Robust Identification of Differential Gene Expression Patterns from Multiple Transcriptomics Datasets for Early Diagnosis, Prognosis, and Therapies for Breast Cancer

Background and Objectives: Breast cancer (BC) is one of the major causes of cancer-related death in women globally. Proper identification of BC-causing hub genes (HubGs) for prognosis, diagnosis, and therapies at an earlier stage may reduce such death rates. However, most of the previous studies detected HubGs through non-robust statistical approaches that are sensitive to outlying observations. Therefore, the main objectives of this study were to explore BC-causing potential HubGs from robustness viewpoints, highlighting their early prognostic, diagnostic, and therapeutic performance. Materials and Methods: Integrated robust statistics and bioinformatics methods and databases were used to obtain the required results. Results: We robustly identified 46 common differentially expressed genes (cDEGs) between BC and control samples from three microarrays (GSE26910, GSE42568, and GSE65194) and one scRNA-seq (GSE235168) dataset. Then, we identified eight cDEGs (COL11A1, COL10A1, CD36, ACACB, CD24, PLK1, UBE2C, and PDK4) as the BC-causing HubGs by the protein-protein interaction (PPI) network analysis of cDEGs. The performance of BC and survival probability prediction models with the expressions of HubGs from two independent datasets (GSE45827 and GSE54002) and the TCGA (The Cancer Genome Atlas) database showed that our proposed HubGs might be considered as diagnostic and prognostic biomarkers, where two genes, COL11A1 and CD24, exhibit better performance. The expression analysis of HubGs by Box plots with the TCGA database in different stages of BC progression indicated their early diagnosis and prognosis ability. The HubGs set enrichment analysis with GO (Gene ontology) terms and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways disclosed some BC-causing biological processes, molecular functions, and pathways. Finally, we suggested the top-ranked six drug molecules (Suramin, Rifaximin, Telmisartan, Tukysa Tucatinib, Lynparza Olaparib, and TG.02) for the treatment of BC by molecular docking analysis with the proposed HubGs-mediated receptors. Molecular docking analysis results also showed that these drug molecules may inhibit cancer-related post-translational modification (PTM) sites (Succinylation, phosphorylation, and ubiquitination) of hub proteins. Conclusions: This study's findings might be valuable resources for diagnosis, prognosis, and therapies at an earlier stage of BC.

Peptide-based targeted polymeric nanoparticles for siRNA delivery

The development of polymer-based nanoparticulate delivery systems for siRNA is important for the clinical success of gene therapy. However, there are some major drawbacks that need to be overcome. Short interfering RNA (siRNA) has been investigated as a potential therapeutic drug to silence disease-associated genes, but its usage is limited due to the lack of effective and safe nanocarriers. In this study, DOPE-PEI, a nanoparticle consisting of the fusogenic lipid 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) conjugated with low-molecular-weight, 600 Da, branched polyethylenimine (PEI) was produced and optimized for siRNA delivery. This delivery system was modified with other components such as 1,2-dioleoyl-sn-glycerol-3-phosphoethanolamine-N-[methoxy(polyethyleneglycol)2000] (DOPE-PEG2K), DOPE-PEG3.4K-bombesin and 1,2-dioleoyl-sn-glycerol-3-phosphoethanolamine/1,2-dioleoyl-3-trimethylammonium-propane (DOPE/DOTAP) and tested on PC-3 cells. The conjugation of DOPE to PEI polymer (DOPE-PEI) improved the efficiency of PEI to deliver siRNA into the cytosol and knockdown genes, but demonstrated high toxicity. The addition of DOPE-PEG2K reduced cellular toxicity by masking the surface positive charge of the DOPE-PEI/siRNA complex, with the incorporation of a gastrin-releasing peptide receptor (GRPR) targeting peptide and DOPE/DOTAP components improving the cellular uptake of siRNA into targeted cells and the siRNA knockdown efficiency.

