Improving the reporting quality of intervention trials addressing the inter-individual variability in response to the consumption of plant bioactives: quality index and recommendations

PURPOSE: The quality of the study design and data reporting in human trials dealing with the inter-individual variability in response to the consumption of plant bioactives is, in general, low. There is a lack of recommendations supporting the scientific community on this topic. This study aimed at developing a quality index to assist the assessment of the reporting quality of intervention trials addressing the inter-individual variability in response to plant bioactive consumption. Recommendations for better designing and reporting studies were discussed. METHODS: The selection of the parameters used for the development of the quality index was carried out in agreement with the scientific community through a survey. Parameters were defined, grouped into categories, and scored for different quality levels. The applicability of the scoring system was tested in terms of consistency and effort, and its validity was assessed by comparison with a simultaneous evaluation by experts' criteria. RESULTS: The "POSITIVe quality index" included 11 reporting criteria grouped into four categories (Statistics, Reporting, Data presentation, and Individual data availability). It was supported by detailed definitions and guidance for their scoring. The quality index score was tested, and the index demonstrated to be valid, reliable, and responsive. CONCLUSIONS: The evaluation of the reporting quality of studies addressing inter-individual variability in response to plant bioactives highlighted the aspects requiring major improvements. Specific tools and recommendations favoring a complete and transparent reporting on inter-individual variability have been provided to support the scientific community on this field

SeaConditions: a web and mobile service for safer professional and recreational activities in the Mediterranean Sea

Abstract. Reliable and timely information on the environmental conditions at sea is key to the safety of professional and recreational users as well as to the optimal execution of their activities. The possibility of users obtaining environmental information in due time and with adequate accuracy in the marine and coastal environment is defined as sea situational awareness (SSA). Without adequate information on the environmental meteorological and oceanographic conditions, users have a limited capacity to respond, which has led to loss of lives and to large environmental disasters with enormous consequent damage to the economy, society and ecosystems. Within the framework of the TESSA project, new SSA services for the Mediterranean Sea have been developed. In this paper we present SeaConditions, which is a web and mobile application for the provision of meteorological and oceanographic observation and forecasting products. Model forecasts and satellite products from operational services, such as ECMWF and CMEMS, can be visualized in SeaConditions. In addition, layers of information related to bathymetry, sea level and ocean-colour data (chl a and water transparency) are displayed. Ocean forecasts at high spatial resolutions are included in the version of SeaConditions presented here. SeaConditions provides a user-friendly experience with a fluid zoom capability, facilitating the appropriate display of data with different levels of detail. SeaConditions is a single point of access to interactive maps from different geophysical fields, providing high-quality information based on advanced oceanographic models. The SeaConditions services are available through both web and mobile applications. The web application is available at www.sea-conditions.com and is accessible and compatible with present-day browsers. Interoperability with GIS software is implemented. User feedback has been collected and taken into account in order to improve the service. The SeaConditions iOS and Android apps have been downloaded by more than 105 000 users to date (May 2016), and more than 100 000 users have visited the web version

Colorectal Cancer Stage at Diagnosis Before vs During the COVID-19 Pandemic in Italy

IMPORTANCE Delays in screening programs and the reluctance of patients to seek medical attention because of the outbreak of SARS-CoV-2 could be associated with the risk of more advanced colorectal cancers at diagnosis. OBJECTIVE To evaluate whether the SARS-CoV-2 pandemic was associated with more advanced oncologic stage and change in clinical presentation for patients with colorectal cancer. DESIGN, SETTING, AND PARTICIPANTS This retrospective, multicenter cohort study included all 17 938 adult patients who underwent surgery for colorectal cancer from March 1, 2020, to December 31, 2021 (pandemic period), and from January 1, 2018, to February 29, 2020 (prepandemic period), in 81 participating centers in Italy, including tertiary centers and community hospitals. Follow-up was 30 days from surgery. EXPOSURES Any type of surgical procedure for colorectal cancer, including explorative surgery, palliative procedures, and atypical or segmental resections. MAIN OUTCOMES AND MEASURES The primary outcome was advanced stage of colorectal cancer at diagnosis. Secondary outcomes were distant metastasis, T4 stage, aggressive biology (defined as cancer with at least 1 of the following characteristics: signet ring cells, mucinous tumor, budding, lymphovascular invasion, perineural invasion, and lymphangitis), stenotic lesion, emergency surgery, and palliative surgery. The independent association between the pandemic period and the outcomes was assessed using multivariate random-effects logistic regression, with hospital as the cluster variable. RESULTS A total of 17 938 patients (10 007 men [55.8%]; mean [SD] age, 70.6 [12.2] years) underwent surgery for colorectal cancer: 7796 (43.5%) during the pandemic period and 10 142 (56.5%) during the prepandemic period. Logistic regression indicated that the pandemic period was significantly associated with an increased rate of advanced-stage colorectal cancer (odds ratio [OR], 1.07; 95%CI, 1.01-1.13; P = .03), aggressive biology (OR, 1.32; 95%CI, 1.15-1.53; P < .001), and stenotic lesions (OR, 1.15; 95%CI, 1.01-1.31; P = .03). CONCLUSIONS AND RELEVANCE This cohort study suggests a significant association between the SARS-CoV-2 pandemic and the risk of a more advanced oncologic stage at diagnosis among patients undergoing surgery for colorectal cancer and might indicate a potential reduction of survival for these patients

