Functional classification and validation of yeast prenylation motifs using machine learning and genetic reporters

Protein prenylation by farnesyltransferase (FTase) is often described as the targeting of a cysteine-containing motif (CaaX) that is enriched for aliphatic amino acids at the a1 and a2 positions, while quite flexible at the X position. Prenylation prediction methods often rely on these features despite emerging evidence that FTase has broader target specificity than previously considered. Using a machine learning approach and training sets based on canonical (prenylated, proteolyzed, and carboxymethylated) and recently identified shunted motifs (prenylation only), this study aims to improve prenylation predictions with the goal of determining the full scope of prenylation potential among the 8000 possible Cxxx sequence combinations. Further, this study aims to subdivide the prenylated sequences as either shunted (i.e., uncleaved) or cleaved (i.e., canonical). Predictions were determined for Saccharomyces cerevisiae FTase and compared to results derived using currently available prenylation prediction methods. In silico predictions were further evaluated using in vivo methods coupled to two yeast reporters, the yeast mating pheromone a-factor and Hsp40 Ydj1p, that represent proteins with canonical and shunted CaaX motifs, respectively. Our machine learning based approach expands the repertoire of predicted FTase targets and provides a framework for functional classification.

External or subcomissural annuloplasty in bicuspid aortic valve repair: which is better?

Patients with a bicuspid aortic valve (BAV) are at increased risk of valvular regurgitation compared to their counterparts with a tri-leaflet aortic valve. There is now increasing emphasis to offer BAV repair to mitigate the risks of prosthesis-related complications, including thromboembolism, haemorrhage and endocarditis, as well as structural valve deterioration and future re-operation with conventional valve replacement, particularly in younger populations. Furthermore, over the preceding two decades, our greater understanding of the functional anatomy of the BAV, pathophysiological mechanisms of BAV insufficiency and the development of a functional classification of aortic regurgitation have significantly contributed to the evolution of aortic valve reconstructive surgery. In this commentary, we discuss a recent article from the Journal of Cardiac Surgery comparing external annuloplasty and subcommissural annuloplasty as techniques for BAV repair.

Underground Built Heritage (UBH) as Valuable Resource in China, Japan and Italy

Recent research about the theoretical approach to elements of cultural heritage that can be included in the newly born class Underground Built Heritage (UBH), has provided several instruments for the functional classification and the static and dynamic analysis of all artefacts coherent with the given definition, while introducing several criteria for their reuse and the evaluation of connected enhancement processes as well. These guidelines can be adopted to analyze single artefacts, groups of homogenous or heterogeneous elements, and also selected territorial assets or national systems, even at a comparative level. With reference to this potential, research results from the application of this new methodological approach to the outputs of three ongoing projects by the National Research Council of Italy, all focusing on UBH, in three countries: China, Japan and Italy, are presented. With reference to the above-mentioned geographical contests, the research introduces a comparative study focusing on selected examples of artefacts that have been historically built underground to manage three functions: living space, religion and economy. This study, carried out based on data collected during onsite visits by the authors, consists in three steps: selection and analysis of case studies, definition of level of reuses on the basis of a given scale, and analysis of the different tools adopted for their conservation and enhancement. In the conclusions, possible future implementations of reuses of the analyzed elements are pointed out.

INVESTIGATING LEXICAL BUNDLES IN THE CORPORA OF ENGLISH AND INDONESIAN RESEARCH ARTICLES WITH THE SKETCH ENGINE

The low publication rate of Indonesian researchers in reputable international journals, particularly in arts and humanities,is caused, among others, by difficulties they faced in producing precise expository texts in English, which are differentfrom texts in Indonesian. The present study examines lexical bundles in the corpora of English and Indonesian researcharticles (RA) on literature and linguistics to describe the similarities and differences of conventionalized phraseology inthe scientific genre of English and Indonesian by using corpus software, namely Sketch Engine. The study focuses onthe frequency, structural and functional characteristics of lexical bundles using a mixed-method research design. TheEnglish corpus comprises 1,351,048 words derived from 124 RA, while the Indonesian corpus consists of 637,910 wordscollected from 124 RA. We found that three-word lexical bundles are more prevalent than four-word lexical bundles inboth corpora. Based on the structural forms, prepositional-based bundles are the most frequent form in English RA, whilenoun-based bundles are the most common form in Indonesian RA. There were no participant-oriented bundles foundin the Indonesian RA corpus in terms of functional classification, whereas the English RA corpus involved more variedfunctional categories of lexical bundles. The findings provide an understanding of phraseological combinations in Englishand Indonesian scientific writing, characterizing disciplinary discourse as well as native and non-native English speakers’rhetorical style, and have pedagogical implications for EAP practitioners.

