MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts

<p>Abstract</p> <p>Background</p> <p>Multiple Sequence Alignment (MSA) is a basic tool for bioinformatics research and analysis. It has been used essentially in almost all bioinformatics tasks such as protein structure modeling, gene and protein function prediction, DNA motif recognition, and phylogenetic analysis. Therefore, improving the accuracy of multiple sequence alignment is important for advancing many bioinformatics fields.</p> <p>Results</p> <p>We designed and developed a new method, MSACompro, to synergistically incorporate predicted secondary structure, relative solvent accessibility, and residue-residue contact information into the currently most accurate posterior probability-based MSA methods to improve the accuracy of multiple sequence alignments. The method is different from the multiple sequence alignment methods (e.g. 3D-Coffee) that use the tertiary structure information of some sequences since the structural information of our method is fully predicted from sequences. To the best of our knowledge, applying predicted relative solvent accessibility and contact map to multiple sequence alignment is novel. The rigorous benchmarking of our method to the standard benchmarks (i.e. BAliBASE, SABmark and OXBENCH) clearly demonstrated that incorporating predicted protein structural information improves the multiple sequence alignment accuracy over the leading multiple protein sequence alignment tools without using this information, such as MSAProbs, ProbCons, Probalign, T-coffee, MAFFT and MUSCLE. And the performance of the method is comparable to the state-of-the-art method PROMALS of using structural features and additional homologous sequences by slightly lower scores.</p> <p>Conclusion</p> <p>MSACompro is an efficient and reliable multiple protein sequence alignment tool that can effectively incorporate predicted protein structural information into multiple sequence alignment. The software is available at <url>http://sysbio.rnet.missouri.edu/multicom_toolbox/</url>.</p

Improving the Alignment Quality of Consistency Based Aligners with an Evaluation Function Using Synonymous Protein Words

Most sequence alignment tools can successfully align protein sequences with higher levels of sequence identity. The accuracy of corresponding structure alignment, however, decreases rapidly when considering distantly related sequences (<20% identity). In this range of identity, alignments optimized so as to maximize sequence similarity are often inaccurate from a structural point of view. Over the last two decades, most multiple protein aligners have been optimized for their capacity to reproduce structure-based alignments while using sequence information. Methods currently available differ essentially in the similarity measurement between aligned residues using substitution matrices, Fourier transform, sophisticated profile-profile functions, or consistency-based approaches, more recently

Views and experiences of people with intellectual disabilities regarding intimate relationships: a qualitative metasynthesis

The aims of this review were to systematically identify, critically appraise and synthesize the results of existing qualitative literature exploring the views and experiences of intimate relationships amongst people with intellectual disabilities. Fourteen peer-reviewed articles were identified through a systematic search of eight databases, reference lists, citations, and relevant journals. The identified articles were appraised for quality, then synthesized using a metaethnography approach. No study met all quality criteria and references to ethical approval were often lacking. Interpretation of the findings suggested three key themes: the meaning of intimate relationships, external constraints and facilitators, and managing external constraints. Though many people with intellectual disabilities desire and benefit from intimate relationships, they experience restrictions that others do not, which can lead to isolation and loneliness. Intimate relationships are not always necessarily linked with sexual behavior; therefore, intimate relationships warrant their own focus in future research, as well as in education and training for people with intellectual disabilities and their caregivers. Within this, a commitment to transparency over research processes is needed, in particular with reference to how ethical approval was obtained, since this has been a shortcoming of research with this focus to date

Mechanisms of blood homeostasis: lineage tracking and a neutral model of cell populations in rhesus macaques

