Managing the Second Year of Your PHD: Data Collection and Upgrading from an MPhil to a PhD

Your PhD typically takes the following course: Getting to grips with the literature and necessary research skills in the first year, conversion to PhD status and data collection in the second year and third year dedicated to writing up the thesis. This article aims to provide guidance and information for the crucial second year

Predicting soil moisture conditions for arable free draining soils in Ireland under spring cereal crop production

peer-reviewedTemporal prediction of soil moisture and evapotranspiration has a crucial role in agricultural and environmental management. A lack of Irish models for predicting evapotranspiration and soil moisture conditions for arable soils still represents a knowledge gap in this particular area of Irish agro-climatic modelling. The soil moisture deficit (SMD) crop model presented in this paper is based on the SMD hybrid model for Irish grassland (Schulte et al., 2005). Crop and site specific components (free-draining soil) have been integrated in the new model, which was calibrated and tested using soil tension measurements from two experimental sites located on a well-drained soil under spring barley cultivation in south-eastern Ireland. Calibration of the model gave an R2 of 0.71 for the relationship between predicted SMD and measured soil tension, while model testing yielded R2 values of 0.67 and 0.65 (two sites). The crop model presented here is designed to predict soil moisture conditions and effective drainage (i.e., leaching events). The model provided reasonable predictions of soil moisture conditions and effective drainage within its boundaries, i.e., free-draining land used for spring cereal production under Irish conditions. In general, the model is simple and practical due to the small number of required input parameters, and due to model outputs that have good practical applicability, such as for computing the cumulative amount of watersoluble nutrients leached from arable land under spring cereals in free-draining soils

Determination and Occurrence of Phenoxyacetic Acid Herbicides and Their Transformation Products in Groundwater Using Ultra High Performance Liquid Chromatography Coupled to Tandem Mass Spectrometry

This research is funded by the National Development Plan, through the Research Stimulus Fund, administered by the Department of Agriculture, Food and Marine (RS-544) and the Teagasc Walsh Fellowship Scheme.peer-reviewedA sensitive method was developed and validated for ten phenoxyacetic acid herbicides, six of their main transformation products (TPs) and two benzonitrile TPs in groundwater. The parent compounds mecoprop, mecoprop-p, 2,4-D, dicamba, MCPA, triclopyr, fluroxypr, bromoxynil, bentazone, and 2,3,6-trichlorobenzoic acid (TBA) are included and a selection of their main TPs: phenoxyacetic acid (PAC), 2,4,5-trichloro-phenol (TCP), 4-chloro-2-methylphenol (4C2MP), 2,4-dichlorophenol (DCP), 3,5,6-trichloro-2-pyridinol (T2P), and 3,5-dibromo-4-hydroxybenzoic acid (BrAC), as well as the dichlobenil TPs 2,6-dichlorobenzamide (BAM) and 3,5-dichlorobenzoic acid (DBA) which have never before been determined in Irish groundwater. Water samples were analysed using an efficient ultra-high performance liquid chromatography (UHPLC) method in an 11.9 min separation time prior to detection by tandem mass spectrometry (MS/MS). The limit of detection (LOD) of the method ranged between 0.00008 and 0.0047 µg·L−1 for the 18 analytes. All compounds could be detected below the permitted limits of 0.1 µg·L−1 allowed in the European Union (EU) drinking water legislation [1]. The method was validated according to EU protocols laid out in SANCO/10232/2006 with recoveries ranging between 71% and 118% at the spiked concentration level of 0.06 µg·L−1. The method was successfully applied to 42 groundwater samples collected across several locations in Ireland in March 2012 to reveal that the TPs PAC and 4C2MP were detected just as often as their parent active ingredients (a.i.) in groundwater

Leaching of N compounds from swards used for dairying that are N based and irrigated with dirty water/slurry.

