Gene tree reconciliation: new developments in Bayesian concordance analysis with BUCKy

When phylogenetic trees inferred from different genes are incongruent, several methods are available to reconcile gene trees and extract the shared phylogenetic information from the sequence data. Bayesian Concordance Analysis, implemented in BUCKy, aims to extract the vertical signal and to infer clusters of genes that share the same tree topology. The new version of BUCKy includes a quartet-based estimate of the species tree with branch lengths in coalescent units

On-site earthquake early warning: a partially non-ergodic perspective from the site effects point of view

We introduce in the on-site earthquake early warning (EEW) a partially non-ergodic perspective from the site effects point of view. We consider the on-site EEW approach where the peak ground velocity (PGV) for S waves is predicted from an early estimate, over the P waves, of either the peak-displacement (PD) or cumulative squared velocity (IV2). The empirical PD-PGV and IV2-PGV relationships are developed by applying a mixed-effect regression where the site-specific modifications of ground shaking are treated as random effects. We considered a large data set composed of almost 31 000 selected recordings in central Italy, a region struck by four earthquakes with magnitude between 6 and 6.5 since the 2009 L’Aquila earthquake. We split the data set into three subsets used for calibrating and validating the on-site EEW models, and for exemplifying their application to stations installed after the calibration phase. We show that the partially non-ergodic models improve the accuracy of the PGV predictions with respect to ergodic models derived for other regions of the world. Moreover, considering PD and accounting for site effects, we reduce the (apparent) aleatory variability of the logarithm of PGV from 0.31 to 0.36, typical values for ergodic on-site EEW models, to about 0.25. Interestingly, a lower variability of 0.15 is obtained by considering IV2 as proxy, which suggests further consideration of this parameter for the design of on-site EEW systems. Since being site-specific is an inherent characteristic of on-site EEW applications, the improved accuracy and precision of the PGV predicted for a target protection translate in a better customization of the alert protocols for automatic actions

Novel triple therapy in osteoarthritis of knee joint

Background: Regenerative medicine may be defined as the process of replacing or regenerating human tissues or cells of humans to restore or to get very near to normal function of human life. Biological tissues found in humans such as blood, fat, bone marrow are the main resources of regenerative medicine which help in natural process of healing of soft tissue. Extracorporeal shock wave therapy (ESWT) is a physical modality that helps in enhancing healing process of soft tissues. Osteoarthritis of the knee joint is a gradually progressive degenerative condition with the loss of articular cartilage. The early stages of disease are managed conservatively with the aim of retarding the rate of cartilage destruction. Methods: A total of 80 patients underwent the novel triple therapy. The objective is to find out the potential of combination therapy in early degenerative disease of knee with the aim of reduction of inflammation. A protocol was developed which involved three injections of platelet rich plasma (PRP), six sessions of combined ESWT and physiotherapy. Results: Evaluation was mainly based on WOMAC/KSS/VAS scores. Patients in stage 1 and 2 (55+15=70) had excellent results for 36 months, patients in stage 3 (10 cases) had satisfactory outcome at 24 months. Conclusions: Triple therapy is an alternative treatment or in few cases a definitive treatment in degenerative disease of knee joint where medical and surgical management has minimal or no role. Triple therapy in mild to moderate osteoarthritis of knee joint has better outcome

Various forms of tobacco usage and its associated oral mucosal lesions

Background: To study the various forms of tobacco usage and its associated oral mucosal lesions among the patients attending Vishnu Dental College Bhimavaram. Material and Methods: An observational cross-sectional study was conducted in a total of 450 patients who were divided into three groups based upon type of tobacco use, as Group-1 Reverse smoking, Group-2 Conventional smoking, Group-3 Smokeless tobacco group and each group consists of 150 subjects. Results: Reverse smoking was observed to be more prevalent among old females with smoker’s palate and carcinomatous lesions being the most common. Conventional smoking was observed more in male patients with maximum occurrence of leukoplakia and tobacco associated melanosis. Smokeless tobacco habit was predominantly seen in younger males. Habit specific lesions like tobacco pouch keratosis, Oral Submucous Fibrosis (OSMF), Quid induced lichenoid reaction were noticed in smokeless tobacco habit group except for erythroplakia which was noticed only in conventional smoking group and it was not significant statistically . Conclusions: In the present study it was found that the usage of reverse smoking habit was most commonly seen in females and this habit is practiced in and surrounding areas of Bhimavaram with more occurrence of carcinoma compared to conventional smoking and smokeless tobacco

Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains

Acidic activation domains are intrinsically disordered regions of the transcription factors that bind coactivators. The intrinsic disorder and low evolutionary conservation of activation domains have made it difficult to identify the sequence features that control activity. To address this problem, we designed thousands of variants in seven acidic activation domains and measured their activities with a high-throughput assay in human cell culture. We found that strong activation domain activity requires a balance between the number of acidic residues and aromatic and leucine residues. These findings motivated a predictor of acidic activation domains that scans the human proteome for clusters of aromatic and leucine residues embedded in regions of high acidity. This predictor identifies known activation domains and accurately predicts previously unidentified ones. Our results support a flexible acidic exposure model of activation domains in which the acidic residues solubilize hydrophobic motifs so that they can interact with coactivators. A record of this paper\u27s transparent peer review process is included in the supplemental information

Parent-adolescent interaction and risk of adolescent internet addiction: a population-based study in Shanghai

Abstract Background Family-based intervention is essential for adolescents with behavioral problems. However, limited data are available on the relationship between family-based factors and adolescent internet addiction (AIA). We aimed to examine this relationship using a representative sample of Shanghai adolescents. Methods In October 2007, a total of 5122 adolescents were investigated from 16 high schools via stratified-random sampling in Shanghai. Self-reported and anonymous questionnaires were used to assess parent-adolescent interaction and family environments. AIA was assessed by DRM-52 Scale, developed from Young’s Internet-addiction Scale, using seven subscales to evaluate psychological symptoms of AIA. Results Adjusting for adolescents’ ages, genders, socio-economic status, school performances and levels of the consumption expenditure, strong parental disapproval of internet-use was associated with AIA (vs. parental approval, OR = 2.20, 95% CI: 1.24-3.91). Worse mother-adolescent relationships were more significantly associated with AIA (OR = 3.79, 95% CI: 2.22-6.48) than worse father-adolescent relationships (OR = 1.76, 95% CI: 1.10-2.80). Marital status of “married-but-separated” and family structure of “left-behind adolescents” were associated with symptoms of some subscales. When having high monthly allowance, resident students tended to develop AIA but commuter students did not. Family social-economic status was not associated with the development of AIA. Conclusions The quality of parent-adolescent relationship/communication was closely associated with the development of AIA, and maternal factors were more significantly associated with development of AIA than paternal factors. Family social-economic status moderated adolescent internet-use levels but not the development of AIA.http://deepblue.lib.umich.edu/bitstream/2027.42/109471/1/12888_2014_Article_1616.pd

Personal characteristics related to the risk of adolescent internet addiction: a survey in Shanghai, China

Abstract Background Paralleling the rapid growth in computers and internet connections, adolescent internet addiction (AIA) is becoming an increasingly serious problem, especially in developing countries. This study aims to explore the prevalence of AIA and associated symptoms in a large population-based sample in Shanghai and identify potential predictors related to personal characteristics. Methods In 2007, 5,122 adolescents were randomly chosen from 16 high schools of different school types (junior, senior key, senior ordinary and senior vocational) in Shanghai with stratified-random sampling. Each student completed a self-administered and anonymous questionnaire that included DRM 52 Scale of Internet-use. The DRM 52 Scale was adapted for use in Shanghai from Young’s Internet Addiction Scale and contained 7 subscales related to psychological symptoms of AIA. Multiple linear regression and logistic regression were both used to analyze the data. Results Of the 5,122 students, 449 (8.8%) were identified as internet addicts. Although adolescents who had bad (vs. good) academic achievement had lower levels of internet-use (p 100 RMB (all p-values <0.05). Adolescents tended to develop AIA and show symptoms in all subscales when they spent more hours online weekly (however, more internet addicts overused internet on weekends than on weekdays, p < 0.0001) or when they used the internet mainly for playing games or real-time chatting. Conclusions This study provides evidence that adolescent personal factors play key roles in inducing AIA. Adolescents having aforementioned personal characteristics and online behaviors are at high-risk of developing AIA that may compound different psychological symptoms associated with AIA. Spending excessive time online is not in itself a defining symptom of AIA. More attention is needed on adolescent excessive weekend internet-use in prevention of potential internet addicts.http://deepblue.lib.umich.edu/bitstream/2027.42/112717/1/12889_2012_Article_4938.pd

