Mechanism of Enzyme Repair by the AAA+ Chaperone Rubisco Activase.

How AAA+ chaperones conformationally remodel specific target proteins in an ATP-dependent manner is not well understood. Here, we investigated the mechanism of the AAA+ protein Rubisco activase (Rca) in metabolic repair of the photosynthetic enzyme Rubisco, a complex of eight large (RbcL) and eight small (RbcS) subunits containing eight catalytic sites. Rubisco is prone to inhibition by tight-binding sugar phosphates, whose removal is catalyzed by Rca. We engineered a stable Rca hexamer ring and analyzed its functional interaction with Rubisco. Hydrogen/deuterium exchange and chemical crosslinking showed that Rca structurally destabilizes elements of the Rubisco active site with remarkable selectivity. Cryo-electron microscopy revealed that Rca docks onto Rubisco over one active site at a time, positioning the C-terminal strand of RbcL, which stabilizes the catalytic center, for access to the Rca hexamer pore. The pulling force of Rca is fine-tuned to avoid global destabilization and allow for precise enzyme repair.

Entanglement and Squeezing of the Optical Field Modes in High Harmonic Generation.

Squeezed optical fields are a powerful resource for a variety of investigations in basic research and technology. However, the generation of intense squeezed light is challenging. Here, we show that intense squeezed light can be produced using strongly laser driven atoms and the so far unrelated process of high harmonic generation. We demonstrate that when the intensity of the driving field significantly depletes the ground state of the atoms, leading to dipole moment correlations, the quantum state of the driving field and the generated high harmonics are entangled and squeezed. Furthermore, we analyze how the resulting quadrature squeezing of the fundamental laser mode after the interaction can be controlled. The findings open the way for the generation of high intensity squeezed light states for a wide range of applications.

Seeing beyond skin deep: High-resolution ultrasound in dermatology-A comprehensive review and future prospects.

High-resolution ultrasound (HRUS), operating at frequencies of 20-25 MHz, is a non-invasive imaging tool that offers dermatologists the ability to visualize structures beneath the skin surface. The objective of this review is to present a comprehensive overview of HRUS applications, emphasising its utility in diagnosing, characterising and managing various dermatological conditions. We undertook a comprehensive literature review on the dermatological application of HRUS across Medline, Embase and Cochrane Library databases, while also incorporating our own clinical experience of over 16 years with the tool. In normal skin, the epidermis and dermis are hyperechoic, and the subcutaneous layer is hypoechoic. Basal cell carcinomas appear hypoechoic with irregular margins, while the presence of hyperechoic inclusion bodies suggests aggressive pathology. Squamous cell carcinomas pose challenges due to acoustic shadow artefacts from the thickened stratum corneum. Melanomas are homogenous hypoechoic lesions, with HRUS used to accurately predict Breslow thickness. HRUS provides dermatologists with a valuable adjunct to traditional clinical examination. Future advancement in image resolution and the standardisation of diagnostic parameters may further expand its utility.

Ultrafast Imaging of Molecular Chirality with Photoelectron Vortices.

Ultrafast imaging of molecular chirality is a key step toward the dream of imaging and interpreting electronic dynamics in complex and biologically relevant molecules. Here, we propose a new ultrafast chiral phenomenon exploiting recent advances in electron optics allowing access to the orbital angular momentum of free electrons. We show that strong-field ionization of a chiral target with a few-cycle linearly polarized 800 nm laser pulse yields photoelectron vortices, whose chirality reveals that of the target, and we discuss the mechanism underlying this phenomenon. Our Letter opens new perspectives in recollision-based chiral imaging.

Visual and Patient-Reported Outcomes of a Diffractive Trifocal Intraocular Lens Compared with Those of a Monofocal Intraocular Lens.

