Utilization of the Aspergillus nidulans pyrG gene as a selectable marker for transformation and electroporation of Neurospora crassa

We report the complementation of the Neurospora crassa pyr-4 mutation with the Aspergillus nidulans pyrG gene. The use of the pyrG gene as a selectable marker for N. crassa transformation offers several advantages: a non toxic nutritional selection, the ability to put single-copy transformants through a sexual cross without the occurrence of RIP (Repeat-Induced Point mutation) by alleles of the pyr-4 gene, and a relatively-high electroporation efficiency. These traits were exploited for targeted gene replacement in N. crassa. In addition, the high electroporation efficiency of pyrG achieved using supercoiled circular DNA renders it an ideal marker for random insertional mutagenesis studies in N. crassa

CCDB: a curated database of genes involved in cervix cancer

The Cervical Cancer gene DataBase (CCDB, http://crdd.osdd.net/raghava/ccdb) is a manually curated catalog of experimentally validated genes that are thought, or are known to be involved in the different stages of cervical carcinogenesis. In spite of the large women population that is presently affected from this malignancy still at present, no database exists that catalogs information on genes associated with cervical cancer. Therefore, we have compiled 537 genes in CCDB that are linked with cervical cancer causation processes such as methylation, gene amplification, mutation, polymorphism and change in expression level, as evident from published literature. Each record contains details related to gene like architecture (exon–intron structure), location, function, sequences (mRNA/CDS/protein), ontology, interacting partners, homology to other eukaryotic genomes, structure and links to other public databases, thus augmenting CCDB with external data. Also, manually curated literature references have been provided to support the inclusion of the gene in the database and establish its association with cervix cancer. In addition, CCDB provides information on microRNA altered in cervical cancer as well as search facility for querying, several browse options and an online tool for sequence similarity search, thereby providing researchers with easy access to the latest information on genes involved in cervix cancer

PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites

A particular challenge in biomedical text mining is to find ways of handling ‘comprehensive’ or ‘associative’ queries such as ‘Find all genes associated with breast cancer’. Given that many queries in genomics, proteomics or metabolomics involve these kind of comprehensive searches we believe that a web-based tool that could support these searches would be quite useful. In response to this need, we have developed the PolySearch web server. PolySearch supports >50 different classes of queries against nearly a dozen different types of text, scientific abstract or bioinformatic databases. The typical query supported by PolySearch is ‘Given X, find all Y's’ where X or Y can be diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites. PolySearch also exploits a variety of techniques in text mining and information retrieval to identify, highlight and rank informative abstracts, paragraphs or sentences. PolySearch's performance has been assessed in tasks such as gene synonym identification, protein–protein interaction identification and disease gene identification using a variety of manually assembled ‘gold standard’ text corpuses. Its f-measure on these tasks is 88, 81 and 79%, respectively. These values are between 5 and 50% better than other published tools. The server is freely available at http://wishart.biology.ualberta.ca/polysearc

Cancer gene prioritization by integrative analysis of mRNA expression and DNA copy number data: a comparative review

A variety of genome-wide profiling techniques are available to probe complementary aspects of genome structure and function. Integrative analysis of heterogeneous data sources can reveal higher-level interactions that cannot be detected based on individual observations. A standard integration task in cancer studies is to identify altered genomic regions that induce changes in the expression of the associated genes based on joint analysis of genome-wide gene expression and copy number profiling measurements. In this review, we provide a comparison among various modeling procedures for integrating genome-wide profiling data of gene copy number and transcriptional alterations and highlight common approaches to genomic data integration. A transparent benchmarking procedure is introduced to quantitatively compare the cancer gene prioritization performance of the alternative methods. The benchmarking algorithms and data sets are available at http://intcomp.r-forge.r-project.orgComment: PDF file including supplementary material. 9 pages. Preprin

Comparison of the oxidative potential of primary (POA) and secondary (SOA) organic aerosols derived from α-pinene and gasoline engine exhaust precursors [version 2; referees: 2 approved]

Background: Primary (POA) and secondary (SOA) organic aerosols, deriving from both anthropogenic and biogenic sources, represent a major fraction of ambient particulate matter (PM) and play an important role in the etiology of respiratory and cardiovascular diseases, largely through systemic inflammation and cellular oxidative stress. The relative contributions of these species to the inhalation burden, however, are rather poorly characterized. In this study, we measured the in vitro oxidative stress response of alveolar macrophages exposed to primary and secondary PM derived from both anthropogenic and biogenic sources. Methods: POA and SOA were generated within an oxidation flow reactor (OFR) fed by pure, aerosolized α-pinene or gasoline engine exhaust, as representative emissions of biogenic and anthropogenic sources, respectively. The OFR utilized an ultraviolet (UV) lamp to achieve an equivalent atmospheric aging process of several days. Results: Anthropogenic SOA produced the greatest oxidative response (1900 ± 255 µg-Zymosan/mg-PM), followed by biogenic (α-pinene) SOA (1321 ± 542 µg-Zymosan/mg-PM), while anthropogenic POA produced the smallest response (51.4 ± 64.3 µg-Zymosan/mg-PM). Conclusions: These findings emphasize the importance of monitoring and controlling anthropogenic emissions in the urban atmosphere, while also taking into consideration spatial and seasonal differences in SOA composition. Local concentrations of biogenic and anthropogenic species contributing to the oxidative potential of ambient PM may vary widely, depending on the given region and time of year, due to factors such as surrounding vegetation, proximity to urban areas, and hours of daylight