Robust identification of significant interactions between toxicogenomic biomarkers and their regulatory chemical compounds using logistic moving range chart

Identification of significant interactions between genes and chemical compounds/drugs is an important issue in toxicogenomic studies as well as in drug discovery and development. There are some online and offline computational tools for toxicogenomic data analysis to identify the biomarker genes and their regulatory chemical compounds/drugs. However, none of the researchers has considered yet the identification of significant interactions between genes and compounds. Therefore, in this paper, we have discussed two approaches namely moving range chart (MRC) and logistic moving range chart (LMRC) for the identification of significant up-regulatory (UpR) and down-regulatory (DnR) gene-compound interactions as well as toxicogenomic biomarkers and their regulatory chemical compounds/drugs. We have investigated the performance of both MRC and LMRC approaches using simulated datasets. Simulation results show that both approaches perform almost equally in absence of outliers. However, in presence of outliers, the LMRC shows much better performance than the MRC. In case of real life toxicogenomic data analysis, the proposed LMRC approach detected some important down-regulated biomarker genes those were not detected by other approaches. Therefore, in this paper, our proposal is to use LMRC for robust identification of significant interactions between genes and chemical compounds/drugs.

Robust Co-clustering to Discover Toxicogenomic Biomarkers and Their Regulatory Doses of Chemical Compounds Using Logistic Probabilistic Hidden Variable Model

Detection of biomarker genes and their regulatory doses of chemical compounds (DCCs) is one of the most important tasks in toxicogenomic studies as well as in drug design and development. There is an online computational platform "Toxygates" to identify biomarker genes and their regulatory DCCs by co-clustering approach. Nevertheless, the algorithm of that platform based on hierarchical clustering (HC) does not share gene-DCC two-way information simultaneously during co-clustering between genes and DCCs. Also it is sensitive to outlying observations. Thus, this platform may produce misleading results in some cases. The probabilistic hidden variable model (PHVM) is a more effective co-clustering approach that share two-way information simultaneously, but it is also sensitive to outlying observations. Therefore, in this paper we have proposed logistic probabilistic hidden variable model (LPHVM) for robust co-clustering between genes and DCCs, since gene expression data are often contaminated by outlying observations. We have investigated the performance of the proposed LPHVM co-clustering approach in a comparison with the conventional PHVM and Toxygates co-clustering approaches using simulated and real life TGP gene expression datasets, respectively. Simulation results show that the proposed method improved the performance over the conventional PHVM in presence of outliers; otherwise, it keeps equal performance. In the case of real life TGP data analysis, three DCCs (glibenclamide-low, perhexilline-low, and hexachlorobenzene-medium) for glutathione metabolism pathway dataset as well as two DCCs (acetaminophen-medium and methapyrilene-low) for PPAR signaling pathway dataset were incorrectly co-clustered by the Toxygates online platform, while only one DCC (hexachlorobenzene-low) for glutathione metabolism pathway was incorrectly co-clustered by the proposed LPHVM approach. Our findings from the real data analysis are also supported by the other findings in the literature.

A newly developed tool for measuring the availability of human resources for emergency obstetric and newborn care services: prospective analytic study in two district-level public facilities in Bangladesh

BACKGROUND

In Bangladesh, while the infrastructure of public health facilities to provide maternal and newborn care services is adequate, services are not always available due to insufficient staffing. A human resource availability index for health facilities is needed for monitoring and advocacy. This study aimed to develop indices for measuring the availability of different types of human resources to provide round-the-clock emergency obstetric and newborn care (EmONC) service at district-level public facilities.

METHODS

As part of a larger intervention study, 30 days of prospective observation of providers was done at a district hospital (DH) and a mother and child welfare centre (MCWC) in one district of Bangladesh using checklists. A scoring system was developed to create an index to quantify the availability of providers for maternal and newborn care.

RESULTS

Based on the newly developed index, medical doctors in the emergency department of the DH were 100% available, but ranged from 27 to 41% availability in the obstetrics/gynecology (ob/gyn) and pediatric wards. In MCWC, the corresponding indices ranged from 32 to 36%. In the DH, the availability of nurses in the ob/gyn ward (96%) was relatively better than in the pediatric ward (65%) but that in operation theatre was only 31%. In the MCWC, the index for the presence of a paramedic or nursing aid was 82% in the ob/gyn ward and 63% in the operation theatre. However, the availability scores of facility support staff for maintenance and security were generally high (over 90%) in both facilities.

