The DM Environment: From Annotation to Dissemination

DM (formerly Digital Mappaemundi) is an online environment that allows users to easily assemble collections of images and texts for study, produce their own rich analysis data, and publish online resources for individual, group or public use. DM is ready for multi-year work with five partner projects (including a new partnership with the British Library) to implement a publicly available user-friendly environment that enables users to 1) assemble collections of resources from any combination of accessible repositories; 2) create richly linked data (e.g., annotation networks involving combinations of images, texts, fragments, web resources, and other annotations) and collections, sequences and indices that organize this data; 3) export data in a number of linked data formats; and 4) easily produce publicly accessible and interactive websites based on such data and linked data published elsewhere

Rapid Metabolic Recovery Following Vigorous Exercise in Burrow-Dwelling Larval Sea Lampreys (\u3cem\u3ePetromyzon marinus\u3c/em\u3e)

Although the majority of the sea lamprey’s (Petromyzon marinus) life cycle is spent as a burrow-dwelling larva, or ammocoete, surprisingly little is known about intermediary metabolism in this stage of the lamprey’s life history. In this study, larval sea lampreys (ammocoetes) were vigorously exercised for 5 min, and their patterns of metabolic fuel depletion and replenishment and oxygen consumption, along with measurements of net whole-body acid and ion movements, were followed during a 4–24-h postexercise recovery period. Exercise led to initial five- to sixfold increases in postexercise oxygen consumption, which remained significantly elevated by 1.5–2.0 times for the next 3 h. Exercise also led to initial 55% drops in whole-body phosphocreatine, which was restored by 0.5 h, but no significant changes in whole-body adenosine triphosphate were observed. Whole-body glycogen concentrations dropped by 70% immediately following exercise and were accompanied by a simultaneous ninefold increase in lactate. Glycogen and lactate were quickly restored to resting levels after 0.5 and 2.0 h, respectively. The presence of an associated metabolic acidosis was supported by very high rates of metabolic acid excretion, which approached 1,000 nmol g-1 during the first 2 h of postexercise recovery. Exercise-induced ion imbalances were also rapidly alleviated, as initially high rates of net Na+ and Cl- loss (—1,200 nmol g-1h-1 and —1,800 nmol g-1h-1 respectively) were corrected within 1–2 h. Although larval sea lampreys spend most of their time burrowed, they are adept at performing and recovering from vigorous anaerobic exercise. Such attributes could be important when these animals are vigorously swimming or burrowing as they evade predators or forage

Using citation-context to reduce topic drifting on pure citation-based recommendation

Recent works in the area of academic recommender systems have demonstrated the effectiveness of co-citation and citation closeness in related-document recommendations. However, documents recommended from such systems may drift away from the main theme of the query document. In this work, we investigate whether incorporating the textual information in close proximity to a citation as well as the citation position could reduce such drifting and further increase the performance of the recommender system. To investigate this, we run experiments with several recommendation methods on a newly created and now publicly available dataset containing 53 million unique citation-based records. We then conduct a user-based evaluation with domain-knowledgeable participants. Our results show that a new method based on the combination of Citation Proximity Analysis (CPA), topic modelling and word embeddings achieves more than 20% improvement in Normalised Discounted Cumulative Gain (nDCG) compared to CPA

Mapping Computational Thinking Skills to the South African Secondary School Mathematics Curriculum

Computational thinking (CT) is gaining recognition as an important skill for learners in both Computer Science (CS) and several other disciplines, including mathematics. In addition, researchers have shown that there is a direct correlation between poor mathematical skills and the high attrition rate of CS undergraduates. This research investigates the use of nine core CT skills in the South African Grades 10–12 Mathematics curriculum by mapping these skills to the objectives given in each of the topics in the curriculum. The artefact developed shows that all the identified CT skills are used in the curriculum. With the use of this mapping, future research on interventions to develop these skills through mathematics at secondary school, should produce school leavers with better mathematical and problem solving abilities, which in turn, might contribute to better success rates in CS university courses

Raman Spectroscopy of Lymphocytes for the Identification of Prostate Cancer Patients with Late Radiation Toxicity Following Radiotherapy

