A new automata for parsing semi-bracketed contextual grammars

Bracketed and fully bracketed contextual grammars were introduced to bring the concept of tree structure to the strings by associating a pair of parentheses to the adjoined contexts in the derivation. But these grammars fail to generate the basic non-context free languages thus unable to provide a syntactical representation to natural languages. To overcome this problem, a new variant called semi-bracketed contextual grammar was introduced recently, where the selectors can also be non-minimally Dyck covered strings. The membership problem for the new variant is left unsolved. In this paper, we propose a parsing algorithm (for non-projected strings) of maximal semi-bracketed contextual grammars. In this process, we introduce a new automaton called k-queue Self Modifying Weighted Automata (k-quSMWA)

Bone health after menopause: effect of surgical menopaus on bone mineral density and osteoporosis

Background: Natural menopause or surgical menopause is associated with endocrinological changes and alteration in bone and mineral metabolism. Hence this study was conducted to assess the bone mineral density changes in women with surgical menopause. Methods: This is a prospective observational study conducted in the department of obstetrics and gynaecology at Sri Ramachandra medical college, which is a tertiary care teaching hospital. 60 women with surgical menopause were included in the study. BMD was assessed by dual energy X-ray absorptiometry at the lumbar spine and hip joint. All the data was entered in Microsoft excel spread sheet and analysed by using SPSS software.Results: Among 60 study subjects, 41 individuals had a normal BMD, 16 had osteopenia, and 3 were diagnosed with osteoporosis. Osteopenia and osteoporosis is significantly higher in patients who had undergone hysterectomy with removal of ovaries. Observations of osteopenia and osteoporosis were significantly higher with increasing number of years post hysterectomy.Conclusions: Prevalence of osteoporosis is high in patients who undergo hysterectomy. Oophorectomy is associated with postoperative bone loss. Targeted management strategies should include routine BMD assessment and hormone therapy improves management of bone health in this population. Further more studies are needed in large populations to test alternative treatments for post oophorectomy osteoporosis

De novo germ-line mutation of APC gene in periampullary carcinoma with familial adenomatous polyps – A novel familial case report in South India

AbstractPeriampullary carcinoma is a malignant tumour arising from the ampulla of vater. Adenomatous polyposis coli (APC) gene has a key role in stabilizing β-catenin pathway, in which hypermethylation in APC gene could lead to proteasome degradation of β-catenin. The aim of this case report is to identify the APC gene mutation and its influence on β-catenin pathway in patient with periampullary carcinoma. A 51-year-old woman was diagnosed with yellow discolouration of sclera, passing deep yellow coloured urine and pruritus. A family history of ovarian cancer had been reported in her mother. Her radiological, pathological and laboratory examination confirmed periampullary carcinoma. She underwent whipple's pancreaticoduodenectomy, and the histopathology of the resected specimen showed a well differentiated adenocarcinoma involving the ampulla of vater. Further, the tumour region was subjected to genetic screening by polymerase chain reaction – restriction fragment length polymorphism (PCR-RFLP), cytogenetic analyses such as karyotyping and immunohistochemical techniques. These results showed non-sense mutation in APC gene at codon 1309, chromosomal alterations at 5q21 and irregular accumulation of β-catenin in nuclear membrane. The family history revealed a strong association of ovarian cancer (maternal) with a similar APC gene mutation. We conclude that periampullary carcinoma patient exhibit FAP due to de novo germ-line mutation of APC gene that engenders an inactivation of β-catenine/TCF mediated transcription function, which is linked with a family history of ovarian cancer

Modelling Intermolecular Structures and Defining Ambiguity in Gene Sequences using Matrix Insertion-Deletion Systems

International audienceGene insertion and deletion are considered as the basic operations in DNA processing and RNA editing. Based on these evolutionary transformations, a computing model has been formulated in formal language theory known as insertion-deletion systems. Recently, in [6], a new computing model named Matrix insertion-deletion system has been introduced to model various bio-molecular structures such as hairpin, stem and loop, pseudoknot, attenuator, cloverleaf, dumbbell that occur at intramolecular level. In this paper, we model some of the intermolecular structures such as double strand languages, nick languages, hybrid molecules (with R-loops), holliday structure, replication fork and linear hybridization (ligated) languages using Matrix insertion-deletion system. In [2], the ambiguity in gene sequence was defined as deriving more than one structure for a single gene sequence. Here, we propose a different view of understanding the ambiguity in gene sequences: A gene sequence is obtained by more than one way such that their intermediate sequences are different. We further classify the ambiguity into many levels based on the components axiom, string (order of deletion/insertion) and contexts (order of the used contexts). We notice that some of the inter and intramolecular structures obey the newly defined ambiguity levels.L'insertion et l'effacement de gènes sont considérés comme les opérations de base dans le traitement de l'ADN et l'édition de l'ARN. Fondé sur ces méchanismes de l'évolution, un modèle de calcul a été formulé dans le cadre de la théorie des langages formels en tant que système d'ajout-effacement. Récemment, un nouveau modèle dénommé "système matriciel d'ajout-effacement" a été introduit pour modéliser différentes structures bio-moléculaires qui apparaissent au niveau intra-moléculaire. Dans ce papier, nous modélisons certaines de ces structures

