180 research outputs found

    Inquiry-based Experiments for Large-scale Introduction to PCR and Eestriction Enzyme Digests

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    Polymerase chain reaction and restriction endonuclease digest are important techniques that should be included in all Biochemistry and Molecular Biology laboratory curriculums. These techniques are frequently taught at an advanced level, requiring many hours of student and faculty time. Here we present two inquiry-based experiments that are designed for introductory laboratory courses and combine both techniques. In both approaches, students must determine the identity of an unknown DNA sequence, either a gene sequence or a primer sequence, based on a combination of PCR product size and restriction digest pattern. The experimental design is flexible, and can be adapted based on available instructor preparation time and resources, and both approaches can accommodate large numbers of students. We implemented these experiments in our courses with a combined total of 584 students and have an 85% success rate. Overall, students demonstrated an increase in their understanding of the experimental topics, ability to interpret the resulting data, and proficiency in general laboratory skills

    Skewed recoil polarization in (e,e'p) reactions from polarized nuclei

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    The general formalism describing A(e,ep)B\vec{A}(\vec{e},e'\vec{p})B reactions, involving polarization of the electron beam, target and ejected proton, is presented within the framework of the relativistic plane wave impulse approximation for medium and heavy nuclei. It is shown that the simultaneous measurement of the target and ejected proton polarization can provide new information which is not contained in the separate analysis of the A(e,ep)B\vec{A}(\vec{e},e'p)B and A(e,ep)BA(\vec{e},e'\vec{p})B reactions. The polarization transfer mechanism in which the electron interacts with the initial nucleon carrying the target polarization, making the proton exit with a fractional polarization in a different direction, is referred to here as ``skewed polarization''. The new observables characterizing the process are identified, and written in terms of polarized response functions and asymmetries which are of tensor nature. The corresponding half-off-shell single-nucleon responses are analyzed using different prescriptions for the electromagnetic vertex and for different kinematics. Numerical predictions are presented for selected perpendicular and parallel kinematics in the case of 39^{39}K as polarized target.Comment: 30 pages, 8 figure

    Bacterial vaccines and serotype replacement: lessons from Haemophilus influenzae and prospects for Streptococcus pneumoniae.

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    Conjugate vaccines have reduced the incidence of invasive disease caused by Haemophilus influenzae, type b (Hib), in industrialized countries and may be highly effective against Streptococcus pneumoniae. However, the serotype specificity of these vaccines has led to concern that their use may increase carriage of and disease from serotypes not included in the vaccine. Replacement has not occurred with the use of Hib vaccines but has occurred in trials of pneumococcal vaccines. Mathematical models can be used to elucidate these contrasting outcomes, predict the conditions under which serotype replacement is likely, interpret the results of conjugate vaccine trials, design trials that will better detect serotype replacement (if it occurs), and suggest factors to consider in choosing the serotype composition of vaccines

    Refinement type contracts for verification of scientific investigative software

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    Our scientific knowledge is increasingly built on software output. User code which defines data analysis pipelines and computational models is essential for research in the natural and social sciences, but little is known about how to ensure its correctness. The structure of this code and the development process used to build it limit the utility of traditional testing methodology. Formal methods for software verification have seen great success in ensuring code correctness but generally require more specialized training, development time, and funding than is available in the natural and social sciences. Here, we present a Python library which uses lightweight formal methods to provide correctness guarantees without the need for specialized knowledge or substantial time investment. Our package provides runtime verification of function entry and exit condition contracts using refinement types. It allows checking hyperproperties within contracts and offers automated test case generation to supplement online checking. We co-developed our tool with a medium-sized (\approx3000 LOC) software package which simulates decision-making in cognitive neuroscience. In addition to helping us locate trivial bugs earlier on in the development cycle, our tool was able to locate four bugs which may have been difficult to find using traditional testing methods. It was also able to find bugs in user code which did not contain contracts or refinement type annotations. This demonstrates how formal methods can be used to verify the correctness of scientific software which is difficult to test with mainstream approaches

    Managing international branch campuses: what do we know? [forthcoming]

