Automated Plankton Classification With a Dynamic Optimization and Adaptation Cycle

With recent advances in Machine Learning techniques based on Deep Neural Networks (DNNs), automated plankton image classification is becoming increasingly popular within the marine ecological sciences. Yet, while the most advanced methods can achieve human-level performance on the classification of everyday images, plankton image data possess properties that frequently require a final manual validation step. On the one hand, this is due to morphological properties manifesting in high intra-class and low inter-class variability, and, on the other hand is due to spatial-temporal changes in the composition and structure of the plankton community. Composition changes enforce a frequent updating of the classifier model via training with new user-generated training datasets. Here, we present a Dynamic Optimization Cycle (DOC), a processing pipeline that systematizes and streamlines the model adaptation process via an automatic updating of the training dataset based on manual-validation results. We find that frequent adaptation using the DOC pipeline yields strong maintenance of performance with respect to precision, recall and prediction of community composition, compared to more limited adaptation schemes. The DOC is therefore particularly useful when analyzing plankton at novel locations or time periods, where community differences are likely to occur. In order to enable an easy implementation of the DOC pipeline, we provide an end-to-end application with graphical user interface, as well as an initial dataset of training images. The DOC pipeline thus allows for high-throughput plankton classification and quick and systematized model adaptation, thus providing the means for highly-accelerated plankton analysis

Risk factors of post renal transplant anaemia among Sudanese patients, a study in three renal transplant centres

<p>Abstract</p> <p>Background</p> <p>There is a relative lack of recent information about late post kidney transplantation anaemia (PTA), especially in the developing countries; data are scarce about the prevalence and risk factors of PTA. Sudan was a leading country in Africa and Arab world in kidney transplantation. The first kidney transplantation in Sudan was in 1973.</p> <p>Methods</p> <p>This is a cross-sectional hospital analytic study enrolling all kidney transplanted recipients following in the transplant referral clinics at Ahmed Gassim, Selma and Ibn Sina Hospitals, Khartoum/Sudan, in the period from 1/8/2010 to 1/9/2010, clinical and laboratory data were obtained from 114 patients, anaemia was defined as Hb levels of < 13 g/dl for male patients and < 12 g/dl for female patients, exclusion criteria were pregnancy, below 18 years old patients, multiple organ transplantation, and patients with less than one year from the transplantation.</p> <p>Results</p> <p>The study showed that 39.5% of the patients were anaemic. Univariate analysis showed that late PTA is significantly associated with not using Erythropoietin (EPO) in the pre-transplant period (p = < 0.001), history of rejection (p = 0.003), longer time from transplantation (p = 0.015), and eGFR (p < 0.0001). Multivariate analysis showed that eGFR (p = < 0.001) and not use of EPO in the pre transplant period (p < 0.001) are strong predictors of PTA. The use of Angiotensin converting enzyme inhibitors/Angiotensin receptors blockers (ACEI/ARB), immunosuppressive treatments, presence or absence of co-morbidities, donor type and donor age are not significantly associated with late PTA.</p> <p>Conclusion</p> <p>The study concluded that late PTA is common and under recognized. Risk factors for late PTA include renal dysfunction, history of rejection, longer duration of transplantation and not using EPO in the pre-transplant period. Renal dysfunction and not using EPO in the pre-transplant period are major predictors of late PTA.</p

A self-rating scale for patient-perceived side effects of inhaled corticosteroids

BACKGROUND: Patient-reported side effect questionnaires offer a simple method for the systematic measurement of drug-related side effects. In order to measure patients' inhaled corticosteroids (ICS) related side effect perceptions the 14-day retrospective Inhaled Corticosteroid Questionnaire (ICQ) was developed. In this research we aim to assess the construct validity and reliability of the ICQ and test its responsiveness to dose changes in adult asthma patients. METHODS: In a cross-sectional study, current inhaler users with asthma completed the ICQ (27 with non ICS inhaler; 61 BDP equivalent daily ICS low dose ≤400 μg; 62 mid dose 401–800 μg; and 105 with high dose >800 μg). We generated 3 construct validity hypotheses: 1) a hierarchical dose-response pattern for scoring of the individual items on the ICQ, and statistically significant differences in the scores of each of the 15 ICQ domains by ICS dose group 2) an association between ICS dose and ICQ scoring after adjusting for appropriate confounders in multiple regression; 3) greater convergence between local side effect domains than between systemic and local domains of the scale. Test-retest reliability was assessed on a randomly selected subgroup of patients (n = 73) who also completed the ICQ a second time after 7 days. In a separate longitudinal study, 61 patients with asthma completed the ICQ at baseline and after changing their daily ICS dose, at 2- and 6- months, in order to test the ICQ's responsiveness. RESULTS: All three construct validity hypotheses were well supported: 1) a statistically significant difference existed in scores for 14 domains, the high ICS dose group scoring highest; 2) ICS dose independently predicted ICQ scoring after adjusting for confounders; 3) greater convergence existed between local ICQ domains than between local and systemic domains. The ICQ had good reproducibility: test-retest intraclass correlation coefficients were ≥0.69 for all but the 'Facial Oedema' domain. In the longitudinal study, ICQ scores for 'Voice Problems' changed significantly at 2- and 6-months from baseline and other ICQ domains displayed trends in scoring change accordant with dose modulation at 6-months. CONCLUSION: The ICQ has good dose-related discriminative properties, is valid, reliable, and shows potential responsiveness to ICS dose change

Benzothiazinones kill Mycobacterium tuberculosis by blocking arabinan synthesis

New drugs are required to counter the tuberculosis (TB) pandemic. Here, we describe the synthesis and characterization of 1,3-benzothiazin-4-ones (BTZs), a new class of antimycobacterial agents that kill Mycobacterium tuberculosis in vitro, ex vivo, and in mouse models of TB. Using genetics and biochemistry, we identified the enzyme decaprenylphosphoryl-beta-d-ribose 2'-epimerase as a major BTZ target. Inhibition of this enzymatic activity abolishes the formation of decaprenylphosphoryl arabinose, a key precursor that is required for the synthesis of the cell-wall arabinans, thus provoking cell lysis and bacterial death. The most advanced compound, BTZ043, is a candidate for inclusion in combination therapies for both drug-sensitive and extensively drug-resistant TB

Is upper gastrointestinal radiography a cost-effective alternative to a Helicobacter pylori “Test and Treat” strategy for patients with suspected peptic ulcer disease?

