Antigenic cartography using variant-specific hamster sera reveals substantial antigenic variation among Omicron subvariants.

Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) has developed substantial antigenic variability. As the majority of the population now has pre-existing immunity due to infection or vaccination, the use of experimentally generated animal immune sera can be valuable for measuring antigenic differences between virus variants. Here, we immunized Syrian hamsters by two successive infections with one of nine SARS-CoV-2 variants. Their sera were titrated against 16 SARS-CoV-2 variants, and the resulting titers were visualized using antigenic cartography. The antigenic map shows a condensed cluster containing all pre-Omicron variants (D614G, Alpha, Delta, Beta, Mu, and an engineered B.1+E484K variant) and considerably more diversity among a selected panel of Omicron subvariants (BA.1, BA.2, BA.4/BA.5, the BA.5 descendants BF.7 and BQ.1.18, the BA.2.75 descendant BN.1.3.1, the BA.2-derived recombinants XBB.2 and EG.5.1, and the BA.2.86 descendant JN.1). Some Omicron subvariants were as antigenically distinct from each other as the wildtype is from the Omicron BA.1 variant. Compared to titers measured in human sera, titers in hamster sera are of higher magnitude, show less fold change, and result in a more compact antigenic map topology. The results highlight the potential of sera from hamsters for the continued antigenic characterization of SARS-CoV-2.

Complete genome sequence of multidrug-resistant Raoultella terrigena strain RT01-5M1 isolated from farmed salmon in Canada.

The genome sequence of multidrug-resistant Raoultella terrigena RT01-5M1 strain isolated from Canadian farmed salmon was determined using Oxford nanopore and Illumina MiSeq sequencers. The assembled chromosome was estimated at 5,699,993 bp in size, with two plasmids, 164,879 bp and 82,046 bp. The chromosome and smaller plasmid contained antimicrobial resistance genes.

Prevention and Management of Osteoradionecrosis in Patients With Head and Neck Cancer Treated With Radiation Therapy: ISOO-MASCC-ASCO Guideline.

PURPOSE: To provide evidence-based recommendations for prevention and management of osteoradionecrosis (ORN) of the jaw secondary to head and neck radiation therapy in patients with cancer. METHODS: The International Society of Oral Oncology-Multinational Association for Supportive Care in Cancer (ISOO-MASCC) and ASCO convened a multidisciplinary Expert Panel to evaluate the evidence and formulate recommendations. PubMed, EMBASE, and Cochrane Library databases were searched for randomized controlled trials and observational studies, published between January 1, 2009, and December 1, 2023. The guideline also incorporated systematic reviews conducted by ISOO-MASCC, which included studies published from January 1, 1990, through December 31, 2008. RESULTS: A total of 1,539 publications were initially identified. There were 487 duplicate publications, resulting in 1,052 studies screened by abstract, 104 screened by full text, and 80 included for systematic review evaluation. RECOMMENDATIONS: Due to limitations of available evidence, the guideline relied on informal consensus for some recommendations. Recommendations that were deemed evidence-based with strong evidence by the Expert Panel were those pertaining to best practices in prevention of ORN and surgical management. No recommendation was possible for the utilization of leukocyte- and platelet-rich fibrin or photobiomodulation for prevention of ORN. The use of hyperbaric oxygen in prevention and management of ORN remains largely unjustified, with limited evidence to support its practice.Additional information is available at www.asco.org/head-neck-cancer-guidelines.

Comparative analysis of SARS-CoV-2 neutralization titers reveals consistency between human and animal model serum and across assays.

The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires ongoing monitoring to judge the ability of newly arising variants to escape the immune response. A surveillance system necessitates an understanding of differences in neutralization titers measured in different assays and using human and animal serum samples. We compared 18 datasets generated using human, hamster, and mouse serum and six different neutralization assays. Datasets using animal model serum samples showed higher titer magnitudes than datasets using human serum samples in this comparison. Fold change in neutralization of variants compared to ancestral SARS-CoV-2, immunodominance patterns, and antigenic maps were similar among serum samples and assays. Most assays yielded consistent results, except for differences in fold change in cytopathic effect assays. Hamster serum samples were a consistent surrogate for human first-infection serum samples. These results inform the transition of surveillance of SARS-CoV-2 antigenic variation from dependence on human first-infection serum samples to the utilization of serum samples from animal models.

Direct comparison of SARS-CoV-2 variant specific neutralizing antibodies in human and hamster sera.

