Retrospective SARS-CoV-2 human antibody development trajectories are largely sparse and permissive.

Immunological interventions, like vaccinations, are enabled by the predictive control of humoral responses to novel antigens. While the development trajectories for many broadly neutralizing antibodies (bnAbs) have been measured, it is less established how human subtype-specific antibodies develop from their precursors. In this work, we evaluated the retrospective development trajectories for eight anti-SARS-CoV-2 Spike human antibodies (Abs).

Inter-assay variability in the measurement of urinary C-terminal cross-linked telopeptide of type II collagen following anterior cruciate ligament reconstruction.

Objective: To compare urinary C-terminal cross-linked telopeptide of type II collagen (u-CTX-II) concentrations and trends as measured by two different commercially available enzyme-linked immunosorbent assays (ELISA) in a cohort of patients in the first year following anterior cruciate ligament (ACL) reconstruction.

Design: 22 ACL-injured patients undergoing reconstructive surgery (mean age 25.2 (SD 8.

Auditory Hallucinations in Borderline Personality Disorder and Schizophrenia: A Quantitative Comparison Using Patient Records.

The phenomenological differences in auditory hallucinations between schizophrenia and borderline personality disorder (BPD) are unclear in the existing literature, in part due to underpowered studies and heterogeneous research populations that do not represent those in the acute clinical setting. This study addresses this by using patient records to compare auditory hallucinations at the point of clinical psychiatric assessment for 341 unique patients, 165 with BPD and 176 with schizophrenia. Patients with BPD were found to have more subjectively distressing and objectively negative hallucinations, as well as more command hallucinations.

Engineered Stop and Go T7 RNA Polymerases.

Precise, stringent, post-translational activation of enzymes is essential for many synthetic biology applications. For example, even a few intracellular molecules of unregulated T7 RNA polymerase can result in growth cessation in a bacterium. We sought to mimic the properties of natural enzymes, where activity is regulated ubiquitously by endogenous metabolites.

Development and validation of a novel method for assessing physical activity profiles after anterior cruciate ligament reconstruction: The Sports and Physical Activity scale.

Objectives: To describe and evaluate the preliminary validity of a novel scoring system for assessing the physical activity of patients after anterior cruciate ligament (ACL) reconstruction.

Methods: The Sports and Physical Activity (SPA) scale consists of thirty options of sports and physical activities, followed by four frequency options for each option selected. Factors used to develop the scoring system were frequency of participation and intensity of the sports or physical activities.

New functions of pirin proteins and a 2-ketoglutarate: Ferredoxin oxidoreductase ortholog in Bacteroides fragilis metabolism and their impact on antimicrobial susceptibility to metronidazole and amixicile.

The understanding of how central metabolism and fermentation pathways regulate antimicrobial susceptibility in the anaerobic pathogen Bacteroides fragilis is still incomplete. Our study reveals that B. fragilis encodes two iron-dependent, redox-sensitive regulatory pirin protein genes, pir1 and pir2.

Modelling the nicotine pharmacokinetic profile for e-cigarettes using real time monitoring of consumers' physiological measurements and mouth level exposure.

Pharmacokinetic (PK) studies can provide essential information on abuse liability of nicotine and tobacco products but are intrusive and must be conducted in a clinical environment. The objective of the study was to explore whether changes in plasma nicotine levels following use of an e-cigarette can be predicted from real time monitoring of physiological parameters and mouth level exposure (MLE) to nicotine before, during, and after e-cigarette vaping, using wearable devices. Such an approach would allow an -effective pre-screening process, reducing the number of clinical studies, reducing the number of products to be tested and the number of blood draws required in a clinical PK study Establishing such a prediction model might facilitate the longitudinal collection of data on product use and nicotine expression among consumers using nicotine products in their normal environments, thereby reducing the need for intrusive clinical studies while generating PK data related to product use in the real world.

Rationalizing Diverse Binding Mechanisms to the Same Protein Fold: Insights for Ligand Recognition and Biosensor Design.

