Nevin Manimala

Bio Protoc. 2023 Sep 5;13(17):e4812. doi: 10.21769/BioProtoc.4812. eCollection 2023 Sep 5.

ABSTRACT

The centrosome governs many pan-cellular processes including cell division, migration, and cilium formation. However, very little is known about its cell type-specific protein composition and the sub-organellar domains where these protein interactions take place. Here, we outline a protocol for the spatial interrogation of the centrosome proteome in human cells, such as those differentiated from induced pluripotent stem cells (iPSCs), through co-immunoprecipitation of protein complexes around selected baits that are known to reside at different structural parts of the centrosome, followed by mass spectrometry. The protocol describes expansion and differentiation of human iPSCs to dorsal forebrain neural progenitors and cortical projection neurons, harvesting and lysis of cells for protein isolation, co-immunoprecipitation with antibodies against selected bait proteins, preparation for mass spectrometry, processing the mass spectrometry output files using MaxQuant software, and statistical analysis using Perseus software to identify the enriched proteins by each bait. Given the large number of cells needed for the isolation of centrosome proteins, this protocol can be scaled up or down by modifying the number of bait proteins and can also be carried out in batches. It can potentially be adapted for other cell types, organelles, and species as well.

PMID:37727868 | PMC:PMC10505934 | DOI:10.21769/BioProtoc.4812

Res Pract Thromb Haemost. 2023 Aug 9;7(6):102167. doi: 10.1016/j.rpth.2023.102167. eCollection 2023 Aug.

ABSTRACT

BACKGROUND: Acute kidney injury (AKI) in patients with COVID-19 is partly mediated by thromboinflammation. In noncritically ill patients with COVID-19, therapeutic-dose anticoagulation with heparin increased the probability of survival to hospital discharge with reduced use of cardiovascular or respiratory organ support.

OBJECTIVES: We investigated whether therapeutic-dose heparin reduces the incidence of AKI or death in noncritically ill patients hospitalized for COVID-19.

METHODS: We report a prespecified secondary analysis of the ACTIV4a and ATTACC open-label, multiplatform randomized trial of therapeutic-dose heparin vs usual-care pharmacologic thromboprophylaxis on the incidence of severe AKI (≥2-fold increase in serum creatinine or initiation of kidney replacement therapy (KDIGO stage 2 or 3) or all-cause mortality in noncritically ill patients hospitalized for COVID-19. Bayesian statistical models were adjusted for age, sex, D-dimer, enrollment period, country, site, and platform.

RESULTS: Among 1922 enrolled, 23 were excluded due to pre-existing end stage kidney disease and 205 were missing baseline or follow-up creatinine measurements. Severe AKI or death occurred in 4.4% participants assigned to therapeutic-dose heparin and 5.5% assigned to thromboprophylaxis (adjusted relative risk [aRR]: 0.72; 95% credible interval (CrI): 0.47, 1.10); the posterior probability of superiority for therapeutic-dose heparin (relative risk < 1.0) was 93.6%. Therapeutic-dose heparin was associated with a 97.7% probability of superiority to reduce the composite of stage 3 AKI or death (3.1% vs 4.6%; aRR: 0.64; 95% CrI: 0.40, 0.99) compared to thromboprophylaxis.

CONCLUSION: Therapeutic-dose heparin was associated with a high probability of superiority to reduce the incidence of in-hospital severe AKI or death in patients hospitalized for COVID-19.

PMID:37727846 | PMC:PMC10506136 | DOI:10.1016/j.rpth.2023.102167

Cureus. 2023 Sep 18;15(9):e45473. doi: 10.7759/cureus.45473. eCollection 2023 Sep.

ABSTRACT

Background The escalating overload and saturation of emergency services, primarily caused by non-urgent cases overwhelming the system, have spurred a critical necessity for innovative solutions that can effectively differentiate genuine emergencies from situations that could be managed through alternative means, such as using AI chatbots. This study aims to evaluate and compare the accuracy in differentiating between a medical emergency and a non-emergency of three of the most popular AI chatbots at the moment. Methods In this study, patient questions from the online forum r/AskDocs on Reddit were collected to determine whether their clinical cases were emergencies. A total of 176 questions were reviewed by the authors, with 75 deemed emergencies and 101 non-emergencies. These questions were then posed to AI chatbots, including ChatGPT, Google Bard, and Microsoft Bing AI, with their responses evaluated against each other and the authors’ responses. A criteria-based system categorized the AI chatbot answers as “yes,” “no,” or “cannot determine.” The performance of each AI chatbot was compared in both emergency and non-emergency cases, and statistical analysis was conducted to assess the significance of differences in their performance. Results In general, AI chatbots considered around 12-15% more cases to be an emergency than reviewers, while they considered a very low number of cases as non-emergency compared to reviewers (around 35% fewer cases). Google Bard detected the most true emergency cases (87%) and true non-emergency cases (36%). However, no real difference in performance between the three AI chatbots was found in detecting true emergencies (p-value = 0.35) and non-emergency cases (p-value = 0.16). Conclusions These AI systems require further refinement to identify emergency situations accurately, but they could potentially be an innovative tool for emergency care and improving patient outcomes. The integration of AI chatbots like ChatGPT, Google Bard, and Microsoft Bing Chat offers a promising avenue to mitigate ED strain and enhance emergency management.

