MRF-ANN: a machine learning approach for automated ER scoring of breast cancer immunohistochemical images.

Molecular pathology, especially immunohistochemistry, plays an important role in evaluating hormone receptor status along with diagnosis of breast cancer. Time-consumption and inter-/intraobserver variability are major hindrances for evaluating the receptor score. In view of this, the paper proposes an automated Allred Scoring methodology for estrogen receptor (ER). White balancing is used to normalize the colour image taking into consideration colour variation during staining in different labs. Markov random field model with expectation-maximization optimization is employed to segment the ER cells. The proposed segmentation methodology is found to have F-measure 0.95. Artificial neural network is subsequently used to obtain intensity-based score for ER cells, from pixel colour intensity features. Simultaneously, proportion score - percentage of ER positive cells is computed via cell counting. The final ER score is computed by adding intensity and proportion scores - a standard Allred scoring system followed by pathologists. The classification accuracy for classification of cells by classifier in terms of F-measure is 0.9626. The problem of subjective interobserver ability is addressed by quantifying ER score from two expert pathologist and proposed methodology. The intraclass correlation achieved is greater than 0.90. The study has potential advantage of assisting pathologist in decision making over manual procedure and could evolve as a part of automated decision support system with other receptor scoring/analysis procedure.

Chest wall lymphomas: Fine needle aspiration cytodiagnosis and review of the literature.

OBJECTIVE: Compared to other chest wall malignancies, lymphoma is a common disease. However, published literature on a series of lymphoma cases involving the chest wall is scarce. The aim of the present study, was to describe experience with chest wall swellings diagnosed as lymphoid neoplasms on fine needle aspiration (FNA) cytology. METHODS: Eleven chest wall swellings were diagnosed as lymphoid neoplasms on FNA over a period of 15 years (January 2000-December 2014). The age of patients ranged from 19 to 73 years (median, 46). The male-to -emale ratio was 7:4. Ten cases had an anterior or lateral chest wall mass, and one swelling was in the scapular region. Six cases had concurrent lymphadenopathy, and one had bone involvement. The FNA smears were reviewed and classified under WHO Classification of Hematopoietic Neoplasms. The histopathological diagnoses were available in eight cases. RESULTS: The preliminary cytodiagnoses in 11 cases of chest wall lymphoid neoplasms were anaplastic large cell lymphoma (ALCL) in two cases, and ALCL/malignant melanoma, ALCL/T-cell-rich-B-cell lymphoma (TCRBCL)/Hodgkin's lymphoma (HL), plasmacytoma/neuroendocrine carcinoma, Hodgkin's lymphoma, small cell NHL/CLL, NHL, suggestive of NHL, post-transplant peripheral T-cell lymphoma (PTCL), and a malignant plasma cell tumour in one case each. The reviewed cytodiagnoses of lymphoid neoplasms were as follows: ALCL ( five cases), centroblastic lymphoma (two cases), and small cell lymphoma/CLL, post-transplant peripheral T-cell lymphoma, Hodgkin's lymphoma and plasmacytoma (one case each). Histopathological diagnoses available in eight cases confirmed the presence of lymphoid neoplasms. CONCLUSION: A variety of lymphoid neoplasms involved the chest wall, and among them, ALCL was a common form.

Computational microscopic imaging for malaria parasite detection: a systematic review.

Malaria, being an epidemic disease, demands its rapid and accurate diagnosis for proper intervention. Microscopic image-based characterization of erythrocytes plays an integral role in screening of malaria parasites. In practice, microscopic evaluation of blood smear image is the gold standard for malaria diagnosis; where the pathologist visually examines the stained slide under the light microscope. This visual inspection is subjective, error-prone and time consuming. In order to address such issues, computational microscopic imaging methods have been given importance in recent times in the field of digital pathology. Recently, such quantitative microscopic techniques have rapidly evolved for abnormal erythrocyte detection, segmentation and semi/fully automated classification by minimizing such diagnostic errors for computerized malaria detection. The aim of this paper is to present a review on enhancement, segmentation, microscopic feature extraction and computer-aided classification for malaria parasite detection.

