ABSTRACT: Alternative course formats are gaining increasing attention in higher education. The literature provides a number of examples and studies of flipped classrooms in the medical sciences and liberal arts and sciences. However, fewer than five papers on flipped classes in graduate public health courses have been published, and none in health management. Because graduate public health education is competency based, it seems that a flipped approach with its applied nature would be an appropriate form of teaching public health courses. This paper describes three successfully flipped courses taught in a school of public health. We provide a rationale for flipping, description of each course, and lessons learned. Once some of the challenges are overcome, we believe flipping courses can provide an alternative approach that enhances active learning in applied, public health, and health management courses.
Project description:Background:Flipped classroom (FC) instruction has become increasingly common in graduate medical education (GME). Objective:The purpose of this study was to profile the use of FC in the GME setting and assess the current status of research quality. Methods:We conducted a systematic literature search of major health and social science databases from July 2017 to July 2018. Articles were screened to ensure they described use of the FC method in an Accreditation Council for Graduate Medical Education-accredited residency program and included research outcomes. Resulting articles were analyzed, described, and evaluated for research quality using the Kirkpatrick framework and the Medical Education Research Study Quality Instrument (MERSQI). Results:Twenty-two articles were identified, all of which were recently published. Five were only indirectly related to FC methods. Most studies reported Kirkpatrick-level outcomes. Studies involving resident learner opinions were generally positive. Pre-posttest studies resulted in large positive improvements in knowledge or skills attainment. Control group study results ranged from large positive (1.56) to negative effects (-0.51). Average MERSQI scores of 12.1 (range, 8.5-15.5) were comparable to GME research norms. Conclusions:Varying methods for implementing and studying the FC in GME has led to variable results. While residents expressed a positive attitude toward FC learning, shortcomings were reported. Approximately half of the studies comparing the flipped to the traditional classroom reported better achievement under the FC design. As indicated by the MERSQI score, studies captured by this review, on average, were as rigorous as typical research on residency education.
Project description:PspGI is a representative of a group of restriction endonucleases that recognize a pentameric sequence related to CCNGG. Unlike the previously investigated Ecl18kI, which does not have any specificity for the central base pair, PspGI prefers A/T over G/C in its target site. Here, we present a structure of PspGI with target DNA at 1.7 A resolution. In this structure, the bases at the center of the recognition sequence are extruded from the DNA and flipped into pockets of PspGI. The flipped thymine is in the usual anti conformation, but the flipped adenine takes the normally unfavorable syn conformation. The results of this and the accompanying manuscript attribute the preference for A/T pairs over G/C pairs in the flipping position to the intrinsically lower penalty for flipping A/T pairs and to selection of the PspGI pockets against guanine and cytosine. Our data show that flipping can contribute to the discrimination between normal bases. This adds a new role to base flipping in addition to its well-known function in base modification and DNA damage repair.
Project description:The bacterial Tn5 and Tn10 transposases have a single active site that cuts both strands of DNA at their respective transposon ends. This is achieved using a hairpin intermediate that requires the DNA to change conformation during the reaction. In Tn5 these changes are controlled in part by a flipped nucleoside that is stacked on a tryptophan residue in a hydrophobic pocket of the transposase. Here we have investigated the base flipping mechanism in Tn10 transposition. As in Tn5 transposition, we find that base flipping takes place after the first nick and is required for efficient hairpin formation and resolution. Experiments with an abasic substrate show that the role of base flipping in hairpin formation is to remove the base from the DNA helix. Specific interactions between the flipped base and the stacking tryptophan residue are required for hairpin resolution later in the reaction. We show that base flipping in Tn10 transposition is not a passive reaction in which a spontaneously flipped base is captured and retained by the protein. Rather, it is driven in part by a methionine probe residue that helps to force the flipped base from the base stack. Overall, it appears that base flipping in Tn10 transposition is similar to that in Tn5 transposition.
