Structural and functional characterization of nanobodies that neutralize Omicron variants of SARS-CoV-2.

The Omicron strains of SARS-CoV-2 pose a significant challenge to the development of effective antibody-based treatments as immune evasion has compromised most available immune therapeutics. Therefore, in the 'arms race' with the virus, there is a continuing need to identify new biologics for the prevention or treatment of SARS-CoV-2 infections. Here, we report the isolation of nanobodies that bind to the Omicron BA.1 spike protein by screening nanobody phage display libraries previously generated from llamas immunized with either the Wuhan or Beta spike proteins. The structure and binding properties of three of these nanobodies (A8, H6 and B5-5) have been characterized in detail providing insight into their binding epitopes on the Omicron spike protein. Trimeric versions of H6 and B5-5 neutralized the SARS-CoV-2 variant of concern BA.5 both in vitro and in the hamster model of COVID-19 following nasal administration. Thus, either alone or in combination could serve as starting points for the development of new anti-viral immunotherapeutics.

Identifying X (Formerly Twitter) Posts Relevant to Dementia and COVID-19: Machine Learning Approach.

BACKGROUND: During the pandemic, patients with dementia were identified as a vulnerable population. X (formerly Twitter) became an important source of information for people seeking updates on COVID-19, and, therefore, identifying posts (formerly tweets) relevant to dementia can be an important support for patients with dementia and their caregivers. However, mining and coding relevant posts can be daunting due to the sheer volume and high percentage of irrelevant posts. OBJECTIVE: The objective of this study was to automate the identification of posts relevant to dementia and COVID-19 using natural language processing and machine learning (ML) algorithms. METHODS: We used a combination of natural language processing and ML algorithms with manually annotated posts to identify posts relevant to dementia and COVID-19. We used 3 data sets containing more than 100,000 posts and assessed the capability of various algorithms in correctly identifying relevant posts. RESULTS: Our results showed that (pretrained) transfer learning algorithms outperformed traditional ML algorithms in identifying posts relevant to dementia and COVID-19. Among the algorithms tested, the transfer learning algorithm A Lite Bidirectional Encoder Representations from Transformers (ALBERT) achieved an accuracy of 82.92% and an area under the curve of 83.53%. ALBERT substantially outperformed the other algorithms tested, further emphasizing the superior performance of transfer learning algorithms in the classification of posts. CONCLUSIONS: Transfer learning algorithms such as ALBERT are highly effective in identifying topic-specific posts, even when trained with limited or adjacent data, highlighting their superiority over other ML algorithms and applicability to other studies involving analysis of social media posts. Such an automated approach reduces the workload of manual coding of posts and facilitates their analysis for researchers and policy makers to support patients with dementia and their caregivers and other vulnerable populations.

Mitral valve repair in a regional quality collaborative: Respect or resect?

Objective: Mitral valve repair is the gold standard for treatment of mitral regurgitation, but the optimal technique remains debated. By using a regional collaborative, we sought to determine the change in repair technique over time. Methods: We identified all patients undergoing isolated mitral valve repair from 2012 to 2022 for degenerative mitral disease. Those with endocarditis, transcatheter repair, or tricuspid intervention were excluded. Continuous variables were analyzed via Wilcoxon rank sum, and categorical variables were analyzed via chi-square testing. Results: We identified 1653 patients who underwent mitral valve repair, with 875 (59.2%) undergoing a no resection repair. Over the last decade, there was no significant trend in the proportion of repair techniques across the region (P = .96). Those undergoing no resection repairs were more likely to have undergone prior cardiac surgery (5.0% vs 2.2%, P = .002) or minimally invasive approaches (61.4% vs 24.7%, P < .001) with similar predicted risk of mortality (median 0.6% vs 0.6%, P = .75). Intraoperatively, no resection repairs were associated with longer bypass times (140 [117-167] minutes vs 122 [91-159] minutes, P < .001). Operative mortality was similar between both groups (1.1% vs 1.0%, P = .82), as were other postoperative outcomes. Anterior leaflet prolapse (odds ratio, 11.16 [6.34-19.65], P < .001) and minimally invasive approach (odds ratio, 6.40 [5.06-8.10], P < .001) were most predictive of no resection repair. Conclusions: Despite minor differences in operative times, statewide over the past decade there remains a diverse mix of both classic "resect" and newer "respect" strategies with comparable short-term outcomes and no major timewise trends. These data may suggest that both approaches are equivocal.

