A Quantitative Real-Time PCR Method to Detect the Quinoa Downy Mildew Pathogen, Peronospora variabilis.

Quinoa downy mildew, caused by Peronospora variabilis, is the most devastating disease of quinoa globally. Rapid, sensitive diagnostic methods are needed to detect and quantify this pathogen in seeds and plant tissue. A hydrolysis probe-based quantitative real-time PCR (qPCR) assay including a competitive internal control was developed for P. variabilis detection. This assay could detect as low as 20 ag of DNA or approximately 25 internal transcribed spacer (ITS) copies per reaction with efficiencies ranging from 93.9 to 98.2%. No nontarget amplification was observed when tested against DNA from other downy mildew pathogens and related oomycetes. P. variabilis strains from multiple countries were detected using this assay. The assay was successfully applied to quantify the pathogen in quinoa seeds from a field trial conducted in the state of Washington. Downy mildew disease was recorded on all 14 genotypes, with the genotypes 104.88 and 106.49 recording the highest area under the disease progress curve values (mean ± SE; 3,236 ± 303 and 2,851 ± 198, respectively) and J6 and Dutchess recording the lowest (441 ± 107 and 409 ± 129, respectively). Seed washes obtained from field samples were subjected to the qPCR assay, and the pathogen was detected in all samples. The highest pathogen ITS copy number was recorded with 106.49 (194,934 ± 38,171), and the lowest was observed in Pasto (5,971 ± 1,435) and Riobamba (9,954 ± 4,243). This qPCR assay could lead to improved detection and quantification of P. variabilis as well as increased understanding of quinoa-P. variabilis interactions and epidemiology.

A Quantitative PCR Method to Detect the Tomato Corky Root Rot Pathogens, Pseudopyrenochaeta lycopersici and P. terrestris.

Corky root rot is an important disease in tomato production systems and is caused by Pseudopyrenochaeta terrestris and P. lycopersici (formerly Pyrenochaeta lycopersici Types 1 and 2, respectively). The corky root rot pathogens are slow growing and difficult to isolate and quantify in soil and plant tissue. A multiplex hydrolysis probe-based qPCR assay was designed to allow for simultaneous detection and quantification of P. lycopersici and P. terrestris with a competitive internal control to indicate if qPCR inhibitors are present. Single species and multiplex assays for Pseudopyrenochaeta spp. detected DNA levels above 0.013 pg of DNA per reaction. These highly specific assays had no nontarget amplification of other fungal and oomycete pathogens or rhizosphere-associated fungi of tomatoes that were tested. This assay can be used to quantify Pseudopyrenochaeta populations in roots and soils in tomato production systems to better determine the impacts of disease management strategies on Pseudopyrenochaeta spp. and provides a tool to study the biology of Pseudopyrenochaeta spp.

Retrorectus mesh reinforcement of ileostomy site fascial closure: stoma closure and reinforcement (SCAR) trial phase I/II results.

PURPOSE: Loop ileostomy (LI) is commonly employed during colorectal surgeries to reduce the consequences of anastomotic leak. Unfortunately, LI is associated with a 10-30% incisional hernia (IH) rate after closure. We hypothesized that prophylactic mesh reinforcement during LI takedown would safely prevent subsequent IH formation. METHODS: This single-center, phase I/II prospective study evaluated adult patients undergoing LI closure after left-sided colorectal cancer procedures. After LI closure, the posterior rectus sheath was mobilized and reapproximated with absorbable suture. A reduced-weight, macroporous, polypropylene mesh (Softmesh, BD) was placed in the retrorectus position to allow 3 cm of overlap and secured with fibrin sealant. The anterior fascia was closed with slowly absorbable suture. CT images obtained for cancer surveillance were reviewed by a radiologist blinded to the study intervention to evaluate for evidence of hernia or surgical site occurrence (SSO). RESULTS: Twenty patients were included with mean defect and mesh sizes of 11.2 cm2 and 64.2 cm2, respectively. Mean operative time for LI takedown and mesh augmented closure was 84 min with mesh implantation time being 16.4 min. Two patients were readmitted within 30 days for ileus, no patient required procedural intervention. Over a mean follow-up period of 20 ± 7 months, no SSO or hernias were observed clinically or on CT imaging. CONCLUSION: In our small series, retromuscular mesh reinforcement of LI closure appears feasible, safe and effective. This mesh reinforcement approach should be further investigated to evaluate its long-term effectiveness.

