Paving the way forward: Escherichia coli bacteriophages in a One Health approach.

Escherichia coli is one of the most notorious pathogens for its ability to adapt, colonize, and proliferate in different habitats through a multitude of acquired virulence factors. Its presence affects the food-processing industry and causes food poisoning, being also a major economic burden for the food, agriculture, and health sectors. Bacteriophages are emerging as an appealing strategy to mitigate bacterial pathogens, including specific E. coli pathovars, without exerting a deleterious effect on humans and animals. This review globally analyzes the applied research on E. coli phages for veterinary, food, and human use. It starts by describing the pathogenic E. coli pathotypes and their relevance in human and animal context. The idea that phages can be used as a One Health approach to control and interrupt the transmission routes of pathogenic E. coli is sustained through an exhaustive revision of the recent literature. The emerging phage formulations, genetic engineering and encapsulation technologies are also discussed as a means of improving phage-based control strategies, with a particular focus on E. coli pathogens.

Assessing Acinetobacter baumannii virulence and treatment with a bacteriophage using zebrafish embryos.

Acinetobacter baumannii is the leading bacteria causative of nosocomial infections, with high fatality rates, mostly due to their multi-resistance to antibiotics. The capsular polysaccharide (k-type) is a major virulence factor. Bacteriophages are viruses that specifically infect bacteria and have been used to control drug-resistant bacterial pathogens. In particular, A. baumannii phages can recognize specific capsules, from a diversity of >125 that exist. This high specificity demands the in vivo identification of the most virulent A. baumannii k-types that need to be targeted by phage therapy. Currently, the zebrafish embryo has particularly attained interest for in vivo infection modeling. In this study, an A. baumannii infection was successfully established, through the bath immersion of tail-injured zebrafish embryos, to study the virulence of eight capsule types (K1, K2, K9, K32, K38, K44, K45, and K67). The model revealed itself as capable of discerning the most virulent (K2, K9, K32, and K45), middle (K1, K38, and K67), and the less virulent (K44) strains. Additionally, the infection of the most virulent strains was controlled in vivo resorting to the same technique, with previously identified phages (K2, K9, K32, and K45 phages). Phage treatments were able to increase the average survival from 35.2% to up to 74.1% (K32 strain). All the phages performed equally well. Collectively, the results show the potential of the model to not only evaluate virulence of bacteria such as A. baumannii but also assess novel treatments' effectiveness.

Palliative care and end stage liver disease: A cohort analysis of palliative care use and factors associated with referral.

INTRODUCTION AND OBJECTIVES: Prevalence and mortality of chronic liver disease have risen significantly. In end stage liver disease, the survival of patients is approximately two years. Despite the poor prognosis and high symptom burden of these patients, integration of palliative care is limited. We aim to assess associated factors and trends in palliative care use in recent years. MATERIALS AND METHODS: A Multicenter retrospective cohort of patients with end stage liver disease who suffered in-hospital mortality between 2017 and 2019. Information regarding patient demographics, hospital characteristics, comorbidities, etiology, decompensations, and interventions was collected. Two-sided tests and logistic regression analysis were used to identify factors associated with palliative care use. RESULTS: A total of 201 patients were analyzed, with a yearly increase in palliative care consultation: 26.7 % in 2017 to 38.3 % in 2019. Patients in palliative care were older (65.72 ± 11.70 vs. 62.10 ± 11.44; p = 0.003), had a lower Karnofsky functionality scale (χ=18.104; p = 0.000) and had higher rates of hepatic encephalopathy (32.1 % vs. 17.4 %, p = 0.007) and hepatocarcinoma (61.7 % vs. 26.2 %; p = 0.000). No differences were found for Model for End-stage Liver Disease (19.28 ± 6.60 vs. 19,90 ± 5.78; p = 0.507) or Child-Pugh scores (p = 0.739). None of the patients who die in the intensive care unit receive palliative care (0 % vs 31.6 %; p = 0.000). Half of the palliative care consultations occurred 6,5 days before death. CONCLUSIONS: Palliative care use differs based on demographics, disease complications, and severity. Despite its increasing implementation, palliative care intervention occurs late. Future investigations should identify approaches to achieve an earlier and concurrent care model.