From Llama to Nanobody: A Streamlined Workflow for the Generation of Functionalised VHHs.

Nanobodies are recombinant antigen-specific single domain antibodies (VHHs) derived from the heavy chain-only subset of camelid immunoglobulins. Their small molecular size, facile expression, high affinity, and stability have combined to make them unique targeting reagents with numerous applications in the biomedical sciences. From our work in producing nanobodies to over sixty different proteins, we present a standardised workflow for nanobody discovery from llama immunisation, library building, panning, and small-scale expression for prioritisation of binding clones. In addition, we introduce our suites of mammalian and bacterial vectors, which can be used to functionalise selected nanobodies for various applications such as in imaging and purification. Key features • Standardise the process of building nanobody libraries and finding nanobody binders so that it can be repeated in any lab with reasonable equipment. • Introduce two suites of vectors to functionalise nanobodies for production in either bacterial or mammalian cells.

Artificial Intelligence Language Models Are Useful Tools for Patients Undergoing Total Ankle Replacement.

BACKGROUND: Artificial intelligence (AI) large language models (LLMs), such as Chat Generative Pre-trained Transformer (ChatGPT), have gained traction as both augmentative tools in patient care but also as powerful synthesizing machines. The use of ChatGPT in orthopaedic foot and ankle surgery, particularly as an informative resource for patients, has not been described to date. The purpose of this study was to assess the quality of information provided by ChatGPT in response to commonly asked questions about total ankle replacement (TAR). METHODS: ChatGPT was asked 10 frequently asked questions about TAR in a conversational thread. Responses were recorded without follow-up, and subsequently graded A, B, C, or F, corresponding with "excellent response," "adequate response needing mild clarification," "inadequate response needing moderate clarification," and "poor response needing severe clarification." RESULTS: Of the 10 responses, 2 were grade "A," 6 were grade "B," 2 were grade "C," and none were grade "F." Overall, the LLM provided good-quality responses to the posed prompts. Conclusion. Overall, the provided responses were understandable and representative of the current literature surrounding TAR. This study highlights the potential role LLMs in augmenting patient understanding of foot and ankle operative procedures. LEVELS OF EVIDENCE: IV.

Rapid and Definitive Identification of Cyclic Peptide Soft Spots by Isotope-Labeled Reductive Dimethylation and Mass Spectrometry Fragmentation.

Cyclic peptides are an emerging therapeutic modality over the past few decades. To identify drug candidates with sufficient proteolytic stability for oral administration, it is critical to pinpoint the amide bond hydrolysis sites, or soft spots, to better understand their metabolism and provide guidance on further structure optimization. However, the unambiguous characterization of cyclic peptide soft spots remains a significant challenge during early stage discovery studies, as amide bond hydrolysis forms a linearized isobaric sequence with the addition of a water molecule, regardless of the amide hydrolysis location. In this study, an innovative strategy was developed to enable the rapid and definitive identification of cyclic peptide soft spots by isotope-labeled reductive dimethylation and mass spectrometry fragmentation. The dimethylated immonium ion with enhanced MS signal at a distinctive m/z in MS/MS fragmentation spectra reveals the N-terminal amino acid on a linearized peptide sequence definitively and, thus, significantly simplifies the soft spot identification workflow. This approach has been evaluated to demonstrate the potential of isotope-labeled dimethylation to be a powerful analytical tool in cyclic peptide drug discovery and development.

Hands-Free Haptic Navigation Devices for Actual Walking.