Modelling Intermolecular Structures and Defining Ambiguity in Gene Sequences using Matrix Insertion-Deletion Systems

International audienceGene insertion and deletion are considered as the basic operations in DNA processing and RNA editing. Based on these evolutionary transformations, a computing model has been formulated in formal language theory known as insertion-deletion systems. Recently, in [6], a new computing model named Matrix insertion-deletion system has been introduced to model various bio-molecular structures such as hairpin, stem and loop, pseudoknot, attenuator, cloverleaf, dumbbell that occur at intramolecular level. In this paper, we model some of the intermolecular structures such as double strand languages, nick languages, hybrid molecules (with R-loops), holliday structure, replication fork and linear hybridization (ligated) languages using Matrix insertion-deletion system. In [2], the ambiguity in gene sequence was defined as deriving more than one structure for a single gene sequence. Here, we propose a different view of understanding the ambiguity in gene sequences: A gene sequence is obtained by more than one way such that their intermediate sequences are different. We further classify the ambiguity into many levels based on the components axiom, string (order of deletion/insertion) and contexts (order of the used contexts). We notice that some of the inter and intramolecular structures obey the newly defined ambiguity levels.L'insertion et l'effacement de gènes sont considérés comme les opérations de base dans le traitement de l'ADN et l'édition de l'ARN. Fondé sur ces méchanismes de l'évolution, un modèle de calcul a été formulé dans le cadre de la théorie des langages formels en tant que système d'ajout-effacement. Récemment, un nouveau modèle dénommé "système matriciel d'ajout-effacement" a été introduit pour modéliser différentes structures bio-moléculaires qui apparaissent au niveau intra-moléculaire. Dans ce papier, nous modélisons certaines de ces structures

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy

Predictors of unfavorable responses to therapy in rifampicin-sensitive pulmonary tuberculosis using an integrated approach of radiological presentation and sputum mycobacterial burden

INTRODUCTION: Despite the exalted status of sputum mycobacterial load for gauging pulmonary tuberculosis treatment and progress, Chest X-rays supplement valuable information for taking instantaneous therapeutic decisions, especially during the COVID-19 pandemic. Even though literature on individual parameters is overwhelming, few studies have explored the interaction between radiographic parameters denoting severity with mycobacterial burden signifying infectivity. By using a sophisticated approach of integrating Chest X-ray parameters with sputum mycobacterial characteristics, evaluated at all the three crucial time points of TB treatment namely pre-treatment, end of intensive phase and completion of treatment, utilizing the interactive Cox Proportional Hazards model, we aimed to precisely deduce predictors of unfavorable response to TB treatment. MATERIALS AND METHOD: We extracted de-identified data from well characterized clinical trial cohorts that recruited rifampicin-sensitive Pulmonary TB patients without any comorbidities, taking their first spell of anti-tuberculosis therapy under supervision and meticulous follow up for 24 months post treatment completion, to accurately predict TB outcomes. Radiographic data independently obtained, interpreted by two experienced pulmonologists was collated with demographic details and, sputum smear and culture grades of participants by an independent statistician and analyzed using the Cox Proportional Hazards model, to not only adjust for confounding factors including treatment effect, but also explore the interaction between radiological and bacteriological parameters for better therapeutic application. RESULTS: Of 667 TB patients with data available, cavitation, extent of involvement, lower zone involvement, smear and culture grade at baseline were significant parameters predisposing to an unfavorable TB treatment outcome in the univariate analysis. Reduction in radiological lesions in Chest X-ray by at least 50% at 2 months and 75% at the end of treatment helped in averting unfavorable responses. Smear and Culture conversion at the end of 2 months was highly significant as a predictor (p2 zones, were 3.05 (95% CI: 1.12–8.23) and 1.92 (95% CI: 0.72–5.08) respectively. Patients without cavitation, zonal involvement 2 zones and 3+ smear grade individually and independently forecasted a poorer TB outcome. The interaction model revealed that Zonal involvement confined to 2 zones, without a cavity and smear grade up to 2+, constituting “minimal disease”, had a better prognosis. Radiological clearance >50% along with smear conversion at the end of intensive phase of treatment, observed to be a reasonable alternative to culture conversion in predicting a successful outcome. These parameters may potentially take up key positions as stratification factors for future trials contemplating on shorter TB regimens

Effects of antiplatelet therapy after stroke due to intracerebral haemorrhage (RESTART): a randomised, open-label trial