BACKGROUND: How a potentially diverse population of hematopoietic stem cells (HSCs) differentiates and proliferates to supply more than 10(11) mature blood cells every day in humans remains a key biological question. We investigated this process by quantitatively analyzing the clonal structure of peripheral blood that is generated by a population of transplanted lentivirus-marked HSCs in myeloablated rhesus macaques. Each transplanted HSC generates a clonal lineage of cells in the peripheral blood that is then detected and quantified through deep sequencing of the viral vector integration sites (VIS) common within each lineage. This approach allowed us to observe, over a period of 4-12 years, hundreds of distinct clonal lineages. RESULTS: While the distinct clone sizes varied by three orders of magnitude, we found that collectively, they form a steady-state clone size-distribution with a distinctive shape. Steady-state solutions of our model show that the predicted clone size-distribution is sensitive to only two combinations of parameters. By fitting the measured clone size-distributions to our mechanistic model, we estimate both the effective HSC differentiation rate and the number of active HSCs. CONCLUSIONS: Our concise mathematical model shows how slow HSC differentiation followed by fast progenitor growth can be responsible for the observed broad clone size-distribution. Although all cells are assumed to be statistically identical, analogous to a neutral theory for the different clone lineages, our mathematical approach captures the intrinsic variability in the times to HSC differentiation after transplantation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12915-015-0191-8) contains supplementary material, which is available to authorized users

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هدف از این تحقیق، ارائه این عوامل در قالب یک مدل و بیان ارتباط می ان این عوامل است . تحقیقاتگوناگونی در مورد عوامل تأثیرگذار بر تمایل دانشجویان به ادامۀ به کارگیری این سیستم ها انجام شده استکه در هر یک از این تحقیقات، عوامل مختلفی در نظر گرفته شده است . پس از مطالعه ادبیات موضوع ومدلهای ارائه شده در تحقیقات قبلی، عوامل مهم تر، استخراج شده و مدلی ارائه شده است. مدل حاصل درطی چند مرحله و با در نظر گرفتن نظر تعدادی از خبرگان، تغییر یافته و در نهایت، مدل نهایی ار ائ ه شدهاست. به منظور اعتبار سنجی مدل پیشنهادی تحقیق، پرسشنامهای طراحی شد . دانشجویان دانشگاه علم وصنعت ایران به عنوان جامعه آماری انتخاب شدند . پرسشنام ۀ طراحی شده بین دانشجویان دوره هاییادگیری الکترونیکی این دانشگاه توزیع شد. نتایج حاصل نشان میدهد که ارتباطی بسیار قوی بین رضایت وتمایل به ادامۀ به کارگیری سیستم یادگیری الکترونیکی وجود دارد. همچنین، به نظر میرسد در کشور ما درحال حاضر فنّاوری، بعدی است که بیشترین اهمیت را داشته و رضایت از آن بیشترین تأثیر را بر تمایل افرادبه ادامه به کارگیری سیستم یادگیری الکترونیکی دارا است

Simulation Of Temperature Changes In Iran Under The Atmosphere Carbon Dioxide Duplication Condition

The present research intends to show the effect of global warming on the trend and patterns of temperature in Iran. The study has been divided into two primary parts, the first of which is an analysis of the country&apos;s temperature trend using the following data measures: the minimum, maximum, and mean seasonal night temperature (the minimum temperature) components, the day temperature (the maximum temperature) component and the mean daily temperature component. This data is specific to the time frame 1951 to 2005 and it was obtained from 92 synoptic and climatology stations around the country. The second part of this research involved simulating and forecasting the effects of global warming on temperature values under conditions in which greenhouse gases have increased. For analyzing these simulations and forecasts the MAGICC SCENGEN model was used and different climate change scenarios were taken into consideration. The results are quite interesting. In the analysis of the country’s current temperature trend and in the forecasting’s, specifically related to time, a significant temperature increase was observed during the summer months. Also, with regard to altitudinal levels, it was evident that stations at higher altitudes show a more significant increase in daily and mean daily temperatures. Taking into account the output mean of the different climate change scenarios, the temperature simulations show a 4.41° C increase in Iran’s mean temperature by 2100. Most of these temperature increases would occur in the southern and eastern parts of Bushehr, certain coastal regions of the Persian Gulf, eastern and western parts of Fars, Kohgilooye, Boyerahmad, southern parts of Yazd, as well as southern and southeastern parts of Esfahan

