DeepChestGNN: A Comprehensive Framework for Enhanced Lung Disease Identification through Advanced Graphical Deep Features.

Lung diseases are the third-leading cause of mortality in the world. Due to compromised lung function, respiratory difficulties, and physiological complications, lung disease brought on by toxic substances, pollution, infections, or smoking results in millions of deaths every year. Chest X-ray images pose a challenge for classification due to their visual similarity, leading to confusion among radiologists. To imitate those issues, we created an automated system with a large data hub that contains 17 datasets of chest X-ray images for a total of 71,096, and we aim to classify ten different disease classes. For combining various resources, our large datasets contain noise and annotations, class imbalances, data redundancy, etc. We conducted several image pre-processing techniques to eliminate noise and artifacts from images, such as resizing, de-annotation, CLAHE, and filtering. The elastic deformation augmentation technique also generates a balanced dataset. Then, we developed DeepChestGNN, a novel medical image classification model utilizing a deep convolutional neural network (DCNN) to extract 100 significant deep features indicative of various lung diseases. This model, incorporating Batch Normalization, MaxPooling, and Dropout layers, achieved a remarkable 99.74% accuracy in extensive trials. By combining graph neural networks (GNNs) with feedforward layers, the architecture is very flexible when it comes to working with graph data for accurate lung disease classification. This study highlights the significant impact of combining advanced research with clinical application potential in diagnosing lung diseases, providing an optimal framework for precise and efficient disease identification and classification.

Characterization of textile effluent treatment plant sludge and its industrial application in fired clay bricks with health risk assessment.

The textile industry in Bangladesh faces environmental and health challenges due to the disposal of solid waste from Effluent Treatment Plants (ETPs). To address this issue, a study was conducted using soil from a brick industry near Dhaka, amending it with varying amounts of dry sludge to create clay bricks. The original soil had a loam texture and medium plasticity. The research found that adding 9 wt% of sludge resulted in Grade A commercial bricks with a compressive strength of 15.33 MPa and water absorption of 13.33 wt%, meeting BDS 208 standards. However, these sludge-incorporated bricks experienced more shrinkage during the burning process due to organic content, requiring additional soil to maintain conventional dimensions. Also, to assess the health hazards of these sludge-incorporated bricks, a leaching test was performed, revealing that no toxic heavy metals (Pb, Cd, Cr, Cu, Ni, and Zn) in the leachate exceeded the limits set by the United States Environmental Protection Agency (USEPA). The study indicates that textile ETP sludge can serve as a sustainable raw material for bricks, potentially reducing the environmental burden caused by textile sludge disposal by 28.75%. This innovative approach offers a promising solution to both environmental and health concerns associated with textile waste in Bangladesh's industrial sector.

Antimicrobial Susceptibility Patterns of Enterococcus Species and Molecular Detection of Enterococcus faecalis Isolated from Patients with Urinary Tract Infection in a Tertiary Care Hospital in Bangladesh.

One of the most prevalent infectious diseases identified in both communities and hospitalized patients is urinary tract infection (UTI). Enterococcus is evolved into a clinically pertinent uropathogen due to its evolving resistance to multiple antimicrobial agents.This study, detects antimicrobial susceptibility patterns of Enterococcus species and molecular detection of Enterococcus faecalis from patients with urinary tract infections. In this cross-sectional observational study, 165 urine samples were obtained from clinically diagnosed patients with UTIs of different ages and gender. Enterococcus species were identified by standard microbiological procedure and PCR (by using species-specific primers for Enterococcus faecalis). A modified Kirby Bauer Disc diffusion method was used to identify the antimicrobial susceptibility pattern following Clinical and Laboratory Standards Institute (CLSI) guidelines. Out of 165 urine samples, 134 samples yielded positive cultures. Enterococcus species were isolated from 23 (17.1%) urine samples. Among all Enterococcus, 16 (69.6%) isolates were E. faecalis, detected by PCR assay. A higher (30.4%) proportion of Enterococcus-positive patients were from the age group 48-57 years and female patients (78.2%) had a higher prevalence. Enterococcal infection was found in 56.5% of non-catheterized patients and 43.5% of catheterized patients. Vancomycin and linezolid (78.3%) and meropenem (73.9%) sensitivity was prevalent among all Enterococcus species. They showed 100% resistance towards ceftriaxone, cefixime 95.7%, cefuroxime 91.3%, azithromycin 82.6%. This research indicated the occurrence of Enterococcus species and the advent of multidrug-resistant E. faecalis in patients with UTIs. Routine speciation and antimicrobial susceptibility testing of Enterococcus in various clinical samples is encouraged.

