Mechanisms of fast and stringent search in homologous pairing of double-stranded DNA

Self-organization in the cell relies on the rapid and specific binding of molecules to their cognate targets. Correct bindings must be stable enough to promote the desired function even in the crowded and fluctuating cellular environment. In systems with many nearly matched targets, rapid and stringent formation of stable products is challenging. Mechanisms that overcome this challenge have been previously proposed, including separating the process into multiple stages; however, how particular in vivo systems overcome the challenge remains unclear. Here we consider a kinetic system, inspired by homology dependent pairing between double stranded DNA in bacteria. By considering a simplified tractable model, we identify different homology testing stages that naturally occur in the system. In particular, we first model dsDNA molecules as short rigid rods containing periodically spaced binding sites. The interaction begins when the centers of two rods collide at a random angle. For most collision angles, the interaction energy is weak because only a few binding sites near the collision point contribute significantly to the binding energy. We show that most incorrect pairings are rapidly rejected at this stage. In rare cases, the two rods enter a second stage by rotating into parallel alignment. While rotation increases the stability of matched and nearly matched pairings, subsequent rotational fluctuations reduce kinetic trapping. Finally, in vivo chromosome are much longer than the persistence length of dsDNA, so we extended the model to include multiple parallel collisions between long dsDNA molecules, and find that those additional interactions can greatly accelerate the searching

Causal networks of phytoplankton diversity and biomass are modulated by environmental context

Untangling causal links and feedbacks among biodiversity, ecosystem functioning, and environmental factors is challenging due to their complex and context-dependent interactions (e.g., a nutrient-dependent relationship between diversity and biomass). Consequently, studies that only consider separable, unidirectional effects can produce divergent conclusions and equivocal ecological implications. To address this complexity, we use empirical dynamic modeling to assemble causal networks for 19 natural aquatic ecosystems (N24◦~N58◦) and quantified strengths of feedbacks among phytoplankton diversity, phytoplankton biomass, and environmental factors. Through a cross-system comparison, we identify macroecological patterns; in more diverse, oligotrophic ecosystems, biodiversity effects are more important than environmental effects (nutrients and temperature) as drivers of biomass. Furthermore, feedback strengths vary with productivity. In warm, productive systems, strong nitrate-mediated feedbacks usually prevail, whereas there are strong, phosphate-mediated feedbacks in cold, less productive systems. Our findings, based on recovered feedbacks, highlight the importance of a network view in future ecosystem management

Probe a family non-universal Z' boson effects in B(s)-> phi mu(+) mu(-)decay

Motivated by the recent measurement on ${\cal B}(\bar{B}_s\to \phi \mu^+\mu^-)$ by CDF collaboration, we study the effects of a family non-universal $Z^{\prime}$ boson on rare semileptonic $\bar{B}_s \to \phi\mu^+\mu^-$ decay. In our evaluations, we analyze the dependences of the dimuon invariant mass spectrum and normalized forward-backward asymmetry on $Z^{\prime}$ couplings and show that these observables are highly sensitive to new $Z^{\prime}$ contributions. Three limiting scenarios are presented in the detailed analyses. Numerically, within the allowed ranges of $Z^{\prime}$ couplings under the constraints from $\bar{B}_s-B_s$ mixing, $B\to\pi K$, $\bar{B}_d\to(X_s,K,K^{\ast})\mu^+\mu^-$ decays and so on, ${\cal B}(\bar{B}_s\to \phi \mu^+\mu^-)$ and $A_{FB}^{(L)}(\bar{B}_s\to \phi \mu^+\mu^-)$ could be enhanced by about 96% and $17$ respectively at most by $Z^{\prime}$ contributions. However, ${\cal B}(\bar{B}_s\to \phi \mu^+\mu^-)$ is hardly to be reduced. Furthermore, the zero crossing in $A_{FB}(\bar{B}_s\to \phi \mu^+\mu^-)$ spectrum at low dimuon mass always exists.Comment: 16 pages, 3 figures, 4 table; accepted by Nucl. Phys.