PMID:37727841 | PMC:PMC10506659 | DOI:10.7759/cureus.45473

Turk Arch Otorhinolaryngol. 2023 Jun;61(2):83-90. doi: 10.4274/tao.2023.2022-11-9. Epub 2023 Sep 18.

ABSTRACT

OBJECTIVE: In hopes of contributing to the decision about the best surgical option in tonsillectomy, we performed this work to compare the effectiveness of the thermal welding system (TW) and monopolar electrocautery (ME) tonsillectomy in terms of postoperative pain, postoperative bleeding, and operation time in patients undergoing tonsillectomy, to determine which procedure is most expected to enhance the postoperative quality of life.

METHODS: Digital databases, including PubMed, Scopus, Cochrane, Web of Science, and Google Scholar, were systematically screened from inception up to October 2022. The included randomized controlled trials (RCTs) were evaluated for risk of bias via the Cochrane tool (version 2). The outcomes were summarized as risk ratio (RR) or mean difference/standardized mean difference (MD/SMD) with a 95% confidence interval (CI) in a random-effects model.

RESULTS: The three RCTs that met our criteria were included in the study. Overall, 151 patients had been enrolled in these three RCTs, in which 75 and 76 were allocated to the TW and ME groups, respectively. The postoperative pain levels were substantially reduced, favoring the TW arm over the ME arm [n=2 RCTs, SMD=-0.39, 95% CI (-0.67, -0.12), p=0.005]. Also, the analysis revealed a substantial variation between the TW and ME arms in terms of operation time [n=2 RCTs, MD=3.29 minutes, 95% CI (1.42, 5.17), p=0.0006]. However, the analysis revealed no substantial variation between the TW and ME arms in term of postoperative bleeding [n=3 RCTs, RR=0.40, 95% CI (0.06, 2.62), p=0.34].

CONCLUSION: This meta-analysis revealed that postoperative bleeding for tonsillectomy were similar between the ME and TW techniques. However, TW showed lower postoperative pain levels than ME statistically but without achieving significant clinical advantage.

PMID:37727819 | PMC:PMC10506519 | DOI:10.4274/tao.2023.2022-11-9

Turk Arch Otorhinolaryngol. 2023 Jun;61(2):58-65. doi: 10.4274/tao.2023.2023-3-5. Epub 2023 Sep 18.

ABSTRACT

OBJECTIVE: To analyze the demographic characteristics and the pathological results of neck dissection in primary parotid gland (PG) cancer patients, and to investigate the effects of histopathological parameters (perineural invasion, lymphovascular invasion, and extracapsular spread), neck metastasis, stage and lymph node ratio (LNR) on survival.

METHODS: Patients who underwent parotidectomy for malignant PG tumors between 2000 and 2019 years were retrospectively reviewed from the medical records. Thirty patients who were treated with parotidectomy and neck dissection were included in the study. Lymph node ratio was calculated as the ratio of the number of metastatic lymph nodes (LN) to the total number of excised LNs. Tumor stage, regional LN metastasis, LNR, perineural invasion, lymphovascular invasion, and extracapsular spread were reviewed for the effects on survival with the Kaplan-Meier analysis.

RESULTS: The study included 17 (57%) male and 13 (43%) female patients. Their mean age was 67.93±16.90 years (range, 50-85 years). The average number of the excised LN was 26.03±11.79 (range, 3-50). Mean LNR was 0.16±0.26. The Kaplan-Meier analysis showed that neck metastasis (p=0.001) and LNR (p<0.001) were associated with shorter survival times compared to perineural invasion (p=0.818), lymphovascular invasion (p=0.154), extracapsular spread (p=0.410) and stage (p=0.294). In multivariate COX regression analysis, only LNR had a statistically significant difference (p=0.027) compared to the other parameters.

CONCLUSION: The present study suggests that LNR and neck metastasis are associated with shorter survival times in PG cancers. Lymph node ratio can be used as a prognostic marker in these patients.

