Implications of use of different intraoperative ultrasound modalities during glioma surgery - A comparative study of factors affecting outcomes

BACKGROUND

The main goal of glioma surgery is to remove the maximum amount of tumor without worsening the patient's neurological condition. Intraoperative ultrasound (US) imaging technologies (2D and 3D) are available to assist surgeons, providing real-time updates. Considering additional time, personnel, and cost, we investigate if comparable outcomes can be achieved using basic (2D) and advanced (3D) technology.

OBJECTIVE

We propose predictive models for (i) glioma tumor resectability (ii) surgical outcome, and (iii) a model to predict the outcome of surgery aided with a particular ultrasound and compare outcomes between 2D and 3D US.

METHODOLOGY

We used real-world surgery data from a tertiary cancer centre. Three groups of cases were analyzed (2D US used, 3D US used, and no US used during resection). The data analysis uses hypothesis testing, bootstrap sampling, and logistic regression.

RESULTS

The preoperatively anticipated extent of tumor removal correlated with the postoperative MRI measurement of tumor removal for US-supported surgery (p=0.01) but not for no US-supported surgeries (p = 0.13). A combination of delineation, eloquence, and the multifocal/multicentric nature of the tumor effectively predicted resectability. The eventual outcome of surgery (actual extent of resection achieved) can be predicted by prior treatment status, delineation, eloquence, and satellite nodules. Based on our prediction model (training set of 350 cases and test of 40 cases of US-guided surgeries), we identify some cases where 3D US seems to offer superior EORs.

CONCLUSION

The resectability of glioma tumors is crucial in determining surgical objectives, and the type of ultrasound used as support impacts tumor removal. The findings in this study aid informed decision-making and optimize imaging technology usage, providing a decision flow for selecting ultrasound based on tumor characteristics.

Novel educational training of para medical professionals in cervical cancer screening

Background

Cervical cancer is a public health problem in India due to weak national screening policy compounded by lack of resources including scarcity of trained personnel to carry out community-based screening program. Para medical professionals (PMPs) are closely related to women in local communities. Hence, training PMPs by incorporating novel technology and reduced time duration to achieve adequate competence in screening is an area underutilized and needs to be explored.

Materials and methods

A pilot cross sectional analytical study was conducted at a tertiary referral cancer center using a shorter version of educational intervention of 2 weeks duration (EI2W) involving PMPs. Pre- and post-training assessment of knowledge, attitude, and practice (KAP) was done using questionnaires consisting of 5 domains viz. awareness of cervical cancer, awareness of cervical pre-cancer, practical screening methodology (practice oriented), data management and aspects of human papilloma virus (HPV). Wilcoxon signed-rank test was used for comparison and the degree of change was measured using analysis of covariance (ANCOVA). A p value of <0.05 was considered significant.

Results

118 PMPs were included. There was a significant improvement in scores of all domains (except cervical pre-cancer domain), following introduction of EI2W. Knowledge scores, post EI2W was better in Auxiliary Nurse Midwives (ANMs) than other participants. Awareness regarding cervical cancer was higher with more years of experience. The KAP analysis showed excellent interrater reliability in the practice 0.726 (0.649-0.792) followed by knowledge domain 0.711 (0.626-0.783).

Conclusion

EI2W was effective in significantly improving the competence of PMPs, thus reducing human resource constraints in cervical cancer prevention and elimination.

Choice of intraoperative ultrasound adjuncts for brain tumor surgery

Background

Gliomas are among the most typical brain tumors tackled by neurosurgeons. During navigation for surgery of glioma brain tumors, preoperatively acquired static images may not be accurate due to shifts. Surgeons use intraoperative imaging technologies (2-Dimensional and navigated 3-Dimensional ultrasound) to assess and guide resections. This paper aims to precisely capture the importance of preoperative parameters to decide which type of ultrasound to be used for a particular surgery.

Methods

This paper proposes two bagging algorithms considering base classifier logistic regression and random forest. These algorithms are trained on different subsets of the original data set. The goodness of fit of Logistic regression-based bagging algorithms is established using hypothesis testing. Furthermore, the performance measures for random-forest-based bagging algorithms used are AUC under ROC and AUC under the precision-recall curve. We also present a composite model without compromising the explainability of the models.

Results

These models were trained on the data of 350 patients who have undergone brain surgery from 2015 to 2020. The hypothesis test shows that a single parameter is sufficient instead of all three dimensions related to the tumor ($$p < 0.05$$ p < 0.05 ). We observed that the choice of intraoperative ultrasound depends on the surgeon making a choice, and years of experience of the surgeon could be a surrogate for this dependence.

Conclusion

This study suggests that neurosurgeons may not need to focus on a large set of preoperative parameters in order to decide on ultrasound. Moreover, it personalizes the use of a particular ultrasound option in surgery. This approach could potentially lead to better resource management and help healthcare institutions improve their decisions to make the surgery more effective.