CkP1 bacteriophage, a S16-like myovirus that recognizes Citrobacter koseri lipopolysaccharide through its long tail fibers.

Citrobacter koseri is an emerging Gram-negative bacterial pathogen, which causes urinary tract infections. We isolated and characterized a novel S16-like myovirus CKP1 (vB_CkoM_CkP1), infecting C. koseri. CkP1 has a host range covering the whole C. koseri species, i.e., all strains that were tested, but does not infect other species. Its linear 168,463-bp genome contains 291 coding sequences, sharing sequence similarity with the Salmonella phage S16. Based on surface plasmon resonance and recombinant green florescence protein fusions, the tail fiber (gp267) was shown to decorate C. koseri cells, binding with a nanomolar affinity, without the need of accessory proteins. Both phage and the tail fiber specifically bind to bacterial cells by the lipopolysaccharide polymer. We further demonstrate that CkP1 is highly stable towards different environmental conditions of pH and temperatures and is able to control C. koseri cells in urine samples. Altogether, CkP1 features optimal in vitro characteristics to be used both as a control and detection agent towards drug-resistant C. koseri infections. KEY POINTS: • CkP1 infects all C. koseri strains tested • CkP1 recognizes C. koseri lipopolysaccharide through its long tail fiber • Both phage CkP1 and its tail fiber can be used to treat or detect C. koseri pathogens.

A Prototype Implantable Artificial Bronchus Reduces Lung Hyperinflation in Recently Deceased Patients with Emphysema.

BACKGROUND: Several minimally invasive treatments have been offered to patients with severe emphysema over the last two decades. Currently, endobronchial valves (EBVs) are the only approved therapeutic option, but this method has drawbacks: only a few can undergo this therapy and the incidence of pneumothorax remains high. A minimally invasive technique, appropriate for a broader patient population and posing fewer risks, would represent a desirable alternative to improve lung function in these patients. OBJECTIVE: The objective of this study was to demonstrate whether a new prototype implantable artificial bronchus (IAB) releases trapped air from the lungs of recently deceased patients with emphysema. METHOD: Seven recently deceased patients with emphysema were mechanically ventilated and the respiratory rate increased from 12 bpm (resting) to 30 bpm (exercise), inducing air trapping and dynamic hyperinflation. This protocol was performed twice, before and after IAB placement. Ventilation parameters and the fraction of inspired oxygen were similar in all patients. Respiratory system plateau pressure (Pplat,rs) and intrinsic positive end-expiratory pressure (iPEEP) were measured. RESULTS: IAB implantation significantly reduced Pplat,rs (p = 0.017) in 6 of 7 deceased patients with emphysema and iPEEP (p = 0.03) in 5 of 7 patients. CONCLUSIONS: Placement of one or two IABs in segmental bronchi (up to 15th generation) proved to be feasible and improved lung function. These findings should provide a basis for subsequent clinical studies to assess the safety and efficacy of IAB in patients with emphysema, as well as identify short- and long-term effects of this innovative procedure.

Automatic generation of creative text in Portuguese: an overview.

Creativity is an inherently human skill, and thus one of the goals of Artificial Intelligence. Specifically, linguistic computational creativity deals with the autonomous generation of linguistically-creative artefacts. Here, we present four types of text that can be tackled in this scope-poetry, humour, riddles, and headlines-and overview computational systems developed for their generation in Portuguese. Adopted approaches are described and illustrated with generated examples, and the key role of underlying computational linguistic resources is highlighted. The future of such systems is further discussed together with the exploration of neural approaches for text generation. While overviewing such systems, we hope to disseminate the area among the community of the computational processing of the Portuguese language.

Transformers for Energy Forecast.

Forecasting energy consumption models allow for improvements in building performance and reduce energy consumption. Energy efficiency has become a pressing concern in recent years due to the increasing energy demand and concerns over climate change. This paper addresses the energy consumption forecast as a crucial ingredient in the technology to optimize building system operations and identifies energy efficiency upgrades. The work proposes a modified multi-head transformer model focused on multi-variable time series through a learnable weighting feature attention matrix to combine all input variables and forecast building energy consumption properly. The proposed multivariate transformer-based model is compared with two other recurrent neural network models, showing a robust performance while exhibiting a lower mean absolute percentage error. Overall, this paper highlights the superior performance of the modified transformer-based model for the energy consumption forecast in a multivariate step, allowing it to be incorporated in future forecasting tasks, allowing for the tracing of future energy consumption scenarios according to the current building usage, playing a significant role in creating a more sustainable and energy-efficient building usage.

