ESTimating plant phylogeny: lessons from partitioning

BACKGROUND: While Expressed Sequence Tags (ESTs) have proven a viable and efficient way to sample genomes, particularly those for which whole-genome sequencing is impractical, phylogenetic analysis using ESTs remains difficult. Sequencing errors and orthology determination are the major problems when using ESTs as a source of characters for systematics. Here we develop methods to incorporate EST sequence information in a simultaneous analysis framework to address controversial phylogenetic questions regarding the relationships among the major groups of seed plants. We use an automated, phylogenetically derived approach to orthology determination called OrthologID generate a phylogeny based on 43 process partitions, many of which are derived from ESTs, and examine several measures of support to assess the utility of EST data for phylogenies. RESULTS: A maximum parsimony (MP) analysis resulted in a single tree with relatively high support at all nodes in the tree despite rampant conflict among trees generated from the separate analysis of individual partitions. In a comparison of broader-scale groupings based on cellular compartment (ie: chloroplast, mitochondrial or nuclear) or function, only the nuclear partition tree (based largely on EST data) was found to be topologically identical to the tree based on the simultaneous analysis of all data. Despite topological conflict among the broader-scale groupings examined, only the tree based on morphological data showed statistically significant differences. CONCLUSION: Based on the amount of character support contributed by EST data which make up a majority of the nuclear data set, and the lack of conflict of the nuclear data set with the simultaneous analysis tree, we conclude that the inclusion of EST data does provide a viable and efficient approach to address phylogenetic questions within a parsimony framework on a genomic scale, if problems of orthology determination and potential sequencing errors can be overcome. In addition, approaches that examine conflict and support in a simultaneous analysis framework allow for a more precise understanding of the evolutionary history of individual process partitions and may be a novel way to understand functional aspects of different kinds of cellular classes of gene products

Greenhouse Cultivation of Cucumber (Cucumis sativus L.) in Standard Soilless Media Amended with Biochar and Compost

Peat is one of the most commonly used substrates in soilless cultivation. However, peat mining produces a negative carbon footprint, which raises the need for alternative sustainable substrate media. To address this, we studied the impact of peat replacement with a combination of various biochars and cotton burr compost on the growth and yield of cucumber (Cucumis sativus L.), and nutrient concentration of media, plant leaf, and fruit in greenhouse conditions. Two experiments were conducted from Nov 2020 through Jan 2021 (Trial 1) and from Feb to Apr 2021 (Trial 2). The treatments were control (peat, vermiculite, and perlite at 2:1:1) and in the control peat was either fully replaced (hardwood biochar+compost, softwood biochar+compost, and hemp biochar+compost) or partially replaced up to 50% (v/v) (hardwood biochar+compost, softwood biochar+compost, and hemp biochar+compost). The control media was more acidic with lowest electrical conductivity than the other treatments. The leaf chlorophyll content and the photosynthetic assimilation rate varied among the treatments in both trials. The final dry shoot biomass was lowest in peat-dominated control treatment suggesting biochar-compost in the substrate media contributed in increased dry biomass of the cucumber plant. The total number of fruits per plant and total yield per plant was significantly increased in all the treatments with the highest in hardwood biochar+compost, compared with the control. The nutrient concentration of media, leaf, and fruit indicates that biochar-compost enhances the nutritional status of the media, which supplies essential nutrients to the plant leaf and fruit while growing in different substrate compositions. Our results suggest that the replacement of peat with full or partial proportions of biochar-compost can produce similar and, in some cases, even better growth, yield, and physiology in potted cucumber than in the unamended control treatment

Minimal Change in Cardiac Index With Increasing PEEP in Pediatric Acute Respiratory Distress Syndrome

Objective: To determine if increasing positive end expiratory pressure (PEEP) leads to a change in cardiac index in children with Pediatric Acute Respiratory Distress Syndrome ranging from mild to severe.Design: Prospective interventional study.Setting: Multidisciplinary Pediatric Intensive Care Unit in a University teaching hospital.Patients: Fifteen intubated children (5 females, 10 males) with a median age of 72 months (IQR 11, 132) and a median weight of 19.3 kg (IQR 7.5, 53.6) with a severity of Pediatric Acute Respiratory Distress Syndrome that ranged from mild to severe with a median lung injury score of 2.3 (IQR 2.0, 2.7).Measurements: Cardiac index (CI) and stroke volume (SV) were measured on baseline ventilator settings and subsequently with a PEEP 4 cmH2O higher than baseline. Change in CI and SV from baseline values was evaluated using Wilcoxon signed rank test.Results: A total of 19 paired measurements obtained. The median baseline PEEP was 8 cmH2O (IQR 8, 10) Range 6–14 cmH2O. There was no significant change in cardiac index or stroke volume with change in PEEP. Baseline median CI 4.4 L/min/m2 (IQR 3.4, 4.8) and PEEP 4 higher median CI of 4.3 L/min/m2 (IQR 3.6, 4.8), p = 0.65. Baseline median SV 26 ml (IQR 13, 44) and at PEEP 4 higher median SV 34 ml (IQR 12, 44) p = 0.63.Conclusion: There is no significant change in cardiac index or stroke volume with increasing PEEP by 4 cmH2O in a population of children with mild to severe PARDS.Clinical Trial Registration: The study is registered on Clinical trails.gov under the Identifier: NCT02354365

