ChemTextMiner: An open source tool kit for mining medical literature abstracts

Text mining involves recognizing patterns from a wealth of information hidden latent in unstructured text and deducing explicit relationships among data entities by using data mining tools. Text mining of Biomedical literature is essential for building biological network connecting genes, proteins, drugs, therapeutic categories, side effects etc. related to diseases of interest. We present an approach for textmining biomedical literature mostly in terms of not so obvious hidden relationships and build biological network applied for the textmining of important human diseases like MTB, Malaria, Alzheimer and Diabetes. The methods, tools and data used for building biological networks using a distributed computing environment previously used for ChemXtreme[1] and ChemStar[2] applications are also described

Comparative study of serum urea, creatinine and C-reactive protein level in chronic kidney disease patients with healthy subjects

Background: Chronic diseases are a leading cause of morbidity and mortality in India. Globally, chronic kidney disease is the 12th cause of death and the 17th cause of disability, respectively. CKD is defined as kidney damage or glomerular filtration rate (GFR) <60 mL/min/1.73 m2 for 3 months or more, irrespective of cause. The present study aimed to find out correlation between serum urea, creatinine and C-reactive protein (CRP) level among patients suffering from chronic kidney disease in an urban based tertiary care hospital in Bikaner, western Rajasthan, India.Methods: This study was conducted at Sardar Patel Medical College and Associated Hospitals at Bikaner, Rajasthan from August 2015 to December 2016. There were 50 cases and 50 controls in the age groups from 10 to 60 yearrs. We took fresh samples and performed required tests following standard protocol. CRP has been done by Antigen Antibody reaction (latex method). RFT has been performed on semi-automatic analyzer.Results: Levels of serum urea and creatinine were significantly raised in CKD patients (p-value<0.005) and CRP level was raised in 52% cases. While 48% cases having normal level %), which requires further study.  Renal function tests were significantly higher in cases than controls.Conclusions: Serum creatinine and urea level were significantly higher in cases as compared to control group

Correlation between prostate specific antigen and prostate volume with disease symptom severity assessed by international prostate symptom score

Background: Benign prostatic hyperplasia (BPH) is clinically defined as prostate adenoma, resulting in bladder outlet obstruction (BOO), which may eventually harm the bladder and even kidneys. For differential diagnosis of male LUTS, uroflowmetry can be used together with non-invasive ultrasound to ascertain the flow rate and IPP. PSA is also an important indicator for differential diagnosis. International prostate symptoms score (IPSS) is used to assess the severity of the symptoms for clinical BPH. There is also a recommendation to consider the quality of life (QoL) index, where a QoL score of ≥3 is considered as worrisome. Methods: This was a retro-prospective study based on secondary and primary data collection and analysis, pertaining to BPH patients who visited the study site previously as well as those who are coming for regular follow-up since 2019. Patient enrolment was done at a teaching hospital Shree Krishna Hospital affiliated to the Pramukh Swami Medical College, Bhaikaka University, Karamsad. About 100 patients presenting with lower urinary tract symptoms (LUTS) and histo-pathologically proven cases of BPH were enrolled to pursue research objectives. All patients were followed up to a period of 3-months after initiating the treatment and disease severity through IPSS and quality of life upon completion of treatment were also assessed. Results: PSA is also an important indicator for differential diagnosis, which is generally less than 1 μg/l in patients in absence of clinically confirmed BPH. In our study, mean prostate volume was reported to be 43.46±19.35 cc. A positive correlation was observed between prostate volume and serum PSA with disease severity. Conclusions: Our study evaluated the IPSS to predict the disease severity and correlated it with quality of life, prostate volume and serum PSA. Our findings were in line with currently available evidences, and suggested that QoL, prostate volume and serum PSA are better predictors of disease severity, IPSS

Genome-wide characterization, molecular evolution and mexpression profiling of the metacaspases in potato (Solanum tuberosum L.)

