Projecting the global impact of fossil fuel production from the Former Soviet Union.

Detailed projections of the Former Soviet Union (FSU) fossil fuel production has been created. Russian production has been modelled at the region (oblast) level where possible. The projections were made using the Geologic Resource Supply-Demand Model (GeRS-DeMo). Low, Best Guess and High scenarios were created. FSU fossil fuels are projected to peak between 2027 and 2087 with the range due to spread of Ultimately Recoverable Resources (URR) values used. The Best Guess (BG) scenario anticipates FSU will peak in 2087 with production over 170 EJ per year. The FSU projections were combined with rest of the world projections (Mohr et al. 2015b), the emissions from the High scenario for the world are similar to the IPCC A1 AIM scenario. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s40789-021-00449-x.

Validation and in-field testing of a new on-site qPCR system for quantification of Legionella pneumophila according to ISO/TS 12869:2012 in HVAC cooling towers.

Legionella pneumophila, found in engineered water systems such as HVAC cooling towers, poses a significant public health risk. Culture, though routinely used to quantify L. pneumophila, has several disadvantages including long turnaround time, low sensitivity, and inter-laboratory variability. In this study, we validated the performance of an on-site quantitative polymerase chain reaction (qPCR) detection system for L. pneumophila in accordance with International Standards Organization Technical Specification 12869:2012. We evaluated specificity, limit of detection and quantification, and calibration curve linearity. Additionally, we evaluated whole system recovery and robustness using samples taken from taps and evaporative cooling towers. We then compared the system's performance against laboratory culture and laboratory qPCR across 53 cooling towers in a 12-week in-field study. We found that concordance between on-site qPCR and culture was both laboratory- and site/sample-dependent. Comparison of laboratory qPCR with on-site qPCR revealed that laboratory results were highly variable and showed little concordance. Some discordance may be explained by time delay between sample collection and testing ('shipping effect') which may lead to inaccurate reporting. Overall, our study highlights the value of on-site qPCR detection of L. pneumophila, demonstrates that laboratories are prone to misreporting results due to shipping effects, and reveals significant discordance between laboratory qPCR and culture.

Visualizing Alternative Phosphorus Scenarios for Future Food Security.

The impact of global phosphorus scarcity on food security has increasingly been the focus of scientific studies over the past decade. However, systematic analyses of alternative futures for phosphorus supply and demand throughout the food system are still rare and provide limited inclusion of key stakeholders. Addressing global phosphorus scarcity requires an integrated approach exploring potential demand reduction as well as recycling opportunities. This implies recovering phosphorus from multiple sources, such as food waste, manure, and excreta, as well as exploring novel opportunities to reduce the long-term demand for phosphorus in food production such as changing diets. Presently, there is a lack of stakeholder and scientific consensus around priority measures. To therefore enable exploration of multiple pathways and facilitate a stakeholder dialog on the technical, behavioral, and institutional changes required to meet long-term future phosphorus demand, this paper introduces an interactive web-based tool, designed for visualizing global phosphorus scenarios in real time. The interactive global phosphorus scenario tool builds on several demand and supply side measures that can be selected and manipulated interactively by the user. It provides a platform to facilitate stakeholder dialog to plan for a soft landing and identify a suite of concrete priority options, such as investing in agricultural phosphorus use efficiency, or renewable fertilizers derived from phosphorus recovered from wastewater and food waste, to determine how phosphorus demand to meet future food security could be attained on a global scale in 2040 and 2070. This paper presents four example scenarios, including (1) the potential of full recovery of human excreta, (2) the challenge of a potential increase in non-food phosphorus demand, (3) the potential of decreased animal product consumption, and (4) the potential decrease in phosphorus demand from increased efficiency and yield gains in crop and livestock systems.

Is Decoupling GDP Growth from Environmental Impact Possible?

The argument that human society can decouple economic growth-defined as growth in Gross Domestic Product (GDP)-from growth in environmental impacts is appealing. If such decoupling is possible, it means that GDP growth is a sustainable societal goal. Here we show that the decoupling concept can be interpreted using an easily understood model of economic growth and environmental impact. The simple model is compared to historical data and modelled projections to demonstrate that growth in GDP ultimately cannot be decoupled from growth in material and energy use. It is therefore misleading to develop growth-oriented policy around the expectation that decoupling is possible. We also note that GDP is increasingly seen as a poor proxy for societal wellbeing. GDP growth is therefore a questionable societal goal. Society can sustainably improve wellbeing, including the wellbeing of its natural assets, but only by discarding GDP growth as the goal in favor of more comprehensive measures of societal wellbeing.

