Gender Inequity in Clinical Clerkships and its Influence on Career Selection: A Cross-Sectional Survey.

Objective: The aim of this study was to identify the frequency, form, and underlying factors contributing to gender inequity experienced by medical undergraduates and assess its influence on their career choices. Method: This was a cross-sectional, retrospective survey with a 100% response rate. This survey was distributed among medical students of clinical years in Karachi's private and government medical colleges from September 10th, 2021-March 30th, 2022. 430 participants were enrolled using a simple-random-sampling-technique. Chi-square/Fisher's Exact tests are employed to assess the relationships between gender and gender-based inequity in various specialties, including their characteristics, influence on career choices, adverse psychological effects, and potential mitigation strategies. Results: Among 430 respondents, 28.6% were male, and 71.4% were female. 89.1% reported gender inequity, evenly distributed in government (80.4%) and private institutions (88.1%). The general surgery and gynecology disciplines stood out, each with a 56% prevalence. In gynecology and surgery clinical-clerkships, both genders experienced similar rates, with females at 54.5% and 42.3%, and males at 56.7% and 61.6%, respectively (P-value = .000*). Disrespect from staff/professors/patients (48.8%) was the most common manifestation, driven by factors like preferences (73.7%), gender superiority (62.6%), societal attitudes (54%), and cultural norms (50.9%). Furthermore, 82.6% of students reported that gender inequity had a negative impact on their career decision (Male = 82.9%;Female = 82.4%, P-value = .899). Additionally, gender inequity also caused demotivation (78.1%), poor self-esteem (67.2%), helplessness/hopelessness (48.6%), and frustration (45.8%). Conclusions: Gender inequity is widely prevalent in the clinical-clerkships, affecting medical students' career decisions and mental health, stressing the need to prioritize and implement solutions at the undergraduate clinical-clerkship level.

Cancer drug sensitivity prediction from routine histology images.

Drug sensitivity prediction models can aid in personalising cancer therapy, biomarker discovery, and drug design. Such models require survival data from randomised controlled trials which can be time consuming and expensive. In this proof-of-concept study, we demonstrate for the first time that deep learning can link histological patterns in whole slide images (WSIs) of Haematoxylin & Eosin (H&E) stained breast cancer sections with drug sensitivities inferred from cell lines. We employ patient-wise drug sensitivities imputed from gene expression-based mapping of drug effects on cancer cell lines to train a deep learning model that predicts patients' sensitivity to multiple drugs from WSIs. We show that it is possible to use routine WSIs to predict the drug sensitivity profile of a cancer patient for a number of approved and experimental drugs. We also show that the proposed approach can identify cellular and histological patterns associated with drug sensitivity profiles of cancer patients.

SynCLay: Interactive synthesis of histology images from bespoke cellular layouts.

Automated synthesis of histology images has several potential applications in computational pathology. However, no existing method can generate realistic tissue images with a bespoke cellular layout or user-defined histology parameters. In this work, we propose a novel framework called SynCLay (Synthesis from Cellular Layouts) that can construct realistic and high-quality histology images from user-defined cellular layouts along with annotated cellular boundaries. Tissue image generation based on bespoke cellular layouts through the proposed framework allows users to generate different histological patterns from arbitrary topological arrangement of different types of cells (e.g., neutrophils, lymphocytes, epithelial cells and others). SynCLay generated synthetic images can be helpful in studying the role of different types of cells present in the tumor microenvironment. Additionally, they can assist in balancing the distribution of cellular counts in tissue images for designing accurate cellular composition predictors by minimizing the effects of data imbalance. We train SynCLay in an adversarial manner and integrate a nuclear segmentation and classification model in its training to refine nuclear structures and generate nuclear masks in conjunction with synthetic images. During inference, we combine the model with another parametric model for generating colon images and associated cellular counts as annotations given the grade of differentiation and cellularities (cell densities) of different cells. We assess the generated images quantitatively using the Frechet Inception Distance and report on feedback from trained pathologists who assigned realism scores to a set of images generated by the framework. The average realism score across all pathologists for synthetic images was as high as that for the real images. Moreover, with the assistance from pathologists, we showcase the ability of the generated images to accurately differentiate between benign and malignant tumors, thus reinforcing their reliability. We demonstrate that the proposed framework can be used to add new cells to a tissue images and alter cellular positions. We also show that augmenting limited real data with the synthetic data generated by our framework can significantly boost prediction performance of the cellular composition prediction task. The implementation of the proposed SynCLay framework is available at https://github.com/Srijay/SynCLay-Framework.