Antigenic characterization of newly emerging SARS-CoV-2 variants is important to assess their immune escape and judge the need for future vaccine updates. To bridge data obtained from animal sera with human sera, we analyzed neutralizing antibody titers in human and hamster single infection sera in a highly controlled setting using the same authentic virus neutralization assay performed in one laboratory. Using a Bayesian framework, we found that titer fold changes in hamster sera corresponded well to human sera and that hamster sera generally exhibited higher reactivity.

Unanticipated mid-flight external trunk perturbation increased frontal plane ACL loading variables during sidestep cuttings.

Unanticipated trunk perturbation is commonly observed when anterior cruciate ligament (ACL) injuries occur during direction-changing manoeuvres. This study aimed to quantify the effect of mid-flight medial-lateral external trunk perturbation directions/locations on ACL loading variables during sidestep cuttings. Thirty-two recreational athletes performed sidestep cuttings under combinations of three perturbation directions (no-perturbation, ipsilateral-perturbation, and contralateral-perturbation relative to the cutting leg) and two perturbation locations (upper-trunk versus lower-trunk). The pushing perturbation was created by customised devices releasing a slam ball to contact participants near maximum jump height prior to cutting. Perturbation generally resulted in greater peak vertical ground reaction force and slower cutting velocity. Upper-trunk contralateral perturbation showed the greatest lateral trunk bending away from the travel direction, greatest peak knee flexion and abduction angles, and greatest peak internal knee adduction moments compared to other conditions. Such increased ACL loading variables were likely due to the increased lateral trunk bending and whole-body horizontal velocity away from the cutting direction caused by the contralateral perturbation act at the upper trunk. The findings may help understand the mechanisms of indirect contact ACL injuries and develop effective cutting techniques for ACL injury prevention.

Two common and distinct forms of variation in human functional brain networks.

The cortex has a characteristic layout with specialized functional areas forming distributed large-scale networks. However, substantial work shows striking variation in this organization across people, which relates to differences in behavior. While most previous work treats individual differences as linked to boundary shifts between the borders of regions, here we show that cortical 'variants' also occur at a distance from their typical position, forming ectopic intrusions. Both 'border' and 'ectopic' variants are common across individuals, but differ in their location, network associations, properties of subgroups of individuals, activations during tasks, and prediction of behavioral phenotypes. Border variants also track significantly more with shared genetics than ectopic variants, suggesting a closer link between ectopic variants and environmental influences. This work argues that these two dissociable forms of variation-border shifts and ectopic intrusions-must be separately accounted for in the analysis of individual differences in cortical systems across people.

Local Anesthetic Systemic Toxicity in Cardiac Surgery Patient with Erector Spinae Plane Catheter: A Case Report.

Regional anesthesia nerve blocks are increasingly used for patients undergoing cardiac surgery as part of multimodal pain management. Though rare, local anesthetic systemic toxicity (LAST) is a severe complication that requires vigilant monitoring. We present a case of a postcardiac surgery patient who developed LAST multiple days after surgery from lidocaine via an erector spinae plane catheter. This episode was determined to be a result of impaired lidocaine metabolism from liver shock caused by worsening pulmonary hypertension. Even under continuous monitoring, patients with cardiac or liver dysfunction are at increased risk of complications from local anesthetics.

The accuracy of anal self- and companion exams among sexual minority men and transgender women: a prospective analysis.

Background: Squamous cell carcinoma of the anus (SCCA) annual incidence among sexual minority men with and without HIV is 85/100,000 and 19/100,000 persons, respectively, which is significantly higher than the overall incidence (2/100,000). Incidence may also be higher in transgender women. Since SCCA tumours average ≥30 mm at diagnosis, we assessed the accuracy of individuals to self-detect smaller anal abnormalities. Methods: Using convenience sampling, the study enrolled sexual minority men and transgender women, aged 25-81 years, in Chicago, Illinois and Houston, Texas, USA, during 2020-2022. Individuals were taught the anal self-examination and anal companion examination (ASE/ACE). Then, a clinician performed a digital anal rectal examination (DARE) before participants conducted the ASE or ACE. The sensitivity, specificity and concordance of the ASE/ACE to detect an abnormality were measured along with factors associated with ASE/ACE and DARE concordance. Findings: Among 714 enrolled individuals, the median age was 40 years (interquartile range, 32-54), 36.8% (259/703) were living with HIV, and 47.0% (334/710), 23.4% (166/710), and 23.0% (163/710) were non-Hispanic white, non-Hispanic Black, and Hispanic, respectively. A total of 94.1% (671/713) identified as cisgendered men, and 5.9% (42/713) as gender minorities. A total of 658 participants completed an ASE and 28 couples (56 partners) completed an ACE. Clinicians detected abnormalities in 34.3% (245/714) of individuals. The abnormalities were a median of 3 mm in diameter. Sensitivity and specificity of the ASE/ACE was 59.6% (95% CI 53.5-65.7%) and 80.2% (95% CI 76.6-83.8%), respectively. Overall concordance was 0.73 (95% CI 0.70-0.76) between ASE/ACE and DARE and increased with increasing anal canal lesion size (p = 0.02). Concordance was lower when participants were older and received ASE/ACE training from a lay person rather than a clinician. Interpretation: Sexual minority men/transgender women may self-detect SCCA when malignant lesions are much smaller than the current mean dimension at presentation of ≥30 mm. Funding: National Cancer Institute.