Navigating the genomic instability mine field of osteosarcoma to better understand implications of non-coding RNAs.

Osteosarcoma is one of the most genomically complex cancers and as result, it has been difficult to assign genomic aberrations that contribute to disease progression and patient outcome consistently across samples. One potential source for correlating osteosarcoma and genomic biomarkers is within the non-coding regions of RNA that are differentially expressed. However, it is unsurprising that a cancer classification that is fraught with genomic instability is likely to have numerous studies correlating non-coding RNA expression and function have been published on the subject. This review undertakes the formidable task of evaluating the published literature of noncoding RNAs in osteosarcoma. This is not the first review on this topic and will certainly not be the last. The review is organized with an introduction into osteosarcoma and the epigenetic control of gene expression before reviewing the molecular function and expression of long non-coding RNAs, circular RNAs, and short non-coding RNAs such as microRNAs, piwi RNAs, and short-interfering RNAs. The review concludes with a review of the literature and how the biology of non-coding RNAs can be used therapeutically to treat cancers, especially osteosarcoma. We conclude that non-coding RNA expression and function in osteosarcoma is equally complex to understanding the expression differences and function of coding RNA and proteins; however, with the added lens of both coding and non-coding genomic sequence, researchers can begin to identify the patterns that consistently associate with aggressive osteosarcoma.

Singular Nuclei Segmentation for Automatic HER2 Quantification Using CISH Whole Slide Images.

Human epidermal growth factor receptor 2 (HER2) quantification is performed routinely for all breast cancer patients to determine their suitability for HER2-targeted therapy. Fluorescence in situ hybridization (FISH) and chromogenic in situ hybridization (CISH) are the US Food and Drug Administration (FDA) approved tests for HER2 quantification in which at least 20 cancer-affected singular nuclei are quantified for HER2 grading. CISH is more advantageous than FISH for cost, time and practical usability. In clinical practice, nuclei suitable for HER2 quantification are selected manually by pathologists which is time-consuming and laborious. Previously, a method was proposed for automatic HER2 quantification using a support vector machine (SVM) to detect suitable singular nuclei from CISH slides. However, the SVM-based method occasionally failed to detect singular nuclei resulting in inaccurate results. Therefore, it is necessary to develop a robust nuclei detection method for reliable automatic HER2 quantification. In this paper, we propose a robust U-net-based singular nuclei detection method with complementary color correction and deconvolution adapted for accurate HER2 grading using CISH whole slide images (WSIs). The efficacy of the proposed method was demonstrated for automatic HER2 quantification during a comparison with the SVM-based approach.

Oral health status, behaviours, food and beverage consumption of aboriginal children in Australia.

ISSUE ADDRESSED: Dental decay is prevalent among Australian Aboriginal children, yet little is known about their oral health-related behaviours. This study explored the oral health status, behaviours, food and beverage consumption of Aboriginal school children aged 7-9 years in Sydney, Australia. METHODS: Parents who were part of an existing longitudinal birth cohort ("Gudaga") were surveyed when their child was between 7 and 9 years. Children (n = 110) also received oral health screening by a trained nurse. RESULTS: A number of children (62%-91%) had at least one visible oral health problem across the 2 years. Around two thirds (62%-67%) of parents rated their child's oral health as excellent/very good and less than half the children (32%-45%) had received dental check-ups. Most children (79%-90%) brushed their teeth and drank water (97%) but more than half (57%-70%) also drank sugar sweetened beverages daily. CONCLUSIONS: Parents are instilling good oral health behaviours, however, the oral health screening suggests children are experiencing oral health issues of which parents may be unaware. Parents also seem to be unaware of beverage consumption practices that can increase the risk of childhood decay. SO WHAT?: The findings highlight the need for greater oral health awareness among Aboriginal families on how to recognise early symptoms dental decay and risk factors like sugar sweetened beverages among school going children. This suggests that existing health promotion strategies may not be reaching many Aboriginal families in the urban areas and more culturally appropriate programs may be needed.

