d/Deafness and the Basic Course: A Case Study of Universal Instructional Design and Students Who are d/Deaf in the (aural) Communication Classroom

The primary purpose of this essay is to suggest ways to create a universally inclusive curriculum, which, by definition, addresses the learning needs of all students, including students with disabilities or, in this case, students who are deaf or hard-of-hearing. Presented with the opportunity of having a d/Deaf students in a public speaking class, we reflect on the accommodations made, the assumptions inherent in an inclusive classroom, and the ideology of ableism. Because d/Deafness is as much a cultural identity as an auditory condition, we also address how to create safe learning environments for diverse student populations through the use of Universal Instructional Design

Combined quantification of the global proteome, phosphoproteome, and proteolytic cleavage to characterize altered platelet functions in the human Scott syndrome

The Scott syndrome is a very rare and likely underdiagnosed bleeding disorder associated with mutations in the gene encoding anoctamin-6. Platelets from Scott patients are impaired in various Ca(2+)-dependent responses, including phosphatidylserine exposure, integrin closure, intracellular protein cleavage, and cytoskeleton-dependent morphological changes. Given the central role of anoctamin-6 in the platelet procoagulant response, we used quantitative proteomics to understand the underlying molecular mechanisms and the complex phenotypic changes in Scott platelets compared with control platelets. Therefore, we applied an iTRAQ-based multi-pronged strategy to quantify changes in (1) the global proteome, (2) the phosphoproteome, and (3) proteolytic events between resting and stimulated Scott and control platelets. Our data indicate a limited number of proteins with decreased (70) or increased (64) expression in Scott platelets, among those we confirmed the absence of anoctamin-6 and the strong up-regulation of aquaporin-1 by parallel reaction monitoring. The quantification of 1566 phosphopeptides revealed major differences between Scott and control platelets after stimulation with thrombin/convulxin or ionomycin. In Scott platelets, phosphorylation levels of proteins regulating cytoskeletal or signaling events were increased. Finally, we quantified 1596 N-terminal peptides in activated Scott and control platelets, 180 of which we identified as calpain-regulated, whereas a distinct set of 23 neo-N termini was caspase-regulated. In Scott platelets, calpain-induced cleavage of cytoskeleton-linked and signaling proteins was downregulated, in accordance with an increased phosphorylation state. Thus, multipronged proteomic profiling of Scott platelets provides detailed insight into their protection against detrimental Ca(2+)-dependent changes that are normally associated with phosphatidylserine exposure

High Arctic aircraft measurements characterising black carbon vertical variability in spring and summer

The vertical distribution of black carbon (BC) par- ticles in the Arctic atmosphere is one of the key parameters controlling their radiative forcing and thus role in Arctic cli- mate change. This work investigates the presence and prop- erties of these light-absorbing aerosols over the High Cana- dian Arctic ( > 70 degree N). Airborne campaigns were performed as part of the NETCARE project (Network on Climate and Aerosols: Addressing Key Uncertainties in Remote Canadian Environments) and provided insights into the variability of the vertical distributions of BC particles in summer 2014 and spring 2015. The observation periods covered evolutions of cyclonic disturbances at the polar front, which favoured the transport of air pollution into the High Canadian Arctic, as otherwise this boundary between the air masses largely im- pedes entrainment of pollution from lower latitudes. A total of 48 vertical profiles of refractory BC (rBC) mass concen- tration and particle size, extending from 0.1 to 5.5 km altitude were obtained with a Single-Particle Soot Photometer (SP2). Generally, the rBC mass concentration decreased from spring to summer by a factor of 10. Such depletion was as- sociated with a decrease in the mean rBC particle diameter, from approximately 200 to 130 nm at low altitude. Due to the very low number fraction, rBC particles did not substantially contribute to the total aerosol population in summer. The analysis of profiles with potential temperature as ver- tical coordinate revealed characteristic variability patterns within specific levels of the cold and stably stratified, dome- like, atmosphere over the polar region. The associated his- tory of transport trajectories into each of these levels showed that the variability was induced by changing rates and effi- ciencies of rBC import. Generally, the source areas affecting the polar dome extended southward with increasing potential temperature (i.e. altitude) level in the dome. While the lower dome was mostly only influenced by low-level transport from sources within the cold central and marginal Arctic, for the mid-dome and upper dome during spring it was found that a cold air outbreak over eastern Europe caused intensified northward transport of air from a corridor over western Rus- sia to central Asia. This sector was affected by emissions from gas flaring, industrial activity and wildfires. The devel- opment of transport caused rBC concentrations in the second lowest level to gradually increase from 32 to 49 ng

