Use Of Sequences Research Articles

Magnetic resonance imaging sequence evaluation of an MR Linac system; early clinical experience.

To systematically identify the preferred magnetic resonance imaging (MRI) sequences following volunteer imaging on a 1.5 Tesla (T) MR-Linear Accelerator (MR Linac) for future protocol development. Non-patient volunteers were recruited to a Research and Ethics committee approved prospective MR-only imaging study on a 1.5T MR Linac system. Volunteers attended 1-3 imaging sessions that included a combination of mDixon, T1w, T2w sequences using 2-dimensional (2D) and 3-dimensional (3D) acquisitions. Each sequence was acquired over 2-7 minutes and reviewed by a panel of 3 observers to evaluate image quality using a visual grading analysis based on a 4-point Likert scale. Sequences were acquired and modified iteratively until deemed fit for purpose (online image matching or re-planning) and all observers agreed they were suitable in 3 volunteers. 26 volunteers underwent 31 imaging sessions of six general anatomical regions. Images were acquired in one or two of six general anatomical regions: male pelvis (n = 9), female pelvis (n = 4), chestwall/breast (n = 5), lung/oesophagus (n = 5), abdomen (n = 3) and head and neck (n = 5). Images were acquired using a pre-defined exam-card that on average, included six sequences (range 2-10), with a maximum scan time of approximately one hour. The majority of observers preferred T2-weighted sequences. The thorax teams were the only groups to prefer T1-weighted imaging. An iterative process identified sequence agreement in all anatomical regions. These sequences will now be evaluated in patient volunteers. This manuscript is the first publication sharing the results of the first systematic selection of MRI sequences for use in on-board MRI-guided radiotherapy by end-users (therapeutic radiographers and clinical oncologists) in healthy volunteers.

Exploring the Design Space of Innovation Canvases

Designerly innovation tools, such as canvases, are widely used for facilitating team and collaboration processes. This paper outlines the potential design space of such innovation canvases. Based on a systematic analysis of 123 existing canvases we developed a morphological box that distinguishes between six different parameters identified as relevant: (1) addressed process step, (2) involved media, (3) sequence of use, (4) available instructions, (5) number of elements, and (6) design specifics, as well as possible choices among them. The analysis also yielded several research gaps. Furthermore, we present an in-depth discussion of the possible theoretical underpinnings of innovation canvases and summarize them in a theoretical framework. The results of this paper provide references for other researchers and practitioners to better understand working mechanisms and fields of application of existing canvases and for developing such visual innovation tools for their own purposes.

ANALYSIS OF COMPLICATIONS WITH LAPAROSCOPIC CHOLECYSTECTOMY (CLINICAL EXPERIENCE FOR 10 YEARS)

The results of treatment of 5166 patients, on calculous cholecystitis, who had undergone laparoscopic cholecystectomy (LXE) from 2009 till 2019 and were in one medical institution, were analyzed. It was established that complications in the performance of LXE occurred in 136 patients and required conversion. Bleeding occurred in 23 patients with acute calculous cholecystitis (GCS) and 1 patient with chronic calculous cholecystitis (0.46%). As a rule, due to the rapid development of the situation, it was not possible to stop the bleeding. The conversion allowed to stop the bleeding by flashing the blood vessels. The destruction of the wall of the gallbladder, which occurred in 4 patients with GCS (0.08 %), prevented any manipulation of the conversion and cholecystectomy. Self-amputation of the bladder duct took place in inflammatory infiltration with GCS in 3 patients (0.06 %). Conversion and cholecystectomy. In the defect of the common bile duct drained Kerah, sealed with seamy sutures. Inflammatory infiltrates occurred in 79 patients with GKH (1.53 %). As in most cases in inflammatory infiltrates it is not possible to verify the structure of the conversion and cholecystectomy. In the case of bile duct lesions, the following options were used to solve this problem. So in two patients with GCS when the infiltration is divided, a common bile duct is crossed. There is a hepatocyanoanmostomy in Ru on a sheltered drainage, and in two patients with GCS in such a situation, hepatocytes-duodenal ulcer is an end-to-side anastomosis in a sheltered drainage. The experience of the occurrence of various complications in the performance of LHE is generalized. They led to the solution of extremely difficult and complicated problems in the future, and the sequence of use of diagnostic techniques was not the same for all patients. A scrupulous analysis of the mistakes made is made. Effectiveness of the use of various methods of treatment at any given complications has been investigated.

