Small-scale intraspecific life history variation in herbivorous spider mites (Tetranychus pacificus) is associated with host plant cultivar.

Life history variation is a general feature of arthropod systems, but is rarely included in models of field or laboratory data. Most studies assume that local processes occur identically across individuals, ignoring any genetic or phenotypic variation in life history traits. In this study, we tested whether field populations of Pacific spider mites (Tetranychus pacificus) on grapevines (Vitis vinifera) display significant intraspecific life history variation associated with host plant cultivar. To address this question we collected individuals from sympatric vineyard populations where either Zinfandel or Chardonnay were grown. We then conducted a "common garden experiment" of mites on bean plants (Phaseolus lunatus) in the laboratory. Assay populations were sampled non-destructively with digital photography to quantify development times, survival, and reproductive rates. Two classes of models were fit to the data: standard generalized linear mixed models and a time-to-event model, common in survival analysis, that allowed for interval-censored data and hierarchical random effects. We found a significant effect of cultivar on development time in both GLMM and time-to-event analyses, a slight cultivar effect on juvenile survival, and no effect on reproductive rate. There were shorter development times and a trend towards higher juvenile survival in populations from Zinfandel vineyards compared to those from Chardonnay vineyards. Lines of the same species, originating from field populations on different host plant cultivars, expressed different development times and slightly different survival rates when reared on a common host plant in a common environment

Isothermal microwave biology : catalysis and fermentation

This thesis looks directly into the controversial subject of the microwave field effect by the production of a versatile prototype isothermal microwave reactor for the investigation of enzymatic and microbiological reactions. The observed results from the prototype reactor and experiments conducted conclude that there is a nonthermal, nonlinear response between the exposure microwave power and rate and yield of cellulose saccharification. The nature of the nonthermal response is controversial and may be dependent on the definition of "nonthermal,' leading to ambiguity of exact mechanism. Enzymatic and microbial conversion of cellulosic material to ethanol is a highly desirable industrial process. Whether the demand is for the mitigation of climate change, political obligations or energy independence, the use of arable land for energy crops limits the available glucose carbon sources for conversion to bioproducts. To prevent this limitation, cellulose (~-l,4-linked glucose polymers) are touted as the "silver bullet" to prevent carbon exhaustion or impinging on food crops. The technical constraint for the industrialization of cellulose based processing is the rate limitation in the cellulase enzymatic action on cellulose. The enzyme rate is limited by feedback cycles and limited mechanical freedom, therefore a relatively high enzyme concentration is required to speed up the process. To date, the associated enzyme production costs and infrastructure prevents bulk volume exploitation. Biomolecular advances (amino acid substitutions, recombination of expression vectors etc) have gone some way to increase either enzymatic rate or enzyme concentration. The work presented in this thesis differs by increasing the rate of the enzyme without molecular modification. Using a microwave field, the work presented shows that by separating the system into its base units, irradiation of the enzyme/substrate complex in an aqueous environment can increase both the initial enzyme rate and the saccharification yield without alteration of the temperature set point. This study shows that the rate increase is not proportional to the microwave field power. An optimal power in each study is either found or suggested. The results cited show that in the three systems (Endoglucanase and cellobiohydrolase with cellulose, endoglucanase and cellobiohydrolase and ~- glucosidase with cellulose, and ~-glucosidase with cellobiose) the initial rates can be increased by 201 %, 65.5% and 69% respectively. In the total hydrolytic process (endoglucanase and cellobiohydrolase and ~-glucosidase on a cellulose substrate) the final glucose yield was increased by 43% in comparison to the conventional thermal control reaction. This is shown in Figure 1. 10.000 1 9.000 1 8.000 j 7.000 6.000 o 20 40 60 80 100 120 140 160 180 I I 1 I U 5.000 r:: o u 4.000 3.000 2.000 j i t t , f 1.000 0.000 Time (hours) =->=OOOW Glucose' ?012W Glucose ?p025W Glucose ~050W Glucose ?075W Glucose Figure 1. Microwave irradiated "cellulase" enzymes with cellulose substrate I For development into an industrial system and looking towards simultaneous saccharification and fermentation (SSF), the yeast Saccharomyces cerevisiae was subjected to irradiated microwave fermentations on a glucose substrate. Although inconclusive in terms of rate increase, cell density 1 was comparable across the power range showing that the irradiation does not have a derogatory effect. ! The natural evolution of the conclusions drawn would be development of the system into a SSF or SSCF configuration for bio-product formation is possible with irradiation up to SOW. ii The novelty of the experiments conducted is twofold. Firstly, the reactor has been designed to ensure that the microwave irradiation is independent of the bulk temperature therefore allowing the exploration of the microwave field effect independently to the thermal effect. Secondly, the microwave source is a continuous microwave irradiation (none pulse irradiation) ensuring that the reaction is subjected to the microwave field for the entire reaction