Enhanced Natural Attenuation of Groundwater Cr(VI) Pollution Using Electron Donors: Yeast Extract vs. Polyhydroxybutyrate

Remediation interventions based on the native bacteria’s capability to reduce Cr(VI) represent a valid strategy in terms of economic and environmental sustainability. In this study, a bioremediation test was carried out using viable microcosms set with groundwater and deep soil (4:1), collected from the saturated zone of an industrial site in Southern Italy that was polluted by ~130 µg L−1 of Cr(VI). Conditions simulating the potential natural attenuation were compared to the enhanced natural attenuation induced by supplying yeast extract or polyhydroxybutyrate. Sterile controls were set up to study the possible Cr(VI) abiotic reduction. No pollution attenuation was detected in the unamended viable reactors, whereas yeast extract provided the complete Cr(VI) removal in 7 days, and polyhydroxybutyrate allowed ~70% pollutant removal after 21 days. The incomplete abiotic removal of Cr(VI) was observed in sterile reactors amended with yeast extract, thus suggesting the essential role of native bacteria in Cr(VI) remediation. This was in accordance with the results of Pearson’s coefficient test, which revealed that Cr(VI) removal was positively correlated with microbial proliferation (n = 0.724), and also negatively correlated with pH (n = −0.646), dissolved oxygen (n = −0.828) and nitrate (n = −0.940). The relationships between the Cr(VI) removal and other monitored parameters were investigated by principal component analysis, which explained 76.71% of the total variance

Optimized protocol proposal to extract eDNA from oligotrophic and degraded water samples

Aquifer represents an oligotrophic environment that sustains a relatively small amount of microbial cells, mostly non-culturable. Due to this dominance of unculturable microorganisms in natural ecosystems, studying microbial communities and their functionality should include culture-independent approaches based on molecular techniques using DNA analysis (Purswani et al. 2011). For practical reasons, aquifer routine analyses focus on groundwater samples, while solid aquifer samples are typically not included (Ritalahti et al. 2010). The amount of groundwater collected, together with the types and concentrations of inhibitory compounds if present, determine the abundance of the target biomarker(s) available for subsequent analyses. Hence, filtering large volumes of groundwater seems beneficial, but for practical purposes, 0.5–2 L of water are typically collected, depending on groundwater characteristics (Ritalahti et al. 2010).In this work, environmental DNA (eDNA) was extracted from groundwater samples, filtering three different initial volumes (1000 ml, 500 ml, and 250 ml) of water samples, using 0.22 µm membranes. Also, two DNA extraction commercial kits were tested, DNeasy PowerWater Kit and DNeasy PowerSoil kit (Qiagen, Germantown, MD) specific for water samples and solid matrix, respectively.For DNeasy PowerWater Kit the standard protocol was carried out, whereas a modified protocol equipped with the Inhibitor Removal Technology® (IRT) was selected for testing DNeasy PowerSoil kit. In order to minimize operator bias, both the protocols were made semi-automated by using a QIAcube provided by Qiagen for genomic DNA extraction. Additional steps to the PowerSoil IRT protocol were performed for optimizing chemical and mechanical cell lysis processes and facilitating the sample dispersion into the buffer solutions. eDNA was verified via electrophoresis and quantified fluorometrically. eDNA extracted from 250 ml of groundwater sample using the DNeasy PowerSoil kit with modified IRT protocol was also tested in downstream applications, including Polymerase Chain Reactions (PCRs) with specific primer pairs for the identification of microbial targets.Results suggest that the PowerSoil modified IRT protocol was the best performing one, allowing a higher eDNA yield from all the water sample volumes tested. In addition, plotting on a graph eDNA concentration values against sample volumes filtered, the yield of PowerSoil modified IRT protocol appeared more similar to an ideal direct proportionality than the yield of PowerWater standard protocol. eDNA quality was suitable for PCR analyses and the identification of bacterial targets, including bacterial subgroups (α and β-proteobacteria) and single species of interest, such as Shewanella oneidensis capable of hexavalent chromium reduction (Tumolo et al. 2020). Under these good performances, the PowerSoil optimized IRT protocol was also applied in a further experiment about bioremediation to extract eDNA from 50 ml of water spiked with 1000 µg/l of hexavalent chromium. The resulting genomic material was successfully used in quantitative PCR (qPCR) assays for monitoring the relative abundance of Shewanella oneidensis during the bioremediation process, allowing to highlight the hexavalent chromium inhibitor effect on the selected microbial target (Ancona et al. 2020).Downstream applications of eDNA obtained using DNeasy PowerSoil kit resulted in positive outcomes for both the experiments previously described. In light of this, it is possible to conclude that this kit combined with the protocol adjustments proposed in this work, can be a performing tool for eDNA extraction, also from small amounts of water sample collected from oligotrophic or degraded environments.Further investigations will be oriented to optimize eDNA extraction from the aquifer solid portion characterized by few nutrients and microbial cells to better understand how microbial populations can distribute themselves between solid and aqueous phases

