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

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

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

Changes in gene expression of neo-squamous mucosa after endoscopic treatment for dysplastic Barrett’s esophagus and intramucosal adenocarcinoma

Author version made available in accordance with publisher copyright policy.Abstract Background: Endoscopic therapy, including by radiofrequency ablation (RFA) or endoscopic mucosal resection (EMR), is first line treatment for Barrett’s esophagus (BE) with high-grade dysplasia (HGD) or intramucosal cancer (IMC) and may be appropriate for some patients with low-grade dysplasia (LGD). Objective: The purpose of this study was to investigate the molecular effects of endotherapy. Methods: mRNA expression of 16 genes significantly associated with different BE stages was measured in paired pretreatment BE tissues and post-treatment neo-squamous biopsies from 36 patients treated by RFA (19 patients, 3 IMC, 4 HGD, 12 LGD) or EMR (17 patients, 4 IMC, 13 HGD). EMR was performed prior to RFA in eight patients. Normal squamous esophageal tissues were from 20 control individuals. Results: Endoscopic therapy resulted in significant change towards the normal squamous expression profile for all genes. The neo-squamous expression profile was significantly different to the normal control profile for 11 of 16 genes. Conclusion: Endotherapy results in marked changes in mRNA expression, with replacement of the disordered BE dysplasia or IMC profile with a more ‘‘normal’’ profile. The neo-squamous mucosa was significantly different to the normal control squamous mucosa for most genes. The significance of this finding is uncertain but it may support continued endoscopic surveillance after successful endotherapy

L’accompagnement-citoyen en soutien à la participation sociale des aînés ayant un traumatisme craniocérébral

Hautement valorisée par les aînés, la participation sociale a des effets bénéfiques sur leur santé biopsychosociale. Tous n’ont pas cependant les mêmes opportunités pour s’investir dans ce type d’activités; particulièrement ceux ayant un traumatisme craniocérébral (TCC) qui sont plus susceptibles d’être limités dans leurs capacités à participer à la vie de la communauté. Les initiatives les plus courantes pour aider ces personnes consistent en une assistance humaine visant àpallierleurs limitations et ne misent pas, en priorité, sur la promotion de leurs compétences. Afin d’optimiser l’aide reçue, un accompagnementcitoyen personnalisé à l’intégration communautaire (APIC) a été développé, implanté et évalué. Cet article documente l’impact de l’APIC sur la participation sociale d’aînés ayant un TCC. Une analyse de contenu thématique a été réalisée sur les données issues d’entrevues semi-dirigées auprès des participants et des journaux de bord des accompagnateurs. Les résultats montrent trois grandes retombées de l’APIC : une meilleure assurance et un plus grand sentiment d’autonomie, un goût retrouvé de s’investir dans des activités de loisirs signifiantes, et une plus grande ouverture vers de nouvelles possibilités de relations.Abstract : Highly valued by seniors, community integration has beneficial effects on their biopsychosocial health. However, not all of them have the same opportunities to engage in social participation activities, particularly those with traumatic brain injury (TBI) who are more likely to be limited in their abilities to participate in the life of the community. The most common initiatives to help these people consist of human assistance to overcome their limitations and which do not focus on skills promotion. In order to optimize the available services and resources, personalized citizen assistance for community integration (APIC) has been developed, implemented, and evaluated. This article documents the impact of APIC on the community integration of seniors with TBI. A thematic content analysis was conducted on data from semi-structured interviews with participants and from attendant logbooks. The results show three major spin-offs from APIC: better insurance and a greater sense of autonomy, a renewed taste for investing in meaningful leisure activities, and greater openness to new relationship opportunities