Automated system for characterization and classification of malaria-infected stages using light microscopic images of thin blood smears.

In this paper, we propose a comprehensive image characterization cum classification framework for malaria-infected stage detection using microscopic images of thin blood smears. The methodology mainly includes microscopic imaging of Leishman stained blood slides, noise reduction and illumination correction, erythrocyte segmentation, feature selection followed by machine classification. Amongst three-image segmentation algorithms (namely, rule-based, Chan-Vese-based and marker-controlled watershed methods), marker-controlled watershed technique provides better boundary detection of erythrocytes specially in overlapping situations. Microscopic features at intensity, texture and morphology levels are extracted to discriminate infected and noninfected erythrocytes. In order to achieve subgroup of potential features, feature selection techniques, namely, F-statistic and information gain criteria are considered here for ranking. Finally, five different classifiers, namely, Naive Bayes, multilayer perceptron neural network, logistic regression, classification and regression tree (CART), RBF neural network have been trained and tested by 888 erythrocytes (infected and noninfected) for each features' subset. Performance evaluation of the proposed methodology shows that multilayer perceptron network provides higher accuracy for malaria-infected erythrocytes recognition and infected stage classification. Results show that top 90 features ranked by F-statistic (specificity: 98.64%, sensitivity: 100%, PPV: 99.73% and overall accuracy: 96.84%) and top 60 features ranked by information gain provides better results (specificity: 97.29%, sensitivity: 100%, PPV: 99.46% and overall accuracy: 96.73%) for malaria-infected stage classification.

Thermodynamics of cadmium sorption on different soils of West Bengal, India.

A sorption study was conducted on different soils collected from five agroecological zones of West Bengal, India, to understand the soil environmental behavior and fate of cadmium. For this purpose batch adsorption experiments were carried out at the native soil pH and at three different temperatures (25°C, 35°C, and 45°C). The adsorption data fitted by a linear least squares technique to the different sorption isotherms. Most data obtained give the good fit to both Freundlich and modified Langmuir isotherms, but they are not consistent with the linear Langmuir adsorption model. Thermodynamic parameters, namely, thermodynamics equilibrium constant at a particular temperature T (K T (0)), Gibbs free energy at a particular temperature T (ΔG T (0)), and change of enthalpy (ΔH (0)) and change of entropy at temperature T (ΔS T (0)), were also determined by applying sorption value and concentrations of Cd in equilibrium solution within the temperature range. The thermodynamic parameters revealed that Cd sorption increases as the values of K T (0), ΔG T (0), ΔH (0), and ΔS T (0) were increased on reaction temperatures. The spontaneous sorption reaction can be concluded due to high values of ΔG T (0). The positive values of ΔH (0) indicated that the Cd sorption is an endothermic one. Under these present conditions, the soil and its components possibly supply a number of sites having different adsorption energies for cadmium sorption.

Quantitative microscopy approach for shape-based erythrocytes characterization in anaemia.

Anaemia is one of the most common diseases in the world population. Primarily anaemia is identified based on haemoglobin level; and then microscopically examination of peripheral blood smear is required for characterizing and confirmation of anaemic stages. In conventional approach, experts visually characterize abnormality present in the erythrocytes under light microscope, and this evaluation process is subjective in nature and error prone. In this study, we have proposed a methodology using machine learning techniques for characterizing erythrocytes in anaemia associated with anaemia using microscopic images of peripheral blood smears. First, peripheral blood smear images are preprocessed based on grey world assumption technique and geometric mean filter for reducing unevenness of background illumination and noise reduction. Then erythrocyte cells are segmented using marker-controlled watershed segmentation technique. The erythrocytes in anaemia, such as, tear drop, echinocyte, acanthocyte, elliptocyte, sickle cells and normal erythrocytes cells have been characterized and classified based on their morphological changes. Optimal subset of features, ranked by information gain measure provides highest classification performance using logistic regression classifier in comparison with other standard classifiers.