PURPOSE: To evaluate the effectiveness and safety of a trifocal intraocular lens (IOL), the TFNT00 (Alcon, Fort Worth, TX), versus a monofocal IOL, the SN60AT (Alcon). DESIGN: Food and Drug Administration-approved, prospective, multicenter, nonrandomized, parallel-group, assessor-masked, confirmatory trial. PARTICIPANTS: Patients enrolled were 22 years of age or older with a diagnosis of bilateral cataract with planned removal by phacoemulsification with a clear corneal incision. METHODS: Consented participants selected their preferred IOL, which was implanted sequentially into each eye of patients meeting eligibility criteria. MAIN OUTCOME MEASURES: The coprimary effectiveness outcomes were mean photopic monocular best-corrected distance visual acuity (BCDVA; 4 m) and distance-corrected near visual acuity (DCNVA; 40 cm) at 6 months after surgery. Secondary effectiveness outcomes included mean monocular distance-corrected intermediate visual acuity (DCIVA; 66 cm) and proportion of participants responding "never" to question 1 of the Intraocular Lens Satisfaction questionnaire (regarding frequency of spectacle use in the past 7 days). Safety outcomes included frequency of "severe" and "most bothersome" visual disturbances. RESULTS: Two hundred forty-three patients underwent cataract surgery with bilateral implantation of the TFNT00 (n = 129) or SN60AT (n = 114) and were followed up for 6 months. Noninferiority of TFNT00 to SN60AT in mean photopic monocular BCDVA (95% upper confidence limit of the difference was <0.1 logarithm of the minimum angle of resolution [logMAR] margin), and superiority in mean photopic monocular DCNVA (difference of 0.42 logMAR; P < 0.001) and DCIVA (difference of 0.26 logMAR; P < 0.001) were demonstrated. The proportion of patients never requiring glasses overall was superior for TFNT00 versus SN60AT (80.5% and 8.2%, respectively). Starbursts, halos, and glare were the most frequently rated severe symptoms with TFNT00; however, less than 5% of patients were very bothered at month 6. CONCLUSIONS: The TFNT00 exhibited superior monocular DCNVA and DCIVA to a spherical monofocal IOL, with comparable monocular BCDVA. Binocular visual acuity was 20/25 or better for distance to near (+0.5 D to -2.5 D), resulting in high levels of spectacle independence. Less than 5% of patients were very bothered by the photic visual disturbances associated with the TFNT00 at 6 months after surgery.

Symphony on strong field approximation.

This paper has been prepared by the Symphony collaboration (University of Warsaw, Uniwersytet Jagiellonski, DESY/CNR and ICFO) on the occasion of the 25th anniversary of the 'simple man's models' which underlie most of the phenomena that occur when intense ultrashort laser pulses interact with matter. The phenomena in question include high-harmonic generation (HHG), above-threshold ionization (ATI), and non-sequential multielectron ionization (NSMI). 'Simple man's models' provide both an intuitive basis for understanding the numerical solutions of the time-dependent Schrödinger equation and the motivation for the powerful analytic approximations generally known as the strong field approximation (SFA). In this paper we first review the SFA in the form developed by us in the last 25 years. In this approach the SFA is a method to solve the TDSE, in which the non-perturbative interactions are described by including continuum-continuum interactions in a systematic perturbation-like theory. In this review we focus on recent applications of the SFA to HHG, ATI and NSMI from multi-electron atoms and from multi-atom molecules. The main novel part of the presented theory concerns generalizations of the SFA to: (i) time-dependent treatment of two-electron atoms, allowing for studies of an interplay between electron impact ionization and resonant excitation with subsequent ionization; (ii) time-dependent treatment in the single active electron approximation of 'large' molecules and targets which are themselves undergoing dynamics during the HHG or ATI processes. In particular, we formulate the general expressions for the case of arbitrary molecules, combining input from quantum chemistry and quantum dynamics. We formulate also theory of time-dependent separable molecular potentials to model analytically the dynamics of realistic electronic wave packets for molecules in strong laser fields. We dedicate this work to the memory of Bertrand Carré, who passed away in March 2018 at the age of 60.

Deep learning architectures for multi-label classification of intelligent health risk prediction.

BACKGROUND: Multi-label classification of data remains to be a challenging problem. Because of the complexity of the data, it is sometimes difficult to infer information about classes that are not mutually exclusive. For medical data, patients could have symptoms of multiple different diseases at the same time and it is important to develop tools that help to identify problems early. Intelligent health risk prediction models built with deep learning architectures offer a powerful tool for physicians to identify patterns in patient data that indicate risks associated with certain types of chronic diseases. RESULTS: Physical examination records of 110,300 anonymous patients were used to predict diabetes, hypertension, fatty liver, a combination of these three chronic diseases, and the absence of disease (8 classes in total). The dataset was split into training (90%) and testing (10%) sub-datasets. Ten-fold cross validation was used to evaluate prediction accuracy with metrics such as precision, recall, and F-score. Deep Learning (DL) architectures were compared with standard and state-of-the-art multi-label classification methods. Preliminary results suggest that Deep Neural Networks (DNN), a DL architecture, when applied to multi-label classification of chronic diseases, produced accuracy that was comparable to that of common methods such as Support Vector Machines. We have implemented DNNs to handle both problem transformation and algorithm adaption type multi-label methods and compare both to see which is preferable. CONCLUSIONS: Deep Learning architectures have the potential of inferring more information about the patterns of physical examination data than common classification methods. The advanced techniques of Deep Learning can be used to identify the significance of different features from physical examination data as well as to learn the contributions of each feature that impact a patient's risk for chronic diseases. However, accurate prediction of chronic disease risks remains a challenging problem that warrants further studies.