Immediate postoperative care on high dependency unit or ward following microvascular free tissue transfer: lessons learnt from a change in practice imposed during the COVID-19 pandemic.

The COVID-19 pandemic resulted in sudden changes to the established practice of using the high dependency unit (HDU) for the first night of postoperative care following microvascular free tissue transfer. Patients were managed instead on the head and neck ward. This retrospective case-note review aimed to report outcomes in consecutive patients treated before and during the pandemic, and to reflect on the implications of ward-based rather than HDU care. A total of 235 patients had free tissue transfer between 3 January 2019 and 25 February 2021: 125 before (lockdown 23 March 2020), and 110 during the pandemic (52 ward-managed and 58 HDU-managed). There were subtle case-mix differences during the pandemic, with 92% of ward-treated patients having oral cancers compared with 64% of HDU patients, and 73% of ward patients having a tracheostomy compared with 40% of HDU patients. Ward patients were less likely to receive electrolyte replacement (45% HDU vs 0% ward) and inotropes (12% HDU vs 2% ward). There were fewer returns to theatre for evacuation of a haematoma or re-anastomosis during the pandemic than there were before it. Other than fewer haematoma complications during the pandemic, the nature of complications was similar. In conclusion, the dramatic changes imposed by the pandemic have shown that the ward is a safe place for patients to be cared for immediately postoperatively, and it alleviates the bed pressures experienced in HDU. Careful case selection and clear criteria are required to identify patients who need the HDU.

Quantifying citrate-enhanced phosphate root uptake using microdialysis.

AIMS: Organic acid exudation by plant roots is thought to promote phosphate (P) solubilisation and bioavailability in soils with poorly available nutrients. Here we describe a new combined experimental (microdialysis) and modelling approach to quantify citrate-enhanced P desorption and its importance for root P uptake. METHODS: To mimic the rhizosphere, microdialysis probes were placed in soil and perfused with citrate solutions (0.1, 1.0 and 10 mM) and the amount of P recovered from soil used to quantify rhizosphere P availability. Parameters in a mathematical model describing probe P uptake, citrate exudation, P movement and citrate-enhanced desorption were fit to the experimental data. These parameters were used in a model of a root which exuded citrate and absorbed P. The importance of soil citrate-P mobilisation for root P uptake was then quantified using this model. RESULTS: A plant needs to exude citrate at a rate of 0.73 µmol cm-1 of root h-1 to see a significant increase in P absorption. Microdialysis probes with citrate in the perfusate were shown to absorb similar quantities of P to an exuding root. CONCLUSION: A single root exuding citrate at a typical rate (4.3 × 10-5 µmol m-1 of root h-1) did not contribute significantly to P uptake. Microdialysis probes show promise for measuring rhizosphere processes when calibration experiments and mathematical modelling are used to decouple microdialysis and rhizosphere mechanisms.

Outcomes of microvascular composite reconstruction for mandibular osteoradionecrosis.

The aim of this retrospective study was to compare outcomes and reconstruction-related complications in patients receiving a composite free flap reconstruction of the mandible for ORN with those reconstructed for other indications. The records of all patients who underwent composite reconstruction of a mandibular defect at Aintree University Hospital, Liverpool, were reviewed and analysed. Based on radiotherapy exposure and ORN history, the study cohort was divided into three separate case-matched groups. Local wound healing issues were markedly more common in the ORN setting, as was infection and subsequent osteosynthesis plate(s) removal. Free flap survival was similar among all three case-matched groups. Advanced mandibular ORN may be safely and predictably reconstructed with composite free flaps, and that while the rate of local complications is greater than non-irradiated, and non-ORN case-matched controls, the free flap survival rate compares favourably.

Modeling radiative and non-radiative pathways at both the Franck-Condon and Herzberg-Teller approximation level.