Point-of-care detection of 16S rRNA of Staphylococcus aureus based on multiple biotin-labeled DNA probes

A visual method that combines multiple biotin-labeled DNA probes and lateral-flow nucleic acid biosensor was developed to detect Staphylococcus aureus. The 16S rRNA from Staphyloccocus aureus (S. aureus), coupled with multiple biotin-labeled DNA probes, was functionalized in a signal structure for lateral-flow point-of-care detection. The secondary structure of the 16S rRNA was unwound by two specific capture probes modified by Fam and multiple bridge probes, which extended additional sequences for use as initiators. By utilizing the initiators, each target 16S rRNA with multiple DNA probes could tether a number of biotin molecules, so that a large number of streptavidin-labeled gold nanoparticles could be introduced in the lateral flow assay. The images of the lateral flow detection results obtained using a smartphone were transmitted to a computer via Wi-Fi or Bluetooth connection for quantitative processing by ImageJ. The limit of detection was 103 cfu/mL without sample enrichment, and decreased to 0.12 cfu/mL following a 3-h enrichment of samples in growth medium. Notably, this method presented high specificity and applicability for the detection of S. aureus in food samples. In short, the developed visual non-specific operation method is very suitable for point-of-care diagnosis of pathogens in resource-limited countries.

In Vitro Assessment of Putative PD-1/PD-L1 Inhibitors: Suggestions of an Alternative Mode of Action

The programmed cell death protein 1 (PD-1) signaling axis is among the most important therapeutic targets in modern oncology. Aurigene Discovery Technologies Ltd. (Aurigene) has patented a series of peptidomimetic small molecules derived from the PD-1 protein sequence for use in targeting the interaction between PD-1 and its ligand, PD-L1. We evaluated three of Aurigene's most potent compounds in SPR binding assays. Our results showed that these compounds-each of which is known to be potently effective in a splenocyte recovery assay-do not directly inhibit the PD-1/PD-L1 interaction nor do they appear to bind to either of the constituent proteins, indicating that another mechanism is at play. As a result of these studies and upon consideration of structural features within the PD-1/PD-L1 complex, we hypothesize that the Aurigene molecules may interact with a currently unknown protein capable of regulating the PD-1 axis.

Potential interaction of radiation therapy, antibiotic, and steroid use in non-small cell lung cancer patients treated with checkpoint inhibitors: A retrospective analysis.

e20724 Background: The activity of Checkpoint inhibitors (CPI) can be predicted by PD-L1 expression. Recent studies showed that other factors can also have an impact including radiation which is beneficial but the use of antibiotics and steroids can have a deleterious effect. We performed a retrospective analysis of stage IV lung cancer patients treated with CPI at our institution and the impact of radiation treatment as well as the use of antibiotics or steroids in their outcome. Methods: We reviewed the data of 121 patients with stage IV non-small cell lung that were treated with CPI from 2015 to 2017 and analyzed the impact of PD-L1 expression, radiation treatment, steroid and antibiotic use on their progression-free survival (PFS) and overall survival (OS). We determined the use of antibiotics and steroids during any time within 30 days of initiation of treatment with CPI. Results: The median age was 66; there were 57 females and 64 males;23 current smokers, 11 non-smokers and 87 previous smokers; 87 adenocarcinomas, 24 squamous cell histology, and 10 others; 38 patients had low PD-L1 ( < 50%), 46 had high PD-L1 (≥50%) and 37 was unknown. The PFS and OS of patients treated with CPI who had radiation (RT) were not different from patients that did not have RT by Gehan-Breslow Wilcoxon test nor there was a difference based on the PD-L1 expression. The use of steroids (S) had a beneficial impact on PFS but it was numerically better but not significant on OS. Antibiotic (AB) use also had a beneficial impact on PFS and OS. Patients that had CPI as first-line therapy had shorter PFS than patients that had CPI as second-line therapy. There was no difference whether RT was used or not in patients that had antibiotics or steroids. Conclusions: Our analysis showed that several factors can potentially impact the PFS and OS of patients treated with CPI. Contrary to the previous report, the use of Ab or S did not affect adversely the PFS and OS. We did not observe a beneficial effect of RT. The sequence of use of CPI could potentially affect the PFS. This data should be taken with caution as it is a retrospective analysis with a small sample number but it reflects the real-life practice of patients treated outside of a clinical trial setting. [Table: see text]