Synthesis and biological evaluation of santacruzamate A analogues for anti-proliferative and immunomodulatory activity.

Santacruzamate A (SCA) is a natural product isolated from a Panamanian marine cyanobacterium, previously reported to have potent and selective histone deacetylase (HDAC) activity. To optimize the enzymatic and cellular activity, 40 SCA analogues were synthesized in a systematic exploration of the zinc-binding group (ZBG), cap terminus, and linker region. Two cap group analogues inhibited proliferation of MCF-7 breast cancer cells, with analogous increased degranulation of cytotoxic T cells (CTLs), while one cap group analogue reduced CTL degranulation, indicative of suppression of the immune response. Additional testing of these analogues resulted in reevaluation of the previously reported SCA mechanism of action. These analogues and the resulting structure-activity relationships will be of interest for future studies on cell proliferation and immune modulation.

SeqAssist: a novel toolkit for preliminary analysis of next-generation sequencing data.

BACKGROUND: While next-generation sequencing (NGS) technologies are rapidly advancing, an area that lags behind is the development of efficient and user-friendly tools for preliminary analysis of massive NGS data. As an effort to fill this gap to keep up with the fast pace of technological advancement and to accelerate data-to-results turnaround, we developed a novel software package named SeqAssist ("Sequencing Assistant" or SA). RESULTS: SeqAssist takes NGS-generated FASTQ files as the input, employs the BWA-MEM aligner for sequence alignment, and aims to provide a quick overview and basic statistics of NGS data. It consists of three separate workflows: (1) the SA_RunStats workflow generates basic statistics about an NGS dataset, including numbers of raw, cleaned, redundant and unique reads, redundancy rate, and a list of unique sequences with length and read count; (2) the SA_Run2Ref workflow estimates the breadth, depth and evenness of genome-wide coverage of the NGS dataset at a nucleotide resolution; and (3) the SA_Run2Run workflow compares two NGS datasets to determine the redundancy (overlapping rate) between the two NGS runs. Statistics produced by SeqAssist or derived from SeqAssist output files are designed to inform the user: whether, what percentage, how many times and how evenly a genomic locus (i.e., gene, scaffold, chromosome or genome) is covered by sequencing reads, how redundant the sequencing reads are in a single run or between two runs. These statistics can guide the user in evaluating the quality of a DNA library prepared for RNA-Seq or genome (re-)sequencing and in deciding the number of sequencing runs required for the library. We have tested SeqAssist using a synthetic dataset and demonstrated its main features using multiple NGS datasets generated from genome re-sequencing experiments. CONCLUSIONS: SeqAssist is a useful and informative tool that can serve as a valuable "assistant" to a broad range of investigators who conduct genome re-sequencing, RNA-Seq, or de novo genome sequencing and assembly experiments.

Comment on Miyamoto et al. Laryngopharyngeal Mucosal Injury Due to Nasogastric Tube Insertion during Cardiopulmonary Resuscitation: A Retrospective Cohort Study. J. Clin. Med. 2024, 13, 261.

I read with great interest the study from Miyamoto et al [...].

Differential reconstructed gene interaction networks for deriving toxicity threshold in chemical risk assessment.

