The Fusion of Wide Field Optical Coherence Tomography and AI: Advancing Breast Cancer Surgical Margin Visualization.

This study explores the integration of Wide Field Optical Coherence Tomography (WF-OCT) with an AI-driven clinical decision support system, with the goal of enhancing productivity and decision making in breast cancer surgery margin assessment. A computationally efficient convolutional neural network (CNN)-based binary classifier is developed using 585 WF-OCT margin scans from 151 subjects. The CNN model swiftly identifies suspicious areas within margins with an on-device inference time of approximately 10 ms for a 420 × 2400 image. In independent testing on 155 pathology-confirmed margins, including 31 positive margins from 29 patients, the classifier achieved an AUROC of 0.976, a sensitivity of 0.93, and a specificity of 0.98. At the margin level, the deep learning model accurately identified 96.8% of pathology-positive margins. These results highlight the clinical viability of AI-enhanced margin visualization using WF-OCT in breast cancer surgery and its potential to decrease reoperation rates due to residual tumors.

Examining the Prevailing Negative Sentiments Surrounding Measles Vaccination: Unsupervised Deep Learning of Twitter Posts from 2017 to 2022.

Despite the proven safety and clinical efficacy of the Measles vaccine, many countries are seeing new heights of vaccine hesitancy or refusal, and are experiencing a resurgence of measles infections as a consequence. With the use of novel machine learning tools, we investigated the prevailing negative sentiments related to Measles vaccination through an analysis of public Twitter posts over a 5-year period. We extracted original tweets using the search terms related to "measles" and "vaccine," and posted in English from January 1, 2017, to December 15, 2022. Of these, 155,363 tweets were identified to be negative sentiment tweets from unique individuals, through the use of Bidirectional Encoder Representations from Transformers (BERT) Named Entity Recognition and SieBERT, a pretrained sentiment in English analysis model. This was followed by topic modeling and qualitative thematic analysis performed inductively by the study investigators. A total of 11 topics were generated after applying BERTopic. To facilitate a global discussion of results, the topics were grouped into four different themes through iterative thematic analysis. These include (a) the rejection of "anti-vaxxers" or antivaccine sentiments, (b) misbeliefs and misinformation regarding Measles vaccination, (c) negative transference due to COVID-19 related policies, and (d) public reactions to contemporary Measles outbreaks. Theme 1 highlights that the current public discourse may further alienate those who are vaccine hesitant because of the disparaging language often used, while Themes 2 and 3 highlight the typology of misperceptions and misinformation underlying the negative sentiments related to Measles vaccination and the psychological tendency of disconfirmation bias. Nonetheless, the analysis was based solely on Twitter and only tweets in English were included; hence, the findings may not necessarily generalize to non-Western communities. It is important to further understand the thinking and feeling of those who are vaccine hesitant to address the issues at hand.

Performance of the paracetamol-aminotransferase multiplication product in risk stratification after paracetamol (acetaminophen) poisoning: a systematic review and meta-analysis.

BACKGROUND: Risk stratification in paracetamol (acetaminophen) poisoning is crucial because hepatotoxicity is common and can be mitigated with treatment. However, current risk stratification tools have limitations. AIMS: We evaluated the diagnostic performance of the paracetamol concentration × aminotransferase multiplication product, for predicting hepatotoxicity after paracetamol overdose. METHODS: Medline, Cochrane Library and Embase were searched for eligible papers. We used random effects models to obtain pooled estimates of the likelihood ratios and diagnostic odds ratios, from which sensitivity and specificity were computed. We assessed two commonly used cut-off values of paracetamol × aminotransferase, 1500 mg/L × IU/L and 10,000 mg/L × IU/L. Using the confusion matrices of these two cut-offs, area under the summary receiver operator characteristic curve and optimal cut-off values in different clinical scenarios were established. RESULTS: Six studies comprising 5036 participants were included. In 4051 patients, using the cut-off of 1500 mg/L × IU/L, a diagnostic odds ratio of 31.90 (95%CI: 9.52-106.90), sensitivity of 0.98 (95%CI: 0.94-1.00) and specificity of 0.66 (95%CI: 0.49-0.89) were obtained. In 3983 patients, using the cut-off of 10,000 mg/L × IU/L, a diagnostic odds ratio of 99.34 (95%CI: 12.26-804.87), sensitivity of 0.65 (95%CI: 0.51-0.82) and specificity of 0.97 (95%CI: 0.95-1.00) were obtained. For staggered ingestions, the 1500 mg/L × IU/L cut-off yielded a diagnostic odds ratio of 69.53 (95%CI: 4.03-1199.75), sensitivity of 1.00 (95%CI: 0.87-1.00) and specificity of 0.74 (95%CI: 0.43-1.00). Next, using the 10,000 mg/L × IU/L cut-off in this scenario yielded a diagnostic odds ratio of 254.58 (95%CI: 11.12-5827.60), sensitivity of 0.79 (95%CI: 0.59-1.00) and specificity of 0.98 (95%CI: 0.94-1.00). The overall summary receiver operator characteristic curve was 0.91 (95%CI: 0.75-0.97), and the optimal cut-off value was 3840 mg/L × IU/L. The summary receiver operator characteristic curve in patients with staggered ingestions was 0.96 (95%CI: 0.85-0.99). The summary receiver operator characteristic curve in patients with staggered ingestions and whose paracetamol concentration was below the detectable limit of 10 mg/L at presentation was 0.97 (95%CI: 0.94-0.99). CONCLUSION: In this first meta-analysis, paracetamol × aminotransferase demonstrates its use in prognosticating hepatotoxicity in patients with paracetamol poisoning. It complements the Rumack-Matthew nomogram as it has shown promise in addressing two key limitations of the nomogram: it is usable after more than 24 h between overdose and acetylcysteine treatment, and it is applicable in staggered ingestions.