Profiling of grazed cultures of the chlorophyte alga Dunaliella tertiolecta using an untargeted LC-MS approach

Extracellular signals are reported to mediate chemical cross-talk among pelagic microbes, including microalgal prey and predators. Water-soluble mediator compounds play a crucial role in extracellular communication which is vital for prey recognition, attraction, capture, and predator deterrence. A range of exo-metabolites including oxylipins and vitamins are released by prey in response to grazing stress. The temporal dynamics of such exo-metabolites largely remains unknown, especially in large-scale cultivation of microalgae such as closed or open ponds. In open ponds, infestation of predators is almost inevitable but highly undesirable due to the imminent threat of culture collapse. The early production of exo-metabolites emitted by microalgal prey in response to predator attack could be leveraged as diagnostic markers of possible culture collapse. This study uses an untargeted approach for temporal profiling of Dunaliella tertiolecta-specific exo-metabolites under grazing pressure from Oxyrrhis marina. We report 24 putatively identified metabolites, belonging to various classes such as short peptides, lipids, indole-derivatives, and free amino acids, as potential markers of grazing-mediated stress. In addition, this study outlines a clear methodology for screening of exo-metabolites in marine algal samples, the analysis of which is frequently hindered by high salt concentrations. In future, a chemistry-based targeted detection of these metabolites could enable a quick and on-site screening of predators in microalgal cultures.

A unified citywide dashboard for allocation and scheduling dialysis for COVID-19 patients on maintenance hemodialysis

Introduction:

The coronavirus disease 2019 (COVID-19) pandemic has caused significant global disruption, especially for chronic care like hemodialysis treatments. Approximately 10,000 end-stage kidney disease (ESKD) patients are receiving maintenance hemodialysis (MHD) at 174 dialysis centers in Greater Mumbai. Because of the fear of transmission of infection and inability to isolate patients in dialysis centers, chronic hemodialysis care was disrupted for COVID-19-infected patients. Hence, we embarked on a citywide initiative to ensure uninterrupted dialysis for these patients.

Materials and Methods:

The Municipal Corporation of Greater Mumbai (MCGM) designated 23 hemodialysis facilities as COVID-positive centers, two as COVID-suspect centers, and the rest continued as COVID-negative centers to avoid transmission of infection and continuation of chronic hemodialysis treatment. Nephrologists and engineers of the city developed a web-based-portal so that information about the availability of dialysis slots for COVID-infected patients was easily available in real time to all those providing care to chronic hemodialysis patients.

Results:

The portal became operational on May 20, 2020, and as of December 31, 2020, has enrolled 1,418 COVID-positive ESKD patients. This initiative has helped 97% of enrolled COVID-infected ESKD patients to secure a dialysis slot within 48 hours. The portal also tracked outcomes and as of December 31, 2020, 370 (27%) patients died, 960 patients recovered, and 88 patients still had an active infection.

Conclusions:

The portal aided the timely and smooth transfer of COVID-19-positive ESKD patients to designated facilities, thus averting mortality arising from delayed or denied dialysis. Additionally, the portal also documented the natural history of the COVID-19 pandemic in the city and provided information on the overall incidence and outcomes. This aided the city administration in the projected resource needs to handle the pandemic.

Data-Independent-Acquisition-Based Proteomic Approach towards Understanding the Acclimation Strategy of Oleaginous Microalga Microchloropsis gaditana CCMP526 in Hypersaline Conditions

Salinity is one of the significant factors that affect growth and cellular metabolism, including photosynthesis and lipid accumulation, in microalgae and higher plants. Microchloropsis gaditana CCMP526 can acclimatize to different salinity levels by accumulating compatible solutes, carbohydrates, and lipids as energy storage molecules. We used proteomics to understand the molecular basis for acclimation of M. gaditana to increased salinity levels [55 and 100 PSU (practical salinity unit)]. Correspondence analysis was used for the identification of salinity-responsive proteins (SRPs). The highest number of salinity-induced proteins was observed in 100 PSU. Gene ontology enrichment analysis revealed a separate path of acclimation for cells exposed to 55 and 100 PSU. Osmolyte and lipid biosynthesis were upregulated in hypersaline conditions. Concomitantly, lipid oxidation pathways were also upregulated in hypersaline conditions, providing acetyl-CoA for energy metabolism through the tricarboxylic acid cycle. Carbon fixation and photosynthesis were tightly regulated, while chlorophyll biosynthesis was affected in hypersaline conditions. Importantly, temporal proteome analysis of salinity-induced M. gaditana revealed vital SRPs which could be used for engineering salinity resilient microalgal strains for improved productivity in hypersaline culture conditions.

