Surgical procedure prediction using medical ontological information

BACKGROUND AND OBJECTIVE

Predicting the duration of surgical procedures is an important step in scheduling operating rooms. Many factors have been shown to influence the duration of a procedure, in this research we aim to use medical ontological information to improve the predictions.

METHODS

This paper presents two methods for incorporating the medical information about a surgical procedure into the prediction of the duration of the procedure. The first method uses the Systematised Nomenclature of Medicine Clinical Terms to relate different procedures to each other. The second uses simple text fragments. The relationships between types of procedures are included in a regression model for the procedure duration. These methods are applied to data from New Zealand healthcare facilities and the accuracy of the estimations of the durations is compared. In addition a simulation of scheduling the procedures in an operating room is performed.

RESULTS

It is shown that both of the methods provide an improvement in the prediction of procedure durations. When compared to a traditional categorical encoding, the ontological information provides an improvement in the continuous ranked probability scores of the prediction of procedure durations from 18.4 min to 17.1 min, and from 25.3 to 21.3 min for types of procedures that are not performed very often.

CONCLUSIONS

Different methods for encoding medical ontological information in surgery procedure duration predictions are presented, and show an improvement over traditional models. The improvement in duration prediction is shown to improve the efficiency of scheduling in a simple simulation.

Homologous recombination suppresses transgenerational DNA end resection and chromosomal instability in fission yeast

Chromosomal instability (CIN) drives cell-to-cell heterogeneity, and the development of genetic diseases, including cancer. Impaired homologous recombination (HR) has been implicated as a major driver of CIN, however, the underlying mechanism remains unclear. Using a fission yeast model system, we establish a common role for HR genes in suppressing DNA double-strand break (DSB)-induced CIN. Further, we show that an unrepaired single-ended DSB arising from failed HR repair or telomere loss is a potent driver of widespread CIN. Inherited chromosomes carrying a single-ended DSB are subject to cycles of DNA replication and extensive end-processing across successive cell divisions. These cycles are enabled by Cullin 3-mediated Chk1 loss and checkpoint adaptation. Subsequent propagation of unstable chromosomes carrying a single-ended DSB continues until transgenerational end-resection leads to fold-back inversion of single-stranded centromeric repeats and to stable chromosomal rearrangements, typically isochromosomes, or to chromosomal loss. These findings reveal a mechanism by which HR genes suppress CIN and how DNA breaks that persist through mitotic divisions propagate cell-to-cell heterogeneity in the resultant progeny.

The first patients treated with MR-CBCT soft-tissue matching in a MR-only prostate radiotherapy pathway

INTRODUCTION

Magnetic Resonance (MR)-only radiotherapy for prostate cancer has previously been reported using fiducial markers for on-treatment verification. MR-Cone Beam Computed Tomography (CBCT) soft-tissue matching does not require invasive fiducial markers and enables MR-only treatments to other pelvic cancers. This study evaluated the first clinical implementation of MR-only prostate radiotherapy using MR-CBCT soft-tissue matching.

METHODS

Twenty prostate patients were treated with MR-only radiotherapy using a synthetic (s)CT-optimised plan with MR-CBCT soft-tissue matching. Two MR sequences were acquired: small Field Of View (FOV) for target delineation and large FOV for organs at risk delineation, sCT generation and on-treatment verification. Patients also received a CT for validation. The prostate was independently contoured on the small FOV MR, copied to the registered CT and modified if there were MR-CT soft-tissue alignment differences (MR-CT volume). This was compared to the MR-only volume with a paired t-test. The treatment plan was recalculated on CT and the doses compared. Independent offline CT-CBCT matches for 5/20 fractions were performed by three therapeutic radiographers using the MR-only contours and compared to the online MR-CBCT matches using two one-sided paired t-tests for equivalence within ±1 mm.

RESULTS

The MR-only volumes were significantly smaller than MR-CT (p = 0.003), with a volume ratio 0.92 ± 0.02 (mean ± standard error). The sCT isocentre dose difference to CT was 0.2 ± 0.1%. MR-CBCT soft-tissue matching was equivalent to CT-CBCT (p < 0.001), with differences of 0.1 ± 0.2 mm (vertical), -0.1 ± 0.2 mm (longitudinal) and 0.0 ± 0.1 mm (lateral).

CONCLUSIONS

MR-only radiotherapy with soft-tissue matching has been successfully clinically implemented. It produced significantly smaller target volumes with high dosimetric and on-treatment matching accuracy.

IMPLICATIONS FOR PRACTICE

MR-only prostate radiotherapy can be safely delivered without using invasive fiducial markers. This enables MR-only radiotherapy to be extended to other pelvic cancers where fiducial markers cannot be used.

