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Background: Laboratory resurrection of ancient coagulation factor (F) IX variants generated through ancestral sequence reconstruction led to the discovery of a FIX variant, designated An96, which possesses enhanced specific activity independent of and additive to that provided by human p.Arg384Lys, referred to as FIX-Padua., Objectives: The goal of the current study was to identify the amino acid substitution(s) responsible for the enhanced activity of An96 and create a humanized An96 FIX transgene for gene therapy application., Methods: Reductionist screening approaches, including domain swapping and scanning residue substitution, were used and guided by one-stage FIX activity assays. In vitro characterization of top candidates included recombinant high-purity preparation, specific activity determination, and enzyme kinetic analysis. Final candidates were packaged into adeno-associated viral (AAV) vectors and delivered to hemophilia B mice., Results: Five of 42 total amino acid substitutions in An96 appear sufficient to retain the enhanced activity of An96 in an otherwise human FIX variant. Additional substitution of the Padua variant further increased the specific activity 5-fold. This candidate, designated ET9, demonstrated 51-fold greater specific activity than hFIX. AAV2/8-ET9 treated hemophilia B mice produced plasma FIX activities equivalent to those observed previously for AAV2/8-An96-Padua, which were 10-fold higher than AAV2/8-hFIX-Padua., Conclusion: Starting from computationally inferred ancient FIX sequences, novel amino acid substitutions conferring activity enhancement were identified and translated into an AAV-FIX gene therapy cassette demonstrating high potency. This ancestral sequence reconstruction discovery and sequence mapping refinement approach represents a promising platform for broader protein drug and gene therapy candidate optimization., Competing Interests: Declaration of competing interests H.C.B., G.D., S.N.G., C.B.D., H.T.S., K.A.K., and C.W.C. are inventors on patents and patent applications describing the ancestral FIX technology filed by Expression Therapeutics, Emory University, Children’s Healthcare of Atlanta, and Georgia Institute of Technology. C.B.D., H.T.S., and H.C.B. are inventors on liver-directed codon-optimization and promoter technology filed by Emory University and Children’s Healthcare of Atlanta. H.T.S. and C.B.D. are cofounders of Expression Therapeutics, Inc, and own equity in the company. H.C.B., G.D., and S.N.G. are employees of Expression Therapeutics, Inc and own equity in the company. Expression Therapeutics, Inc has obtained licenses for FIX-An96, liver codon-optimized FIX, and synthetic liver-directed promoter intellectual property. K.C.C., P.C.S., and G.M.B. declare no conflicts of interest. The terms of these arrangements have been reviewed and approved by Emory University in accordance with its conflict of interest policies., (Copyright © 2023 International Society on Thrombosis and Haemostasis. Published by Elsevier Inc. All rights reserved.)

Objective: Endoscopy is a medical diagnostic procedure used to see inside the human body with the help of a camera-attached system called the endoscope. Endoscopic images and videos suffer from specular reflections (or highlight) and can have an adverse impact on the diagnostic quality of images. These scattered white regions severely affect the visual appearance of images for both endoscopists and the computer-aided diagnosis of diseases. Methods & Results: We introduce a new parameter-free matrix decomposition technique to remove the specular reflections. The proposed method decomposes the original image into a highlight-free pseudo-low-rank component and a highlight component. Along with the highlight removal, the approach also removes the boundary artifacts present around the highlight regions, unlike the previous works based on family of Robust Principal Component Analysis (RPCA). The approach is evaluated on three publicly available endoscopy datasets: Kvasir Polyp, Kvasir Normal-Pylorus and Kvasir Capsule datasets. Our evaluation is benchmarked against 4 different state-of-the-art approaches using three different well-used metrics such as Structural Similarity Index Measure (SSIM), Percentage of highlights remaining and Coefficient of Variation (CoV). Conclusions: The results show significant improvements over the compared methods on all three metrics. The approach is further validated for statistical significance where it emerges better than other state-of-the-art approaches. Clinical and Translational Impact Statement- The mathematical concepts of low rank and rank decomposition in matrix algebra are translated to remove specularities in the endoscopic images The result shows the impact of the proposed method in removing specular reflections from endoscopic images indicating improved diagnosis efficiency for both endoscopists and computer-aided diagnosis systems., (This work is licensed under a Creative Commons Attribution 4.0 License. For more information, see https://creativecommons.org/licenses/by/4.0/.)