What to expect from a non-suspicious prostate MRI? A review = Que peut-on attendre d’une IRM prostatique non suspecte ? Une revue de la littérature

BACKGROUND: Many guidelines now recommend multiparametric MRI (mpMRI) prior to an initial or repeat prostate biopsy. However, clinical decision making for men with a non-suspicious mpMRI (Likert or PIRADS score 1-2) varies. OBJECTIVES: To review the most recent literature to answer three questions. (1) Should we consider systematic biopsy if mpMRI is not suspicious? (2) Are there additional predictive factors that can help decide which patient should have a biopsy? (3) Can the low visibility of some cancers be explained and what are the implications? SOURCES: A narrative review was performed in Medline databases using two searches with the terms "MRI" and "prostate cancer" and ("diagnosis" or "biopsy") and ("non-suspicious" or "negative" or "invisible"); "prostate cancer MRI visible". References of the selected articles were screened for additional articles. STUDY SELECTION: Studies published in the last 5 years in English language were assessed for eligibility and selected if data was available to answer one of the three study questions. RESULTS: Considering clinically significant cancer as ISUP grade≥2, the negative predictive value (NPV) of mpMRI in various settings and populations ranges from 76% to 99%, depending on cancer prevalence and the type of confirmatory reference test used. NPV is higher among patients with prior negative biopsy (88-96%), and lower for active surveillance patients (85-90%). The PSA density (PSAd) with a threshold of PSAd<0.15ng/ml/ml was the most studied and relevant predictive factor used in combination with mpMRI to rule out clinically significant cancer. Finally, mpMRI-invisible tumours appear to differ from a histopathological and genetic point of view, conferring clinical advantage to invisibility. LIMITATIONS: Most published data come from expert centres and results may not be reproducible in all settings. CONCLUSION: mpMRI has high diagnostic accuracy and in cases of negative mpMRI, PSA density can be used to determine which patient should have a biopsy. Growing knowledge of the mechanisms and genetics underlying MRI visibility will help develop more accurate risk calculators and biomarkers

Boundary-RL: Reinforcement Learning for Weakly-Supervised Prostate Segmentation in TRUS Images

We propose Boundary-RL, a novel weakly supervised segmentation method that utilises only patch-level labels for training. We envision the segmentation as a boundary detection problem, rather than a pixel-level classification as in previous works. This outlook on segmentation may allow for boundary delineation under challenging scenarios such as where noise artefacts may be present within the region-of-interest (ROI) boundaries, where traditional pixel-level classification-based weakly supervised methods may not be able to effectively segment the ROI. Particularly of interest, ultrasound images, where intensity values represent acoustic impedance differences between boundaries, may also benefit from the boundary delineation approach. Our method uses reinforcement learning to train a controller function to localise boundaries of ROIs using a reward derived from a pre-trained boundary-presence classifier. The classifier indicates when an object boundary is encountered within a patch, as the controller modifies the patch location in a sequential Markov decision process. The classifier itself is trained using only binary patch-level labels of object presence, which are the only labels used during training of the entire boundary delineation framework, and serves as a weak signal to inform the boundary delineation. The use of a controller function ensures that a sliding window over the entire image is not necessary. It also prevents possible false-positive or -negative cases by minimising number of patches passed to the boundary-presence classifier. We evaluate our proposed approach for a clinically relevant task of prostate gland segmentation on trans-rectal ultrasound images. We show improved performance compared to other tested weakly supervised methods, using the same labels e.g., multiple instance learning.Comment: Accepted to MICCAI Workshop MLMI 2023 (14th International Conference on Machine Learning in Medical Imaging