Determinants of exposure to endocrine disruptors following hurricane Harvey

Hurricane Harvey was a category four storm that induced catastrophic flooding in the Houston metropolitan area. Following the hurricane there was increased concern regarding chemical exposures due to damage caused by flood waters and emergency excess emissions from industrial facilities. This study utilized personal passive samplers in the form of silicone wristbands in Houston, TX to both assess chemical exposure to endocrine disrupting chemicals (EDCs) immediately after the hurricane and determine participant characteristics associated with higher concentrations of exposure. Participants from the Houston-3H cohort (n = 172) wore a wristband for seven days and completed a questionnaire to determine various flood-related and demographic variables. Bivariate and multivariate analysis indicated that living in an area with a high Area Deprivation Index (ADI) (indicative of low socioeconomic status), identifying as Black/African American or Latino, and living in the Houston neighborhoods of Baytown and East Houston were associated with increased exposure to EDCs. These results provide evidence of racial/ethnic and socioeconomic injustices in exposure to EDCs in the Houston Metropolitan Area. Since the multiple regression models conducted did not fully explain exposure (0.047 < R2 < 0.34), more research is needed on the direct sources of EDCs within this area to create effective exposure mitigation strategies.

Toxicity Profiles and Protective Effects of Antifreeze Proteins From Insect in Mammalian Models

Antifreeze proteins (AFPs), found in many cold-adapted organisms, can protect them from cold and freezing damages and have thus been considered as additional protectants in current cold tissue preservation solutions that generally include electrolytes, osmotic agents, colloids and antioxidants, to reduce the loss of tissue viability associated with cold-preservation. Due to the lack of toxicity profile studies on AFPs, their inclusion in cold preservation solutions has been a trial-and-error process limiting the development of AFPs' application in cold preservation. To assess the feasibility of translating the technology of AFPs for mammalian cell cold or cryopreservation, we determined the toxicity profile of two highly active beetle AFPs, DAFP1 and TmAFP, from Dendroides canadensis and Tenebrio molitor in this study. Toxicity was examined on a panel of representative mammalian cell lines including testicular spermatogonial stem cells and Leydig cells, macrophages, and hepatocytes. Treatments with DAFP1 and TmAFP at up to 500μg/mL for 48 and 72hours were safe in three of the cell lines, except for a 20% decrease in spermatogonia treated with TmAFP. However, both AFPs at 500μg/mL or below reduced hepatocyte viability by 20 to 40% at 48 and 72h. At 1000μg/mL, DAFP1 and TmAFP reduced viability in most cell lines. While spermatogonia and Leydig cell functions were not affected by 1000μg/mL DAFP1, this treatment induced inflammatory responses in macrophages. Adding 1000μg/ml DAFP1 to rat kidneys stored at 4°C for 48hours protected the tissues from cold-related damage, based on tissue morphology and gene and protein expression of two markers of kidney function. However, DAFP1 and TmAFP did not prevent the adverse effects of cold on kidneys over 72hours. Overall, DAFP1 is less toxic at high dose than TmAFP, and has potential for use in tissue preservation at doses up to 500μg/mL. However, careful consideration must be taken due to the proinflammatory potential of DAFP1 on macrophages at higher doses and the heighten susceptibility of hepatocytes to both AFPs.

Anchoring the species Rhizophagus intraradices (formerly Glomus intraradices)

The nomenclatural type material of Rhizophagus intraradices (basionym Glomus intraradices) was originally described from a trap pot culture established with root fragments, subcultures of which later became registered in the INVAM culture collection as FL 208. Subcultures of FL 208 (designated as strain ATT 4) and a new strain, independently isolated from the type location (ATT 1102), were established as both pot cultures with soil-like substrate and in vitro root organ culture. Long-term sampling of these cultures shows spores of the species to have considerable morphological plasticity, not described in the original description. Size, shape and other features of the spores were much more variable than indicated in the protologue. Phylogenetic analyses confirmed earlier published evidence that sequences from all R. intraradices cultures formed a monophyletic clade, well separated from, and not representing a sister clade to, R. irregularis. Moreover, new phylogenetic analyses show that Rhizoglomus venetianum and R. irregularis are synonymous. The morphological characters used to separate these species exemplify the difficulties in species recognition due to the high phenotypic plasticity in the genus Rhizophagus. Rhizophagus intraradices is morphologically re-described, an epitype is designated from a single-spore isolate derived from ATT 4, and R. venetianum is synonymised with R. irregularis.