Iatrogenic endometriosis harbors somatic cancer-driver mutations.

Does incisional endometriosis (IE) harbor somatic cancer-driver mutations? We found that approximately one-quarter of IE cases harbor somatic-cancer mutations, which commonly affect components of the MAPK/RAS or PI3K-Akt-mTor signaling pathways. Despite the classification of endometriosis as a benign gynecological disease, it shares key features with cancers such as resistance to apoptosis and stimulation of angiogenesis and is well-established as the precursor of clear cell and endometrioid ovarian carcinomas. Our group has recently shown that deep infiltrating endometriosis (DE), a form of endometriosis that rarely undergoes malignant transformation, harbors recurrent somatic mutations. In a retrospective study comparing iatrogenically induced and endogenously occurring forms of endometriosis unlikely to progress to cancer, we examined endometriosis specimens from 40 women with IE and 36 women with DE. Specimens were collected between 2004 and 2017 from five hospital sites in either Canada, Germany or the Netherlands. IE and DE cohorts were age-matched and all women presented with histologically typical endometriosis without known history of malignancy. Archival tissue specimens containing endometriotic lesions were macrodissected and/or laser-capture microdissected to enrich endometriotic stroma and epithelium and a hypersensitive cancer hotspot sequencing panel was used to assess for presence of somatic mutations. Mutations were subsequently validated using droplet digital PCR. PTEN and ARID1A immunohistochemistry (IHC) were performed as surrogates for somatic events resulting in functional loss of respective proteins. Overall, we detected somatic cancer-driver events in 11 of 40 (27.5%) IE cases and 13 of 36 (36.1%) DE cases, including hotspot mutations in KRAS, ERBB2, PIK3CA and CTNNB1. Heterogeneous PTEN loss occurred at similar rates in IE and DE (7/40 vs 5/36, respectively), whereas ARID1A loss only occurred in a single case of DE. While rates of detectable somatic cancer-driver events between IE and DE are not statistically significant (P > 0.05), KRAS activating mutations were more prevalent in DE. Detection of somatic cancer-driver events were limited to hotspots analyzed in our panel-based sequencing assay and loss of protein expression by IHC from archival tissue. Whole genome or exome sequencing, or epigenetic analysis may uncover additional somatic alterations. Moreover, because of the descriptive nature of this study, the functional roles of identified mutations within the context of endometriosis remain unclear and causality cannot be established. The alterations we report may be important in driving the growth and survival of endometriosis in ectopic regions of the body. Given the frequency of mutation in surgically displaced endometrium (IE), examination of similar somatic events in eutopic endometrium, as well as clinically annotated cases of other forms of endometriosis, in particular endometriomas that are most commonly linked to malignancy, is warranted. This study was funded by a Canadian Cancer Society Impact Grant [701603, PI Huntsman], Canadian Institutes of Health Research Transitional Open Operating Grant [MOP-142273, PI Yong], the Canadian Institutes of Health Research Foundation Grant [FDN-154290, PI Huntsman], the Canadian Institutes of Health Research Project Grant [PJT-156084, PIs Yong and Anglesio], and the Janet D. Cottrelle Foundation through the BC Cancer Foundation [PI Huntsman]. D.G. Huntsman is a co-founder and shareholder of Contextual Genomics Inc., a for profit company that provides clinical reporting to assist in cancer patient treatment. R. Aguirre-Hernandez, J. Khattra and L.M. Prentice have a patent MOLECULAR QUALITY ASSURANCE METHODS FOR USE IN SEQUENCING pending and are current (or former) employees of Contextual Genomics Inc. The remaining authors have no competing interests to declare. Not applicable.