Mice with endogenous TDP-43 mutations exhibit gain of splicing function and characteristics of amyotrophic lateral sclerosis.

TDP-43 (encoded by the gene TARDBP) is an RNA binding protein central to the pathogenesis of amyotrophic lateral sclerosis (ALS). However, how TARDBP mutations trigger pathogenesis remains unknown. Here, we use novel mouse mutants carrying point mutations in endogenous Tardbp to dissect TDP-43 function at physiological levels both in vitro and in vivo Interestingly, we find that mutations within the C-terminal domain of TDP-43 lead to a gain of splicing function. Using two different strains, we are able to separate TDP-43 loss- and gain-of-function effects. TDP-43 gain-of-function effects in these mice reveal a novel category of splicing events controlled by TDP-43, referred to as "skiptic" exons, in which skipping of constitutive exons causes changes in gene expression. In vivo, this gain-of-function mutation in endogenous Tardbp causes an adult-onset neuromuscular phenotype accompanied by motor neuron loss and neurodegenerative changes. Furthermore, we have validated the splicing gain-of-function and skiptic exons in ALS patient-derived cells. Our findings provide a novel pathogenic mechanism and highlight how TDP-43 gain of function and loss of function affect RNA processing differently, suggesting they may act at different disease stages.

Morphological Study of Root Canals of Maxillary Molars by Cone-Beam Computed Tomography.

The aim of this study was to evaluate the root canal morphology of permanent maxillary molars by cone-beam computed tomography (CBCT) using the classifications of Weine et al. and Vertucci and to correlate the findings with sex, age, position in the dental arch, and prevalence of a second canal in the mesiobuccal root (MB2). A total of 414 scans were evaluated, corresponding to 1,000 teeth. The assessment consisted of coronal, axial, and sagittal reconstructions using i-CAT Workstation®. Type 0 was assigned when neither classification could be applied. The data were entered into an Excel spreadsheet and analyzed using SPSS. The chi-squared test or Fisher's exact test was used to compare the distribution of root canal morphology classified using the two systems. Analysis of the distribution of Weine types showed a predominance of type III in mesiobuccal roots, while type 0 predominated in distobuccal and palatal roots. Vertucci type IV predominated in mesiobuccal and distobuccal roots and type VII in palatal roots. There was no difference in the distribution of morphological canal types in permanent maxillary molars evaluated by CBCT according to sex, age group, or position in the dental arch of the patients. MB2 canals were identified in 68.4% of the teeth evaluated.

Sound Classification and Processing of Urban Environments: A Systematic Literature Review.

Audio recognition can be used in smart cities for security, surveillance, manufacturing, autonomous vehicles, and noise mitigation, just to name a few. However, urban sounds are everyday audio events that occur daily, presenting unstructured characteristics containing different genres of noise and sounds unrelated to the sound event under study, making it a challenging problem. Therefore, the main objective of this literature review is to summarize the most recent works on this subject to understand the current approaches and identify their limitations. Based on the reviewed articles, it can be realized that Deep Learning (DL) architectures, attention mechanisms, data augmentation techniques, and pretraining are the most crucial factors to consider while creating an efficient sound classification model. The best-found results were obtained by Mushtaq and Su, in 2020, using a DenseNet-161 with pretrained weights from ImageNet, and NA-1 and NA-2 as augmentation techniques, which were of 97.98%, 98.52%, and 99.22% for UrbanSound8K, ESC-50, and ESC-10 datasets, respectively. Nonetheless, the use of these models in real-world scenarios has not been properly addressed, so their effectiveness is still questionable in such situations.

Transformers for Urban Sound Classification-A Comprehensive Performance Evaluation.