Use of probiotics in the NICU: Evaluating the stability of a three-strain probiotic blend in various media for enteral feeding

BACKGROUND

There is little published data on how to prepare probiotic supplements for enteral delivery in the NICU. The objective of this study was to determine how a three-strain probiotic blend (Bb-02, TH-4® and BB-12®) would behave when mixed and held for 4 hours with saline water, sterile water, dextrose 5% in water (D5W), 24 kcal preterm formula, and human milk.

METHODS

A packet of a three-strain probiotic supplement was mixed with 3 mL of saline water, sterile water, D5W, 24 kcal preterm formula, and human milk (tested at 3 mL and 2 mL). Samples were stored at room temperature for 60 minutes then refrigerated for 180 minutes. Probiotic survival, using quantitative enumeration, and pH were monitored over 4 hours. Samples were passed through a 5 French (Fr) feeding tube at the end of the study to evaluate viscosity.

RESULTS

The largest variation in total cell count from 0-time was sterile water with a + 0.26 log(CFU)/mL change at 90 minutes and typical variation is considered±0.50 log units indicating no significant change between samples in 4 hours. Saline water had the lowest final pH at 4.88. All samples easily passed through a 5 Fr feeding tube.

CONCLUSION

The study showed minimal change in cell counts across solutions for 4 hours of storage, indicating health care facilities may be able to prepare probiotic supplements with a variety of solutions in pharmacies or milk rooms. This allows greater flexibility for probiotic delivery to preterm infants.

Understanding the impact of SNPs associated with autism spectrum disorder on biological pathways in the human fetal and adult cortex

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by significant and complex genetic etiology. GWAS studies have identified genetic variants associated with ASD, but the functional impacts of these variants remain unknown. Here, we integrated four distinct levels of biological information (GWAS, eQTL, spatial genome organization and protein-protein interactions) to identify potential regulatory impacts of ASD-associated SNPs (p < 5 × 10^-8) on biological pathways within fetal and adult cortical tissues. We found 80 and 58 SNPs that mark regulatory regions (i.e. expression quantitative trait loci or eQTLs) in the fetal and adult cortex, respectively. These eQTLs were also linked to other psychiatric disorders (e.g. schizophrenia, ADHD, bipolar disorder). Functional annotation of ASD-associated eQTLs revealed that they are involved in diverse regulatory processes. In particular, we found significant enrichment of eQTLs within regions repressed by Polycomb proteins in the fetal cortex compared to the adult cortex. Furthermore, we constructed fetal and adult cortex-specific protein-protein interaction networks and identified that ASD-associated regulatory SNPs impact on immune pathways, fatty acid metabolism, ribosome biogenesis, aminoacyl-tRNA biosynthesis and spliceosome in the fetal cortex. By contrast, in the adult cortex they largely affect immune pathways. Overall, our findings highlight potential regulatory mechanisms and pathways important for the etiology of ASD in early brain development and adulthood. This approach, in combination with clinical studies on ASD, will contribute to individualized mechanistic understanding of ASD development.

Markers of human endometrial hypoxia can be detected in vivo and ex vivo during physiological menstruation

STUDY QUESTION

Can markers of human endometrial hypoxia be detected at menstruation in vivo?

SUMMARY ANSWER

Our in vivo data support the presence of hypoxia in menstrual endometrium of women during physiological menstruation.

WHAT IS KNOWN ALREADY

Current evidence from animal models and human in vitro studies suggests endometrial hypoxia is present at menstruation and drives endometrial repair post menses. However, detection of human endometrial hypoxia in vivo remains elusive.

STUDY DESIGN, SIZE, DURATION

We performed a prospective case study of 16 women with normal menstrual bleeding.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Reproductively aged female participants with a regular menstrual cycle underwent objective measurement of their menstrual blood loss using the alkaline haematin method to confirm a loss of <80 ml per cycle. Exclusion criteria were exogenous hormone use, an intrauterine device, endometriosis or fibroids >3 cm. Participants attended for two MRI scans; during days 1-3 of menstruation and the early/mid-secretory phase of their cycle. The MRI protocol included dynamic contrast-enhanced MRI and T2* quantification. At each visit, an endometrial sample was also collected and hypoxia-regulated repair factor mRNA levels (ADM, VEGFA, CXCR4) were quantified by RT-qPCR.

MAIN RESULTS AND THE ROLE OF CHANCE

Women had reduced T2* during menstrual scans versus non-menstrual scans (P = 0.005), consistent with menstrual hypoxia. Plasma flow (Fp) was increased at menstruation compared to the non-menstrual phase (P = 0.0005). Laboratory findings revealed increased ADM, VEGF-A and CXCR4 at menstruation on examination of paired endometrial biopsies from the menstrual and non-menstrual phase (P = 0.008; P = 0.03; P = 0.009). There was a significant correlation between T2* and these ex vivo hypoxic markers (P < 0.05).

