Prediction of efficiencies for diverse prime editing systems in multiple cell types.

Applications of prime editing are often limited due to insufficient efficiencies, and it can require substantial time and resources to determine the most efficient pegRNAs and prime editors (PEs) to generate a desired edit under various experimental conditions. Here, we evaluated prime editing efficiencies for a total of 338,996 pairs of pegRNAs including 3,979 epegRNAs and target sequences in an error-free manner. These datasets enabled a systematic determination of factors affecting prime editing efficiencies. Then, we developed computational models, named DeepPrime and DeepPrime-FT, that can predict prime editing efficiencies for eight prime editing systems in seven cell types for all possible types of editing of up to 3 base pairs. We also extensively profiled the prime editing efficiencies at mismatched targets and developed a computational model predicting editing efficiencies at such targets. These computational models, together with our improved knowledge about prime editing efficiency determinants, will greatly facilitate prime editing applications.

Development of innate and adaptive immunity to RSV in young children.

Infection of the respiratory tract with respiratory syncytial virus (RSV) is common and occurs repeatedly throughout life with most severe disease occurring at the extremes of age: in young infants and the elderly. Effective anti-viral therapeutics are not available and therefore prevention has been the primary strategy for reducing the disease burden. Our current understanding of respiratory mucosal cell biology and the immune response within the respiratory tract is inadequate to prevent infection caused by a pathogen like RSV that does not disseminate outside of this environment. Gaps in our understanding of the activation of innate and adaptive immunity in response to RSV and the role of age upon infection also limit improvements in the design of therapeutics and vaccines for young infants. However, advancements in structural biology have improved our ability to characterize antibodies against viral proteins and in 2023 the first vaccines for those over 60 years and pregnant women became available, potentially reducing the burden of disease. This review will examine our current understanding of the critical facets of anti-RSV immune responses in infants and young children as well as highlight areas where more research is needed.

Fabrication of a light screen-aperture integrated flexible thin film micro-lens array for a biomimetic superposition compound eye.

Micro-lens array, an artificial compound eye vision system, provides a wide field of view and multi-perspective view. However, it has not been adopted as a computer vision application due to its limited visible range and high optical interference. In this research, a novel fabrication method for the flexible polydimethylsiloxane micro-lens array with a polytetrafluoroethylene light screen-aperture integrated layer was established by the simple protrusion method. The integrated layer provided longer visible range by one meter while maintaining the wide field-of-view of 100 °. The resulting images were used for obtaining depth information of a target as an example and for analyzing the rectangular and hexagonal arrangements of the micro-lenses for the future applications. With the improved visual range, wide field-of-view and flexibility, the fabricated micro-lens array can be applied to the small and curved CMOS image sensors in the future.

Marker-Based Structural Displacement Measurement Models with Camera Movement Error Correction Using Image Matching and Anomaly Detection.

To prevent collapse accidents at construction sites, the marker-based displacement measurement method was developed. However, it has difficulty in obtaining accurate measurements at long distances (>50 m) in an outdoor environment because of camera movements. To overcome this problem, marker-based structural displacement measurement models using image matching and anomaly detection were designed in this study. Then, the performance of each model in terms of camera movement error correction was verified through comparison with that of a conventional model. The results show that the systematic errors due to camera movements (<1.7°) were corrected. The detection rate of markers with displacement reached 95%, and the probability that the error size would be less than 10 mm was ≥ 95% with a 95% confidence interval at a distance of more than 100 m. Moreover, the normalized mean square error was less than 0.1. The models developed in this study can measure the pure displacement of an object without the systematic errors caused by camera movements. Furthermore, these models can be used to measure the displacements of distant structures using closed-circuit television cameras and markers in an outdoor environment with high accuracy.

RIDDLE: Race and ethnicity Imputation from Disease history with Deep LEarning.

Anonymized electronic medical records are an increasingly popular source of research data. However, these datasets often lack race and ethnicity information. This creates problems for researchers modeling human disease, as race and ethnicity are powerful confounders for many health exposures and treatment outcomes; race and ethnicity are closely linked to population-specific genetic variation. We showed that deep neural networks generate more accurate estimates for missing racial and ethnic information than competing methods (e.g., logistic regression, random forest, support vector machines, and gradient-boosted decision trees). RIDDLE yielded significantly better classification performance across all metrics that were considered: accuracy, cross-entropy loss (error), precision, recall, and area under the curve for receiver operating characteristic plots (all p < 10-9). We made specific efforts to interpret the trained neural network models to identify, quantify, and visualize medical features which are predictive of race and ethnicity. We used these characterizations of informative features to perform a systematic comparison of differential disease patterns by race and ethnicity. The fact that clinical histories are informative for imputing race and ethnicity could reflect (1) a skewed distribution of blue- and white-collar professions across racial and ethnic groups, (2) uneven accessibility and subjective importance of prophylactic health, (3) possible variation in lifestyle, such as dietary habits, and (4) differences in background genetic variation which predispose to diseases.

