Draft genome sequence of plastic degrading Bacillus sp. AIIW2 isolated from the Arabian ocean

The endemic spread of plastic in the environment requires urgent need of a sustainable approach. Marine microbes found to have vast bioactivity and play a central role in biogeochemical cycling in the ocean; however, very few of them had been explored for biochemical cycling or plastic degradation. In the present study, we report the draft genome sequence of marine Bacillus sp. AIIW2 which was found to utilize plastic as a carbon source. The Bacillus sonorensis SRCM101395 was used as a reference genome for mapping the reads. The genome size of strain AIIW2 was approximately 4.4 Mb and composed of 4737 coding sequences with 45.7% G + C contents. The whole genome comparison of strain AIIW2 with three closest Bacillus strains showed strain specificity, the 16S ribosomal RNA sequence shows 99.93% similarity with Bacillus paralicheniformis KJ-16^T (KY694465). This genome data would provide the genetic basis in developing plastic bioremediation approaches and discover the enzymes pertinent in the biodegradation processes.     

Clinical Concept-Based Radiology Reports Classification Pipeline for Lung Carcinoma

Rising incidence and mortality of cancer have led to an incremental amount of research in the field. To learn from preexisting data, it has become important to capture maximum information related to disease type, stage, treatment, and outcomes. Medical imaging reports are rich in this kind of information but are only present as free text. The extraction of information from such unstructured text reports is labor-intensive. The use of Natural Language Processing (NLP) tools to extract information from radiology reports can make it less time-consuming as well as more effective. In this study, we have developed and compared different models for the classification of lung carcinoma reports using clinical concepts. This study was approved by the institutional ethics committee as a retrospective study with a waiver of informed consent. A clinical concept-based classification pipeline for lung carcinoma radiology reports was developed using rule-based as well as machine learning models and compared. The machine learning models used were XGBoost and two more deep learning model architectures with bidirectional long short-term neural networks. A corpus consisting of 1700 radiology reports including computed tomography (CT) and positron emission tomography/computed tomography (PET/CT) reports were used for development and testing. Five hundred one radiology reports from MIMIC-III Clinical Database version 1.4 was used for external validation. The pipeline achieved an overall F1 score of 0.94 on the internal set and 0.74 on external validation with the rule-based algorithm using expert input giving the best performance. Among the machine learning models, the Bi-LSTM_dropout model performed better than the ML model using XGBoost and the Bi-LSTM_simple model on internal set, whereas on external validation, the Bi-LSTM_simple model performed relatively better than other 2. This pipeline can be used for clinical concept-based classification of radiology reports related to lung carcinoma from a huge corpus and also for automated annotation of these reports.

     

TP53 polymorphisms in gliomas from Indian patients: Study of codon 72 genotype, rs1642785, rs1800370 and 16 base pair insertion in intron-3

Several single nucleotide polymorphisms of the TP53 gene have been reported, amongst which polymorphism in codon 72 (rs1042522) has received significant attention and shown to be associated with disease susceptibility in different cancer types. However, there are variable reports on this polymorphism in gliomas from worldwide with inconsistent results. In addition, the implications of other polymorphic loci are not much explored in gliomas. Hence, in the present study the TP53 sequence was analyzed for all polymorphism and mutations in a total of 84 gliomas of different types and grades from patients of Indian origin. The complete sequence of all coding exons (2 to 11) and introns 2, 3, 5 and 8 of TP53 gene were studied while for introns 1, 4, 6, 7, 9 and 10, only exon flanking regions could be studied. The polymorphic loci were compared with control population. In addition to the well known codon 72 polymorphism (rs1042522), three other polymorphisms rs1642785, rs1800370 and a 16 base pair insertion in intron-3 were found. At codon 72, our study showed higher Arg/Arg genotype in gliomas compared to normal population (38% versus 13%). The Arg allele frequency in glioma patients was comparatively higher than controls (0.55 versus 0.45; P = 0.037). The Arg allele frequency was also high in adult glioblastomas compared to paediatric counterparts (0.55 versus 0.36). However, there was no significant association of TP53 mutations with any genotype of codon 72. At rs1642785, the G allele frequency was significantly higher in gliomas than in control population (0.55 versus 0.36, P = 0.005). The genotype at a 16 base pair insertion in intron-3 was almost similar in case and control. However, the polymorphism at rs1800370 was exclusive to gliomas. This is the first report of TP53 gene polymorphism in glioma patients from India. Our study also delineates the frequency of four polymorphisms in gliomas for the first time. The codon 72 variant (rs1042522) and rs1642785 polymorphisms possibly poses risk to glioma development in Indian population. However, the functional significance of these polymorphism needs further elucidation.     