End of Project ReportA study was carried out to investigate nitrate leaching on a dairy farm in Co. Cork. The farm had a history of high nitrate-N in borehole waters and the study aimed to elucidate the causative factors for this. Physical and chemical data regarding the soils, the hydrology, and the N input/output balances were determined and collated. Results showed that nitrate-N concentrations > the EU maximum allowable concentration (MAC) of 11.3 mg/l for drinking water occurred in soil drainage from the light textured soils studied due to a large imbalance between N inputs and outputs. High fertiliser N usage, animal manure and dirty water applications, atmospheric N depositions and soil organic N mineralisation in combination produced these results . While it is recognised that nitrate leaching will vary in amount from year to year the lessons from the study are clear - light textured soils that are used for intensive dairying and which receive high inputs of N are prone to release drainage water high in nitrate.European Union Structural Funds (EAGGF

Mustard catch crop enhances denitrification in shallow groundwater beneath a spring barley field

The study was funded by Department of Agriculture and Food through the Research Stimulus Fund Programme (Grant RSF 06383) in collaboration with the Department of Civil, Structural & Environmental Engineering, Trinity College Dublin, Ireland.peer-reviewedOver-winter green cover crops have been reported to increase dissolved organic carbon (DOC) concentrations in groundwater, which can be used as an energy source for denitrifiers. This study investigates the impact of a mustard catch crop on in situ denitrification and nitrous oxide (N2O) emissions from an aquifer overlain by arable land. Denitrification rates and N2O-N/(N2O-N + N2-N) mole fractions were measured in situ with a push–pull method in shallow groundwater under a spring barley system in experimental plots with and without a mustard cover crop. The results suggest that a mustard cover crop could substantially enhance reduction of groundwater nitrate NO3--N via denitrification without significantly increasing N2O emissions. Mean total denitrification (TDN) rates below mustard cover crop and no cover crop were 7.61 and 0.002 μg kg−1 d−1, respectively. Estimated N2O-N/(N2O-N + N2-N) ratios, being 0.001 and 1.0 below mustard cover crop and no cover crop respectively, indicate that denitrification below mustard cover crop reduces N2O to N2, unlike the plot with no cover crop. The observed enhanced denitrification under the mustard cover crop may result from the higher groundwater DOC under mustard cover crop (1.53 mg L−1) than no cover crop (0.90 mg L−1) being added by the root exudates and root masses of mustard. This study gives insights into the missing piece in agricultural nitrogen (N) balance and groundwater derived N2O emissions under arable land and thus helps minimise the uncertainty in agricultural N and N2O-N balances

Simplifying and improving the extraction of nitrate from freshwater for stable isotope analyses

Determining the isotopic composition of nitrate (NO3_) in water can prove useful to identify NO3_ sources and to understand its dynamics in aquatic systems. Among the procedures available, the ‘ionexchange resin method’ involves extracting NO3_ from freshwater and converting it into solid silver nitrate (AgNO3), which is then analysed for 15N/14N and 18O/16O ratios. This study describes a simplified methodology where water was not pre-treated to remove dissolved organic carbon (DOC) or barium cations (added to precipitate O-bearing contaminants), which suited samples with high NO3_ ($400 mM or 25 mg L_1 NO3_) and low DOC (typically <417 mM of C or 5 mg L_1 C) levels. % N analysis revealed that a few AgNO3 samples were of low purity (compared with expected % N of 8.2), highlighting the necessity to introduce quality control/quality assurance procedures for silver nitrate prepared from field water samples. Recommendations are then made to monitor % N together with % O (expected at 28.6, i.e. 3.5 fold % N) in AgNO3 in order to better assess the type and gravity of the contamination as well as to identify potentially unreliable data

In situ denitrification rates in shallow groundwater beneath a springbarley - mustard cover crop system

Abstract of Conference poster presentatio

Groundwater nitrate reduction versus dissolved gas production: A tale of two catchments

peer-reviewedAt the catchment scale, a complex mosaic of environmental, hydrogeological and physicochemical characteristics combine to regulate the distribution of groundwater and stream nitrate (NO3−). The efficiency of NO3− removal (via denitrification) versus the ratio of accumulated reaction products, dinitrogen (excess N2) & nitrous oxide (N2O), remains poorly understood. Groundwater was investigated in two well drained agricultural catchments (10 km2) in Ireland with contrasting subsurface lithologies (sandstone vs. slate) and landuse. Denitrification capacity was assessed by measuring concentration and distribution patterns of nitrogen (N) species, aquifer hydrogeochemistry, stable isotope signatures and aquifer hydraulic properties. A hierarchy of scale whereby physical factors including agronomy, water table elevation and permeability determined the hydrogeochemical signature of the aquifers was observed. This hydrogeochemical signature acted as the dominant control on denitrification reaction progress. High permeability, aerobic conditions and a lack of bacterial energy sources in the slate catchment resulted in low denitrification reaction progress (0–32%), high NO3− and comparatively low N2O emission factors (EF5g1). In the sandstone catchment denitrification progress ranged from 4 to 94% and was highly dependent on permeability, water table elevation, dissolved oxygen concentration solid phase bacterial energy sources. Denitrification of NO3 − to N2 occurred in anaerobic conditions, while at intermediate dissolved oxygen; N2O was the dominant reaction product. EF5g1 (mean: 0.0018) in the denitrifying sandstone catchment was 32% less than the IPCC default. The denitrification observations across catchments were supported by stable isotope signatures. Stream NO3− occurrence was 32% lower in the sandstone catchment even though N loading was substantially higher than the slate catchment.Teagasc Walsh Fellowship Programm