Metal accumulation, biochemical response and yield of Indian mustard grown in soil amended with rural roadside pond sediment.

This present study aims to discern the effect of roadside pond sediments on Brassica juncea (L.) Czern. (cv. Rohini) by examining heavy metal uptake by different parts of the plant and its influence on biochemical properties, biomass, yield and oil content in plant. Although the treated soils were clearly contaminated with heavy metals (HMs) after application of pond sediments and chemical fertilizers, but the metal content in mustard leaves and seeds are below the permissible limit of consumable food. HMs accumulation was proportionally lesser in grains than in shoots and roots. All the biochemical characteristics were significantly (p<0.05) responded to the pond sediments application as compared to the control. Increase in photosynthetic pigment was also observed during growing period while pond sediment was used as amendment. This study revealed that Brassica juncea is well adapted to tolerate and accumulate high quantities of HMs due to increased level of antioxidants (cysteine and ascorbic acid) in roots, shoots and leaves. Multivariate techniques like principal component analysis and cluster analysis (CA) were used as classification techniques. On the basis of factor loadings and principal component scores, different parameters were grouped based on their similarity or closeness, separately in leaves, roots and seeds. A very similar grouping was also obtained using CA. However, pond sediment did not thwart the enhancement of mustard yield and oil content. Therefore, pond sediment would be a valuable resource for mustard as an alternative soil amendment for nutrients, but long-term use may require the cessation to restrict HMs contamination in soils.

Characterisation and in silico analysis of interleukin-4 cDNA of nilgai (Boselaphus tragocamelus) and Indian buffalo (Bubalus bubalis).

Interleukin-4 (IL-4) produced from Th2 cells modulates both innate and adaptive immune responses. It is a common belief that wild animals possess better immunity against diseases than domestic and laboratory animals; however, the immune system of wild animals is not fully explored yet. Therefore, a comparative study was designed to explore the wildlife immunity through characterisation of IL-4 cDNA of nilgai, a wild ruminant, and Indian buffalo, a domestic ruminant. Total RNA was extracted from peripheral blood mononuclear cells of nilgai and Indian buffalo and reverse transcribed into cDNA. Respective cDNA was further cloned and sequenced. Sequences were analysed in silico and compared with their homologues available at GenBank. The deduced 135 amino acid protein of nilgai IL-4 is 95.6% similar to that of Indian buffalo. N-linked glycosylation sequence, leader sequence, Cysteine residues in the signal peptide region, and 3' UTR of IL-4 were found to be conserved across species. Six nonsynonymous nucleotide substitutions were found in Indian buffalo compared to nilgai amino acid sequence. Tertiary structure of this protein in both species was modeled, and it was found that this protein falls under 4-helical cytokines superfamily and short chain cytokine family. Phylogenetic analysis revealed a single cluster of ruminants including both nilgai and Indian buffalo that was placed distinct from other nonruminant mammals.

Isoniazid preventive therapy among child contacts of TB patients, India.

BACKGROUND: Isoniazid preventive therapy (IPT) for child contacts of TB patients, a globally accepted intervention, needs to be evaluated in diverse geographical regions.OBJECTIVES: To assess the extent of IPT coverage and adherence, to ascertain its sociodemographic and programmatic correlates and to explore existing constraints from service providers and beneficiaries´ perspectives.METHODS: A mixed-method study was conducted in January-June 2021 in Paschim Bardhaman District, West Bengal, India. Quantitative assessment was done among 280 child contacts of TB cases registered between January and December 2020 in all TB units in the district. Primary caregivers were interviewed using a pre-designed questionnaire. Two focus group discussions with all senior treatment supervisors of the district and in-depth interviews with 12 purposively selected caregivers of the children were undertaken. Qualitative data were analysed thematically.RESULTS: Only 48.9% (137/280) of child contacts were screened; 58.9% (165/280) were initiated on IPT and 40% (66/165) adhered to a full course. Coverage of the full 6-month IPT among total study participants was 23.6% (66/280). Household visits by health personnel and initial screening significantly predicted increased coverage. Programmatic inadequacies, poor understanding, social stigma and COVID situation were major constraints.CONCLUSION: Coverage of IPT remains unacceptably low and requires health system strengthening for effectively implementing current recommendations of TB preventive treatment.