Ultrasound biomicroscopic characteristics of the anterior segment in primary congenital glaucoma

PURPOSE: To evaluate qualitatively and quantitatively ultrasound biomicroscopic (UBM) features of the anterior segment in eyes with primary congenital glaucoma. METHODS: UBM of 45 eyes of patients with primary congenital glaucoma (39 previously operated and 6 unoperated eyes) and 28 control eyes were included in this study. UBM parameters were correlated with ocular biometry. Iris thickness, ciliary body thickness, ciliary body-lens distance, posterior chamber depth, and anterior chamber angle were measured and compared with control eyes. Other features of the anterior segment were qualitatively evaluated. RESULTS: A thin, stretched-out ciliary body and abnormal tissue at the iridocorneal angle were features seen in 90% of UBM scans. Iris thickness and stretched zonules correlated with the axial length (r = -0.6 and 0.58, respectively; p = 0.04) but not with the mean corneal diameter. Abnormal insertion of the ciliary body to the posterior surface of the iris was noted in eight eyes (17%). CONCLUSIONS: The present study documents characteristic anterior segment dysplasia and ciliary body anomalies in patients with primary congenital glaucoma.     

Adverse drug event detection in a community hospital utilising computerised medication and laboratory data.

OBJECTIVE: Computerised monitors can detect and, with clinical intervention, often prevent or ameliorate adverse drug events (ADEs). We evaluated whether a computer-based alerting system was useful in a community hospital setting. METHODS: We evaluated 6 months of retrospectively collected medication and laboratory data from a 140-bed community hospital, and applied the rules from a computerised knowledge base to determine if the resulting alerts might have allowed a clinician to prevent or lessen harm related to medication toxicity. We randomly selected 11% (n = 58, of which 56 were available) of charts deemed to be high- or critical-priority alerts, based on the likelihood of the alerts being associated with injury, to determine the frequencies of ADEs and preventable ADEs. RESULTS: In 6 months, there were 8829 activations of the rule set, generating a total of 3547 alerts. Of these, 528 were of high or critical priority, 664 were of medium priority and 2355 were of low priority. Chart review among the sample (56 charts) of high- or critical-priority alerts found five non-preventable and two preventable ADEs, suggesting that among the total high- or critical-priority alerts alone, there would be approximately 94 non-preventable ADEs and 37 preventable ADEs annually in this hospital that could be detected using this method. CONCLUSIONS: Computer-based rules engines have the potential to identify and, with clinical intervention, mitigate preventable ADEs, and implementation is feasible in community hospitals without an advanced information technology application.     

Variation in content of taxol and related taxanes in Eastern Himalayan populations of Taxus wallichiana

Extraction and analysis of paclitaxel and other taxanes in bark, needle leaves and stem segments of male and female plants of Taxus wallichiana, representing several populations, indicate that significant variation in taxane content exists within the population. Bark accumulated maximum amount of paclitaxel in almost all plants. Populations located at higher altitude tended to accumulate more paclitaxel than lower altitude plants. Seasons in which samples were collected and plant age have also been shown to affect paclitaxel accumulation. No effects of plant sex on paclitaxel content of the plants analyzed were observed. Significant differences in baccatin-III and 10-deacetylbaccatin III content were found to exist in the trees analyzed in this study.     

Development of transferable skills during short special study modules: students' self-appraisal

Special study modules (SSMs) were introduced into the Leeds undergraduate medical curriculum following recommendations by the General Medical Council (GMC). The main rationale behind such project work is to enable students to develop the skills and attitudes necessary for future self-directed learning along with the knowledge required to practise as competent doctors. At the University of Leeds, the students complete SSM monitoring forms for each SSM in the fourth year, aimed at allowing students to self-evaluate the SSMs. In addition, it provides useful feedback from the students on the themes of the projects as well as on the transferable skills developed by the students during their individual SSMs. The aim of the study was to identify the themes pursued in each project, look at the transferable skills developed and evaluate the differences or similarities between the type of project pursued and the themes and skills identified in the different specialities. A total of 181 monitoring forms of fourth-year students were analysed for the themes and the transferable skills identified. There were 55 students each in Obstetrics and Gynaecology and Paediatrics and 50 students each in Psychiatry and General Practice/Public Health. The results from the four specialities were compared for themes and skills identified. Overall, health and prevention was the commonest theme identified followed by communication skills (64.4% and 62.7% respectively). All transferable skills were well represented in the different specialities with information gathering and learning/organizational skills identified by most students as the major component. The feedback from the students is positive in terms of a wide range of transferable skills developed and most of the themes identified by the GMC are being pursued.     

Depletion of norepinephrine decreases the proliferation,but does not influence the survival and differentiation,of granule cell progenitors in the adult rat hippocampus

The dentate gyrus region retains the ability to generate neurons throughout adulthood. A few studies have examined the neurotransmitter regulation of adult hippocampal neurogenesis and have shown that this process is regulated by serotonin and glutamate. Given the strong noradrenergic innervation of the adult hippocampus and the ability of norepinephrine to influence proliferation during development, we examined the influence of norepinephrine on adult hippocampal neurogenesis. Our study indicates that depletion of norepinephrine by the selective noradrenergic neurotoxin, N-(2-chloroethyl)-N-ethyl-2-bromo benzylamine hydrochloride (DSP-4), results in a 63% reduction in the proliferation of dentate gyrus progenitor cells identified through 5-bromo-2'-deoxyuridine (BrdU) labelling. In contrast, the survival of BrdU-positive cells labelled prior to treatment with DSP-4 is not influenced by norepinephrine depletion. The differentiation of BrdU labelled progenitors into neurons or glia was also not sensitive to noradrenergic depletion. These results indicate that the proliferation, but not the survival or differentiation, of adult hippocampal granule cell progenitors is affected by norepinephrine depletion.