All Washed Out? Foliar Nutrient Resorption and Leaching in Senescing Switchgrass

Ideal bioenergy feedstocks are low in nutrients that act as anti-quality factors during conversion processes. Research has shown that delaying harvest of temperate perennial grasses until late winter reduces nutrient content, primarily due to end-season resorption, but also indicates a role for foliar nutrient leaching. While end-season resorption has been estimated, foliar nutrient leaching has not, and is a factor that could refine harvest recommendations. Additionally, establishing a baseline of mineral loss during switchgrass senescence will improve our understanding of leaf-level nutrient resorption. Therefore, we applied simulated rainfall to replicated (n = 5) plots within a previously established switchgrass stand to determine if heavy precipitation can induce nutrient leaching in senescing, unharvested foliage. Hour-long simulated rainfalls of ∼120 mm were applied every 2 weeks from early September to a killing frost in 2014 and 2015. Leaf samples were taken from the upper and lower canopy before and after simulated rainfalls and from no-rain controls and analyzed for elemental N, P, K, S, Mg, and Ca. Nutrient resorption estimates ranged from 33 to 82% in control plots. Comparison of rainfall plots to controls indicated that lower canopy leaves, upon reaching ≥50% senescence, were slightly susceptible to foliar nutrient leaching, with losses ranging from 0.3 to 2.8 g kg−1dry matter for K, P, and Mg. Nitrogen, Ca, and S were not susceptible to foliar leaching. Although statistically significant (P ≤ 0.05), these values suggested that foliar leaching was not a strong driver of nutrient loss during senescence

Survival outcomes and interval between lymphoscintigraphy and SLNB in cutaneous melanoma- findings of a large prospective cohort study

Introduction: Sentinel lymph node biopsy (SLNB) in cutaneous melanoma (CM) is performed to identify patient at risk of regional and distant relapse. We hypothesized that timing of lymphoscintigraphy may influence the accuracy of SLNB and patient outcomes. Methods: We reviewed prospective data on patients undergoing SLNB for CM at a large university cancer-center between 2008-2015, examining patient and tumor demographics and time between lymphoscintigraphy (LS) and SLNB. Kaplan-Meier survival analysis assessed disease-specific (DSS) and overall-survival (OS), stratified by timing of LS. Cox multivariate regression analysis assessed independent risk factors for survival. Results: We identified 1015 patients. Median follow-up was 45 months (IQR 26-68 months). Univariate analysis showed a 6.8% absolute DSS (HR 1.6 [1.03-2.48], p= 0.04) benefit and a 10.7% absolute OS (HR 1.64 [1.13-2.38], p=0.01) benefit for patients whose SLNB was performed 12 hours (n=652). Multivariate analysis identified timing of LS as an independent predictor of OS (p=0.007) and DSS (p=0.016) when competing with age, sex, Breslow thickness (BT) and SLN status. No difference in nodal relapse rates (5.2% v 4.6%; p=0.67) was seen. Both groups were matched for age, sex, BT and SLN status. Conclusion: These data have significant implications for SLNB services, suggesting delaying SLNB >12 hours after LS using a Tc99-labelled nanocolloid has a significant negative survival impact for patients and should be avoided. We hypothesise that temporal tracer migration is the underlying cause and advocate further trials investigating alternative, 'stable' tracer-agents

A feasibility study of indocyanine green fluorescence mapping for sentinel lymph node detection in cutaneous melanoma

