Construction of a novel phagemid to produce custom DNA origami scaffolds.

DNA origami, a method for constructing nanoscale objects, relies on a long single strand of DNA to act as the 'scaffold' to template assembly of numerous short DNA oligonucleotide 'staples'. The ability to generate custom scaffold sequences can greatly benefit DNA origami design processes. Custom scaffold sequences can provide better control of the overall size of the final object and better control of low-level structural details, such as locations of specific base pairs within an object. Filamentous bacteriophages and related phagemids can work well as sources of custom scaffold DNA. However, scaffolds derived from phages require inclusion of multi-kilobase DNA sequences in order to grow in host bacteria, and those sequences cannot be altered or removed. These fixed-sequence regions constrain the design possibilities of DNA origami. Here, we report the construction of a novel phagemid, pScaf, to produce scaffolds that have a custom sequence with a much smaller fixed region of 393 bases. We used pScaf to generate new scaffolds ranging in size from 1512 to 10 080 bases and demonstrated their use in various DNA origami shapes and assemblies. We anticipate our pScaf phagemid will enhance development of the DNA origami method and its future applications

First principles study of topological phase in chains of 3d3d transition metals

Recent experiments have shown the signatures of Majorana bound states at the ends of magnetic chains deposited on a superconducting substrate. Here, we employ first principles calculations to directly investigate the topological properties of $3d$ transition metal nanochains (i.e., Mn, Cr, Fe and Co). In contrast to the previous studies [Nadj-Perge et al. Science 346, 602 (2014) and Ruby et al. Nano Lett. 17, 4473 (2017)], we found the exact tight binding models in the Wannier orbital basis for the isolated chains as well as for the surface--deposited wires. Based on these models, we calculate topological invariant of $\mathbb{Z}_2$ phase for all systems. Our results for the isolated chains demonstrate the existence of the topological phase only in the Mn and Co systems. We considered also a non-collinear magnetic order as a source of the non--trivial topological phase and found that this type of magnetic order is not a stable ground state in the Fe and Co isolated chains. Further studies showed that a coupling between the chain and substrate leads to strong modification of the band structure. Moreover, the analysis of the topological invariant indicates a possibility of emergence of the topological phase in all studied nanochains deposited on the Pb surface. Therefore, our results demonstrate an important role of the coupling between deposited atoms and a substrate for topological properties of nanosystems.Comment: 11 pages, 7 figure

STATISTICS OF GYNECOLOGICAL MALIGNANCIES

The paper analyzes data on the state-of-the-art of oncological care given to patients with gynecological cancer, considers differences in morbidity rates between individual population groups and regions, and compares the maximum and minimum cancer morbidity rates among different populations

Eddy genesis and manipulation in plane laminar shear flow

Eddy formation and presence in a plane laminar shear flow configuration consisting of two infinitely long plates orientated parallel to each other is investigated theoretically. The upper plate, which is planar, drives the flow; the lower one has a sinusoidal profile and is fixed. The governing equations are solved via a full finite element formulation for the general case and semi-analytically at the Stokes flow limit. The effects of varying geometry (involving changes in the mean plate separation or the amplitude and wavelength of the lower plate) and inertia are explored separately. For Stokes flow and varying geometry, excellent agreement between the two methods of solution is found. Of particular interest with regard to the flow structure is the importance of the clearance that exists between the upper plate and the tops of the corrugations forming the lower one. When the clearance is large, an eddy is only present at sufficiently large amplitudes or small wavelengths. However, as the plate clearance is reduced, a critical value is found which triggers the formation of an eddy in an otherwise fully attached flow for any finite amplitude and arbitrarily large wavelength. This is a precursor to the primary eddy to be expected in the lid-driven cavity flow which is formed in the limit of zero clearance between the plates. The influence of the flow driving mechanism is assessed by comparison with corresponding solutions for the case of gravity-driven fluid films flowing over an undulating substrate. When inertia is present, the flow generally becomes asymmetrical. However, it is found that for large mean plate separations the flow local to the lower plate becomes effectively decoupled from the inertia dominated overlying flow if the wavelength of the lower plate is sufficiently small. In such cases the local flow retains its symmetry. A local Reynolds number based on the wavelength is shown to be useful in characterising these large-gap flows. As the mean plate separation is reduced, the form of the asymmetry caused by inertia changes, and becomes strongly dependent on the plate separation. For lower plate wavelengths which do not exhibit a cinematically induced secondary eddy, an inertially induced secondary eddy can be created if the mean plate separation is sufficiently small and the global Reynolds number sufficiently large