Discovery of compounds that reactivate p53 mutants in vitro and in vivo.

The tumor suppressor p53 is the most frequently mutated protein in human cancer. The majority of these mutations are missense mutations in the DNA binding domain of p53. Restoring p53 tumor suppressor function could have a major impact on the therapy for a wide range of cancers. Here we report a virtual screening approach that identified several small molecules with p53 reactivation activities. The UCI-LC0023 compound series was studied in detail and was shown to bind p53, induce a conformational change in mutant p53, restore the ability of p53 hotspot mutants to associate with chromatin, reestablish sequence-specific DNA binding of a p53 mutant in a reconstituted in vitro system, induce p53-dependent transcription programs, and prevent progression of tumors carrying mutant p53, but not p53null or p53WT alleles. Our study demonstrates feasibility of a computation-guided approach to identify small molecule corrector drugs for p53 hotspot mutations.

CSF neurofilament light may predict progression from amnestic mild cognitive impairment to Alzheimer's disease dementia.

Neurofilament light (NfL) is a promising biomarker of neurodegeneration in Alzheimer's disease (AD). In this study, cerebrospinal fluid (CSF) NfL was measured in a 24-month longitudinal cohort consisting of control (n = 52), amnestic mild cognitive impairment (aMCI) (n = 55), and probable AD dementia (n = 28) individuals. The cohort was reevaluated after 6-10 years. Baseline CSF NfL was significantly elevated in aMCI and probable AD dementia groups compared to controls (p < 0.0001). CSF NfL was significantly lower in stable aMCI patients compared to aMCI patients who converted to probable AD dementia within the 24-month period (p = 0.004). Substituting T-tau for NfL in the core AD biomarkers model (Aß42/P-tau/T-tau) did not improve ability to separate control and AD, or stable and converter aMCI patients. Our results support that elevated CSF NfL could predict progression in aMCI patients, but its utility cannot improve the core AD biomarkers.

Plasma Protein Profiling by Proximity Extension Assay Technology Reveals Novel Biomarkers of Traumatic Brain Injury-A Pilot Study.

BACKGROUND: Traumatic brain injury (TBI) is a significant public health issue affecting nearly 69 million patients worldwide per year. Reliable diagnostic biomarkers are urgently needed to aid in disease diagnosis and prognosis and to guide patient aftercare. Blood biomarkers represent an attractive modality to quickly, cheaply, and objectively evaluate clinical status. We hypothesize that deep and quantitative plasma proteomic profiling with a novel technology, proximity extension assay, may lead to the discovery of diagnostic and/or prognostic biomarkers of TBI. METHODS: We used high-throughput proximity extension assays (PEA) to quantify the relative abundance of over 1000 unique proteins in plasma. PEA is a highly sensitive multiplex immunoassay capable of detecting very low-abundance proteins (down to fg/mL) in complex biological matrices. Our patient cohort consisted of severe TBI (sTBI) patients, matched healthy controls, and another non-TBI group that was included in the analysis to validate the specificity of the candidates during the selection process. The obtained protein quantification data was then filtered to identify candidate biomarkers through statistical analysis, literature searches, and comparison to our reference control groups. RESULTS: Overall, we identified 6 novel candidate TBI biomarkers. Candidates exhibit a significant increase in plasma protein abundance in sTBI when comparing between healthy controls and sTBI patients. Candidates generally had low expression in our reference groups compared with the sTBI group. CONCLUSIONS: Our preliminary findings represent a starting point for future validation. These biomarkers, either alone or in combination, may have significant clinical utility in aiding in TBI diagnosis, prognosis, and/or management.

