Henderson Delaney (atticfile1)

Clostridium (Ruminiclostridium) thermocellum is recognized for its ability to ferment cellulosic biomass directly, but it cannot naturally grow on xylose. Recently, C. thermocellum (KJC335) was engineered to utilize xylose through expressing a heterologous xylose catabolizing pathway. Here, we compared KJC335's transcriptomic responses to xylose versus cellobiose as the primary carbon source and assessed how the bacteria adapted to utilize xylose. Our analyses revealed 417 differentially expressed genes (DEGs) with log2 fold change (FC) >|1| and 106 highly DEGs (log2 FC >|2|). Among the DEGs, two putative sugar transporters, cbpC and cbpD, were up-regulated, suggesting their contribution to xylose transport and assimilation. Moreover, the up-regulation of specific transketolase genes (tktAB) suggests the importance of this enzyme for xylose metabolism. Results also showed remarkable up-regulation of chemotaxis and motility associated genes responding to xylose feeding, as well as widely varying gene expression in those encoding cellulosomal enzymes. For the down-regulated genes, several were categorized in gene ontology terms oxidation-reduction processes, ATP binding and ATPase activity, and integral components of the membrane. This study informs potentially critical, enabling mechanisms to realize the conceptually attractive Next-Generation Consolidated BioProcessing approach where a single species is sufficient for the co-fermentation of cellulose and hemicellulose.The use of raw amino acid sequences as input for deep learning models for protein functional prediction has gained popularity in recent years. This scheme obliges to manage proteins with different lengths, while deep learning models require same-shape input. To accomplish this, zeros are usually added to each sequence up to a established common length in a process called zero-padding. However, the effect of different padding strategies on model performance and data structure is yet unknown. We propose and implement four novel types of padding the amino acid sequences. Then, we analysed the impact of different ways of padding the amino acid sequences in a hierarchical Enzyme Commission number prediction problem. Results show that padding has an effect on model performance even when there are convolutional layers implied. Contrastingly to most of deep learning works which focus mainly on architectures, this study highlights the relevance of the deemed-of-low-importance process of padding and raises awareness of the need to refine it for better performance. The code of this analysis is publicly available at https//github.com/b2slab/padding_benchmark .Surgical hand hygiene reduces the risk of surgical site infections (SSIs). SSIs are not considered an issue in endourological surgery, whereas febrile urinary tract infections (f-UTIs) and urological sepsis are becoming problematic. We wondered whether surgical hand hygiene is necessary for endourological surgery. Therefore, we aimed to evaluate the influence of surgical hand hygiene on f-UTI onset in endourological surgery by comparing procedures in which surgical hand hygiene with double gloving was used with those in which regular hand hygiene with double gloving was used between April 2016 and July 2020. In this prospective cohort study of 477 patients who underwent endourological surgeries, surgeons in the surgical hand hygiene and regular hygiene groups performed surgery on 259 and 218 patients, respectively. There was no significant difference in patient background, and multivariate analyses revealed no significant differences in f-UTI onset (odds ratio, 0.87; p = 0.74) between the two groups. In conclusion, regular hand hygiene with double gloving may be considered an alternative to surgical hand hygiene to prevent endourological f-UTIs, which could alter operational protocols for endourological surgery. Further studies are needed to validate our fin