Human-interpretable image features derived from densely mapped cancer pathology slides predict diverse molecular phenotypes

Computational methods have made substantial progress in improving the accuracy and throughput of pathology workflows for diagnostic, prognostic, and genomic prediction. Still, lack of interpretability remains a significant barrier to clinical integration. We present an approach for predicting clinically-relevant molecular phenotypes from whole-slide histopathology images using human-interpretable image features (HIFs). Our method leverages >1.6 million annotations from board-certified pathologists across >5700 samples to train deep learning models for cell and tissue classification that can exhaustively map whole-slide images at two and four micron-resolution. Cell- and tissue-type model outputs are combined into 607 HIFs that quantify specific and biologically-relevant characteristics across five cancer types. We demonstrate that these HIFs correlate with well-known markers of the tumor microenvironment and can predict diverse molecular signatures (AUROC 0.601-0.864), including expression of four immune checkpoint proteins and homologous recombination deficiency, with performance comparable to 'black-box' methods. Our HIF-based approach provides a comprehensive, quantitative, and interpretable window into the composition and spatial architecture of the tumor microenvironment.

Evaluation of regeneration of semitendinosus tendon using ultrasound imaging and isokinetic strength testing after graft harvest for arthroscopic anterior cruciate ligament reconstruction

Background

A lot of the research has been done worldwide evaluating the capacity of the semitendinosus tendon to regenerate which has not been conducted in the Indian population.

Study design

31 patients who underwent unilateral ACL reconstruction with hamstrings were taken into study. All patients underwent ultrasonography imaging of both knees and bilateral isokinetic flexion strength assessment at a one-year postoperative period. Images were obtained at three levels and their dimensions are compared with normal side. Isokinetic testing of the knee is done to evaluate the flexion deficit and is compared to the uninvolved knee.

Results

Out of a total of 31 patients, 14 patients showed no regeneration, 17 showed regeneration at various levels. On isokinetic testing patients with no regeneration showed the highest mean flexion deficit.

Conclusion

The semitendinosus tendon and its regeneration can be visualized well using ultrasonography. After semitendinosus harvesting, the flexion strength will be decreased as compared to the normal knee. The flexion strength in patients who have a regenerated tendon will be higher as compared to those who have no regeneration.

Morbidity profile of communities in Bhopal city (India) vis-à-vis distance of residence from Union Carbide India Limited plant and drinking water usage pattern

Objective:

A cross-sectional study was undertaken to assess the prevalence of morbidities in communities residing at variable distances from the closed down insecticide manufacturing plant premises of Union Carbide India Limited (UCIL), Bhopal, India and to determine association of morbidities, if any, with their drinking water usage pattern and distance of localities from the UCIL plant.

Materials and Methods:

A total of 10,827 individuals belonging to 2,184 families, residing within 0-1 km (Stratum I) and 2.5-5.0 km (Stratum II) radial distances from UCIL plant were surveyed and 9,306 of them (86%) were clinically examined. Data were analyzed to examine the association between the groups of morbidities, likely due to biological and chemical water contamination, and the distance of locality from the UCIL plant. Multiple logistic regression was used to explore the risk factors for morbidities.

Results:

Nearly similar prevalence (25.3% in stratum I, 25.8% in stratum II) and the trend of all-cause morbidities were recorded in the two strata. While morbidities related to gastrointestinal tract system (P < 0.05), auditory system (P < 0.01), neoplasm/cancers (P < 0.01) and congenital anomalies (P < 0.01) were significantly higher in stratum I, the prevalence of hypertension (6.4% stratum II, 4.7% stratum I; P < 0.01) and diabetes mellitus (3.4% stratum II, 2.0% stratum I; P < 0.001) was found significantly higher in stratum II. No association (P > 0.05) was observed between the prevalence of morbidities, likely due to the consumption of biologically or chemically contaminated drinking water, and the distance of locality/stratum from the UCIL plant.

Discussion and Conclusion:

By and large similar pattern of morbidities were recorded in the two strata suggesting that the communities, irrespective of the distance of their residences from UCIL plant or sources of their drinking water, are equally vulnerable to various morbidities.

Quantifying Argonaute 2 (Ago2) expression to stratify breast cancer

BACKGROUND

Argonaute-2 (Ago2) is an essential component of microRNA biogenesis implicated in tumourigenesis. However Ago2 expression and localisation in breast cancer remains undetermined. The aim was to define Ago2 expression (mRNA and protein) and localisation in breast cancer, and investigate associations with clinicopathological details.