Associations between rapid weight gain in infancy and weight status among urban Aboriginal children participating in the Gudaga study: nine-year results from a cohort study.

BACKGROUND: Rapid weight gain (RWG) in infants is associated with overweight and obesity in childhood and beyond, highlighting the need for early intervention. METHODS: Data from a birth cohort of Australian Aboriginal and Torres Strait Islander children living in an urban area were analysed to determine the prevalence of RWG in infancy and the association between RWG and overweight and obesity, categorised using both body mass index and waist to height ratio from birth to 9 years. RESULTS: The prevalence of overweight and obesity is higher in this cohort (at 47%) than the population average. The Australian population as a whole has seen steady increases. In this cohort although the prevalence of combined overweight and obesity remained relatively stable between 2 and 9 years, the proportion of children categorized as obese using BMI has increased. 42% of children who were overweight or obese at 9 years had experienced RWG in infancy. Children were 2.7 and 3.9 times more likely to be overweight at 9 years if they experienced RWG or were overweight at 2 years, respectively. CONCLUSION: RWG was common in this cohort and the strongest predictor of excess weight at 2 years and at 9 years. Early intervention is crucial in the first year of life across the whole population to prevent obesity in children. Culturally appropriate interventions developed with the community are required for Aboriginal and Torres Strait Islander babies and their parents.

Underlying Ossification Phenotype in a Murine Model of Metastatic Synovial Sarcoma.

Synovial sarcoma, an uncommon cancer, typically affects young adults. Survival rates range from 36% to 76%, decreasing significantly when metastases are present. Synovial sarcomas form in soft tissues, often near bones, with about 10% demonstrating ossification in the tumor. The literature is inconclusive on whether the presence of ossification portends a worse prognosis. To this end, we analyzed our genetic mouse models of synovial sarcoma to determine the extent of ossification in the tumors and its relationship with morbidity. We noted higher ossification within our metastatic mouse model of synovial sarcoma. Not only did we observe ossification within the tumors at a frequency of 7%, but an even higher frequency, 72%, of bone reactivity was detected by radiography. An enrichment of bone development genes was associated with primary tumors, even in the absence of an ossification phenotype. In spite of the ossification being intricately linked with the metastatic model, the presence of ossification was not associated with a faster or worse morbidity in the mice. Our conclusion is that both metastasis and ossification are dependent on time, but that they are independent of one another.

Impact of Left Atrial Appendage Closure During Cardiac Surgery on the Occurrence of Early Postoperative Atrial Fibrillation, Stroke, and Mortality: A Propensity Score-Matched Analysis of 10 633 Patients.

BACKGROUND: Prophylactic exclusion of the left atrial appendage (LAA) is often performed during cardiac surgery ostensibly to reduce the risk of stroke. However, the clinical impact of LAA closure in humans remains inconclusive. METHODS: Of 10 633 adults who underwent coronary artery bypass grafting and valve surgery between January 2000 and December 2005, 9792 patients with complete baseline characteristics, surgery procedure, and follow-up data were included in this analysis. A propensity score-matching analysis based on 28 pretreatment covariates was performed and 461 matching pairs were derived and analyzed to estimate the association of LAA closure with early postoperative atrial fibrillation (POAF) (atrial fibrillation ≤30 days of surgery), ischemic stroke, and mortality. RESULTS: In the propensity-matched cohort, the overall incidence of POAF was 53.9%. In this group, the rate of early POAF among the patients who underwent LAA closure was 68.6% versus 31.9% for those who did not undergo the procedure (P<0.001). LAA closure was independently associated with an increased risk of early POAF (adjusted odds ratio, 3.88; 95% confidence interval, 2.89-5.20), but did not significantly influence the risk of stroke (adjusted hazard ratio, 1.07; 95% confidence interval, 0.72-1.58) or mortality (adjusted hazard ratio, 0.92; 95% confidence interval, 0.75-1.13). CONCLUSIONS: After adjustment for treatment allocation bias, LAA closure during routine cardiac surgery was significantly associated with an increased risk of early POAF, but it did not influence the risk of stroke or mortality. It remains uncertain whether prophylactic exclusion of the LAA is warranted for stroke prevention during non-atrial fibrillation-related cardiac surgery.

