TopoRoot+: computing whorl and soil line traits of field-excavated maize roots from CT imaging.

BACKGROUND: The use of 3D imaging techniques, such as X-ray CT, in root phenotyping has become more widespread in recent years. However, due to the complexity of the root structure, analyzing the resulting 3D volumes to obtain detailed architectural root traits remains a challenging computational problem. When it comes to image-based phenotyping of excavated maize root crowns, two types of root features that are notably missing from existing methods are the whorls and soil line. Whorls refer to the distinct areas located at the base of each stem node from which roots sprout in a circular pattern (Liu S, Barrow CS, Hanlon M, Lynch JP, Bucksch A. Dirt/3D: 3D root phenotyping for field-grown maize (zea mays). Plant Physiol. 2021;187(2):739-57. https://doi.org/10.1093/plphys/kiab311 .). The soil line is where the root stem meets the ground. Knowledge of these features would give biologists deeper insights into the root system architecture (RSA) and the below- and above-ground root properties. RESULTS: We developed TopoRoot+, a computational pipeline that produces architectural traits from 3D X-ray CT volumes of excavated maize root crowns. Building upon the TopoRoot software (Zeng D, Li M, Jiang N, Ju Y, Schreiber H, Chambers E, et al. Toporoot: A method for computing hierarchy and fine-grained traits of maize roots from 3D imaging. Plant Methods. 2021;17(1). https://doi.org/10.1186/s13007-021-00829-z .) for computing fine-grained root traits, TopoRoot + adds the capability to detect whorls, identify nodal roots at each whorl, and compute the soil line location. The new algorithms in TopoRoot + offer an additional set of fine-grained traits beyond those provided by TopoRoot. The addition includes internode distances, root traits at every hierarchy level associated with a whorl, and root traits specific to above or below the ground. TopoRoot + is validated on a diverse collection of field-grown maize root crowns consisting of nine genotypes and spanning across three years. TopoRoot + runs in minutes for a typical volume size of [Formula: see text] on a desktop workstation. Our software and test dataset are freely distributed on Github. CONCLUSIONS: TopoRoot + advances the state-of-the-art in image-based phenotyping of excavated maize root crowns by offering more detailed architectural traits related to whorls and soil lines. The efficiency of TopoRoot + makes it well-suited for high-throughput image-based root phenotyping.

Capecitabine-Induced Genital Hand-Foot Syndrome Treated With Topical Tacrolimus.

We describe a rare case of capecitabine-induced palmar-plantar erythrodysesthesia (PPE), or hand-foot syndrome (HFS), involving the genitals, which resolved with tacrolimus therapy, in a patient with cT3dN3 stage IIIc moderately differentiated proximal rectal adenocarcinoma who was undergoing neoadjuvant chemotherapy. Given its severe impact on the quality of life, HFS often requires independent local anti-inflammatory treatment and subsequent dose delay and/or modification of the patient's chemotherapy. We believe that our findings in this report can aid clinicians in the early recognition and management of capecitabine-associated HFS resulting in balanitis, as prompt treatment may reduce morbidity and avoid prolonged interruption of chemotherapy in these patients.

Comprehensive safety assessment of serendipity berry sweet protein produced from Komagataella phaffii.

Serendipity berry plant (Dioscoreophyllum cumminsii (Stapf) Diels) is the source of a naturally sweet protein referred to as monellin. The safety of serendipity berry sweet protein (SBSP) containing single polypeptide monellin (MON) expressed in Komagataella phaffii (formerly Pichia pastoris) and produced via precision fermentation was examined comprehensively through assessments of in vitro and in silico protein digestion, in silico allergenicity, in vitro genotoxicity (reverse mutation and mammalian micronucleus assays), and 14-day and 90-day oral (dietary) toxicity studies in rats. There was no indication of allergenicity for SBSP in the in silico analyses. Results from both in vitro and in silico protein digestibility assessments indicated that SBSP is digested upon ingestion and would therefore be unlikely to pose a toxigenic or allergenic risk to consumers. SBSP was non-genotoxic in in vitro assays and showed no adverse effects in the 14-day or 90-day toxicity studies up to the highest dose tested. The 90-day toxicity study supports a NOAEL for SBSP of 1954 mg/kg bw/day, which corresponds to a NOAEL for MON of 408 mg/kg bw/day.