The success of radiotherapy in tumour control depends on the total dose given. However, the tolerance of the normal tissues surrounding the tumour limits this dose. It is not known why some patients develop radiation toxicity and, currently, it is not possible to predict before treatment which patients will experience adverse effects. Thus, there is an unmet clinical need for a new test to identify patients at risk of radiation toxicity. Here, we report a new approach based on Raman spectroscopy.Blood samples were collected from 42 patients who had undergone radiotherapy for prostate cancer and had shown either severe or no/minimal late radiation toxicity in follow up. Radiation response was assessed following in vitro irradiation using Raman spectroscopy in addition to the G2 chromosomal radiosensitivity assay and the H2AX DNA damage assay.A Partial Least Squares Discriminant Analysis model was developed to classify patients using known radiation toxicity scores. A sensitivity of 95%, specificity of 92% and overall accuracy of 93% was achieved. In the future, this technology may have potential to lead to individualised patient radiotherapy by identifying which patients are at risk of radiation toxicity

Vibrational Spectroscopy of Liquid Biopsies for Prostate Cancer Diagnosis

Background: Screening for prostate cancer with prostate specific antigen and digital rectal examination allows early diagnosis of prostate malignancy but has been associated with poor sensitivity and specificity. There is also a considerable risk of over-diagnosis and overtreatment, which highlights the need for better tools for diagnosis of prostate cancer. This study investigates the potential of high throughput Raman and Fourier Transform Infrared (FTIR) spectroscopy of liquid biopsies for rapid and accurate diagnosis of prostate cancer. Methods: Blood samples (plasma and lymphocytes) were obtained from healthy control subjects and prostate cancer patients. FTIR and Raman spectra were recorded from plasma samples, while Raman spectra were recorded from the lymphocytes. The acquired spectral data was analysed with various multivariate statistical methods, principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA) and classical least squares (CLS) fitting analysis. Results: Discrimination was observed between the infrared and Raman spectra of plasma and lymphocytes from healthy donors and prostate cancer patients using PCA. In addition, plasma and lymphocytes displayed differentiating signatures in patients exhibiting different Gleason scores. A PLS-DA model was able to discriminate these groups with sensitivity and specificity rates ranging from 90% to 99%. CLS fitting analysis identified key analytes that are involved in the development and progression of prostate cancer. Conclusions: This technology may have potential as an alternative first stage diagnostic triage for prostate cancer. This technology can be easily adaptable to many other bodily fluids and could be useful for translation of liquid biopsy-based diagnostics into the clinic

Effect of hemolysis on Fourier transform infrared and Raman spectra of blood plasma

Hemolysis is a very common phenomenon and is referred as the release of intracellular components from red blood cells to the extracellular fluid. Hemolyzed samples are often rejected in clinics due to the interference of hemoglobin and intracellular components in laboratory measurements. Plasma and serum based vibrational spectroscopy studies are extensively applied to generate spectral biomarkers for various diseases. However, no studies have reported the effect of hemolysis in blood based vibrational spectroscopy studies. This study was undertaken to evaluate the effect of hemolysis on infrared and Raman spectra of blood plasma. In this study, prostate cancer plasma samples (n = 30) were divided into three groups (nonhemolyzed, mildly hemolyzed, and moderately hemolyzed) based on the degree of hemolysis and FTIR and Raman spectra were recorded using high throughput (HT)-FTIR and HT-Raman spectroscopy. Discrimination was observed between the infrared and Raman spectra of nonhemolyzed and hemolyzed plasma samples using principal component analysis. A classical least square fitting analysis showed differences in the weighting of pure components in nonhemolyzed and hemolyzed plasma samples. Therefore, it is worth to consider the changes in spectral features due to hemolysis when comparing the results within and between experiments

Prediction of DNA Damage and G2 Chromosomal Radio-Sensitivity Ex-vivo in Peripheral Blood Mononuclear Cells with Label-Free Raman Microspectroscopy

Liquid biopsies are a potentially rich store of biochemical information that can be linked to an individual’s response to therapeutic treatments, including radiotherapy, and which may ultimately play a role in the individualization of treatment regimens. Peripheral blood mononuclear cells (PBMCs) can be used for the biochemical profiling of the individual, but also, being living cells, can provide insights into the individuals response to ionizing radiation exposure

Adapting to 4 Degrees C World

The Paris Agreement\u27s goal to hold warming to 1.50-2 0 C above pre-industrial levels now appears unrealistic. Profs. Robin Kundis Craig and J.B. Ruhl have recently argued that because a 40 C world may be likely, we must recognize the disruptive consequences of such a world and respond by reimagining governance structures to meet the challenges of adapting to it. In this latest in a biannual series of essays, they and other members of the Environmental Law Collaborative explore what 40 C might mean for a variety of current legal doctrines, planning policies, governance structures, and institutions