Temporal acclimation of Microchloropsis gaditana CCMP526 in response to hypersalinity

Evaporation from culture ponds and raceways can subject algae to hypersalinity stress, and this is exacerbated by global warming. We investigated the effect of salinity on a marine microalga, Microchloropsis gaditana, which is of industrial significance because of its high lipid-accumulating capability. Both short-term (hours) and medium-term (days) effects of salinity were studied across various salinities (37.5, 55, 70 and 100 PSU). Salinity above 55 PSU suppressed cell growth and specific growth rate was significantly reduced at 100 PSU. Photosynthesis (F_v/F_m, rETR_max and I_k) was severely affected at high salinity conditions. Total carbohydrate per cell increased ∼1.7-fold after 24 h, which is consistent with previous findings that salinity induces osmolyte production to counter osmotic shock. In addition, accumulation of lipid increased by ∼4.6-fold in response to salinity. Our findings indicate a possible mechanism of acclimation to salinity, opening up new frontiers for osmolytes in pharmacological and cosmetics applications.

Epidemic of Chemical Peritonitis in Patients on Continuous Ambulatory Peritoneal Dialysis: A Report from Western India

While non-infectious etiologies like chemical irritants are rare causes of epidemics of peritonitis, this possibility should be considered when one encounters an unusual clustering of peritonitis cases. We describe here an epidemic of chemical peritonitis at our center.

Toward more transparent and reproducible omics studies through a common metadata checklist and data publications

Biological processes are fundamentally driven by complex interactions between biomolecules. Integrated high-throughput omics studies enable multifaceted views of cells, organisms, or their communities. With the advent of new post-genomics technologies, omics studies are becoming increasingly prevalent; yet the full impact of these studies can only be realized through data harmonization, sharing, meta-analysis, and integrated research. These essential steps require consistent generation, capture, and distribution of metadata. To ensure transparency, facilitate data harmonization, and maximize reproducibility and usability of life sciences studies, we propose a simple common omics metadata checklist. The proposed checklist is built on the rich ontologies and standards already in use by the life sciences community. The checklist will serve as a common denominator to guide experimental design, capture important parameters, and be used as a standard format for stand-alone data publications. The omics metadata checklist and data publications will create efficient linkages between omics data and knowledge-based life sciences innovation and, importantly, allow for appropriate attribution to data generators and infrastructure science builders in the post-genomics era. We ask that the life sciences community test the proposed omics metadata checklist and data publications and provide feedback for their use and improvement.

Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications

Biological processes are fundamentally driven by complex interactions between biomolecules. Integrated high-throughput omics studies enable multifaceted views of cells, organisms, or their communities. With the advent of new post-genomics technologies, omics studies are becoming increasingly prevalent; yet the full impact of these studies can only be realized through data harmonization, sharing, meta-analysis, and integrated research. These essential steps require consistent generation, capture, and distribution of metadata. To ensure transparency, facilitate data harmonization, and maximize reproducibility and usability of life sciences studies, we propose a simple common omics metadata checklist. The proposed checklist is built on the rich ontologies and standards already in use by the life sciences community. The checklist will serve as a common denominator to guide experimental design, capture important parameters, and be used as a standard format for stand-alone data publications. The omics metadata checklist and data publications will create efficient linkages between omics data and knowledge-based life sciences innovation and, importantly, allow for appropriate attribution to data generators and infrastructure science builders in the post-genomics era. We ask that the life sciences community test the proposed omics metadata checklist and data publications and provide feedback for their use and improvement.

Distinctive microRNA signature of medulloblastomas associated with the WNT signaling pathway

AIM

Medulloblastoma is a malignant brain tumor that occurs predominantly in children. Current risk stratification based on clinical parameters is inadequate for accurate prognostication. MicroRNA expression is known to be deregulated in various cancers and has been found to be useful in predicting tumor behavior. In order to get a better understanding of medulloblastoma biology, miRNA profiling of medulloblastomas was carried out in parallel with expression profiling of protein-coding genes.

MATERIALS AND METHODS

miRNA profiling of medulloblastomas was carried out using Taqman Low Density Array v 1.0 having 365 human microRNAs. In parallel, genome-wide expression profiling of protein-coding genes was carried out using Affymetrix gene 1.0 ST arrays.

RESULTS

Both the profiling studies identified four molecular subtypes of medulloblastomas. Expression levels of select protein-coding genes and miRNAs could classify an independent set of medulloblastomas. Twelve of 31 medulloblastomas were found to overexpress genes belonging to the canonical WNT signaling pathway and carry a mutation in CTNNB1 gene. A number of miRNAs like miR-193a, miR-224/miR-452 cluster, miR-182/miR-183/miR-96 cluster, and miR-148a having potential tumor/metastasis suppressive activity were found to be overexpressed in the WNT signaling associated medulloblastomas. Exogenous expression of miR-193a and miR-224, two miRNAs that have the highest WNT pathway specific upregulation, was found to inhibit proliferation, increase radiation sensitivity and reduce anchorage-independent growth of medulloblastoma cells.