Background: Antiplatelet therapy reduces the risk of major vascular events for people with occlusive vascular disease, although it might increase the risk of intracranial haemorrhage. Patients surviving the commonest subtype of intracranial haemorrhage, intracerebral haemorrhage, are at risk of both haemorrhagic and occlusive vascular events, but whether antiplatelet therapy can be used safely is unclear. We aimed to estimate the relative and absolute effects of antiplatelet therapy on recurrent intracerebral haemorrhage and whether this risk might exceed any reduction of occlusive vascular events. Methods: The REstart or STop Antithrombotics Randomised Trial (RESTART) was a prospective, randomised, open-label, blinded endpoint, parallel-group trial at 122 hospitals in the UK. We recruited adults (≥18 years) who were taking antithrombotic (antiplatelet or anticoagulant) therapy for the prevention of occlusive vascular disease when they developed intracerebral haemorrhage, discontinued antithrombotic therapy, and survived for 24 h. Computerised randomisation incorporating minimisation allocated participants (1:1) to start or avoid antiplatelet therapy. We followed participants for the primary outcome (recurrent symptomatic intracerebral haemorrhage) for up to 5 years. We analysed data from all randomised participants using Cox proportional hazards regression, adjusted for minimisation covariates. This trial is registered with ISRCTN (number ISRCTN71907627). Findings: Between May 22, 2013, and May 31, 2018, 537 participants were recruited a median of 76 days (IQR 29–146) after intracerebral haemorrhage onset: 268 were assigned to start and 269 (one withdrew) to avoid antiplatelet therapy. Participants were followed for a median of 2·0 years (IQR [1·0– 3·0]; completeness 99·3%). 12 (4%) of 268 participants allocated to antiplatelet therapy had recurrence of intracerebral haemorrhage compared with 23 (9%) of 268 participants allocated to avoid antiplatelet therapy (adjusted hazard ratio 0·51 [95% CI 0·25–1·03]; p=0·060). 18 (7%) participants allocated to antiplatelet therapy experienced major haemorrhagic events compared with 25 (9%) participants allocated to avoid antiplatelet therapy (0·71 [0·39–1·30]; p=0·27), and 39 [15%] participants allocated to antiplatelet therapy had major occlusive vascular events compared with 38 [14%] allocated to avoid antiplatelet therapy (1·02 [0·65–1·60]; p=0·92). Interpretation: These results exclude all but a very modest increase in the risk of recurrent intracerebral haemorrhage with antiplatelet therapy for patients on antithrombotic therapy for the prevention of occlusive vascular disease when they developed intracerebral haemorrhage. The risk of recurrent intracerebral haemorrhage is probably too small to exceed the established benefits of antiplatelet therapy for secondary prevention

Effects of antiplatelet therapy after stroke due to intracerebral haemorrhage (RESTART): a randomised, open-label trial

Background: Antiplatelet therapy reduces the risk of major vascular events for people with occlusive vascular disease, although it might increase the risk of intracranial haemorrhage. Patients surviving the commonest subtype of intracranial haemorrhage, intracerebral haemorrhage, are at risk of both haemorrhagic and occlusive vascular events, but whether antiplatelet therapy can be used safely is unclear. We aimed to estimate the relative and absolute effects of antiplatelet therapy on recurrent intracerebral haemorrhage and whether this risk might exceed any reduction of occlusive vascular events. Methods: The REstart or STop Antithrombotics Randomised Trial (RESTART) was a prospective, randomised, open-label, blinded endpoint, parallel-group trial at 122 hospitals in the UK. We recruited adults (≥18 years) who were taking antithrombotic (antiplatelet or anticoagulant) therapy for the prevention of occlusive vascular disease when they developed intracerebral haemorrhage, discontinued antithrombotic therapy, and survived for 24 h. Computerised randomisation incorporating minimisation allocated participants (1:1) to start or avoid antiplatelet therapy. We followed participants for the primary outcome (recurrent symptomatic intracerebral haemorrhage) for up to 5 years. We analysed data from all randomised participants using Cox proportional hazards regression, adjusted for minimisation covariates. This trial is registered with ISRCTN (number ISRCTN71907627). Findings: Between May 22, 2013, and May 31, 2018, 537 participants were recruited a median of 76 days (IQR 29–146) after intracerebral haemorrhage onset: 268 were assigned to start and 269 (one withdrew) to avoid antiplatelet therapy. Participants were followed for a median of 2·0 years (IQR [1·0– 3·0]; completeness 99·3%). 12 (4%) of 268 participants allocated to antiplatelet therapy had recurrence of intracerebral haemorrhage compared with 23 (9%) of 268 participants allocated to avoid antiplatelet therapy (adjusted hazard ratio 0·51 [95% CI 0·25–1·03]; p=0·060). 18 (7%) participants allocated to antiplatelet therapy experienced major haemorrhagic events compared with 25 (9%) participants allocated to avoid antiplatelet therapy (0·71 [0·39–1·30]; p=0·27), and 39 [15%] participants allocated to antiplatelet therapy had major occlusive vascular events compared with 38 [14%] allocated to avoid antiplatelet therapy (1·02 [0·65–1·60]; p=0·92). Interpretation: These results exclude all but a very modest increase in the risk of recurrent intracerebral haemorrhage with antiplatelet therapy for patients on antithrombotic therapy for the prevention of occlusive vascular disease when they developed intracerebral haemorrhage. The risk of recurrent intracerebral haemorrhage is probably too small to exceed the established benefits of antiplatelet therapy for secondary prevention