BACKGROUND: Pathway alterations reflected as changes in gene expression regulation and gene interaction can result from cellular exposure to toxicants. Such information is often used to elucidate toxicological modes of action. From a risk assessment perspective, alterations in biological pathways are a rich resource for setting toxicant thresholds, which may be more sensitive and mechanism-informed than traditional toxicity endpoints. Here we developed a novel differential networks (DNs) approach to connect pathway perturbation with toxicity threshold setting. METHODS: Our DNs approach consists of 6 steps: time-series gene expression data collection, identification of altered genes, gene interaction network reconstruction, differential edge inference, mapping of genes with differential edges to pathways, and establishment of causal relationships between chemical concentration and perturbed pathways. A one-sample Gaussian process model and a linear regression model were used to identify genes that exhibited significant profile changes across an entire time course and between treatments, respectively. Interaction networks of differentially expressed (DE) genes were reconstructed for different treatments using a state space model and then compared to infer differential edges/interactions. DE genes possessing differential edges were mapped to biological pathways in databases such as KEGG pathways. RESULTS: Using the DNs approach, we analyzed a time-series Escherichia coli live cell gene expression dataset consisting of 4 treatments (control, 10, 100, 1000 mg/L naphthenic acids, NAs) and 18 time points. Through comparison of reconstructed networks and construction of differential networks, 80 genes were identified as DE genes with a significant number of differential edges, and 22 KEGG pathways were altered in a concentration-dependent manner. Some of these pathways were perturbed to a degree as high as 70% even at the lowest exposure concentration, implying a high sensitivity of our DNs approach. CONCLUSIONS: Findings from this proof-of-concept study suggest that our approach has a great potential in providing a novel and sensitive tool for threshold setting in chemical risk assessment. In future work, we plan to analyze more time-series datasets with a full spectrum of concentrations and sufficient replications per treatment. The pathway alteration-derived thresholds will also be compared with those derived from apical endpoints such as cell growth rate.

Dr Google - assessing the reliability and readability of information on general surgical procedures found via search engines.

BACKGROUND: The most common general surgical emergency operations are laparoscopic appendicectomy, laparoscopic cholecystectomy, hernia repair, hemorrhoidectomy and colectomy. Patients commonly perform an internet search for more information prior to undergoing surgery, which can lead to an inappropriate understanding of their procedure. The aim is to assess the quality of information available on three of the most used search engines. METHODS: A search was conducted on Google.com, Bing.com and Yahoo.com using the terms related to laparoscopic appendicectomy, laparoscopic cholecystectomy, hemorrhoidectomy, hernia repair and colectomy. First 20 results from each search engine were collected for evaluation. Results were excluded if they were sponsored, duplicates, academic publications, advertisements, forums, audiovisual tools, social media or any non-English information. Included results were assessed for reliability using DISCERN and JAMA benchmark score. Readability was assessed using Flesch Reading Ease (FRE) Score and Simple Measure of Gobbledygook (SMOG). RESULTS: Hundred and ninety-seven websites were analysed, 44.7% were published by institutions, 34.5% by health websites and 20.8% by independent surgeons. Mean DISCERN scores for Institutions was 54.6 ± 11.3, independent surgeons 45.9 ± 11.4 and health websites 58.7 ± 10.3. Mean JAMA score for Institutions was 1.0 ± 1.0, independent surgeons 0.1 ± 0.4 and health websites 1.7 ± 1.1. FRE scores for institutions was 51.6 ± 10.3, independent surgeons 40.9 ± 10.2, and health websites 45.7 ± 12.3. SMOG scores were 9.8 ± 1.5 for institutions, 11.4 ± 1.6 for independent surgeons and 10.6 ± 1.7 for health websites. CONCLUSION: Health information on common general surgical procedures found on search engines are generally fair to good quality but still above the suggested reading level of the population. Information on surgical procedures should be written at recommended reading level of 13-14 years old.

A covalent BTK ternary complex compatible with targeted protein degradation.

Targeted protein degradation using heterobifunctional chimeras holds the potential to expand target space and grow the druggable proteome. Most acutely, this provides an opportunity to target proteins that lack enzymatic activity or have otherwise proven intractable to small molecule inhibition. Limiting this potential, however, is the remaining need to develop a ligand for the target of interest. While a number of challenging proteins have been successfully targeted by covalent ligands, unless this modification affects form or function, it may lack the ability to drive a biological response. Bridging covalent ligand discovery with chimeric degrader design has emerged as a potential mechanism to advance both fields. In this work, we employ a set of biochemical and cellular tools to deconvolute the role of covalent modification in targeted protein degradation using Bruton's tyrosine kinase. Our results reveal that covalent target modification is fundamentally compatible with the protein degrader mechanism of action.

Clinical Outcomes After Bilateral Implantation of a Diffractive Trifocal Intraocular Lens: A Worldwide Pooled Analysis of Prospective Clinical Investigations.