Many relevant sound events occur in urban scenarios, and robust classification models are required to identify abnormal and relevant events correctly. These models need to identify such events within valuable time, being effective and prompt. It is also essential to determine for how much time these events prevail. This article presents an extensive analysis developed to identify the best-performing model to successfully classify a broad set of sound events occurring in urban scenarios. Analysis and modelling of Transformer models were performed using available public datasets with different sets of sound classes. The Transformer models' performance was compared to the one achieved by the baseline model and end-to-end convolutional models. Furthermore, the benefits of using pre-training from image and sound domains and data augmentation techniques were identified. Additionally, complementary methods that have been used to improve the models' performance and good practices to obtain robust sound classification models were investigated. After an extensive evaluation, it was found that the most promising results were obtained by employing a Transformer model using a novel Adam optimizer with weight decay and transfer learning from the audio domain by reusing the weights from AudioSet, which led to an accuracy score of 89.8% for the UrbanSound8K dataset, 95.8% for the ESC-50 dataset, and 99% for the ESC-10 dataset, respectively.

Insights into the genome architecture and evolution of Shiga toxin encoding bacteriophages of Escherichia coli.

BACKGROUND: A total of 179 Shiga toxin-producing Escherichia coli (STEC) complete genomes were analyzed in terms of serotypes, prophage coding regions, and stx gene variants and their distribution. We further examined the genetic diversity of Stx-converting phage genomes (Stx phages), focusing on the lysis-lysogeny decision and lytic cassettes. RESULTS: We show that most STEC isolates belong to non-O157 serotypes (73 %), regardless the sources and geographical regions. While the majority of STEC genomes contain a single stx gene (61 %), strains containing two (35 %), three (3 %) and four (1 %) stx genes were also found, being stx2 the most prevalent gene variant. Their location is exclusively found in intact prophage regions, indicating that they are phage-borne. We further demonstrate that Stx phages can be grouped into four clusters (A, B, C and D), three subclusters (A1, A2 and A3) and one singleton, based on their shared gene content. This cluster distribution is in good agreement with their predicted virion morphologies. Stx phage genomes are highly diverse with a vast number of 1,838 gene phamilies (phams) of related sequences (of which 677 are orphams i.e. unique genes) and, although having high mosaicism, they are generally organized into three major transcripts. While the mechanisms that guide lysis-lysogeny decision are complex, there is a strong selective pressure to maintain the stx genes location close to the lytic cassette composed of predicted SAR-endolysin and pin-holin lytic proteins. The evolution of STEC Stx phages seems to be strongly related to acquiring genetic material, probably from horizontal gene transfer events. CONCLUSIONS: This work provides novel insights on the genetic structure of Stx phages, showing a high genetic diversity throughout the genomes, where the various lysis-lysogeny regulatory systems are in contrast with an uncommon, but conserved, lytic system always adjacent to stx genes.

Expert Statement: Pneumothorax Associated with One-Way Valve Therapy for Emphysema: 2020 Update.

For selected patients with advanced emphysema, bronchoscopic lung volume reduction with one-way valves can lead to clinically relevant improvements of airflow obstruction, hyperinflation, exercise capacity, and quality of life. The most common complication of this procedure is pneumothorax with a prevalence of up to ±34% of the treated patients. Patients who develop a pneumothorax also experience meaningful clinical benefits once the pneumothorax is resolved. Timely resolution of a post-valve treatment pneumothorax requires skilled and adequate pneumothorax management. This expert panel statement is an updated recommendation of the 2014 statement developed to help guide pneumothorax management after valve placement. Additionally, mechanisms for pneumothorax development, risk assessment, prevention of pneumothorax, and outcomes after pneumothorax are addressed. This recommendation is based on a combination of the current scientific literature and expert opinion, which was obtained through a modified Delphi method.

Urban Safety: An Image-Processing and Deep-Learning-Based Intelligent Traffic Management and Control System.