Genetic diversity study on 12 X-STR loci of investigator® Argus X STR kit in Bangladeshi population.

The X-chromosome short tandem repeat (STR) loci are of particular interest for solving complex kinship and paternity cases. Here, we report the genetic data from 209 unrelated Bangladeshi individuals (102 males and 107 females) that were genotyped using the 12 X-chromosomal STR markers included in the Investigator® Argus X-12 kit (Qiagen). The 12 X-STR markers are located in four linkage groups (linkage group I: DXS10135, DXS10148, and DXS8378; linkage group II: DXS7132, DXS10079, and DXS10074; linkage group III: DXS10103, HPRTB, and DXS10101; and linkage group IV: DXS10146, DXS10134, and DXS7423). Allelic frequencies of the 12 X-STR loci and haplotype frequencies of the four linkage groups were investigated. No significant difference was observed in the allele frequencies of males and females. Distributions of heterozygosity were observed from 64.5 to 92.5% among the studied 12 X STR loci. DXS10135 and DXS10101 loci were found to be most polymorphic. For all the four linkage groups, the haplotype diversity was found to be greater than 0.986. A total of 95, 73, 66, and 74 haplotypes were observed in linkage groups I, II, III, and IV, respectively. Hardy-Weinberg equilibrium tests showed no significant deviation from expected values for all 12 loci (p > 0.05). The exact test for pairwise linkage disequilibrium for the 12 loci in the male samples did not show any significant linkage disequilibrium except the DXS10103 and DXS10101 loci after the p values were corrected by Bonferroni's correction for multiple testing (p > 0.05/66). A combined power of discrimination in male and female individuals were 0.999999998159791 and 0.999999999999993, respectively. The combined mean exclusion chance were 0.999997635 in deficiency cases, 0.999999996 in normal trio cases, and 0.999999178 in duo cases. The currently investigated Bangladeshi population showed significant differences when compared with previously reported X-STR data from other 12 populations. The results of the data analysis indicated that all the loci in the Investigator® Argus X 12 kit were fairly informative and might be useful in forensic application and kinship analysis in Bangladeshi population.

Knowledge attitude and practice regarding diabetes mellitus among Nondiabetic and diabetic study participants in Bangladesh.

BACKGROUND: Increased awareness amongst large population groups is a major determinant for the prevention of diabetes and its complications as well as related metabolic disorders. Knowledge and attitude are the principal markers of awareness that need to be studied in various population groups in specific racial and cultural contexts. The present study was undertaken to explore knowledge, attitude and practice (KAP) regarding -diabetes mellitus (DM) among nondiabetic (nonDM) and type 2 diabetes mellitus (T2DM) patients in Bangladesh. METHODS: A cross-sectional study was conducted among 18,697 adults (aged 18 years and above; 7796 male and 10,901 female; 6780 nonDM and 11,917 T2DM) selected purposively from the OPD of 19 healthcare centres in and around Dhaka and in northern parts of Bangladesh. KAP were assessed by a pre-structured, interviewer-administered questionnaire and categorised using predefined scores of poor (mean + 1 SD). Univariate and bivariate statistical analysis were done as appropriate. Multivariate linear regression was done to examine the association between diabetes related KAP and other covariates. RESULTS: The mean (±SD) age (years) of all the study participants was 46 ± 14, mean BMI 24.4 ± 4.1 and mean waist-hip ratio (WHR) was 0.93 ± 0.07. The proportion of poor, average and good knowledge scores among T2DM subjects were 17%, 68% and 15% respectively. The corresponding values for attitude score were 23%, 67% and 10% respectively. The KAP regarding diabetes was found to be better among people who were living with diabetes compared to their counterparts. DM males showed better knowledge and practice regarding diabetes, compared to nonDM counterparts (M ± SD; 44.18 ± 16.13 vs 40.88 ± 15.62, p = <0.001; 66.00 ± 29.68 vs 64.21 ± 31.79, p < 0.001, respectively). Females showed better attitude score compared to males. Overall KAP were found to be significantly higher (p < 0.001) in middle aged (31-50 years) participants in each group. Participants from urban residents, higher educational background and upper socio-economic class demonstrated significantly greater score in terms of KAP in both nonDM and T2DM groups (p < 0.001). On linear regression analysis, knowledge scores correlated strongly with education, income, residence, diabetic state, BMI and attitude. CONCLUSIONS: The overall level of knowledge and practice concerning diabetes among Bangladeshi population is average, but the overall level of attitude is good both in nonDM and T2DM subjects. To prevent diabetes and its complications there is an urgent need for coordinated educational campaigns with a prioritized focus on poorer, rural and less educated groups.

