Performance evaluation of three DNA sample tracking tools in a whole exome sequencing workflow

Next-generation sequencing applications are becoming the building blocks for clinical diagnostics. These experiments require numerous wet- and drylab steps, each one increasing the probability of a sample swap and/or contamination. Therefore, an identity confirmation at the end of the process is required to ensure the right data is used for each patient. We tested three commercially available, SNP bases sample tracking kits in a diagnostic workflow to evaluate their performance. The coverage uniformity, on-target specificity, sample identification and genotyping performance were determined to measure the reliability and estimate the cost-effectiveness of each kit. Our findings showed that the kit from Swift did not perform up to standards as only 20 out of the 46 samples were correctly genotyped. The kit provided by Nimagen identified all but one sample and the kit from pxlence unambiguously identified all samples, making it the most reliable and robust kit of this evaluation. The kit from Nimagen showed poor on-target rates, resulting in deeper sequencing needs and higher sequencing costs compared to the other two kits.

Automated Intracranial Hematoma Classification in Traumatic Brain Injury (TBI) Patients Using Meta-Heuristic Optimization Techniques

Traumatic Brain Injury (TBI) is a devastating and life-threatening medical condition that can result in long-term physical and mental disabilities and even death. Early and accurate detection of Intracranial Hemorrhage (ICH) in TBI is crucial for analysis and treatment, as the condition can deteriorate significantly with time. Hence, a rapid, reliable, and cost-effective computer-aided approach that can initially capture the hematoma features is highly relevant for real-time clinical diagnostics. In this study, the Gray Level Occurrence Matrix (GLCM), the Gray Level Run Length Matrix (GLRLM), and Hu moments are used to generate the texture features. The best set of discriminating features are obtained using various meta-heuristic algorithms, and these optimal features are subjected to different classifiers. The synthetic samples are generated using ADASYN to compensate for the data imbalance. The proposed CAD system attained 95.74% accuracy, 96.93% sensitivity, and 94.67% specificity using statistical and GLRLM features along with KNN classifier. Thus, the developed automated system can enhance the accuracy of hematoma detection, aid clinicians in the fast interpretation of CT images, and streamline triage workflow.

Substituent Effects Impact Surface Charge and Aggregation of Thiophenol-Labeled Gold Nanoparticles for SERS Biosensors

SERS immunoassay biosensors hold immense potential for clinical diagnostics due to their high sensitivity and growing interest in multi-marker panels. However, their development has been hindered by difficulties in designing compatible extrinsic Raman labels. Prior studies have largely focused on spectroscopic characteristics in selecting Raman reporter molecules (RRMs) for multiplexing since the presence of well-differentiated spectra is essential for simultaneous detection. However, these candidates often induce aggregation of the gold nanoparticles used as SERS nanotags despite their similarity to other effective RRMs. Thus, an improved understanding of factors affecting the aggregation of RRM-coated gold nanoparticles is needed. Substituent electronic effects on particle stability were investigated using various para-substituted thiophenols. The inductive and resonant effects of functional group modifications were strongly correlated with nanoparticle surface charge and hence their stability. Treatment with thiophenols diminished the negative surface charge of citrate-stabilized gold nanoparticles, but electron-withdrawing substituents limited the magnitude of this diminishment. It is proposed that this phenomenon arises by affecting the interplay of competing sulfur binding modes. This has wide-reaching implications for the design of biosensors using thiol-modified gold surfaces. A proof-of-concept multiplexed SERS biosensor was designed according to these findings using the two thiophenol compounds with the most electron-withdrawing substitutions: NO2 and CN.

Oral Hygiene Considerations in Adult Patients with Leukemia during a Cycle of Chemotherapy

The oral cavity is the place where the first symptoms of systemic diseases may appear. Leukemia is the malignancy of the hematopoietic system in which abnormal leukocytes are produced in the bone marrow and these cells spread to the peripheral blood. It is classified clinically on the basis of the duration and nature of the disease (acute or chronic), the type of cell involved (myeloid, lymphoid, or monocytes), and a rise in the number of abnormal cells in the blood. The study aimed to assess and compare the oral hygiene and periodontium status based on the indices in leukemic patients before and after one cycle of chemotherapy and whether the therapy had an impact on the change of these parameters. Dental indices used in clinical diagnostics were calculated: API (approximal plaque index), SBI (sulcus bleeding index), and CPI (community periodontal index). The research project was conducted at the Clinic of Hematooncology and Bone Marrow Transplantation of the Independent Public Clinical Hospital No. 1 in Lublin. The target population consisted of 102 adults with leukemia who were over 18 years of age. The time since diagnosis of the disease ranged from 1 to 10 years. The data were evaluated in the Statistica 12 software with the respective tests. In the majority of patients, both before and after chemotherapy, improper oral hygiene and severe generalized periodontitis were confirmed. The cycle of chemotherapy that was used did not correlate with the change of patients’ oral hygiene and periodontium state. Unsatisfactory oral hygiene and periodontal health has to be addressed with urgent dental treatment to avoid systemic complications in leukemic patients.

