A Novel Experimental Approach to Understand the Transport of Nanodrugs.

Nanoparticle-based drugs offer attractive advantages like targeted delivery to the diseased site and size and shape-controlled properties. Therefore, understanding the particulate flow of the nanodrugs is important for effective delivery, accurate prediction of required dosage, and developing efficient drug delivery platforms for nanodrugs. In this study, the transport of nanodrugs including flow velocity and deposition is investigated using three model metal oxide nanodrugs of different sizes including iron oxide, zinc oxide, and combined Cu-Zn-Fe oxide synthesized via a modified polyol approach. The hydrodynamic size, size, morphology, chemical composition, crystal phase, and surface functional groups of the water-soluble nanodrugs were characterized via dynamic light scattering, transmission electron microscopy, scanning electron microscopy-energy dispersive X-ray, X-ray diffraction, and fourier transform infrared spectroscopy, respectively. Two different biomimetic flow channels with customized surfaces are developed via 3D printing to experimentally monitor the velocity and deposition of the different nanodrugs. A diffusion dominated mechanism of flow is seen in size ranges 92 nm to 110 nm of the nanodrugs, from the experimental velocity and mass loss profiles. The flow velocity analysis also shows that the transport of nanodrugs is controlled by sedimentation processes in the larger size ranges of 110-302 nm. However, the combined overview from experimental mass loss and velocity trends indicates presence of both diffusive and sedimentation forces in the 110-302 nm size ranges. It is also discovered that the nanodrugs with higher positive surface charges are transported faster through the two test channels, which also leads to lower deposition of these nanodrugs on the walls of the flow channels. The results from this study will be valuable in realizing reliable and cost-effective in vitro experimental approaches that can support in vivo methods to predict the flow of new nanodrugs.

Clarke Error Grid Analysis for Performance Evaluation of Glucometers in a Tertiary Care Referral Hospital.

Glucometer is the most commonly used POCT device and guides monitoring of blood glucose level in both clinical settings and outside. Inaccurate glucometer readings resulting in erroneous therapeutic intervention has critical consequences on patient care. Regulatory guidelines for performance evaluation of glucometers are not available in many countries. A robust program implemented by the hospital is essential to ensure accuracy and precision of glucometers to produce optimal results. The objective of this study was to design a quality assurance program for the evaluation of glucometers in a high volume tertiary care referral hospital and evaluate the results from July'18 to July'19. Seventy three glucometers used across the hospital were subjected to Internal Quality Control checks and Proficiency Testing performed once a month and every 3 months respectively. The results were reviewed and plotted on a Bland Altman Graph. Clarke Error Grid Analysis was done to evaluate the clinical significance of inaccuracies in the measurement of blood glucose concentration as per ISO 15197: 2013. Eight devices were identified as unacceptable by ISO standards and replaced subsequently. 96.83% and 3.17% of the values were in Zone A and B of Clarke Error Grid Analysis. The study complied with the standard which requires that 99% of the values fall within zones A and B. The review of the program after one year and its ability to identify defective glucometers has validated the efficacy of the model. The method used may be suggested as a prototype for quality management of glucometers in a clinical setting.

Retrospective Analysis of Clinical Laboratory Parameters, Therapeutics and Outcome in Patients Infected with SARS-CoV2.

SARS-CoV-2 is the third coronavirus to have caused severe disease in humans in the last two decades, with approximately 5% of all patients and 20% of hospitalized patients experiencing severe symptoms, necessitating intensive care. The occurrence of Cytokine Storm has been implicated in the immune-pathogenesis of severe COVID-19. This is associated with cardiac injury, precipitated by cytokine mediated imbalance of coagulation and fibrinolysis, in the lung alveoli. In the absence of proven therapeutic agents, combinations of anti-viral drugs, immune-modulators and other adjunctive therapies have been tried in different clinical settings. A total of 128 confirmed cases of severe COVID-19 admitted to BLK-MAX Super Speciality Hospital between 16th of June to 31st of July, 2020 were included in this study. The correlation of age, gender, first value (on admission) of serum IL-6 and D-dimer, and impact of Tocilizumab and Remdesivir therapy on clinical outcome (28-day mortality), was evaluated in confirmed cases of severe COVID-19. The mortality rate was highest in the age group above 70 years. The incidence of death was significantly higher in males above 50 years, when age and gender were considered together. IL-6 and D-dimer levels >70 pg/mL and > 0.5µg FEU/mL respectively, were associated with poor outcome. 85.3% of patients treated with Remdesivir showed clinical improvement. When Tocilizumab and Remdisivir were administered together, 44.0% of patients survived while 56% expired. 79.7% of patients survived while 20.3% expired when neither Tocilizumab nor Remdesivir was administered.