Assessment of the antigenic evolution of a clade 6B.1 human H1N1pdm influenza virus revealed differences between ferret and human convalescent sera.

BACKGROUND: Influenza viruses continually acquire mutations in the antigenic epitopes of their major viral antigen, the surface glycoprotein haemagglutinin (HA), allowing evasion from immunity in humans induced upon prior influenza virus infections or vaccinations. Consequently, the influenza strains used for vaccine production must be updated frequently. METHODS: To better understand the antigenic evolution of influenza viruses, we introduced random mutations into the HA head region (where the immunodominant epitopes are located) of a pandemic H1N1 (H1N1pdm) virus from 2015 and incubated it with various human sera collected in 2015-2016. Mutants not neutralized by the human sera were sequenced and further characterized for their haemagglutination inhibition (HI) titers with human sera and with ferret sera raised to H1N1pdm viruses from 2009 to 2015. FINDINGS: The largest antigenic changes were conferred by mutations at HA amino acid position 187; interestingly, these antigenic changes were recognized by human, but not by ferret serum. H1N1pdm viruses with amino acid changes at position 187 were very rare until the end of 2018, but have become more frequent since; in fact, the D187A amino acid change is one of the defining changes of clade 6B.1A.5a.1 viruses, which emerged in 2019. INTERPRETATION: Our findings indicate that amino acid substitutions in H1N1pdm epitopes may be recognized by human sera, but not by homologous ferret sera. FUNDING: This project was supported by funding from the NIAID-funded Center for Research on Influenza Pathogenesis (CRIP, HHSN272201400008C).

Factors associated with decreased anal sphincter tone and the accuracy of forced anal examinations to detect individuals having receptive anal intercourse: An observational study.

Objective and Design: Forced anal examinations are used to prosecute sexual and gender minorities (SGM) in at least seven countries under the presumption that decreased sphincter tone, estimated by a finger inserted into the anal canal, can detect persons practicing receptive anal intercourse. In a cross-sectional analysis of the baseline data from a longitudinal study, we aimed to determine factors associated with sphincter tone and the accuracy of sphincter tonality to detect persons engaging in receptive anal intercourse. Setting: Clinicians in Chicago, Houston, and Milwaukee, USA conducted digital anal rectal examinations (DARE) on 838 participants, 94.0% of whom were cisgendered males. Clinicians used the Digital Rectal Examination Scoring System to score sphincter resting tone (RT) and squeeze tone (ST). On a separate survey, individuals reported their preferred position for anal intercourse: i.e., either always/mostly insertive anal intercourse, always/mostly receptive anal intercourse, or both receptive and insertive anal intercourse. Multivariable regression assessed factors associated with decreased sphincter tone while area under the Receiver Operating Characteristic curves (AUC) estimated the accuracy of sphincter tonality to detect receptive anal intercourse. Results: 11.3% had decreased RT (95/838) and 6.3% had decreased ST (53/838). The accuracy of DARE to detect any receptive anal intercourse was little better than random guessing (AUC 0.53, 95% CI 0.51 to 0.55, and AUC 0.51, 95% CI 0.49 to 0.53, respectively. RT and ST decreased with age regardless of sexual behavior (p trend <0.01 for both). Compared to individuals having always/mostly insertive anal intercourse, individuals having always/mostly receptive anal intercourse was associated with decreased RT, but not ST, while those equally preferring both insertive and receptive anal intercourse were not associated with decreased RT or ST. Conclusions: Decreased sphincter tone is uncommon among SGM who prefer receptive anal intercourse. Given virtually no accuracy, a finger inserted into the anus has no utility to detect individuals practicing receptive anal intercourse and thus should not be used as such. Trial registration: NCT04090060. Summary Box: What is already known on this topic: To gather evidence for prosecution of sexual and gender minorities, forced anal exams are used in multiple countries. The examination includes inserting the index finger into the anal canal to detect decreased sphincter tone which is considered evidence of receptive anal intercourse. We found only two small studies (n= 58 and n=24) assessing factors associated with decreased sphincter tone and none assessing the accuracy of sphincter tone to detect sexual and gender minorities having receptive anal intercourse.What this study adds: Our study suggests that a finger inserted into the anal canal is not useful to detect a history of receptive anal intercourse. As such, the sexual practices of individuals cannot be known using a forced anal examination.