In this survey, we give an overview of hands-free haptic devices specifically designed for navigation guidance while walking. We present and discuss the devices by body part, namely devices for the arm, foot and leg, back, belly and shoulders, waist and finally the head. Although the majority of the experimental tests were successful in terms of reaching the target while being guided by the device, the experimental requirements were wide-ranging. The distances to be covered ranged from just a few meters to more than a kilometer, and while some of the devices worked autonomously, others required the experimenter to act as Wizard of Oz. To compare the usefulness and potential of these devices, we created a table in which we rated several relevant aspects such as autonomy, conspicuity and compactness. Major conclusions are that outdoor devices have the highest technology readiness level, because these allow autonomous navigation through GPS, and that the most compact devices still require the action of an experimenter. Unfortunately, none of the hands-free devices are at a level of readiness where they could be useful to people with visual impairments. The most important factor that should be improved is localization accuracy, which should be high and available at all times.

Safety of early discharge after elective lumbar spine surgery with subfascial drains and association with significant reduction in length of stay.

OBJECTIVE: After lumbar spine surgery, postoperative drain removal often delays discharge. Whether inpatient drain removal reduces the risk of surgical site infection (SSI) or hematoma remains controversial. Therefore, in patients undergoing elective lumbar spine surgery, the authors sought to determine the impact of inpatient versus outpatient drain removal on the following variables: 1) length of hospital stay (LOS), and 2) postoperative complications. METHODS: A single-center retrospective cohort study in which the authors used prospectively collected data of patients undergoing primary, elective, 1- or 2-level lumbar spine decompression and/or fusion was undertaken between 2016 and 2022. Patients with intraoperative or postoperative CSF leaks were excluded. The primary exposure variable was inpatient versus outpatient drain removal. The primary outcome was LOS, and secondary outcomes were postoperative complications, including 90-day postoperative SSI or hematoma. Multivariable logistic and linear regression were performed, controlling for age, body mass index, instrumentation, number of levels, antibiotics at discharge, and surgeons involved. RESULTS: Of 483 patients included, 325 (67.3%) had inpatient drain removal and 158 (32.7%) had outpatient drain removal. Patients with outpatient drain removal were significantly younger (58.6 ± 12.4 vs 61.2 ± 13.2 years, p = 0.040); more likely to have 1-level surgery (75.9% vs 56.6%, p < 0.001); and less likely to receive instrumentation (50.6% vs 69.5%, p < 0.001). Postoperatively, patients with outpatient drain removal had a shorter LOS (0.7 ± 0.6 vs 2.3 ± 1.6 days, p < 0.001); were more likely to be discharged home (98.1% vs 92.3%, p = 0.015); were more likely to be discharged on antibiotics (76.6% vs 3.1%, p < 0.001); were less likely to be on opioids (32.3% vs 88.3%, p < 0.001); and were more likely to have Jackson-Pratt compared to Hemovac drains (96.2% vs 34.5%, p < 0.001). No difference was found in SSI (3.7% vs 3.8%, p > 0.999) or hematoma (0.9% vs 0.6%, p > 0.999), as well as reoperation or readmission due to SSI or hematoma. On multivariable regression, outpatient drain removal was significantly associated with shorter LOS (ß = -1.15, 95% CI -1.56 to -0.73, p < 0.001). No association was found with SSI/hematoma (p > 0.05). CONCLUSIONS: Outpatient drain removal after elective lumbar spine surgery was associated with a significantly decreased LOS without a significant increase in postoperative SSI or hematoma. Although the choice of drain removal and the LOS may be subject to surgeons' preference, these results may support the feasibility and safety of outpatient drain removal, and the potential cost savings resulting from shortened hospital stays. Drawbacks may exist regarding added burden to the patient and the surgeon's team to accommodate 1-week follow-up appointments for drain removal.

Piperazate-Guided Isolation of Caveamides A and B, Cyclohexenylalanine-Containing Nonribosomal Peptides from a Cave Actinomycete.

Hybrid genome-mining/15N-NMR was used to target compounds containing piperazate (Piz) residues, leading to the discovery of caveamides A (1) and B (2) from Streptomyces sp. strain BE230, isolated from New Rankin Cave (Missouri). Caveamides are highly dynamic molecules containing an unprecedented ß-ketoamide polyketide fragment, two Piz residues, and a new N-methyl-cyclohexenylalanine residue. Caveamide B (2) exhibited nanomolar cytotoxicity against several cancer cell lines and nanomolar antimicrobial activity against MRSA and E. coli.