Programme and policy perspectives towards a tobacco-free generation in India: findings from a qualitative study

Objective This study explored multistakeholder perspectives on existing adolescent-specific tobacco control policies and programmes, to advance India’s transition towards a tobacco-free generation.Design Qualitative semi-structured interviews.Setting Interviews were conducted with officials involved in tobacco control at the national (India), state (Karnataka), district (Udupi) and village level. Interviews were audio recorded, transcribed verbatim and analysed thematically.Participants Thirty-eight individuals representing national (n=9), state (n=9), district (n=14) and village (n=6) levels, participated.Results The study findings highlighted the need to strengthen and amend the existing Tobacco Control Law (2003) provisions, particularly in the vicinity of schools (Sections 6a and 6b). Increasing the minimum legal age to buy tobacco from 18 to 21 years, developing an ‘application’ for ‘compliance and monitoring indicators’ in Tobacco-Free Educational Institution guidelines were proposed. Policies to address smokeless tobacco use, stricter enforcement including regular monitoring of existing programmes, and robust evaluation of policies was underscored. Engaging adolescents to co-create interventions was advocated, along with integrating national tobacco control programmes into existing school and adolescent health programmes, using both an intersectoral and whole-societal approach to prevent tobacco use, were recommended. Finally, stakeholders mentioned that when drafting and implementing a comprehensive national tobacco control policy, there is a need to adopt a vision striving toward a tobacco-free generation.Conclusion Strengthening and developing tobacco control programmes and policies are warranted which are monitored and evaluated rigorously, and where adolescents should be involved, accordingly

Acute cholecystitis with massive upper gastrointestinal bleed: A case report and review of the literature

BACKGROUND: Cystic artery pseudoaneurysm is a rare complication following cholecystitis. Its presentation with upper gastrointestinal hemorrhage (UGIH) is even rarer. Thirteen patients with cystic artery pseudoaneurysm have been reported in the literature but only 2 of them presented with UGIH alone. CASE PRESENTATION: We report a 43-year-old woman who developed a cystic artery pseudoaneurysm following an episode of acute cholecystitis. She presented with haematemesis and melaena associated with postural symptoms. Upper gastrointestinal endoscopy revealed a duodenal ulcer with adherent clots in the first part of the duodenum. Ultrasonography detected gallstones and a pseudoaneurysm at the porta hepatis. Selective hepatic angiography showed two small pseudoaneurysms in relation to the cystic artery, which were selectively embolized. However, the patient developed abdominal signs suggestive of gangrene of the gall bladder and underwent an emergency laparotomy. Cholecystectomy with common bile duct exploration along with repair of the duodenal rent, and pyloric exclusion and gastrojejunostomy was done. CONCLUSION: This case illustrates the occurrence of a rare complication (pseudoaneurysm) following cholecystitis with an unusual presentation (UGIH). Cholecystectomy, ligation of the pseudoaneurysm and repair of the intestinal communication is an effective modality of treatment

Management of Hypertriglyceridemia in the Diabetic Patient

The hypertriglyceridemia of diabetes can be classified into mild to moderate (triglycerides between 150–499 mg/dL) and severe hypertriglyceridemia (triglycerides ≥500 mg/dL). As in any other individuals with hypertriglyceridemia, secondary causes need to be excluded. The management of severe hypertriglyceridemia (chylomicronemia syndrome) includes aggressive reduction of triglycerides with intravenous insulin, fibrates, omega-3 fatty acids, and/or niacin therapy to avert the risk of pancreatitis. In patients with mild to moderate hypertriglyceridemia, the treatment of choice is statin therapy to achieve the low-density lipoprotein (LDL) and non-high-density lipoprotein (HDL) target goals. The evidence base would favor niacin therapy in combination with statin therapy to achieve the goals pertaining to LDL cholesterol and non-HDL cholesterol. The data about the combination of fibrate therapy with statin therapy are disappointing