Development of the Pulmonary Hypertension Functional Classification Self-Report: a patient version adapted from the World Health Organization Functional Classification measure

Background Pulmonary arterial hypertension (PAH) is characterized by progressive limitations on physical activity, right heart failure, and premature death. The World Health Organization functional classification (WHO-FC) is a clinician-rated assessment used widely to assess PAH severity and functioning, but no equivalent patient-reported version of PAH symptoms and activity limitations exists. We developed a version of the WHO-FC for self-completion by patients: the Pulmonary Hypertension Functional Classification Self-Report (PH-FC-SR). Methods Semistructured interviews were conducted with three health care providers (HCPs) via telephone to inform development of the draft PH-FC-SR. Two rounds of semi-structured interviews were conducted with 14 US patients with a self-reported PAH diagnosis via telephone/online to elicit concepts and iteratively refine the PH-FC-SR. Results HCPs reported that the WHO-FC was a useful tool for evaluating patients’ PAH severity over time and for making treatment decisions but acknowledged that use of the measure is subjective. Patients in round 1 interviews (n = 6) reported PAH symptoms, including shortness of breath (n = 6), fatigue (n = 5), syncope (n = 5), chest pains (n = 3), and dizziness (n = 3). Round 1 patients identified challenges with the original WHO-FC, including comprehensibility of clinical terms and overlapping descriptions of class II and III, and preferred the Draft 1 PH-FC-SR over the original WHO-FC. After minor changes were made to Draft 2, round 2 interviews (n = 8) confirmed patients understood the PH-FC-SR class descriptions, interpreting them consistently. Conclusions The HCP and patient interviews identified and confirmed certain limitations inherent within the clinician-rated WHO-FC, including subjective assessment and overlapping definitions for class II and III. The PH-FC-SR includes patient-appropriate language, symptoms, and physical activity impacts relevant to patients with PAH. Future research is recommended to validate the PH-FC-SR and explore its correlation with the physician-assessed WHO-FC and other outcomes.

Development of a City-Scale Approach for Façade Color Measurement with Building Functional Classification Using Deep Learning and Street View Images

Precise measuring of urban façade color is necessary for urban color planning. The existing manual methods of measuring building façade color are limited by time and labor costs and hardly carried out on a city scale. These methods also make it challenging to identify the role of the building function in controlling and guiding urban color planning. This paper explores a city-scale approach to façade color measurement with building functional classification using state-of-the-art deep learning techniques and street view images. Firstly, we used semantic segmentation to extract building façades and conducted the color calibration of the photos for pre-processing the collected street view images. Then, we proposed a color chart-based façade color measurement method and a multi-label deep learning-based building classification method. Next, the field survey data were used as the ground truth to verify the accuracy of the façade color measurement and building function classification. Finally, we applied our approach to generate façade color distribution maps with the building classification for three metropolises in China, and the results proved the transferability and effectiveness of the scheme. The proposed approach can provide city managers with an overall perception of urban façade color and building function across city-scale areas in a cost-efficient way, contributing to data-driven decision making for urban analytics and planning.

VIEWS ON THE STRUCTURAL-SEMANTIC AND FUNCTIONAL CLASSIFICATION OF SYMBOLS

This article reflects the views of scholars from various fields of science on symbols and their classification, and the symbols used in the Uzbek language are divided into groups from a linguistic point of view.

Circle the Cardiac Remodeling With circRNAs

Cardiac remodeling occurs after the heart is exposed to stress, which is manifested by pathological processes such as cardiomyocyte hypertrophy and apoptosis, dendritic cells activation and cytokine secretion, proliferation and activation of fibroblasts, and finally leads to heart failure. Circular RNAs (circRNAs) are recently recognized as a specific type of non-coding RNAs that are expressed in different species, in different stages of development, and in different pathological conditions. Growing evidences have implicated that circRNAs play important regulatory roles in the pathogenesis of a variety of cardiovascular diseases. In this review, we summarize the biological origin, characteristics, functional classification of circRNAs and their regulatory functions in cardiomyocytes, endothelial cells, fibroblasts, immune cells, and exosomes in the pathogenesis of cardiac remodeling.