Cross-linking breast tumor transcriptomic states and tissue histology.

Identification of the gene expression state of a cancer patient from routine pathology imaging and characterization of its phenotypic effects have significant clinical and therapeutic implications. However, prediction of expression of individual genes from whole slide images (WSIs) is challenging due to co-dependent or correlated expression of multiple genes. Here, we use a purely data-driven approach to first identify groups of genes with co-dependent expression and then predict their status from WSIs using a bespoke graph neural network. These gene groups allow us to capture the gene expression state of a patient with a small number of binary variables that are biologically meaningful and carry histopathological insights for clinical and therapeutic use cases. Prediction of gene expression state based on these gene groups allows associating histological phenotypes (cellular composition, mitotic counts, grading, etc.) with underlying gene expression patterns and opens avenues for gaining biological insights from routine pathology imaging directly.

Unravelling the genetic basis of retinal dystrophies in Pakistani consanguineous families.

BACKGROUND: Retinitis Pigmentosa (RP) is a clinically and genetically progressive retinal dystrophy associated with severe visual impairments and sometimes blindness, the most common syndromic form of which is Usher syndrome (USH). This study aimed to further increase understanding of the spectrum of RP in the Khyber Pakhtunkhwa region of Pakistan. METHODOLOGY: Four consanguineous families of Pashtun ethnic group were investigated which were referred by the local collaborating ophthalmologists. In total 42 individuals in four families were recruited and investigated using whole exome and dideoxy sequencing. Among them, 20 were affected individuals including 6 in both family 1 and 2, 5 in family 3 and 3 in family 4. RESULT: Pathogenic gene variants were identified in all four families, including two in cone dystrophy and RP genes in the same family (PDE6C; c.480delG, p.Asn161ThrfsTer33 and TULP1; c.238 C > T, p.Gln80Ter) with double-homozygous individuals presenting with more severe disease. Other pathogenic variants were identified in MERTK (c.2194C > T, p.Arg732Ter), RHO (c.448G > A, p.Glu150Lys) associated with non-syndromic RP, and MYO7A (c.487G > A, p.Gly163Arg) associated with USH. In addition, the reported variants were of clinical significance as the PDE6C variant was detected novel, whereas TULP1, MERTK, and MYO7A variants were detected rare and first time found segregating with retinal dystrophies in Pakistani consanguineous families. CONCLUSIONS: This study increases knowledge of the genetic basis of retinal dystrophies in families from Pakistan providing information important for genetic testing and diagnostic provision particularly from the Khyber Pakhtunkhwa region.

Evaluation of phytoremediation potential and resistance of Gladiolus grandiflora L. against cadmium stress.