A blood-based biomarker panel for stratifying current risk for colorectal cancer.

Colorectal cancer (CRC) is often curable and preventable using current screening modalities. Unfortunately, screening compliance remains low, partly due to patient dissatisfaction with faecal/endoscopic testing. Recent guidelines advise CRC screening should begin with risk stratification. A blood-based test providing clinically actionable CRC risk information would likely improve screening compliance and enhance clinical decision making. We analyzed 196 gene expression profiles to select candidate CRC biomarkers. qRT-PCR was performed on 642 samples to develop a 7-gene biomarker panel using 112 CRC/120 controls (training set) and 202 CRC/208 controls (independent, blind test set). Panel performance characteristics and disease prevalence (0.7%) were then used to develop a scale assessing an individual's current risk of having CRC based on his/her gene signature. A 7-gene panel (ANXA3, CLEC4D, LMNB1, PRRG4, TNFAIP6, VNN1 and IL2RB) discriminated CRC in the training set (area under the receiver-operating-characteristic curve (ROC AUC), 0.80; accuracy, 73%; sensitivity, 82%; specificity 64%). The independent blind test set confirmed performance (ROC AUC, 0.80; accuracy, 71%; sensitivity, 72%; specificity, 70%). Individual gene profiles were compared against the population results and used to calculate the current relative risk for CRC. We have developed a 7-gene, blood-based biomarker panel that can stratify subjects according to their current relative risk across a broad range in an average-risk population. Across the continuous spectrum of risk as defined by the current relative risk scale, it is possible to identify clinically meaningful reference points that can assist patients and physicians in CRC screening decision making.

The peripheral-blood transcriptome: new insights into disease and risk assessment.

Future personalized medicine strategies for assessing an individual's health require, ideally, a noninvasive system that is capable of integrating numerous interactive factors, including gender, age, genetics, behavior, environment and comorbidities. Several microarray-based methods developed to meet this goal are currently under investigation. However, most rely on tissue biopsies, which are not readily available or accessible. As an alternative, several recent studies have investigated the use of human peripheral blood cells as surrogate biopsy material. Such studies are based on the assumption that molecular profiling of circulating blood might reflect physiological and pathological events occurring in different tissues of the body. This has led to the development of novel methods for identifying and monitoring blood biomarkers to probe an individual's health status. Here, we discuss the rationale and clinical potential of profiling the peripheral-blood transcriptome.

[Asbestos and malignant pleural mesothelioma: molecular, cellular and physiopathological aspects]. / Amiante et mésothéliome pleural malin: aspects moléculaires, cellulaires et physiopathologiques.

Asbestos is known as mutagenic and carcinogenic for human and is responsible for many pulmonary diseases including asbestosis, bronchogenic carcinoma and malignant pleural mesothelioma. Occupational exposure to asbestos is involved in 70-80% of all malignant pleural mesothelioma. The later presents a growing challenge for both researcher and clinician. The diagnosis of malignant pleural mesothelioma is difficult and the current treatments did not show significant improvement of the survival. The increasing incidence of malignant pleural mesothelioma, its gravity and its human, social and financial consequences are of high concern in public health. In this paper we summarize the so far knowledge on cellular, molecular and pathophysiological events involved in genesis and development of malignant pleural mesothelioma. Finally, the paper also report recent data sourced from the study of malignant pleural mesothelioma transcriptome using high-throughput technologies such as gene expression array. These data should improve the accuracy of mesothelioma diagnosis and therapy.

Microdissection, mRNA amplification and microarray: a study of pleural mesothelial and malignant mesothelioma cells.

