Protein structural variation in computational models and crystallographic data

Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the validation is typically limited to individual modes for a single protein. We use anisotropic displacement parameters from crystallography to test the quality of prediction of both the magnitude and directionality of conformational variance. Normal modes from four simple elastic network model potentials and from the CHARMM forcefield are calculated for a data set of 83 diverse, ultrahigh resolution crystal structures. While all five potentials provide good predictions of the magnitude of flexibility, the methods that consider all atoms have a clear edge at prediction of directionality, and the CHARMM potential produces the best agreement. The low-frequency modes from different potentials are similar, but those computed from the CHARMM potential show the greatest difference from the elastic network models. This was illustrated by computing the dynamic correlation matrices from different potentials for a PDZ domain structure. Comparison of normal mode results with anisotropic temperature factors opens the possibility of using ultrahigh resolution crystallographic data as a quantitative measure of molecular flexibility. The comprehensive evaluation demonstrates the costs and benefits of using normal mode potentials of varying complexity. Comparison of the dynamic correlation matrices suggests that a combination of topological and chemical potentials may help identify residues in which chemical forces make large contributions to intramolecular coupling.Comment: 17 pages, 4 figure

The usefulness of feedback

Feedback can occur before and after assessment submission, but needs to be useful in order for students to improve their subsequent performance. Arguably, undergraduate students, and particularly international, online and new students, are especially in need of feedback to effectively engage in academic and disciplinary expectations. Therefore, this article draws on survey data from students, disaggregated by mode of study, citizenship of enrolment and year of study, to explore their experiences of feedback usefulness both before and after assessment submission. Overall, undergraduate students were positive; however, this perception decreased according to their year level. Comparisons between online and international students also revealed key differences. A conclusion is that undergraduate students cannot be treated homogeneously, and educators need to attend to the feedback experiences of different student groups as they progress through their programme

What makes for effective feedback: staff and student perspectives

Since the early 2010s the literature has shifted to view feedback as a process that students do where they make sense of information about work they have done, and use it to improve the quality of their subsequent work. In this view, effective feedback needs to demonstrate effects. However, it is unclear if educators and students share this understanding of feedback. This paper reports a qualitative investigation of what educators and students think the purpose of feedback is, and what they think makes feedback effective. We administered a survey on feedback that was completed by 406 staff and 4514 students from two Australian universities. Inductive thematic analysis was conducted on data from a sample of 323 staff with assessment responsibilities and 400 students. Staff and students largely thought the purpose of feedback was improvement. With respect to what makes feedback effective, staff mostly discussed feedback design matters like timing, modalities and connected tasks. In contrast, students mostly wrote that high-quality feedback comments make feedback effective – especially comments that are usable, detailed, considerate of affect and personalised to the student’s own work. This study may assist researchers, educators and academic developers in refocusing their efforts in improving feedbac

Integer programming for minimal perturbation problems in university course timetabling

In this paper we present a general integer programming-based approach for the minimal perturbation problem in university course timetabling. This problem arises when an existing timetable contains hard constraint violations, or infeasibilities, which need to be resolved. The objective is to resolve these infeasibilities while minimising the disruption or perturbation to the remainder of the timetable. This situation commonly occurs in practical timetabling, for example when there are unexpected changes to course enrolments or available rooms. Our method attempts to resolve each infeasibility in the smallest neighbourhood possible, by utilising the exactness of integer programming. Operating within a neighbourhood of minimal size keeps the computations fast, and does not permit large movements of course events, which cause widespread disruption to timetable structure. We demonstrate the application of this method using examples based on real data from the University of Auckland

Three Chemically Distinct Floral Ecotypes in Drakaea livida, an Orchid Pollinated by Sexual Deception of Thynnine Wasps

Sexually deceptive orchids are unusual among plants in that closely related species typically attract different pollinator species using contrasting blends of floral volatiles. Therefore, intraspecific variation in pollinator attraction may also be underpinned by differences in floral volatiles. Here, we tested for the presence of floral ecotypes in the sexually deceptive orchid Drakaea livida and investigated if the geographic range of floral ecotypes corresponded to variation in pollinator availability. Pollinator choice trials revealed the presence of three floral ecotypes within D. livida that each attracts a different species of thynnine wasp as a pollinator. Surveys of pollinator distribution revealed that the distribution of one of the ecotypes was strongly correlated with that of its pollinator, while another pollinator species was present throughout the range of all three ecotypes, demonstrating that pollinator availability does not always correlate with ecotype distribution. Floral ecotypes differed in chemical volatile composition, with a high degree of separation evident in principal coordinate analysis. Some compounds that differed between ecotypes, including pyrazines and (methylthio)phenols, are known to be electrophysiologically active in thynnine wasp antennae. Based on differences in pollinator response and floral volatile profile, the ecotypes represent distinct entities and should be treated as such in conservation management

