Predicting base editing outcomes using position-specific sequence determinants

Nucleotide-level control over DNA sequences is poised to power functional genomics studies and lead to new therapeutics. CRISPR/Cas base editors promise to achieve this ability, but the determinants of their activity remain incompletely understood. We measured base editing frequencies in two human cell lines for two cytosine and two adenine base editors at ~14,000 target sequences. Base editing activity is sequence-biased, with largest effects from nucleotides flanking the target base, and is correlated with measures of Cas9 guide RNA efficiency. Whether a base is edited depends strongly on the combination of its position in the target and the preceding base, with a preceding thymine in both editor types leading to a wider editing window, while a preceding guanine in cytosine editors and preceding adenine in adenine editors to a narrower one. The impact of features on editing rate depends on the position, with guide RNA efficacy mainly influencing bases around the centre of the window, and sequence biases away from it. We use these observations to train a machine learning model to predict editing activity per position for both adenine and cytosine editors, with accuracy ranging from 0.49 to 0.72 between editors, and with better generalization performance across datasets than existing tools. We demonstrate the usefulness of our model by predicting the efficacy of potential disease mutation correcting guides, and find that most of them suffer from more unwanted editing than corrected outcomes. This work unravels the position-specificity of base editing biases, and provides a solution to account for them, thus allowing more efficient planning of base edits in experimental and therapeutic contexts.

Positional Differences in Peak- and Accumulated- Training Load Relative to Match Load in Elite Football

Quantification of training and match load is an important method to personalize the training stimulus’ prescription to players according to their match demands. The present study used time-motion analysis and triaxial-accelerometer to quantify and compare: a) The most demanding passages of play in training sessions and matches (5-min peaks); b) and the accumulated load of typical microcycles and official matches, by playing position. Players performance data in 15 official home matches and 11 in-season microcycles were collected for analysis. Players were divided into four different playing positions: Centre-backs, wing-backs, centre midfielders, and centre forwards. The results show that match demands were overperformed for acceleration counts (acccounts) (131%–166%) and deceleration counts (deccounts) (108%–134%), by all positions. However, relative to match values, training values for sprint distance (sprintdist) and high-intensity run distance (HIRdist) were considerably lower (36%–61% and 57%–71%) than for accelerations and decelerations. The most pronounced difference on the 5-min peaks was observed in sprints (sprintpeak), with wing-backs achieving during the microcycle only 64% of the sprintpeak in matches, while centre backs, centre midfielders, and centre forwards levelled and overperformed the match values (107%, 100%, and 107%, respectively). Differences observed across playing positions in matches and microcycles underline the lack of position specificity of common training drills/sessions adopted by coaches in elite football.

Anthropometric Profile of Soccer Players as a Determinant of Position Specificity and Methodological Issues of Body Composition Estimation

The aim of the present study was (a) to describe the anthropometric profile of a large group of soccer players based on different age groups and their playing positions on the field, and (b) to examine the variations of body composition among adult soccer players using diverse equations based on skinfold thickness. A total of 618 Greek soccer players who were grouped by age (i.e., 12–14, 14–16, 16–18, and 18–37 years) and playing position (i.e., goalkeeper, defender, midfielder, and forward) were evaluated for weight, height, and skinfolds. The Pařízková formula was used to estimate the percentage of body fat. Furthermore, for players who were 18 years or older the Reilly and Evans formulas was used to estimate the percentage of body fat. Independent of the age, in this large sample, goalkeepers presented higher values for weight, height and the percentage of body fat estimation as compared with other field positions. An anthropometric pattern was observed in each tactical position, namely, across a specific age of increasing maturation process (14–16 years). With the Pařízková formula, we found a mean (SD) range of variation in the percentage of body fat estimation between 4.87 ± 1.46 and 5.51 ± 1.46 as compared with the Evans formula. The same pattern of differences was found when the Reilly equation was considered. In conclusion, we observed a position specificity of anthropometric characteristics across different age categories. Additionally, the same data supported different validated equations which resulted in large differences in the final outcome estimations.

Investigating the Influence of Designers’ Cognitive Characteristics and Interaction Behaviors in Design Concept Generation

This paper investigates relationships among the cognitive characteristics, interaction behaviors, and ideation outcomes of 14 engineering design teams engaged in concept generation. Cognitive characteristics were measured using the Kirton Adaption-Innovation Inventory (KAI), which assesses an individual’s cognitive preference for structure in generating and working with ideas in problem solving. Team interactions were assessed using the Interaction Dynamics Notation (IDN), which allows interaction behaviors to be quantitatively analyzed, while team outcomes were measured in terms of ideation utterances (ideas and unique ideas). Our analyses revealed that cognitive style (KAI) did not correlate significantly with interaction response behaviors (IDN) or with the quantity of ideas/unique ideas produced. However, the cognitive style diversity of the teams did influence the number of topics they discussed, as well as the interconnectedness of those topics. In addition, several specific interaction responses were associated with the occurrence of ideas/unique ideas, although the sequences associated with those responses varied widely; the more adaptive teams also had greater position specificity in these sequences than the more innovative teams. Our findings highlight the importance of forming cognitively diverse design teams and suggest that specific interaction behaviors should be encouraged or taught as a means to increase the occurrence of ideas and/or unique ideas during team concept generation.

Synthesis of p-methoxyphenyl sulfated β-GalNAc derivatives with inhibitory activity against Japanese encephalitis virus

The N-acetylgalactosamine (GalNAc) residue is one of the units of chondroitin sulfate E (CS-E) which has been reported to have inhibitory activity against Japanese encephalitis virus (JEV). Herein, we describe the synthesis of a series of p-methoxyphenyl β-GalNAc derivatives with a sulfate group at 3-, 4-, and/or 6-positions using an efficient route through a common synthetic intermediate. By measuring the inhibition activity of these compounds that bear different numbers and positions of sulfate groups, the effect of position specificity for interaction with the virus was determined. From these results, GalNAc6S and GalNAc4S6S derivatives inhibited JEV infections well; we suggest the 6-O-sulfate group is necessary for selective recognition by the virus.