Functional recovery of diabetic mouse hearts by glutaredoxin-1 gene therapy: role of Akt-FoxO-signaling network.

Recent studies suggest that glutaredoxin-1 (Glrx-1) may serve as therapeutic target for diabetic hearts. As the level of reactive oxygen species (ROS) is increased in the pathologic hearts including ischemia/reperfusion (I/R) and diabetes, we assumed that upregulation of Glrx-1 could reduce the cardiac risk factors associated with I/R and/or diabetes. Diabetes was induced in mice by i.p. injection of streptozotocin (150 mg kg(-1)). Eight days after when the blood glucose was elevated to 400 mg per 100 ml, the animals were randomly assigned to one of the following three groups, which received either empty vector, or LacZ or Glrx-1 adenoviral construct. Four days later, isolated working hearts were subjected to 30 min ischemia followed by 2 h reperfusion. Glrx-1 gene therapy significantly enhanced the Glrx-1 level, which prevented I/R-mediated reduction of ventricular recovery, increased myocardial infarct size and cardiomyocyte apoptosis in diabetic myocardium. In concert, Glrx-1 prevented diabetes and ischemia-reperfusion induced reduction of cardioprotective proteins including Akt, FoxO-1, and hemeoxygenase-1, and abolished the death signal triggered by Jnk, p38 mitogen-activated protein kinase, and c-Src. Glrx-1 gene therapy seems to prevent cardiac complications in diabetic heart due to the I/R by switching the death signal into survival signal by activating Akt-FoxO-signaling network.

Poisoning, stings and bites in children-- what is new? An experience from a tertiary care hospital in Kolkata.

Poisonings, stings and bites continue to be important cause of pediatric morbidity and hospitalization. The toxic product involved in the poisoning varies in different geographical areas and in same area over time. A retrospective study was conducted amongst the children of the age group up to 12 years admitted to a tertiary care hospital in Kolkata from January 2005 to December 2008. Total number of admissions was 17019 and that for accidental poisoning was 451 (2.65%). Kerosene constituted the largest group (54.55%). Mosquito coil and refill liquid were the new additions to the list of poisons and their ingestion was cause for admission of 15 (3.33%) children. The number of admissions due to stings and bites was 108 (0.63% of all admissions) during the above period. Of all the cases, 9 (1.83%) cases of accidental poisoning and 4 (3.7%) cases of stings and bites died.

Molecular characterization of toll-like receptor 2 of ruminants and comparative expression in nilgai (Boselaphus tragocamelus) vs. buffalo (Bubalus bubalis).

Toll-like receptors play role in the innate immune responses and orchestrate the adaptive immunity by induction of proinflammatory cytokines and up-regulation of costimulatory molecules. The present study has characterized TLR2 cDNA in nilgai, buffalo, sheep and goat that recognizes the peptidoglycan of Gram-positive bacteria. TLR2 coding sequences were amplified from monocytes cDNA and cloned in pGEMT-easy vector for nucleotide sequencing. Sequence analysis revealed 2355-bp-long TLR2 open reading frame encoding 784 amino acids in all the species studied. Nilgai TLR2 has 97.8% to 95.1% identity at nucleotide level and 96.2% to 92.7% identity at amino acid level with other ruminant species studied. Nonsynonymous substitutions exceeding synonymous substitutions indicated evolution of this receptor through positive selection among ruminants. Furthermore, basal TLR2 messenger RNA expression in different immune cells and tissues quantified by real-time polymerase chain reaction revealed highest level in in vitro derived dendritic cells followed by peripheral blood mononuclear cells. Skin and testes also expressed significant level in both nilgai and buffalo. Comparatively, nilgai immune cells and tissues expressed more TLR2 transcript than buffalo, thus elucidating stronger armamentarium of antibacterial immunity in nilgai as compared to buffalo.

