PURE: A webserver for the prediction of domains in unassigned regions in proteins

<p>Abstract</p> <p>Background</p> <p>Protein domains are the structural and functional units of proteins. The ability to parse proteins into different domains is important for effective classification, understanding of protein structure, function, and evolution and is hence biologically relevant. Several computational methods are available to identify domains in the sequence. Domain finding algorithms often employ stringent thresholds to recognize sequence domains. Identification of additional domains can be tedious involving intense computation and manual intervention but can lead to better understanding of overall biological function. In this context, the problem of identifying new domains in the unassigned regions of a protein sequence assumes a crucial importance.</p> <p>Results</p> <p>We had earlier demonstrated that accumulation of domain information of sequence homologues can substantially aid prediction of new domains. In this paper, we propose a computationally intensive, multi-step bioinformatics protocol as a web server named as <b>PURE </b>(<b>P</b>rediction of <b>U</b>nassigned <b>RE</b>gions in proteins) for the detailed examination of stretches of unassigned regions in proteins. Query sequence is processed using different automated filtering steps based on length, presence of coiled-coil regions, transmembrane regions, homologous sequences and percentage of secondary structure content. Later, the filtered sequence segments and their sequence homologues are fed to PSI-BLAST, cd-hit and Hmmpfam. Data from the various programs are integrated and information regarding the probable domains predicted from the sequence is reported.</p> <p>Conclusion</p> <p>We have implemented PURE protocol as a web server for rapid and comprehensive analysis of unassigned regions in the proteins. This server integrates data from different programs and provides information about the domains encoded in the unassigned regions.</p

An ensemble of intelligent water drop algorithm for feature selection optimization problem

Master River Multiple Creeks Intelligent Water Drops (MRMC-IWD) is an ensemble model of the intelligent water drop, whereby a divide-and-conquer strategy is utilized to improve the search process. In this paper, the potential of the MRMC-IWD using real-world optimization problems related to feature selection and classification tasks is assessed. An experimental study on a number of publicly available benchmark data sets and two real-world problems, namely human motion detection and motor fault detection, are conducted. Comparative studies pertaining to the features reduction and classification accuracies using different evaluation techniques (consistency-based, CFS, and FRFS) and classifiers (i.e., C4.5, VQNN, and SVM) are conducted. The results ascertain the effectiveness of the MRMC-IWD in improving the performance of the original IWD algorithm as well as undertaking real-world optimization problems

Creativity in a COVID-19 Virtual Learning Space

The COVID-19 pandemic has changed the world, and education too has been affected in many ways. In particular, much learning in higher education has moved to synchronous virtual spaces. Regardless of context, the principles of learning and teaching remain at the foreground, and the importance of developing active and creative learning spaces has never been greater. We are a group of one faculty member, six graduate students, and one teaching assistant who came together to write this paper so that we could share our online experiences in a clinical education course during the summer of 2020. We used a variety of active-learning and creative-teaching approaches. In this paper, we share our virtual use of video-based learning, gaming/crosswords, speed dating, blowing bubbles as a way to learn how to teach a psychomotor skill, image-based art, forum theatre, and found poetry. We share a crossword designed specifically for readers with which to grapple and our summary is presented as a found poem. Student author quotes are interspersed throughout the paper. Résumé La pandémie de COVID-19 a changé le monde et du même coup, a fait basculer le domaine de l’éducation. Principalement en enseignement supérieur une grande partie de l’apprentissage a maintenant lieu dans des espaces virtuels synchrones. Mais peu importe le contexte, les principes d’apprentissage et d’enseignement restent à l’avant-plan et le besoin de développer des espaces d’apprentissage actifs et créatifs est plus important que jamais. Notre groupe, composé d’un membre du corps professoral, de six étudiantes des cycles supérieurs et d’une auxiliaire d’enseignement, fut créé pour rédiger cet article et ainsi partager nos expériences d’un cours en ligne de formation clinique à l’été 2020, dans lequel une variété d’approches d’apprentissage actif et d’enseignement créatif ont été utilisées. Dans cet article, nous partageons notre utilisation virtuelle d’outils d’apprentissage tels les vidéos, jeux/mots croisés, rencontres express (speed dating), faire des bulles pour apprendre à enseigner une habileté psychomotrice, l’art visuel par l’image, le théâtre-forum et la poésie retrouvée. Nous partageons également un mot croisé conçu spécifiquement à l’intention de nos lecteurs et lectrices et notre résumé est présenté comme un poème retrouvé. Quelques citations d’étudiantes ayant participé à la rédaction, ont été insérées çà et là à travers l’articl