Magnetically treated water for removal of surface contamination by Malathion on Chinese Kale (Brassica oleracea L.).

Malathion® is a persistent organophosphate pesticide used against biting and chewing insects on vegetables. It is a difficult-to-remove surface contaminant of vegetables and contaminates surface and ground water and soils. Malathion® is only partially water soluble, but use of detergent carriers makes adhering Malathion® residues difficult to subsequently remove. Magnetically treated water (MTW) successfully removed Malathion® from Chinese Kale (Brassica oleracea L.), meeting Maximum Residue Load (MRL) standards. Samples were soaked in MTW for 30 min prior to detection with GC/MS/MS, 98.5±3.02% of Malathion® was removed after washing by MTW. Removal by simple washing was only ≈42±1.2% which was not nearly sufficient to meet MRL criteria.

Patients with Hip Osteoarthritis Have a Higher Rate of Spinal Reoperation Following Lumbar Spinal Fusion.

BACKGROUND: Lumbar spinal pathology is known to affect outcomes following total hip arthroplasty (THA). However, the effect of hip osteoarthritis (OA) on outcomes following lumbar fusion has not been well studied. The purpose of this study was to determine the association between hip OA and spinal reoperation following lumbar spinal fusion. METHODS: The 5% Medicare Part B claims database was queried for all patients who underwent primary elective lumbar fusion from 2005 to 2019. Patients were divided into 2 groups: those who underwent elective THA within 1 year after primary lumbar fusion, indicating that they had severe hip OA at the time of lumbar fusion, and those who underwent lumbar fusion with no diagnosed hip OA and no THA during the study period. Exclusion criteria included THA as a result of trauma, revision THA or primary THA in the 5-year period before primary lumbar fusion, <65 years of age, and no enrollment in the database for 5 years before and 1 year after primary lumbar fusion. The primary outcome was spinal reoperation within 1, 3, and 5 years. Multivariable Cox regression was performed with age, sex, diabetes, heart disease, obesity, smoking status, osteoporosis, number of levels fused, use of posterior instrumentation, use of an interbody device, use of bone graft, and surgical approach as covariates. RESULTS: Overall, 1,123 patients (63.4% female; 91.3% White; mean age, 76.8 ± 4.1 years) were included in the hip OA group and 8,893 patients (56.2% female; 91.3% White; mean age, 74.8 ± 4.9 years) were included in the control group. After multivariable analysis, patients with severe hip OA had significantly greater rates of revision surgery at 3 years (odds ratio [OR], 1.61; p < 0.001) and 5 years (OR, 1.87; p < 0.001) after the index lumbar fusion. CONCLUSIONS: Patients with severe hip OA at the time of primary lumbar fusion had a significantly increased risk of spinal reoperation at 3 and 5 years postoperatively. These data provide further evidence to support performing THA prior to lumbar fusion in the unsettled debate regarding which surgery should be prioritized for patients with simultaneous degenerative diseases of the hip and lumbar spine. LEVEL OF EVIDENCE: Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.

Highly oxygenated cyclohexenes from Uvaria dac Pierre ex Finet & Gagnep. and their α-glucosidase inhibitory activity.

Phytochemical investigations of the twig and leaf extracts of Uvaria dac Pierre ex Finet & Gagnep. resulted in the isolation and identification of five new highly oxygenated cyclohexenes, uvaridacols M - Q (1-3, 5, and 6), and six known compounds (4 and 7-11). All new structures were elucidated by spectroscopic methods and HRESITOFMS data. The absolute configuration of 1, 5, and 6 was confirmed by single X-ray diffraction analysis with Cu Kα radiation. In contrast, other compounds were established by comparing their specific rotation and ECD spectra with those of known compounds. Some of the isolated compounds with sufficient quantity were evaluated for their α-glucosidase inhibitory activity. Of these, (-)-1,6-desoxypipoxide (10) showed α-glucosidase inhibitory activity with an IC50 value of 28.6 µM. The in silico molecular docking of active compounds was also studied.

Reactivation strength during cued recall is modulated by graph distance within cognitive maps.