LIMITATIONS, REASONS FOR CAUTION

This study examined the in vivo detection of endometrial hypoxic markers at specific timepoints in the menstrual cycle in women with a menstrual blood loss <80 ml/cycle and without significant uterine structural abnormalities. Further research is required to determine the presence of endometrial hypoxia in those experiencing abnormal uterine bleeding with and without fibroids/adenomyosis.

WIDER IMPLICATIONS OF THE FINDINGS

Heavy menstrual bleeding (HMB) is a common, debilitating condition. Understanding menstrual physiology may improve therapeutics. To our knowledge, this is the first in vivo data supporting the presence of menstrual hypoxia in the endometrium of women with normal menstrual bleeding. If aberrant in those with HMB, these non-invasive tests may aid diagnosis and facilitate personalized treatments for HMB.

STUDY FUNDING/COMPETING INTEREST(S)

This work was funded by Wellbeing of Women grant RG1820, Wellcome Trust Fellowship 209589/Z/17/Z and undertaken in the MRC Centre for Reproductive Health, funded by grants G1002033 and MR/N022556/1. H.O.D.C. has clinical research support for laboratory consumables and staff from Bayer AG and provides consultancy advice (but with no personal remuneration) for Bayer AG, PregLem SA, Gedeon Richter, Vifor Pharma UK Ltd, AbbVie Inc; Myovant Sciences GmbH. H.O.D.C. receives royalties from UpToDate for articles on abnormal uterine bleeding.

TRIAL REGISTRATION NUMBER

N/A.

130 Improving Documentation of Bowel Movement on Geriatric Wards

Introduction

Constipation is a widely prevalent issue in older adults that may result in complications such as urinary retention, delirium and bowel obstruction. Previous studies have indicated that while stool charts are well completed by nursing staff, they are infrequently monitored by doctors. This project aimed to improve the documentation of bowel movement by doctors on ward rounds to 85%, by the end of a 3-month period.

Methods

Formulation of the project was achieved using group work and a fishbone diagram which focussed on how doctors can improve on documenting bowel movements. Baseline data were collected from inpatient notes on weekdays over a three-week period on a geriatric ward in Northern General Hospital, Sheffield. Interventions of posters and stickers of the poo emoji were placed on walls and in inpatient notes respectively as a reminder. Post-intervention data were collected on weekdays over two weeks, and then repeated a month later to assess for a sustained change.

Results

The data on bowel activity documentation were collected from 28 patients. The baseline data showed that bowel activity was monitored daily on the ward 56.25% of the time. There was a significant increase in documentation of 85.75% following the interventions. The sustainability study showed that bowel activity was documented on the ward 59.09% of the time.

Conclusions

This study shows how a strong effect on behavioural change can be accomplished through simple interventions such as stickers and posters. As most wards currently still use paper notes, this is a generalisable model that other wards can trial. However, this study also shows the difficulty in maintaining behavioural change over extended periods of time. Further PDSA cycles should examine the reasons behind the difficulty sustaining the change and implement new changes that aim to overcome them.

Figs S1-S3 & Tables S1-S2

Fig. S1. Rhizophagus intraradices: culturing history of the type and successful ex-type culture attempts (ATT 4) and a new isolate (ATT 1102) from the type location established approx. 30 years later. Both pot cultures (PC) and root organ cultures (ROC) are shown with dates of establishment and voucher numbers for samples that yielded specimens for preservation in herbaria. Sun bags are item B7062, Sigma Aldrich (https://www.sigmaaldrich.com). Location of cultures: Forestry Commission Northern Research Station or other localities in UK; Université catholique de Louvain (UCL); Ludwig Maximilian University of Munich (LMU). Gel refers to a small portion of substrate from a parent ROC, with a single spore, several spores, or root fragments (usually with attached mycelium).Fig. S2. Phylogenetic maximum likelihood phylogenetic tree of Rhizophagus species and isolates characterised for the SSU-ITS-LSU rDNA region, with Sclerocystis as outgroup. Bootstrap (BS) values below 60 % and BS values of terminal sister relations are not shown. “Rhizoglomus venetianum” (= R. irregularis) sequences are marked in red, sequence variants characterised in a Rhizophagus irregularis genome project are marked in blue. Sequences of Rhizophagus intraradices cultures derived from the ex-type culture FL 208, including the epitype (voucher W 5719 from MUCL 52327 = ATT 4-83), are shown in green and sequences of the new isolate collected from the type locality (MUCL 49410 = ATT 1102-12) in brown.Table S1. Rhizophagus intraradices: lengths and widths (µm) of extra- and intraradical spores from two strains, ATT 4 and ATT 1102 spores with inferential statistics (number of spores observed (n), minimum value (Min), first quartile of the data (Q1), median, third quartile of data (Q3), maximum value (Max), mean, standard deviation (SD) and % coefficient of variation (CV %)). Table S2. Rhizophagus intraradices: spore colours from two strains (ATT 4 – type and ex-type) and ATT 1102 (new culture from type locality) from pot cultures (PC) and root organ cultures (ROC). Where possible, colours were matched with charts from Royal Botanic Garden Edinburgh, Munsell, or Methuen Handbook of Colour.