CONCLUSIONS

Our newly developed index on availability of providers demonstrated huge gaps in availability of providers in evening and night shifts in most of the disciplines in the study facilities. This provider availability index is easy to create and can be used as a meaningful tool to quantify gaps in human resources by type in various types of district-level health facilities. Further studies are needed for adaptation of this tool in different types of health facilities and to assess its implication as an advocacy tool.

Toxic Dose prediction of Chemical Compounds to Biomarkers using an ANOVA based Gene Expression Analysis

The aim of toxicogenomic studies is to optimize the toxic dose levels of chemical compounds (CCs) and their regulated biomarker genes. This is also crucial in drug discovery and development. There are popular online computational tools such as ToxDB and Toxygates to identify toxicogenomic biomarkers using t-test. However, they are not suitable for the identification of biomarker gene regulatory dose of corresponding CCs. Hence, we describe a one-way ANOVA model together with Tukey's HSD test for the identification of toxicogenomic biomarker genes and their influencing CC dose with improved efficiency. Glutathione metabolism pathway data analysis shows high and middle dose for acetaminophen, and nitrofurazone as well as high dose for methapyrilene as significant toxic CC dose. The corresponding regulated top seven toxicogenomic biomarker genes found in this analysis is Gstp1, Gsr, Mgst2, Gclm, G6pd, Gsta5 and Gclc.

Market Assessment and Product Evaluation of Probiotic Containing Dietary Supplements Available in Bangladesh Market

Probiotics containing food supplements available in Bangladesh market were identified and collected for assessment. To assess their label claim, they were resuspended into sterile distilled water. Then, series dilutions of each sample solution were prepared and immediately plated out, in duplicate, into De Man Rogosa Sharpe (MRS) agar. These plates were then incubated at 37°C for 48 hours and colonies were counted. Viable cell numbers stated on the labels were compared with actual viable cell numbers. To assess the viability of the probiotics included in the products, probiotic strains were isolated from each of the four products and screened for inhibitory activity against six indicator strains. It was surprisingly found that although the viable cell numbers of all supplements were three to four log cycles lower than label claim of the products, however, this problem did not affect the inhibitory activity of the probiotic strains against indicator strains according to in vitro assessment. Legislation and regulation regarding prebiotic-probiotic containing products should be built up in Bangladesh to ensure quality products supply to the consumers. Moreover, manufacturers of probiotic containing products should take the responsibility for providing the consumer with scientifically and legally correct information.

Role of early serum beta human chorionic gonadotropin measurement in predicting multiple pregnancy and pregnancy wastage in an in vitro ET fertilization cycle

OBJECTIVE:

This study was performed to assess the prognostic value of serum beta human chorionic gonadotropin (βhCG), measured on day 14 post embryo transfer (ET) for predicting multiple gestation and pregnancy wastage in women undergoing in vitro fertilization ET (IVF-ET).

MATERIALS AND METHODS:

This retrospective study was performed between May 2009 and November 2012. Out of the 181 women who conceived, 168 were included and the remaining 13 were excluded as their pregnancy was biochemical. Serum βhCG was measured using a chemiluminescent enzyme immunometric assay. The predictive values of serum βhCG for establishing multiple pregnancy and pregnancy wastages were calculated by receiver operating characteristic (ROC) curve analysis. Median values of serum βhCG and outcome of all pregnancies were compared.

RESULTS:

Out of the 168 patients who conceived after IVF treatment, 114 (68%) were viable pregnancies (delivered/ongoing). Among the viable pregnancies, 97 (85%) had a successful pregnancy outcome and the remaining 17 patients are ongoing pregnancies. Median values of βhCG (625 IU/L) among viable pregnancies was significantly (P < 0.05) higher than that of nonviable pregnancies (174 IU/L). The median values of βhCG for singleton (502 IU/L), twins (1093 IU/L), and triplets (2160 IU/L) was statistically significant (P < 0.05). Using ROC curve it was predicted that for a value of βhCG at 375 IU/L, the sensitivity of viable pregnancy was 65% and specificity of viable pregnancy was also 65%, with positive and negative predictive values of 65 and 68%, respectively. Similarly for multiple pregnancy and pregnancy wastage the predictive values of βhCG were 808 and 375 IU/L, respectively; while the sensitivity and specificity is more than 65% each.