Protection of Water Resources from Agriculture Pollution: An Integrated Methodological Approach for the Nitrates Directive 91–676-EEC Implementation

Nitrogen is a vital nutrient helpful to plants and crop growth. However, among the leading causes of water resources pollution is the excess nitrogen from agricultural sources. In European Union countries, the Nitrates Directive has been approved to reduce this problem monitoring of water bodies with regard to nitrate concentrations, designation of Nitrate Vulnerable Zones (NVZs), and establishing codes of good agricultural practices and measures to prevent and reduce water pollution from nitrates. In light of this, we propose an integrated methodological approach to better manage a environmental issue as the perimeter of NVZs with the prospective that our approach could be used in the future by other member states representing a Best Practice in that direction. The methodology is based on data integration applied in a GIS environment. Different available data representing the knowledge of the territory were harmonised, systematised and georeferenced, in order to increase the environmental framework, preserve the contamination of the water resource and give indications on the measures to be implemented to apply in the best way possible the Nitrates Directive. Finally, it was also possible to overcome the infringement procedure in progress for Italy and the Puglia region and proceed to new designation of NVZs

Evaluating the Influence of Nitrogen Fertilizers and Biochar on Brassica oleracea L. var. botrytis by the Use of Fourier Transform Infrared (FTIR) Spectroscopy

The exponential growth of the human population requires an increasing application of nitrogen (N) fertilizers, causing environmental pollution. Biochar (B) amended soil has been suggested as a sustainable agricultural practice to improve crop yield and mitigate agricultural pollutants’ contamination. Evaluating the effect of fertilization on Brassica crops, in combination with spectral analysis, may specify changes in the chemical composition of the vegetable as a result of N fertilization. This study characterized cauliflower tissues treated with N fertilizer and biochar, employing Fourier Transform Infrared spectroscopy. The experiment was conducted in cauliflower mesocosms treated with two doses of N fertilizer (130 and 260 kg N ha−1) with or without B. Attenuated total reflectance fractions were used to characterize fractions of curds, leaves, stems, and roots in the infrared using a Fourier transform. Principal component analysis was performed to classify the main differences among cauliflower tissues concerning treatments. FTIR spectra of Brassica oleracea L. var. botrytis tissues were related to nitrogen-based agricultural practices. The specific molecules associated with functional groups in cauliflower tissues were phenols, amides, proteins, amines, and glucosinolates. Biochar amended soil resulted in higher peaks that correspond to the stretching of phenols and proteins. The application of sustainable nitrogen fertilizers might influence the absorption bands characteristic of cauliflower’s typical metabolites. The research allows the identification of Brassicaceae’s functional molecules with a potential agronomic application

Validation of bacterial markers to discriminate against the source of nitrate contamination: a promising application within the EU Nitrates Directive