Genetic population structure of the alpine species Rhododendron pseudochrysanthum sensu lato (Ericaceae) inferred from chloroplast and nuclear DNA

<p>Abstract</p> <p>Background</p> <p>A complex of incipient species with different degrees of morphological or ecological differentiation provides an ideal model for studying species divergence. We examined the phylogeography and the evolutionary history of the <it>Rhododendron pseudochrysanthum </it>s. l.</p> <p>Results</p> <p>Systematic inconsistency was detected between gene genealogies of the cpDNA and nrDNA. Rooted at <it>R. hyperythrum </it>and <it>R. formosana</it>, both trees lacked reciprocal monophyly for all members of the complex. For <it>R. pseudochrysanthum </it>s.l., the spatial distribution of the cpDNA had a noteworthy pattern showing high genetic differentiation (F_ST= 0.56-0.72) between populations in the Yushan Mountain Range and populations of the other mountain ranges.</p> <p>Conclusion</p> <p>Both incomplete lineage sorting and interspecific hybridization/introgression may have contributed to the lack of monophyly among <it>R. hyperythrum</it>, <it>R. formosana </it>and <it>R. pseudochrysanthum </it>s.l. Independent colonizations, plus low capabilities of seed dispersal in current environments, may have resulted in the genetic differentiation between populations of different mountain ranges. At the population level, the populations of Central, and Sheishan Mountains may have undergone postglacial demographic expansion, while populations of the Yushan Mountain Range are likely to have remained stable ever since the colonization. In contrast, the single population of the Alishan Mountain Range with a fixed cpDNA haplotype may have experienced bottleneck/founder's events.</p

Tooth Position Determination by Automatic Cutting and Marking of Dental Panoramic X-ray Film in Medical Image Processing

This paper presents a novel method for automatic segmentation of dental X-ray images into single tooth sections and for placing every segmented tooth onto a precise corresponding position table. Moreover, the proposed method automatically determines the tooth’s position in a panoramic X-ray film. The image-processing step incorporates a variety of image-enhancement techniques, including sharpening, histogram equalization, and flat-field correction. Moreover, image processing was implemented iteratively to achieve higher pixel value contrast between the teeth and cavity. The next image-enhancement step is aimed at detecting the teeth cavity and involves determining the segment and points separating the upper and lower jaw, using the difference in pixel values to cut the image into several equal sections and then connecting each cavity feature point to extend a curve that completes the description of the separated jaw. The curve is shifted up and down to look for the gap between the teeth, to identify and address missing teeth and overlapping. Under FDI World Dental Federation notation, the left and right sides receive eight-code sequences to mark each tooth, which provides improved convenience in clinical use. According to the literature, X-ray film cannot be marked correctly when a tooth is missing. This paper utilizes artificial center positioning and sets the teeth gap feature points to have the same count. Then, the gap feature points are connected as a curve with the curve of the jaw to illustrate the dental segmentation. In addition, we incorporate different image-processing methods to sequentially strengthen the X-ray film. The proposed procedure had an 89.95% accuracy rate for tooth positioning. As for the tooth cutting, where the edge of the cutting box is used to determine the position of each tooth number, the accuracy of the tooth positioning method in this proposed study is 92.78%

Caries and Restoration Detection Using Bitewing Film Based on Transfer Learning with CNNs

Caries is a dental disease caused by bacterial infection. If the cause of the caries is detected early; the treatment will be relatively easy; which in turn prevents caries from spreading. The current common procedure of dentists is to first perform radiographic examination on the patient and mark the lesions manually. However; the work of judging lesions and markings requires professional experience and is very time-consuming and repetitive. Taking advantage of the rapid development of artificial intelligence imaging research and technical methods will help dentists make accurate markings and improve medical treatments. It can also shorten the judgment time of professionals. In addition to the use of Gaussian high-pass filter and Otsu’s threshold image enhancement technology; this research solves the problem that the original cutting technology cannot extract certain single teeth; and it proposes a caries and lesions area analysis model based on convolutional neural networks (CNN); which can identify caries and restorations from the bitewing images. Moreover; it provides dentists with more accurate objective judgment data to achieve the purpose of automatic diagnosis and treatment planning as a technology for assisting precision medicine. A standardized database established following a defined set of steps is also proposed in this study. There are three main steps to generate the image of a single tooth from a bitewing image; which can increase the accuracy of the analysis model. The steps include (1) preprocessing of the dental image to obtain a high-quality binarization; (2) a dental image cropping procedure to obtain individually separated tooth samples; and (3) a dental image masking step which masks the fine broken teeth from the sample and enhances the quality of the training. Among the current four common neural networks; namely; AlexNet; GoogleNet; Vgg19; and ResNet50; experimental results show that the proposed AlexNet model in this study for restoration and caries judgments has an accuracy as high as 95.56% and 90.30%; respectively. These are promising results that lead to the possibility of developing an automatic judgment method of bitewing film

