Multiple Insertions Research Articles

Rare case of calcified fibrin sheath causing central venous occlusion, mimicking a retained catheter fragment

BackgroundLong-term placements of central venous catheters (CVCs) are known to cause various complications, among which include fibrin sheath formation, causing catheter dysfunction, infection and thrombosis. Post-catheter removal, these sheaths may sometimes be retained in the vein; however, are rarely calcified. When retained sheaths are calcified, they may cause diagnostic confusion on imaging, as they may mimic a retained catheter fragment.Case presentationWe report a case of a patient with end-stage renal disease and a history of multiple prior CVC insertions presenting with symptoms of central venous occlusion post-revascularization of his stenosed arteriovenous fistula. CT venography revealed a linear tubular hyperdensity within the right brachiocephalic vein and superior vena cava, which at first glance looked like a retained catheter fragment. However, further scrutiny revealed a retained calcified intravascular fibrin sheath as the cause of occlusion.ConclusionsAwareness of the radiological discriminating features of calcified fibrin sheaths are important to prevent misdiagnosis and unnecessary interventions as these sheaths may mimic retained catheter fragments. Calcified fibrin sheaths should also be considered as a differential diagnosis of radio-opaque intravascular structures or venous calcifications post-CVC removal.

Investigation of cutting force components and surface roughness in face milling with different cutting ratios

During the face milling process, the choice of technological parameters plays an important role. The two most important parameters are the feed and the depth of cut, the ratio of which is also called the cutting ratio. The main topic of the paper is to examine how different values of the chip ratio affect the components of the cutting force and the roughness of the machined surface. It is also shown how important it is to know the exact geometry of the cutting insert, as well as - in the case of cutting with multiple inserts - the knowledge of the run-out between the individual inserts. Based on the performed investigations, it was determined that the use of a chip ratio close to 1 is not recommended either in terms of cutting force components or surface roughness.

Maintaining Single-Channel Recordings on a Silver Nanoneedle through Probe Design and Feedback Tip Positioning Control.

Ion channel proteins showed great promise in the field of nanopore sensing and molecular flux imaging applications due to the atomic-level precision of the pore size and a high signal-to-noise ratio. More specifically, ion channel probes, where the protein channels are integrated at the end of a solid probe, can achieve highly localized detection. Metal probe materials such as gold and silver have been developed to support lipid bilayers and enable the use of smaller probes, or nanoneedles, compared to more traditional glass micropipette ion channel probes. Silver probes are preferable because they support sustained DC stable channel current due to the AgCl layer formed around the tip during the fabrication process. However, one of the current challenges in ion channel measurements is maintaining a single-channel recording. Multiple protein insertions complicate data analysis and destabilize the bilayer. Herein, we combine the promising probe material (Ag/AgCl) with an approach based on current feedback-controlled tip positioning to maintain long-term single-channel recordings for up to 3 h. We develop a hybrid positioning control system, where the channel current is used as feedback to control the vertical movement of the silver tip and, subsequently, control the number of protein channels inserted in the lipid membrane. Our findings reveal that the area of the lipid bilayer decreases with moving the silver tip up (i.e., decreasing the displacement in the z-direction). By reducing the bilayer area around the fine silver tip, we minimize the probability of multiple insertions and remove unwanted proteins. In addition, we characterize the effect of lipid properties such as fluidity on the lipid membrane area. We believe that the use of silver nanoneedles, which enables DC stable channel current, coupled with the developed tip displacement mechanism will offer more opportunities to employ these probes for chemical imaging and mapping different surfaces.

Form-factors and complete basis of observables via separation of variables for higher rank spin chains

Integrable mathfrak{sl} (N) spin chains, which we consider in this paper, are not only the prototypical example of quantum integrable systems but also systems with a wide range of applications. For these models we use the Functional Separation of Variables (FSoV) technique with a new tool called Character Projection to compute all matrix elements of a complete set of operators, which we call principal operators, in the basis diagonalising the tower of conserved charges as determinants in Q-functions. Building up on these results we then derive similar determinant forms for the form-factors of combinations of multiple principal operators between arbitrary factorizable states, which include, in particular, off-shell Bethe vectors and Bethe vectors with arbitrary twists. We prove that the set of principal operators generates the complete spin chain Yangian. Furthermore, we derive the representation of these operators in the SoV bases allowing one to compute correlation functions with an arbitrary number of principal operators. Finally, we show that the available combinations of multiple insertions includes Sklyanin’s SoV B operator. As a result, we are able to derive the B operator for mathfrak{sl} (N) spin chains using a minimal set of ingredients, namely the FSoV method and the structure of the SoV basis.