A Conceptual Framework for Social, Behavioral, and Environmental Change through Stakeholder Engagement in Water Resource Management

Incorporating stakeholder engagement into environmental management may help in the pursuit of novel approaches for addressing complex water resource problems. However, evidence about how and under what circumstances stakeholder engagement enables desirable changes remains elusive. In this paper, we develop a conceptual framework for studying social and environmental changes possible through stakeholder engagement in water resource management, from inception to outcomes. We synthesize concepts from multiple literatures to provide a framework for tracing linkages from contextual conditions, through engagement process design features, to social learning, community capacity building, and behavioral change at individual, group, and group network levels, and ultimately to environmental change. We discuss opportunities to enhance the framework including through empirical applications to delineate scalar and temporal dimensions of social, behavioral, and environmental changes resulting from stakeholder engagement, and the potential for negative outcomes thus far glossed over in research on change through engagement

Rapid Immunomagnetic Negative Enrichment of Neutrophil Granulocytes from Murine Bone Marrow for Functional Studies In Vitro and In Vivo

Polymorphonuclear neutrophils (PMN) mediate early immunity to infection but can also cause host damage if their effector functions are not controlled. Their lack or dysfunction is associated with severe health problems and thus the analysis of PMN physiology is a central issue. One prerequisite for PMN analysis is the availability of purified cells from primary organs. While human PMN are easily isolated from peripheral blood, this approach is less suitable for mice due to limited availability of blood. Instead, bone marrow (BM) is an easily available reservoir of murine PMN, but methods to obtain pure cells from BM are limited. We have developed a novel protocol allowing the isolation of highly pure untouched PMN from murine BM by negative immunomagnetic isolation using a complex antibody cocktail. The protocol is simple and fast (∼1 h), has a high yield (5–10*106 PMN per animal) and provides a purity of cells equivalent to positive selection (>80%). Most importantly, cells obtained by this method are non-activated and remain fully functional in vitro or after adoptive transfer into recipient animals. This method should thus greatly facilitate the study of primary murine PMN in vitro and in vivo

iTRAQ protein quantification: a quality-controlled workflow

Reporter ion-based methods are among the major techniques to quantify peptides and proteins. Two main labels, tandem mass tag (TMT) and iTRAQ, are widely used by the proteomics community. They are, however, often applied as out-of-the-box methods, without thorough quality control. Thus, due to undiscovered limitations of the technique, irrelevant results might be trusted. To address this issue, we here propose a step-by-step quality control of the iTRAQ workflow. From sample preparation to final ratio calculation we provide metrics and techniques assessing the actual effectiveness of iTRAQ quantification as well as a novel method for more reliable protein ratio estimation

Peptide identification quality control

Identification of large proteomics data sets is routinely performed using sophisticated software tools called search engines. Yet despite the importance of the identification process, its configuration and execution is often performed according to established lab habits, and is mostly unsupervised by detailed quality control. In order to establish easily obtainable quality control criteria that can be broadly applied to the identification process, we here introduce several simple quality control methods. An unbiased quality control of identification parameters will be conducted using target/decoy searches providing significant improvement over identification standards. MASCOT identifications were for instance increased by 13% at a constant level of confidence. The target/decoy approach can however not be universally applied. We therefore also quality control the application of this strategy itself, providing useful and intuitive metrics for evaluating the precision and robustness of the obtained false discovery rate

A complex standard for protein identification, designed by evolution

Shotgun proteomic investigations rely on the algorithmic assignment of mass spectra to peptides. The quality of these matches is therefore a cornerstone in the analysis and has been the subject of numerous recent developments. In order to establish the benefits of novel algorithms, they are applied to reference samples of known content. However, these were recently shown to be either too simple to resemble typical real-life samples or as leading to results of lower accuracy as the method itself. Here, we describe how to use the proteome of Pyrococcus furiosus, a hyperthermophile, as a standard to evaluate proteomics identification workflows. Indeed, we prove that the Pyrococcus furiosus proteome provides a valid method for detecting random hits, comparable to the decoy databases currently in popular use, but we also prove that the Pyrococcus furiosus proteome goes squarely beyond the decoy approach by also providing many hundreds of highly reliable true positive hits. Searching the Pyrococcus furiosus proteome can thus be used as a unique test that provides the ability to reliably detect both false positives as well as proteome-scale true positives, allowing the rigorous testing of identification algorithms at the peptide and protein level