Objectives: Sentinel lymph node biopsy (SLNB) is standard of care for staging regional LN in AJCC stage IB-IIC melanoma; using dual localization with radiolabelled colloid and blue dye. Combining these gives optimal accuracy; drawbacks include cumulative radiation exposure for healthcare workers, coordination between disciplines and anaphylaxis. An alternative tracer agent is indocyanine green (ICG); an optical enhancer that fluoresces in the near infrared range. This prospective cohort study assesses the feasibility of using ICG as a tracer agent to detect SLN in cutaneous melanoma. Methods: Primary melanoma patients diagnosed with pT1b-pT4b tumours undergoing SLNB were recruited over a 6-month period at a tertiary referral centre. All underwent standard preoperative lymphoscintigraphy (LSG) using 20-40MBq of Tc99radiolabelled nanocolloid plus intraoperative Patent Blue dye (PBD). ICG was administered as a third tracer agent intraoperatively. Results: 62 patients (33M/29F) were recruited; median age was 61 years. Median melanoma Breslow thickness was 1.6mm. 144 specimens containing 135 SLN were excised. Concordance rate for all 3 tracer agents was 88.1%(119/135 LN); that for radioisotope/PBD was 88.2%(95%CI:82.2,93.7). There were no discordance pairs between radioisotope/PBD compared to radioisotope/PBD/ICG. Radioisotope/ICG significantly increased the sensitivity of detecting SLN to 98.5%(95%CI:94.8,99.8); p<0.00001 compared to radioisotope/PBD. Concordance rate of intraoperative ICG drainage pattern with LSG was 22.6%. Conclusion: ICG utilization showed comparable sensitivity with gold standard. Technical challenges e.g. ICG leakage into biopsy field, poor concordance with LSG limits its efficacy in melanoma SLNB. We therefore do not recommend replacing current practice with ICG alone or by using a combination with TC99

The oxygen isotopic composition of phosphate in river water and its potential sources in the Upper River Taw catchment, UK

The need to reduce both point and diffuse phosphorus pollution to aquatic ecosystems is widely recognised and in order to achieve this, identification of the different pollutant sources is essential. Recently, a stable isotope approach using oxygen isotopes within phosphate (δ18OPO4) has been used in phosphorus source tracing studies. This approach was applied in a one-off survey in September 2013 to the River Taw catchment in south-west England where elevated levels of phosphate have been reported. River water δ18OPO4 along the main channel varied little, ranging from + 17.1 to + 18.8‰. This was no > 0.3‰ different to that of the isotopic equilibrium with water (Eδ18OPO4). The δ18OPO4 in the tributaries was more variable (+ 17.1 to + 18.8‰), but only deviated from Eδ18OPO4 by between 0.4 and 0.9‰. Several potential phosphate sources within the catchment were sampled and most had a narrow range of δ18OPO4 values similar to that of river Eδ18OPO4. Discharge from two waste water treatment plants had different and distinct δ18OPO4 from one another ranging between + 16.4 and + 19.6‰ and similar values to that of a dairy factory final effluent (+ 16.5 to + 17.8‰), mains tap water (+ 17.8 to + 18.4‰), and that of the phosphate extracted from river channel bed sediment (+ 16.7 to + 17.6‰). Inorganic fertilizers had a wide range of values (+ 13.3 to + 25.9‰) while stored animal wastes were consistently lower (+ 12.0 to + 15.0‰) than most other sources and Eδ18OPO4. The distinct signals from the waste water treatment plants were lost within the river over a short distance suggesting that rapid microbial cycling of phosphate was occurring, because microbial cycling shifts the isotopic signal towards Eδ18OPO4. This study has added to the global inventory of phosphate source δ18OPO4 values, but also demonstrated the limitations of this approach to identifying phosphate sources, especially at times when microbial cycling is high

Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes.

Methods to deconvolve single-cell RNA-sequencing (scRNA-seq) data are necessary for samples containing a mixture of genotypes, whether they are natural or experimentally combined. Multiplexing across donors is a popular experimental design that can avoid batch effects, reduce costs and improve doublet detection. By using variants detected in scRNA-seq reads, it is possible to assign cells to their donor of origin and identify cross-genotype doublets that may have highly similar transcriptional profiles, precluding detection by transcriptional profile. More subtle cross-genotype variant contamination can be used to estimate the amount of ambient RNA. Ambient RNA is caused by cell lysis before droplet partitioning and is an important confounder of scRNA-seq analysis. Here we develop souporcell, a method to cluster cells using the genetic variants detected within the scRNA-seq reads. We show that it achieves high accuracy on genotype clustering, doublet detection and ambient RNA estimation, as demonstrated across a range of challenging scenarios.We acknowledge the Wellcome Sanger Institute’s DNA Pipelines for construction of the 10x sequencing libraries. We thank Allan Muhwezi and Andrew Russell for assistance with parasite culture and 10x Single-cell 3’ RNA-seq respectively. In addition, we would like to thank Matthew Young for useful conversations about ambient RNA, Mirjana Efremova for providing information about the maternal/fetal data, and Katie Gray for assistance in interpreting the previously unannotated cluster. The Wellcome Sanger Institute is funded by the Wellcome Trust (grant 206194/Z/17/Z), which supports MKNL and MH. This work was supported by an MRC Career Development Award (G1100339) to MKNL. We would like to acknowledge the Wellcome Trust Sanger Institute as the source of the human induced pluripotent cell lines that were generated under the Human Induced Pluripotent Stem Cell Initiative funded by a grant from the Wellcome Trust and Medical Research Council, supported by the Wellcome Trust (WT098051) and the NIHR/Wellcome Trust Clinical Research Facility, and acknowledges Life Science Technologies Corporation as the provider of Cytotune (HipSci.org). The Cardiovascular Epidemiology Unit is supported by core funding from the UK Medical Research Council (MR/L003120/1), the British Heart Foundation (RG/13/13/30194; RG/18/13/33946) and the National Institute for Health Research [Cambridge Biomedical Research Centre at the Cambridge University Hospital’s NHS Foundation Trust]. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health and Social Care