Machine Learning Combined with Restriction Enzyme Mining Assists in the Design of Multi-Point Mutagenic Primers

The polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) experiment has the characteristics of low-cost, rapidity, simplicity, convenience, high sensitivity and high specificity; thus, many small and medium laboratories use it to perform all kinds of single nucleotide polymorphisms (SNPs) genotyping works, and as a molecular biotechnology for disease-related analysis. However, many single nucleotide polymorphisms lack available restriction enzymes to distinguish the specific genotypes on a target SNP, and that causes the PCR-RFLP assay which is unavailable to be called mismatch PCR-RFLP. In order to completely solve the problem of mismatch PCR-RFLP, we have created a teaching–learning-based optimization (TLBO) multi-point mutagenic primer design algorithm which, combined with REHUNT, provides a complete and specific restriction enzyme mining solution. The proposed method not only introduces several search strategies suitable for multi-point mutagenesis primers, but also enhances the reliability of mutagenic primer design. In addition, this study is also designed for more complex SNP structures (with multiple dNTPs and insertion and deletion) to provide specific solutions for SNP diversity. We tested against fifteen mismatch PCR-RFLP SNPs in the human SLC6A4 gene on the NCBI dbSNP database as experimental templates. The experimental results indicate that the proposed method is helpful for providing the multi-point mutagenic primers that meet the constrain conditions of PCR experiments.

Labeling Ebola Virus with a Self-Splicing Fluorescent Reporter.

Inteins (intervening proteins) are polypeptides that interrupt the sequence of other proteins and remove themselves through protein splicing. In this intein-catalyzed reaction, the two peptide bonds surrounding the intein are rearranged to release the intein from the flanking protein sequences, termed N- and C-exteins, which are concurrently joined by a peptide bond. Because of this unique functionality, inteins have proven exceptionally useful in protein engineering. Previous work has demonstrated that heterologous proteins can be inserted within an intein, with both the intein and inserted protein retaining function, allowing for intein-containing genes to coexpress additional coding sequences. Here, we show that a fluorescent protein (ZsGreen) can be inserted within the Pyrococcus horikoshii RadA intein, with the hybrid protein (ZsG-Int) maintaining fluorescence and splicing capability. We used this system to create a recombinant Ebola virus expressing a fluorescent protein. We first tested multiple potential insertion sites for ZsG-Int within individual Ebola virus proteins, identifying a site within the VP30 gene that facilitated efficient intein splicing in mammalian cells while also preserving VP30 function. Next, we successfully rescued a virus containing the ZsG-Int-VP30 fusion protein, which displayed fluorescence in the infected cells. We thus report a new intein-based application for adding reporters to systems without the need to add additional genes. Further, this work highlights a novel reporter design, whereby the reporter is only made if the protein of interest is translated and does not remain fused to the protein of interest.

Emoji-like structure in the right atrium: identified as blood cyst and removed by interventional venous drainage cannula.

Intracardiac blood cysts are thin-walled, blood-filled and round-shaped malformations, commonly located to the endocardium of semilunar or atrioventricular valves. Blood cysts with a diameter of a few millimetres are a frequent finding in neonates and infants 2 years of age or younger,1 but in adults they are rare. On echocardiography, blood cysts have usually a round or oval shape, about the half are pedunculated or mobile, their size varies in adults, but cysts up to a diameter of 40 mm have been reported, and usually the trapped blood within the cyst appears echo-free.2,3 The aetiology of acquired blood cysts in adults remains unknown. Furthermore, the management of adult patients with a blood cyst is controversial. We present a 56-year-old male patient in whom a mobile blood cyst in the right atrium was found by transesophageal echocardiography as part of preoperative diagnostic investigation in pocket infection of a cardiac contractility modulation device. The patient had a history with multiple lead implantations since 28 years due to AV block and dilatative cardiomyopathy. The blood cyst has been successfully removed by a venous drainage cannula (AngioVac system). In this case, the evolution of blood cyst is compatible with a possible mechanical injury of endocardium due to multiple insertions and high number of leads in the right heart. To the best of our knowledge, here we report for the first time on the removal of a blood cyst using a large venous drainage cannula (22 french size).