With the rapid growth and development of cities, Intelligent Traffic Management and Control (ITMC) is becoming a fundamental component to address the challenges of modern urban traffic management, where a wide range of daily problems need to be addressed in a prompt and expedited manner. Issues such as unpredictable traffic dynamics, resource constraints, and abnormal events pose difficulties to city managers. ITMC aims to increase the efficiency of traffic management by minimizing the odds of traffic problems, by providing real-time traffic state forecasts to better schedule the intersection signal controls. Reliable implementations of ITMC improve the safety of inhabitants and the quality of life, leading to economic growth. In recent years, researchers have proposed different solutions to address specific problems concerning traffic management, ranging from image-processing and deep-learning techniques to forecasting the traffic state and deriving policies to control intersection signals. This review article studies the primary public datasets helpful in developing models to address the identified problems, complemented with a deep analysis of the works related to traffic state forecast and intersection-signal-control models. Our analysis found that deep-learning-based approaches for short-term traffic state forecast and multi-intersection signal control showed reasonable results, but lacked robustness for unusual scenarios, particularly during oversaturated situations, which can be resolved by explicitly addressing these cases, potentially leading to significant improvements of the systems overall. However, there is arguably a long path until these models can be used safely and effectively in real-world scenarios.

µCT trait analysis reveals morphometric differences between domesticated temperate small grain cereals and their wild relatives.

Wheat and barley are two of the founder crops domesticated in the Fertile Crescent, and currently represent crops of major economic importance in temperate regions. Due to impacts on yield, quality and end-use, grain morphometric traits remain an important goal for modern breeding programmes and are believed to have been selected for by human populations. To directly and accurately assess the three-dimensional (3D) characteristics of grains, we combine X-ray microcomputed tomography (µCT) imaging techniques with bespoke image analysis tools and mathematical modelling to investigate how grain size and shape vary across wild and domesticated wheat and barley. We find that grain depth and, to a lesser extent, width are major drivers of shape change and that these traits are still relatively plastic in modern bread wheat varieties. Significant changes in grain depth are also observed to be associated with differences in ploidy. Finally, we present a model that can accurately predict the wild or domesticated status of a grain from a given taxa based on the relationship between three morphometric parameters (length, width and depth) and suggest its general applicability to both archaeological identification studies and breeding programmes.

Functional Analysis and Antivirulence Properties of a New Depolymerase from a Myovirus That Infects Acinetobacter baumannii Capsule K45.

Acinetobacter baumannii is an important pathogen causative of health care-associated infections and is able to rapidly develop resistance to all known antibiotics, including colistin. As an alternative therapeutic agent, we have isolated a novel myovirus (vB_AbaM_B9) which specifically infects and makes lysis from without in strains of the K45 and K30 capsule types, respectively. Phage B9 has a genome of 93,641 bp and encodes 167 predicted proteins, of which 29 were identified by mass spectrometry. This phage holds a capsule depolymerase (B9gp69) able to digest extracted exopolysaccharides of both K30 and K45 strains and remains active in a wide range of pH values (5 to 9), ionic strengths (0 to 500 mM), and temperatures (20 to 80°C). B9gp69 was demonstrated to be nontoxic in a cell line model of the human lung and to make the K45 strain fully susceptible to serum killing in vitro Contrary to the case with phage, no resistance development was observed by bacteria targeted with the B9gp69. Therefore, capsular depolymerases may represent attractive antimicrobial agents against A. baumannii infections.IMPORTANCE Currently, phage therapy has revived interest for controlling hard-to-treat bacterial infections. Acinetobacter baumannii is an emerging Gram-negative pathogen able to cause a variety of nosocomial infections. Additionally, this species is becoming more resistant to several classes of antibiotics. Here we describe the isolation of a novel lytic myophage B9 and its recombinant depolymerase. While the phage can be a promising alternative antibacterial agent, its success in the market will ultimately depend on new regulatory frameworks and general public acceptance. We therefore characterized the phage-encoded depolymerase, which is a natural enzyme that can be more easily managed and used. To our knowledge, the therapeutic potential of phage depolymerase against A. baumannii is still unknown. We show for the first time that the K45 capsule type is an important virulence factor of A. baumannii and that capsule removal via the recombinant depolymerase activity helps the host immune system to combat the bacterial infection.

Predicting promoters in phage genomes using PhagePromoter.