Design, synthesis and evaluation of novel N-hydroxybenzamides/N-hydroxypropenamides incorporating quinazolin-4(3H)-ones as histone deacetylase inhibitors and antitumor agents.

In our search for novel small molecules targeting histone deacetylases, we have designed and synthesized several series of novel N-hydroxybenzamides/N-hydroxypropenamides incorporating quinazolin-4(3H)-ones (4a-h, 8a-d, 10a-d). Biological evaluation showed that these hydroxamic acids were generally cytotoxic against three human cancer cell lines (SW620, colon; PC-3, prostate; NCI-H23, lung cancer). It was found that the N-hydroxypropenamides (10a-d) were the most potent, both in term of HDAC inhibition and cytotoxicity. Several compounds, e.g. 4e, 8b-c, and 10a-c, displayed up to 4-fold more potent than SAHA (suberoylanilide hydroxamic acid, vorinostat) in term of cytotoxicity. These compounds also comparably inhibited HDACs with IC50 values in sub-micromolar range. Docking experiments on HDAC2 isozyme revealed some important features contributing to the inhibitory activity of synthesized compounds, especially for propenamide analogues. Importantly, the free binding energy computed was found to have high quantitative correlation (R2 ∼ 95%) with experimental results.

Novel N-hydroxybenzamides incorporating 2-oxoindoline with unexpected potent histone deacetylase inhibitory effects and antitumor cytotoxicity.

In our search for novel small molecules targeting histone deacetylases, we have designed and synthesized two series of novel N-hydroxybenzamides incorporating 2-oxoindolines (4a-g, 6a-g). Biological evaluation showed that these benzamides potently inhibited HDAC2 with IC50 values in sub-micromolar range. In three human cancer cell lines the synthesized compounds were up to 4-fold more cytotoxic than SAHA. Docking experiments indicated that the compounds tightly bound to HDAC2 at the active binding site with binding affinities much higher than that of SAHA. Our present results demonstrate that these novel and simple N-hydroxybenzamides are potential for further development as anticancer agents and further investigation of similarly simple N-hydroxybenzamides should be warranted to obtain more potent HDAC inhibitors.

Fabrication of Localized Surface Plasmon Resonance Sensor Based on Optical Fiber and Micro Fluidic Channel.

This paper proposes Fiber-Optic Localized Surface Plasmon Resonance (FO LSPR) sensor combined with a micro fluidic channel, which enables continuous supply of fluid for bio-reaction. The proposed method prevents degradation of the sensing performance due to changes in measurement conditions. The feasibility of the FO LSPR sensor with a micro fluidic channel was demonstrated by computational fluid dynamics (CFD) simulation. Also, the proposed method was assessed by measuring the output intensity of the FO LSPR sensor at various refractive index solutions. Finally, a prostate-specific antigen (PSA) immunoassay was performed to evaluate the possibility of the fabricated sensor system as a biosensor.

Robust Video Stabilization Using Particle Keypoint Update and l1-Optimized Camera Path.

Acquisition of stabilized video is an important issue for various type of digital cameras. This paper presents an adaptive camera path estimation method using robust feature detection to remove shaky artifacts in a video. The proposed algorithm consists of three steps: (i) robust feature detection using particle keypoints between adjacent frames; (ii) camera path estimation and smoothing; and (iii) rendering to reconstruct a stabilized video. As a result, the proposed algorithm can estimate the optimal homography by redefining important feature points in the flat region using particle keypoints. In addition, stabilized frames with less holes can be generated from the optimal, adaptive camera path that minimizes a temporal total variation (TV). The proposed video stabilization method is suitable for enhancing the visual quality for various portable cameras and can be applied to robot vision, driving assistant systems, and visual surveillance systems.

Mini-review on river eutrophication and bottom improvement techniques, with special emphasis on the Nakdong River.