Assessing the content validity of the Manchester–Oxford Foot Questionnaire in surgically treated ankle fracture patients: a qualitative study

Background Roughly 10% of fractures in adults are ankle fractures. These injuries are found in both sexes and present with different fracture characteristics. The treatment varies with the patients’ biology and fracture type, and the goals are to restore stability, prevent pain and maintain ankle function. Clinicians generally use outcomes like assessment of radiography, pain level, or function. The use of patient-reported outcome measures is increasing, and the Manchester–Oxford Foot Questionnaire (MOXFQ) has been shown to have good measurement properties when validated in patients with foot and ankle disorders. However, the instrument has not been validated for ankle fracture patients. This study aims to assess the content validity of the items in MOXFQ in surgically treated ankle fracture patients. Methods A qualitative deductive design was used to investigate patients’ response process of the MOXFQ. Individual interviews were conducted using cognitive interviewing based on the theoretical framework of the 4-step model by Tourangeau. Adult patients that were surgically treated for an ankle fracture between four weeks and 18 months were purposively sampled, and interviews followed a semi-structured interview guide. The predetermined categories were comprehension, retrieval, judgement, and response. Results Seventeen respondents (65% females) were interviewed. Respondents’ age ranged from 27 to 76 years. Some of the respondents in the early recovery phase were limited by post-operative restrictions and did not find the items in the walking/standing domain relevant. Respondents that were allowed weight-bearing as tolerated (WBAT) were able to recall relevant information for most items. Respondents with time since surgery more than 12 months had less pain and remembered fewer relevant episodes in the recall period. Items in the social interaction domain contained ambiguous questions and were generally considered less important by respondents. The summary index score lacked important concepts in measuring overall quality of life. Conclusions Pain was a central concept in the post-operative recovery of ankle fracture patients. The MOXFQ-subscales for pain and walking/standing had acceptable content validity in patients that were allowed WBAT. The social interaction-subscale and the summary index score had insufficient content validity for this patient population.publishedVersio

Interactive Multiple Object Tracking (iMOT)

We introduce a new task for exploring the relationship between action and attention. In this interactive multiple object tracking (iMOT) task, implemented as an iPad app, participants were presented with a display of multiple, visually identical disks which moved independently. The task was to prevent any collisions during a fixed duration. Participants could perturb object trajectories via the touchscreen. In Experiment 1, we used a staircase procedure to measure the ability to control moving objects. Object speed was set to 1°/s. On average participants could control 8.4 items without collision. Individual control strategies were quite variable, but did not predict overall performance. In Experiment 2, we compared iMOT with standard MOT performance using identical displays. Object speed was set to 2°/s. Participants could reliably control more objects (M = 6.6) than they could track (M = 4.0), but performance in the two tasks was positively correlated. In Experiment 3, we used a dual-task design. Compared to single-task baseline, iMOT performance decreased and MOT performance increased when the two tasks had to be completed together. Overall, these findings suggest: 1) There is a clear limit to the number of items that can be simultaneously controlled, for a given speed and display density; 2) participants can control more items than they can track; 3) task-relevant action appears not to disrupt MOT performance in the current experimental context

Three-body recombination rates near a Feshbach resonance within a two-channel contact interaction model

We calculate the three-body recombination rate into a shallow dimer in a gas of cold bosonic atoms near a Feshbach resonance using a two-channel contact interaction model. The two-channel model naturally describes the variation of the scattering length through the Feshbach resonance and has a finite effective range. We confront the theory with the available experimental data and show that the two-channel model is able to quantitatively describe the existing data. The finite effective range leads to a reduction of the scaling factor between the recombination minima from the universal value of 22.7. The reduction is larger for larger effective ranges or, correspondingly, for narrower Feshbach resonances.Comment: 9 pages, 7 figure