Simulation of global warming effect on outdoor thermal comfort conditions

In the coming decades, global warming and increase in temperature, in different regions of the world, may change indoor and outdoor thermal comfort conditions and human health. The aim of this research was to study the effects of global warming on thermal comfort conditions in indoor ambiences in Iran. To study the increase in temperature, model for assessment of greenhouse-gas induced climate change scenario generator compound model has been used together with four scenarios and to estimate thermal comfort conditions, adaptive model of the American Society of Heating, Refrigerating and Air-conditioning Engineers has been used. In this study, Iran was divided into 30 zones, outdoor conditions were obtained using meteorological data of 80 climatological stations and changes in neutral comfort conditions in 2025, 2050, 2075 and 2100 were predicted. In accordance with each scenario, findings from this study showed that temperature in the 30 zones will increase by 2100 to between 3.4 °C and 5.6 °C. In the coming decades and in the 30 studied zones, neutral comfort temperature will increase and be higher and more intense in the central and desert zones of Iran. The low increase in this temperature will be connected to the coastal areas of the Caspian and Oman Sea in southeast Iran. This increase in temperature will be followed by a change in thermal comfort and indoor energy consumption from 8.6 % to 13.1 % in air conditioning systems. As a result, passive methods as thermal inertia are proposed as a possible solution

The Influence of Civil Behaviour on Social Capital: A Case Study by Cooperative General Administration, Zahedan Province

Amidst today's challenging world, in order for doing well in the competition which relies on satisfying customer expectations as well as adaptation with the changing nature of occupations,  organizations tend to hire employees who are capable of doing more than their job descriptions on the belief that such capabilities would influence the employee participation in organizational policies. Bateman and Organ (1983) coined the term "Organizational Civil Behaviour" (OCB) to refer to a set of useful behaviours which are not officially cited in a job description, yet are expressed obviously by employees in order to help others out. This seems to stand in close relation with social capital which includes the whole of social norms contributing to an enhanced level of participation through the members of the society. The present research aims at studying the relation between OCB and Social capital in 1388-89 (2009-10). The statistical population consists in the entire employees of the provincial Cooperative General Administration, Cooperative Development Bank as well as cooperative offices at the township level. The data were collected through clustered stratified sampling from 197 employees. Questionnaire was the data collection tool and Pierson and Regression correlations were the tests applied for data analysis. Briefly speaking, the results indicated that there is a significant relation between OCB and social capita

Effects of Distraction on Physiologic Indices and Pain Intensity in children aged 3-6 Undergoing IV Injection

Background &amp;amp; Objective: Illness, hospitalization and pain are often first crisis children faced with in their early life. Performing painful procedures such as IV injections for medical purposes are inevitable and stressful events in pediatric wards. Distraction is an inexpensive, practical, and nonpharmacological nursing intervention for pain relief. This study aimed to determine the effects of distraction on some physiological indices (heart rate and O2 saturation (and intensity of pain in the hospitalized children aged 3-6 years undergoing IV injection. Methods &amp;amp; Materials: In this clinical trial, 72 children aged 3-6 years who were undergoing IV insertion were recruited for the study. The participants were randomly allocated into two groups of intervention and control. Distraction technique was applied using bubble-maker in the intervention group. After 10 minutes, pain intensity was measured using OUCHER scale. Moreover, heart rate and blood oxygen saturation were measured for three minutes in both groups using Pulse Oxymeter pre- and post-intervention. Results: The findings showed statistically significant differences in the average heart rate (P&amp;lt;0.01) and the amount of saturated oxygen (P&amp;lt;0.009) and the pain intensity (P&amp;lt;0.001) between two groups after the intervention. The pain decreased significantly in the intervention group in comparison with the control group. Conclusion: According to the research findings, distraction with bubble-maker resulted in decreasing the physiological responses and intensity of pain in children aged 3- 6 years. This method can be useful in reliving the pain in preschool children undergoing IV insertion. &amp;nbsp