Water quality in rivers is vital to humans and to maintenance of biotic and ecological integrity. During the Four Major Rivers restoration of South Korea, remarkable attempts have been made to decrease external nutrient loads and moveable weirs were designed to discharge silt that may deposit in pools. However, recently eutrophication of the Nakdong River, which was limited to the lower reaches, is seen to be spreading upstream. The reduction of external nutrient loads to rivers is a long-term goal that is unlikely to lead to reductions in algal blooms for many years because of the time required to implement effective land management strategies. It would therefore be desirable to implement complementary strategies. Regulating the amount of water released is effective at preventing algae blooms in weir pools; so, the relationship between discharge, stratification and bloom formation should be understood in this regard. However, pollutants are likely to accumulate in the riverbed upstream from release points. Thus, to control phosphorus levels, total phosphorus density should be lowered by applying in-river techniques as well. As many ecosystem properties are controlled by multiple processes, simultaneous river bottom improvement techniques, such as combined dissolved oxygen supply and nutrient inactivation, are likely to be effective. The purpose of this review is to present a series of technological approaches that can be used to improve the river bottom area and hence sediment nutrient release, and to illustrate the application of these techniques to the Nakdong River.

The effects of isometric trunk exercises and dynamic trunk exercises on gait in elderly people.

The purpose of this study was to compare the effects of dynamic trunk exercises and isometric trunk exercises on gait in elderly people. [Subjects] This study randomly allocated 20 elderly people to an isometric trunk exercise group (n=10) and a dynamic trunk exercise group (n=10). The exercises were performed for 30 minutes three times a week for 12 weeks. Gait speed, stride length, cadence, and step width were measured at a normal pace using GAITRite. All groups were evaluated before and after 12 weeks. [Results] The isometric exercise group showed a significant change in gait velocity, cadence, and left and right step lengths. The dynamic trunk exercise group showed a significant change in gait velocity, cadence, left and right step lengths, left and right step times, and left and right stride lengths. Moreover, a comparison of the exercise effect between the two groups showed a significant difference in gait velocity. [Conclusion] The results of this study suggest that isometric trunk exercises and dynamic trunk exercises have a positive effect on gait function in elderly people. In particular, isometric trunk exercises are recommended to promote gait velocity.

Sulforaphane alleviates scopolamine-induced memory impairment in mice.

Sulforaphane, an organosulfur compound present in cruciferous vegetables, has been shown to exert neuroprotective effects in experimental in vitro and in vivo models of neurodegeneration. To determine whether sulforaphane can preserve cognitive function, we examined its effects on scopolamine-induced memory impairment in mice using the Morris water maze test. Sulforaphane (10 or 50mg/kg) was administered to C57BL/6 mice by oral gavage for 14 days (days 1-14), and memory impairment was induced by intraperitoneal injection of scopolamine (1mg/kg) for 7 days (days 8-14). Mice that received scopolamine alone showed impaired learning and memory retention and considerably decreased cholinergic system reactivity in the hippocampus and frontal cortex, as indicated by a decreased acetylcholine (ACh) level and an increased acetylcholinesterase (AChE) activity. Sulforaphane significantly attenuated the scopolamine-induced memory impairment and improved cholinergic system reactivity, as indicated by an increased ACh level, decreased AChE activity, and increased choline acetyltransferase (ChAT) expression in the hippocampus and frontal cortex. These effects of sulforaphane on cholinergic system reactivity were confirmed in vitro. Sulforaphane (10 or 20µM) increased the ACh level, decreased the AChE activity, and increased ChAT expression in scopolamine-treated primary cortical neurons. These observations suggest that sulforaphane might exert a significant neuroprotective effect on cholinergic deficit and cognitive impairment.

Implantable Neural Electrodes Fabrication Based on Perfluoroalkoxyalkane Film.

OBJECTIVE: In this paper, the fabrication of perfluoro-alkoxy alkane (PFA) film-based planar neural electrodes was proposed. METHODS: The fabrication of PFA-based electrodes started with cleaning of PFA film. The argon plasma pretreatment was performed on the PFA film surface and attached to a dummy silicon wafer. Metal layers were deposited and patterned using the standard Micro Electro Mechanical Systems (MEMS) process. Electrode-sites and pads were opened using reactive ion etching (RIE). Lastly, the electrode patterned PFA substrate film was thermally laminated with the other bare PFA film. Electrical-physical evaluation tests were conducted along with in vitro tests, ex vivo tests and soak tests to evaluate the electrode performance and biocompatibility. RESULTS: The electrical and physical performance of PFA-based electrodes had better performances compared to other biocompatible polymer-based electrodes. Also, the biocompatibility and longevity were verified by cytotoxicity test, elution test, and accelerated life test. CONCLUSION: The PFA film-based planar neural electrode fabrication was established and evaluated. The PFA based electrodes showed excellent benefits such as long-term reliability, low water absorption rate, and flexibility using the neural electrode. SIGNIFICANCE: For implantable neural electrodes, hermetic sealing is required for in vivo durability. PFA fulfilled a low water absorption rate with relatively low Young's modulus to increase the longevity and biocompatibility of the devices.