The effect of frailty and age on outcomes in elective paraesophageal hernia repair.

INTRODUCTION: Paraesophageal hernia repair (PEHR) is a safe and effective operation. Previous studies have described risk factors for poor peri-operative outcomes such as emergent operations or advanced patient age, and pre-operative frailty is a known risk factor in other major surgery. The goal of this retrospective cohort study was to determine if markers of frailty were predictive of poor peri-operative outcomes in elective paraesophageal hernia repair. METHODS: Patients who underwent elective PEHR between 1/2011 and 6/2022 at a single university-based institution were identified. Patient demographics, modified frailty index (mFI), and post-operative outcomes were recorded. A composite peri-operative morbidity outcome indicating the incidence of any of the following: prolonged length of stay (≥ 3 days), increased discharge level of care, and 30-day complications or readmissions was utilized for statistical analysis. Descriptive statistics and logistic regression were used to analyze the data. RESULTS: Of 547 patients who underwent elective PEHR, the mean age was 66.0 ± 12.3, and 77.1% (n = 422) were female. Median length of stay was 1 [IQR 1, 2]. ASA was 3-4 in 65.8% (n = 360) of patients. The composite outcome occurred in 32.4% (n = 177) of patients. On multivariate analysis, increasing age (OR 1.021, p = 0.02), high frailty (OR 2.02, p < 0.01), ASA 3-4 (OR 1.544, p = 0.05), and redo-PEHR (OR 1.72, p = 0.02) were each independently associated with the incidence of the composite outcome. On a regression of age for the composite outcome, a cutoff point of increased risk is identified at age 72 years old (OR 2.25, p < 0.01). CONCLUSION: High frailty and age over 72 years old each independently confer double the odds of a composite morbidity outcome that includes prolonged post-operative stay, peri-operative complications, the need for a higher level of care after elective paraesophageal hernia repair, and 30-day readmission. This provides additional information to counsel patients pre-operatively, as well as a potential opportunity for targeted pre-habilitation.

Novel insights into the role of long non-coding RNA in the human malaria parasite, Plasmodium falciparum.

The complex life cycle of Plasmodium falciparum requires coordinated gene expression regulation to allow host cell invasion, transmission, and immune evasion. Increasing evidence now suggests a major role for epigenetic mechanisms in gene expression in the parasite. In eukaryotes, many lncRNAs have been identified to be pivotal regulators of genome structure and gene expression. To investigate the regulatory roles of lncRNAs in P. falciparum we explore the intergenic lncRNA distribution in nuclear and cytoplasmic subcellular locations. Using nascent RNA expression profiles, we identify a total of 1768 lncRNAs, of which 718 (~41%) are novels in P. falciparum. The subcellular localization and stage-specific expression of several putative lncRNAs are validated using RNA-FISH. Additionally, the genome-wide occupancy of several candidate nuclear lncRNAs is explored using ChIRP. The results reveal that lncRNA occupancy sites are focal and sequence-specific with a particular enrichment for several parasite-specific gene families, including those involved in pathogenesis and sexual differentiation. Genomic and phenotypic analysis of one specific lncRNA demonstrate its importance in sexual differentiation and reproduction. Our findings bring a new level of insight into the role of lncRNAs in pathogenicity, gene regulation and sexual differentiation, opening new avenues for targeted therapeutic strategies against the deadly malaria parasite.

Lytic efficiency of immunosuppressive drug-resistant armoured T cells against circulating HBV-related HCC in whole blood.