Although irrigation water is a fundamental need for plant growth, it is also a source of pollutants if contaminated with harmful materials like cadmium (Cd). Irrigation water possessing abundant Cd causes damage to soil, plants, animals and ultimately human beings through the food chain. A pot experiment was conducted to evaluate the gladiolus (Gladiolus grandiflora L.) potential of Cd accumulation and the capability of the plant to be an economically beneficial choice in presence of high Cd irrigation water supply. Artificially prepared four levels of Cd irrigation water were applied to the plants viz., 30, 60, 90 and 120 mg L-1. The results revealed that 30 mg L-1 Cd had no difference in all growth-related parameters when compared to the control. Photosynthesis rate, stomatal conductance and transpiration rate along with plant height and spike length were reduced with high accumulation levels of Cd in plants. The main plant portion for Cd storage found in Gladiolus grandiflora L was corm where the amount of Cd was 10-12 times higher than the amount found in leaves, and 2-4 times more than the stem. This deportment was further established by the translocation factor (TF). In corm to shoot TF and corm to stem TF, the factor reduced with increasing Cd levels, while, in corm to leaves TF, Cd levels were statistically non-significant. From corm to shoot TF value of 0.68 and 0.43 in case of 30 and 60 mg L-1, Cd treatments indicates good phytoremediation potential of Gladiolus in low and moderate Cd-polluted environments. Conclusively, the study reveals the good capability of Gladiolus grandiflora L. to harvest Cd from the soil and water in reasonably good amount with sufficient potential to grow under irrigation-based Cd stress. Under revelations of the study, Gladiolus grandiflora L appeared as a Cd accumulator which could potentially be used as a sustainable approach for phytoremediation of Cd.

Prevalence of low back pain among medical doctors of the teaching hospitals in Karachi, Pakistan: A cross-sectional survey.

Objective: Our goal was to deduce the prevalence of low back pain among medical doctors in the teaching hospitals of Karachi, Pakistan, along with its associated variables and the functional disability accompanying it. Methods: This cross-sectional study was conducted among medical doctors from Creek General Hospital and United Hospital, affiliated with United Medical and Dental College, Karachi, Pakistan. A sample of 80 participants was included in this study, and a non-probability convenient sampling with randomization was utilized. Using a three-part questionnaire that included the Oswestry Disability Index, all participants were scrutinized for low back pain with its characteristics, associated risk factors, and functional disability. Results: Seventy percent of medical doctors included in this study suffered from the problem of low back pain, with 68% experiencing it over the last 3 months to 1 year. Furthermore, 89% and 11% suffered from minimal and moderate disability, respectively, affecting day-to-day and work life. Moreover, this study also found a significantly positive association (p value < 0.05*) of low back pain with age and work-related characteristics and was more common in those with work experience between 1 and 10 years, >8 working hours, >4 standing hours, and belonging to the surgery and medicine specialties. The association was significantly positive according to the chi-square/Fischer exact test. Conclusion: Our study addressed the evidence that low back pain is prevalent among medical doctors in teaching hospitals in Karachi, Pakistan, potentially affecting patient treatment and student education and accentuating the need for further intervention and research among doctors worldwide.

SlideGraph+: Whole slide image level graphs to predict HER2 status in breast cancer.

Human epidermal growth factor receptor 2 (HER2) is an important prognostic and predictive factor which is overexpressed in 15-20% of breast cancer (BCa). The determination of its status is a key clinical decision making step for selection of treatment regimen and prognostication. HER2 status is evaluated using transcriptomics or immunohistochemistry (IHC) through in-situ hybridisation (ISH) which incurs additional costs and tissue burden and is prone to analytical variabilities in terms of manual observational biases in scoring. In this study, we propose a novel graph neural network (GNN) based model (SlideGraph+) to predict HER2 status directly from whole-slide images of routine Haematoxylin and Eosin (H&E) stained slides. The network was trained and tested on slides from The Cancer Genome Atlas (TCGA) in addition to two independent test datasets. We demonstrate that the proposed model outperforms the state-of-the-art methods with area under the ROC curve (AUC) values > 0.75 on TCGA and 0.80 on independent test sets. Our experiments show that the proposed approach can be utilised for case triaging as well as pre-ordering diagnostic tests in a diagnostic setting. It can also be used for other weakly supervised prediction problems in computational pathology. The SlideGraph+ code repository is available at https://github.com/wenqi006/SlideGraph along with an IPython notebook showing an end-to-end use case at https://github.com/TissueImageAnalytics/tiatoolbox/blob/develop/examples/full-pipelines/slide-graph.ipynb.

USH2A gene variants cause Keratoconus and Usher syndrome phenotypes in Pakistani families.

