Terahertz (THz) spectroscopy is a powerful tool for unambiguously extracting complex-valued material properties (e.g., refractive index, conductivity, etc.) from a wide range of samples, with ...applications ranging from materials science to biology. However, extracting complex refractive indices from THz time-domain spectroscopy data can prove challenging, especially for multilayer samples. These challenges arise from the large number of transmission-reflection paths the THz pulse can take through the sample layers, leading to unwieldy strings of Fresnel coefficients. This issue has often been addressed using various approximations. However, these approximations are only applicable to specific classes of samples and can give erroneous results when misapplied. An alternative to this approach is to programmatically model all possible paths through the sample. The many paths through the sample layers can be modeled as a tree that branches at every point where the paths diverge, i.e., whenever the pulse can either be transmitted or reflected. This tree can then be used to generate expressions relating the unknown refractive index to the observed time domain data. Here, we provide a freely available open-source package implementing this method as both a MATLAB library and a corresponding graphical user interface, which can also be run without a MATLAB license (https://github.com/YaleTHz/nelly). We have tested this method for a range of samples and compared the results to commonly used approximations to demonstrate its accuracy and wide applicability. Our method consistently gives better agreement than common approximations.
► Single-molecule analyses revealed diffusive behaviors of DNA repair proteins. ► 1D and 3D search and intersegmental transfer are used to locate the target loci. ► MutS forms distinct clamps on DNA ...before and after mismatch recognition. ► RAD52 uses 1D sliding to impose quality control on annealing of complementary strands. ► Homology search by RecA is facilitated by intersegmental transfer and 1D sliding.
Cellular DNA repair machines are constantly at work supporting the integrity of our genomes. Numerous proteins cooperate to form a complex and adaptive system dedicated to detection and timely processing of DNA damage. The molecular underpinnings of how these proteins locate and discriminate DNA lesions, match homologous sequences, mend the DNA and attend to a replication in distress are of a paramount biomedical importance, but in many cases remain unclear. Combined with more conventional tools, single-molecule biochemistry has been stepping in to address the age-old problems in the DNA repair field. This review will address new insights into diffusive properties of three DNA repair systems: I will discuss the emerging model of how MutS homologues locate and respond to mismatches in the dsDNA; the mechanism by which RAD52 promotes annealing of complementary DNA strands coated with ssDNA binding protein RPA; and how the nucleoprotein filament formed by RecA recombinase on ssDNA searches for homology within duplex DNA. These three distinct DNA repair factors exemplify the dynamic nature of cellular DNA repair machines revealed by single-molecule studies.
Canker and wood rot pathogens cause dieback and, in severe cases, the death of young apple trees. Recently, a higher occurrence of cankers was observed on 1-year-old apple trees in the Western Cape ...Province of South Africa. This study aimed to assess the phytosanitary status of nursery trees and propagation material as possible inoculum sources for canker pathogens. Thirteen 1-year-old apple orchards showing canker or dieback symptoms were sampled. Certified nursery apple trees were collected from four nurseries as well as scion and rootstock mother plant material. Isolations were made from the discoloration observed in the vascular tissue of the plant parts and from asymptomatic material. Possible canker and wood rot species were identified with PCR and sequence comparisons of the relevant gene regions and phylogenetic analyses. Similar canker and wood rot species were isolated from 1-year-old diseased apple trees, nursery apple trees, and the propagation material. Forty-five fungal species associated with canker or wood rot symptoms were identified. The top five most abundant fungal species found causing disease on commercial 1-year-old trees were also found in high numbers causing latent infection in certified apple nursery trees. These species were Didymosphaeria rubi-ulmifolii sensu lato, Diplodia seriata, Schizophyllum commune, Didymella pomorum, and Coniochaeta fasciculata, with D. rubi-ulmifolii sensu lato being the dominant species in both sampling materials. In all, 65% of certified nursery apple trees, 5% of scion shoots used for budding, and 21% of rooted rootstock cuttings from layer blocks had latent infections of canker and wood rot pathogens. Pathogenicity trials were conducted with isolates of 39 species, inoculated onto 2-year-old branches of 14-year-old Golden Delicious trees. All species caused lesions that were significantly longer than the control. This study confirmed the presence of canker and wood rot pathogens in apple propagation material as well as certified nursery apple trees, which will aid the improvement of management practices in nurseries.