Elimination of iodine deficiency disorders--current status in Purba Medinipur district of West Bengal, India.

BACKGROUND AND OBJECTIVES: Towards sustainable elimination of iodine deficiency disorders (IDD), the existing programme needs to be monitored through recommended methods and indicators. Thus, we conducted the study to assess the current status of IDD in Purba Medinipur district, West Bengal. METHODS: It was a community based cross-sectional study; undertaken from October 2006-April 2007. 2400 school children, aged 8-10 years were selected by '30 cluster' sampling technique. Indicators recommended by the WHO/UNICEF/ICCIDD were used. Subjects were clinically examined by standard palpation technique for goitre, urinary iodine excretion was estimated by wet digestion method and salt samples were tested by spot iodine testing kit. RESULTS: The total goitre rate (TGR) was 19.7% (95% CI = 18.1-21.3 %) with grade I and grade II (visible goitre) being 16.7% and 3% respectively. Goitre prevalence did not differ by age but significant difference was observed in respect of sex. Median urinary iodine excretion level was 11.5 mcg/dL and none had value less than 5 mcg/dL. Only 50.4% of the salt samples tested were adequately iodised (> or = 15 ppm). CONCLUSION: The district is in a phase of transition from iodine deficiency to iodine sufficiency as evident from the high goitre prevalence (19.7%) and median urinary iodine excretion (11.5 mcg/dL) within optimum limit. But, salt iodisation level far below the recommended goal highlights the need for intensified efforts towards successful transition.

Persistence of gaps in implementation of revised national tuberculosis control program in an area of West Bengal.

A study was conducted to evaluate the RNTCP in Habra TB, unit North 24 Parganas district, in February 2004. We collected both primary and secondary data, cross-checked registers and records. The TB unit was catering 23% more population; 54% of patients belonged to backward section. All patients received free drugs and free microscopy services; 90% received DOT during intensive phase and 67% during continuation phase; DOT time was inconvenient to 20% patients and 30% in attending DOT; 14% patients did not give three sputum samples at diagnosis; 28.3% centers lacked expected facilities; inconsistency in 27.8% drug boxes; records lacking in address verification (74.4%) and defaulter retrieval activity (47.2%). Delay in diagnosis and initiation of treatment was also prevailed.

Targeted disruption of the mouse Sod I gene makes the hearts vulnerable to ischemic reperfusion injury.

The role of Cu/Zn-superoxide dismutase (SOD) in myocardial ischemic reperfusion injury was studied by using a mouse model with targeted disruption of the mouse Sod I gene. Inactivation of the functional mouse Sod I gene in hearts by gene targeting (Sod I(+/-)) resulted in a 50% reduction of Cu/Zn-SOD mRNA and significant reduction of Cu/Zn-SOD enzyme activity compared with that of wild-type Sod I(+/+) mice. Cu/Zn-SOD mRNA could not be detected in Sod I(-/-) heart. The isolated buffer-perfused hearts from the knockout mice devoid of any functional copy of the Sod I (Sod I(-/-)) and matched nontransgenic control mice were subjected to 30 minutes of global ischemia followed by 2 hours of reperfusion. For both groups of mice, the postischemic functional recovery for the hearts was lower than the baseline, but the recovery for the Sod I(-/-) was less compared with the wild-type mice. Thus, the postischemic recovery of the developed force and the maximum first derivative of the developed force were consistently lower for the Sod I(-/-) mouse hearts compared with wild-type control hearts. The coronary flow was lower compared with the baseline levels for both groups of hearts, but there was no significant difference between the groups. The myocardial infarction determined from the ratio of infarct size/area of risk was higher for the Sod I(-/-) mice compared with the control mice. The amount of creatine kinase release from the wild-type mouse hearts was less compared with the Sod I(-/-) mouse hearts. In concert, a reduced amount of oxidative stress was found in the hearts of wild-type mice compared with Sod I(-/-) mouse hearts. These results documented that Sod I(-/-) mouse hearts were more susceptible to ischemic reperfusion injury compared with corresponding wild-type mouse hearts, suggesting that the Sod I gene constitutes an important defense element for the hearts.