Short-term predictive ability of selected cardiovascular risk prediction models in a rural Bangladeshi population: a case-cohort study.

BACKGROUND: Prediction of absolute risk of cardiovascular diseases (CVDs) has important clinical and public health significance, but the predictive ability of the available tools has not yet been tested in the rural Bangladeshi population. The present study was undertaken to test the hypothesis that both laboratory-based (Framingham equation and WHO/ISH laboratory-based charts) and non-laboratory-based tools may be used to predict CVDs on a short-term basis. METHODS: Data from a case-cohort study (52989 cohort and 439 sub-cohort participants), conducted on a rural Bangladeshi population, were analysed using modified Cox PH model with a maximum follow-up of 2.5 years. The outcome variable, coronary heart diseases (CHDs), was assessed in 2014 using electrocardiography, and it was used as a surrogate marker for CVDs in Bangladesh. The predictive power of the models was assessed by calculating C-statistics and generating ROC curves with other measures of diagnostic tests. RESULTS: All the models showed high negative prediction values (NPVs, 84 % to 92 %) and these did not differ between models or gender. The sensitivity of the models substantially changed based on the risk prediction thresholds (between 5-30 %); however, the NPVs and PPVs were relatively stable at various threshold levels. Hypertension and dyslipidaemia were significantly associated with CHD outcome in males and ABSI (a body shape index) in females. All models showed similar C-statistics (0.611-0.685, in both genders). Overall, the non-laboratory-based model showed better performance (0.685) in women but equal performance in men. CONCLUSIONS: Existing CVD risk prediction tools may identify future CHD cases with fairly good confidence on a short-term basis. The non-laboratory-based tool, using ABSI as a predictor, may provide better predictive accuracy among women.

Clinical and biochemical characterization of high risk and not high risk for cardiovascular disease adults in a population from peripheral region of Bangladesh.

BACKGROUND: A group of 63708 Bangladeshi adults from a rural area were screened in 2011-12 for cardiovascular diseases (CVD) risk using a questionnaire based tool developed as part of the 'WHO CVD-RISK Management Package for low-and medium resource setting'. In the current study participants who were found to be high risk and a sample of the not high risk participants from the screening were further characterized clinically and biochemically to explore the burden and determinants of CVD risk factors in a remote rural Bangladeshi population. METHODS: The high risk participants comprised all 1170 subjects who screened positive in 2011-12 and the not high risk group comprised 563 randomly sampled participants from the 62538 who screened negative. Socio-demographic, behavioral, anthropometric, clinical and biochemical data (glucose and lipids) were collected by standardized procedures. Body Mass Index (BMI) was classified following Asian BMI criteria. Data was analyzed using univariable and multivariable methods. RESULTS: On univariable analysis in high risk and not high risk participants respectively, age in years (M ± SD) was 50 ± 11 for both groups, ratio of male: female was 40:60 and 66:44, current smoking 28.5% and 50.6%; smokeless tobacco use 37.1% and 34.8%; overweight and obesity measured by body mass index (BMI) was 39.1% and 20.5%; high waist circumference (WC) 36.1% and 11.9%; high waist to hip ratio (WHR) 53.8% and 26.3%; and with high waist to height ratio (WHtR) 56.4% and 28.4%, existence of hypertension (HTN) was 15.8% and 3.6%, pre-HTN 43.8% and 12.1%, diabetes (DM) 14.0% and 10.5%, pre-DM 16.9% and 12.1% and dyslipidaemia 85.8% and 89.5%. In multivariable logistic regression analysis female sex, BMI, WC, WHR and WHtR, HTN and dyslipidaemia remain significantly more common among high risk participants (p < 0.05 and p < 0.001). CONCLUSIONS: The prevalence of clinical and biochemical risk factors of CVDs are quite high even in this rural population and this may be related to the socioeconomic and cultural transition in Bangladeshi society. Surprisingly more of the high risk group was female and there were fewer smokers. Obesity and hypertension were more frequent in high risk participants.