Alzheimer Disease Pathogenesis: The Role of Autoimmunity.

BACKGROUND: In addition to deposits of amyloid ß (Aß) plaques and neurofibrillary tangles, growing evidence demonstrates that complex and multifaceted biological processes can arise during Alzheimer disease (AD) pathogenesis. The recent failures of clinical trials based on the amyloid hypothesis and the presence of Aß plaques in cognitively healthy elderly persons without AD point toward a need to explore novel pathobiological mechanisms of AD. CONTENT: In the search for alternative AD mechanisms, numerous genome-wide association studies and mechanistic discoveries suggest a potential immunologic component of the disease. However, new experimental tools are needed to uncover these immunogenic components. The current methods, such as ELISAs or protein microarrays, have limitations of low throughput and/or sensitivity and specificity. In this article, we briefly discuss evidence of potential autoimmune contributions to AD pathobiology, describe the current methods for identifying autoantibodies in patient fluids, and outline our own efforts to develop new techniques for novel autoantibody biomarker discovery. SUMMARY: Uncovering the putative autoimmune components of AD may be crucial in paving the way to new concepts for pathogenesis, diagnosis, and therapy. IMPACT STATEMENT: In addition to deposits of amyloid ß plaques and neurofibrillary tangles, growing evidence demonstrates that complex and multifaceted biological processes can arise during Alzheimer disease (AD) pathogenesis. Numerous research directions, including genome-wide association, clinical correlation, and mechanistic studies, have pointed to a potential autoimmunologic contribution to AD pathology. We present research suggesting the association between autoimmunity and AD and demonstrate the need for new laboratory techniques to further characterize potential brain antigen-specific autoantibodies. Uncovering the putative autoimmune components of AD may be crucial in paving the way to new concepts for pathogenesis, diagnosis, and therapy.

Decreased cerebrospinal fluid neuronal pentraxin receptor is associated with PET-Aß load and cerebrospinal fluid Aß in a pilot study of Alzheimer's disease.

Multifactorial pathological processes of Alzheimer's disease (AD) begin decades prior to clinical onset. Early identification of patients at risk of developing AD using biomarkers reflecting various aspects of pathogenesis is necessary for prevention and early intervention. Cortical ß-amyloid (Aß) burden assessed by positron emission tomography (PET) or cerebrospinal fluid (CSF) levels of Aß42 are validated biomarkers for early identification. Recently, alterations in levels of neuronal proteins, neuronal pentraxin receptor (NPTXR) and neurofilament light (NfL), in the CSF have emerged as promising AD biomarkers. However, their association with Aß deposition is not well understood. In this pilot study, we evaluate whether CSF NfL and NPTXR are associated with PET-Aß imaging and core CSF biomarkers (Aß42, T-tau, and P-tau). CSF samples were collected from a sub-cohort of participants from the Australian Imaging Biomarkers and Lifestyle study of aging (AIBL) and categorized as either PET-Aß positive (n = 15) or negative (n = 15). NPTXR was significantly lower in PET-Aß positive than negative individuals (p =  0.04), and correlated with Aß42 (rho = 0.69, p <  0.0001), T-tau (rho = 0.45, p =  0.01), and P-tau (rho = 0.51, p =  0.004). However, CSF NfL was not significantly different between PET-Aß positive and negative individuals and did not correlate with any of the core CSF biomarkers. Similar associations of NPTXR and the core CSF biomarkers persisted in the cognitively normal individuals. Together, NPTXR concentration in CSF may be more sensitive NfL to identify AD risk during the preclinical stage, warranting further investigation into its contribution to AD pathogenesis.

Understanding the effects of chronic benzodiazepine use in depression: a focus on neuropharmacology.

Benzodiazepines are frequently prescribed on an ongoing basis to individuals with depression, mainly to alleviate anxiety or insomnia, despite current guideline recommendations that continuous use should not exceed 4 weeks. Currently, there are no efficacy trials published beyond 8 weeks. Several antidepressant trials demonstrate that the concomitant use of a benzodiazepine is associated with poorer depressive outcomes and functional status; however, it is unclear why this is the case. Patients with depression receiving a benzodiazepine may reflect a more ill or high anxiety group, although even within anxiety disorders, the use of a benzodiazepine is associated with poorer outcomes. The neuroadaptive consequences of long-term benzodiazepine use may be a factor underlying these findings. Chronic benzodiazepine use results in decreased gamma-aminobutyric acid and monoaminergic function, as well as interference with neurogenesis, which are all purported to play a role in antidepressant efficacy. This review will discuss the oppositional neuropharmacological interactions between chronic benzodiazepine use and antidepressant mechanism of action, which could result in reduced antidepressant efficacy and function in depression.