Recurrence of hepatitis B virus-related hepatocellular carcinoma (HBV-HCC) after liver transplant (LT) is mediated by circulating tumour cells (CTCs) and exacerbated by the immunosuppressants required to prevent graft rejection. To circumvent the effects of immunosuppressants, we developed immunosuppressive drug-resistant armoured HBV-specific T-cell receptor-redirected T cells (IDRA HBV-TCR). However, their ability to eliminate HBV-HCC circulating in the whole blood has never been tested, and whether their lytic efficacy is compatible with the number of adoptively transferred T cells in vivo has never been measured. Hence, we developed a microscopy-based assay to quantify CTCs in whole blood. The assay was then used to quantify the efficacy of IDRA HBV-TCRs to lyse free-floating HBV-HCC cells in the presence of Tacrolimus and Mycophenolate Mofetil (MMF). We demonstrated that a panel of antibodies (AFP, GPC3, Vimentin, pan-Cytokeratin, and CD45) specific for HCC tumour antigens and immune cells can effectively differentiate HCC-CTCs in whole blood. Through dose-titration experiments, we observed that in the presence of immunosuppressive drugs, a minimum of 20 000 IDRA HBV-TCR T cells/ml of whole blood is necessary to lyse ~63.5% of free-floating HBV-HCC cells within 16 hours. In conclusion, IDRA HBV-TCR T cells can lyse free-floating HBV-HCC cells in whole blood in the presence of Tacrolimus and MMF. The quantity of IDRA-HBV TCR T cells required can be achieved by the adoptive transfer of 5 × 106 IDRA-HBV TCR-T cells/kg, supporting the utilisation of IDRA HBV-TCR T cells to eliminate CTCs as prophylaxis against recurrence after LT.

Assessing the effects of smoking status on outcomes of elective minimally invasive paraesophageal hernia repair.

BACKGROUND: Patients are often advised on smoking cessation prior to elective surgical interventions, but the impact of active smoking on paraesophageal hernia repair (PEHR) outcomes is unclear. The objective of this cohort study was to evaluate the impact of active smoking on short-term outcomes following PEHR. METHODS: Patients who underwent elective PEHR at an academic institution between 2011 and 2022 were retrospectively reviewed. The National Surgical Quality Improvement Program (NSQIP) database from 2010 to 2021 was queried for PEHR. Patient demographics, comorbidities, and 30-day post-operative data were collected and maintained in an IRB-approved database. Cohorts were stratified by active smoking status. Primary outcomes included rates of death or serious morbidity (DSM) and radiographically identified recurrence. Bivariate and multivariable regressions were performed, and p value < 0.05 was considered statistically significant. RESULTS: 538 patients underwent elective PEHR in the single-institution cohort, of whom 5.8% (n = 31) were smokers. 77.7% (n = 394) were female, median age was 67 [IQR 59, 74] years, and median follow-up was 25.3 [IQR 3.2, 53.6] months. Rates of DSM (non-smoker 4.5% vs smoker 6.5%, p = 0.62) and hernia recurrence (33.3% vs 48.4%, p = 0.09) did not differ significantly. On multivariable analysis, smoking status was not associated with any outcome (p > 0.2). On NSQIP analysis, 38,284 PEHRs were identified, of whom 8.6% (n = 3584) were smokers. Increased DSM was observed among smokers (non-smoker 5.1%, smoker 6.2%, p = 0.004). Smoking status was independently associated with increased risk of DSM (OR 1.36, p < 0.001), respiratory complications (OR 1.94, p < 0.001), 30-day readmission (OR 1.21, p = 0.01), and discharge to higher level of care (OR 1.59, p = 0.01). No difference was seen in 30-day mortality or wound complications. CONCLUSION: Smoking status confers a small increased risk of short-term morbidity following elective PEHR without increased risk of mortality or hernia recurrence. While smoking cessation should be encouraged for all active smokers, minimally invasive PEHR in symptomatic patients should not be delayed on account of patient smoking status.

Equestrian-Related Musculoskeletal Injuries Presenting to a Chiropractic Practice: A Retrospective Chart Review of 19 Patients.