The studies of molecular alterations in tumor cells with microarrays are often hampered by inherent tissue heterogeneity. The emergence of Laser Capture Microdissection (LCM) allowed us to overcome this challenge since it gives selective access to cancer cells that are isolated from their native tissue environment. In this report, we microdissected mesothelial cells and malignant mesothelioma cells of ex vivo resected specimens using LCM. Amplified RNA from mesothelial and mesothelioma microdissected cells allowed us to measure global gene expression with 10 K-microarrays in four independent experiments. We screened 9850 annotated human genes, 1275 of which have satisfied our data analysis requirements. They included 302 overexpressed genes and 160 downregulated genes in mesothelioma microdissected cells as compared to mesothelial microdissected cells. Among them, the expression levels of eight genes, namely BF, FTL, IGFBP7, RARRES1, RARRES2, RBP1, SAT, and TXN according to HUGO nomenclature, were increased, whereas six: ALOX5AP, CLNS1A, EIF4A2, ELK3, REQ and SYPL, were found to be underexpressed in mesothelioma microdissected cells. The ferritin light polypeptide (FTL) gene overexpression was confirmed by real time quantitative PCR. Our approach allowed a comprehensive in situ examination of mesothelioma and provided an accurate way to find new marker genes that may be useful for diagnosis and treatment of malignant pleural mesothelioma.

Cell protection, resistance and invasiveness of two malignant mesotheliomas as assessed by 10K-microarray.

Malignant pleural mesothelioma (MPM) is an aggressive serosal tumor, strongly associated with former exposure to asbestos fibers and for which there is currently no effective treatment available. In human, MPM is characterized by a high local invasiveness, poor prognosis and therapeutic outcomes. In order to assess molecular changes that specify this phenotype, we performed a global gene expression profiling of human MPM. Using a 10,000-element microarray, we analyzed mRNA relative gene expression levels by comparing a mesothelioma cell line to either a pleural cell line or tumor specimens. To analyze these gene expression data, we used various bioinformatics softwares. Hierarchical clustering methods were used to group genes and samples with similar expression in an unsupervised mode. Genes of known function were further sorted by enzyme, function and pathway clusters using a supervised software (IncyteGenomics). Taken together, these data defined a molecular fingerprint of human MPM with more than 700 up- or down-regulated genes related to several traits of the malignant phenotype, specially associated with MPM invasiveness, protection and resistance to anticancer defenses. This portrait is meaningful in disease classification and management, and relevant in finding new specific markers of MPM. These molecular markers should improve the accuracy of mesothelioma diagnosis, prognosis and therapy.

From transcriptomics to bibliomics.

BACKGROUND: Current biological investigations tend to operate with genomes, instead of genes as during the last century. It is possible to compare entire genomes, transcriptomes or proteomes, using alphanumeric data corresponding to the differential expression levels of thousands of genes. What remains difficult is to link array results to factual or bibliographical data and retrieve information that is highly structured and - in Shannon's sense - rare. MATERIAL/METHODS: We have developed a tool, Documentation and Information LIBrary (DILIB), that enables us to retrieve, organize and analyze huge amounts of data available on the Internet and related to microarray experiments. DILIB can link hundreds of differentially expressed genes - through their Single Identifier or GenBank accession number - to hundreds of Medline records, and can retrieve, analyze, and compare automatically thousands of non-trivial descriptors related to gene clusters. RESULTS: As exemplified with frequency comparison of MEdical Subject Headings and Registry Number descriptors, we reanalyzed the involvement of 'integrin', 'interleukin' and 'CD Antigens' in mesotheliomas. Thus, DILIB allowed us to: (i). associate literature to expressed genes, (ii). link functional transcriptomes in various experiments, (iii). associate specific descriptors to experiments, (iv). define new research areas, and eventually (v). find new functions for co-expressed genes. CONCLUSIONS: We propose a new concept, 'bibliomics', representing a subset of high quality and rare information, retrieved and organized by systematic literature-searching tools from existing databases, and related to a subset of genes functioning together in '-omic' sciences.

Microarrays as cancer keys: an array of possibilities.

Malignant transformation results from accumulation of genetic and epigenetic events. Functional studies of cancer will be crucial to our understanding of its complexity and polymorphism. There is no doubt that emerging genomic and proteomic technologies will facilitate such investigations. Microarray technology is a new and efficient approach to extract data of biomedical relevance for a wide range of applications. In cancer research, it will provide high-throughput and valuable insights into differences in an individual's tumor as compared with constitutional DNA, mRNA expression, and protein expression and activity. Across individuals, comparisons could provide tissue-specific disease signatures that provide diagnosis based on hundreds of informative genes. The resulting product should be a wealth of tumor-associated and tumor-specific biomarkers, which may help in cancer etiology, diagnosis, and therapy and ultimately lead to "molecular nosology" of cancers. This review highlights the recent developments in microarray technologies in cancer research, focuses on the results obtained so far, and describes the eventual use of microarray technology for clinical applications.