Real-Time Shape Estimation of Hyper-Redundant Flexible Manipulator Using Coiled Fiber Sensors.

The shape of flexible endoscopic surgical robot should be obtained to increase control accuracy and prevent unwanted tissue damage. To estimate the shape of flexible manipulator, space efficiency, cost-effectiveness, system complexity, and ease of calibration should be considered to integrate sensors into the manipulator. In this article, we propose a real-time method to estimate the shape of a hyper-redundant manipulator having embedded coiled fiber sensors. The main advantage of this method is guaranteeing shape recognition even when the manipulator is subjected to an external load. The fiber sensors are highly flexible, compact, and inexpensive, as well as they can functionally measure both compressive and tensile strain of hyper-redundant manipulator. The sensor design was optimized to achieve durability and sensitivity. The numbers of sensor and the placements were determined by the analysis of the kinematics and moment distribution of the manipulator. The accuracy of shape estimation was validated experimentally under both free-loading and loading conditions. The proposed method achieved real-time estimating capability with a mean maximum error of each joint position smaller than 3.54% in free-loading condition and 5.47% in loading condition.

Fabrication and validation of flexible neural electrodes based on polyimide tape and gold sheet.

This research was conducted to apply polyimide tape, which has the advantages of low price ans strong adhesive strength, to the neural electrode process. In addition, to maximize the low-cost characteristics, a fabrication process based on UV laser patterning rather than a photolithography process was introduced. The fabrication process started by attaching the gold sheet on the conductive double-sided tape without being torn or crushed. Then, the gold sheet and the double-sided tape were patterned together using UV laser. The patterned layer was transferred to the single-side polyimide tape. For insulation layer, electrode site opened single-sided polyimide tape was prepared. Polydimethylsiloxane was used as an adhesion layer, and alignment between electrode sites and opening sites was processed manually. The minimum line width achieved through the proposed fabrication process was approximately 100 µm, and the sheet resistance of the conductive layer was 0.635 Ω/sq. Measured cathodal charge storage capacity was 0.72 mC/cm2 and impedance at 1 kHz was 4.07 kΩ/cm2. Validation of fabricated electrode was confirmed by conducting 30 days accelerated soak test, flexibility test, adhesion test and ex vivo stimulation test. The novel flexible neural electrodes based on single-sided polyimide tape and UV laser patterned gold sheet was fabricated successfully. Conventional neural electrode fabrication processes based on polyimide substrate has a disadvantages such as long fabrication time, expensive costs, and probability of delamination between layers. However, the novel fabrication process which we introduced can overcome many shortcomings of existing processes, and offers great advantages such as simplicity of fabrication, inexpensiveness, flexibility and long-term reliability.

Tobacco-induced hyperglycemia promotes lung cancer progression via cancer cell-macrophage interaction through paracrine IGF2/IR/NPM1-driven PD-L1 expression.

Tobacco smoking (TS) is implicated in lung cancer (LC) progression through the development of metabolic syndrome. However, direct evidence linking metabolic syndrome to TS-mediated LC progression remains to be established. Our findings demonstrate that 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone and benzo[a]pyrene (NNK and BaP; NB), components of tobacco smoke, induce metabolic syndrome characteristics, particularly hyperglycemia, promoting lung cancer progression in male C57BL/6 J mice. NB enhances glucose uptake in tumor-associated macrophages by increasing the expression and surface localization of glucose transporter (GLUT) 1 and 3, thereby leading to transcriptional upregulation of insulin-like growth factor 2 (IGF2), which subsequently activates insulin receptor (IR) in LC cells in a paracrine manner, promoting its nuclear import. Nuclear IR binds to nucleophosmin (NPM1), resulting in IR/NPM1-mediated activation of the CD274 promoter and expression of programmed death ligand-1 (PD-L1). Restricting glycolysis, depleting macrophages, or blocking PD-L1 inhibits NB-mediated LC progression. Analysis of patient tissues and public databases reveals elevated levels of IGF2 and GLUT1 in tumor-associated macrophages, as well as tumoral PD-L1 and phosphorylated insulin-like growth factor 1 receptor/insulin receptor (pIGF-1R/IR) expression, suggesting potential poor prognostic biomarkers for LC patients. Our data indicate that paracrine IGF2/IR/NPM1/PD-L1 signaling, facilitated by NB-induced dysregulation of glucose levels and metabolic reprogramming of macrophages, contributes to TS-mediated LC progression.