Prognostic significance of serum inflammatory markers in esophageal cancer

Background The aim of this study was to assess the relative prognostic value of biomarkers to measure the systemic inflammatory response (SIR) and potentially improve prognostic modeling in patients undergoing potentially curative surgery for esophageal adenocarcinoma (EC). Methods Consecutive 330 patients undergoing surgery for EC between 2004 and 2018 within a regional UK cancer network were identified. Serum measurements of haemoglobin, C-reactive protein, albumin, modified Glasgow Prognostic Score (mGPS), and differential neutrophil to lymphocyte ratio (NLR) were obtained before surgery, and correlated with histopathological factors and outcomes. Primary outcome measures were disease-free (DFS) and overall survival (OS). Results Of 330 OC patients, 294 underwent potentially curative esophagectomy. Univariable DFS analysis revealed pT, pN, pTNM stage (all p < 0.001), poor differentiation (p = 0.001), vascular invasion (p < 0.001), R1 status (p < 0.001), perioperative chemotherapy (p = 0.009), CRP (p = 0.010), mGPS (p = 0.011), and NLR (p < 0.001), were all associated with poor survival. Multivariable Cox regression analysis of DFS revealed only NLR [Hazard Ratio (HR) 3.63, 95% Confidence Interval (CI) 2.11–6.24, p < 0.001] retained significance. Multivariable Cox regression analysis of OS revealed similar findings: NLR [HR 2.66, (95% CI 1.58–4.50), p < 0.001]. Conclusion NLR is an important SIR prognostic biomarker associated with DFS and OS in EC

Triazacyclohexane Chromium Triflate Complexes as Precursors for the Catalytic Selective Olefin Trimerisation and its Investigation by Mass Spectrometry

A novel set of linear α-olefin trimerisation pre-catalysts is presented. The R3TACCr(OTf)3 (R3TAC = 1,3,5-trialkyl-1,3,5-triazacyclohexane) complexes produce an active system after facile activation with less than 10 equivalents of trialkylaluminium. Isomerisation was observed in many cases, which is proposed to occur via the π-allyl complex mechanism, though this was minimised by optimisation of the reaction conditions. The pre-catalysts can be synthesised from R3TACCrCl3 in neat TfOH or by addition of R3TAC to Cr(OTf)3 or better Cr(OTf)3(THF)3, the synthesis and structure of which is presented here. The use of this highly defined system allowed the identification of 2-methyl-1-hexene as a side product of activation with AlMe3, in agreement with the proposed metallacyclic mechanism. Isomer distribution of the trimer product is similar to R3TACCrCl3/MAO activated systems and depends mostly on the ligand substituent R. ESI mass spectrometry of an ortho-difluorobenzene solution of the activated catalyst was analysed at different stages of reaction. A series of signals was observed that matched those expected for cationic chromium species predicted by the metallacyclic mechanism. In particular, [R3TACCrMe2]+ was observed to form immediately after alkylation with AlMe3, while [R3TACCr(olefin)n]+ (n = 0, 1, 2, 3, 4 and olefin = 1-hexene or 1-octene) formed after addition of 1-hexene. Absence of any detected tetramer and observation of [R3TACCr(olefin)4]+ leads to the conclusion that a metallacycloheptane-olefin complex may lead to β-H abstraction rather than insertion and may even be required to avoid formation of [R3TACCr(olefin)1]+ which is observed in only very small amounts indicating a low stability. Chromium(I) complexes [R3TACCr(arene)]+ with the arene solvent can also be observed and their signal intensity indicate a relative stability of o-C6H4F2 &lt; cymene &lt; benzene &lt; PhF, toluene &lt; p-xylene