PMID:37727816 | PMC:PMC10506524 | DOI:10.4274/tao.2023.2023-3-5

Infect Dis Model. 2023 Sep 9;8(4):1079-1087. doi: 10.1016/j.idm.2023.09.002. eCollection 2023 Dec.

ABSTRACT

This work addresses the problem of supervised classification for highly correlated high-dimensional data describing non-independent observations to identify SNPs related to a phenotype. We use a general penalized linear mixed model with a single random effect that performs simultaneous SNP selection and population structure adjustment in high-dimensional prediction models. Specifically, the model simultaneously selects variables and estimates their effects, taking into account correlations between individuals. Single nucleotide polymorphisms (SNPs) are a type of genetic variation and each SNP represents a difference in a single DNA building block, namely a nucleotide. Previous research has shown that SNPs can be used to identify the correct source population of an individual and can act in isolation or simultaneously to impact a phenotype. In this regard, the study of the contribution of genetics in infectious disease phenotypes is of great importance. In this study, we used uncorrelated variables from the construction of blocks of correlated variables done in a previous work to describe the most related observations of the dataset. The model was trained with 90% of the observations and tested with the remaining 10%. The best model obtained with the generalized information criterion (GIC) identified the SNP named rs2493311 located on the first chromosome of the gene called PRDM16 ((PR/SET domain 16)) as the most decisive factor in malaria attacks.

PMID:37727806 | PMC:PMC10505671 | DOI:10.1016/j.idm.2023.09.002

Front Immunol. 2023 Sep 1;14:1215302. doi: 10.3389/fimmu.2023.1215302. eCollection 2023.

ABSTRACT

INTRODUCTION: In the absence of clinical efficacy data, vaccine protective effect can be extrapolated from animals to humans, using an immunological biomarker in humans that correlates with protection in animals, in a statistical approach called immunobridging. Such an immunobridging approach was previously used to infer the likely protective effect of the heterologous two-dose Ad26.ZEBOV, MVA-BN-Filo Ebola vaccine regimen. However, this immunobridging model does not provide information on how the persistence of the vaccine-induced immune response relates to durability of protection in humans.

METHODS AND RESULTS: In both humans and non-human primates, vaccine-induced circulating antibody levels appear to be very stable after an initial phase of contraction and are maintained for at least 3.8 years in humans (and at least 1.3 years in non-human primates). Immunological memory was also maintained over this period, as shown by the kinetics and magnitude of the anamnestic response following re-exposure to the Ebola virus glycoprotein antigen via booster vaccination with Ad26.ZEBOV in humans. In non-human primates, immunological memory was also formed as shown by an anamnestic response after high-dose, intramuscular injection with Ebola virus, but was not sufficient for protection against Ebola virus disease at later timepoints due to a decline in circulating antibodies and the fast kinetics of disease in the non-human primates model. Booster vaccination within three days of subsequent Ebola virus challenge in non-human primates resulted in protection from Ebola virus disease, i.e. before the anamnestic response was fully developed.

DISCUSSION: Humans infected with Ebola virus may benefit from the anamnestic response to prevent disease progression, as the incubation time is longer and progression of Ebola virus disease is slower as compared to non-human primates. Therefore, the persistence of vaccine-induced immune memory could be considered as a potential correlate of long-term protection against Ebola virus disease in humans, without the need for a booster.

PMID:37727795 | PMC:PMC10505757 | DOI:10.3389/fimmu.2023.1215302

Front Immunol. 2023 Sep 1;14:1231813. doi: 10.3389/fimmu.2023.1231813. eCollection 2023.

ABSTRACT

BACKGROUND: Vitamin D deficiency is a substantial public health problem. The present study evaluated the association between vitamin D concentration and hospitalization and mortality risk in patients with coronavirus disease 19 (COVID-19).

METHODS: This study used the COronavirus in LOwer Silesia (COLOS) dataset collected between February 2020 and June 2021. The medical records of 474 patients with confirmed severe acute respiratory syndrome 2 (SARS-CoV-2) infection, and whose vitamin D concentration was measured, were analyzed.

RESULTS: We determined a significant difference in vitamin D concentration between discharged patients and those who died during hospitalization (p = 0.0096). We also found an effect of vitamin D concentration on the risk of death in patients hospitalized due to COVID-19. As vitamin D concentration increased, the odds ratio (OR) for death slightly decreased (OR = 0.978; 95% confidence interval [CI] = 0.540-0.669). The vitamin D concentration cutoff point was 15.40 ng/ml. In addition, patients with COVID-19 and serum 25-hydroxyvitamin D (25(OH)D) concentrations < 30 ng/ml had a lower survival rate than those with serum 25(OH)D ≥ 30 ng/ml (log-rank test p = 0.0018). Moreover, a Cox regression model showed that patients with an estimated glomerular filtration rate (eGFR) ≥ 60 ml/min/1.73 m² and higher vitamin D concentrations had a 2.8% reduced risk of mortality (hazard ratio HR = 0.972; CI = 0.95-0,99; p = 0.0097).