Comparison of the oxidative potential of primary (POA) and secondary (SOA) organic aerosols derived from α-pinene and gasoline engine exhaust precursors [version 1; referees: 2 approved]

Background: Primary (POA) and secondary (SOA) organic aerosols, deriving from both anthropogenic and biogenic sources, represent a major fraction of ambient particulate matter (PM) and play an important role in the etiology of respiratory and cardiovascular diseases, largely through systemic inflammation and cellular oxidative stress. The relative contributions of these species to the inhalation burden, however, are rather poorly characterized. In this study, we measured the in vitro oxidative stress response of alveolar macrophages exposed to primary and secondary PM derived from both anthropogenic and biogenic sources. Methods: POA and SOA were generated within an oxidation flow reactor (OFR) fed by pure, aerosolized α-pinene or gasoline engine exhaust, as representative emissions of biogenic and anthropogenic sources, respectively. The OFR utilized an ultraviolet (UV) lamp to achieve an equivalent atmospheric aging process of several days. Results: Anthropogenic SOA produced the greatest oxidative response (1900 ± 255 µg-Zymosan/mg-PM), followed by biogenic (α-pinene) SOA (1321 ± 542 µg-Zymosan/mg-PM), while anthropogenic POA produced the smallest response (51.4 ± 64.3 µg-Zymosan/mg-PM). Conclusions: These findings emphasize the importance of monitoring and controlling anthropogenic emissions in the urban atmosphere, while also taking into consideration spatial and seasonal differences in SOA composition. Local concentrations of biogenic and anthropogenic species contributing to the oxidative potential of ambient PM may vary widely, depending on the given region and time of year, due to factors such as surrounding vegetation, proximity to urban areas, and hours of daylight

An exploratory randomized controlled trial evaluating text prompts in Lebanon to encourage health‐seeking behavior for hypertension

Aims of the study The current study evaluates the effectiveness of an opportunistic mobile screening on the percentage of people who are aware of whether they may be hypertensive (in an observational study) and the effectiveness of reminder prompts on the percentage of people who seek further medical attention (in a randomized controlled trial). Methods used to conduct the study The screening of 1227 participants (529 female) was conducted during the registration period of the 2018 Beirut International Marathon in Lebanon. Next, 266 participants whose screening indicated hypertension (64 Female) were randomly allocated to a treatment group or a control group in a 1:1 fashion. The treatment group received a reminder prompt to seek further medical attention for their potential hypertension and the control group did not. The overt nature of the text message meant that participants in the treatment group could not be blinded to their group allocation. The primary outcome is participants’ self‐reports of whether they sought further medical attention. Results of the study For the opportunistic screening, a 25% prevalence rate and a 24% awareness rate of hypertension was indicated. A McNemar analysis suggested that the screening increased participant awareness (X2 (N =1227)=72.16, p <0.001). For the randomized controlled trial, 219 participants provided follow‐up data via a phone call (82% retention). A Chi‐squared analysis suggested that the reminder prompt successfully encouraged more participants to seek further medical attention, 45.5% treatment group vs. 28.0% control group (X 2(1, N =219)=7.19, p =0.007, φ =0.18). Conclusions drawn and clinical implications Extra support in the form of a brief reminder message can increase the percentage of people who seek further medical attention after attending an opportunistic screening at a marathon event. The discussion reviews how the results align with previous research, strengths and limitations of the current study, and implications for future research and practice

Water hammer with column separation: A historical review

Column separation refers to the breaking of liquid columns in fully filled pipelines. This may occur in a water-hammer event when the pressure in a pipeline drops to the vapor pressure at specific locations such as closed ends, high points or knees (changes in pipe slope). The liquid columns are separated by a vapor cavity that grows and diminishes according to the dynamics of the system. The collision of two liquid columns, or of one liquid column with a closed end, may cause a large and nearly instantaneous rise in pressure. This pressure rise travels through the entire pipeline and forms a severe load for hydraulic machinery, individual pipes and supporting structures. The situation is even worse: in one water-hammer event many repetitions of cavity formation and collapse may occur. This paper reviews water hammer with column separation from the discovery of the phenomenon in the late 19th century, the recognition of its danger in the 1930s, the development of numerical methods in the 1960s and 1970s, to the standard models used in commercial software packages in the late 20th century. A comprehensive survey of laboratory tests and field measurements is given. The review focuses on transient vaporous cavitation. Gaseous cavitation and steam condensation are beyond the scope of the paper. © 2005 Elsevier Ltd. All rights reserved.A. Bergant, A.R. Simpson, and A.S. Tijsselinghttp://www.elsevier.com/wps/find/journaldescription.cws_home/622877/description#descriptio