THE GOLD AND SILVER VESSELS AND OTHER PRECIOUS FINDS FROM THE THOLOS TOMB AT KOKLA IN THE ARGOLID

The Late Helladic IIB–IIIA1 tholos in the Kokla necropolis is a particularly important and intriguing tomb that can provide us with interesting insights into the wider social landscape of the Argolid just prior to the emergence of the Mycenaean palaces. Architecturally, the tomb itself is a unique mix of features derived from tholoi and chamber tombs; its entrance is adorned with what must be one of the earliest-surviving Mycenaean frescoes. This tholos tomb had not been looted, a rare phenomenon for such tombs, and the precious finds, that is to say the gold, silver and ivory objects, are presented here in detail. These artworks include both Minoan and Mycenaean influences. The group of metal vessels is significant as it is one of the largest assemblages of metalware found from the post-Shaft Grave period on the Mycenaean Greek mainland. It appears that some of these objects were used for funerary ritual activity in conjunction with the bench in the tholos, whereas other objects seem to have been part of an assemblage of grave-goods. As no human remains were discovered, it is difficult to piece together the sequence of use for the tomb. Nevertheless, the publication of this material from the Kokla tholos is an important contribution to our knowledge of the Argolid during this period.

Estimating conductive sapwood area in diffuse and ring porous trees with electronic resistance tomography

Accurately estimating sapwood area is essential for modelling whole-tree or stand-scale transpiration from point-flow sap-flux observations. In this study, we tested the validity of electrical resistance tomography (ERT) to locate the sapwood-heartwood (SW/HW) interface for two ring porous (Quercus nigra L. and Quercus virginiana Mill.) and one diffuse porous (Acer rubrum L.) species. Estimates derived from the ERT analyses were compared with the SW/HW interface measured following dye perfusion testing. The ERT results revealed spatial variation in electrical resistance, with higher resistivity in the inner part of the cross sections. Regression analyses showed that ERT was able to accurately account for 97% and 80% of the variation in sapwood area (calculated as R2) for Q. virginiana (n = 19) and Q. nigra (n = 7), respectively, and 56% of the variation in the diffuse porous species (n = 8). Root mean square error (RMSE) values for sapwood areas of the ring porous species were 11.12 cm2 (19%) and 25.98 cm2 (33%) for Q. virginiana and Q. nigra, respectively. Sapwood area estimates for diffuse wood carried greater error (RMSE = 33.52 cm2 (131%)). Model bias for all sapwood area estimates was negative, suggesting that ERT had a tendency to overestimate sapwood areas. Electrical resistance tomography proved to be a significant predictor of sapwood area in the three investigated species, although it was more reliable for ring porous wood. In addition to the results, a comprehensive code sequence for use with R statistical software is provided, so that other investigators may follow the same method.

Library of Synthetic Streptomyces Regulatory Sequences for Use in Promoter Engineering of Natural Product Biosynthetic Gene Clusters.