Objective: The purpose of this study was to describe the types of equestrian-related musculoskeletal injuries and their management. Methods: We retrospectively reviewed the charts of 19 patients who presented with injuries from equestrian activities at a chiropractic practice from December 2000 to December 2020. Deidentified data were extracted from the charts and summarized. Results: Of the 19 patients, 42.3% presented with acute trauma, 38.5% had overuse injuries, and 19.2% had chronic injuries as a result of previous trauma. We found that 90% of overuse injuries and 18.2% of acute injuries led to chronic conditions that needed ongoing management. Conclusion: From this sample of patients, there was a high percentage of overuse and chronic injuries for patients who participated in equestrian activities.

Management of Anticoagulation/Antiplatelet Medication and Venous Thromboembolism Prophylaxis in Elective Spine Surgery: Concise Clinical Recommendations Based on a Modified Delphi Process.

STUDY DESIGN: Delphi method. OBJECTIVE: To gain consensus on the following questions: (1) When should anticoagulation/antiplatelet (AC/AP) medication be stopped before elective spine surgery?; (2) When should AC/AP medication be restarted after elective spine surgery?; (3) When, how, and in whom should venous thromboembolism (VTE) chemoprophylaxis be started after elective spinal surgery? SUMMARY OF BACKGROUND DATA: VTE can lead to significant morbidity after adult spine surgery, yet postoperative VTE prophylaxis practices vary considerably. The management of preoperative AC/AP medication is similarly heterogeneous. MATERIALS AND METHODS: Delphi method of consensus development consisting of three rounds (January 26, 2021, to June 21, 2021). RESULTS: Twenty-one spine surgeons were invited, and 20 surgeons completed all rounds of questioning. Consensus (>70% agreement) was achieved in 26/27 items. Group consensus stated that preoperative Direct Oral Anticoagulants should be stopped two days before surgery, warfarin stopped five days before surgery, and all remaining AC/AP medication and aspirin should be stopped seven days before surgery. For restarting AC/AP medication postoperatively, consensus was achieved for low-risk/medium-risk/high-risk patients in 5/5 risk factors (VTE history/cardiac/ambulation status/anterior approach/operation). The low/medium/high thresholds were POD7/POD5/POD2, respectively. For VTE chemoprophylaxis, consensus was achieved for low-risk/medium-risk/high-risk patients in 12/13 risk factors (age/BMI/VTE history/cardiac/cancer/hormone therapy/operation/anterior approach/staged separate days/staged same days/operative time/transfusion). The one area that did not gain consensus was same-day staged surgery. The low-threshold/medium-threshold/high-threshold ranges were postoperative day 5 (POD5) or none/POD3-4/POD1-2, respectively. Additional VTE chemoprophylaxis considerations that gained consensus were POD1 defined as the morning after surgery regardless of operating finishing time, enoxaparin as the medication of choice, and standardized, rather than weight-based, dose given once per day. CONCLUSIONS: In the first known Delphi study to address anticoagulation/antiplatelet recommendations for elective spine surgery (preoperatively and postoperatively); our Delphi consensus recommendations from 20 spine surgeons achieved consensus on 26/27 items. These results will potentially help standardize the management of preoperative AC/AP medication and VTE chemoprophylaxis after adult elective spine surgery.

Change in gliding properties of the iliotibial tract in hypermobile Ehlers-Danlos Syndrome.

PURPOSE: Fascial changes in hypermobile Ehlers-Danlos syndrome (hEDS), a heritable connective tissue disorder, can be used visualized with sonoelastography. The purpose of this study was to explore the inter-fascial gliding characteristics in hEDS. METHODS: In 9 subjects, the right iliotibial tract was examined with ultrasonography. Tissue displacements of the iliotibial tract were estimated from ultrasound data using cross-correlation techniques. RESULTS: In hEDS subjects, shear strain was 46.2%, lower than those with lower limb pain without hEDS (89.5%) and in control subjects without hEDS and without pain (121.1%). CONCLUSION: Extracellular matrix changes in hEDS may manifest as reduced inter-fascial plane gliding.