Image quality assessment for machine learning tasks using meta-reinforcement learning

In this paper, we consider image quality assessment (IQA) as a measure of how images are amenable with respect to a given downstream task, or task amenability. When the task is performed using machine learning algorithms, such as a neural-network-based task predictor for image classification or segmentation, the performance of the task predictor provides an objective estimate of task amenability. In this work, we use an IQA controller to predict the task amenability which, itself being parameterised by neural networks, can be trained simultaneously with the task predictor. We further develop a meta-reinforcement learning framework to improve the adaptability for both IQA controllers and task predictors, such that they can be fine-tuned efficiently on new datasets or meta-tasks. We demonstrate the efficacy of the proposed task-specific, adaptable IQA approach, using two clinical applications for ultrasound-guided prostate intervention and pneumonia detection on X-ray images

Natural history of prostate cancer on active surveillance: stratification by MRI using the PRECISE recommendations in a UK cohort

Objectives: The PRECISE recommendations for magnetic resonance imaging (MRI) in patients on active surveillance (AS) for prostate cancer (PCa) include repeated measurement of each lesion, and attribution of a PRECISE radiological progression score for the likelihood of clinically significant change over time. We aimed to compare the PRECISE score with clinical progression in patients who are managed using an MRI-led AS protocol. Methods: A total of 553 patients on AS for low- and intermediate-risk PCa (up to Gleason score 3 + 4) who had two or more MRI scans performed between December 2005 and January 2020 were included. Overall, 2161 scans were retrospectively re-reported by a dedicated radiologist to give a PI-RADS v2 score for each scan and assess the PRECISE score for each follow-up scan. Clinical progression was defined by histological progression to ≥ Gleason score 4 + 3 (Gleason Grade Group 3) and/or initiation of active treatment. Progression-free survival was assessed using Kaplan-Meier curves and log-rank test was used to assess differences between curves. Results: Overall, 165/553 (30%) patients experienced the primary outcome of clinical progression (median follow-up, 74.5&nbsp;months; interquartile ranges, 53–98). Of all patients, 313/553 (57%) did not show radiological progression&nbsp;on MRI (PRECISE 1–3), of which 296/313 (95%) had also no clinical progression. Of the remaining 240/553 patients (43%) with radiological progression&nbsp;on MRI (PRECISE 4–5), 146/240 (61%) experienced clinical progression (p &lt; 0.0001). Patients with radiological progression&nbsp;on&nbsp;MRI (PRECISE 4-5) showed a trend to an increase in PSA density. Conclusions: Patients without radiological progression on MRI (PRECISE 1-3) during AS had a very low likelihood of clinical progression and many could avoid routine re-biopsy. Key Points: • Patients&nbsp;without radiological progression on MRI (PRECISE 1–3) during&nbsp;AS had a very low likelihood of clinical progression and many could avoid routine re-biopsy. • Clinical progression was almost always detectable in patients with radiological progression on MRI (PRECISE 4–5)&nbsp;during AS. • Patients with radiological progression&nbsp;on MRI (PRECISE 4–5)&nbsp;during AS showed a trend to an increase in PSA density

Linking farmer and beekeeper preferences with ecological knowledge to improve crop pollination

1. Pollination by insects is a key input into many crops, with managed honeybees often being hired to support pollination services. Despite substantial research into pollination management, no European studies have yet explored how and why farmers managed pollination services and few have explored why beekeepers use certain crops. 2. Using paired surveys of beekeepers and farmers in 10 European countries, this study examines beekeeper and farmer perceptions and motivations surrounding crop pollination. 3. Almost half of the farmers surveyed believed they had pollination service deficits in one or more of their crops. 4. Less than a third of farmers hired managed pollinators, however most undertook at least one form of agri-environment management known to benefit pollinators, although few did so to promote pollinators. 5. Beekeepers were ambivalent towards many mass flowering crops, with some beekeepers using crops for their honey that other beekeepers avoid because of perceived pesticide risks. 6. The findings highlight a number of largely overlooked knowledge gaps that will affect knowledge exchange and co-operation between the two groups