Preparation of amino-substituted indenes and 1,4-dihydronaphthalenes using a one-pot multireaction approach: total synthesis of oxybenzo[c]phenanthridine alkaloids

Allylic trichloroacetimidates bearing a 2-vinyl or 2-allylaryl group have been designed as substrates for a one-pot, two-step multi-bond-forming process leading to the general preparation of aminoindenes and amino-substituted 1,4-dihydronaphthalenes. The synthetic utility of the privileged structures formed from this one-pot process was demonstrated with the total synthesis of four oxybenzo[c]phenanthridine alkaloids, oxychelerythrine, oxysanguinarine, oxynitidine, and oxyavicine. An intramolecular biaryl Heck coupling reaction, catalyzed using the Hermann–Beller palladacycle was used to effect the key step during the synthesis of the natural products

Preliminary fabrication and characterization of electron beam melted Ti-6Al-4V customized dental implant

The current study was aimed to fabricate customized root form dental implant using additive manufacturing technique for the replacement of missing teeth. The root form dental implant was designed using Geomagic (TM) and Magics (TM), the designed implant was directly manufactured by layering technique using ARCAM A2 (TM) electron beam melting system by employing medical grade Ti- 6Al-4V alloy powder. Furthermore, the fabricated implant was characterized in terms of certain clinically important parameters such as surface microstructure, surface topography, chemical purity and internal porosity. Results confirmed that, fabrication of customized dental implants using additive rapid manufacturing technology offers an attractive method to produce extremely pure form of customized titanium dental implants, the rough and porous surface texture obtained is expected to provide better initial implant stabilization and superior osseointegration. (C) 2016 The Authors. Production and hosting by Elsevier B.V. on behalf of King Saud University

Vascular and Cardiac Impairments in Rats Inhaling Ozone and Diesel Exhaust Particles

BackgroundMechanisms of cardiovascular injuries from exposure to gas and particulate air pollutants are unknown.ObjectiveWe sought to determine whether episodic exposure of rats to ozone or diesel exhaust particles (DEP) causes differential cardiovascular impairments that are exacerbated by ozone plus DEP.Methods and resultsMale Wistar Kyoto rats (10–12 weeks of age) were exposed to air, ozone (0.4 ppm), DEP (2.1 mg/m3), or ozone (0.38 ppm) + DEP (2.2 mg/m3) for 5 hr/day, 1 day/week for 16 weeks, or to air, ozone (0.51 or 1.0 ppm), or DEP (1.9 mg/m3) for 5 hr/day for 2 days. At the end of each exposure period, we examined pulmonary and cardiovascular biomarkers of injury. In the 16-week study, we observed mild pulmonary pathology in the ozone, DEP, and ozone + DEP exposure groups, a slight decrease in circulating lymphocytes in the ozone and DEP groups, and decreased platelets in the DEP group. After 16 weeks of exposure, mRNA biomarkers of oxidative stress (hemeoxygenase-1), thrombosis (tissue factor, plasminogen activator inhibitor-1, tissue plasminogen activator, and von Willebrand factor), vasoconstriction (endothelin-1, endothelin receptors A and B, endothelial NO synthase) and proteolysis [matrix metalloprotease (MMP)-2, MMP-3, and tissue inhibitor of matrix metalloprotease-2] were increased by DEP and/or ozone in the aorta, but not in the heart. Aortic LOX-1 (lectin-like oxidized low-density lipoprotein receptor-1) mRNA and protein increased after ozone exposure, and LOX-1 protein increased after exposure to ozone + DEP. RAGE (receptor for advanced glycation end products) mRNA increased in the ozone + DEP group. Exposure to ozone or DEP depleted cardiac mitochondrial phospholipid fatty acids (DEP > ozone). The combined effect of ozone and DEP exposure was less pronounced than exposure to either pollutant alone. Exposure to ozone or DEP for 2 days (acute) caused mild changes in the aorta.ConclusionsIn animals exposed to ozone or DEP alone for 16 weeks, we observed elevated biomarkers of vascular impairments in the aorta, with the loss of phospholipid fatty acids in myocardial mitochondria. We conclude that there is a possible role of oxidized lipids and protein through LOX-1 and/or RAGE signaling