High-throughput detection of T-DNA insertion sites for multiple transgenes in complex genomes

BackgroundGenetic engineering of crop plants has been successful in transferring traits into elite lines beyond what can be achieved with breeding techniques. Introduction of transgenes originating from other species has conferred resistance to biotic and abiotic stresses, increased efficiency, and modified developmental programs. The next challenge is now to combine multiple transgenes into elite varieties via gene stacking to combine traits. Generating stable homozygous lines with multiple transgenes requires selection of segregating generations which is time consuming and labor intensive, especially if the crop is polyploid. Insertion site effects and transgene copy number are important metrics for commercialization and trait efficiency.ResultsWe have developed a simple method to identify the sites of transgene insertions using T-DNA-specific primers and high-throughput sequencing that enables identification of multiple insertion sites in the T1 generation of any crop transformed via Agrobacterium. We present an example using the allohexaploid oil-seed plant Camelina sativa to determine insertion site location of two transgenes.ConclusionThis new methodology enables the early selection of desirable transgene location and copy number to generate homozygous lines within two generations.

Vendor independent coronary calcium scoring improves individual risk assessment – the Multi-Ethnic Study of Atherosclerosis (MESA)

Abstract Background Coronary artery calcium (CAC) scoring improves event prediction of coronary heart disease (CHD) and can be used to guide initiation or deferral of statin therapy in asymptomatic individuals at low-to-intermediate risk. However, there is substantial variation of CAC scores acquired with different CT scanners. Therefore, CAC scoring discrepancies may lead to suboptimal patients' treatment and harmonization is needed. Purpose The aim of our study was twofold. Our first aim was to develop a calibration tool resulting in vendor neutral Agatston Score (vnAS). Second, we aimed to assess the effect of using this calibration tool in the existing Multi-Ethnic Study of Atherosclerosis (MESA) study cohort on both risk prediction of coronary heart disease (CHD), and initiation of statin therapy. Methods Two static anthropomorphic phantoms containing multiple CAC inserts were imaged on seven different CT systems and one EBT system. For each CT system, the vnAS calculator parameters were derived using regression analysis based on Agatston scores from EBT and CT. To validate our vnAS, we used CAC scoring information and clinical data of participants from MESA study. All included participants (Cohort I, n=3181) were assigned to one out of four calcium groups, which were defined as zero-calcium (AS and vnAS of 0), low-calcium (AS and vnAS of 1–99) high-calcium (AS and vnAS ≥100), and reclassified individuals (AS <100 and vnAS ≥100). The occurrence of CHD events in each group was assessed and multivariable Cox regression models were used to assess the added value of the vnAS in the prediction of CHD events For a sub-cohort of 890 participants at intermediate cardiovascular risk, the potential benefit from statin therapy was estimated based on the number needed to treat (NNT). NNT were determined for patients with vnAS ≥100 and vnAS ≥300 with original AS below 100 (group I) or 300 (group II), respectively. Results For all CT systems, a high degree of correlation with EBT Agatston scores was shown (R2 >0.932). Using the vnAS, 85 individuals (2.7%) were reclassified from a lower to a higher risk category. For the reclassified participants, CHD event rates increased significantly from 7% to 15% (p=0.008) with a CHD hazard ratio of 3.39 (95% CI 1.82–6.35, p=0.001) (Figure 1). In intermediate risk cohort, the NNT was smaller for reclassified individuals as compared to their original (low) calcium group, at 7 vs 12 for group I and 2 vs 15 for group II, respectively. The summary of vnAS applicability is depicted in Figure 2. Conclusions We developed a calibration tool, which enables to calculate vendor neutral AS (vnAS). Based on vnAS, 85 individuals from MESA study, who were reclassified from a lower to a higher calcium category, did indeed have a higher CHD event rate. Consequently, the potential benefit from statin therapy, based on vnAS, was also increased for reclassified participants at intermediate cardiovascular risk. Funding Acknowledgement Type of funding sources: None.

Single- and duplex TaqMan-quantitative PCR for determining the copy numbers of integrated selection markers during site-specific mutagenesis in Toxoplasma gondii by CRISPR-Cas9.