Naked Mole-Rat Cortex Maintains Reactive Oxygen Species Homeostasis During In Vitro Hypoxia or Ischemia and Reperfusion.

Neuronal injury during acute hypoxia, ischemia, and following reperfusion are partially attributable to oxidative damage caused by deleterious fluctuations of reactive oxygen species (ROS). In particular, mitochondrial superoxide (O2•-) production is believed to upsurge during lowoxygen conditions and also following reperfusion, before being dismutated to H2O2 and released into the cell. However, disruptions of redox homeostasis may be beneficially attenuated in the brain of hypoxia-tolerant species, such as the naked mole-rat (NMR, Heterocephalus glaber). As such, we hypothesized that ROS homeostasis is better maintained in the brain of NMRs during severe hypoxic/ ischemic insults and following reperfusion. We predicted that NMR brain would not exhibit substantial fluctuations in ROS during hypoxia or reoxygenation, unlike previous reports from hypoxiaintolerant mouse brain. To test this hypothesis, we measured cortical ROS flux using corrected total cell fluorescence measurements from live brain slices loaded with the MitoSOX red superoxide (O2•-) indicator or chloromethyl 2',7'-dichlorodihydrofluorescein diacetate (CM-H2-DCFDA; which fluoresces with whole-cell hydrogen peroxide (H2O2) production) during various low-oxygen treatments, exogenous oxidative stress, and reperfusion. We found that NMR cortex maintained ROS homeostasis during low-oxygen conditions, while mouse cortex exhibited a ~40% increase and a ~30% decrease in mitochondrial O2•- and cellular H2O2 production, respectively. Mitochondrial ROS homeostasis in NMRs was only disrupted following sodium cyanide application, which was similarly observed in mice. Our results suggest that NMRs have evolved strategies to maintain ROS homeostasis during acute bouts of hypoxia and reoxygenation, potentially as an adaptation to life in an intermittently hypoxic environment.

COVID-19 Vaccination Rates and Vaccine Hesitancy Among Spanish-Speaking Free Clinic Patients.

We sought to assess COVID-19 vaccination rates, as well as attitudes and beliefs towards the vaccine, of patients in a Spanish-speaking student-run free clinic in Columbus, Ohio. A cross-sectional study was performed. Surveys were distributed to all individuals over 18 years who presented to La Clínica Latina between July, 2022 and September, 2022. A convenience sample was used: patients in the waiting room and their accompanying family members or friends were invited to participate. Subjects were excluded if under the age of 18 or over the age of 75, or if non-Spanish speaking. Of the 158 individuals who agreed to participate in our study, 146 responded to the question regarding vaccination status, revealing 90.4% of respondents had received a COVID-19 vaccination. Most respondents learned about the vaccine from social media (26.4%) or television (22.7%). The majority of participants sought answers to questions surrounding the vaccine by asking their doctor (49.1%). The most common reason among unvaccinated participants for not undergoing vaccination was fear of an adverse reaction to the vaccine (n = 11). We found that a large proportion (90.4%) of individuals seeking care at a Spanish-speaking free clinic were vaccinated against COVID-19. Our study also provides perspective on the means of health knowledge acquisition and behaviors in this predominantly Latinx patient population in central Ohio. We can utilize our results to optimize and tailor clinic services and initiatives for COVID-19 boosters to meet the needs of this community.

High-throughput continuous evolution of compact Cas9 variants targeting single-nucleotide-pyrimidine PAMs.