BACKGROUND: Retinitis pigmentosa (RP) is the most common inherited retinal dystrophy, affecting approximately 1 in 4000 individuals worldwide. The most common form of syndromic RP is Usher syndrome (USH) accounting for approximately 20-30 % of RP cases. Mutations in the USH2A gene cause a significant proportion of recessive non-syndromic RP and USH type II (USH2). This study aimed to determine the causative role of the USH2A gene in autosomal recessive inherited ocular diseases and to establish genotype-phenotype correlation associated with USH2A variants. METHODS: We performed direct Sanger sequencing and co-segregation analysis of the USH2A gene to identify disease causing variants in a non-syndromic RP family, two USH2 families and two Keratoconus (KC) families. RESULTS: Disease causing variants in the USH2A gene were identified in two families displayed KC and USH2 phenotypes. A novel variant c.4029T > G, p.Asn1343Lys in the USH2A gene was detected in a Pakistani family with KC phenotype. In addition, a missense variant (c.7334 C > T, p. Ser2445Phe) in the USH2A gene was found segregating in another Pakistani family with USH2 phenotype. Homozygosity of identified missense USH2A variants was found associated with autosomal recessive inherited KC and USH2 phenotypes in investigated families. These variants were not detected in ethnically matched healthy controls. Moreover, the USH2A variants were predicted to be deleterious or potentially disease causing by PolyPhen-2, PROVEAN and SIFT. CONCLUSIONS: This study provided first evidence for association of a novel USH2A variant with KC phenotype in a Pakistani family as well as established the phenotype-genotype correlation of a USH2A variant (c.7334 C > T, p. Ser2445Phe) with USH2 phenotype in another Pakistani family. The phenotype-genotype correlations established in present study may improve clinical diagnosis of affected individuals for better management and counseling.

Role of brassinosteroids in alleviating toxin-induced stress of Verticillium dahliae on cotton callus growth.

Brassinosteroids are well known to mitigate biotic stresses; however, their role to induce tolerance against Verticillium dahliae is unknown. The current study employed V. dahliae (Vd) toxin as pathogen-free model system to induce stress on cotton callus growth, and its amelioration was investigated using 24-epibrassinolide (EBR). Results revealed that EBR has ameliorative effects against Vd toxin with greater seen effect when callus was treated with EBR prior to its exposure to Vd toxin (pre-EBR treatment) than EBR applied along with Vd toxin simultaneously (co-EBR treatment). Pre-EBR-treated calli remained green, while 65 and 90% callus browning was observed in co-EBR- and Vd toxin-alone-treated callus, respectively. Likewise, the fresh weight of the pre-EBR-treated callus was 52% higher than Vd toxin-alone treatment, whereas this increase was only 23% in co-EBR-treated callus. Meanwhile, EBR treatment of the cotton callus has also increased the contents of chlorophylls a and b, carotenoids, total phenols, flavonoids, soluble sugars, and proteins and increased the activity of enzymes involved in secondary metabolism like polyphenol oxidase (PPO), phenylalanine ammonialyase (PAL), cinnamyl alchol dehydrogenase (CAD), and shikimate dehydrogenase (SKDH) over Vd toxin-alone treatment with higher increments being observed in pre-EBR-treated callus. Furthermore, EBR treatment mimicked the DNA damage and improved the structure of mitochondria, granum, stroma thylakoids, and the attachment of ribosomes with the endoplasmic reticulum. This EBR-mediated mitigation was primarily associated with substantially increased contents of photosynthetic pigments and regulation of secondary metabolism.

Leaf-based physiological, metabolic, and ultrastructural changes in cultivated cotton cultivars under cadmium stress mediated by glutathione.