Spatially interacting phosphorylation sites and mutations in cancer.

Advances in mass-spectrometry have generated increasingly large-scale proteomics datasets containing tens of thousands of phosphorylation sites (phosphosites) that require prioritization. We develop a bioinformatics tool called HotPho and systematically discover 3D co-clustering of phosphosites and cancer mutations on protein structures. HotPho identifies 474 such hybrid clusters containing 1255 co-clustering phosphosites, including RET p.S904/Y928, the conserved HRAS/KRAS p.Y96, and IDH1 p.Y139/IDH2 p.Y179 that are adjacent to recurrent mutations on protein structures not found by linear proximity approaches. Hybrid clusters, enriched in histone and kinase domains, frequently include expression-associated mutations experimentally shown as activating and conferring genetic dependency. Approximately 300 co-clustering phosphosites are verified in patient samples of 5 cancer types or previously implicated in cancer, including CTNNB1 p.S29/Y30, EGFR p.S720, MAPK1 p.S142, and PTPN12 p.S275. In summary, systematic 3D clustering analysis highlights nearly 3,000 likely functional mutations and over 1000 cancer phosphosites for downstream investigation and evaluation of potential clinical relevance.

Ultrasound assessment of fetal hearing response to vibroacoustic stimulation.

Background: Assessment of fetal responses to external stimuli could be a vital clue for understanding development of fetal neurophysiology, which is extremely challenging to explore. To study hearing development in growing human fetus, we assessed sonographic fetal movement responses to external auditory stimulus at increasing period of gestation.Method: In 123 normal pregnant women between 16 and 40 weeks' gestation, sonographic assessment of fetal movements (gross body movement, isolated limb movement, breathing movement and startle response) was carried out before and after administering vibroacoustic stimulation (VAS). Types and number of fetal movements during 5-min period each - immediately before and after application of VAS - were compared.Results: With increasing gestational age, spontaneous gross body movement decreased significantly between 16-28 and 29-40 weeks of gestation (93.3 versus 66.6%; p < .001). However, VAS significantly increased gross body movement at 29-40 weeks of gestation (66.6 versus 93.6%; p < .001). Incidence of isolated limb movement was inversely related to increasing gestational age. However, VAS was associated with significantly increase in isolated limb movement during 29-40 weeks' gestation (57.1 versus 80.9%; p = .007). VAS induced almost similar pattern of response for both fetal startle and breathing movements.Conclusions: Fetal movement responses to VAS are consistent after 28 weeks' gestation. These findings suggest fetal hearing develops at or before 28 weeks of intrauterine life.

Database of evidence for precision oncology portal.

Summary: A database of curated genomic variants with clinically supported drug therapies and other oncological annotations is described. The accompanying web portal provides a search engine with two modes: one that allows users to query gene, cancer type, variant type or position for druggable mutations, and another to search for and to visualize, on three-dimensional protein structures, putative druggable sites that cluster with known druggable mutations. Availability and implementation: http://dinglab.wustl.edu/depo.

Integrative omics analyses broaden treatment targets in human cancer.

BACKGROUND: Although large-scale, next-generation sequencing (NGS) studies of cancers hold promise for enabling precision oncology, challenges remain in integrating NGS with clinically validated biomarkers. METHODS: To overcome such challenges, we utilized the Database of Evidence for Precision Oncology (DEPO) to link druggability to genomic, transcriptomic, and proteomic biomarkers. Using a pan-cancer cohort of 6570 tumors, we identified tumors with potentially druggable biomarkers consisting of drug-associated mutations, mRNA expression outliers, and protein/phosphoprotein expression outliers identified by DEPO. RESULTS: Within the pan-cancer cohort of 6570 tumors, we found that 3% are druggable based on FDA-approved drug-mutation interactions in specific cancer types. However, mRNA/phosphoprotein/protein expression outliers and drug repurposing across cancer types suggest potential druggability in up to 16% of tumors. The percentage of potential drug-associated tumors can increase to 48% if we consider preclinical evidence. Further, our analyses showed co-occurring potentially druggable multi-omics alterations in 32% of tumors, indicating a role for individualized combinational therapy, with evidence supporting mTOR/PI3K/ESR1 co-inhibition and BRAF/AKT co-inhibition in 1.6 and 0.8% of tumors, respectively. We experimentally validated a subset of putative druggable mutations in BRAF identified by a protein structure-based computational tool. Finally, analysis of a large-scale drug screening dataset lent further evidence supporting repurposing of drugs across cancer types and the use of expression outliers for inferring druggability. CONCLUSIONS: Our results suggest that an integrated analysis platform can nominate multi-omics alterations as biomarkers of druggability and aid ongoing efforts to bring precision oncology to patients.

