverse electron demand Diels-Alder reaction between tetrazine (Tz) and trans-cyclooctene (TCO). Pretargeted PET imaging and RIT using TCO-modified antibodies in conjunction with Tz-bearing radioligands produce high activity concentrations in target tissues as well as reduced radiation doses to healthy organs compared to directly labeled radioimmunoconjugates. Herein, we describe how to prepare a TCO-modified antibody (humanized A33-TCO) as well as how to synthesize two Tz-bearing radioligands: one labeled with the positron-emitting radiometal copper-64 ([Cu-64]Cu-SarAr-Tz) and one labeled with the beta-emitting radiolanthanide lutetium-177 ([Lu-177]Lu-DOTA-PEG(7)-Tz). We also provide a detailed description of pretargeted PET and pretargeted RIT experiments in a murine model of human colorectal carcinoma. Proper training in both radiation safety and the handling of laboratory mice is required for the successful execution of this protocol.Peer reviewe

High-Dimensional Feature Selection by Feature-Wise Kernelized Lasso

The goal of supervised feature selection is to find a subset of input features that are responsible for predicting output values. The least absolute shrinkage and selection operator (Lasso) allows computationally efficient feature selection based on linear dependency between input features and output values. In this paper, we consider a feature-wise kernelized Lasso for capturing non-linear input-output dependency. We first show that, with particular choices of kernel functions, non-redundant features with strong statistical dependence on output values can be found in terms of kernel-based independence measures. We then show that the globally optimal solution can be efficiently computed; this makes the approach scalable to high-dimensional problems. The effectiveness of the proposed method is demonstrated through feature selection experiments with thousands of features.Comment: 18 page

Enzymatic, immunological and phylogenetic characterization of Brucella suis urease

<p>Abstract</p> <p>Background</p> <p>The sequenced genomes of the <it>Brucella </it>spp. have two urease operons, <it>ure</it>-1 and <it>ure</it>-2, but there is evidence that only one is responsible for encoding an active urease. The present work describes the purification and the enzymatic and phylogenomic characterization of urease from <it>Brucella suis </it>strain 1330. Additionally, the urease reactivity of sera from patients diagnosed with brucellosis was examined.</p> <p>Results</p> <p>Urease encoded by the <it>ure</it>-1 operon of <it>Brucella suis </it>strain 1330 was purified to homogeneity using ion exchange and hydrophobic interaction chromatographies. The urease was purified 51-fold with a recovery of 12% of the enzyme activity and 0.24% of the total protein. The enzyme had an isoelectric point of 5, and showed optimal activity at pH 7.0 and 28–35°C. The purified enzyme exhibited a Michaelis-Menten saturation kinetics with a <it>K</it>_{<it>m </it>}of 5.60 ± 0.69 mM. Hydroxyurea and thiourea are competitive inhibitors of the enzyme with K_iof 1.04 ± 0.31 mM and 26.12 ± 2.30 mM, respectively. Acetohydroxamic acid also inhibits the enzyme in a competitive way. The molecular weight estimated for the native enzyme was between 130–135 kDa by gel filtration chromatography and 157 ± 7 kDa using 5–10% polyacrylamide gradient non-denaturing gel. Only three subunits in SDS-PAGE were identified: two small subunits of 14,000 Da and 15,500 Da, and a major subunit of 66,000 Da. The amino terminal sequence of the purified large subunit corresponded to the predicted amino acid sequence encoded by <it>ureC1</it>. The UreC1 subunit was recognized by sera from patients with acute and chronic brucellosis. By phylogenetic and cluster structure analyses, <it>ureC1 </it>was related to the <it>ureC </it>typically present in the <it>Rhizobiales</it>; in contrast, the <it>ureC2 </it>encoded in the <it>ure</it>-2 operon is more related to distant species.</p> <p>Conclusion</p> <p>We have for the first time purified and characterized an active urease from <it>B. suis</it>. The enzyme was characterized at the kinetic, immunological and phylogenetic levels. Our results confirm that the active urease of <it>B. suis </it>is a product of <it>ure</it>-1 operon.</p

Hospital survey on patient safety culture (HSOPSC) : a multi-method approach for target-language instrument translation, adaptation, and validation to improve the equivalence of meaning for cross-cultural research

Altres ajuts: This research project was partially funded through a research dissemination grant from the Universidad Cooperativa de Colombia received by Dr. Doriam E. Camacho-Rodríguez.The Hospital Survey on Patient Safety Culture (HSOPSC) is widely utilized in multiple languages across the world. Despite culture and language variations, research studies from Latin America use the Spanish language HSOPSC validated for Spain and the United States. Yet, these studies fail to report the translation method, cultural adaptation process, and the equivalence assessment strategy. As such, the psychometric properties of the HSOPSC are not well demonstrated for cross-cultural research in Latin America, including Peru. The purpose of this study was to develop a target-language HSOPSC for cross-cultural research in Peru that asks the same questions, in the same manner, with the same intended meaning, as the source instrument. This study used a mixed-methods approach adapted from the translation guideline recommended by Agency for Healthcare Research and Quality. The 3-phase, 7-step process incorporated translation techniques, pilot testing, cognitive interviews, clinical participant review, and subject matter expert evaluation. The instrument was translated and evaluated in 3 rounds of cognitive interview (CI). There were 37 problem items identified in round 1 (14 clarity, 12 cultural, 11 mixed); and resolved to 4 problems by round 3. The pilot-testing language clarity inter-rater reliability was S-CVI/Avg = 0.97 and S-CVI/UA = 0.86; and S-CVI/Avg = 0.96 and S-CVI/UA = 0.83 for cultural relevance. Subject matter expert agreement in matching items to the correct dimensions was substantially equivalent (Kappa = 0.72). Only 1 of 12 dimensions had a low Kappa (0.39), borderline fair to moderate. The remaining dimensions performed well (7 = almost perfect, 2 = substantial, and 2 = moderate). The HSOPSC instrument developed for Peru was markedly different from the other Spanish-language versions. The resulting items were equivalent in meaning to the source, despite the new language and different cultural context. The analysis identified negatively worded items were problematic for target-language translation. With the limited literature about negatively worded items in the context of cross-cultural research, further research is necessary to evaluate this finding and the recommendation to include negatively worded items in instruments. This study demonstrates cross-cultural research with translated instruments should adhere to established guidelines, with cognitive interviews, based on evidence-based strategies