Current clinical consensus supports an initial Helicobacter pylori (HP) “test and treat” approach when compared to immediate endoscopy for patients with suspected peptic ulcer disease. Alternative diagnostic approaches that incorporate upper GI radiography (UGI) have not been previously evaluated. We sought to determine the cost effectiveness of UGI compared to a HP test and treat strategy, incorporating recent data addressing the reduced prevalence of HP, lower cost of diagnostic interventions, and reduced attribution of PUD to HP. METHODS : Using decision analysis, three diagnostic and treatment strategies were evaluated: 1) Test and Treat —initial HP serology, treat patients who test positive with HP eradication and antiulcer therapy; 2) Initial UGI series —treat all patients with documented ulcer disease with HP eradication and antiulcer therapy; and 3) Initial UGI series, HP serology if ulcer present — treat ulcer and HP based on diagnostic test results. RESULTS : The estimated cost per ulcer cured for each strategy were as follows: test and treat, $3,025; initial UGI,$3,690; and UGI with serology, $3,790. The estimated cost per patient treatment were: test and treat,$498; initial UGI, $610; and UGI with serology,$620. When UGI reimbursement was decreased to less than $50, the UGI strategies yielded a lower cost per patient treated than the test and treat strategy. CONCLUSION : At the current level of reimbursement, UGI should not be considered a cost-effective alternative to the HP test and treat strategy for the initial evaluation of patients with suspected peptic ulcer disease.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73722/1/j.1572-0241.2000.01837.x.pd

Visions of the Victorian Scientist

This project surveys the scientist as a character in British novels from 1818 to 1909. Almost every major nineteenth-century novelist wrote at least one “scientist novel,” including Wilkie Collins, Charles Dickens, George Eliot, Elizabeth Gaskell, Thomas Hardy, Mary Shelley, and H. G. Wells. I argue that this happened because the realist novel is an ideal experimental space for epistemologies: its protracted engagement with ways of thinking allows it to test both the accuracy and ethics of epistemologies. These novels depict science as a way of seeing with ethical repercussions in order to explore what happens when science turns its gaze upon human beings. In doing so, these novelists were both responding to and shaping a new vision of science in British culture: During this period, “science” became codified as a distinct epistemological practice, the amateur “man of science” was replaced by the professional “scientist,” and science turned its gaze upon the human realm in the form of new sciences such as sociology and psychology. If the new scientist’s way of seeing left him unable to perceive even his lover with accuracy or caused him to behave unethically toward his community, then how could science’s claims about human thought and human society be trusted? I trace how novelists engage with these questions by exploring the way the novel depicts science as a unique visual practice that manifests in different human realms—such as romantic relationships, projects of social reform, the domestic space, and war—while contextualizing these novels in the ways the Victorians themselves talked about the ethical implications of seeing like a scientist. In doing so, I intervene in the study of Victorian science and literature by suggesting that the Victorian novel was not only responding to the new disciplines and discoveries of science, but to the new way of seeing the world that the scientist embodied

Comparative analysis European wide marine ecosystem shifts - a large scale approach for developing the basis for ecosystem-based management

Abrupt and rapid ecosystem shifts (where major reorganizations of food-web and community structures occur), commonly termed regime shifts, are changes between contrasting and persisting states of ecosystem structure and function. These shifts have been increasingly reported for exploited marine ecosystems around the world from the North Pacific to the North Atlantic. Understanding the drivers and mechanisms leading to marine ecosystem shifts is crucial in developing adaptive management strategies to achieve sustainable exploitation of marine ecosystems. An international workshop on a comparative approach to analysing these marine ecosystem shifts was held at Hamburg University, Institute for Hydrobiology and Fisheries Science, Germany on 1-3 November 2010. Twenty-seven scientists from 14 countries attended the meeting, representing specialists from seven marine regions, including the Baltic Sea, the North Sea, the Barents Sea, the Black Sea, the Mediterranean Sea, the Bay of Biscay and the Scotian Shelf off the Canadian East coast. The goal of the workshop was to conduct the first large-scale comparison of marine ecosystem regime shifts across multiple regional areas, in order to support the development of ecosystem-based management strategies

Stable landings mask irreversible community reorganizations in an overexploited Mediterranean ecosystem

Cumulative human pressures and climate change can induce nonlinear discontinuous dynamics in ecosystems, known as regime shifts. Regime shifts typically imply hysteresis, a lacking or delayed system response when pressures are reverted, which can frustrate restoration efforts. Here, we investigate whether the northern Adriatic Sea fish and macroinvertebrate community, as depicted by commercial fishery landings, has undergone regime shifts over the last 40 years, and the reversibility of such changes. We use a stochastic cusp model to show that, under the interactive effect of fishing pressure and water warming, the community reorganized through discontinuous changes. We found that part of the community has now reached a new stable state, implying that a recovery towards previous baselines might be impossible. Interestingly, total landings remained constant across decades, masking the low resilience of the community. Our study reveals the importance of carefully assessing regime shifts and resilience in marine ecosystems under cumulative pressures and advocates for their inclusion into management