CONCLUSION:

βhCG cutoff values determined on day 14 post ET by ROC curve analysis are useful in discriminating between multiple pregnancy and pregnancy losses. The cutoff value might aid in the prognosis, clinical management, and counseling of the IVF patients.

Lifestyle pattern in selected slums in Mymensingh Municipal area

Lifestyle is composed of cultural and behavioural patterns and lifelong personal habits that developed through processes of socialization. Lifestyle may be health promotive or detrimental to health. Health requires the promotion of healthy lifestyle. Many current day health problems are associated with lifestyle changes. Because of rising urban population, the number of slum dwellers is rising. The mobility of people from rural to urban areas is the main reason of the growing slum population in cities. This Descriptive, cross-sectional study was directed to assess lifestyle pattern in four purposively selected slums in Mymensingh Municipal area. Non-Probability purposive type of sampling technique was used for selecting the study unit. Sample size was one hundred and twenty-three (123) families. Data were collected by interview with one of the adult family members, preferably with the head of the family, with mixed type of interviewer administered questionnaire. There were 494 family members with an average family size of 4.02, while mean age was 24.58 years with a standard deviation (SD) of 17.79 years. Male-female ratio was 103:100. Of 409 members over 5 years, 174(42.54%) did not have schooling and were illiterate. At least 105(33.02%) members were house-wives, and 99(81.15%) members were smokers. An overwhelming majority (79, 64.23%) families had monthly income between 2000 to 4999 taka. As many as 55(44.72%) families lived in kaccha house, while 40(32.52%) had to live in "Jhupree". In cent per cent families, tube well was the source of water for drinking and other household purposes. A highest majority 121(98.37%) of the families had latrine, while the remaining 2(1.63%) did not have any latrine, and defecate in open air. Of 121 families, 78(64.46%) families had sanitary latrine, while 43(37.54%) did not have sanitary latrine. It was revealed that 86(69.92%) families had cell-phone, while 65(52.85%) families had television, 10(8.13%) families had radio, and 5(4.06%) families had DVD/VCR for recreational facilities. As many as 75(60.98%) respondents had correct knowledge, while the rest 48(39.02%) had incorrect knowledge on hand washing. Of 75, at least 66(88.00%) respondents practiced hand washing, while 9(12.00%) respondents did not practice it. As many as 110(89.43%) members sought medical help for major and minor illness of their family members, whereas the rest 13(10.57%) families did not. Of 110, 62(56.36%) families paid visit to government Hospital, while 22(20.00%) visited to private clinic, 12(10.90%) to pharmacy, 10(9.10%) to qualified doctors and 4(3.64%) to the traditional healers. As many as 58(52.71%) respondents mentioned that they preferred as the facilities cater service free of cost, while 32(29.10%) preferred for better and effective treatment, 16(14.55%) for close to their residence and 4(7.27%) for their belief. Living condition of slum dwellers is considerably low due to low income and inadequate education. Moreover, poor physical environment with unsanitary excreta disposal method is commonplace in slum areas. Existing lifestyle of slum dwellers is unacceptable, and should be improved so that they can contribute to the national development.

Correlation of ultrasonographic findings with ultrasound guided fine needle aspiration of liver lesion

Ultrasonographic findings of liver were correlated with cytological findings in a series of 50 patients. Multiple lesions described by ultrasonography and suggested as HCC/TB were proved to be metastatic in 60% cases and hepatocellular carcinoma in 40% cases by cytological examination. Multiple lesions suggested as metastatic lesions in ultrasonography was proved as such by cytology in 83% cases. Solitary lesion suggested as neoplastic in ultrasonography was proved as such in cytology in 90% cases. Of the 2 patients suggested as diffuse parenchymal lesion revealed cytological findings of cirrhosis in one case and that of TB in other. Serum alpha-feto protein and Carcinoembryogenic antigen (CEA) was done in all the cases. Serum alpha-feto protein was higher in hepatocellular carcinoma and CEA was higher in metastatic lesions. Ultrasound guided fine needle aspiration of liver can play more role in diagnosis and classification of liver disease than ultrasonographic comment alone, as it requires greater degree of precision to reach diagnostic accuracy.