Comprehensive Characterization of Cancer Driver Genes and Mutations.

Identifying molecular cancer drivers is critical for precision oncology. Multiple advanced algorithms to identify drivers now exist, but systematic attempts to combine and optimize them on large datasets are few. We report a PanCancer and PanSoftware analysis spanning 9,423 tumor exomes (comprising all 33 of The Cancer Genome Atlas projects) and using 26 computational tools to catalog driver genes and mutations. We identify 299 driver genes with implications regarding their anatomical sites and cancer/cell types. Sequence- and structure-based analyses identified >3,400 putative missense driver mutations supported by multiple lines of evidence. Experimental validation confirmed 60%-85% of predicted mutations as likely drivers. We found that >300 MSI tumors are associated with high PD-1/PD-L1, and 57% of tumors analyzed harbor putative clinically actionable events. Our study represents the most comprehensive discovery of cancer genes and mutations to date and will serve as a blueprint for future biological and clinical endeavors.

Systematic Analysis of Splice-Site-Creating Mutations in Cancer.

For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creating mutations (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated mutations having clear evidence of creating alternative splice junctions. TP53 and GATA3 have 26 and 18 SCMs, respectively, and ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including PARP1, BRCA1, and BAP1, were experimentally validated for splice-site-creating function. Notably, we found that neoantigens induced by SCMs are likely several folds more immunogenic compared to missense mutations, exemplified by the recurrent GATA3 SCM. Further, high expression of PD-1 and PD-L1 was observed in tumors with SCMs, suggesting candidates for immune blockade therapy. Our work highlights the importance of integrating DNA and RNA data for understanding the functional and the clinical implications of mutations in human diseases.

Systematic Functional Annotation of Somatic Mutations in Cancer.

The functional impact of the vast majority of cancer somatic mutations remains unknown, representing a critical knowledge gap for implementing precision oncology. Here, we report the development of a moderate-throughput functional genomic platform consisting of efficient mutant generation, sensitive viability assays using two growth factor-dependent cell models, and functional proteomic profiling of signaling effects for select aberrations. We apply the platform to annotate >1,000 genomic aberrations, including gene amplifications, point mutations, indels, and gene fusions, potentially doubling the number of driver mutations characterized in clinically actionable genes. Further, the platform is sufficiently sensitive to identify weak drivers. Our data are accessible through a user-friendly, public data portal. Our study will facilitate biomarker discovery, prediction algorithm improvement, and drug development.

Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.

The advent of next-generation sequencing has dramatically decreased the cost for whole-genome sequencing and increased the viability for its application in research and clinical care. The Personal Genome Project (PGP) provides unrestricted access to genomes of individuals and their associated phenotypes. This resource enabled the Critical Assessment of Genome Interpretation (CAGI) to create a community challenge to assess the bioinformatics community's ability to predict traits from whole genomes. In the CAGI PGP challenge, researchers were asked to predict whether an individual had a particular trait or profile based on their whole genome. Several approaches were used to assess submissions, including ROC AUC (area under receiver operating characteristic curve), probability rankings, the number of correct predictions, and statistical significance simulations. Overall, we found that prediction of individual traits is difficult, relying on a strong knowledge of trait frequency within the general population, whereas matching genomes to trait profiles relies heavily upon a small number of common traits including ancestry, blood type, and eye color. When a rare genetic disorder is present, profiles can be matched when one or more pathogenic variants are identified. Prediction accuracy has improved substantially over the last 6 years due to improved methodology and a better understanding of features.

Anatomical variation of posterior slope of tibial plateau in adult Eastern Indian population.