Particulate matter-induced metabolic recoding of epigenetics in macrophages drives pathogenesis of chronic obstructive pulmonary disease.

Chronic obstructive pulmonary disease (COPD) is a group of illnesses associated with unresolved inflammation in response to toxic environmental stimuli. Persistent exposure to PM is a major risk factor for COPD, but the underlying mechanism remains unclear. Using our established mouse model of PM-induced COPD, we find that repeated PM exposure provokes macrophage-centered chronic inflammation and COPD development. Mechanistically, chronic PM exposure induces transcriptional downregulation of HAAO, KMO, KYNU, and QPRT in macrophages, which are the enzymes of de novo NAD+ synthesis pathway (kynurenine pathway; KP), via elevated chromatin binding of the CCCTC-binding factor (CTCF) near the transcriptional regulatory regions of the enzymes. Subsequent reduction of NAD+ and SIRT1 function increases histone acetylation, resulting in elevated expression of pro-inflammatory genes in PM-exposed macrophages. Activation of SIRT1 by nutraceutical resveratrol mitigated PM-induced chronic inflammation and COPD development. In agreement, increased levels of histone acetylation and decreased expression of KP enzymes were observed in pulmonary macrophages of COPD patients. We newly provide an evidence that dysregulated NAD+ metabolism and consecutive SIRT1 deficiency significantly contribute to the pathological activation of macrophages during PM-mediated COPD pathogenesis. Additionally, targeting PM-induced intertwined metabolic and epigenetic reprogramming in macrophages is an effective strategy for COPD treatment.

A case report of T cell/histiocyte-rich large B cell lymphoma misdiagnosed as lymphomatoid papulosis.

RATIONALE: T cell/histiocyte-rich large B cell lymphoma (THRLBCL) is an uncommon B cell lymphoma characterized by < 10% large neoplastic B cells in a background of abundant T cells and frequent histiocytes. If a skin lesion is the first clinical sign of lymphoma, the diagnosis might be difficult and misdiagnosed. PATIENT CONCERNS: A 60-year-old woman presented with multiple erythematous umbilicated nodules on her left upper back for 3 months. DIAGNOSES: Through punch biopsy of the back lesion and additional excisional right inguinal lymph node biopsy, the patient was diagnosed with cutaneous metastasis of THRLBCL. INTERVENTIONS: The patient was referred to the Hemato-oncology Department for chemotherapy. OUTCOMES: R-CHOP chemotherapy is currently in progress, and some skin lesions show improvement. LESSONS: Skin lesions might be the first clinical sign of THRLBCL and when THRLBCL is suspected, careful further evaluation is essential for accurate diagnosis and treatment.

A Scalp Scar-Reducing Procedure for the Hair Transplant Donor Area Using a Columnar Trichophytic Suture: A Case Report.

BACKGROUND: One of the main concerns of patients who undergo hair transplantation surgery such as follicular unit strip surgery is scar widening on surgical sites. Until now, trichophytic suture, double-layer suture, tattoos, follicular unit transplantation on scars are suggested as a solution. CASE REPORT: A 23-year-old man with frontal hair loss underwent follicular unit strip surgery. To reduce hair donor area scarring, we tried a new trichophytic suture method. After surgery, the patient's hair loss degree was corrected with about C1 in the basic and specific (BASP) classification. Also, there was less scar in the columnar trichophytic suture part, compared with almost 7 mm of scar widening in the simple primary closure part. CONCLUSION: This study highlights that a columnar trichophytic suture may be useful for patients undergoing scalp surgery for cosmetic purposes.

Statistical discrimination using different machine learning models reveals dissimilar key compounds of soybean leaves in targeted polyphenol-metric metabolomics in terms of traits and cultivation.

Soybean (SB) leaves (SLs) contain diverse flavonoids with health-promoting properties. To investigate the chemical constituents of SB and their correlations across phenotypes, growing periods, and environmental factors, a validated separation method for mass detection was used with targeted metabolomics. Thirty-six polyphenols (1 coumestrol, 5 flavones, 18 flavonols, and 12 isoflavones) were identified in SLs, 31 of which were quantified. Machine learning (ML) modelling was used to differentiate between the variety, bean color, growing period, and cultivation area and identify the key compounds responsible for these differences. The isoflavone and flavonol profiles were influenced by the growing period and cultivation area based on bootstrap forest modelling. The neural model showed the best predictive capacity for SL differences among the various ML models. Discriminant polyphenols can differ depending on the ML method applied; therefore, a cautious approach should be ensured when using statistical ML outputs, including orthogonal partial least squares discriminant analysis.