Project description:Base flipping in DNA is an important process involved in genomic repair and epigenetic control of gene expression. The driving forces for these processes are not fully understood, especially in the context of the underlying dynamics of the DNA and solvent effects. We studied double-stranded DNA oligomers that have been previously characterized by imino proton exchange NMR using both additive and polarizable force fields. Our results highlight the importance of induced polarization on the base flipping process, yielding near-quantitative agreement with experimental measurements of the equilibrium between the base-paired and flipped states. Further, these simulations allow us to quantify for the first time the energetic implications of polarization on the flipping pathway. Free energy barriers to base flipping are reduced by changes in dipole moments of both the flipped bases that favor solvation of the bases in the open state and water molecules adjacent to the flipping base.
Project description:As for UV-induced DNA damage, which may induce skin cancer in animals and growth inhibition in plants, there are two types of photoproducts, namely cis-sin cyclobutane pyrimidine dimers (CPD) and pyrimidine-pyrimidone (6-4) photoproducts. When they are to be repaired, base-flipping occurs, and they bind to enzymes. However, this process remains relatively unknown at a molecular level. We analyze conformation and interaction energy changes upon base-flipping using classical molecular dynamics (CMD) simulations and ab initio electronic structure calculations. CMD simulations starting with a CPD in the flipped-in and flipped-out states showed that both states were unchanged for 500 ns, indicating the flipped-in and flipped-out processes do not occur spontaneously (without any help of the enzyme) after photo-damage. To deeply understand the reasons, we investigated interaction energy changes among bases upon structure changes during the flipped-in and flipped-out processes using Parallel Cascade Selection-MD (PaCS-MD) simulations at 400 K, followed by a fragment molecular orbital (FMO) method. The total inter-fragment interaction energy (IFIE) between CPD and other bases at the flipped-in state is estimated to be -60.08 kcal/mol. In particular, four bases strongly interact with CPD with interaction energies being -10.96, -13.70, -21.52, and -14.46 kcal/mol each. On the other hand, the total IFIE at the obtained flipped-out state increased to -10.40 kcal/mol by partly losing hydrogen bonds and ?-? stacking interactions, respectively. These results clearly indicate that the base-flipping process of DNA lesions occurs with the help of external forces like interactions with appropriate enzymes such as photolyases.
Project description:The photo-induced cis-syn-cyclobutane pyrimidine (CPD) dimer is a frequent DNA lesion. In bacteria photolyases efficiently repair dimers employing a light-driven reaction after flipping out the CPD damage to the active site. How the repair enzyme identifies a damaged site and how the damage is flipped out without external energy is still unclear. Employing molecular dynamics free energy calculations, the CPD flipping process was systematically compared to flipping undamaged nucleotides in various DNA global states and bound to photolyase enzyme. The global DNA deformation alone (without protein) significantly reduces the flipping penalty and induces a partially looped out state of the damage but not undamaged nucleotides. Bound enzyme further lowers the penalty for CPD damage flipping with a lower free energy of the flipped nucleotides in the active site compared to intra-helical state (not for undamaged DNA). Both the reduced penalty and partial looping by global DNA deformation contribute to a significantly shorter mean first passage time for CPD flipping compared to regular nucleotides which increases the repair likelihood upon short time encounter between repair enzyme and DNA.
Project description:Base flipping is a common strategy utilized by many enzymes to gain access to the functional groups of nucleic acid bases in duplex DNA which are otherwise protected by the DNA backbone and hydrogen bonding with their partner bases. Several X-ray crystallography studies have revealed flipped conformations of nucleotides bound to enzymes. However, little is known about the base-flipping process itself, even less about the role of the enzymes. Computational studies have used umbrella sampling to elicit the free energy profile of the base-flipping process using a pseudodihedral angle to represent the reaction coordinate. In this study, we have used an unrestrained trajectory in which a flipped base spontaneously reinserted into the helix in order to evaluate and improve the previously defined pseudodihedral angle. Our modified pseudodihedral angles use a new atom selection to improve the numerical stability of the restraints and also provide better correlation to the extent of flipping observed in simulations. Furthermore, on the basis of the comparison of potential of mean force (PMF) generated using different reaction coordinates, we observed that the shape of a flipping PMF profile is strongly dependent on the definition of the reaction coordinate, even for the same data set.