CONCLUSION

Expression level of tumor/metastasis suppressive miRNAs in the WNT signaling associated medulloblastomas is likely to determine their response to treatment, and thus, these miRNAs would be important biomarkers for risk stratification within the WNT signaling associated medulloblastomas.

Protein structure prediction aided by geometrical and probabilistic constraints

Database-assisted ab initio protein structure prediction methods have exhibited considerable promise in the recent past, with several implementations being successful in community-wide experiments (CASP). We have employed combinatorial optimization techniques toward solving the protein structure prediction problem. A Monte Carlo minimization algorithm has been employed on a constrained search space to identify minimum energy configurations. The search space is constrained by using radius of gyration cutoffs, the loop backbone dihedral probability distributions, and various secondary structure packing conformations. Simulations have been carried out on several sequences and 1000 conformations have been initially generated. Of these, 50 best candidates have then been selected as probable conformations. The search for the optimum has been simplified by incorporating various geometrical constraints on secondary structural elements using distance restraint potential functions. The advantages of the reported methodology are its simplicity, and modifiability to include other geometric and probabilistic restraints.

Prevalence of dementia in an urban Indian population

This article reports the findings of a 3-year epidemiological survey for dementia in an urban community-resident population in Mumbai (Bombay), India, wherein the prevalence of all types of dementia was determined.

METHOD

The study was conducted in three stages. Stage 1: From a potential pool of 30,000 subjects aged 40 years or more, 24,488 (male = 11,875; female = 12,613) persons completed self-report or interviewer-rated protocols based on the Sandoz Clinical Assessment Geriatric Scale, but 5,512 (18.37%) persons refused to participate. Scores on the protocol had a possible range from 0 through 34. Stage 2: Persons with a score +2 SD above the mean were selected in this stage where the persons were screened for cognitive functioning using a modified and translated version of the Mini-Mental State Examination. Individuals who scored below the 5th percentile were included in Stage 3 and underwent a detailed neurological, psychiatric, and neuropsychological evaluation as well as hematological, radiological, electrocardiographic, and electroencephalographic investigations. Diagnoses were made jointly by a neurologist, psychiatrist, and psychologist using the DSM-IV diagnostic criteria. Subjects were also rated on the Clinical Dementia Rating (CDR) scale and assessed for activities of daily living.

RESULTS

One hundred five subjects with dementia (CDR > or = 0.5) were identified in this population of 24,488 persons. The prevalence rate for dementia in those aged 40 years and more was 0.43% and for persons aged 65 and above was 2.44%. Seventy-eight individuals had a CDR of > or = 1 yielding an overall prevalence rate of 0.32%, and a prevalence rate of 1.81% for those aged 65 years and older. The overall prevalence rate for Alzheimer's disease (AD) in the population was 0.25%, and 1.5% for those aged 65 years and above. AD (n = 62; 65%) was the most common cause of dementia followed byvascular dementia (n = 23; 22%). There were more women (n = 38) than men (n = 24) in the AD group. Increasing age was associated with a higher prevalence of the dementia syndrome in general as well as AD specifically.

CONCLUSION

In the population surveyed, the prevalence of AD and other dementias is less than that reported from developed countries but similar to results of other studies in India. Prevalence of the dementia syndrome increased with age and was not related to gender. AD was the most common dementia and the prevalence was higher in women than in men. Results are discussed with respect to shorter life expectancy, relocation of affected persons, and differences in the risk factors as compared to developed countries.

Use of streamline chelating for capture and purification of poly-His-tagged recombinant proteins

Expression of recombinant proteins with poly-histidine tags enables their convenient capture and purification using immobilized metal affinity chromatography (IMAC). The 6 x His-tagged protein binds to a chelating resin charged with metal ions such as Ni2+, Cu2+ or Zn2+, and can therefore be separated from proteins which have lower, or no, affinity for the resin. Two recombinant proteins, a malaria transmission-blocking vaccine candidate secreted extracellularly by S. cerevisiae and a modified diphtheria toxin produced intracellularly by E. coli, were expressed with 6 x His tags and could therefore be purified using IMAC. In an effort to further simplify the initial capture of these proteins, an expanded bed adsorption technique using a chelating resin (Streamline Chelating) was introduced. It was possible to capture the intracellular diphtheria protein from E. coli directly after cell lysis, without prior centrifugation or filtration. The extracellular malaria vaccine candidate was also directly captured from a high cell density yeast culture. Detailed information on the experimental work performed, and the capture processes developed, is provided.