Unveiling the link between arsenic toxicity and diabetes: an in silico exploration into the role of transcription factors.

Arsenic-induced diabetes, despite being a relatively newer finding, is now a growing area of interest, owing to its multifaceted nature of development and the diversity of metabolic conditions that result from it, on top of the already complicated manifestation of arsenic toxicity. Identification and characterization of the common and differentially affected cellular metabolic pathways and their regulatory components among various arsenic and diabetes-associated complications may aid in understanding the core molecular mechanism of arsenic-induced diabetes. This study, therefore, explores the effects of arsenic on human cell lines through 14 transcriptomic datasets containing 160 individual samples using in silico tools to take a systematic, deeper look into the pathways and genes that are being altered. Among these, we especially focused on the role of transcription factors due to their diverse and multifaceted roles in biological processes, aiming to comprehensively investigate the underlying mechanism of arsenic-induced diabetes as well as associated health risks. We present a potential mechanism heavily implying the involvement of the TGF-ß/SMAD3 signaling pathway leading to cell cycle alterations and the NF-κB/TNF-α, MAPK, and Ca2+ signaling pathways underlying the pathogenesis of arsenic-induced diabetes. This study also presents novel findings by suggesting potential associations of four transcription factors (NCOA3, PHF20, TFDP1, and TFDP2) with both arsenic toxicity and diabetes; five transcription factors (E2F5, ETS2, EGR1, JDP2, and TFE3) with arsenic toxicity; and one transcription factor (GATA2) with diabetes. The novel association of the transcription factors and proposed mechanism in this study may serve as a take-off point for more experimental evidence needed to understand the in vivo cellular-level diabetogenic effects of arsenic. Supplementary Information: The online version contains supplementary material available at 10.1007/s43188-024-00255-y.

Occurrence of microplastics in fish gastrointestinal tracts belongs to different feeding habits from the Bangladesh coast of the Bay of Bengal.

The Bay of Bengal (BoB) is home to a range of commercially important species with different food habits and feeding features. Microplastic (MP) contamination in the fish of BoB, like in many other marine environments, is a significant environmental concern. The study aimed to investigate the presence of microplastics (MPs) in the gastrointestinal tracts (GITs) of selected commercial marine fishes from the Bangladesh coast of the BoB. Six fish species (Escualosa thoracata, Tenualosa ilisha, Johnius belangerii, Trichiurus lepturus, Planiliza parsia, and Mystus gulio) were investigated (n = 120) following hydrogen peroxide digestion, and floatation (saline solution) protocols. After analyses, a total number of 696 MPs (dimension 0.3 to 5 mm) were identified. Moreover, the highest occurrence of MPs in fish GITs was found in planktivorous fish (average of 7.7 items/individual), followed by omnivorous (average of 5.2 items/individual), and carnivorous fish (average of 4.6 items/individual) (p < 0.001). However, planktivorous E. thoracata showed the highest number of MPs per g of GIT (average of 30.99 items/g GIT), whereas T. ilisha showed the lowest count (average of 0.77 items/g GIT). Different types of MPs (fibers (19 to 76%), fragments (6 to 61%), films (8 to 35%), microbeads (0 to 5%), and foams (0 to 2%)) were also observed. In terms of the color of MPs, the transparent, black, green, and blue types were the most common. Polymers were found as polyethylene (35 to 43%), polyethylene terephthalate (28 to 35%), polyamide (20 to 31%), and polystyrene (0 to 7%). The study provides a significant incidence of MPs in fish from the Bangladesh part of the BoB, which is very concerning. Therefore, long-term research is indispensable to ascertain the variables affecting the presence of MPs in fish, their origins, and their potential effects on the BoB fisheries. Stringent policies on plastic use and disposal should be strongly urged in this coastal region.