Complex approach to assessment of functional status of patients with chronic obstructive pulmonary disease

BACKGROUND: Considering the economic costs of managing patients with chronic obstructive pulmonary disease (COPD), as well as the high mortality and disability rate, it is necessary to improve the diagnosis of the disease, to look for new approaches to assessing the functional status of patients. AIM: Is to study the functional status of patients with COPD. MATERIALS AND METHODS: A comprehensive approach was applied to assess the functional status of patients: the data of the 6-minute walk test (6MWT), heart rate variability (HRV) was studied, ergoreflex was assessed according to HRV data. 64 patients with COPD and 41 male volunteers without respiratory diseases older than 40 years were examined. Statistical processing of the obtained results was carried out using the licensed package of applied statistical programs Excel 2010 and Statistica 10. RESULTS: The group of patients with COPD and the respondents of the control group were comparable in terms of body mass index, heart rate, respiratory rate, index of indicators of activity of regulatory systems (p > 0.05). As expected, during the 6MWT, differences were obtained between the studied groups in terms of the distance covered (p < 0.01). Similarly, the results of the study of the function of external respiration showed a statistically significant difference in all the studied parameters (p < 0.01). The results obtained confirmed the presence of impaired respiratory function in the group of patients with COPD. Analysis of HRV values, when conducting a test with external peripheral vascular occlusion, confirmed ergoreflex hyperactivity in patients with COPD. CONCLUSION: The integration of methods for routine clinical diagnostics of patients condition (spirometry, 6-minute walk test, assessment of autonomic status) and the introduction of the study of ergoreflex activity made it possible to expand the understanding of the functional state of patients with COPD and is of great interest for further research.

Bimetallic Nanomaterials-Based Electrochemical Biosensor Platforms for Clinical Applications

Diabetes is a foremost health issue that results in ~4 million deaths every year and ~170 million people suffering globally. Though there is no treatment for diabetes yet, the blood glucose level of diabetic patients should be checked closely to avoid further problems. Screening glucose in blood has become a vital requirement, and thus the fabrication of advanced and sensitive blood sugar detection methodologies for clinical analysis and individual care. Bimetallic nanoparticles (BMNPs) are nanosized structures that are of rising interest in many clinical applications. Although their fabrication shares characteristics with physicochemical methodologies for the synthesis of corresponding mono-metallic counterparts, they can display several interesting new properties and applications as a significance of the synergetic effect between their two components. These applications can be as diverse as clinical diagnostics, anti-bacterial/anti-cancer treatments or biological imaging analyses, and drug delivery. However, the exploitation of BMNPs in such fields has received a small amount of attention predominantly due to the vital lack of understanding and concerns mainly on the usage of other nanostructured materials, such as stability and bio-degradability over extended-time, ability to form clusters, chemical reactivity, and biocompatibility. In this review article, a close look at bimetallic nanomaterial based glucose biosensing approaches is discussed, concentrating on their clinical applications as detection of glucose in various real sample sources, showing substantial development of their features related to corresponding monometallic counterparts and other existing used nanomaterials for clinical applications.

Dual-Functional Peroxidase-Copper Phosphate Hybrid Nanoflowers for Sensitive Detection of Biological Thiols

An effective strategy to detect biological thiols (biothiols), including glutathione (GSH), cysteine (Cys), and homocysteine (Hcy), holds significant incentive since they play vital roles in many cellular processes and are closely related to many diseases. Here, we demonstrated that hybrid nanoflowers composed of crystalline copper phosphate and horseradish peroxidase (HRP) served as a functional unit exhibiting dual catalytic activities of biothiol oxidase and HRP, yielding a cascade reaction system for a sensitive one-pot fluorescent detection of biothiols. The nanoflowers were synthesized through the anisotropic growth of copper phosphate petals coordinated with the amine/amide moieties of HRP, by simply incubating HRP and copper(II) sulfate for three days at room temperature. Copper phosphates within the nanoflowers oxidized target biothiols to generate H2O2, which activated the entrapped HRP to oxidize the employed Amplex UltraRed substrate to produce intense fluorescence. Using this strategy, biothiols were selectively and sensitively detected by monitoring the respective fluorescence intensity. This nanoflower-based strategy was also successfully employed for reliable quantification of biothiols present in human serum, demonstrating its great potential for clinical diagnostics.

SARS-CoV-2 seroprevalence in Delhi, India: September October 2021: a population based seroepidemiological study

Background We conducted a repeat serosurvey in Delhi, India to estimate the seroprevalence of SARS-CoV-2 in the general population and compare the antibody prevalence in the vaccinated and non-vaccinated groups. Methods This cross sectional study was conducted from September 24 to October 14 2021 in 280 wards of Delhi among 27811 participants selected through a multistage sampling technique with housing settlement based stratification. The SARS-CoV-2 immunoglobulin (IgG) antibodies were screened with the VITROS (Ortho Clinical Diagnostics, Raritan, NJ, USA) assay (90% sensitivity, 100% specificity). Results A total of 24895 (89.5%) samples were seropositive. The crude seroprevalence was 87.99% (95% CI 89.1, 89.8), weighted for age and sex was 88% (95% CI 87.6, 88.4), and after adjustment of assay performance was estimated as 97.5% (95% CI 97.0, 98.0). The weighted seroprevalence in the 11 districts ranged from 84.9% (South-West district) to 90.8% (East district) Females in all the age-groups (<18, 18-49 and ≥50) had significantly higher odds of seropositivity (p<0.001). On adjusted analysis, the odds of seroconversion in the participants vaccinated with at-least one dose of either Covid-19 vaccine (Covishield/Covaxin) was more than four times compared to the unvaccinated (aRR 4.2 (3.8, 4.6)). The seroprevalence was also comparable among the complete and partially vaccinated subgroups for both vaccines (Table 4). Most (86.8%) seropositive individuals had a SARS-CoV-2 signal/cut-off ≥4.0 except in children Conclusions We observed IgG antibodies against SARS-CoV-2 in most of the general population of Delhi with likely higher antibody titers in the vaccinated compared to the unvaccinated groups.