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    peer-reviewedOver the last decade, the growth of the international branch campus (IBC) has been one of the most striking developments in the internationalisation of higher education. There are now over 200 IBCs across the world, mostly in the Middle East and East and South‐east Asia. Despite the growing numbers of IBCs and the considerable financial and reputational risk they pose to their home universities, relatively little is known about the challenges of managing these foreign outposts. This paper reviews the growing, but still fragmented, literature in this increasingly important sector of higher education. It finds that managers of IBCs are faced with a range of challenges, which primarily stem from dealing with key stakeholder groups: students, staff, home and host country quality regulators, the home university and the host government, as well as the IBC's local joint venture partners. It concludes that further work is required to better understand the factors which influence and constrain IBC managers in balancing the competing interests of stakeholders.ACCEPTEDpeer-reviewe

    Glucose Depletion in the Airway Surface Liquid Is Essential for Sterility of the Airways

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    Diabetes mellitus predisposes the host to bacterial infections. Moreover, hyperglycemia has been shown to be an independent risk factor for respiratory infections. The luminal surface of airway epithelia is covered by a thin layer of airway surface liquid (ASL) and is normally sterile despite constant exposure to bacteria. The balance between bacterial growth and killing in the airway determines the outcome of exposure to inhaled or aspirated bacteria: infection or sterility. We hypothesized that restriction of carbon sources –including glucose– in the ASL is required for sterility of the lungs. We found that airway epithelia deplete glucose from the ASL via a novel mechanism involving polarized expression of GLUT-1 and GLUT-10, intracellular glucose phosphorylation, and low relative paracellular glucose permeability in well-differentiated cultures of human airway epithelia and in segments of airway epithelia excised from human tracheas. Moreover, we found that increased glucose concentration in the ASL augments growth of P. aeruginosa in vitro and in the lungs of hyperglycemic ob/ob and db/db mice in vivo. In contrast, hyperglycemia had no effect on intrapulmonary bacterial growth of a P. aeruginosa mutant that is unable to utilize glucose as a carbon source. Our data suggest that depletion of glucose in the airway epithelial surface is a novel mechanism for innate immunity. This mechanism is important for sterility of the airways and has implications in hyperglycemia and conditions that result in disruption of the epithelial barrier in the lung

    Equal opportunities: Do shareable interfaces promote more group participation than single users displays?

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    Computers designed for single use are often appropriated suboptimally when used by small colocated groups working together. Our research investigates whether shareable interfaces–that are designed for more than one user to inter-act with–can facilitate more equitable participation in colocated group settings compared with single user displays. We present a conceptual framework that characterizes Shared Information Spaces (SISs) in terms of how they constrain and invite participation using different entry points. An experiment was conducted that compared three different SISs: a physical-digital set-up (least constrained), a multitouch tabletop (medium), and a laptop display (most constrained). Statistical analyses showed there to be little difference in participation levels between the three conditions other than a predictable lack of equity of control over the interface in the laptop condition. However, detailed qualitative analyses revealed more equitable participation took place in the physical-digital condition in terms of verbal utterances over time. Those who spoke the least contributed most to the physical design task. The findings are discussed in relation to the conceptual framework and, more generally, in terms of how to select, design, and combine different display technologies to support collaborative activities

    Partner relationship satisfaction and maternal emotional distress in early pregnancy

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    <p>Abstract</p> <p>Background</p> <p>Recognition of maternal emotional distress during pregnancy and the identification of risk factors for this distress are of considerable clinical- and public health importance. The mental health of the mother is important both for herself, and for the physical and psychological health of her children and the welfare of the family. The first aim of the present study was to identify risk factors for maternal emotional distress during pregnancy with special focus on partner relationship satisfaction. The second aim was to assess interaction effects between relationship satisfaction and the main predictors.</p> <p>Methods</p> <p>Pregnant women enrolled in the Norwegian Mother and Child Cohort Study (n = 51,558) completed a questionnaire with questions about maternal emotional distress, relationship satisfaction, and other risk factors. Associations between 37 predictor variables and emotional distress were estimated by multiple linear regression analysis.</p> <p>Results</p> <p>Relationship dissatisfaction was the strongest predictor of maternal emotional distress (β = 0.25). Other predictors were dissatisfaction at work (β = 0.11), somatic disease (β = 0.11), work related stress (β = 0.10) and maternal alcohol problems in the preceding year (β = 0.09). Relationship satisfaction appeared to buffer the effects of frequent moving, somatic disease, maternal smoking, family income, irregular working hours, dissatisfaction at work, work stress, and mother's sick leave (<it>P </it>< 0.05).</p> <p>Conclusions</p> <p>Dissatisfaction with the partner relationship is a significant predictor of maternal emotional distress in pregnancy. A good partner relationship can have a protective effect against some stressors.</p
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