Sensitivity of transcritical cycle and turbine design to dopant fraction in CO2-based working fluids

Supercritical CO2 (sCO2) power cycles have gained prominence for their expected excellent performance and compactness. Among their benefits, they may potentially reduce the cost of Concentrated Solar Power (CSP) plants. Because the critical temperature of CO2 is close to ambient temperatures in areas with good solar irradiation, dry cooling may penalise the efficiency of sCO2 power cycles in CSP plants. Recent research has investigated doping CO2 with different materials to increase its critical temperature, enhance its thermodynamic cycle performance, and adapt it to dry cooling in arid climates. This paper investigates the use of CO2/TiCl4, CO2/NOD (an unnamed Non-Organic Dopant), and CO2/C6F6 mixtures as working fluids in a transcritical Rankine cycle implemented in a 100 MWe power plant. Specific focus is given to the effect of dopant type and fraction on optimal cycle operating conditions and on key parameters that influence the expansion process. Thermodynamic modelling of a simple recuperated cycle is employed to identify the optimal turbine pressure ratio and recuperator effectiveness that achieve the highest cycle efficiency for each assumed dopant molar fraction. A turbine design model is then used to define the turbine geometry based on optimal cycle conditions. It was found that doping CO2 with any of the three dopants (TiCl4, NOD, or C6F6) increases the cycle’s thermal efficiency. The greatest increase in efficiency is achieved with TiCl4 (up to 49.5%). The specific work, on the other hand, decreases with TiCl4 and C6F6, but increases with NOD. Moreover, unlike the other two dopants, NOD does not alleviate recuperator irreversibility. In terms of turbine design sensitivity, the addition of any of the three dopants increases the pressure, temperature, and expansion ratios across the turbine. The fluid’s density at turbine inlet increases with all dopants as well. Conversely, the speed of sound at turbine inlet decreases with all dopants, yet higher Mach numbers are expected in CO2/C6F6 turbines

Financial toxicity of cancer care in low and middle-income countries: a systematic review and meta-analysis

Introduction: The costs associated with cancer diagnosis, treatment and care present enormous financial toxicity. However, evidence of financial toxicity associated with cancer in low and middle-income countries (LMICs) is scarce. Aim: To identify the extent of cancer-related financial toxicity and how it has been measured in LMICs. Methods: : Four electronic databases were searched to identify studies of any design that reported financial toxicity among cancer patients in LMICs. Random-effects meta-analysis was used to derive the pooled prevalence of financial toxicity. Sub-group analyses were performed according to: costs; and determinants of financial toxicity. Results: : A total of 31 studies were included in this systematic review and meta-analysis. The pooled prevalence of financial toxicity was 56.96% [95% CI, 30.51, 106.32]. In sub-group meta-analyses, the financial toxicity was higher among cancer patients with household size of more than four (1.17% [95% CI, 1.03, 1.32]; p = 0.02; I 2 = 0%), multiple cycles of chemotherapy (1.94% [95% CI, 1.00, 3.75]; p = 0.05; I 2 = 43%) and private health facilities (2.87% [95% CI, 1.89, 4.35]; p Conclusions: : This study indicates that cancer diagnosis, treatment and care impose high financial toxicity on cancer patients in LMICs. Further rigorous research on cancer-related financial toxicity is needed

Suicidal Behavior and Psychological Distress in University Students: A 12-Nation Study. Archives of Suicide Research