Arid1a Loss Enhances Disease Progression in a Murine Model of Osteosarcoma.

Osteosarcoma is an aggressive bone malignancy, molecularly characterized by acquired genome complexity and frequent loss of TP53 and RB1. Obtaining a molecular understanding of the initiating mutations of osteosarcomagenesis has been challenged by the difficulty of parsing between passenger and driver mutations in genes. Here, a forward genetic screen in a genetic mouse model of osteosarcomagenesis initiated by Trp53 and Rb1 conditional loss in pre-osteoblasts identified that Arid1a loss contributes to OS progression. Arid1a is a member of the canonical BAF (SWI/SNF) complex and a known tumor suppressor gene in other cancers. We hypothesized that the loss of Arid1a increases the rate of tumor progression and metastasis. Phenotypic evaluation upon in vitro and in vivo deletion of Arid1a validated this hypothesis. Gene expression and pathway analysis revealed a correlation between Arid1a loss and genomic instability, and the subsequent dysregulation of genes involved in DNA DSB or SSB repair pathways. The most significant of these transcriptional changes was a concomitant decrease in DCLRE1C. Our findings suggest that Arid1a plays a role in genomic instability in aggressive osteosarcoma and a better understanding of this correlation can help with clinical prognoses and personalized patient care.

DNA Quantity and Quality Comparisons between Cryopreserved and FFPE Tumors from Matched Pan-Cancer Samples.

Personalized cancer care requires molecular characterization of neoplasms. While the research community accepts frozen tissues as the gold standard analyte for molecular assays, the source of tissue for testing in clinical cancer care comes almost universally from formalin-fixed, paraffin-embedded tissue (FFPE). As newer technologies emerge for DNA characterization that requires higher molecular weight DNA, it was necessary to compare the quality of DNA in terms of DNA length between FFPE and cryopreserved samples. We hypothesized that cryopreserved samples would yield higher quantity and superior quality DNA compared to FFPE samples. We analyzed DNA metrics by performing a head-to-head comparison between FFPE and cryopreserved samples from 38 human tumors representing various cancer types. DNA quantity and purity were measured by UV spectrophotometry, and DNA from cryopreserved tissue demonstrated a 4.2-fold increase in DNA yield per mg of tissue (p-value < 0.001). DNA quality was measured on a fragment microelectrophoresis analyzer, and again, DNA from cryopreserved tissue demonstrated a 223% increase in the DNA quality number and a 9-fold increase in DNA fragments > 40,000 bp (p-value < 0.0001). DNA from the cryopreserved tissues was superior to the DNA from FFPE samples in terms of DNA yield and quality.

Enhancing rice growth and yield with weed endophytic bacteria Alcaligenes faecalis and Metabacillus indicus under reduced chemical fertilization.

Endophytic bacteria, recognized as eco-friendly biofertilizers, have demonstrated the potential to enhance crop growth and yield. While the plant growth-promoting effects of endophytic bacteria have been extensively studied, the impact of weed endophytes remains less explored. In this study, we aimed to isolate endophytic bacteria from native weeds and assess their plant growth-promoting abilities in rice under varying chemical fertilization. The evaluation encompassed measurements of mineral phosphate and potash solubilization, as well as indole-3-acetic acid (IAA) production activity by the selected isolates. Two promising strains, tentatively identified as Alcaligenes faecalis (BTCP01) from Eleusine indica (Goose grass) and Metabacillus indicus (BTDR03) from Cynodon dactylon (Bermuda grass) based on 16S rRNA gene phylogeny, exhibited noteworthy phosphate and potassium solubilization activity, respectively. BTCP01 demonstrated superior phosphate solubilizing activity, while BTDR03 exhibited the highest potassium (K) solubilizing activity. Both isolates synthesized IAA in the presence of L-tryptophan, with the detection of nifH and ipdC genes in their genomes. Application of isolates BTCP01 and BTDR03 through root dipping and spraying at the flowering stage significantly enhanced the agronomic performance of rice variety CV. BRRI dhan29. Notably, combining both strains with 50% of recommended N, P, and K fertilizer doses led to a substantial increase in rice grain yields compared to control plants receiving 100% of recommended doses. Taken together, our results indicate that weed endophytic bacterial strains BTCP01 and BTDR03 hold promise as biofertilizers, potentially reducing the dependency on chemical fertilizers by up to 50%, thereby fostering sustainable rice production.