Here, we present a concise model that can predict the photoluminescent properties of a given compound from first principles, both within and beyond the Franck-Condon approximation. The formalism required to compute fluorescence, Internal Conversion (IC), and Inter-System Crossing (ISC) is discussed. The IC mechanism, in particular, is a difficult pathway to compute due to difficulties associated with the computation of required bosonic configurations and non-adiabatic coupling elements. Here, we offer a discussion and breakdown on how to model these pathways at the Density Functional Theory (DFT) level with respect to its computational implementation, strengths, and current limitations. The model is then used to compute the photoluminescent quantum yield (PLQY) of a number of small but important compounds: anthracene, tetracene, pentacene, diketo-pyrrolo-pyrrole (DPP), and Perylene Diimide (PDI) within a polarizable continuum model. Rate constants for fluorescence, IC, and ISC compare well for the most part with respect to experiment, despite triplet energies being overestimated to a degree. The resulting PLQYs are promising with respect to the level of theory being DFT. While we obtained a positive result for PDI within the Franck-Condon limit, the other systems require a second order correction. Recomputing quantum yields with Herzberg-Teller terms yields PLQYs of 0.19, 0.08, 0.04, 0.70, and 0.99 for anthracene, tetracene, pentacene, DPP, and PDI, respectively. Based on these results, we are confident that the presented methodology is sound with respect to the level of quantum chemistry and presents an important stepping stone in the search for a tool to predict the properties of larger coupled systems.

A model of COVID-19 propagation based on a gamma subordinated negative binomial branching process.

We build a parsimonious Crump-Mode-Jagers continuous time branching process of COVID-19 propagation based on a negative binomial process subordinated by a gamma subordinator. By focusing on the stochastic nature of the process in small populations, our model provides decision making insight into mitigation strategies as an outbreak begins. Our model accommodates contact tracing and isolation, allowing for comparisons between different types of intervention. We emphasize a physical interpretation of the disease propagation throughout which affords analytical results for comparison to simulations. Our model provides a basis for decision makers to understand the likely trade-offs and consequences between alternative outbreak mitigation strategies particularly in office environments and confined work-spaces. Combining the asymptotic limit of our model with Bayesian hierarchical techniques, we provide US county level inferences for the reproduction number from cumulative case count data over July and August of this year.

Clinical characteristics, treatment intent, and outcome in a consecutive 10-year cohort of oral cancer patients aged 75 years and older.

The prevalence of oral squamous cell carcinoma (OSCC) in the elderly is expected to increase by nearly a third in the next decade. Its management in older patients is potentially more challenging due to their pre-existing medical comorbidities, frailty, reduced life expectancy, and social issues. The aim of this retrospective review was to report on treatment given to patients aged 75 years and over, case mix, and survival. All patients aged 75 years and over who were diagnosed with OSCC in Merseyside between 1 January 2007 and 31 December 2016, and treated with either curative or palliative intent, were included. Their hospital notes were reviewed. Fisher's exact test and Kaplan-Meier analysis were used for data analysis. There were 236 patients (median (IQR) age 81 (78-86) years); 67% were treated curatively and 33% palliatively. Factors associated with palliation included older age, advanced tumour stage, cognitive impairment, and residence in a nursing or residential home. Of the 165 patients who were offered curative treatment, six (4%) declined due to personal or family reasons. Overall survival for palliative patients was 12% at one year and 7% at two years, whereas for patients treated curatively it was 74% at one year, 56% at two years, and 34% at five years. Patients over 85 years of age were less likely to have composite free flaps and postoperative radiotherapy. Perioperative mortality was 2.6%. Improvements in surgical techniques and perioperative management have enabled clinicians to offer treatment with curative intent to older frail patients, and with careful case selection outcomes can be very good.

Chest CT screening for COVID-19 in elective and emergency surgical patients: experience from a UK tertiary centre.

AIM: To determine the incidence of possible COVID-19-related lung changes on preoperative screening computed tomography (CT) for COVID-19 and how their findings influenced decision-making. To also to determine whether the patients were managed as COVID-19 patients after their imaging findings, and the proportion who had SARS-CoV2 reverse transcriptionpolymerase chain reaction (RT-PCR) testing. MATERIALS AND METHODS: A retrospective study was undertaken of consecutive patients having imaging prior to urgent elective surgery (n=156) or acute abdominal imaging (n=283). Lung findings were categorised according to the British Society of Thoracic Imaging (BSTI) guidelines. RT-PCR testing, management, and outcomes were determined from the electronic patient records. RESULTS: 3% (13/439) of CT examinations demonstrated findings of classic/probable COVID-19 pneumonia, whilst 4% (19/439) had findings indeterminate for COVID-19. Of the total cohort, 1.6% (7/439) subsequently had confirmed RT-PCR-positive COVID-19. Importantly, all the patients with a normal chest or alternative diagnoses on CT who had PCR testing within the next 7 days, had a negative RT-PCR (92/407). There was a change in surgical outcome in 6% (10/156) of the elective surgical cohort with no change to surgical management was demonstrated in the acute abdominal emergency cohort requiring surgery (2/283). CONCLUSION: There was a 7% (32/439) incidence of potential COVID-19-related lung changes in patients having preoperative CT. Although this altered surgical management in the elective surgical cohort, no change to surgical management was demonstrated in the acute abdominal emergency cohort requiring surgery.