Herein, we developed a single and a duplex TaqMan quantitative PCR (qPCR) for absolute quantification of copy numbers of integrated dihydrofolate reductase-thymidylate synthase (mdhfr-ts) drug selectable marker for pyrimethamine resistance in Toxoplasma gondii knockouts (KOs). The single TaqMan qPCR amplifies a 174 bp DNA fragment of the inserted mdhfr-ts and of the wild-type (WT) dhfr-ts (wtdhfr-ts) which is present as single copy gene in Toxoplasma and encodes a sensitive enzyme to pyrimethamine. Thus, the copy number of the dhfr-ts fragment in a given DNA quantity from KO parasites with a single site-specific integration should be twice the number of dhfr-ts copies recorded in the same DNA quantity from WT parasites. The duplex TaqMan qPCR allows simultaneous amplification of the 174 bp dhfr-ts fragment and the T. gondii 529-bp repeat element. Accordingly, for a WT DNA sample, the determined number of tachyzoites given by dhfr-ts amplification is equal to the number of tachyzoites determined by amplification of the Toxoplasma 529-bp, resulting thus in a ratio of 1. However, for a KO clone having a single site-specific integration of mdhfr-ts, the calculated ratio is 2. We then applied both approaches to test T. gondii RH mutants in which the major surface antigen (SAG1) was disrupted through insertion of mdhfr-ts using CRISPR-Cas9. Results from both assays were in correlation showing a high accuracy in detecting KOs with multiple integrated mdhfr-ts. Southern blot analyses using BsaBI and DraIII confirmed qPCRs results. Both TaqMan qPCRs are needed for reliable diagnostic of T. gondii KOs following CRISPR-Cas9-mediated mutagenesis, particularly with respect to off-target effects resulting from multiple insertions of mdhfr-ts. The principle of the duplex TaqMan qPCR is applicable for other selectable markers in Toxoplasma. TaqMan qPCR tools may contribute to more frequent use of WT Toxoplasma strains during functional genomics.

A novel parallel overlapping mode for complete ablation of large benign thyroid nodules in a single-session radiofrequency ablation.

BackgroundRadiofrequency ablation (RFA) has been widely applied in patients with benign thyroid nodules (BTNs), and complete ablation in a single-session treatment brings great benefits to patients. While how the ablation should be planned and performed to achieve complete ablation in a single-session treatment in large BTNs remains unknown.PurposeTo determine a more suitable ablation strategy for sufficient treatment in a single-session treatment.Materials and MethodsThis retrospective study included 108 BTNs receiving RFA treatment. These patients were divided into two groups: group A using one insertion point with a fan-shaped overlapping mode and group B using multiple insertion points with a novel parallel overlapping mode. All the treatments used a hydrodissection approach and moving-shot technique. Contrast-enhanced ultrasonography (CEUS) was used to guide the supplementary ablation. Follow-ups were performed at 1, 3, 6 and 12 months. The rates of supplementary ablation, initial ablation ratio (IAR), the rates of complete ablation (CAR), treatment effects and complications between the two groups were compared.ResultsThe group B had larger treated nodules (10.2ml vs 6.4ml, P<0.001) than group A, while group B had a lower rate of supplementary ablation (21.6% vs 75.4%, P<0.001), especially in the BTNs with craniocaudal diameters ≥30mm (22.0% vs 100%, P<0.001). With the assistance of supplementary ablation, both groups achieved similar IAR (100% vs 100%, P=0.372) and CAR (94.7% vs 94.1%, P=1.000). Two groups showed similar VRRs at 12-month follow-up (77.9% vs 77.5%, P=0.894) and similar rates of complications (3.5% vs 2.0%, P=1.000).ConclusionsNeedle placement using the multiple insertion points with a novel parallel overlapping mode would be easier to achieve complete ablation with less supplementary ablation, especially in large nodules.

Transthoracic intracardiac lines-A double edged sword.

Routine use of central venous access is needed in children undergoing open heart surgery for pressure monitoring and inotrope infusion. We sought to evaluate the efficiency and safety of routine use of transthoracic intracardiac lines (ICLs) in patients undergoing cardiac surgery and to compare them to patients who have been previously treated with traditional central venous lines (non-ICLs). Retrospective review of charts of all patients who underwent cardiac surgery and had an ICL inserted in the operating room. Case control matching was done with similar patient in which ICL was not inserted. Patients characteristics, diagnosis, operative, and intensive care datawere collected for each patient and analyzed. A total number of 376 patient records were reviewed (198 ICL patientsand 178 non-ICL patients). Umbilical line and non-ICL durations were longer in the non-ICL group. ICL duration was the longest of all lines, averaging 12.87 ± 10.82 days. The necessity for multiple line insertions (˃2 insertions) was significantly higher in the non-ICL group, with a relative risk ratio of 3.24 (95% confidence interval: 1.617-6.428). There was no statistical difference of infections rate and line complications between the two groups. ICLs are safe in infants undergoing cardiac surgery and can be kept in place for a long period of time with a low rate of line complications and infection. Routine use of ICLs reduces the number of central venous catheter placement in this complex patient population.