Prevalence of and factors associated with zero-dose and under-immunized children in selected areas of Bangladesh: Findings from Lot Quality Assurance Sampling Survey.

BACKGROUND: In the era of Gavi's 5.0 vision of "leaving no one behind with immunization", childhood routine vaccination in missed communities is considered as a priority concern. Despite having a success story at the national level, low uptake of immunization is still persistent in selected pocket areas of Bangladesh. However, prevalence and the associated factors of zero-dose (ZD) and under-immunization (UI) are still unknown at those geo-pockets of Bangladesh. Thus, the study aims to report and identify the factors associated with ZD and UI in selected geographical locations. METHODS: This study used data from a Lot Quality Assurance Sampling (LQAS) survey where 504 households from 18 clusters of four hard to reach (HTR) and one urban slum were included. Caregivers of children aged 4.5 to 23 months were interviewed. Three outcome variables- ZD, UI and ZD/UI were considered and several related attributes were considered as independent variables. Data were analyzed through bivariate analysis, binary logistic regression and dominance analysis. RESULTS: Overall, 32% of the children were either ZD (8%) or UI (26%) in the selected areas. The adjusted odds of ZD/UI for urban slum and haor (wetlands) areas were 5.62 and 3.61 respectively considering coastal areas as reference. However, distance of nearest EPI center, availability of EPI card, age of caregivers, education and occupation of mother and number of earning members in household were influential factors for ZD/UI. According to dominance analysis, availability of EPI card can explain the most of the variation of ZD/UI in this study. CONCLUSION: The study findings highlight the high prevalence ZD/UI in certain geo-pockets of the country. It provided a powerful insight of current situation and associated factors in regards to ZD/UI in the country which will help policy-makers and programme managers in designing programmes to reduce missed communities in Bangladesh.

Zinc trafficking: 1,10-phenanthroline, glutathione, and other metal binding ligands form adducts with proteomic Zn2.

Hypotheses were tested that the proteome of pig kidney LLC-PK1 cells (i) contains Zn-proteins that react with a diversity of native and pharmacologically active metal-binding ligands to form ternary complexes and (ii) includes proteins that bind Zn2+ nonspecifically and together form ternary adducts with a variety of metal-binding agents. The method to observe ternary complex formation with Zn-proteins and proteome•Zn involved preformation of fluorescent TSQ [6-Methoxy-(8-p-toluenesulfonamido)quinoline]-Zn-proteins and/or proteome•Zn-TSQ adducts followed by competitive reaction with selected ligands. The loss of TSQ-dependent fluorescence signaled the replacement of TSQ by the competing ligand in the starting adducts. In vitro, 1,10-phenanthroline competed effectively with TSQ for binding to Zn-proteins in the proteome. The successful competition of 1,10-phenanthroline with TSQ-Zn-proteins was also observed in cells. Similarly, 1,10-phenanthroline was shown to bind to a sizable fraction of Zn2+ associated adventitiously with proteome (proteome•Zn). Other synthetic ligands that bind to Zn-proteins and proteome•Zn include 2,2-bipyridyl, 8-hydroxyquinoline, 2,2'-dicarboxypyridine, and pyrithione. Such results suggest that ligand binding to such sites may play a role in the observed biological effects of these and other metal-binding molecules. Although cysteine does not significantly compete with TSQ, glutathione displaces TSQ from Zn-proteins and proteome•Zn at concentrations well below those found in cells, implying that ternary complex formation involving glutathione may be physiologically significant.