Project description:Individual DNA bases are known to be able to flip out of the helical stack, providing enzymes with access to the genetic information otherwise hidden inside the helix. Consequently, base flipping is a necessary first step to many more complex biological processes such as DNA transcription or replication. Much remains unknown about this elementary step, despite a wealth of experimental and theoretical studies. From the theoretical point of view, the involved timescale of milliseconds or longer requires the use of enhanced sampling techniques. In contrast to previous theoretical studies employing umbrella sampling along a predefined flipping coordinate, this study attempts to induce flipping without prior knowledge of the pathway, using information from a molecular dynamics simulation of a B-DNA fragment and the conformational flooding method. The relevance to base flipping of the principal components of the simulation is assayed, and a combination of modes optimally related to the flipping of the base through either helical groove is derived for each of the two bases of the central guanine-cytosine basepair. By applying an artificial flooding potential along these collective coordinates, the flipping mechanism is accelerated to within the scope of molecular dynamics simulations. The associated free energy surface is found to feature local minima corresponding to partially flipped states, particularly relevant to flipping in isolated DNA; further transitions from these minima to the fully flipped conformation are accelerated by additional flooding potentials. The associated free energy profiles feature similar barrier heights for both bases and pathways; the flipped state beyond is a broad and rugged attraction basin, only a few kcal/mol higher in energy than the closed conformation. This result diverges from previous works but echoes some aspects of recent experimental findings, justifying the need for novel approaches to this difficult problem: this contribution represents a first step in this direction. Important structural factors involved in flipping, both local (sugar-phosphate backbone dihedral angles) and global (helical axis bend), are also identified.
Project description:Invoice printing just has two-color printing, so invoice font image can be seen as binary image. To embed watermarks into invoice image, the pixels need to be flipped. The more huge the watermark is, the more the pixels need to be flipped. We proposed a new pixels flipping method in invoice image for huge watermarking capacity. The pixels flipping method includes one novel interpolation method for binary image, one flippable pixels evaluation mechanism, and one denoising method based on gravity center and chaos degree. The proposed interpolation method ensures that the invoice image keeps features well after scaling. The flippable pixels evaluation mechanism ensures that the pixels keep better connectivity and smoothness and the pattern has highest structural similarity after flipping. The proposed denoising method makes invoice font image smoother and fiter for human vision. Experiments show that the proposed flipping method not only keeps the invoice font structure well but also improves watermarking capacity.
Project description:Sequestration of soil organic carbon (SOC) has been recognized as an opportunity to off-set global carbon dioxide (CO<sub>2</sub> ) emissions. Flipping (full inversion to 1-3 m) is a practice used on New Zealand's South Island West Coast to eliminate water-logging in highly podzolized sandy soils. Flipping results in burial of SOC formed in surface soil horizons into the subsoil and the transfer of subsoil material low in SOC to the "new" topsoil. The aims of this study were to quantify changes in the storage and stability of SOC over a 20-year period following flipping of high-productive pasture grassland. Topsoils (0-30 cm) from sites representing a chronosequence of flipping (3-20 years old) were sampled (2005/07) and re-sampled (2017) to assess changes in topsoil carbon stocks. Deeper samples (30-150 cm) were also collected (2017) to evaluate the changes in stocks of SOC previously buried by flipping. Density fractionation was used to determine SOC stability in recent and buried topsoils. Total SOC stocks (0-150 cm) increased significantly by 69 ± 15% (179 ± 40 Mg SOC ha<sup>-1</sup> ) over 20 years following flipping. Topsoil burial caused a one-time sequestration of 160 ± 14 Mg SOC ha<sup>-1</sup> (30-150 cm). The top 0-30 cm accumulated 3.6 Mg SOC ha<sup>-1</sup> year<sup>-1</sup> . The chronosequence and re-sampling revealed SOC accumulation rates of 1.2-1.8 Mg SOC ha<sup>-1</sup> year<sup>-1</sup> in the new surface soil (0-15 cm) and a SOC deficit of 36 ± 5% after 20 years. Flipped subsoils contained up to 32% labile SOC (compared to <1% in un-flipped subsoils) thus buried SOC was preserved. This study confirms that burial of SOC and the exposure of SOC depleted subsoil results in an overall increase of SOC stocks of the whole soil profile and long-term SOC preservation.