Simulation of fertilizer requirement for irrigated wheat in eastern India using the QUEFTS model.

Crop modeling can provide us with information about fertilizer dose to achieve the target yield, crop conditions, etc. Due to conventional and imbalanced fertilizer application, nutrient use efficiency in wheat is low. Estimation of fertilizer requirements based on quantitative approaches can assist in improving yields and nutrient use efficiency. Field experiments were conducted at 20 sites in eastern India (Nadia district of West Bengal) to assess the soil supply, requirement, and internal efficiency of N, P, K, and Zn in wheat. The data were used to calibrate the QUEFTS (Quantitative Evaluation of the Fertility of Tropical Soils) model for site-specific, balanced fertilizer recommendations. The parameters of maximum accumulation (a) and maximum dilution (d) in wheat were calculated for N (35, 100), P (129, 738), K (17, 56), and Zn (21502, 140244). Grain yield of wheat showed statistically significant correlation with N (R2 = 0.937**), P (R2 = 0.901**), and K uptake (R2 = 0.801**). The NPK ratio to produce 1 tonne grain yield of wheat was calculated to be 4.9:1.0:8.9. The relationships between chemical properties and nutrient-supplying capacity of soils were also established. The model was validated using the data from four other experiments. Observed yields with different amounts of N, P, K, and Zn were in good agreement with the predicted values, suggesting that the validated QUEFTS model can be used for site-specific nutrient management of wheat.

Hemoglobin Detroit: beta95 (FG2) lysine leads to asparagine.

Hb Detroit is a mutant which migrates between Hb A and Hb J Baltimore on cellulose acetate (pH 8.5), and with Hb A on citrate agar (pH 6.0). Globin chain analyses in alkaline and acid buffers reveal an abnormal beta chain with a mobility between the betaA and betaJ Baltimore chains. Structural characterization of this abnormal chain shows that lysine at position 95 is replaced by asparagine. No hematological abnormalities could be attributed to the presence of the mutant, and the oxygen affinity properties of the stripped hemoglobin are similar to those of Hb A. The beta95 residue which is substituted in Hb Detroit and also in Hb N Baltimore ((beta95 Lys leads to Glu) does not appear to be in a critical functional area of the molecule.

Release of fatty acid-binding protein from ischemic-reperfused rat heart and its prevention by mepacrine.

In an attempt to resolve the issue of whether there is a loss of fatty acid binding protein (H-FABP) from heart during ischemia and reperfusion, and to further examine the role of this protein in ischemic-reperfusion injury, the amount of H-FABP of heart was monitored during ischemia and reperfusion. Excellent correlation was obtained between the loss of H-FABP from heart and its appearance in the perfusate buffer when examined by Western blot using the specific antibody to H-FABP. Further quantitation was achieved by densitometric scanning of the Western blot and rocket electrophoresis. Maximum release of H-FABP was observed within 20 min of reperfusion, the total release being 10% of the H-FABP content of the heart. Mepacrine, a membrane stabilizer and a phospholipase inhibitor, reduced the release of H-FABP from the heart and prevented the accumulation of nonesterified fatty acids in the tissue during ischemia and reperfusion. In view of the established role of H-FABP in the preservation of membrane phospholipids by either scavenging free radicals during ischemia and reperfusion or by modulating the enzymes of phospholipid synthesis, it seems likely that the loss of H-FABP may have some contribution towards the ischemic-reperfusion injury.