Fold classification based on secondary structure – how much is gained by including loop topology?

BACKGROUND: It has been proposed that secondary structure information can be used to classify (to some extend) protein folds. Since this method utilizes very limited information about the protein structure, it is not surprising that it has a higher error rate than the approaches that use full 3D fold description. On the other hand, the comparing of 3D protein structures is computing intensive. This raises the question to what extend the error rate can be decreased with each new source of information, especially if the new information can still be used with simple alignment algorithms. We consider the question whether the information about closed loops can improve the accuracy of this approach. While the answer appears to be obvious, we had to overcome two challenges. First, how to code and to compare topological information in such a way that local alignment of strings will properly identify similar structures. Second, how to properly measure the effect of new information in a large data sample. We investigate alternative ways of computing and presenting this information. RESULTS: We used the set of beta proteins with at most 30% pairwise identity to test the approach; local alignment scores were used to build a tree of clusters which was evaluated using a new log-odd cluster scoring function. In particular, we derive a closed formula for the probability of obtaining a given score by chance.Parameters of local alignment function were optimized using a genetic algorithm. Of 81 folds that had more than one representative in our data set, log-odds scores registered significantly better clustering in 27 cases and significantly worse in 6 cases, and small differences in the remaining cases. Various notions of the significant change or average change were considered and tried, and the results were all pointing in the same direction. CONCLUSION: We found that, on average, properly presented information about the loop topology improves noticeably the accuracy of the method but the benefits vary between fold families as measured by log-odds cluster score

The current state of graphical abstracts and how to create good graphical abstracts

Graphical abstracts (GAs), also known as visual abstracts, are powerful tools for communicating complex information and ideas clearly and concisely. These visual representations aim to capture the essential findings and central message of a research study, allowing the audience to understand and remember its content quickly. This review article describes the current state of GAs, including their benefits, limitations, and future directions in the development of GAs. It also presents methods and tips for producing a GA. In Korea, more than 10 medical journals have introduced GAs from 2021 to 2022. The number of citations was higher in articles with GAs than in those without GAs in the top 10 gastroenterology journals. There are five types of GAs: conceptual diagrams, flowcharts, infographics, iconographic abstracts, and photograph-like illustrations. A limitation of the GA system is the absence of a universal standard for GAs. The key steps for creating a GA are as follows: (1) start by identifying the main message; (2) choose an appropriate visual style; (3) draw an easy-to-understand graphic; (4) use colors and other design elements; and (5) request feedback. Available tools that are useful for creating GAs include Microsoft PowerPoint, Mind the Graph, Biorender, and Canva. Another effective method is collaborating with experts. Artificial intelligence will soon be able to produce GAs more efficiently from raw data or manuscripts, which will help researchers draw GAs more easily. GAs have become a crucial art for researchers to master, and their use is expected to expand in the future

An Analysis of Research Trends in Brain-based Learning in Adult Education and HRD Fields: The Content Analysis and Network Text Analysis

The purpose of this study is to address the trends of the research on brain-based learning and to present an integrative theoretical framework to provide new insights and future directions in adult education and HRD fields. Based on the neuroscientific perspective, the implications of which the ways to conceptually broaden educational research and practice were discussed

Influence of the molecular structure of metal-phthalocyanine on electrocatalytic reactions

The demand for new catalysts for renewable energy production has become crucial. As an alternative to metal catalysts for electrocatalysis to produce energy sources, metal-phthalocyanine (MPc) electrocatalysts have shown potential. Their physicochemical and electrochemical properties depend on the chemical structure of the MPc and the central metal atom. Recent reviews of MPcs focused on their electrochemical performance in specific catalytic reactions, such as oxygen reduction reaction and CO2 reduction reaction. However, understanding the structure of MPcs in depth is important, since their electrochemical catalytic activity is affected by structural modifications of MPcs. Therefore, this minireview focuses on how the molecular structure of MPcs affects electrochemical catalysis

Prenatal Diagnosis of Bilateral Pulmonary Agenesis: a Case Report

We report a case of bilateral pulmonary agenesis (BPA), which was suspected during a prenatal US examination and diagnosed by fetal magnetic resonance imaging (MRI). BPA is an extremely rare congenital anomaly and, although many fetal structural defects can be detected with a high degree of confidence after introducing high-resolution US, the prenatal diagnosis of BPA remains problematic. Other thoracic abnormalities, such as a congenital diaphragmatic hernia, congenital cystic adenomatoid malformation, and pulmonary sequestration, should be excluded from the list of possible diagnoses before coming to the conclusion of BPA, because BPA is absolutely incompatible with extrauterine life, and an accurate internal diagnosis can prevent a futile intervention from being performed.Lee EY, 2008, RADIOLOGY, V247, P632, DOI 10.1148/radiol.2473062124Moreno-Alvarez O, 2008, ULTRASOUND OBST GYN, V31, P164, DOI 10.1002/uog.5201Obenauer S, 2008, CLIN IMAG, V32, P48, DOI 10.1016/j.clinimag.2007.08.019Joshi S, 2007, EARLY HUM DEV, V83, P789, DOI 10.1016/j.earlhumdev.2007.09.007Jeanty C, 2007, ULTRASOUND OBST GYN, V29, P378, DOI 10.1002/uog.3958Nazir Z, 2006, J PEDIATR SURG, V41, P1165, DOI 10.1016/j.jpedsurg.2006.02.012Gabarre JA, 2005, J ULTRAS MED, V24, P865Levine D, 2003, RADIOLOGY, V228, P379, DOI 10.1148/radiol.2282020604Vettraino IM, 2003, J ULTRAS MED, V22, P723Yang JI, 2003, J CLIN ULTRASOUND, V31, P214, DOI 10.1002/jcu.10157Laudy JAM, 2000, ULTRASOUND OBST GYN, V16, P284Kalache KD, 1997, FETAL DIAGN THER, V12, P360ENGELLENNER W, 1989, PEDIATR PATHOL, V9, P725