Promoter engineering has emerged as a powerful tool to activate transcriptionally silent natural product biosynthetic gene clusters found in bacterial genomes. Since biosynthetic gene clusters are composed of multiple operons, their promoter engineering requires the use of a set of regulatory sequences with a similar level of activities. Although several successful examples of promoter engineering have been reported, its widespread use has been limited due to the lack of a library of regulatory sequences suitable for use in promoter engineering of large, multiple operon-containing biosynthetic gene clusters. Here, we present the construction of a library of constitutively active, synthetic Streptomyces regulatory sequences. The promoter assay system has been developed using a single-module nonribosomal peptide synthetase that produces the peptide blue pigment indigoidine, allowing for the rapid screening of a large pool of regulatory sequences. The highly randomized regulatory sequences in both promoter and ribosome binding site regions were screened for their ability to produce the blue pigment, and they are classified into the strong, medium, and weak regulatory sequences based on the strength of a blue color. We demonstrated the utility of our synthetic regulatory sequences for promoter engineering of natural product biosynthetic gene clusters using the actinorhodin gene cluster as a model cluster. We believe that the set of Streptomyces regulatory sequences we report here will facilitate the discovery of new natural products from silent, cryptic biosynthetic gene clusters found in sequenced Streptomyces genomes.

IMAGE INFORMATION VALUE OF VARIATION ANALYSIS VALUE SENSITIVIY ENCHODING (SENSE) USING T2 WEIGHTED TURBO BALANCE FIELD ECHO (BTFE) SEQUENCE IN THE MRCP IN RADIOLOGICAL INSTALLATION SILOAM HOSPITAL SURABAYA

Background : MRCP is an examination used to evaluate the system billiary, pancreas and gall bladder with channel because of the possible presence of stones, tumors and other diseases. To diagnose the MRCP examination,one sequence in use is T2 weighted Turbo Field Echo Balance (T2W BTFE) which in its parameters No Sensitivity Enchoding (SENSE). The purpose of this study was to determine the Information analysis Anatomical differences with variation of Sensitivity Encoding (SENSE) on T2-weighted sequences BTFE the MRCP examination, And to investigate value Sensitivity Encoding (SENSE) optimal T2-weighted sequences BTFE the MRCP examination. Methods : The method of this research is experimental with approach quasi-experimental design with control. This research is done in Siloam Hospital Surabaya. MRCP image data in the form of axial 40 of the 10 patients with 4 variation of Sensitivity Encoding (SENSE), which are 1.4, 1.6, 1.8, and 2. Assessment of information image data done by 3 respondents. Analysing process done with Friedman test. Results : The results showed that there MRCP image information differences with variation in sensitivity encoding (SENSE) on T2-weighted sequences BTFE with a significance level of p value <0.001. Differences in image information occurs in liver, Gall Blader, Pancreas and CBD (Common Bile Duct). The use value Sensitivity Encoding (SENSE) on T2-weighted sequences for optimal BTFE MRCP is a 1.8 with a mean rank 3.85. Conclusion : The optimal use value Sensitivity Encoding (SENSE) on T2-weighted sequences for optimal BTFE MRCP is a 1.8.

순위 기반 분기한정법과 군집분석을 활용한 인간공학적 콘솔 배치 최적화 방법 개발

Designing an optimal component layout for an ergonomic console is important for the effective and efficient operation by its users. This study developed a console layout optimization method using a priority-based branch-and-bound algorithm and a clustering analysis. The proposed method starts with a priority-based branch and bound algorithm which searches all feasible layouts having scores higher than a designated score (e.g., 80 out of 100). Next, the objective function computes scores for the searched layouts by considering four allocation criteria (importance, frequency, sequence of use, and functional grouping) and two ergonomic criteria (reach and visibility). Lastly, the clustering analysis on the searched layouts extracts a small number of representative layouts for a designer to select the most preferred. The proposed layout optimization method was applied to component layout design of a radar console to examine its effectiveness.

Carotid Intraplaque Hemorrhage Imaging with Quantitative Vessel Wall T1 Mapping: Technical Development and Initial Experience.