Metacaspases are distant relatives of animal caspases found in plants, protozoa and fungi. Some recent studies have demonstrated that metacaspases are involved in regulating the developmental and environmentally induced programmed cell death in plants. In this study, we identified metacaspase gene family in potato (Solanum tuberosum L.) and analyzed their expression pattern in various developmental tissues and stress responses of plants. There were eight metacaspase genes identified in the Peptidase (Cysteine protease) C14 family and based upon sequence alignment and phylogenetic analysis, a systematic nomenclature of potato metacaspases (SotubMCs) has been proposed. Three of the eight candidate genes showing homology with Arabidopsis thaliana type I metacaspase, AtMC1 were given name SotubMC1, SotubMC2 and SotubMC3 as per the degree of relatedness. Similarly, the next three being homologous to A. thaliana type I metacaspase, AtMC3 were named SotubMC4, SotubMC5, and SotubMC6. The remaining two were named SotubMC7 and SotubMC8, showing significant similarity with type II metacaspases of A. thaliana, AtMC4 and AtMC9, respectively. Evolutionary divergence analysis of SotubMCs from its orthologs in seven other members of Solanaceae family as well as with A. thaliana, Vitis vinifera and Oryza sativa was also carried out. The dN/dS ratios of the orthologous pairs suggested the SotubMCs were under purifying (negative) selection in course of plant evolution. Splicing patterns of potato metacaspases were also analyzed. Amongst all SotubMCs, SotubMC2, SotubMC4, SotubMC6 and SotubMC7 genes appeared to produce multiple alternative spliced variants of different lengths. Furthermore using protein modeling tools, we have predicted the protein structure of identified metacaspases. The cis-regulatory elements analysis was also performed exhibiting the presence of development, stress and hormones related cis-elements in the promoter regions of the SotubMCs. This indicates that potato metacaspases might be playing important roles in the development, stress and hormone responsive pathways. Moreover, relative expression analysis of identified genes was carried out using qRT-PCR in various developmental tissues that also include stolons and tubers. The eight metacaspases showed differential expression in different tissues. Some of the tissues such as leaf undergoing senescence among different leaf developmental stages (immature, mature and senescent) displayed higher relative expression of some of the metacaspases, implying their involvement in leaf senescence. The expression pattern of SotubMCs under various abiotic, biotic and hormonal stresses was also analysed. The results showed that many members of the potato metacaspase gene family displayed differential expression patterns under various stress conditions. Taken together, the study could provide crucial resources for further investigations to understand the functional roles of the identified metacaspases in potato

Thoracic outlet syndrome due to compression of subclavian artery at first rib

Thoracic Outlet Syndrome (TOS) refers to a constellation of signs and symptoms that arise from compression of the neurovascular bundle within the confined space of the thoracic outlet. Neurogenic (nTOS) from brachial plexus compression (95%), venous (vTOS) from subclavian vein compression (3%), & arterial (aTOS) from subclavian artery compression (1%). Most common clinical presentation of aTOS patients is distal upper extremity arterial emboli in otherwise healthy patient. Presenting a case report of arterial thoracic outlet syndrome.

Certain expansion formulae involving incomplete I-functions

The aim of this paper is to derive the expansion formulae for the incomplete I-function. Furthermore, their special cases are illustrated in terms of various types of special functions (incomplete I-function, incomplete H-function, and incomplete H-function) that are common in nature and very useful for further analysis.Publisher's Versio

Rare case of Hirayama’s disease

Hirayama’s disease is a rare benign neurological disorder also known as monomelic amyotrophy, Sobue disease,Juvenile Muscular Atrophy of Distal Upper Extremity (JMADUE). It mainly affects young males in their second or third decades and is most commonly seen in Asian countries like Japan, Malaysia and India. In majority of the cases the cause of the disease is unknown. An 18 year male came with weakness in his right hand and forearm since 1 year. Examination revealed weakness and wasting of muscles of forearm and hand without lower limb involvement and normal deep tendon reflexes. MRI showed focal short segment hyperintense signal in the ventral and right lateral aspect of the cervical cord at C5-C6 level with the involved segment measuring 4x3mm in size. Based on clinical and radiological features a diagnosis of focal amyotrophy was made. Patient is given a cervical collar to prevent flexion at the neck and physiotherapy in the form of hand and forearm exercises were started. Regular follow up of the patient once every 2 months is being done. Hirayama’s disease is a rare, benign, self-limiting neurological disorder. Early diagnosis and management by preventing cervical flexion with the help of a cervical collar has shown to halt the progression of the disease

Predictive role of fragmented QRS in patients with ST-elevation myocardial infarction undergoing primary percutaneous coronary intervention

Objective: Fragmented QRS (fQRS), as defined by additional spikes in the QRS complex of a 12-lead electrocardiogram (ECG), is a marker of scarred myocardium. In patients with coronary artery disease (CAD), fQRS is a predictor of heart failure (HF) and other major adverse cardiac events (MACE). The study was aimed to evaluate the role of fQRS in prediction of HF in patients with ST-elevation myocardial infarction (STEMI) undergoing primary percutaneous coronary intervention (PCI). Methods: In a prospective, non-randomized, small observational study, we enrolled 188 consecutive patients with STEMI undergoing primary PCI. Patients were grouped according to the presence or absence of fQRS and their in-hospital, 1 and 6-month MACE outcomes were assessed. Results: Of the 188 patients, fQRS were noted in 92 (48.94%) patients. Patients with fQRS were more likely to have Killip class II/III/IV. Patients with fQRS had a significantly higher corrected QT interval, lower left ventricular ejection fraction (LVEF), and higher N-terminal pro brain natriuretic peptide (NT-pro BNP) at 24 hours and 48 hours compared to patients without fQRS. The in-hospital (P=0.001), 30-day (P=0.03) and 6-month (p=0.01) MACE were higher in patients with fQRS. On logistic multiple analysis, fQRS in anterior leads (OR=3.70, CI=1.68-10.02, p=0.001), fQRS in more than 2 leads (OR=5.20, CI=1.51-12.83, p=0.01), NT-proBNP (OR=1.05, CI=1.03-1.08, p=0.02) and Killip class II/III/IV were found to be significant predictors for HF hospitalization. Conclusion: Our findings suggest that fQRS can be a predictor for HF in patients with STEMI and provide a simple and readily available technique for predicting prognosis. Larger studies are required to validate these findings