CONCLUSIONS: The results indicate an association between 25(OH)D levels in patients with COVID-19 and the final course of hospitalization and risk of death.

PMID:37727794 | PMC:PMC10505823 | DOI:10.3389/fimmu.2023.1231813

J Pharm Policy Pract. 2023 Sep 19;16(1):102. doi: 10.1186/s40545-023-00606-4.

ABSTRACT

BACKGROUND: Chronic kidney disease (CKD) poses a significant public health challenge. CKD patients have compromised renal function, which not only alters the pharmacokinetics of drugs but also their pharmacodynamics. Adjusting drug doses for these patients is essential to achieve the intended clinical outcomes, prevent adverse drug events, and halt further progression of the disease. Pharmacists play a pivotal role in ensuring safe and appropriate therapy for CKD patients. However, there is a noticeable absence of national dosing guidelines for CKD in Pakistan, coupled with a scarcity of studies exploring the knowledge, attitude, and perception of renal dose adjustments in the country. This study aimed to evaluate the knowledge, attitudes, and perceptions of pharmacists in the Khyber Pakhtunkhwa province and Islamabad regarding renal dose adjustments.

METHODOLOGY: A cross-sectional study was conducted to gauge the knowledge, attitude, and perception of pharmacists working in various cities of Khyber Pakhtunkhwa and the capital city, Islamabad, from February to May 2023. The Renal Dosing Questionnaire-13 (RDQ-13) scale was employed for this purpose. The survey link was disseminated through emails, and the RDQ-13 scale was also completed in person by pharmacists from hospitals, clinics, community, and retail settings who interact with CKD patients. Univariate linear regression was employed, and factors with a p value < 0.25 were subjected to multivariate linear regression. For comparing knowledge, attitude, and perception scores of pharmacists, the independent t test and one-way ANOVA were utilized as appropriate. A p value < 0.05 was deemed statistically significant.

RESULTS: Of the 384 pharmacists approached, 270 completed the RDQ-13 scale, resulting in a response rate of 70.3%. The overall knowledge score regarding renal dose adjustment was 21.24 ± 2.18 (mean ± SD). Attitude scores averaged at 10.04 ± 1.81, and perception scores at 7.19 ± 2.15. Multivariate analysis indicated a positive correlation between the pharmacists’ perception scores and gender, with male pharmacists scoring higher than their female counterparts.

CONCLUSIONS: The study underscores the importance of instituting targeted training programs for pharmacists, ensuring access to dependable resources, and promoting research and results dissemination in the realm of renal pharmacotherapy to enhance public health outcomes.

PMID:37726861 | DOI:10.1186/s40545-023-00606-4

J Cheminform. 2023 Sep 19;15(1):84. doi: 10.1186/s13321-023-00755-3.

ABSTRACT

Many recently proposed structure-based virtual screening models appear to be able to accurately distinguish high affinity binders from non-binders. However, several recent studies have shown that they often do so by exploiting ligand-specific biases in the dataset, rather than identifying favourable intermolecular interactions in the input protein-ligand complex. In this work we propose a novel approach for assessing the extent to which machine learning-based virtual screening models are able to identify the functional groups responsible for binding. To sidestep the difficulty in establishing the ground truth importance of each atom of a large scale set of protein-ligand complexes, we propose a protocol for generating synthetic data. Each ligand in the dataset is surrounded by a randomly sampled point cloud of pharmacophores, and the label assigned to the synthetic protein-ligand complex is determined by a 3-dimensional deterministic binding rule. This allows us to precisely quantify the ground truth importance of each atom and compare it to the model generated attributions. Using our generated datasets, we demonstrate that a recently proposed deep learning-based virtual screening model, PointVS, identified the most important functional groups with 39% more efficiency than a fingerprint-based random forest, suggesting that it would generalise more effectively to new examples. In addition, we found that ligand-specific biases, such as those present in widely used virtual screening datasets, substantially impaired the ability of all ML models to identify the most important functional groups. We have made our synthetic data generation framework available to facilitate the benchmarking of new virtual screening models. Code is available at https://github.com/tomhadfield95/synthVS .

PMID:37726844 | DOI:10.1186/s13321-023-00755-3