Declarative memory retrieval is thought to involve reinstatement of neuronal activity patterns elicited and encoded during a prior learning episode. Furthermore, it is suggested that two mechanisms operate during reinstatement, dependent on task demands: individual memory items can be reactivated simultaneously as a clustered occurrence or, alternatively, replayed sequentially as temporally separate instances. In the current study, participants learned associations between images that were embedded in a directed graph network and retained this information over a brief 8 min consolidation period. During a subsequent cued recall session, participants retrieved the learned information while undergoing magnetoencephalographic recording. Using a trained stimulus decoder, we found evidence for clustered reactivation of learned material. Reactivation strength of individual items during clustered reactivation decreased as a function of increasing graph distance, an ordering present solely for successful retrieval but not for retrieval failure. In line with previous research, we found evidence that sequential replay was dependent on retrieval performance and was most evident in low performers. The results provide evidence for distinct performance-dependent retrieval mechanisms, with graded clustered reactivation emerging as a plausible mechanism to search within abstract cognitive maps.

An Ovine Model Yields Histology and Gene Expression Changes Consistent with Laryngotracheal Stenosis.

OBJECTIVES: Animal models for laryngotracheal stenosis (LTS) are critical to understand underlying mechanisms and study new therapies. Current animal models for LTS are limited by small airway sizes compared to human. The objective of this study was to develop and validate a novel, large animal ovine model for LTS. METHODS: Sheep underwent either bleomycin-coated polypropylene brush injury to the subglottis (n = 6) or airway stent placement (n = 2) via suspension microlaryngoscopy. Laryngotracheal complexes were harvested 4 weeks following injury or stent placement. For the airway injury group, biopsies (n = 3 at each site) were collected of tracheal scar and distal normal regions, and analyzed for fibrotic gene expression. Lamina propria (LP) thickness was compared between injured and normal areas of trachea. RESULTS: No mortality occurred in sheep undergoing airway injury or stent placement. There was no migration of tracheal stents. After protocol optimization, LP thickness was significantly increased in injured trachea (Sheep #3: 529.0 vs. 850.8 um; Sheep #4: 933.0 vs. 1693.2 um; Sheep #5: 743.7 vs. 1378.4 um; Sheep #6: 305.7 vs. 2257.6 um). A significant 62-fold, 20-fold, 16-fold, 16-fold, and 9-fold change of COL1, COL3, COL5, FN1, and TGFB1 was observed in injured scar specimen relative to unaffected airway, respectively. CONCLUSION: An ovine LTS model produces histologic and transcriptional changes consistent with fibrosis seen in human LTS. Airway stent placement in this model is safe and feasible. This large airway model is a reliable and reproducible method to assess the efficacy of novel LTS therapies prior to clinical translation. LEVEL OF EVIDENCE: N/A Laryngoscope, 2024.

Unmet needs in people with high-grade glioma: Defining criteria for stepped care intervention.

BACKGROUND: We aimed to define levels of unmet supportive care needs in people with primary brain tumour and reach expert consensus on feasibility of addressing patients' needs in clinical practice. METHODS: We conducted secondary analysis of a prospective cohort study of people diagnosed with high-grade glioma (n = 116) who completed the Supportive Care Needs Survey-SF34 during adjuvant chemoradiation therapy. Participants were allocated to one of three categories: no need ('no need' for help on all items), low need ('low need' for help on at least one item, but no 'moderate' or 'high' need), or moderate/high need (at least one 'moderate' or 'high' need indicated). Clinical capacity to respond to the proportion of patients needing to be prioritised was assessed. RESULTS: Overall, 13% (n = 5) were categorised as no need, 23% (n = 27) low need, and 64% (n = 74) moderate/high need. At least one moderate/high need was reported in the physical and daily living domain (42%), and psychological (34%) domain. In recognition of health system capacity, the moderate/high need category was modified to distinguish between: moderate need ('moderate' need indicated for at least one item but 'high' need was not selected for any item) and high need (at least one 'high' need indicated). Results revealed 24% (n = 28) moderate need and 40% (n = 46) high need. Those categorised as high need indicated needing assistance navigating the health system and information. CONCLUSIONS: Using four step allocations resulted in 40% of patients indicating high need. Categories may facilitate appropriate triaging, and guide stepped models of healthcare delivery.