Purpose To develop a three-dimensional (3D) high-spatial-resolution time-efficient sequence for use in quantitative vessel wall T1 mapping. Materials and Methods A previously described sequence, simultaneous noncontrast angiography and intraplaque hemorrhage (SNAP) imaging, was extended by introducing 3D golden angle radial k-space sampling (GOAL-SNAP). Sliding window reconstruction was adopted to reconstruct images at different inversion delay times (different T1 contrasts) for voxelwise T1 fitting. Phantom studies were performed to test the accuracy of T1 mapping with GOAL-SNAP against a two-dimensional inversion recovery (IR) spin-echo (SE) sequence. In vivo studies were performed in six healthy volunteers (mean age, 27.8 years ± 3.0 [standard deviation]; age range, 24-32 years; five male) and five patients with atherosclerosis (mean age, 66.4 years ± 5.5; range, 60-73 years; five male) to compare T1 measurements between vessel wall sections (five per artery) with and without intraplaque hemorrhage (IPH). Statistical analyses included Pearson correlation coefficient, Bland-Altman analysis, and Wilcoxon rank-sum test with data permutation by subject. Results Phantom T1 measurements with GOAL-SNAP and IR SE sequences showed excellent correlation (R2 = 0.99), with a mean bias of -25.8 msec ± 43.6 and a mean percentage error of 4.3% ± 2.5. Minimum T1 was significantly different between sections with IPH and those without it (mean, 371 msec ± 93 vs 944 msec ± 120; P = .01). Estimated T1 of normal vessel wall and muscle were 1195 msec ± 136 and 1117 msec ± 153, respectively. Conclusion High-spatial-resolution (0.8 mm isotropic) time-efficient (5 minutes) vessel wall T1 mapping is achieved by using the GOAL-SNAP sequence. This sequence may yield more quantitative reproducible biomarkers with which to characterize IPH and monitor its progression. © RSNA, 2017.

Revealing the biography of a hidden medieval manuscript using synchrotron and conventional imaging techniques

Reading the content of hidden texts from ancient manuscripts has become an increasingly important endeavor thanks to the variety of non-destructive analytical tools and image processing routines available for this task. In this study, portable macro X-Ray Fluorescence (MA-XRF-tube), Visible Hyperspectral Imaging (HSI) together with Synchrotron based macro X-Ray Fluorescence (MA-XRF-SR) are combined with signal processing methods to reveal the biography of a degraded manuscript recycled as binding material for a 16th century printed edition of Hesiod's Works and Days. The analytical techniques allow visualizing the hidden text, revealing passages from the Institutes Justinian, a 6th century A.D codification of the Roman Law, with further marginal comments on medieval Canon Law. In addition, the identification of the materials (e.g. pigments, inks) part of the original manuscript together with their sequence of use are revealed: i) the preparation of the parchment using a Ca-based preparation layer, ii) drawing of ruled guide lines, using a Pb-based pen or ink, iii) writing of the main text using a rich Fe-gall ink with modulating color pigments (Hg-, Cu- and Pb- based) and iv) addition of two types of comments to the main text, one of the ink used for the comments being a Fe-gall ink rich in Cu.

Lactate dehydrogenase predicts combined progression-free survival after sequential therapy with abiraterone and enzalutamide for patients with castration-resistant prostate cancer.

An array of clinical issues remains to be resolved for castration-resistant prostate cancer (CRPC), including the sequence of drug use and drug cross-resistance. At present, no clear guidelines are available for the optimal sequence of use of novel agents like androgen-receptor axis-targeted (ARAT) agents, particularly enzalutamide, and abiraterone. This study retrospectively analyzed a total of 69 patients with CRPC treated with sequential therapy using enzalutamide followed by abiraterone or vice versa. The primary outcome measure was the comparative combined progression-free survival (PFS) comprising symptomatic and/or radiographic PFS. Patients were also compared for total prostate-specific antigen (PSA)-PFS, overall survival (OS), and PSA response. The predictors of combined PFS and OS were analyzed with a backward-stepwise multivariate Cox model. Of the 69 patients, 46 received enzalutamide first, followed by abiraterone (E-A group), and 23 received abiraterone, followed by enzalutamide (A-E group). The two groups were not significantly different with regard to basic data, except for hemoglobin values. In a comparison with the E-A group, the A-E group was shown to be associated with better combined PFS in Kaplan-Meier analysis (P = 0.043). Similar results were obtained for total PSA-PFS (P = 0.049), while OS did not differ between groups (P = 0.62). Multivariate analysis demonstrated that pretreatment lactate dehydrogenase (LDH) values and age were significant predictors of longer combined PFS (P < 0.05). Likewise, multivariate analysis demonstrated that pretreatment hemoglobin values and performance status were significant predictors of longer OS (P < 0.05). The results of this study suggested the A-E sequence had longer combined PSA and total PSA-PFS compared to the E-A sequence in patients with CRPC. LDH values in sequential therapy may serve as a predictor of longer combined PFS.