BACKGROUND: Upper surface of the proximal tibial end, tibial plateau, has a slope directed posteroinferiorly relative to the long axis of the middle of the shaft. It has important consideration in surgeries such as knee arthroplasty, high tibial osteotomy, and medical imaging of the knee joint. The aim of the present study was to estimate the tibial plateau angle (TPA) by plain radiograph in the adult Eastern Indian population as during literature review, we were unable to find any study, except one (without specific reference axis), on this variable among the Indian population. MATERIALS AND METHODS: A sample was taken from adult patients attending the outpatient department of orthopedics of the institute with minor knee problems. Measurement of the TPA was done in the true lateral radiographs of the knee joints of the selected subjects by a standardized method. RESULTS: TPA varied widely from 6° to 24°, with the mean ± standard deviation value 13.6° ±3.5°. Student's unpaired t-test revealed no significant difference of TPA between left and right knees, both in male (P = 0.748) and female (P = 0.917) separately and in the entire study population irrespective of gender (P = 0.768). Comparison of TPA between male (13.3° ± 3.3°) and female (13.9° ± 3.4°) by Student's unpaired t-test showed no sexual dimorphism (P = 0.248). There were poor correlations of TPA with age and body mass index. CONCLUSION: The present study described the variations of the TPA in the adult Eastern Indian population (range 6°-24°, mean ± SD 13.6° ± 3.5°, no laterality, no sexual dimorphism, poor correlation with age and BMI). Knowledge of this study could be used in different orthopedic surgeries and imaging technique in or around the knee joint.

Protein-structure-guided discovery of functional mutations across 19 cancer types.

Local concentrations of mutations are well known in human cancers. However, their three-dimensional spatial relationships in the encoded protein have yet to be systematically explored. We developed a computational tool, HotSpot3D, to identify such spatial hotspots (clusters) and to interpret the potential function of variants within them. We applied HotSpot3D to >4,400 TCGA tumors across 19 cancer types, discovering >6,000 intra- and intermolecular clusters, some of which showed tumor and/or tissue specificity. In addition, we identified 369 rare mutations in genes including TP53, PTEN, VHL, EGFR, and FBXW7 and 99 medium-recurrence mutations in genes such as RUNX1, MTOR, CA3, PI3, and PTPN11, all mapping within clusters having potential functional implications. As a proof of concept, we validated our predictions in EGFR using high-throughput phosphorylation data and cell-line-based experimental evaluation. Finally, mutation-drug cluster and network analysis predicted over 800 promising candidates for druggable mutations, raising new possibilities for designing personalized treatments for patients carrying specific mutations.

Pilot study demonstrating effectiveness of targeted education to improve informed consent understanding in AIDS clinical trials.

Assessing and improving informed consent understanding is equally important as obtaining consent from participants in clinical trial research, but developing interventions to target gaps in participants' informed consent understanding remains a challenge. We used a randomized controlled study design to pilot test an educational intervention to improve actual informed consent understanding of new enrollees in the Adult AIDS Clinical Trial Group (AACTG). Questionnaires were administered to 24 enrollees to assess their baseline understanding on eight elements of informed consent associated with AIDS clinical trials. Enrollees who scored 18/21(85%) or less were randomly assigned to in-person, targeted education (intervention), or delayed education (control). Two follow-up assessments were administered. Repeated measures ANOVA was performed to determine intervention effectiveness in improving actual informed consent understanding over time. Actual understanding improved at the immediate post-intervention time point with a significant score difference of 2.5 when comparing the intervention and delayed groups. In addition, there was a significant score difference of 3.2 when comparing baseline to three-month follow-up for the two groups, suggesting a statistically significant intervention effect to improve actual understanding of the basic elements of informed consent. The findings demonstrated that one-time targeted education can improve actual informed consent understanding one week after the intervention, but retention of these concepts may require periodic monitoring to ensure comprehension throughout the course of a clinical trial.

Socio-demographic and AIDS-related factors associated with tuberculosis stigma in southern Thailand: a quantitative, cross-sectional study of stigma among patients with TB and healthy community members.