Cerebrospinal fluid neuronal pentraxin receptor as a biomarker of long-term progression of Alzheimer's disease: a 24-month follow-up study.

Lower cerebrospinal fluid (CSF) levels of neuronal pentraxin receptor (NPTXR) are associated with Alzheimer's disease (AD), but few studies show longitudinal changes in CSF NPTXR. In the present study, CSF NPTXR was measured at 0, 12, and 24 months using an enzyme-linked immunosorbent assay. The study groups included 28 patients with mild cognitive impairment (MCI) (MCI-MCI), 27 MCI patients who progressed to AD (MCI-AD) during the study, and 28 AD patients (AD-AD). Baseline levels were assessed for 46 control individuals. AD patients had lower baseline CSF NPTXR than controls (p = 0.023). Linear mixed models estimated a 6.7% annualized decrease in CSF NPTXR in the AD-AD group, significantly different from MCI-MCI (p = 0.03) and MCI-AD groups (p = 0.048). CSF NPTXR did not correlate with CSF Aß42 and weakly correlated with CSF Aß40, T-tau, P-tau (all R2 < 0.22, p < 0.06). These trends suggest CSF NPTXR may be a candidate biomarker of AD progression but not sufficiently sensitive to resolve when patients convert from MCI to dementia.

Mass Spectrometry-Based Assay for Targeting Fifty-Two Proteins of Brain Origin in Cerebrospinal Fluid.

Cerebrospinal fluid (CSF) is a circulatory fluid of the central nervous system and it can reflect the biochemical changes occurring in the brain. Although CSF retrieval through lumbar puncture is invasive, it remains the most commonly used fluid in exploring brain pathology as it is less complex and contains a higher concentration of brain-derived proteins than plasma (Reiber, H. Clin. Chim. Acta 2001, 310, 173-186; Macron et al. J. Proteome Res. 2018, 17, 4315-4319). We hypothesize that proteins produced by the brain will have diagnostic significance for brain pathologies. Hence, we expanded the previously in-house-developed 31-protein panel with more proteins classified as brain-specific by the Human Protein Atlas (HPA). Using the HPA, we selected 76 protein coding genes and screened CSF using liquid chromatography-mass spectrometry (LC-MS) and narrowed the protein list to candidates identified endogenously in CSF. Next, we developed a parallel reaction monitoring (PRM) assay for the 21 new proteins and merged it with the 31-protein assay developed earlier. In the process, we evaluated different screening strategies and optimized MS collision energies and ion isolation windows to achieve the highest possible analyte signal resulting in the PRM assay with an average linear dynamic range of 4.3 × 103. We also assessed the extent of Asn (N)-Gln (Q) deamidation, N-terminal pyro-Glu (E) conversion, and Met (M) oxidation and found that deamidation can be misassigned without high mass accuracy and high-resolution settings. We also assessed how many of these proteins could be reliably measured in 10 individual patient CSF samples. Our approach allows us to measure the relative levels of 52 brain-derived proteins in CSF by a single LC-MS method. This new assay may have important applications in discovering CSF biomarkers for various neurological diseases.

Total Synthesis of Micrococcin P1 through Scalable Thiazole Forming Reactions of Cysteine Derivatives and Nitriles.

Thiopeptides are a class of natural products with untapped therapeutic potential. To expand the methods available for the scaled production of these antibiotics, we report the laboratory synthesis of micrococcin P1 showcasing thiazole forming reactions of cysteine derivatives and nitriles followed by oxidation. In most instances, this thiazole forming sequence does not require chromatography and proved scalable. Using this approach, 199 mg of micrococcin P1 was generated in a single synthetic sequence.

Liquid biopsy of cerebrospinal fluid identifies neuronal pentraxin receptor (NPTXR) as a biomarker of progression of Alzheimer's disease.