Evaluation of deployment capability of a novel outside-the-scope, detachable catheter system for ablation of lung lesions in exvivo human lung models.

ObjectivesEffective transbronchial ablation of lung nodules requires precise catheter delivery to the target lesion and freedom from the bronchoscope for safety throughout the procedure and to allow for multiple catheter insertions. A fully detachable, outside-the-scope (OTS) probe system was developed that attaches to a flexible bronchoscope. Using this system, the operator can deploy the probe in the target and completely detach it from the scope. Our aim was to demonstrate the endobronchial deployment accuracy and feasibility of an OTS, detachable, simulated ablation catheter driven to peripheral lung targets in ex vivo–ventilated human lung models.MethodsA balloon catheter inflated with radiopaque contrast was used as a simulated peripheral target in freshly explanted lungs from lung transplant recipients. A simulated ablation catheter was positioned outside and aligned to the tip of the bronchoscope using the OTS system. Under fluoroscopic guidance, the bronchoscope and the catheter were driven toward the target in mechanically ventilated lungs. Once the catheter tip was confirmed within the target, the OTS system was released and the probe was detached from the scope. The bronchoscope was retracted and fluoroscopy was used to confirm the position of the catheter.ResultsTwelve peripheral targets were simulated. The ablation catheter was successfully deployed with its tip positioned within 5 mm from the target and confirmed stability during multiple cycles of ventilation.ConclusionsA novel, detachable, OTS system can be successfully deployed in peripheral lung targets with potential clinical applications for multiple procedures in advanced bronchoscopy where scope freedom is advantageous.

Integrated multi-objective optimization on the geometrical design of a disk-type milling cutter with multiple inserts applying uniform design, RBF neural network, and PSO algorithm

Integrated multi-objective optimization on the geometrical design of a disk-type milling cutter with multiple inserts applying uniform design, RBF neural network, and PSO algorithm

Accuracy of guide wire placement for femoral neck stabilization using 3D printed drill guides

BackgroundThe goal of stabilization of the femoral neck is to limit morbidity and mortality from fracture. Of three potential methods of fixation, (three percutaneous screws, the Synthes Femoral Neck System, and a dynamic hip screw), each requires guide wire positioning of the implant(s) in the femoral neck and head. Consistent and accurate positioning of these systems is paramount to reduce surgical times, stabilize fractures effectively, and reduce complications. To help expedite surgery and achieve ideal implant positioning in the geriatric population, we have developed and validated a surgical planning methodology using 3D modelling and printing technology.MethodsUsing image processing software, 3D surgical models were generated placing guide wires in a virtual model of an osteoporotic proximal femur sawbone. Three unique drill guides were created to achieve the optimal position for implant placement for each of the three different implant systems, and the guides were 3D printed. Subsequently, a trauma fellowship trained orthopedic surgeon used the 3D printed guides to position 2.8 mm diameter drill bit tipped guide wires into five osteoporotic sawbones for each of the three systems (fifteen sawbones total). Computed Tomography (CT) scans were then taken of each of the sawbones with the implants in place. 3D model renderings of the CT scans were created using image processing techniques and the displacement and angular deviations at guide wire entry to the optimal sawbone model were measured.ResultsAcross all three percutaneous screw guide wires, the average displacement was 3.19 ± 0.12 mm and the average angular deviation was 4.10 ± 0.17o. The Femoral Neck System guide wires had an average displacement of 1.59 ± 0.18 mm and average angular deviation of 2.81 ± 0.64o. The Dynamic Hip Screw had an average displacement of 1.03 ± 0.19 mm and average angular deviation of 2.59 ± 0.39o.ConclusionThe use of custom 3D printed drill guides to assist with the positioning of guide wires proved to be accurate for each of the three types of surgical strategies. Guides which are used to place more than 1 guide wire may have lower positional accuracy, as the guide may shift during multiple wire insertions. We believe that personalized point of care drill guides provide an accurate intraoperative method for positioning implants into the femoral neck.