Pathophysiology, prevention, treatment, and outcomes of intestinal failure-associated liver disease.

Intestinal failure-associated liver disease (IFALD) remains a serious problem in the treatment of infants with nutritional problems and short bowel syndrome. A review of the recent literature from 2010 to 2016, concentrating on articles related to the pathophysiology of IFALD and to outcomes of novel nutritional and pharmacological therapies for neonatal cholestasis in the post-surgical neonate. The pathophysiology of IFALD relates to an increase sensitivity of the neonatal liver to cholestasis in the non-fed state; prolonged cholestasis almost inevitably results in liver damage which will progress from fibrosis to cirrhosis. Clinically discerned risk factors include premature birth, inflammation, sepsis, disruption of the enterohepatic circulation by creation of a proximal stoma, and the duration and type of parenteral nutritional support. Within the hepatocyte, the regulatory enzyme farsanoid receptor X (FXR) appears to play a pivotal role in the development of cholestasis. Recent studies have shown that its activity is suppressed by sepsis, and by plant phytosterols found in soy-based lipid preparations. This paradigm is reflected in the emerging consensus for the care of post-surgical neonates, which is based around a multi-disciplinary team approach. Using an algorithm-driven approach, an appropriate balance between caloric support and prevention of IFALD can be achieved. Further prospective studies are required to further refine the optimal sequence of use of these therapies and the long-term effects on neurological development and hepatic function. However, with optimal care, the number of IF patients progressing to end-stage liver disease because of IFALD should be very low.

Final irrigation protocols may affect intraradicular dentin ultrastructure.

The aim of this study was to evaluate the effect of different irrigation protocols on the root dentin structure using scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Thirty-nine lower bovine incisors were hemisected longitudinally and randomly divided into 13 groups (n=3). After the root halves were reassembled, it was applied a specific irrigation protocol for each group, as following: G1, distilled water (control); G2, 0.9% saline; G3, saline+17% EDTA; G4, saline+PUI; G5, saline+PUI+EDTA; G6 to G9 received the same protocol as above replacing 0.9% saline by 2.5% NaOCl; and G10 to G13 by 2% CHX. One-half of each sample was prepared and evaluated using SEM and the other one by TEM observations. TEM descriptive analysis showed modifications in dentin organic ultrastructure, characterized by the thinning of dentin collagen fibrils, caused by NaOCl, enhanced by EDTA and/or PUI. SEM analysis showed that NaOCl with PUI caused significantly larger erosion of the peritubular dentin than in all the other groups (P<0.05), followed by NaOCl+EDTA and NaOCl+EDTA+PUI. NaOCl caused ultrastructural alterations in the dentin collagen, and enhanced by EDTA and/or PUI, promoted peritubular and intertubular erosion. The effect of irrigating solutions on dentin ultrastructure was still unclear. The acknowledgment about the kind of solution, concentrations, application time, and sequence of use was important to achieve the right sanitization without jeopardizing the dentin ultrastructure quality.