Many physicians do not know how to accurately interpret test results using Bayes' rule. As a remedy, two kinds of interventions have been shown effective: boosting insight and boosting agency with ...natural frequencies. To boost insight, test statistics are provided in natural frequencies (rather than conditional probabilities), without instructions on how to use them. To boost agency, a training is provided on how to translate probabilities into natural frequencies and apply them in Bayes' rule. What has not been shown is whether boosting agency is sufficient or if representing test statistics in natural frequencies may additionally boost insight to maximize accurate test interpretation.
We used a pre/posttest design to assess test interpretation accuracy of 577 medical students before and after a training on two Bayesian reasoning tasks, one providing conditional probabilities, the other natural frequencies. The pretest assessed baseline abilities versus the effect of natural frequencies to boost insight. After participants received a training on how to translate conditional probabilities into natural frequencies and how to apply them in Bayes' rule, test interpretation skills were assessed using the same tasks again, comparing the effects of training-induced agency with versus without additionally boosting insight (i.e., test statistics in natural frequencies versus conditional probabilities).
Compared to the test question formatted in conditional probabilities (34% correct answers), natural frequencies facilitated Bayesian reasoning without training (68%), that is, they increased insight. The training on how to use natural frequencies improved performance for tasks formatted in conditional probabilities (64%). Performance was maximal after training and with test statistics formatted in natural frequencies, that is, with a combination of boosting insight and agency (89%).
Natural frequencies should be used to boost insight and agency to maximize effective use of teaching resources. Thus, mandating that test statistics are provided in natural frequencies and adopting short trainings on how to translate conditional probabilities into natural frequencies and how to apply them in Bayes' rule will help to maximize accurate test interpretation.
The study was a registered with the German Clinical Trial Registry ( DRKS00008723 ; 06/03/2015).
Scanning lidar remote sensing systems have recently become available for use in ecological applications. Unlike conventional microwave and optical sensors, lidar sensors directly measure the ...distribution of vegetation material along the vertical axis and can be used to provide three-dimensional, or volumetric, characterizations of vegetation structure. Ecological applications of scanning lidar have hitherto used one-dimensional indices to characterize canopy height. A novel three-dimensional analysis of lidar waveforms was developed to characterize the total volume and spatial organization of vegetation material and empty space within the forest canopy. These aspects of the physical structure of canopies have been infrequently measured, from either field or remote methods. We applied this analysis to 22 plots in Douglas-fir/western hemlock stands on the west slope of the Cascades Range in Oregon. Each plot had coincident lidar data and field measurements of stand structure. We compared results from the novel analysis to two earlier methods of canopy description. Using the indices of canopy structure from all three methods of description as independent variables in a stepwise multiple regression, we were able to make nonasymptotic predictions of biomass and leaf area index (LAI) over a wide range, up to 1200 Mg ha
−1 of biomass and an LAI of 12, with 90% and 75% of variance explained, respectively. Furthermore, we were able to make accurate estimates of other stand structure attributes, including the mean and standard deviation of diameter at breast height, the number of stems greater than 100 cm in diameter, and independent estimates of the basal area of Douglas-fir and western hemlock. These measurements can be directly related to indices of forest stand structural complexity, such as those developed for old-growth forest characterization. Indices of canopy structure developed using the novel, three-dimensional analysis accounted for most of the variables used in predictive equations generated by the stepwise multiple regression.
In most cases, prosthetic rehabilitation of patients suffering from microstomia is inconvenient for the patient and challenging for both the dentist and dental technician. In such cases, conventional ...impression-taking requires an individualized tray design and modified impression techniques, amplifying the risk for impression and cast deformation and thereby compromising the final outcome. An intraoral scanner (IOS) might overcome these limitations due to its reduced size compared to an impression tray. In the present case history report, a microstomia patient was successfully restored with a telescopic prosthesis by digitizing both retaining teeth and the palate with an IOS.
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