Socio-Economic Inequalities in the Use of Postnatal Care in India

OBJECTIVES: First, our objective was to estimate socio-economic inequalities in the use of postnatal care (PNC) compared with those in the use of care at birth and antenatal care. Second, we wanted to compare inequalities in the use of PNC between facility births and home births and to determine inequalities in the use of PNC among mothers with high-risk births. METHODS AND FINDINGS: Rich-poor ratios and concentration indices for maternity care were estimated using the third round of the District Level Household Survey conducted in India in 2007-08. Binary logistic regression models were used to examine the socio-economic inequalities associated with use of PNC after adjusting for relevant socio-economic and demographic characteristics. PNC for both mothers and newborns was substantially lower than the care received during pregnancy and child birth. Only 44% of mothers in India at the time of survey received any care within 48 hours after birth. Likewise, only 45% of newborns received check-up within 24 hours of birth. Mothers who had home births were significantly less likely to have received PNC than those who had facility births, with significant differences across the socio-economic strata. Moreover, the rich-poor gap in PNC use was significantly wider for mothers with birth complications. CONCLUSIONS: PNC use has been unacceptably low in India given the risks of mortality for mothers and babies shortly after birth. However, there is evidence to suggest that effective use of pregnancy and childbirth care in health facilities led to better PNC. There are also significant socio-economic inequalities in access to PNC even for those accessing facility-based care. The coverage of essential PNC is inadequate, especially for mothers from economically disadvantaged households. The findings suggest the need for strengthening PNC services to keep pace with advances in coverage for care at birth and prenatal services in India through targeted policy interventions

Bronchiectasis in India:results from the European Multicentre Bronchiectasis Audit and Research Collaboration (EMBARC) and Respiratory Research Network of India Registry

BACKGROUND: Bronchiectasis is a common but neglected chronic lung disease. Most epidemiological data are limited to cohorts from Europe and the USA, with few data from low-income and middle-income countries. We therefore aimed to describe the characteristics, severity of disease, microbiology, and treatment of patients with bronchiectasis in India. METHODS: The Indian bronchiectasis registry is a multicentre, prospective, observational cohort study. Adult patients ( 6518 years) with CT-confirmed bronchiectasis were enrolled from 31 centres across India. Patients with bronchiectasis due to cystic fibrosis or traction bronchiectasis associated with another respiratory disorder were excluded. Data were collected at baseline (recruitment) with follow-up visits taking place once per year. Comprehensive clinical data were collected through the European Multicentre Bronchiectasis Audit and Research Collaboration registry platform. Underlying aetiology of bronchiectasis, as well as treatment and risk factors for bronchiectasis were analysed in the Indian bronchiectasis registry. Comparisons of demographics were made with published European and US registries, and quality of care was benchmarked against the 2017 European Respiratory Society guidelines. FINDINGS: From June 1, 2015, to Sept 1, 2017, 2195 patients were enrolled. Marked differences were observed between India, Europe, and the USA. Patients in India were younger (median age 56 years [IQR 41-66] vs the European and US registries; p&lt;0\ub70001]) and more likely to be men (1249 [56\ub79%] of 2195). Previous tuberculosis (780 [35\ub75%] of 2195) was the most frequent underlying cause of bronchiectasis and Pseudomonas aeruginosa was the most common organism in sputum culture (301 [13\ub77%]) in India. Risk factors for exacerbations included being of the male sex (adjusted incidence rate ratio 1\ub717, 95% CI 1\ub703-1\ub732; p=0\ub7015), P aeruginosa infection (1\ub729, 1\ub710-1\ub750; p=0\ub7001), a history of pulmonary tuberculosis (1\ub720, 1\ub707-1\ub734; p=0\ub7002), modified Medical Research Council Dyspnoea score (1\ub732, 1\ub725-1\ub739; p&lt;0\ub70001), daily sputum production (1\ub716, 1\ub703-1\ub730; p=0\ub7013), and radiological severity of disease (1\ub703, 1\ub701-1\ub704; p&lt;0\ub70001). Low adherence to guideline-recommended care was observed; only 388 patients were tested for allergic bronchopulmonary aspergillosis and 82 patients had been tested for immunoglobulins. INTERPRETATION: Patients with bronchiectasis in India have more severe disease and have distinct characteristics from those reported in other countries. This study provides a benchmark to improve quality of care for patients with bronchiectasis in India. FUNDING: EU/European Federation of Pharmaceutical Industries and Associations Innovative Medicines Initiative inhaled Antibiotics in Bronchiectasis and Cystic Fibrosis Consortium, European Respiratory Society, and the British Lung Foundation