Effect of extrudate swell on extrusion foam of polyethylene terephthalate

The effect of extrudate swell on extrusion foam of thermoplastic polymers is presented using an experimental approach supported by a modelling of the phenomenon. Its understanding is fundamental in designing the geometry of a die for extrusion foam and to predict foaming. The extrudate swell is the swelling of a viscoelastic material due to a fast elastic recovery after being subjected to stresses. We show that there exists a link between the extrudate swell and foaming, performing experiments with simple and complex extrusion dies to measure the expansion ratio. It was found that the expansion ratio is anisotropic and the anisotropy in the expansion of the foam is due to the extrudate swell that affects strongly the final shape of the product and it cannot be neglected in standard application for extrusion foam. A simple heuristic model was developed to predict the extrudate swell from geometrical parameters and rheological characterization of the fluid. It was found that the foaming mechanism of polyethylene terephthalate, blown with cyclopentane, changes as function of extrudate swell and the lowest density foam is achieved using the die that has the bigger extrudate swell.

Intracranial haemorrhage associated with systemic anticoagulation in ventilated COVID-19 Intensive care patients

Introduction

COVID-19 induces a pro-inflammatory, hypercoagulable state with marked elevations of ferritin, C-reactive protein, interleukin, and D-dimers. Observed consequences include pro-thrombotic disseminated intravascular coagulation (DIC) with a high rate of venous thromboembolism (VTE) and elevated D-dimers with high fibrinogen and low anti-thrombin levels. Pulmonary congestion appears to be due to micro-vascular thrombosis and occlusion on pathological examination.1 The acquired pro-thrombotic state and associated poorer outcomes seen in critically ill COVID-19 patients 2,3 have led to such patients being treated empirically with systemic anticoagulants. Unfractionated heparin (UFH) or low molecular weight heparin (LMWH) have both been used.2,3

Methods

Review of COVID-19 positive adult patients admitted to the critical care unit between 10th March and 13th May 2020 with severe respiratory failure requiring invasive ventilation.

Results

In that period we admitted 59 patients. 6 (10%) females, 56 (90%) males. 45 (76%) patients required therapeutic anticoagulation (27 UFH, 14 LMWH, 4 argatroban). 4 (8.9%) of the 45 anticoagulated patients suffered catastrophic intracranial haemorrhage and subsequently died.

Discussion

The risk for any significant haemorrhage in patients systemically anticoagulated for VTE with unfractionated heparin (UFH) is 2-3%, 4 and that of anticoagulant-related intracranial haemorrhage (AICH) in patients systemically anticoagulated with UFH is 1-2.7% (in patients treated for ischaemic stroke) and 4% with argatroban.5 We report a much higher incidence of nearly 9%. The cases we present fulfilled the advised criteria for systemic anticoagulation. Despite four-hourly monitoring of APPT and anti-Xa activity on the intensive care unit there were significant fluxes in these laboratory markers of anticoagulation. These may be associated with the uncharted nature of this disease process.It is impossible to disassociate the necessary therapeutic-intensity anticoagulation with the observed heightened frequency of life-ending intracranial haemorrhage in these patients.

Tracheostomy in the coronavirus disease 2019 patient: evaluating feasibility, challenges and early outcomes of the 14-day guidance

OBJECTIVES

To report feasibility, early outcomes and challenges of implementing a 14-day threshold for undertaking surgical tracheostomy in the critically ill coronavirus disease 2019 patient.

METHODS

Twenty-eight coronavirus disease 2019 patients underwent tracheostomy. Demographics, risk factors, ventilatory assistance, organ support and logistics were assessed.