Formaldehyde Densitometry of Galactic Star-Forming Regions Using the H2CO 3(12)-3(13) and 4(13)-4(14) Transitions

We present Green Bank Telescope (GBT) observations of the 3(12)-3(13) (29 GHz) and 4(13)-4(14) (48 GHz) transitions of the H2CO molecule toward a sample of 23 well-studied star-forming regions. Analysis of the relative intensities of these transitions can be used to reliably measure the densities of molecular cores. Adopting kinetic temperatures from the literature, we have employed a Large Velocity Gradient (LVG) model to derive the average hydrogen number density [n(H2)] within a 16 arcsecond beam toward each source. Densities in the range of 10^{5.5}--10^{6.5} cm^{-3} and ortho-formaldehyde column densities per unit line width between 10^{13.5} and 10^{14.5} cm^{-2} (km s^{-1})^{-1} are found for most objects, in general agreement with existing measurements. A detailed analysis of the advantages and limitations to this densitometry technique is also presented. We find that H2CO 3(12)-3(13)/4(13)-4(14) densitometry proves to be best suited to objects with T_K >~ 100 K, above which the H2CO LVG models become relatively independent of kinetic temperature. This study represents the first detection of these H2CO K-doublet transitions in all but one object in our sample. The ease with which these transitions were detected, coupled with their unique sensitivity to spatial density, make them excellent monitors of density in molecular clouds for future experiments. We also report the detection of the 9_2--8_1 A^- (29 GHz) transition of CH3OH toward 6 sources.Comment: 17 pages; 6 figures; Accepted by Ap

Improved perioperative seroma and complication rates following the application of a 2-layer negative pressure wound therapy system after inguinal lymphadenectomy for metastatic cutaneous melanoma

Background: Perioperative complications following inguinal lymphadenectomy, including seroma formation, are frequent. We have employed a 2-layer negative pressure wound therapy (2-LNPWT) as a method to reduce seroma rate and perioperative complications. We present the outcome of our initial experience with 2-LNPWT and compare the outcomes of its use with traditional closed suction drains (CSDs).  Materials and methods: A non-randomised retrospective case–control series was analysed. Surgeons performing inguinal lymphadenectomy for metastatic cutaneous melanoma utilised either the 2-LNPWT therapy or traditional CSDs according to their practice preference.  Results: The study included 111 patients. The cohorts were well matched for gender, disease burden, body mass index and comorbidities. The 2-LNPWT technique was associated with significantly better postoperative outcomes than CSD, in terms of incidence of seroma formation (26.9% vs 49.4%; p < 0.03), period of drainage (15 days vs 20 days; p = 0.005) and return to theatre rate (0% vs 15.3%; p = 0.03). The overall seroma rate was 44.1%. The only significant association with seroma initiation was the type of drainage system used (2-LNPWT 31.2% vs CSD 58.3%; p < 0.03; OR 3.0). The method of drainage did not alter the course of an established seroma. There was no significant difference in overall or disease-specific survival detected between the 2 groups.  Conclusion: This retrospective non-randomised case control study has demonstrated the safe use of a novel application of negative pressure wound therapy that significantly reduced the incidence of seroma formation and postoperative complication rate for inguinal lymphadenectomy for melanoma