This study investigated the prevalence of suicidal behavior and psychological distress in university students across 12 nations. A total of 5572 university students from 12 countries were surveyed about suicide ideation, suicide attempts and psychological distress by means of a self-administered questionnaire. Almost 29% of the samples reported having contemplated suicide and 7% reported attempting suicide. Of the total sample, 51.1% scored above the General Health Questionnaire-12 ≥ 3 cut-off point, 41.6% above the GHQ-12 ≥ 4 cut-off point, and 33.8% scored above the GHQ-12 ≥ 5 cut-off point. While odds of suicide ideation were elevated in Austria and the UK, reduced ORs were detected for China, Italy, Saudi Arabia, Tunisia, and Turkey. Similarly, while odds of suicide attempt were high in Jordan, Palestine, Saudi Arabia, and to some extent in Turkey, reduced ORs were observed for Austria, China, Italy, Japan and the USA. Elevated ORs for psychological distress were seen in Japan, Jordan, Palestine, Saudi Arabia, Tunisia and Turkey but reduced ORs were noted in Austria, China, Iran, Italy and the USA. Psychological distress was strongly associated with reports of suicide ideation and attempts. Suicide ideation, suicide attempt and psychological distress are common in university students but their rates vary depending on the sociocultural context. Due attention should be devoted to the mental health needs of young adults enrolled in higher educational institutions and more cross-cultural research is warranted to better understand the etiology of the observed intersocietal variations in suicidal behavior and psychological distress

The Role of Religion on Suicidal Behavior, Attitudes and Psychological Distress in University Students: A Multinational Study

The purpose of this study was to determine the association of religion to suicidal behavior, attitudes and psychological distress in 5572 students from 12 countries by means of a self-report questionnaire. Our results showed that an affiliation with Islam was associated with reduced risk for suicide ideation, however affiliating with Orthodox Christianity and no religion was related to increased risk for suicide ideation. While affiliating with Buddhism, Catholic religion and no religion associated with lowered risk for attempting suicide, affiliation with Islam was related to heightened risk for attempting suicide. Affiliation with Hinduism, Orthodox Christianity, Protestantism, Catholicism, other religions and with no religion was associated with decreased risk for psychological distress but those reported affiliating with Islam evinced greater risk for psychological distress. The associations of the strength of religious belief to suicidal ideation and attempts were in the expected direction for most but it had a positive relation in respondents affiliating with Catholicism and other religions. Students reporting affiliation with Islam, Orthodox religion and Buddhism were the least accepting of suicide but they displayed a more confronting interpersonal style to an imagined peer with a suicidal decision. It was concluded that the protective function of religion in educated segments of populations (university students) and in university students residing in Muslim countries where freedom from religion is restricted or religion is normative and/or compulsory is likely to be limited. Our findings suggest that public policies supporting religious freedom may augment the protective function of religion against suicide and psychological distress

Cross - national comparisons of attitudes towards suicide and suicidal persons in university students from 12 countries

This paper reports the results of a comparative investigation of attitudes to suicide and suicidal persons in 5,572 university students from 12 countries. Participants filled out two scales measuring attitudes towards suicide and suicidal persons, a measure of psychological distress together with the questions about suicidal behavior. Results showed that the highest suicide acceptance scores were observed in Austrian, UK, Japanese and Saudi Arabian samples and the lowest scores were noted in Tunisian, Turkish, Iranian and Palestinian samples. While the highest social acceptance scores for a suicidal friend were noted in Turkish, US, Italian and Tunisian samples, the lowest scores were seen in Japanese, Saudi Arabian, Palestinian and Jordanian samples. Compared to participants with a suicidal past, those who were never suicidal displayed more internal barriers against suicidal behavior. Men were more accepting of suicide than women but women were more willing to help an imagined suicidal peer. Participants with accepting attitudes towards suicide but rejecting attitudes towards suicidal persons reported more suicidal behavior and psychological distress, and were more often from high suicide rate countries and samples than their counterparts. They are considered to be caught in a fatal trap in which most predominant feelings of suicidality such as hopelessness or helplessness are likely to occur. We conclude that in some societies such as Japan and Saudi Arabia it might be difficult for suicidal individuals to activate and make use of social support systems