Creating a Practice-Based Implementation Network: Facilitating Practice Change Across Health Care Systems.

A proof-of-concept practice-based implementation network was developed in the US Departments of Veteran Affairs (VA) and Defense to increase the speed of implementation of mental health practices, derive lessons learned prior to larger-scale implementation, and facilitate organizational learning. One hundred thirty-four clinicians in 18 VA clinics received brief training in the use of the PTSD checklist (PCL) in clinical care. Two implementation strategies, external facilitation and technical assistance, were used to encourage the use of outcomes data to inform treatment decisions and increase discussion of results with patients. There were mixed results for changes in the frequency of PCL administration, but consistent increases in clinician use of data and incorporation into the treatment process via discussion. Programs and clinicians were successfully recruited to participate in a 2-year initiative, suggesting the feasibility of using this organizational structure to facilitate the implementation of new practices in treatment systems.

Results of flap reconstruction: categorisation to reflect outcomes and process in the management of head and neck defects.

The reporting of the outcomes of flap reconstruction is often based on numerical success rates. Whilst this remains a useful variable with which to measure success, it is limited in its ability to reflect the complex processes involved. The lack of consistency in the categorisation of outcomes of flap reconstruction in the head and neck could potentially lead us to lose the opportunity to fully capture the implications of its success or failure, or both. We propose a classification that moves away from primarily reporting the results of its binary nature, and focuses more on the process of reconstruction, particularly in the head and neck.

Health-related quality of life in patients with T1N0 oral squamous cell carcinoma: selective neck dissection compared with wait and watch surveillance.

Management of the neck in patients with clinical T1N0 oral squamous cell carcinoma (SCC) is controversial. The aim of this study was to report the health-related quality of life (HRQoL) in a consecutive group of patients with stage 1 disease at a time closest to two years after primary surgery. Of 216 patients treated between 2007 and 2012 (after excluding early death and regional recurrence), 195 were eligible. HRQoL was measured using the University of Washington quality of life questionnaire version 4. The overall response rate was 65% (126/195). HRQoL outcomes were good, but compared with patients in the wait and watch group, those who had selective neck dissection (SND) had more problems regarding appearance (14% compared with 1%, p=0.008) and pain (19% compared with 6%, p=0.04). Similar trends were seen for shoulder (14% compared with 8%), mood (16% compared with 8%), and speech (5% compared with 1%), and for poorer overall QoL (30% compared with 16%). It is difficult to establish why patients did or did not have neck dissection in a retrospective sample, but it is likely that those who had SND had larger tumours. The findings highlight the impact that SND has on HRQoL in domains such as appearance, pain, speech, swallowing, and chewing. Previous studies on SND have tended to focus on injury to the accessory nerve and shoulder function, but these new data emphasise the need to include other domains in future trials that compare wait and watch, SND, and sentinel lymph node biopsy.

Application of Bayesian statistics to estimate nitrous oxide emission factors of three nitrogen fertilisers on UK grasslands.

Trapezoidal integration by linear interpolation of data points is by far the most commonly used method of cumulative flux calculations of nitrous oxide (N2O) in studies that use flux chambers; however, this method is incapable of providing accurate uncertainty estimates. A Bayesian approach was used to calculate N2O emission factors (EFs) and their associated uncertainties from flux chamber measurements made after the application of nitrogen fertilisers, in the form of ammonium nitrate (AN), urea (Ur) and urea treated with Agrotain® urease inhibitor (UI) at four grassland sites in the UK. The comparison between the cumulative fluxes estimated using the Bayesian and linear interpolation methods were broadly similar (R2 = 0.79); however, the Bayesian method was capable of providing realistic uncertainties when a limited number of data points is available. The study reports mean EF values (and 95% confidence intervals) of 0.60 ±â€¯0.63, 0.29 ±â€¯0.22 and 0.26 ±â€¯0.17% of applied N emitted as N2O for the AN, Ur and UI treatments, respectively. There was no significant difference between N2O emissions from the Ur and UI treatments. In the case of the automatic chamber data collected at one site in this study, the data did not fit the log-normal model, implying that more complex models may be needed, particularly for measurement data with high temporal resolution.