The massive generation of data, which includes images and videos, has made data management, analysis, information extraction difficult in recent years. To gather relevant information, this large amount of data needs to be grouped. Real-life data may be noise corrupted during data collection or transmission, and the majority of them are unlabeled, allowing for the use of robust unsupervised clustering techniques. Traditional clustering techniques, which vectorize the images, are unable to keep the geometrical structure of the images. Hence, a robust tensor-based submodule clustering method based on l12 regularization with improved clustering capability is formulated. The l12 induced tensor nuclear norm (TNN), integrated into the proposed method, offers better low rankness while retaining the self-expressiveness property of submodules. Unlike existing methods, the proposed method employs a simultaneous noise removal technique by twisting the lateral image slices of the input data tensor into frontal slices and eliminates the noise content in each image, using the principles of the sparse and low rank decomposition technique. Experiments are carried out over three datasets with varying amounts of sparse, Gaussian and salt and pepper noise. The experimental results demonstrate the superior performance of the proposed method over the existing state-of-the-art methods.

The rising demand for surveillance systems naturally necessitates more efficient and noise robust moving object detection (MOD) systems from the captured video streams. Inspired by the challenges in MOD which are yet to be addressed properly, this paper proposes a new MOD scheme using l 1/2 regularization in the tensor framework. It takes advantage of the special features of tensor singular value decomposition ( t -SVD) along with regularizations using l 1/2 -norm with half thresholding operation and tensor total variation (TTV) to develop a noise robust MOD system with improved detection accuracy. While t -SVD exploits the spatio-temporal correlation of the video background, l 1/2 regularization provides noise robustness besides removing the sparser but discontinuous dynamic elements in the spatio-temporal direction. Moreover, TTV enhances the spatio-temporal continuity and fills up the gaps due to the lingering objects and thereby extracting the foreground precisely. The proposed three-way optimization method is designed to address both static and dynamic background cases of MOD separately with the intention to reduce the misclassifications due to moving/cluttered background. The brilliance of this method is confirmed by the impressive visual quality of the background/foreground separation, noise robustness, reduced computational complexity, and rapid response. The quantitative evaluation discloses the predominance of the proposed method with respect to the state-of-the-art techniques.

Low-dose Computed Tomography (CT) imaging is a most commonly used medical imaging modality. Though the reduction in dosage reduces the risk due to radiation, it leads to an increase in noise level. Hence, it is a mandatory requirement to include a noise reduction technique as a pre- and/or post-processing step for better disease diagnosis. The nuclear norm minimization has attracted a great deal of research interest in contemporary years. This paper proposes a low-rank approximation based approach for denoising of CT images by effectively utilizing the global spatial correlation and local smoothness properties. The tensor nuclear norm is used to describe the global properties and the tensor total variation is used to characterize the local smoothness as well as to improve global smoothness. The resulting optimization problem is solved by the Alternative Direction Method of Multipliers (ADMM) technique. Experimental results on simulated and real CT data prove that the proposed methods outperform the state-of-art works., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Potency is a key optimization parameter for hemophilia A gene therapy product candidates. Optimization strategies include promoter engineering to increase transcription, codon optimization of mRNA to improve translation, and amino-acid substitution to promote secretion. Herein, we describe both rational and empirical design approaches to the development of a minimally sized, highly potent AAV-fVIII vector that incorporates three unique elements: a liver-directed 146-nt transcription regulatory module, a target-cell-specific codon optimization algorithm, and a high-expression bioengineered fVIII variant. The minimal synthetic promoter allows for the smallest AAV-fVIII vector genome known at 4,832 nt, while the tissue-directed codon optimization strategy facilitates increased fVIII transgene product expression in target cell types, e.g., hepatocytes, over traditional genome-level codon optimization strategies. As a tertiary approach, we incorporated ancient and orthologous fVIII sequence elements previously shown to facilitate improved biosynthesis through post-translational mechanisms. Together, these technologies contribute to an AAV-fVIII vector that confers sustained, curative levels of fVIII at a minimal dose in hemophilia A mice. Moreover, the first two technologies should be generalizable to all liver-directed gene therapy vector designs.