The engineering of novel protein-ligand binding interactions, particularly for complex drug-like molecules, is an unsolved problem, which could enable many practical applications of protein biosensors. In this work, we analyzed two engineered biosensors, derived from the plant hormone sensor PYR1, to recognize either the agrochemical mandipropamid or the synthetic cannabinoid WIN55,212-2. Using a combination of quantitative deep mutational scanning experiments and molecular dynamics simulations, we demonstrated that mutations at common positions can promote protein-ligand shape complementarity and revealed prominent differences in the electrostatic networks needed to complement diverse ligands.

An integrated technology for quantitative wide mutational scanning of human antibody Fab libraries.

Antibodies are engineerable quantities in medicine. Learning antibody molecular recognition would enable the in silico design of high affinity binders against nearly any proteinaceous surface. Yet, publicly available experiment antibody sequence-binding datasets may not contain the mutagenic, antigenic, or antibody sequence diversity necessary for deep learning approaches to capture molecular recognition.

GMMA Can Stabilize Proteins Across Different Functional Constraints.

Stabilizing proteins without otherwise hampering their function is a central task in protein engineering and design. PYR1 is a plant hormone receptor that has been engineered to bind diverse small molecule ligands. We sought a set of generalized mutations that would provide stability without affecting functionality for PYR1 variants with diverse ligand-binding capabilities.

Rationalizing diverse binding mechanisms to the same protein fold: insights for ligand recognition and biosensor design.

The engineering of novel protein-ligand binding interactions, particularly for complex drug-like molecules, is an unsolved problem which could enable many practical applications of protein biosensors. In this work, we analyzed two engineer ed biosensors, derived from the plant hormone sensor PYR1, to recognize either the agrochemical mandipropamid or the synthetic cannabinoid WIN55,212-2. Using a combination of quantitative deep mutational scanning experiments and molecular dynamics simulations, we demonstrated that mutations at common positions can promote protein-ligand shape complementarity and revealed prominent differences in the electrostatic networks needed to complement diverse ligands.

Enhanced T cell receptor specificity through framework engineering.

Development of T cell receptors (TCRs) as immunotherapeutics is hindered by inherent TCR cross-reactivity. Engineering more specific TCRs has proven challenging, as unlike antibodies, improving TCR affinity does not usually improve specificity. Although various protein design approaches have been explored to surmount this, mutations in TCR binding interfaces risk broadening specificity or introducing new reactivities.

Responsiveness of the Various Short-Form Versions of the Knee Injury and Osteoarthritis Outcome Score Between 2 and 5 Years After Anterior Cruciate Ligament Reconstruction.

Background: Various short-form versions of the Knee injury and Osteoarthritis Outcome Score (KOOS) have been developed in an attempt to minimize responder burden. However, the responsiveness of these short-form measures in patients who have undergone anterior cruciate ligament (ACL) reconstruction has not been compared at midterm follow-up.

Purpose: To determine the responsiveness of 3 short-form versions of the KOOS (KOOS-12, KOOS-Global, and KOOS-ACL) in patients who have undergone ACL reconstruction.

An integrated technology for quantitative wide mutational scanning of human antibody Fab libraries.

Antibodies are engineerable quantities in medicine. Learning antibody molecular recognition would enable the design of high affinity binders against nearly any proteinaceous surface. Yet, publicly available experiment antibody sequence-binding datasets may not contain the mutagenic, antigenic, or antibody sequence diversity necessary for deep learning approaches to capture molecular recognition.

Quantifying the Benefits of Imputation over QSAR Methods in Toxicology Data Modeling.

Imputation machine learning (ML) surpasses traditional approaches in modeling toxicity data. The method was tested on an open-source data set comprising approximately 2500 ingredients with limited and data obtained from the OECD QSAR Toolbox. By leveraging the relationships between different toxicological end points, imputation extracts more valuable information from each data point compared to well-established single end point methods, such as ML-based Quantitative Structure Activity Relationship (QSAR) approaches, providing a final improvement of up to around 0.