RESULTS

The mean time from intubation to tracheostomy formation was 17.0 days (standard deviation = 4.4, range 8-26 days). Mean time to decannulation was 15.8 days (standard deviation = 9.4) and mean time to intensive care unit stepdown to a ward was 19.2 days (standard deviation = 6.8). The time from intubation to tracheostomy was strongly positively correlated with: duration of mechanical ventilation (r(23) = 0.66; p < 0.001), time from intubation to decannulation (r(23) = 0.66; p < 0.001) and time from intubation to intensive care unit discharge (r(23) = 0.71; p < 0.001).

CONCLUSION

Performing a tracheostomy in coronavirus disease 2019 positive patients at 8-14 days following intubation is compatible with favourable outcomes. Multidisciplinary team input is crucial to patient selection.

Effectiveness of the New Extended-release Formulation of Quetiapine as Monotherapy for the Treatment of Acute Bipolar Depression (Trial D144CC00002)

Objectives:

To evaluate the effectiveness of extended-release quetiapine fumarate (quetiapine XR) as once-daily monotherapy for bipolar depression.

Method:

Patients in this double-blind, placebo-controlled study were acutely depressed adults with bipolar I or II disorder (with or without rapid cycling), and were randomized to 8 weeks of once-daily treatment with quetiapine XR 300 mg (n=133) or placebo (n=137). The primary outcome measure was change from baseline to endpoint (Week 8) in Montgomery-Åsberg Depression Rating Scale (MADRS) total score. Secondary outcome measures included response (MADRS total score reduction ≥50%) and remission (MADRS total score ≤12) rates at endpoint, changes from baseline to endpoint in MADRS item scores, and Clinical Global Impressions-Bipolar (CGI-BP) severity of illness and change. Change from baseline was compared between groups with analysis of covariance using last observation carried forward approach.

Results:

Quetiapine XR 300 mg/d was significantly more effective than placebo in improving depressive symptoms, from first assessment (Week 1; P< 0.001) to endpoint (P< 0.001). Compared with placebo, quetiapine XR was associated with higher response (P< 0.001) and remission (P< 0.05) rates and greater improvements from baseline to endpoint in MADRS total score (-17.43 vs -11.92; P< 0.001), MADRS item scores for core symptoms of depression, and CGI-BP-related outcomes at Week 8. Most common adverse events with quetiapine XR were dry mouth, somnolence, and sedation.

Conclusions:

Quetiapine XR (300 mg) once-daily monotherapy was efficacious (from Weeks 1 through 8) compared with placebo and generally well tolerated in bipolar depression.

Supported by funding from AstraZeneca Pharmaceuticals LP.

Homologous recombination repair intermediates promote efficient de novo telomere addition at DNA double-strand breaks

The healing of broken chromosomes by de novo telomere addition, while a normal developmental process in some organisms, has the potential to cause extensive loss of heterozygosity, genetic disease, or cell death. However, it is unclear how de novo telomere addition (dnTA) is regulated at DNA double-strand breaks (DSBs). Here, using a non-essential minichromosome in fission yeast, we identify roles for the HR factors Rqh1 helicase, in concert with Rad55, in suppressing dnTA at or near a DSB. We find the frequency of dnTA in rqh1Δ rad55Δ cells is reduced following loss of Exo1, Swi5 or Rad51. Strikingly, in the absence of the distal homologous chromosome arm dnTA is further increased, with nearly half of the breaks being healed in rqh1Δ rad55Δ or rqh1Δ exo1Δ cells. These findings provide new insights into the genetic context of highly efficient dnTA within HR intermediates, and how such events are normally suppressed to maintain genome stability.

An Evaluation of the Hybrid Model for Predicting Surgery Duration

The degree of accuracy in surgery duration estimation directly impacts on the quality of planned surgical lists. Model selection for the prediction of surgery duration requires technical expertise and significant time and effort. The result is often a collection of viable models, the performance of which varies across different strata of the surgical population. This paper proposes a prediction framework to be used after a comprehensive model selection process has been completed for surgery duration prediction. The framework produces a partition of the surgical cases and a "hybrid model" that allocates different predictors from the collection of viable models to different parts of the surgical population. The intention is a flexible prediction process that can reassign models and adapt as surgical processes change. The framework is tested via a simulation study, and its utility is demonstrated by predicting surgery durations for Ear, Nose and Throat surgeries in a New Zealand hospital. The results indicate that the hybrid model is effective, performing better than standard model selection in two of the three simulation studies, and marginally worse when the selected model was the true underlying process.