Despite the availability of Cas9 variants with varied protospacer-adjacent motif (PAM) compatibilities, some genomic loci-especially those with pyrimidine-rich PAM sequences-remain inaccessible by high-activity Cas9 proteins. Moreover, broadening PAM sequence compatibility through engineering can increase off-target activity. With directed evolution, we generated four Cas9 variants that together enable targeting of most pyrimidine-rich PAM sequences in the human genome. Using phage-assisted noncontinuous evolution and eVOLVER-supported phage-assisted continuous evolution, we evolved Nme2Cas9, a compact Cas9 variant, into variants that recognize single-nucleotide pyrimidine-PAM sequences. We developed a general selection strategy that requires functional editing with fully specified target protospacers and PAMs. We applied this selection to evolve high-activity variants eNme2-T.1, eNme2-T.2, eNme2-C and eNme2-C.NR. Variants eNme2-T.1 and eNme2-T.2 offer access to N4TN PAM sequences with comparable editing efficiencies as existing variants, while eNme2-C and eNme2-C.NR offer less restrictive PAM requirements, comparable or higher activity in a variety of human cell types and lower off-target activity at N4CN PAM sequences.

Epigenetic aging is associated with aberrant neural oscillatory dynamics serving visuospatial processing in people with HIV.

BACKGROUND: Despite effective antiretroviral therapy, cognitive impairment and other aging-related comorbidities are more prevalent in people with HIV (PWH) than in the general population. Previous research examining DNA methylation has shown PWH exhibit accelerated biological aging. However, it is unclear how accelerated biological aging may affect neural oscillatory activity in virally suppressed PWH, and more broadly how such aberrant neural activity may impact neuropsychological performance. METHODS: In the present study, participants (n = 134) between the ages of 23 - 72 years underwent a neuropsychological assessment, a blood draw to determine biological age via DNA methylation, and a visuospatial processing task during magnetoencephalography (MEG). Our analyses focused on the relationship between biological age and oscillatory theta (4-8 Hz) and alpha (10 - 16 Hz) activity among PWH (n=65) and seronegative controls (n = 69). RESULTS: PWH had significantly elevated biological age when controlling for chronological age relative to controls. Biological age was differentially associated with theta oscillations in the left posterior cingulate cortex (PCC) and with alpha oscillations in the right medial prefrontal cortex (mPFC) among PWH and seronegative controls. Stronger alpha oscillations in the mPFC were associated with lower CD4 nadir and lower current CD4 counts, suggesting such responses were compensatory. Participants who were on combination antiretroviral therapy for longer had weaker theta oscillations in the PCC. CONCLUSIONS: These findings support the concept of interactions between biological aging and HIV status on the neural oscillatory dynamics serving visuospatial processing. Future work should elucidate the long-term trajectory and impact of accelerated aging on neural oscillatory dynamics in PWH.

A Modular Scaffold for Controlling Transcriptional Activation via Homomeric Protein-Protein Interactions.

Protein-protein interactions (PPIs) have been extensively utilized in synthetic biology to construct artificial gene networks. However, synthetic regulation of gene expression by PPIs in E. coli has largely relied upon repressors, and existing PPI-controlled transcriptional activators have generally been employed with heterodimeric interactions. Here we report a highly modular, PPI-dependent transcriptional activator, cCadC, that was designed to be compatible with homomeric interactions. We describe the process of engineering cCadC from a transmembrane protein into a soluble cytosolic regulator. We then show that gene transcription by cCadC can be controlled by homomeric PPIs and furthermore discriminates between dimeric and higher-order interactions. Finally, we demonstrate that cCadC activity can be placed under small molecule regulation using chemically induced dimerization or ligand dependent stabilization. This work should greatly expand the scope of PPIs that can be employed in artificial gene circuits in E. coli and complements the existing repertoire of tools for transcriptional regulation in synthetic biology.

Enzyme directed evolution using genetically encodable biosensors.

Directed evolution has been remarkably successful in identifying enzyme variants with new or improved properties, such as altered substrate scope or novel reactivity. Genetically encodable biosensors (GEBs), which convert the concentration of a small molecule ligand into an easily detectable output signal, have seen increasing application to enzyme directed evolution in the last decade. GEBs enable the use of high-throughput methods to assess enzyme activity of very large libraries, which can accelerate the search for variants with desirable activity. Here, we review different classes of GEBs and their properties in the context of enzyme evolution, how GEBs have been integrated into directed evolution workflows, and recent examples of enzyme evolution efforts utilizing GEBs. Finally, we discuss the advantages, challenges, and opportunities for using GEBs in the directed evolution of enzymes.