Detection of Dental Apical Lesions Using CNNs on Periapical Radiograph

Apical lesions, the general term for chronic infectious diseases, are very common dental diseases in modern life, and are caused by various factors. The current prevailing endodontic treatment makes use of X-ray photography taken from patients where the lesion area is marked manually, which is therefore time consuming. Additionally, for some images the significant details might not be recognizable due to the different shooting angles or doses. To make the diagnosis process shorter and efficient, repetitive tasks should be performed automatically to allow the dentists to focus more on the technical and medical diagnosis, such as treatment, tooth cleaning, or medical communication. To realize the automatic diagnosis, this article proposes and establishes a lesion area analysis model based on convolutional neural networks (CNN). For establishing a standardized database for clinical application, the Institutional Review Board (IRB) with application number 202002030B0 has been approved with the database established by dentists who provided the practical clinical data. In this study, the image data is preprocessed by a Gaussian high-pass filter. Then, an iterative thresholding is applied to slice the X-ray image into several individual tooth sample images. The collection of individual tooth images that comprises the image database are used as input into the CNN migration learning model for training. Seventy percent (70%) of the image database is used for training and validating the model while the remaining 30% is used for testing and estimating the accuracy of the model. The practical diagnosis accuracy of the proposed CNN model is 92.5%. The proposed model successfully facilitated the automatic diagnosis of the apical lesion

Effects of Transapical Transcatheter Mitral Valve Implantation

Purpose: In this study, transapical transcatheter mitral valve-in-valve implantation (TAMVI) was compared with surgical redo mitral valve replacement (SRMVR) in terms of clinical outcomes.Methods: We retrospectively identified patients with degenerated mitral bioprosthesis or failed annuloplasty rings who underwent redo SRMVR or TAMVI at our medical center. Clinical outcomes were based on echocardiography results.Results: We retrospectively identified patients with symptomatic mitral bioprosthetic valve dysfunction (n = 58) and failed annuloplasty rings (n = 14) who underwent redo SRMVR (n = 36) or TAMVI (n = 36). The Society of Thoracic Surgeons Predicted Risk of Mortality scores were higher in the TAMVI group (median: 9.52) than in the SRMVR group (median: 5.59) (p-value = 0.02). TAMVI patients were more severe in New York Heart Association (p-value = 0.04). The total procedure time (skin to skin) and length of stay after procedures were significantly shorter in the TAMVI group, and no significant difference in mortality was noted after adjustment for confounding factors (p-value = 0.11). The overall mean mitral valve pressure gradient was lower in the TAMVI group than in the SRMVR group at 24 months (p &lt; 0.01). Both groups presented a decrease in the severity of mitral and tricuspid regurgitation at 3–24 months.Conclusions: In conclusion, the statistical analysis is still not robust enough to make a claim that TAMVI is an appropriate alternative. The outcome of the patient appears only to be related to the patient's pre-operative STS score. Additional multi-center, longitudinal studies are warranted to adequately assess the effect of TAMVI

Introgression Between Cultivars and Wild Populations of Momordica charantia L. (Cucurbitaceae) in Taiwan

The landrace strains of Momordica charantia are widely cultivated vegetables throughout the tropics and subtropics, but not in Taiwan, a continental island in Southeast Asia, until a few hundred years ago. In contrast, the related wild populations with smaller fruit sizes are native to Taiwan. Because of the introduction of cultivars for agricultural purposes, these two accessions currently exhibit a sympatric or parapatric distribution in Taiwan. In this study, the cultivars and wild samples from Taiwan, India, and Korea were collected for testing of their hybridization and evolutionary patterns. The cpDNA marker showed a clear distinction between accessions of cultivars and wild populations of Taiwan and a long divergence time. In contrast, an analysis of eight selectively neutral nuclear microsatellite loci did not reveal a difference between the genetic structures of these two accessions. A relatively short divergence time and frequent but asymmetric gene flows were estimated based on the isolation-with-migration model. Historical and current introgression from cultivars to wild populations of Taiwan was also inferred using MIGRATE-n and BayesAss analyses. Our results showed that these two accessions shared abundant common ancestral polymorphisms, and the timing of the divergence and colonization of the Taiwanese wild populations is consistent with the geohistory of the Taiwan Strait land bridge of the Last Glacial Maximum (LGM). Long-term and recurrent introgression between accessions indicated the asymmetric capacity to receive foreign genes from other accessions. The modern introduction of cultivars of M. charantia during the colonization of Taiwan by the Han Chinese ethnic group enhanced the rate of gene replacement in the native populations and resulted in the loss of native genes