Human rhinovirus (HRV) infection is an important trigger of exacerbations of chronic obstructive pulmonary disease (COPD) but its role in determining exacerbation frequency phenotype or the time-course of HRV infection in naturally occurring exacerbations is unknown. Sputum samples from 77 patients were analysed by real-time quantitative PCR for both HRV (388 samples), and Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis (89 samples). Patients recorded worsening of respiratory symptoms on daily diary cards, from which exacerbations were identified. HRV prevalence and load at exacerbation presentation were significantly higher than in the stable state (prevalence 53.3% versus 17.2%, respectively; p<0.001) but 0% by day 35 post-exacerbation. HRV load was higher in patients with cold symptoms (p=0.046) or sore throats (p=0.006) than those without. 73% of bacterium-negative but HRV-positive exacerbations were bacterium-positive by day 14. Patients with HRV detected at exacerbation had a higher exacerbation frequency (interquartile range) of 3.01 (2.02-5.30) per year compared with patients without HRV (2.51 (2.00-3.51)) (p=0.038). HRV prevalence and load increased at COPD exacerbation, and resolved during recovery. Frequent exacerbators were more likely to experience HRV infection. Secondary bacterial infection is common after HRV infection, and provides a possible mechanism for exacerbation recurrence and a potential target for novel therapies., (© ERS 2014.)

Background: Objective of the present study was to examine the association between adiponectin and hepatic steatosis, and other biochemical and anthropometric parameters in healthy subjects., Results: A total of 1349 subjects (age 18-65 years) underwent ultrasound examination of the liver. Mean adiponectin concentration for the study collective was 11.35 ± 6.28 μg/mL. The following parameters were assessed for their association with adiponectin: body-mass index (BMI); age; sex; arterial blood pressure; nicotine use; alcohol consumption; physical activity; metabolic syndrome; total, low-density lipoprotein (LDL) and high-density lipoprotein (HDL) cholesterol; triglycerides; aspartate aminotransferase (AST); alanine aminotransferase (ALT); γ-glutamyltransferase (GGT); alkaline phosphatase (AP); C-reactive protein (CRP); insulin sensitivity according to the Homeostasis Model Assessment (HOMA); random blood glucose; and the degree of steatosis of the liver. The numerical differences in the variables influencing adiponectin returned in the descriptive analysis were confirmed at bivariate analysis for BMI, ALT, AST, GGT, AP, total and HDL cholesterol, triglycerides, CRP, arterial blood pressure, metabolic syndrome, nicotine use and alcohol consumption. The logistic regression of the multivariate analysis showed that male sex, hepatic steatosis, BMI, metabolic syndrome, tobacco smoking and CRP correlate negatively with adiponectin, while age, moderate alcohol consumption and HDL cholesterol exhibit a positive association., Conclusions: The results of the present study confirm the findings of previous research. Adiponectin correlates negatively with cardiometabolic risk factors and is an independent indicator for non-alcoholic fatty liver disease (NAFLD).

Rationale: Patients with chronic obstructive pulmonary disease (COPD) have elevated cardiovascular risk, and myocardial injury is common during severe exacerbations. Little is known about the prevalence, magnitude, and underlying mechanisms of cardiovascular risk in community-treated exacerbations., Objectives: To investigate how COPD exacerbations and exacerbation frequency impact cardiovascular risk and myocardial injury, and whether this is related to airway infection and inflammation., Methods: We prospectively measured arterial stiffness (aortic pulse wave velocity [aPWV]) and cardiac biomarkers in 98 patients with stable COPD. Fifty-five patients had paired stable and exacerbation assessments, repeated at Days 3, 7, 14, and 35 during recovery. Airway infection was identified using polymerase chain reaction., Measurements and Main Results: COPD exacerbation frequency was related to stable-state arterial stiffness (rho = 0.209; P = 0.040). Frequent exacerbators had greater aPWV than infrequent exacerbators (mean ± SD aPWV, 11.4 ± 2.1 vs. 10.3 ± 2.0 ms(-1); P = 0.025). Arterial stiffness rose by an average of 1.2 ms(-1) (11.1%) from stable state to exacerbation (n = 55) and fell slowly during recovery. In those with airway infection at exacerbation (n = 24) this rise was greater (1.4 ± 1.6 vs. 0.7 ± 1.3 ms(-1); P = 0.048); prolonged; and related to sputum IL-6 (rho = 0.753; P < 0.001). Increases in cardiac biomarkers at exacerbation were higher in those with ischemic heart disease (n = 12) than those without (n = 43) (mean ± SD increase in troponin T, 0.011 ± 0.009 vs. 0.003 ± 0.006 μg/L, P = 0.003; N-terminal pro-brain natriuretic peptide, 38.1 ± 37.7 vs. 5.9 ± 12.3 pg/ml, P < 0.001)., Conclusions: Frequent COPD exacerbators have greater arterial stiffness than infrequent exacerbators. Arterial stiffness rises acutely during COPD exacerbations, particularly with airway infection. Increases in arterial stiffness are related to inflammation, and are slow to recover. Myocardial injury is common and clinically significant during COPD exacerbations, particularly in those with underlying ischemic heart disease.