Potential use of ketoconazole in a dynamic endocrine test to differentiate between biological outliers and testosterone use by athletes

Determination of the ratio of testosterone to epitestosterone (T/E) in urine is used to detect testosterone administration in athletes, with a ratio &gt; 6 considered as evidence of an offense. We show that administration of ketoconazole, which inhibits testosterone biosynthesis, may be useful for differentiating between an athlete who is using testosterone and one who naturally gives a ratio &gt; 6. In a control subject pretreated with testosterone, ketoconazole caused the ratio to increase; conversely, it caused a decrease in the ratio in an athlete under investigation. Repeated administration of ketoconazole to two normal men caused a decrease in the ratio due to a large decrease in the urinary excretion rate of testosterone relative to epitestosterone. Stimulation with human chorionic gonadotropin exacerbated the differences in excretion rates. A single administration of ketoconazole to six normal men caused the T/E ratios to decrease significantly within 8 h, a suitable time scale for use in a dynamic test.

Rapid muscle volume prediction using anthropometric measurements and population-derived statistical models

Knowledge of subject-specific muscle volumes may be used as surrogates for evaluating muscle strength and power generated by 'fat-free' muscle mass. This study presents population-based statistical learning approaches for predicting 'fat-free' muscle volume from known anthropometric measurements. Using computed tomography (CT) imaging data to obtain lower-limb muscle volumes from 50 men and women, this study evaluated six statistical learning methods for predicting muscle volumes from anthropometric measurements: (i) stepwise regression, (ii) linear support vector machine (SVM), (iii) 2nd-order polynomial SVM, (iv) linear partial least squares regression (PLSR), (v) quadratic PLSR, and (vi) 3rd-order spline fit PLSR. These techniques have successfully been demonstrated in bioengineering applications and freely available in open-source toolkits. Analysis revealed that separating a general population into sexes and/or cohorts based on adipose level may improve prediction accuracies. The most important measures that statistically influence muscle volume predictions were shank girth, followed by sex and finally leg length, as identified using stepwise regression. SVM learning predicted muscle volume with an accuracy of 85 ± 4% when using linear interpolation, but performed poorly with an accuracy of 59 ± 6% using polynomial interpolation. The simpler linear PLSR exhibited muscle volume prediction accuracy of 87 ± 2%, while quadratic PLSR was slightly reduced at 82 ± 3%. For the spline fit PLSR, high accuracy was observed on the training data set (~ 99%) but over-fitting (a drawback of high-interpolation methods) resulted in erroneous predictions on testing data, and hence, the model was deemed unsuitable. In conclusion, use of linear PLSR models with variables of sex, leg length, and shank girth is a useful tool for predicting 'fat-free' muscle volume.

Experimental designs of field-based constructed floating wetland studies: A review

A Constructed Floating Wetland (CFW) is a relatively recent innovation in stormwater treatment and is a hydroponic device that is designed to move up and down with changing water levels as urban runoff enters a stormwater retention pond. This floating capability is designed to improve the pollutant removal efficiency of the CFW. The CFW studies undertaken so far have produced encouraging results under a range of conditions such as system size, inflow pollutant concentrations, climatic conditions, and coverage ratio. However, these results have not yet been drawn together to better understand how the various design features of a CFW influence its performance. This paper reviews the available field investigations with the aim of helping guide and improve the experimental designs and installations of future CFW installations. This in turn will improve the knowledge and acceptance of these recently developed stormwater treatment systems. One of the findings of this review was that using a percentage coverage design approach may not be as effective as improving the design efficiency. Understanding the hydraulics of the entire pond and CFW system is also critical to effective design. The review also found that the performance evaluation of future CFW installations would be improved if consideration is given to including both baseline monitoring and experimental controls.

A randomized controlled trial protocol assessing the effectiveness, safety and cost-effectiveness of methotrexate vs. ciclosporin in the treatment of severe atopic eczema in children: the TREatment of severe Atopic eczema Trial (TREAT)

BACKGROUND

Oral systemic immunomodulatory medication is regularly used off-licence in children with severe atopic eczema. However, there is no firm evidence regarding the effectiveness, safety, cost-effectiveness and impact on quality of life from an adequately powered randomized controlled trial (RCT) using systemic medication in children.

OBJECTIVES

To assess whether there is a difference in the speed of onset, effectiveness, side-effect profile and reduction in flares post-treatment between ciclosporin (CyA) and methotrexate (MTX), and also the cost-effectiveness of the drugs. Treatment impact on quality of life will also be examined in addition to whether FLG genotype influences treatment response. In addition, the trial studies the immune-metabolic effects of CyA and MTX.

METHODS

Multicentre, parallel group, assessor-blind, pragmatic RCT of 36 weeks' duration with a 24-week follow-up period. In total, 102 children aged 2-16 years with moderate-to-severe atopic eczema, unresponsive to topical treatment will be randomized (1 : 1) to receive MTX (0·4 mg kg^-1 per week) or CyA (4 mg kg^-1 per day).