Cadmium (Cd) pollution is present in the world over especially in the industrialized parts of the world. To reduce Cd accumulation in various crops especially food crops, alleviating agents such as reduced glutathione (GSH) can be applied, which are capable either to exclude or to sequester Cd contamination. This study investigated the leaf-based spatial distribution of physiological, metabolic, and microstructural changes in two cotton cultivars (Coker 312 and TM-1) under GSH-mediated Cd stress using single levels of Cd (50 µM) and GSH (50 µM) both separately and in mix along with control. Results showed that GSH revived the morphology and physiology of both cotton cultivars alone or in mix with Cd. Cd uptake was enhanced in all segments of leaf and whole leaf upon the addition of GSH. GSH alleviated Cd-induced reduction in the photosynthetic pigment compositions and chlorophyll a fluorescence parameters. Mean data of biomarkers (2,3,5-triphenyltetrazolium (TTC), total soluble protein (TSP), malondialdehyde (MDA), hydrogen peroxide (H2O2)) revealed the adverse effects of Cd stress on leaf segments of both cultivars, which were revived by GSH. The oxidative metabolism induced by Cd stress was profoundly influenced by exogenous GSH application. The microstructural alterations were mainly confined to chloroplastic regions of leaves under Cd-stressed conditions, which were greatly revived upon the GSH addition. As a whole, Cd stress greatly affected TM-1 as compared to Coker 312. These results suggest a positive role of GSH in alleviating Cd-mediated changes in different leaf sections of cotton cultivars.

Comparative study of alleviating effects of GSH, Se and Zn under combined contamination of cadmium and chromium in rice (Oryza sativa).

A hydroponic experiment was conducted to study the ameliorative effects of separate or combined application of exogenous glutathione (GSH), selenium (Se) and zinc (Zn) upon 20 µM cadmium (Cd) plus 20 µM chromium (Cr) heavy metal stress (HM) in rice seedlings. The results showed that HM caused a marked reduction in seedling height, chlorophyll content (SPAD) and biomass, and activities of catalase (CAT) and ascorbate peroxidase (APX) in leaves and H(+)-ATPase in roots/leaves, but elevated superoxide dismutase (SOD) and guaiacol peroxidase (POD) activities in leaves with elevated malondialdehyde (MDA) accumulation both in leaves and roots over the control. The best mitigation effect was recorded in HM+GSH+Zn and HM+GSH (addition of GSH+Zn and GSH to HM solution), which greatly alleviated HM-induced growth inhibition and oxidative stress. Compared with HM alone, HM+GSH and HM+GSH+Zn markedly reduced Cr uptake and translocation but not affected Cd concentration; improved H(+)-ATPase activity and Fe, Zn, Mn uptake and translocation, and repressed MDA accumulation. Meanwhile exogenous GSH and GSH+Zn counteracted HM-induced response of antioxidant enzymes, via suppressing HM-induced dramatic increase of root/leaf SOD and leaf POD activities, and elevating stress-depressed leaf APX and leaf/root CAT activities.

Alleviation of aluminum toxicity by hydrogen sulfide is related to elevated ATPase, and suppressed aluminum uptake and oxidative stress in barley.

Greenhouse hydroponic experiments were performed to evaluate potential role of H(2)S on Al toxicity in barley seedlings. Seedlings pretreated with 200 µM NaHS as a donor of H(2)S for 24h and subsequently exposed to 100 µM AlCl(3) for 24h had significantly longer roots than those without NaHS. The promoted root elongation was correlated with a substantial decrease in Al-induced overproduction of lipid peroxidation, electrolyte leakage and Al accumulation in roots, and a marked increase in Al-induced depress activities of Na(+)K(+)-ATPase and H(+)-ATPase. The alleviating role of H(2)S on Al-induced toxicity was also found in a time- and dose-dependent experiment. Addition of 200 and 400 µM NaHS to 100 µM AlCl(3) effectively alleviated Al-toxicity, markedly diminished Al-induced MDA accumulation, and increased chlorophyll content, net photosynthetic rate (Pn) and maximal photochemical efficiency (Fv/Fm) compared with Al alone. Exogenous H(2)S significantly elevated depressed CAT activities, and further improved root POD activity. Moreover, NaHS decreased Al accumulation, but elevated concentrations of S, P, Ca, Mg and Fe in plants. These data suggest that H(2)S-induced alleviation in Al toxicity is attributed to reduced Al uptake and MDA accumulation, improved uptake of P, Ca, Mg and Fe, and elevated ATPase and photosynthetic performance.