Feedback Reconstruction and Implementations of Pseudorandom Number Generators from Composited De Bruijn Sequences

A binary de Bruijn sequence of order $n$ is a sequence of zeros and ones of period $2^n$ that contains every binary $n$ -tuple exactly once in a period of the sequence. A composited construction of a de Bruijn sequence is a construction of a nonlinear feedback shift register (NLFSR) that generates a de Bruijn sequence where the composited feedback function of the NLFSR is the sum of a feedback function with $k$ th order composition and a sum of $(k+1)$ product-of-sum terms. The goals of this article are to perform a profound analysis of composited de Bruijn sequences for use in cryptography and find an efficient implementation of the composited feedback function. We first determine the lower bound of the linear complexity of a composited de Bruijn sequence and then conduct a profound analysis on the composited construction by introducing the notion of the higher order $D$ -morphic preimages of a binary sequence. Our analysis aims at the reconstruction of a composited de Bruijn sequence from a segment known as $k$ th order $D$ -morphic order $n$ de Bruijn preimages ( $(n,k)$ -DMDPs) of length $(2^n+k)$ and $k$ th order $D$ -morphic order $n$ $m$ -sequence preimages ( $(n,k)$ -DMMPs) of length $(2n+k)$ for a nonlinearly and linearly generated composited de Bruijn sequence, respectively. We also provide the success probability of finding an $(n,k)$ -DMMP/DMDP from a composited de Bruijn sequence for the reconstruction. Furthermore, we develop a new iterative technique with its parallel extension for computing the feedback function and the new technique is faster than other known techniques for producing de Bruijn sequences of long period. In addition, we present three instances of composited de Bruijn sequences of period $2^{64}$ together with their software implementations and performances.

Development of a multiplex PCR assay to discriminate native Hymenoscyphus albidus and introduced Hymenoscyphus fraxineus in Britain and assess their distribution

Two Hymenoscyphus species are associated with ash (Fraxinus) in Europe; the recently arrived ash dieback pathogen Hymenoscyphus fraxineus and apparently native Hymenoscyphus albidus. However, in parts of Europe invasive H. fraxineus appears to be replacing H. albidus which may, therefore, face extinction. We designed primers based on calmodulin sequences for use in singleplex and multiplex PCR assays to detect and discriminate between these two morphologically very similar species. The multiplex assay was tested against 50 isolates and 26 apothecial field samples of H. albidus/H. fraxineus from Europe and Asia, plus isolates of Hymenoscyphus fructigenus, Hymenoscyphus koreanus and Hymenoscyphus occultus. Use of the assay confirmed both H. albidus and H. fraxineus were present across southern Britain between 2014 and 2015, with H. albidus detected at eight geographically distinct sites. The sensitivity, specificity and potential applications of the multiplex assay are discussed.

Germline viral "fossils" guide in silico reconstruction of a mid-Cenozoic era marsupial adeno-associated virus.

Germline endogenous viral elements (EVEs) genetically preserve viral nucleotide sequences useful to the study of viral evolution, gene mutation, and the phylogenetic relationships among host organisms. Here, we describe a lineage-specific, adeno-associated virus (AAV)-derived endogenous viral element (mAAV-EVE1) found within the germline of numerous closely related marsupial species. Molecular screening of a marsupial DNA panel indicated that mAAV-EVE1 occurs specifically within the marsupial suborder Macropodiformes (present-day kangaroos, wallabies, and related macropodoids), to the exclusion of other Diprotodontian lineages. Orthologous mAAV-EVE1 locus sequences from sixteen macropodoid species, representing a speciation history spanning an estimated 30 million years, facilitated compilation of an inferred ancestral sequence that recapitulates the genome of an ancient marsupial AAV that circulated among Australian metatherian fauna sometime during the late Eocene to early Oligocene. In silico gene reconstruction and molecular modelling indicate remarkable conservation of viral structure over a geologic timescale. Characterisation of AAV-EVE loci among disparate species affords insight into AAV evolution and, in the case of macropodoid species, may offer an additional genetic basis for assignment of phylogenetic relationships among the Macropodoidea. From an applied perspective, the identified AAV “fossils” provide novel capsid sequences for use in translational research and clinical applications.