Bradyrhizobium japonicum mutants with enhanced sensitivity to genistein resulting in altered nod gene regulation

Bradyrhizobium japonicum mutants with altered nod gene induction characteristics were isolated by screening mutants for genistein-independent nod gene expression. Plasmid pZB32, carrying a nodY::lacZ transcriptional gene fusion, was introduced into B. japonicum cells that had been subjected to UV mutagenesis. Ten independent transformants producing a blue color on plates containing 5bromo-4chloro-3indolyl-beta-D-galactopyranoside but lacking genistein, indicative of constitutive expression of the nodY::lacZ reporter gene, were isolated. Beta-galactosidase activity assays revealed that while all of the 10 strains were sensitive to low concentrations of genistein, none exhibited truly constitutive nodY::lacZ expression in liquid culture. Soybean plants inoculated with three of the mutants were chlorotic and stunted, with shoot dry weights close to those of the uninoculated plants, indicating the absence of nitrogen fixation. Differences in the kinetics of nodY::lacZ expression and lipochitin oligosaccharide Nod signal production suggested that the strains carried different mutations. Some of these strains may be useful in mitigating the low root zone temperature-associated delay in soybean nodulation at the northern extent of soybean cultivation.

Specific flavonoids induced nod gene expression and pre-activated nod genes of Rhizobium leguminosarum increased pea (Pisum sativum L.) and lentil (Lens culinaris L.) nodulation in controlled growth chamber environments

The gram-negative soil bacteria Rhizobium spp. infect and establish a nitrogen-fixing symbiosis with legume crops which involves the mutual exchange of diffusable signal molecules. In this study, Rhizobium leguminosarum containing a nod-lacZ gene fusion was used to screen the most effective plant-to-bacteria signal molecules for pea and lentil and the induction conditions. Out of a number of signal compounds including apigenin, daidzein, genistein, hesperetin, kaempferol, luteolin, naringenin, and rutin, hesperetin and naringenin were found to be the most effective plant-to-bacteria signal molecules. The induction of nod genes was temperature-dependent, where nod gene induction was decreased with dropping incubation temperature. The combination of hesperetin at 7 microM and naringenin at 3 microM resulted in better induction of nod gene activities compared to either hesperetin or naringenin alone. Nodulation and plant dry matter accumulation of pea and lentil plants receiving preinduced R. leguminosarum were higher than those of plants receiving uninduced R. leguminosarum cells in controlled environment growth chamber conditions. Preinduced Rhizobium with hesperetin at a concentration of 10 microM increased nodule number on average by 60.5% and dry matter accumulation by 14% in field pea at 17 degrees C, while it was 32% and 9% at 24 degrees C, respectively. Similarly, averaged over two rhizobial strains, a 59% and 6% increase in nodule number and biomass production at 17 degrees C, and a 39% and 27% at 24 degrees C, were obtained from lentil inoculated with hesperetin-induced R. leguminosarum, respectively.

Unnatural deaths during Zakat distribution

Zakat is an islamic religious directive to wealthy Muslims to distribute 2.5% of their total annual saving to the poor. Before Eid-ul-Fitr Zakat is distributed to share happiness and joy with the poor. Deaths due to stampede in uncontrolled crowds of poor during Zakat distribution made it a point of study. In this tragic accident during Zakat distribution on 26.4.91 at a Biri (cigarette) factory (10 k.m. away from the port city of Chittagong), the total number of deaths were 32, out of which 27 (84.37%) persons died of Traumatic Asphyxia and 5 (15.63%) from head injury and more than 100 were injured, mostly elderly female and children. The young and elderly male escaped.