RESULTS

The trial has two primary outcomes: change from baseline to 12 weeks in Objective Severity Scoring of Atopic Dermatitis (o-SCORAD) and time to first significant flare following treatment cessation.

CONCLUSIONS

This trial addresses important therapeutic questions, highlighted in systematic reviews and treatment guidelines for atopic eczema. The trial design is pragmatic to reflect current clinical practice.

The effects of serotonin modulation on medial prefrontal connectivity strength and stability: A pharmacological fMRI study with citalopram

BACKGROUND

Static and dynamic functional connectivity are being increasingly used to measure the effects of disease and a range of different interventions on brain networks. While preliminary evidence suggests that static connectivity can be modulated by chronic antidepressants administration in healthy individuals and in major depression, much less is known about the acute effects of antidepressants especially on dynamic functional connectivity changes. Here we examine acute effects of antidepressants on dynamic functional connectivity within the default mode network. The default mode network is a well described network with many functions in which the role of serotonin is not clear.

METHODS

In this work we measured acute pharmacological effects of an infusion of the selective serotonin reuptake inhibitor (SSRI) citalopram (10 mg) in a sample of thirteen healthy volunteers randomised to receive on two occasions the active compound or placebo in a cross over dosing.

RESULTS

Acute citalopram administration relative to placebo increased static connectivity between the medial prefrontal cortex and right dorsolateral prefrontal cortex and posterior cingulate cortex. The SSRI also induced a reduction in variability of connectivity with the medial prefrontal cortex in the precuneus and posterior cingulate cortex.

DISCUSSION

The measured changes are compatible with modified serotonin cortical availability.

Randomised clinical trial: gastrointestinal events in arthritis patients treated with celecoxib, ibuprofen or naproxen in the PRECISION trial

AIM

To evaluate GI safety of celecoxib compared with 2 nonselective (ns) NSAIDs, as a secondary objective of a large trial examining multiorgan safety.

METHODS

This randomised, double-blind controlled trial analysed 24 081 patients. Osteoarthritis or rheumatoid arthritis patients, needing ongoing NSAID treatment, were randomised to receive celecoxib 100-200 mg b.d., ibuprofen 600-800 mg t.d.s. or naproxen 375-500 mg b.d. plus esomeprazole, and low-dose aspirin or corticosteroids if already prescribed. Clinically significant GI events (CSGIE-bleeding, obstruction, perforation events from stomach downwards or symptomatic ulcers) and iron deficiency anaemia (IDA) were adjudicated blindly.

RESULTS

Mean treatment and follow-up durations were 20.3 and 34.1 months. While on treatment or 30 days after, CSGIE occurred in 0.34%, 0.74% and 0.66% taking celecoxib, ibuprofen and naproxen. Hazard ratios (HR) were 0.43 (95% CI 0.27-0.68, P = 0.0003) celecoxib vs ibuprofen and 0.51 (0.32-0.81, P = 0.004) vs naproxen. There was also less IDA on celecoxib: HR 0.43 (0.27-0.68, P = 0.0003) vs ibuprofen; 0.40 (0.25-0.62, P < 0.0001) vs naproxen. Even taken with low-dose aspirin, fewer CSGIE occurred on celecoxib than ibuprofen (HR 0.52 [0.29-0.94], P = 0.03), and less IDA vs naproxen (0.42 [0.23-0.77, P = 0.005]). Corticosteroid use increased total GI events and CSGIE. H. pylori serological status had no influence.

CONCLUSIONS

Arthritis patients taking NSAIDs plus esomeprazole have infrequent clinically significant gastrointestinal events. Co-prescribed with esomeprazole, celecoxib has better overall GI safety than ibuprofen or naproxen at these doses, despite treatment with low-dose aspirin or corticosteroids.

Using Pulsed-Field Gel Electrophoresis to Analyze Schizosaccharomyces pombe Chromosomes and Chromosomal Elements

Pulsed field gel electrophoresis (PFGE) uses alternatively oriented pulsed electrical fields to separate large DNA molecules. Here, we describe PFGE protocols and conditions for separating and visualizing chromosomes between 0.5 and 6 Mb (optimal for analyzing the endogenous fission yeast chromosomes of 5.7, 4.6, and 3.5 Mb), and for shorter chromosomal elements of between 50 and 600 kb, such as the 530 kb Ch¹⁶ minichromosome. In addition to determining chromosome size, this technique has a wide range of applications, including determining whether DNA replication or repair is complete, defining the molecular karyotype of cells, analyzing chromosomal rearrangements, assigning genes or constructs to particular chromosomes, and isolating DNA from specific chromosomes.