Conditions that enable effective feedback

© 2019, © 2019 HERDSA. Despite an increasing focus on assessment feedback, educators continue to find that simply replicating an effective feedback practice from one context does not guarantee success in the next. There is a growing recognition that the contextual factors surrounding successful practices need to be considered. This article reports on a large-scale mixed methods project and proposes 12 conditions that enable successful feedback in higher education. The conditions were distilled from seven rich case studies through multiple stages of thematic analysis, case comparison and reliability checking. The conditions were also evaluated by surveying senior leaders of Australian universities. These conditions highlight the importance of carefully designing feedback processes, along with the need for addressing capacity and culture for feedback. This helps to explain why there are such variances in effective feedback across contexts, and offers insight into how it may be achieved

Evaluation Nonlinear Soil Response In Situ

Evaluation of nonlinear soil properties is an important concern in geotechnical earthquake engineering. Typically, nonlinear properties are expressed in terms of the nonlinear reduction in shear and constrained moduli with strain and the nonlinear increase in material damping in shear and constrained compression with strain. At this time, there is essentially total dependency on laboratory testing to evaluate nonlinear soil properties. The accuracy and limitations involved in modeling in situ properties with laboratory evaluated properties remains to be studied. In an attempt to evaluate nonlinear soil properties directly in the field, an in situ test method is being developed at the University of Texas that dynamically loads a soil deposit while simultaneously measuring strains, soil properties, and pore water pressures. Initial testing with this method has focused on vertically loading an unsaturated sandy soil, evaluating the magnitude of induced strains, and assessing the variation of constrained modulus (in terms of compression wave velocity, VP) with effective vertical stress and vertical strain. Preliminary results show that the test method can be used to: (1) evaluate the increase in small-strain VP with increasing vertical effective stress, (2) induce nonlinear compressional and shear strains, and (3) evaluate the nonlinear reduction in VP with increasing vertical strain

A Systematic Review Including an Additional Pediatric Case Report: Pediatric Cases of Mammary Analogue Secretory Carcinoma

Importance Mammary Analogue Secretory Carcinoma (MASC) is a newly characterized salivary gland carcinoma resembling secretory carcinoma of the breast. Prior to being described, MASC was most commonly misdiagnosed as Acinic Cell Carcinoma. Though MASC is predominantly an adult neoplasm, cases have been reported in the pediatric population. Reporting and summarizing of known cases is imperative to understand the prognosis and clinical behavior of MASC. Objective (1) Report a rare case of pediatric MASC. (2) Review and consolidate the existing literature on MASC in the pediatric population. Evidence review Web of Science, Medline, EMBASE, and The Cochrane Library were searched for studies that included pediatric cases of MASC. Data on clinical presentation, diagnosis and management, and pathology were collected from all pediatric cases. Findings Case Report 14 year old with left-sided parotid mass diagnosed as MASC based on histology and immunohistochemistry. He was managed surgically with left superficial parotidectomy with selective neck dissection. Literature review The majority of MASC cases have been identified via retrospective reclassification of previously misclassified salivary gland tumors. Of all the pediatric cases (N=11) of MASC, the female-to-male ratio is 1:1.2 with an age range of 10-17 years old. The most common clinical presentation was a slowly growing, fixed, and painless mass of the parotid gland, often detected incidentally on physical examination. Common pathological features include eosinophilic vacuolated cytoplasm within cystic, tubular, and/or papillary architecture. Immunohistochemistry showed positivity for S100, mammaglobin, cytokeratin 19, and vimentin. The diagnosis was confirmed by the detection of the characteristic ETV6-NTRK6 fusion gene via fluorescent in-situ hybridization (FISH). Only 4 cases discussed treatment. Each of these underwent successful surgical resection alone with or without lymph node dissection. Conclusions and relevance Since the first case of MASC in the pediatric population was described in 2011, only 12 cases, including this one, have been described in the literature. With this paucity of information, much remains unknown regarding this new pathologic diagnosis. The collection of clinical outcomes data of children with MASC is needed to better understand the behavior of this malignancy as well as determine optimal treatment regimens

Temporal Simultons in Optical Parametric Oscillators

We report the first demonstration of a regime of operation in optical parametric oscillators (OPOs), in which the formation of temporal simultons produces stable femtosecond half-harmonic pulses. Simultons are simultaneous bright-dark solitons of a signal field at frequency ω and the pump field at 2ω, which form in a quadratic nonlinear medium. The formation of simultons in an OPO is due to the interplay of nonlinear pulse acceleration with the timing mismatch between the pump repetition period and the cold-cavity round-trip time and is evidenced by sech^2 spectra with broad instantaneous bandwidths when the resonator is detuned to a slightly longer round-trip time than the pump repetition period. We provide a theoretical description of an OPO operating in a regime dominated by these dynamics, observe the distinct features of simulton formation in an experiment, and verify our results with numerical simulations. These results represent a new regime of operation in nonlinear resonators, which can lead to efficient and scalable sources of few-cycle frequency combs at arbitrary wavelengths