Background Alzheimer's disease (AD) is the most prevalent form of dementia. Currently, the most studied biomarkers of AD are cerebrospinal fluid (CSF) amyloid ß 1-42, total tau and phosphorylated tau. However, misdiagnosis can exceed 20%. Recently, we found that CSF amyloid ß precursor-like protein-1 (APLP1) and neuronal pentraxin receptor (NPTXR) are promising biomarkers of AD. The aim of the present study is to validate CSF APLP1 and NPTXR as biomarkers of AD severity. Methods APLP1 and NPTXR concentrations were measured in the CSF of patients with mild cognitive impairment (MCI) (n = 14), mild AD (n = 21), moderate AD (n = 43) and severe AD (n = 30) using enzyme-linked immunosorbent assays (ELISAs). Results CSF APLP1 and NPTXR were not associated with age or sex. CSF APLP1 was not different between any of the AD severity groups (p = 0.31). CSF NPTXR was significantly different between MCI and mild AD (p = 0.006), mild and moderate AD (p = 0.016), but not between moderate and severe AD (p = 0.36). NPTXR concentration progressively declined from MCI to mild, to moderate and to severe AD patients (p < 0.0001, Kruskal-Wallis test). CSF NPTXR positively correlated with the Mini-Mental Status Examination (MMSE) score (p < 0.001). Conclusions NPTXR concentration in CSF is a promising biomarker of AD severity and could inform treatment success and disease progression in clinical settings.

Putative autoantibodies in the cerebrospinal fluid of Alzheimer's disease patients.

Background: Recent efforts have described an immunogenic component to the pathobiology of Alzheimer's disease (AD) and Parkinson's disease (PD). However, current methods of studying fluid autoantibodies, such as enzyme-linked immunosorbent assays and immunohistochemistry, are hypothesis-driven and not optimal for discovering new autoantibody biomarkers by proteome-wide screening. Recently, we developed a general mass spectrometry-based approach to identify tissue-specific autoantibodies in serum, at a proteome-wide level. In this study, we adapted the method to explore novel autoantibody biomarkers in the cerebrospinal fluid (CSF) of AD and PD patients. Methods: CSF samples were obtained from 10 headache control individuals, 10 AD patients and 10 PD patients. Antibodies present in the CSF were isolated by immobilization to protein-G magnetic beads. These antibodies were incubated with a brain tissue extract, prepared from frontal cortex, pons, cerebellum and brain stem. Protein antigens captured by the protein-G magnetic bead-bound antibodies were digested with trypsin and analyzed using mass spectrometry. Autoantibody candidates were selected by 1) detection in one or less individuals of the control group and 2) identification in at least half of the patient groups. Results: There were 16 putative autoantibody biomarkers selected from the AD group. Glia-derived nexin autoantibody was detected in eight of ten AD patients and was absent in the control group. Other AD pathology-related targets were also identified, such as actin-interaction protein, quinone oxidoreductase, sushi repeat-containing protein, metalloproteinase inhibitor 2, IP3 receptor 1 and sarcoplasmic/endoplasmic reticulum calcium ATPase 2. An additional eleven autoantibody targets were also identified in the present experiment, although their link to AD is not clear. No autoantibodies in the PD group satisfied our selection criteria. Conclusion: Our unbiased mass spectrometry method was able to detect new putative CSF autoantibody biomarkers of AD. Further investigation into the involvement of humoral autoimmunity in AD and PD pathobiology may be warranted.

Neuronal pentraxin receptor-1 is a new cerebrospinal fluid biomarker of Alzheimer's disease progression.

Background: Alzheimer's disease (AD) is the most common type of dementia, with progressive onset of clinical symptoms. The main pathological hallmarks are brain deposits of extracellular amyloid beta plaques and intracellular neurofibrillary tangles (NFT). Cerebrospinal fluid reflects pathological changes in the brain; amyloid beta 1-42 is a marker of amyloid plaques, while total and phosphorylated tau are markers of NFT formation. Additional biomarkers associated with disease pathogenesis are needed, for better prognosis, more specific diagnosis, prediction of disease severity and progression and for improved patient classification in clinical trials. The aim of the present study was to evaluate brain-specific proteins as potential biomarkers of progression of AD. Methods: Overall, 30 candidate proteins were quantified in cerebrospinal fluid (CSF) samples from patients with mild cognitive impairment (MCI) and mild, moderate and severe AD dementia (n=101) using mass spectrometry-based selected reaction monitoring assays. ELISA was used for neuronal pentraxin receptor-1 (NPTXR) confirmation. Results: The best discrimination between MCI and more advanced AD stages (moderate and severe dementia) was observed for protein NPTXR (area under the curve, AUC=0.799). A statistically different abundance of this protein was observed between the two groups, with severe AD patients having progressively lower levels (p<0.05). ELISA confirmed lower levels in AD, in a separate cohort that included controls, MCI and AD patients. Conclusions: We conclude that NPTXR protein in CSF is a novel potential biomarker of AD progression and could have important utility in assessing treatment success in clinical trials.