METHODS

Ago2 protein was stained in breast cancer cell lines and tissue microarrays (TMAs), with intensity and localization assessed. Staining intensity was correlated with clinicopathological details. Using independent databases, Ago2 mRNA expression and gene alterations in breast cancer were investigated.

RESULTS

In the breast cancer TMAs, 4 distinct staining intensities were observed (Negative, Weak, Moderate, Strong), with 64.2% of samples stained weak or negatively for Ago2 protein. An association was found between strong Ago2 staining and, the Her2 positive or basal subtypes, and between Ago2 intensity and receptor status (Estrogen or Progesterone). In tumours Ago2 mRNA expression correlated with reduced relapse free survival. Conversely, Ago2 mRNA was expressed significantly lower in SK-BR-3 (HER2 positive) and BT-20 (Basal/Triple negative) cell lines. Interestingly, high levels of Ago2 gene amplification (10-27%) were observed in breast cancer across multiple patient datasets. Importantly, knowledge of Ago2 expression improves predictions of breast cancer subtype by 20%, ER status by 15.7% and PR status by 17.5%.

CONCLUSIONS

Quantification of Ago2 improves the stratification of breast cancer and suggests a differential role for Ago2 in breast cancer subtypes, based on levels and cellular localisation. Further investigation of the mechanisms affecting Ago2 dysregulation will reveal insights into the molecular differences underpinning breast cancer subtypes.

First case report of spontaneous posterior fossa subdural hemorrhage - A rare cause of neonatal encephalopathy

Posterior fossa subdural hemorrhage (PFSDH) in term neonates is rare and unknown in the absence of obvious trauma. Its management is challenging and decided case to case basis. Here we report two cases of posterior fossa subdural hemorrhage in term babies with normal transition at birth and presenting later with neonatal encephalopathy. First baby was born by elective caesarean section and the second baby by assisted vaginal delivery. They presented at 60 h and 48 h respectively. Both babies had similar clinical presentation in the form of poor feeding, shrill cry and posturing. But they had contrasting clinical course with features of brainstem compression in the first baby requiring ventilation. Coagulation workup was normal in the first baby but fibrinogen level was low in the second baby. Magnetic resonance imaging of the first baby showed PFSDH with tonsillar herniation while in the second baby, there was no midline shift or herniation associated with the PFSDH. Management was tailor made to suit the clinical course and imaging findings. Craniotomy and clot evacuation was done in the first case and in the second baby, management was conservative. Neurological examination was normal at discharge. Both are developmentally normal on follow up. There is no evidence of hydrocephalus in both. Management of PFSDH depends on clinical course and MRI findings. Timely intervention leads to good outcome.

The Importance of Flexion MRI in Hirayama Disease with Special Reference to Laminodural Space Measurements

BACKGROUND AND PURPOSE

Hirayama disease is a benign focal amyotrophy of the distal upper limbs involving C7, C8, and T1 segmental myotomes with sparing of the brachioradialis and proximal muscles of the upper limb innervated by C5-6 myotomes. The objective of the present study was to study the utility of MR imaging in young patients presenting with weakness and wasting of the distal upper extremity and to evaluate the importance of the laminodural space during flexion cervical MR imaging.

MATERIALS AND METHODS

This was a prospective cross-sectional study conducted from January 2014 to July 2017 in a tertiary care center from Northeast India. Forty-five patients with clinically definite Hirayama disease underwent electrophysiologic evaluation followed by MR imaging of the cervical spine.

RESULTS

The mean age at recruitment was 22.8 ± 5.5 years. Forty patients (88.9%) had unilateral and 5 (11.1%) had bilateral upper extremity involvement. Cervical cord T2-weighted hyperintensities were demonstrated in 16 patients (35.6%), of which 15 (33.3%) had anterior horn cell hyperintensities. Flexion MR imaging showed loss of the posterior dural attachment, forward shifting of the posterior dural sac with postcontrast enhancement, and prominent posterior epidural venous plexus in all patients. The laminodural space at maximum forward shifting of the posterior dural sac ranged from 3 to 9.8 mm, with a mean distance of 5.99 mm (95% confidence interval, 5.42-6.57 mm).

CONCLUSIONS

Flexion cervical MR imaging is a very useful investigation in diagnosing Hirayama disease. The increase in the laminodural space and the presence of cervical cord flattening during flexion are essential for diagnosis.