Multiple reaction monitoring assays for large-scale quantitation of proteins from 20 mouse organs and tissues.

Mouse is the mammalian model of choice to study human health and disease due to its size, ease of breeding and the natural occurrence of conditions mimicking human pathology. Here we design and validate multiple reaction monitoring mass spectrometry (MRM-MS) assays for quantitation of 2118 unique proteins in 20 murine tissues and organs. We provide open access to technical aspects of these assays to enable their implementation in other laboratories, and demonstrate their suitability for proteomic profiling in mice by measuring normal protein abundances in tissues from three mouse strains: C57BL/6NCrl, NOD/SCID, and BALB/cAnNCrl. Sex- and strain-specific differences in protein abundances are identified and described, and the measured values are freely accessible via our MouseQuaPro database: http://mousequapro.proteincentre.com . Together, this large library of quantitative MRM-MS assays established in mice and the measured baseline protein abundances represent an important resource for research involving mouse models.

Durability of Cross-Neutralizing Antibodies 5.5 Months After Bivalent Coronavirus Disease 2019 Vaccine Booster.

We analyzed neutralizing antibodies in samples from ancestral + BA.1 and ancestral + BA.4/5 boosted individuals, collected around 5.5 months after booster. Titers of neutralizing antibodies generally decreased compared to a time point early after the bivalent booster immunization. This was more pronounced for individuals without infection history and for recently emerged Omicron variants.

Falling decreased anterior cruciate ligament loading variables during single-leg landings after mid-flight external trunk perturbation.

Mid-flight external upper-trunk perturbation is associated with increased anterior cruciate ligament (ACL) injury risk during landing. This study aimed to assess the effect of natural, soft, and falling landing techniques on knee mechanics and vertical ground reaction forces (VGRF) during single-leg landings with/without mid-flight medial-lateral external upper-trunk pushing perturbation. Twenty-eight participants performed single-leg landings using the three landing techniques with/without mid-flight pushing perturbation. The perturbation was created by a customized apparatus releasing a slam ball and pushing the participants near the peak jump height at the upper trunk. Perturbation resulted in significantly greater lateral trunk bending angles, knee flexion angles at initial contact, peak knee abduction angles, and peak knee adduction moments compared to no perturbation. The falling condition significantly demonstrated the greatest lateral trunk bending angles, knee flexion angles, and peak knee external rotation moments and the smallest peak knee abduction angles, peak VGRF, and peak knee extension moments compared to natural/soft landings regardless of perturbation conditions. Mid-flight external perturbation resulted in variables associated with greater ACL loading during single-leg landings. Falling demonstrated variables associated with smaller ACL loading, particularly for perturbation conditions. Incorporating falling techniques into jump-landing training programs may guide players to safely fall on the ground when perturbation occurs. Falling provides an alternative strategy to potentially decrease indirect contact ACL injury risk when the sports environment allows.

Military accession guidelines: An allergy focus.

Medical evaluation for military applicants is an intricate process that requires an understanding of the terminology, standards, and guidelines. Allergy providers are often called to provide medical evaluations for patients who desire to join the military services. Without understanding the complexities and nuances of military medical evaluations, a provider may delay or not be able to assist their patient in obtaining the desired goal of joining the services. This article reviews the terminology of military medical evaluations and the guidelines and processes for these evaluations. We also focus our discussion on common allergic conditions that may be disqualifying for service and provide expert opinions of the subtleties of these conditions to provide the allergist with a practical approach to medical evaluations. Finally, we provide a list of resources that are accessible to any provider engaged in military medical evaluations for accessions.

The impact of S2 mutations on Omicron SARS-CoV-2 cell surface expression and fusogenicity.