The European Community (EC) Nitrates Directive (ND) (Council Directive 1991/676/EEC) aims to avoid water pollution by nitrates from poor farming practices. Under the ND, Nitrate Vulnerable Zones (NVZs) have been defined as areas where the concentration of agricultural nitrates in surface or groundwater exceeds 50 mg/L. Groundwater is one of the main sources of drinking water in Europe, so ensuring its quality is of significant importance. Monitoring of water parameters, the identification of pollution, the development of good agricultural practice codes is included in ND as measures and action programs. ND provides for the attribution of areas affected by nitrate pollution to the NVZ in which farmers must comply with measures necessary to reduce nitrogen in excess and protect the quality of environmental matrices.However, in some cases the quality of water bodies remains poor, suggesting that some action measures are ineffective or need improvements. Nevertheless, nitrates in excess in groundwater might be related to industrial inputs, untreated waste discharge, and sewage spilling. Due to this, identifying non-agricultural contributions to nitrate groundwater pollution can be of great interest. With this aim, the employment of biomarkers such as microbes associated with the intestinal tract of a specific host is under study for identifying fecal pollution.This strategy is known, in scientific literature, as Microbial Source Tracking (MST)(Furtula et al. 2011)The amplification of 16S rRNA genes of host-specific Bacteroidales allows discriminating against human and livestock fecal sources in samples from nitrate polluted environment.The aim of this work is to evaluate the sensitivity and specificity of these intestinal biomarkers in groundwater samples collected along with the Apulian Region (Southern Italy) in order to assess the applicability of the MST in the employ of ND. A preliminary study was carried out to validate the performance of seven markers for MST using two different approaches: Polimerase Chain Reaction (PCR) and quantitative Real-time PCR (qPCR) assays. For both PCR and qPCR experiments selected primer sets were checked using fecal samples of known origin as positive controls. PCR assay was used for human (HF74 and Enterococcus faecalis) (Bernhard and Field 2000, Jackson et al. 2004), cattle (CF123) (Bernhard and Field 2000), equine (HoF597) (Dick et al. 2005), and pig (Pig163) (Dick et al. 2005) markers screening. Two additional markers were tested through Real-time PCR: human (Human- Bacteroides) (Seurinck et al. 2005) and zootechnical (BacPre I) (Kobayashi et al. 2012).The results indicate that biomarkers can be considered reliable in distinguishing human from animal pollution. Nevertheless, our studies show that the tests conducted with the human Enterococcus faecalis biomarker do not discriminate the zootechnical source from the human one. In some cases, PCR-tested biomarkers cannot determine the source of contamination in environmental matrices due to the detection limit. Animal and human fecal markers were widely detected on eleven groundwater samples through Real Time PCR, highlighting the prevalent source of contamination in the environmental matrix.This research provides evidence that MST technology is a valid tool for local authorities to identify the source of nitrate contamination and review uncertainties during the NVZs definition and the action program development required by the European Nitrate Directive

Enhancement of Chromium (VI) Reduction in Microcosms Amended with Lactate or Yeast Extract: A Laboratory-Scale Study

A laboratory-scale study was carried out to evaluate the groundwater bioremediation potential of hexavalent chromium (Cr(VI)), taking into account the chromate pollution of an industrial site located in Southern Italy (Apulia Region). The reduction of Cr(VI) was studied on laboratory microcosms, set up in different experimental conditions, namely: ABIO (soil and water sterilized), BIO (soil and water not sterilized), LATT (with the addition of lactate), and YE (with the addition of yeast extract). Control test lines, set up by using sterilized matrices and amendments, were employed to assess the occurrence of the pollutant reduction via chemical processes. By combining molecular (microbial abundance, specific chromate reductase genes (ChR) and the Shewanella oinedensis bacterial strain) with chemical analyses of chromium (VI and III) in the matrices (water and soil) of each microcosm, it was possible to investigate the response of microbial populations to different experimental conditions, and therefore, to assess their bioremediation capability in promoting Cr(VI) reduction. The overall results achieved within this work evidenced the key role of amendments (lactate and yeast extract) in enhancing the biological reduction of hexavalent chromium in the contaminated aqueous phase of laboratory microcosms. The highest value of Cr(VI) removal (99.47%) was obtained in the YE amended microcosms at seven days

Use of Biochar to Improve the Sustainable Crop Production of Cauliflower (<i>Brassica oleracea</i> L.)

In agriculture, biochar (B) application has been suggested as a green technology to reduce nitrate pollution from agricultural origins and improve crop yield. The agronomic impact of B use on soil has been extensively studied, while knowledge of its possible effects on horticultural cultivation is still scarce. A greenhouse experiment was conducted to evaluate the effect of using biochar in soils treated with two different rates of nitrogen fertilizers on soil properties and nitrogen (N) leachate. This study also investigated the vegetative parameters during the crop growing season of Brassica oleracea L. var. botrytis. Soil mesocosms were set up to test the following treatments: untreated/control (C); normal dose of N fertilizer (130 kg N ha−1) (ND); ND+B; high dose of N fertilizer (260 kg N ha−1) (HD); and HD+B. Principal component analysis and cluster analysis were exploited to assess biochar’s ability to reduce nitrate leaching and enhance soil–vegetative properties. Biochar addition affected the soil chemical properties of the fertilized microcosms (ND and HD). Biochar increased the NH4+ content in HD soil and the NO3− content in ND soil by 26 mg/L and 48.76 mg/L, respectively. The results showed that biochar application increased the marketable cauliflower yield. In ND+B and HD+B, the curd weight was 880.68 kg and 1097.60 kg, respectively. In addition, a small number of nitrogenous compounds in the leachate were quantified in experimental lines with the biochar. Therefore, biochar use improves the marketable yield of horticulture, mitigating the negative impacts associated with the mass use of N fertilizers in agriculture