Rare Cause of Hyperkalemia in the Newborn Period: Report of Two Cases of Pseudohypoaldosteronism Type 1

Pseudohypoaldosteronism (PHA) Type 1 is characterized by mineralocorticoid resistance, manifesting as neonatal salt wasting, hypotension, hyperkalemia, hyponatremia, and metabolic acidosis in spite of elevated aldosterone levels and plasma renin activity. It is important to differentiate children with systemic PHA from renal PHA, as these children are likely to decompensate even with mild symptoms. Here, we report two neonates with PHA that presented to us with multiorgan involvement.

Improved Tapaswini having four BB resistance genes pyramided with six genes/QTLs, resistance/tolerance to biotic and abiotic stresses in rice

Rice, a major food crop, is grown in a wide range of ecological conditions and suffers significant yield losses as it is constantly exposed to a wide range of environmental and biotic stresses. The prevalence of different biotypes/strains has necessitated assembling of numerous resistance genes/QTLs into elite genotypes to confer a broader scale of resistance. The current study reports successful pyramiding of genes/QTLs that confer tolerance/resistance to submergence (Sub1), salinity (Saltol), blast (Pi2, Pi9) and gall midge (Gm1, Gm4) to supplement the four bacterial blight resistance genes (Xa 4, xa5, xa13, Xa21) present in Improved Tapaswini, an elite cultivar. The precise transfer of genes/QTLs was accomplished through effective foreground selection and suitable gene pyramids were identified. Background selection was practiced using morphological and grain quality traits to enhance the recovery of the recurrent parental genome. In the bioassays, the pyramids exhibited higher levels of resistance/ tolerance against the target stresses. The novel feature of the study was successful pyramidization and demonstration of the function of ten genes/QTLs in a new genotype. This success can stimulate several such studies to realize the full potential of molecular plant breeding as the foundation for rice improvement.

Metabolomics approach discriminates toxicity index of pyrazinamide and its metabolic products, pyrazinoic acid and 5-hydroxy pyrazinoic acid

Pyrazinamide (PYZ)-an essential component of primary drug regimen used for the treatment and management of multidrug resistant or latent tuberculosis-is well known for its hepatoxicity. However, the mechanism of PYZ-induced hepatotoxicity is still unknown to researchers. Studies have shown that the drug is metabolized in the liver to pyrazinoic acid (PA) and 5-hydroxy pyrazinoic acid (5-OHPA) which individually may cause different degrees of hepatotoxicity. To evaluate this hypothesis, PYZ, PA, and 5-OHPA were administered to albino Wistar rats orally (respectively, at 250, 125, and 125 mg kg^-1 for 28 days). Compared to normal rats, PYZ and its metabolic products decreased the weights of dosed rats and induced liver injury and a status of oxidative stress as assessed by combined histopathological and biochemical analysis. Compared to normal controls, the biochemical and morphological changes were more aberrant in PA- and 5-OHPA-dosed rats with respect to those dosed with PYZ. Finally, the serum metabolic profiles of rats dosed with PYZ, PA, and 5-OHPA were measured and compared with those of normal control rats. With respect to normal control rats, the rats dosed with PYZ and 5-OHPA showed most aberrant metabolic perturbations in their sera as compared to those dosed with PA. Altogether, the study suggests that PYZ-induced hepatotoxicity might be associated with its metabolized products, where 5-OHPA contributes to a higher degree in its overall toxicity than PA.

Nano sculpt: A methodology for generating complex realistic configurations for atomistic simulations

Atomistic simulations have now become commonplace in the study of the deformation and failure of materials. Increase in computing power in recent years has made large-scale simulations with billions, or even trillions, of atoms a possibility. Most simulations to-date, however, are still performed with quasi-2D geometries or rather simplistic 3D setups. Although controlled studies on such well-defined structures are often required to obtain quantitative information from atomistic simulations, for qualitative studies focusing on e.g. the identification of mechanisms, researchers would greatly benefit from a methodology that helps realize more realistic configurations. The ideal scenario would be a one-on-one reconstruction of experimentally observed structures. To this end, we propose a new method and software tool called nano sculpt with the following features:•The method allows for easy sample generation for atomistic simulations from any arbitrarily shaped 3D enclosed volume.•The tool can be used to build atomistic samples from artificial geometries, including CAD geometries and structures obtained from simulation methods other than atomistic simulations.•The tool enables the generation of experimentally informed atomistic samples, by e.g. digitization of micrographs or usage of tomography data.