SARS-CoV-2 Omicron subvariants are still emerging and spreading worldwide. These variants contain a high number of polymorphisms in the spike (S) glycoprotein that could potentially impact their pathogenicity and transmission. We have previously shown that the S:655Y and P681H mutations enhance S protein cleavage and syncytia formation. Interestingly, these polymorphisms are present in Omicron S protein. Here, we characterized the cleavage efficiency and fusogenicity of the S protein of different Omicron sublineages. Our results showed that Omicron BA.1 subvariant is efficiently cleaved but it is poorly fusogenic compared to previous SARS-CoV-2 strains. To understand the basis of this phenotype, we generated chimeric S protein using combinations of the S1 and S2 domains from WA1, Delta and Omicron BA.1 variants. We found that the S2 domain of Omicron BA.1 hindered efficient cell-cell fusion. Interestingly, this domain only contains six unique polymorphisms never detected before in ancestral SARS-CoV-2 variants. WA1614G S proteins containing the six individuals S2 Omicron mutations were assessed for their fusogenicity and S surface expression after transfection in cells. Results showed that the S:N856K and N969K substitutions decreased syncytia formation and impacted S protein cell surface levels. However, we observed that "first-generation" Omicron sublineages that emerged subsequently, had convergently evolved to an enhanced fusogenic activity and S expression on the surface of infected cells while "second-generation" Omicron variants have highly diverged and showed lineage-specific fusogenic properties. Importantly, our findings could have potential implications in the improvement and redesign of COVID-19 vaccines.

Structural Elucidation of Intact Rough-type Lipopolysaccharides Using Field Asymmetric Ion Mobility Spectrometry and Kendrick Mass Defect Plots.

Lipopolysaccharides (LPSs) are a hallmark virulence factor of Gram-negative bacteria. They are complex, structurally heterogeneous mixtures due to variations in number, type, and position of their simplest units: fatty acids and monosaccharides. Thus, LPS structural characterization by traditional mass spectrometry (MS) methods is challenging. Here, we describe the benefits of field asymmetric ion mobility spectrometry (FAIMS) for analysis of an intact R-type lipopolysaccharide complex mixture (lipooligosaccharide; LOS). Structural characterization was performed using Escherichia coli J5 (Rc mutant) LOS, a TLR4 agonist widely used in glycoconjugate vaccine research. FAIMS gas-phase fractionation improved the (S/N) ratio and number of detected LOS species. Additionally, FAIMS allowed the separation of overlapping isobars facilitating their tandem MS characterization and unequivocal structural assignments. In addition to FAIMS gas-phase fractionation benefits, extra sorting of the structurally related LOS molecules was further accomplished using Kendrick mass defect (KMD) plots. Notably, a custom KMD base unit of [Na-H] created a highly organized KMD plot that allowed identification of interesting and novel structural differences across the different LOS ion families, i.e., ions with different acylation degrees, oligosaccharides composition, and chemical modifications. Defining the composition of a single LOS ion by tandem MS along with the organized KMD plot structural network was sufficient to deduce the composition of 181 LOS species out of 321 species present in the mixture. The combination of FAIMS and KMD plots allowed in-depth characterization of the complex LOS mixture and uncovered a wealth of novel information about its structural variations.

Descriptive analyses of bacterial communities in marine sediment microcosms spiked with fish wastes, emamectin benzoate, and oxytetracycline.

In marine sediments surrounding salmon aquaculture sites, organic matter (OM) enrichment has been shown to influence resident bacterial community composition; however, additional effects on these communities due to combined use of the sea-lice therapeutant emamectin benzoate (EMB) and the widely used antibiotic oxytetracycline (OTC) are unknown. Here, we use sediment microcosms to assess the influence of OM, EMB, and OTC on benthic bacterial communities. Microcosms consisted of mud or sand sediments enriched with OM (fish and feed wastes) and spiked with EMB and OTC at environmentally-relevant concentrations. Samples were collected from initial matrices at the initiation of the trial and after 110 days for 16 S rRNA gene sequencing of the V3-V4 region and microbiome profiling. The addition of OM in both mud and sand sediments reduced alpha diversities; for example, an average of 1106 amplicon sequence variants (ASVs) were detected in mud with no OM addition, while only 729 and 596 ASVs were detected in mud with low OM and high OM, respectively. Sediments enriched with OM had higher relative abundances of Spirochaetota, Firmicutes, and Bacteroidota. For instance, Spirochaetota were detected in sediments with no OM with a relative abundance range of 0.01-1.2%, while in sediments enriched with OM relative abundance varied from 0.16% to 26.1%. In contrast, the addition of EMB (60 ng/g) or OTC (150 ng/g) did not result in distinct taxonomic shifts in the bacterial communities compared to un-spiked sediments during the timeline of this experiment. EMB and OTC concentrations may have been below effective inhibitor concentrations for taxa in these communities; further work should explore gene content and the presence of antibiotic resistance genes (ARGs) in sediment-dwelling bacteria.