How To Make A Pie: Reproducible Research for Empirical Economics & Econometrics

Empirical economics and econometrics (EEE) research now relies primarily on the application of code to datasets. Handling the workflow linking datasets, programs, results and finally manuscript(s) is essential if one wish to reproduce results, which is now increasingly required by journals and institutions. We underline here the importance of “reproducible research” in EEE and suggest three simple principles to follow. We illustrate these principles with good habits and tools, with particular focus on their implementation in most popular software and languages in applied economics

How To Make A Pie: Reproducible Research for Empirical Economics & Econometrics

Empirical economics and econometrics (EEE) research now relies primarily on the application of code to datasets. Handling the workflow linking datasets, programs, results and finally manuscript(s) is essential if one wish to reproduce results, which is now increasingly required by journals and institutions. We underline here the importance of “reproducible research” in EEE and suggest three simple principles to follow. We illustrate these principles with good habits and tools, with particular focus on their implementation in most popular software and languages in applied economics

Influence of Extraction Solvent on the Biological Properties of Maritime Pine Bark (Pinus pinaster)

Maritime pine bark (Pinus pinaster Aiton subsp. atlantica) is rich in polyphenols with known bioactive properties which are beneficial for human health. However, biological activities of bark extracts depend on the type of polyphenols extracted and the characteristics of these extractives depend on several factors such as the type of solvents used. The in uence of the extraction solvent on the composition and consequently on the properties of the extracts has been poorly described. Thus, in this study the in uence of the extraction solvent (water, ethanol and ethanol-water (50/50 v/v%)) on the antibacterial and anticancer properties of P. pinaster bark samples were evaluated. LC-DAD-MS profiling of the different extracts was also carried out to study their polyphenol composition. Results show that extraction solvent must be carefully chosen with respect to foreseeing use of bark extracts, since ethanolic and hydroethanolic extracts displayed the greatest antibacterial activity whereas water extracts showed increased anticancer properties. © 2022. International Journal of Food Studies.All Rights Reserve

High expression of Cathepsin E in tissues but not blood of patients with Barrett’s esophagus and adenocarcinoma

Background Cathepsin E (CTSE), an aspartic proteinase, is differentially expressed in the metaplasia–dysplasia–neoplasia sequence of gastric and colon cancer. We evaluated CTSE in Barrett’s esophagus (BE) and cancer because increased CTSE levels are linked to improved survival in several cancers, and other cathepsins are up-regulated in BE and esophageal adenocarcinoma (EAC). Methods A total of 273 pretreatment tissues from 199 patients were analyzed [31 normal squamous esophagus (NE), 29 BE intestinal metaplasia, 31 BE with dysplasia (BE/D), 108 EAC]. CTSE relative mRNA expression was measured by real-time polymerase chain reaction, and protein expression was measured by immunohistochemistry. CTSE serum levels were determined by enzyme-linked immunosorbent assay. Results Median CTSE mRNA expression levels were ≥1,000-fold higher in BE/intestinal metaplasia and BE/D compared to NE. CTSE levels were significantly lower in EAC compared to BE/intestinal metaplasia and BE/D, but significantly higher than NE levels. A similar expression pattern was present in immunohistochemistry, with absent staining in NE, intense staining in intestinal metaplasia and dysplasia, and less intense EAC staining. CTSE serum analysis did not discriminate patient groups. In a uni- and multivariable Cox proportional hazards model, CTSE expression was not significantly associated with survival in patients with EAC, although CTSE expression above the 25th percentile was associated with a 41 % relative risk reduction for death (hazard ratio 0.59, 95 % confidence interval 0.27–1.26, p = 0.17). Conclusions CTSE mRNA expression is up-regulated more than any known gene in Barrett intestinal metaplasia and dysplasia tissues. Protein expression is similarly highly intense in intestinal metaplasia and dysplasia tissues

Исследовательская деятельность эколого-биологической направленности в НОУ "Эврика" - эффективное средство профессиональной ориентации учащихся

В статье научно-исследовательская деятельность эколого-биологической направленности старшеклассников НОУ "Эврика" г. Нижнего Новгорода рассматривается как одна из значимых инновационных форм профессионального самоопределения. Материалом исследования послужил анализ программ конференции городского научного общества учащихся "Эврика" и судьбы выпускников данного общества. Отмечена тенденция роста популярности эколого-биологических исследований среди старшеклассников г. Нижнего Новгорода и успешное вхождение в профессию выпускников научного общества учащихся.In the article, the research activity of the ecology and biology of senior pupils of the scientific society of the pupils "Eureka" in Nizhny Novgorod is considered as one of the significant innovative forms of professional self-determination. The material of the study was the analysis of the programs of the conference of the city scientific society of the students "Eureka" and the fate of the graduates of this society. The tendency of growth of popularity of ecological and biological researches among senior pupils of Nizhny Novgorod and successful entry into the profession of graduates of the scientific society of students is noted