Cetuximab is an anti-epidermal growth factor receptor (EGFR) monoclonal antibody approved by the US Food and Drug Administration for the treatment of colorectal (CRC) and head and neck (H&N) cancers. Hypersensitivity-infusion reactions (HIRs) confer moderate morbidity and potential mortality. HIRs have a wide geographic incidence with few identifiable risk factors. Limited data regarding risk-reduction interventions for HIR or post-HIR retreatment are available. All patients treated with cetuximab at a single Veterans Affairs facility were monitored for development of HIRs, with baseline clinical, demographic, and supportive care data recorded. All received standard premedication based on cohort assignment. A total of 51 consecutive patients (30 CRC; 21 H&N) received at least one dose of cetuximab. Grades II-IV HIRs occurred in 14 patients (27%; 6 grade II, 6 grade Ill, 2 grade IV). There was no grade V HIR. All HIRs occurred during the first infusion. There were no differences between age, race, diagnosis, stage, concurrent chemotherapy, or radiotherapy with cetuximab, allergy history, or military service era of patients developing HIRs versus those who did not.There were no identifiable risk factors that predicted the severity of HIR. Neither premedication modifications (P = 0.34) nor bronchodilator use (P= 0.12) impacted the incidence or severity of HIR. A cetuximab test dose successfully elicited an HIR and resulted in an 87% cost savings. None of five patients receiving subsequent retreatment with anti-EGFR MoAb had recurrence of an HIR. An HIR during cetuximab infusion can be a serious and underestimated toxicity. The relatively high incidence reported here is consistent with that previously identified in the Southeastern United States. No clinical, demographic, or historic variables reliably predicted HIR in our population. Use of a test dose to elicit a HIR appears to be feasible and cost-effective. Use of panitumumab after a cetuximab HIR in select patients with CRC appears to be feasible and safe.

Background: Umbilical cord blood (UCB) is an acceptable source of hematopoietic cells for transplantation with success being associated with the nucleated cell count (NCC), CD34+ cells, and colony-forming unit-granulocyte-macrophage (CFU-GM) content infused. A total of 1033 UCB samples with neonatal and paternal characteristics that might influence hematopoietic content were examined., Study Design and Methods: UCB samples were screened, processed, and reevaluated for the above cell counts. These parameters of engraftment potential were analyzed for associations with neonatal and parental characteristics., Results: Postprocessed NCCs (median, 6.53 x 10(8)+/- 2.80 x 10(8) SD; mean 7.30 x 10(8)), CD34+ counts (median, 2.02 x 10(6) +/- 2.20 x 10(6) SD; mean, 2.65 x 10(6); r = 0.66; p < 0.001), and CFU-GM content (median, 2.65 x 10(5) +/- 3.16 x 10(5) SD; mean, 3.54 x 10(5); r = 0.61; p < 0.001) all were strongly interrelated. Both initial volume (median, 77.5 +/- 26.2 mL SD; mean, 81.9 mL) and initial NCC (median, 9.75 x 10(8) +/- 4.88 x 10(8) SD; mean, 10.9 x 10(8)) correlated well with postprocessed NCC (r = 0.60; r = 0.90; p < 0.01), CD34+ count (r = 0.40; r = 0.63; p < 0.01), and CFU-GM content (r = 0.38; r = 0.59; p < 0.01), with a stronger relationship seen with initial NCC. Infant birth weight (specifically, >3000 g), but not sex, gestational age, or cytomegalovirus status correlated strongly with collection volume and UCB cell counts. Units from minority volunteers contained relatively smaller volumes and hematopoietic content., Conclusion: UCB banks should emphasize selecting the heaviest infants and processing large-volume units with high NCCs to optimize hematopoietic potential. Minority recruitment should be encouraged with consideration given to inherent racial differences in cell counts. There does not appear to be a significant relationship between other neonatal and parental characteristics and that of engraftment potential.