BACKGROUND: Tuberculosis (TB) remains one of the most important infectious diseases worldwide. A comprehensive approach towards disease control that addresses social factors including stigma is now advocated. Patients with TB report fears of isolation and rejection that may lead to delays in seeking care and could affect treatment adherence. Qualitative studies have identified socio-demographic, TB knowledge, and clinical determinants of TB stigma, but only one prior study has quantified these associations using formally developed and validated stigma scales. The purpose of this study was to measure TB stigma and identify factors associated with TB stigma among patients and healthy community members. METHODS: A cross-sectional study was performed in southern Thailand among two different groups of participants: 480 patients with TB and 300 healthy community members. Data were collected on socio-demographic characteristics, TB knowledge, and clinical factors. Scales measuring perceived TB stigma, experienced/felt TB stigma, and perceived AIDS stigma were administered to patients with TB. Community members responded to a community TB stigma and community AIDS stigma scale, which contained the same items as the perceived stigma scales given to patients. Stigma scores could range from zero to 30, 33, or 36 depending on the scale. Three separate multivariable linear regressions were performed among patients with TB (perceived and experience/felt stigma) and community members (community stigma) to determine which factors were associated with higher mean TB stigma scores. RESULTS: Only low level of education, belief that TB increases the chance of getting AIDS, and AIDS stigma were associated with higher TB stigma scores in all three analyses. Co-infection with HIV was associated with higher TB stigma among patients. All differences in mean stigma scores between index and referent levels of each factor were less than two points, except for incorrectly believing that TB increases the chance of getting AIDS (mean difference of 2.16; 95% CI: 1.38, 2.94) and knowing someone who died from TB (mean difference of 2.59; 95% CI: 0.96, 4.22). CONCLUSION: These results suggest that approaches addressing the dual TB/HIV epidemic may be needed to combat TB stigma and that simply correcting misconceptions about TB may have limited effects.

Factors associated with utilization of a free HIV VCT clinic by female sex workers in Jinan City, Northern China.

Based on our previous qualitative exploration, this research presents the second phase in our study of factors associated with utilization of a free HIV VCT clinic in Jinan City, Northern China, by female sex workers (FSWs). A total of 970 FSWs from entertainment venues were interviewed and prospectively followed to determine who ultimately sought and received VCT at the clinic, compared to those who did not. Simple and multiple logistic regressions were performed on factors drawn from the Ecological Perspective, hypothesized to be associated with utilization of testing at the VCT clinic. Despite 69% of FSWs expressing willingness to attend the VCT clinic, only 11% were actually tested. The multiple logistic regression model that provided best goodness of fit included the covariates of willingness to attend the VCT clinic (Adjusted OR 3.13, 95% CI: 1.62-6.59), low perceived HIV infection risk (Adjusted OR 0.64, 95% CI: 0.35-1.11), low fear of FSWs status disclosure in the clinic (Adjusted OR 0.55, 95% CI: 0.31-0.94) and influence of acquaintances (Adjusted OR 0.52, 95% CI: 0.29-0.89) and peers (Adjusted OR 2.45, 95% CI: 1.40-4.50). This is the first study in China to follow FSWs longitudinally to measure factors related to VCT utilization. The low utilization of VCT services by participants in our study is similar to prior reports throughout China. FSWs' access to VCT service is associated with intrapersonal, institutional, and particularly, interpersonal factors. Based on these findings, we recommend emphasis on confidentiality of services, VCT education for influential peers, and introduction of HIV rapid testing on site.

HIV interventions to reduce HIV/AIDS stigma: a systematic review.

We reviewed the literature to determine the effectiveness of HIV-related interventions in reducing HIV/AIDS stigma. Studies selected had randomized controlled trial (RCT), pretest-posttest with a non-randomized control group, or pretest-posttest one group study designs in which HIV-related interventions were being evaluated, and in which HIV/AIDS stigma was one of the outcomes being measured. A checklist was used to extract data from accepted studies, assess their internal validity, and overall quality. Data were extracted from 19 studies, and 14 of these studies demonstrated effectiveness in reducing HIV/AIDS stigma. Only 2 of these 14 effective studies were considered good studies, based on quality, the extent to which the intervention focused on reducing HIV/AIDS stigma, and the statistics reported to demonstrate effectiveness. Future studies to reduce HIV/AIDS stigma could improve by designing interventions that pay greater attention to internal validity, use validated HIV/AIDS stigma instruments, and achieve both statistical and public health significance.

Silent endurance and profound loneliness: socioemotional suffering in African Americans living with HIV in the rural south.

We explored how community responses to HIV contribute to distress in African Americans living with HIV in the rural South of the United States. We listened to the voices of community members through focus groups and African Americans with HIV through interviews. Community avoidance of HIV, negative views of HIV, and discriminatory behavior powerfully affected the distress of people living with HIV (PLWH). Ongoing distress, coupled with limited support, led to a life in which many PLWH endured their pain in silence and experienced profound loneliness. We conceptualized their experiences as socioemotional suffering--the hidden emotional burden and inner distress of not only living with HIV, a complex serious illness, but also with the societal attitudes and behaviors that are imposed on the illness and on PLWH. To improve the quality of life and health of PLWH, we cannot focus solely on the individual, but must also focus on the local community and society as a whole.