Comparative Analysis of Face Milling in Dry and Wet Condition of Al 8011 For Minimum Surface Roughness in Face Milling

Abstract: The quality of machined components is evaluated in respect of how closely they adhere to set product finish, and reflective properties. Dimensional accuracy, tool wear and quality of surface finish are three factors that manufacturers must be able to control at the machining operations to ensure better performance and service life of engineering component. Aluminum alloys are extensively used as a main engineering material in various industries such as automotive industries, the mould and the die components manufacture and the industry in which weight is the most important factor. The purpose of this research is to investigate the effect of the main factors of the surface roughness and flatness in aluminum 8011 face milling with dry and wet condition. This experimental investigation to be conducted by using VMC controlled milling machine with 30mm face milling cutter with carbide multiple inserts. The same parameters were executed during the operation only difference minimum quantity lubricant for one set of operation and another set of operation without lubricant. The experimental results were evaluated using Taguchi technique minimum surface finish obtained at medium speed and maximum feed and depth of cut 0.222 µm in the dry condition during the face milling operation. The minimum flatness was obtained 0.012 mm at wet condition. minimum surface finish obtained through dry condition. Optimal control factor and ANNOVA calculations were found for face milling operation of AA8011.

Multiple Criss-Cross Insertion and Deletion Correcting Codes

This paper investigates the problem of correcting multiple criss-cross insertions and deletions in arrays. More precisely, we study the unique recovery of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$n \times n$ </tex-math></inline-formula> arrays affected by <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${t}$ </tex-math></inline-formula> <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-criss-cross deletions</i> defined as any combination of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${t_{\mathrm {r}}}$ </tex-math></inline-formula> row and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${t_{\mathrm {c}}}$ </tex-math></inline-formula> column deletions such that <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${t_{\mathrm {r}}}+ {t_{\mathrm {c}}}= {t}$ </tex-math></inline-formula> for a given <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$t$ </tex-math></inline-formula> . We show an equivalence between correcting <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${t}$ </tex-math></inline-formula> -criss-cross deletions and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${t}$ </tex-math></inline-formula> -criss-cross insertions and show that a code correcting <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${t}$ </tex-math></inline-formula> -criss-cross insertions/deletions has redundancy at least <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${t} n + {t}\log n - \log ({t}!)$ </tex-math></inline-formula> . Then, we present an existential construction of a <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${t}$ </tex-math></inline-formula> -criss-cross insertion/deletion correcting code with redundancy bounded from above by <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${t} n + \mathcal {O}({t}^{2} \log ^{2} n)$ </tex-math></inline-formula> . The main ingredients of the presented code construction are systematic binary <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${t}$ </tex-math></inline-formula> -deletion correcting codes and Gabidulin codes. The first ingredient helps locating the indices of the inserted/deleted rows and columns, thus transforming the insertion/deletion-correction problem into a row/column erasure-correction problem which is then solved using the second ingredient.

Hepatitis B Virus Variants with Multiple Insertions and/or Deletions in the X Open Reading Frame 3' End: Common Members of Viral Quasispecies in Chronic Hepatitis B Patients.

Deletions in the 3′ end region of the hepatitis B virus (HBV) X open reading frame (HBX) may affect the core promoter (Cp) and have been frequently associated with hepatocellular carcinoma (HCC). The aim of this study was to investigate the presence of variants with deletions and/or insertions (Indels) in this region in the quasispecies of 50 chronic hepatitis B (CHB) patients without HCC. We identified 103 different Indels in 47 (94%) patients, in a median of 3.4% of their reads (IQR, 1.3–8.4%), and 25% (IQR, 13.1–40.7%) of unique sequences identified in each quasispecies (haplotypes). Of those Indels, 101 (98.1%) caused 44 different altered stop codons, the most commonly observed were at positions 128, 129, 135, and 362 (putative position). Moreover, 39 (37.9%) Indels altered the TATA-like box (TA) sequences of Cp; the most commonly observed caused TA2 + TA3 fusion, creating a new putative canonical TATA box. Four (8%) patients developed negative clinical outcomes after a median follow-up of 9.4 (8.7–12) years. In conclusion, we observed variants with Indels in the HBX 3′ end in the vast majority of our CHB patients, some of them encoding alternative versions of HBx with potential functional roles, and/or alterations in the regulation of transcription.