Pathogenicity of Candida viswanathii for normal and cortisone-treated mice

The pathogenicity of Candida viswanathii, PCI 501/1 (CBS 4024), originally isolated from CSF of a fatal case of meningitis in India, is reported. Also, included is a global overview of the occurrence of C. viswanathii in clinical and environmental sources. The investigation was done in normal and cortisone-treated albino mice challenged intravenously with variable doses of 1×10(6), 4×10(6) and 16×10(6) actively growing yeast cells of the fungus. The animals were kept under observation up to 3 weeks when they were sacrificed for a mycological and histopathologic study. As apparent from the data on morbidity and mortality, the species exhibited low virulence for normal mice, whereas it caused significantly higher mortality (P<0.0008) and morbidity (macroscopic lesions) (P<0.0004) in cortisone group. Likewise, there was overall higher recovery of C. viswanathii in culture from the cortisone-treated than in the normal group of mice. These observations are indicative of C. viswanathii being an opportunistic pathogen. It is recognized that a definitive identification of C. viswanathii requires mycological expertise for comprehensive phenotypic characterization or the application of expensive techniques such as Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) and molecular techniques, facilities for which are generally lacking in a vast majority of laboratory diagnostic centers especially in developing countries. Consequently, the prevalence of C. viswanathii in clinical and environmental samples is currently likely to be underestimated.

Training-induced Increase in Bone Mineral Density between Growing Male and Female Rats

The purpose of this study was to determine the existence of sex differences in the resistance training-induced elevation in bone mineral density (BMD) and bone strength (Fmax) during the growth period in rats. 16 male (M) and 16 female (F) rats (approx. 8 weeks old) were randomly divided into sedentary control (MC=8, FC=8), and resistance-trained (RT) groups (M-RT=8, F-RT=8). The RT groups were conditioned to climb a vertical ladder 4 consecutive times (per exercise session) with weights attached to their tail 3 days per week for a total of 6 weeks. After 6 weeks, there were no interaction effects (sex×exercise). The main effect of sex indicated no difference in tibial BMD (in g/cm(2)) for males (0.226±0.005) compared to females (0.221±0.004). However, Fmax (in Newtons) was significantly greater for males (131.3±5.3) compared to females (89.9±3.0). The main effect of exercise indicated that tibial BMD and Fmax were significantly greater for RT groups (0.234±0.004 g/cm(2) and 120.9±7.4 Newtons) compared to controls (0.212±0.003 g/cm(2) and 100.3±5.1 Newtons). The results indicate that during growth, there were no sex differences in the training-induced elevation in BMD and bone mechanical properties.

Mitochondrial DNA-based genetic diversity of Anopheles nivipes in North East India

Malaria is a major public health problem in north-east India mainly transmitted by Anopheles baimai and An. minimus while Anopheles nivipes plays an important supportive role. The genetic diversity of An. nivipes in north-east India was investigated by employing two mitochondrial DNA markers namely NADH dehydrogenase 5 (ND5) and cytochrome oxidase sub unit II (COII). High genetic diversity in An. nivipes was observed by the detection of 16 haplotypes among 30 sequences of ND5 gene and 29 haplotypes among 29 COII sequences. Anopheles nivipes of north-east India was significantly differentiated genetically with that of neighboring South-east Asian An. nivipes as revealed by pairwise F_ST values of 0.127 (p < 0.01) and 0.044 (p < 0.001) for ND5 and COII genes, respectively, suggesting geographical barriers to gene flow in this species between the two geographical areas resulting in significant population structuring.

Larvicidal activity of few select indigenous plants of North East India against disease vector mosquitoes (Diptera: Culicidae)

Mosquitoes are the vectors of several life threatening diseases like dengue, malaria, Japanese encephalitis and lymphatic filariasis, which are widely present in the north-eastern states of India. Investigations on five local plants of north-east India, selected on the basis of their use by indigenous communities as fish poison, were carried out to study their mosquito larvicidal potential against Anopheles stephensi (malaria vector), Stegomyia aegypti (dengue vector) and Culex quinquefasciatus (lymphatic filariasis vector) mosquitoes. Crude Petroleum ether extracts of the roots of three plants viz. Derris elliptica, Linostoma decandrum and Croton tiglium were found to have remarkable larvicidal activity; D. elliptica extract was the most effective and with LC50 value of 0.307 μg/ml its activity was superior to propoxur, the standard synthetic larvicide. Half-life of larvicidal activity of D. elliptica and L. decandrum extracts ranged from 2-4 days.