HIV-1 viral blips are associated with repeated and increasingly high levels of cell-associated HIV-1 RNA transcriptional activity

Objective:Some HIV+ patients, virally suppressed on ART, show occasional 'blips' of detectable HIV-1 plasma RNA. We used a new highly sensitive assay of cell-associated HIV-1 RNA to measure transcriptional activity in PBMCs and production of infectious virus from the viral reservoir, in patients with and without 'blips'.Design/methods:RNA and DNA extracted from cells in 6 ml of peripheral blood, from suppressed patients with one to two 'blip' episodes over the past 2 years of ART (n = 55), or no 'blips' (n = 52), were assayed for HIV-1 RNA transcripts and proviral DNA targeting the highly conserved 'R' region of the LTR. Follow-up samples were also collected. Purified CD4+T cells were cultured with anti-CD3/CD28/CD2 T-cell activator to amplify transcription and measure replication competent virus.Results:HIV-1 RNA transcripts ranged from 1.3 to 5415 copies/106white blood cells. 'Blip' patients had significantly higher levels vs. without blips (median 192 vs. 49; P = 0.0007), which correlated with: higher levels of inducible transcripts after activation in vitro, sustained higher HIV-1 transcription levels in follow-up samples along with increasing HIV-1 DNA in some, and production of replication-competent HIV-1.Conclusion:Viral 'blips' are significant reflecting higher transcriptional activity from the reservoir and contribute to the reservoir over time. This sensitive assay can be used in monitoring the size and activity of the HIV-1 reservoir and will be useful in HIV-1 cure strategies

Structures and activities of tiahuramides A–C, cyclic depsipeptides from a tahitian collection of the marine cyanobacterium Lyngbya majuscula

The structures of three new cyclic depsipeptides, tiahuramides A (1), B (2), and C (3), from a French Polynesian collection of the marine cyanobacterium Lyngbya majuscula are described. The planar structures of these compounds were established by a combination of mass spectrometry and 1D and 2D NMR experiments. Absolute configurations of natural and nonproteinogenic amino acids were determined through a combination of acid hydrolysis, derivitization with Marfey’s reagent, and HPLC. The absolute configuration of hydroxy acids was confirmed by Mosher’s method. The antibacterial activities of tiahuramides against three marine bacteria were evaluated. Compound 3 was the most active compound of the series, with an MIC of 6.7 μM on one of the three tested bacteria. The three peptides inhibit the first cell division of sea urchin fertilized eggs with IC50 values in the range from 3.9 to 11 μM. Tiahuramide B (2), the most potent compound, causes cellular alteration characteristics of apoptotic cells, blebbing, DNA condensation, and fragmentation, already at the first egg cleavage. The cytotoxic activity of compounds 1–3 was tested in SH-SY5Y human neuroblastoma cells. Compounds 2 and 3 showed an IC50 of 14 and 6.0 μM, respectively, whereas compound 1 displayed no toxicity in this cell line at 100 μM. To determine the type of cell death induced by tiahuramide C (3), SH-SY5Y cells were costained with annexin V–FITC and propidium iodide and analyzed by flow cytometry. The double staining indicated that the cytotoxicity of compound 3 in this cell line is produced by necrosis

CO-FREE Alternative Test Products for Copper Reduction in Agriculture

The project CO-FREE (2012-2016) aimed to develop strategies to replace/reduce copper use in organic, integrated and conventional farming. CO-FREE alternative test products (CTPs) were tested and integrated together with decision support systems, disease-tolerant varieties, and innovative breeding goals (ideotypes) into improved management strategies. CO-FREE focused on apple/apple scab (Venturia inaequalis), grape/downy mildew (Plasmopara viticola), and tomato and potato/late blight (Phytophthora infestans). Starting point of the project were ten CTPs with direct or indirect modes of action including Trichoderma atroviride SC1 and protein extract SCNB, Lysobacter spp., yeast-based derivatives, Cladosporium cladosporioides H39, the oligosaccharidic complex COS-OGA, Aneurinibacillus migulanus and Xenorhabdus bovienii, sage (Salvia officinalis) extract, liquorice (Glycyrrhiza glabra) extract, PLEX- and seaweed plant extracts. As the project progressed, further promising CTPs were included by the partners. Field trials were performed in different European countries in 2012-2015 following EPPO standards. In the first years, stand-alone applications of CTPs were tested. In the following years these were integrated into complete strategies. Effects on main and further diseases, on yield and on non-target organisms were assessed. Here, field trial results with CTPs are summarized