Gizzard erosions in broiler chickens in Sweden caused by fowl adenovirus serotype 1 (FAdV-1): investigation of outbreaks, including whole-genome sequencing of an isolate

ABSTRACT The present paper describes the investigation of the first outbreaks of adenoviral gizzard erosions (AGE) in Sweden, in five broiler flocks. The investigation included whole viral genome sequencing and investigation of genomic organization and sequence relationships with other adenoviruses. All five flocks had a history of decreased growth and uneven size of birds since 9-10 days of age. Macroscopically, lesions consistent with AGE (detached koilin layers, discolouration, bleeding, erosions) were identified in gizzards in all five flocks. In four flocks histology was performed, and degeneration and inflammation of the koilin layer and gizzard mucosa were identified in all four. In one flock, intranuclear inclusion bodies typical for fowl adenovirus (FAdV) were detected in trapped epithelial cells in the koilin layer. In four flocks in situ hybridization was performed, and cells positive for FAdV serotype 1 (FAdV-1) were demonstrated in the koilin layer and gizzard mucosa. FAdV species A (FAdV-A) was detected in gizzard, liver, caecal tonsils and bursa of Fabricius by polymerase chain reaction (PCR) and sequencing. Ten out of ten examined parent flocks of the affected chickens were seropositive for FAdV, indicating former or on-going infection. However, FAdV was not detected in embryos from seropositive parent flocks and thus vertical transmission was not demonstrated. The entire nucleotide sequence of one sample was determined and found to be 43,856 base pairs (bp) in length. The genome sequence and organization were found to be similar to that of the reference apathogenic avian adenovirus “chicken embryo lethal orphan” (CELO). RESEARCH HIGHLIGHTS AGE in Swedish broilers: necropsy, histopathology, ISH, PCR, whole-genome sequencing. Whole FAdV-genome analysed: 43,856 bp, found to be most similar to CELO (U46933.1). Multiple point mutations, site insertions and deletions identified compared to CELO. Paper adds knowledge about European disease situation and pathogenic FAdV-strains.

Transcriptional regulation via strand displacement DNA repair in G‐quadruplexes

Environmental exposures and lifestyle choices can result in cellular oxidative stress, characterized by the generation of an abundance of reactive oxygen species (ROS). ROS wreak havoc on the structure of DNA bases, with guanine modification yielding the lesion 8‐oxo‐7,8‐ dihydroguanine (8oxoG) being particularly prevalent. If not repaired, 8oxoG is mutagenic, causing G to T transversion mutations that can initiate and promote human disease. Guanine‐rich G‐ quadruplex (G4) forming sequences are enriched at promoter proximal regions of the genome, making these regions hot spots for 8oxoG lesions. The cells primary defense against 8oxoG is base excision repair (BER). Recently, it was shown that the repair of 8oxoG by the BER enzymes OGG1 and APE1 perturbs the structural equilibrium of the VEGFpromoter DNA sequence between duplex and G4 conformations, resulting in epigenetic‐like modifications of gene expression. However, the mechanistic details regulating this equilibrium remain somewhat enigmatic, including the activity and coordination of BER enzymes on an 8oxoG containing G4 promoter. To address this, we determined the requirement and efficiency of each BER factor on G4 substates (including OGG1, APE1, Polβ, and DNA ligase 1) by employing a combination of pre‐steady state kinetics assays and in vitroBER reconstitution assays with G4 DNA substrates. Surprisingly, we observe OGG1 is capable of initiating BER on oxidized G4 VEGFDNA substrates in which the G4 region is flanked by non‐G4, duplex regions of DNA. Pre‐steady state kinetics revealed that compared to abasic duplex DNA, APE1‐mediated strand cleavage is only slightly decreased and that a majority of the reduction in its activity on G4 DNA results from slow product release. Thus, APE1 may have an opportunity to recruit transcription factors to the VEGF promoter during this slow product release step of its reaction. Interestingly, Polβ performs multiple insertions on G4 substates via strand displacement DNA synthesis, with 3 ‐ 5 insertions depending on the position of damage. In contrast, there is only a single insertion by Polβ with corresponding duplex DNA substates and no insertion when the G4 structure lacks an opposing strand with flanking duplex regions. Ligase I does not efficiently ligate G4 substrates, and hence cannot complete the BER repair cycle. Instead, proper repair requires the long‐patch BER enzyme flap‐endonuclease activity of FEN1 in response to the multiple insertions by Polβ prior to ligation.