Heuristics in risky decision-making relate to preferential representation of information.

When making choices, individuals differ from one another, as well as from normativity, in how they weigh different types of information. One explanation for this relates to idiosyncratic preferences in what information individuals represent when evaluating choice options. Here, we test this explanation with a simple risky-decision making task, combined with magnetoencephalography (MEG). We examine the relationship between individual differences in behavioral markers of information weighting and neural representation of stimuli pertinent to incorporating that information. We find that the extent to which individuals (N = 19) behaviorally weight probability versus reward information is related to how preferentially they neurally represent stimuli most informative for making probability and reward comparisons. These results are further validated in an additional behavioral experiment (N = 88) that measures stimulus representation as the latency of perceptual detection following priming. Overall, the results suggest that differences in the information individuals consider during choice relate to their risk-taking tendencies.

Novel pentafluorosulfanyl-containing triclocarban analogs selectively kill Gram-positive bacteria.

Novel antimicrobial agents are needed to combat antimicrobial resistance. This study tested novel pentafluorosulfanyl-containing triclocarban analogs for their potential antibacterial efficacy. Standard procedures were used to produce pentafluorosulfanyl-containing triclocarban analogs. Twenty new compounds were tested against seven Gram-positive and Gram-negative indicator strains as well as 10 clinical isolates for their antibacterial and antibiofilm activity. Mechanistic investigations focused on damage to cell membrane, oxidizing reduced thiols, iron-sulfur clusters, and oxidative stress to explain the compounds' activity. Safety profiles were assessed using cytotoxicity experiments in eukaryotic cell lines. Following screening, selected components had significantly better antibacterial and antibiofilm activity against Gram-positive bacteria in lower concentrations in comparison to ciprofloxacin and gentamycin. For instance, one compound had a minimum inhibitory concentration of <0.0003 mM, but ciprofloxacin had 0.08 mM. Mechanistic studies show that these novel compounds do not affect reduced thiol content, iron-sulfur clusters, or hydrogen peroxide pathways. Their impact comes from Gram-positive bacterial cell membrane damage. Tests on cell culture toxicity and host component safety showed promise. Novel diarylurea compounds show promise as Gram-positive antimicrobials. These compounds offer prospects for study and optimization. IMPORTANCE: The rise of antibiotic resistance among bacterial pathogens poses a significant threat to global health, underscoring the urgent need for novel antimicrobial agents. This study presents research on a promising class of novel compounds with potent antibacterial properties against Gram-positive bacteria, notably Staphylococcus aureus and MRSA. What sets these novel analogs apart is their superior efficacy at substantially lower concentrations compared with commonly used antibiotics like ciprofloxacin and gentamycin. Importantly, these compounds act by disrupting the bacterial cell membrane, offering a unique mechanism that could potentially circumvent existing resistance mechanisms. Preliminary safety assessments also highlight their potential for therapeutic use. This study not only opens new avenues for combating antibiotic-resistant infections but also underscores the importance of innovative chemical approaches in addressing the global antimicrobial resistance crisis.

Joint Modeling of Gene-Environment Correlations and Interactions Using Polygenic Risk Scores in Case-Control Studies.

Polygenic risk scores (PRS) are rapidly emerging as a way to measure disease risk by aggregating multiple genetic variants. Understanding the interplay of PRS with environmental factors is critical for interpreting and applying PRS in a wide variety of settings. We develop an efficient method for simultaneously modeling gene-environment correlations and interactions using PRS in case control studies. We use a logistic-normal regression modeling framework to specify the disease risk and PRS distribution in the underlying population and propose joint inference across the two models using the retrospective likelihood of the case-control data. Extensive simulation studies demonstrate the flexibility of the method in trading-off bias and efficiency for the estimation of various model parameters compared to the standard logistic regression or a case-only analysis for gene-environment interactions, or a control-only analysis for gene-environment correlations. Finally using simulated case-control data sets within the UK Biobank study, we demonstrate the power of our method for its ability to recover results from the full prospective cohort for the detection of an interaction between long-term oral contraceptive use and PRS on the risk of breast cancer. This method is computationally efficient and implemented in a user-friendly R package.