Characteristics of procalcitonin in hospitalized COVID-19 patients and clinical outcomes of antibiotic use stratified by procalcitonin levels.

We examined the characteristics of pro-calcitonin (PCT) in hospitalized COVID-19 patients (cohort 1) and clinical outcomes of antibiotic use stratified by PCT in non-critically ill patients without bacterial co-infection (cohort 2). Retrospective reviews were performed in adult, hospitalized COVID-19 patients during March-May 2020. For cohort 1, we excluded hospital transfers, renal disease and extra-pulmonary infection without isolated pathogen(s). For cohort 2, we further excluded microbiologically confirmed infection, 'do not resuscitate ± do not intubate' status, and intensive care unit (ICU). For cohort 1, PCT was compared between absent/low-suspicion and proven bacterial co-infections. Factors associated with elevated PCT and sensitivity/specificity/PPV/NPV of PCT cutoffs for identifying bacterial co-infections were explored. For cohort 2, clinical outcomes including mechanical ventilation within 5 days (MV5) were compared between the antibiotic and non-antibiotic groups stratified by PCT ≥ 0.25 µg/L. Nine hundred and twenty four non-ICU and 103 ICU patients were included (cohort 1). The median PCT was higher in proven vs. absent/low-suspicion of bacterial co-infection. Elevated PCT was significantly associated with proven bacterial co-infection, ICU status and oxygen requirement. For PCT ≥ 0.25 µg/L, sensitivity/specificity/PPV/NPV were 69/65/6.5/98% (non-ICU) and 75/33/8.6/94% (ICU). For cohort 2, 756/1305 (58%) patients were included. Baseline characteristics were balanced between the antibiotic and non-antibiotic groups except PCT ≥ 0.25 µg/L (antibiotic:non-antibiotic = 59%:24%) and tocilizumab use (antibiotic:non-antibiotic = 5%:2%). 23% (PCT < 0.25 µg/L) and 58% (PCT ≥ 0.25 µg/L) received antibiotics. Antibiotic group had significantly higher rates of MV5. COVID-19 severity inferred from ICU status and oxygen requirement as well as the presence of bacterial co-infections were associated with elevated PCT. PCT showed poor PPV and high NPV for proven bacterial co-infections. The use of antibiotics did not show improved clinical outcomes in COVID-19 patients with PCT ≥ 0.25 µg/L outside of ICU when bacterial co-infections are of low suspicion.

Development of a potent high-affinity human therapeutic antibody via novel application of recombination signal sequence-based affinity maturation.

Therapeutic antibody development requires discovery of an antibody molecule with desired specificities and drug-like properties. For toxicological studies, a therapeutic antibody must bind the ortholog antigen with a similar affinity to the human target to enable relevant dosing regimens, and antibodies falling short of this affinity design goal may not progress as therapeutic leads. Herein, we report the novel use of mammalian recombination signal sequence (RSS)-directed recombination for complementarity-determining region-targeted protein engineering combined with mammalian display to close the species affinity gap of human interleukin (IL)-13 antibody 731. This fully human antibody has not progressed as a therapeutic in part because of a 400-fold species affinity gap. Using this nonhypothesis-driven affinity maturation method, we generated multiple antibody variants with improved IL-13 affinity, including the highest affinity antibody reported to date (34 fM). Resolution of a cocrystal structure of the optimized antibody with the cynomolgus monkey (or nonhuman primate) IL-13 protein revealed that the RSS-derived mutations introduced multiple successive amino-acid substitutions resulting in a de novo formation of a π-π stacking-based protein-protein interaction between the affinity-matured antibody heavy chain and helix C on IL-13, as well as an introduction of an interface-distant residue, which enhanced the light chain-binding affinity to target. These mutations synergized binding of heavy and light chains to the target protein, resulting in a remarkably tight interaction, and providing a proof of concept for a new method of protein engineering, based on synergizing a mammalian display platform with novel RSS-mediated library generation.