Purpose: To investigate visual and safety outcomes of AcrySof® IQ PanOptix® (model TFNT00), a trifocal, presbyopia-correcting intraocular lens (IOL), in patients of different ethnicities across multiple countries, based on a pooled analysis of six prospective multicenter studies. Patients and Methods: This pooled analysis included adult patients from six prospective clinical studies performed across 56 centers worldwide. After cataract removal by phacoemulsification, all patients were implanted with TFNT00; follow-up duration varied from 3 to 12 months according to the studies' design. Binocular defocus curve; absolute manifest refraction spherical equivalent (MRSE); and binocular photopic uncorrected and corrected visual acuities at distance (UCDVA, BCDVA; 4-5 m), intermediate (UCIVA, DCIVA; 60-66 cm), and near (UCNVA, DCNVA; 40 cm) were measured. Results: The study included 557 patients, 547 of whom were implanted bilaterally with the TFNT00 IOL (n = 1094 eyes). Binocular visual data at 1 month and 3-6 months after implantation were available for up to 546 and 542 bilaterally implanted patients, respectively. A continuous range of 0.1 logarithm of the minimum angle of resolution (logMAR) or better vision from distance (0.00 diopter [D], 4-5 m) to near (-3.00 D; optically equivalent to 33 cm) was observed 3-6 months after TFNT00 implantation. At 3-6 months, 88.2% of first eyes achieved an MRSE ≤0.50 D and 88.7% of second eyes achieved an MRSE ≤0.50 D. Overall, 99.3%, 92.3%, and 94.6% of patients bilaterally implanted with TFNT00 achieved binocular photopic BCDVA, DCIVA, and DCNVA of 0.14 logMAR or better, respectively. Ocular adverse device effects and secondary surgical interventions (SSIs) were infrequent. Conclusion: This global pooled analysis showed that TFNT00 provided a continuous range of 0.1 logMAR (~20/25 Snellen) or better vision from distance to 33 cm, with a low incidence of ocular adverse device effects and SSIs.

An inverse agonist of orphan receptor GPR61 acts by a G protein-competitive allosteric mechanism.

GPR61 is an orphan GPCR related to biogenic amine receptors. Its association with phenotypes relating to appetite makes it of interest as a druggable target to treat disorders of metabolism and body weight, such as obesity and cachexia. To date, the lack of structural information or a known biological ligand or tool compound has hindered comprehensive efforts to study GPR61 structure and function. Here, we report a structural characterization of GPR61, in both its active-like complex with heterotrimeric G protein and in its inactive state. Moreover, we report the discovery of a potent and selective small-molecule inverse agonist against GPR61 and structural elucidation of its allosteric binding site and mode of action. These findings offer mechanistic insights into an orphan GPCR while providing both a structural framework and tool compound to support further studies of GPR61 function and modulation.

Biometric assessment of pseudophakic subjects during objective accommodative stimulation: a prospective observational study.

CLINICAL RELEVANCE: Ultrasound biomicroscopy is an objective method for assessing changes in anterior segment biometry. There is a paucity of data on the reliability of this method. A reliable method for assessing anterior segment changes during physiologically driven accommodation can be a useful tool for clinicians, researchers, and industry. BACKGROUND: To assess the test-retest reliability of ultrasound biomicroscopy for measurements of change in anterior chamber depth during a distance to near fixation task in pseudophakic subjects. METHODS: Subjects were adults with monofocal intraocular lenses implanted in both eyes who completed a 6-month post-operative period and had monocular uncorrected distance visual acuity of 6/15 (0.4 logMAR) or better. The change in anterior chamber depth during a distance to near fixation task was measured with a 35-MHz VuMAX HD ultrasound biomicroscopy device (Sonomed Escalon, New Hyde Park, NY) during two separate visits. An asymmetrical vergence paradigm allowed evaluation of anterior segment biometry at 22-µm axial resolution in one eye, while the fellow eye fixated on the target. To assess the test-retest reliability, 2-sided 95% CI from a paired t test was calculated for the difference in anterior chamber depth change from distance to near between visits. RESULTS: The mean (standard deviation) near-focused anterior chamber depth measured by ultrasound biomicroscopy was 4.331 (0.237) and 4.333 (0.241) mm at visits 1 and 2, respectively. In response to a change in fixation from distance (4 m) to near (40 cm), the mean anterior chamber depth change was -0.012 (0.038) and 0.003 (0.039) mm at visits 1 and 2, respectively. Analysis of the difference in the change in anterior chamber depth between visits was -0.015 mm (95% CI, -0.035 to 0.003). CONCLUSION: Ultrasound biomicroscopy is a repeatable, objective method for assessing change in anterior segment biometry during physiological changes in fixation from distance to near.