Meta-analysis reveals that pollinator functional diversity and abundance enhance crop pollination and yield.

How insects promote crop pollination remains poorly understood in terms of the contribution of functional trait differences between species. We used meta-analyses to test for correlations between community abundance, species richness and functional trait metrics with oilseed rape yield, a globally important crop. While overall abundance is consistently important in predicting yield, functional divergence between species traits also showed a positive correlation. This result supports the complementarity hypothesis that pollination function is maintained by non-overlapping trait distributions. In artificially constructed communities (mesocosms), species richness is positively correlated with yield, although this effect is not seen under field conditions. As traits of the dominant species do not predict yield above that attributed to the effect of abundance alone, we find no evidence in support of the mass ratio hypothesis. Management practices increasing not just pollinator abundance, but also functional divergence, could benefit oilseed rape agriculture.

Upgrade to the MAPS neutron time-of-flight chopper spectrometer.

The MAPS direct geometry time-of-flight chopper spectrometer at the ISIS pulsed neutron and muon source has been in operation since 1999, and its novel use of a large array of position-sensitive neutron detectors paved the way for a later generations of chopper spectrometers around the world. Almost two decades of experience of user operations on MAPS, together with lessons learned from the operation of new generation instruments, led to a decision to perform three parallel upgrades to the instrument. These were to replace the primary beamline collimation with supermirror neutron guides, to install a disk chopper, and to modify the geometry of the poisoning in the water moderator viewed by MAPS. Together, these upgrades were expected to increase the neutron flux substantially, to allow more flexible use of repetition rate multiplication and to reduce some sources of background. Here, we report the details of these upgrades and compare the performance of the instrument before and after their installation as well as to Monte Carlo simulations. These illustrate that the instrument is performing in line with, and in some respects in excess of, expectations. It is anticipated that the improvement in performance will have a significant impact on the capabilities of the instrument. A few examples of scientific commissioning are presented to illustrate some of the possibilities.

Ageing in corrective services: from the perspective of prison chaplains.

The number of older inmates in New South Wales prisons has increased over the past ten years but it is unclear whether corrective services can cater for the increase. The current study reports the results of a qualitative study about ageing in prison. Eight prison chaplains from four corrective facilities in NSW were interviewed using a semi-structured interview schedule. The results of a thematic analysis revealed four main themes: the system, the services, the environment and the inmate. The themes reveal a system that is not designed to cope with an ageing population. Inmates become resentful of what has happened to them rather than for the damage they have done to somebody else. The system lacks processes and programmes to enable proper rehabilitation. The issues raised by the chaplains in terms of services, the environment and the inmates decrease the possibility that an older inmate will adapt to the environment and successfully age in place.

Transmission infrared spectroscopy for rapid quantification of fat, protein, and lactose concentrations in human milk.

OBJECTIVE: To develop partial least squares regression (PLSR) calibration models in combination with transmission infrared (TIR) spectroscopy for rapid and optimal quantification of human milk macronutrient concentrations. STUDY DESIGN: Human milk samples (n = 306) were characterized simultaneously by reference chemical analytical methods and TIR spectroscopy. Reference macronutrient concentrations were linked to pre-processed spectra and divided into two (training and test) sets. PLSR was used to develop trial calibration models using training set, and the test set was used to assess the accuracy of the trial analytical methods. RESULTS: For the methods selected as optimal, the concordance correlation coefficients between reference and TIR-based methods were 0.93 for fat, 0.96 for protein, and 0.52 for lactose. The Bland-Altman plots showed no evidence of systematic bias between TIR and reference methods. CONCLUSIONS: TIR spectroscopy provides the basis for accurate and rapid quantification of human milk fat and protein concentrations but is less accurate for measuring lactose concentration.