A high-throughput two-cell assay for interrogating inhibitory signaling pathways in T cells.

The recent success of immunotherapies relying on manipulation of T-cell activation highlights the value of characterising the mediators of immune checkpoint signaling. CRISPR/Cas9 is a popular approach for interrogating signaling pathways; however, the lack of appropriate assays for studying inhibitory signaling in T cells is limiting the use of large-scale perturbation-based approaches. Here, we adapted an existing Jurkat cell-based transcriptional reporter assay to study both activatory and inhibitory (PD-1-mediated) T-cell signaling using CRISPR-based genome screening in arrayed and pooled formats.

Isolated pulmonary valve endocarditis in a patient without structural heart disease or a history of intravenous drug use.

We present a case of a febrile patient in his 70s who was found to have isolated native pulmonary valve vegetations on echocardiography, and on blood cultures. Of note, our patient had none of the typical risk factors associated with this rare form of endocarditis previously described in only a handful of case reports.

An orthogonalized PYR1-based CID module with reprogrammable ligand-binding specificity.

Plants sense abscisic acid (ABA) using chemical-induced dimerization (CID) modules, including the receptor PYR1 and HAB1, a phosphatase inhibited by ligand-activated PYR1. This system is unique because of the relative ease with which ligand recognition can be reprogrammed. To expand the PYR1 system, we designed an orthogonal '*' module, which harbors a dimer interface salt bridge; X-ray crystallographic, biochemical and in vivo analyses confirm its orthogonality.

Standardizing cassette-based deep mutagenesis by Golden Gate assembly.

Protocols for the construction of large, deeply mutagenized protein encoding libraries via Golden Gate assembly of synthetic DNA cassettes employ disparate, system-specific methodology. Here we present a standardized Golden Gate method for building user-defined libraries. We demonstrate that a 25 μL reaction, using 40 fmol of input DNA, can generate a library on the order of 1 × 10 members and that reaction volume or input DNA concentration can be scaled up with no losses in transformation efficiency.

High-Performance Cannabinoid Sensor Empowered by Plant Hormone Receptors and Antifouling Magnetic Nanorods.

The misuse of cannabinoids and their synthetic variants poses significant threats to public health, necessitating the development of advanced techniques for detection of these compounds in biological or environmental samples. Existing methods face challenges like lengthy sample pretreatment and laborious antifouling steps. Herein, we present a novel sensing platform using magnetic nanorods coated with zwitterionic polymers for the simple, rapid, and sensitive detection of cannabinoids in biofluids.

The current state and future of T-cell exhaustion research.

'Exhaustion' is a term used to describe a state of native and redirected T-cell hypo-responsiveness resulting from persistent antigen exposure during chronic viral infections or cancer. Although a well-established phenotype across mice and humans, exhaustion at the molecular level remains poorly defined and inconsistent across the literature. This is, in part, due to an overreliance on surface receptors to define these cells and explain exhaustive behaviours, an incomplete understanding of how exhaustion arises, and a lack of clarity over whether exhaustion is the same across contexts, e.

Is quadriceps strength associated with patellofemoral joint loading after anterior cruciate ligament reconstruction?

Objective: To test whether quadriceps strength is associated with measures of patellofemoral (PF) joint loading during running and hopping in people after an anterior cruciate ligament reconstruction (ACLR).

Design: Cross-sectional study.

Setting: Biomechanics laboratory.

The Resolution of Kaplan Fiber Injuries Is Observed in a Majority of Cases at 9 Months After Acute Primary Anterior Cruciate Ligament Reconstruction: A Radiological Study.

Background: The natural history of Kaplan fiber (KF) injuries after acute primary anterior cruciate ligament (ACL) reconstruction (ACLR) remains unknown.

Purpose/hypothesis: The purpose of this study was to evaluate the temporal change in the magnetic resonance imaging (MRI) appearance of the KF complex after acute primary ACLR. It was hypothesized that KF injuries would resolve with time.