SUMMARY: The growing interest in phages as antibacterial agents has led to an increase in the number of sequenced phage genomes, increasing the need for intuitive bioinformatics tools for performing genome annotation. The identification of phage promoters is indeed the most difficult step of this process. Due to the lack of online tools for phage promoter prediction, we developed PhagePromoter, a tool for locating promoters in phage genomes, using machine learning methods. This is the first online tool for predicting promoters that uses phage promoter data and the first to identify both host and phage promoters with different motifs. AVAILABILITY AND IMPLEMENTATION: This tool was integrated in the Galaxy framework and it is available online at: https://bit.ly/2Dfebfv. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A Tailspike with Exopolysaccharide Depolymerase Activity from a New Providencia stuartii Phage Makes Multidrug-Resistant Bacteria Susceptible to Serum-Mediated Killing.

Providencia stuartii is emerging as a significant drug-resistant nosocomial pathogen, which encourages the search for alternative therapies. Here, we have isolated Providencia stuartii phage Stuart, a novel podovirus infecting multidrug-resistant hospital isolates of this bacterium. Phage Stuart is a proposed member of a new Autographivirinae subfamily genus, with a 41,218-bp genome, direct 345-bp repeats at virion DNA ends, and limited sequence similarity of proteins to proteins in databases. Twelve out of the 52 predicted Stuart proteins are virion components. We found one to be a tailspike with depolymerase activity. The tailspike could form a highly thermostable oligomeric ß-structure migrating close to the expected trimer in a nondenaturing gel. It appeared to be essential for the infection of three out of four P. stuartii hosts infected by phage Stuart. Moreover, it degraded the exopolysaccharide of relevant phage Stuart hosts, making the bacteria susceptible to serum killing. Prolonged exposure of a sensitive host to the tailspike did not cause the emergence of bacteria resistant to the phage or to serum killing, opposite to the prolonged exposure to the phage. This indicates that phage tail-associated depolymerases are attractive antivirulence agents that could complement the immune system in the fight with P. stuartiiIMPORTANCE The pace at which multidrug-resistant strains emerge has been alarming. P. stuartii is an infrequent but relevant drug-resistant nosocomial pathogen causing local to systemic life-threatening infections. We propose an alternative approach to fight this bacterium based on the properties of phage tailspikes with depolymerase activity that degrade the surface bacterial polymers, making the bacteria susceptible to the immune system. Unlike antibiotics, phage tailspikes have narrow and specific substrate spectra, and by acting as antivirulent but not bactericidal agents they do not cause the selection of resistant bacteria.

Phage therapy efficacy: a review of the last 10 years of preclinical studies.

Due to the rise of multidrug-resistant infections in humans, phage therapy is gaining renewed attention in Western medicine. Despite the increasing number of publications focussed on the isolation, characterization and in vitro performance of different phages, there is still a lack of concise pre-clinical information to guide the application of phage therapy in clinical practice. Nevertheless, over the last decade, efforts have been made to conduct more detailed studies of the in vivo efficacy of phages. Here, we review the most relevant in vivo studies performed in the last decade covering phage efficacy in both preclinical and clinical trials. We compare different routes of administration, dosage effect and different animal models of distinct types of infections. Moreover, insights into case studies and results from clinical trials are presented. Challenges and limitations of phage use as evidenced by the current state of research are also discussed in order to improve both the trustworthiness and success of the implementation of phage therapy.

TDP-43 proteinopathies: a new wave of neurodegenerative diseases.

Inclusions of pathogenic deposits containing TAR DNA-binding protein 43 (TDP-43) are evident in the brain and spinal cord of patients that present across a spectrum of neurodegenerative diseases. For instance, the majority of patients with sporadic amyotrophic lateral sclerosis (up to 97%) and a substantial proportion of patients with frontotemporal lobar degeneration (~45%) exhibit TDP-43 positive neuronal inclusions, suggesting a role for this protein in disease pathogenesis. In addition, TDP-43 inclusions are evident in familial ALS phenotypes linked to multiple gene mutations including the TDP-43 gene coding (TARDBP) and unrelated genes (eg, C9orf72). While TDP-43 is an essential RNA/DNA binding protein critical for RNA-related metabolism, determining the pathophysiological mechanisms through which TDP-43 mediates neurodegeneration appears complex, and unravelling these molecular processes seems critical for the development of effective therapies. This review highlights the key physiological functions of the TDP-43 protein, while considering an expanding spectrum of neurodegenerative diseases associated with pathogenic TDP-43 deposition, and dissecting key molecular pathways through which TDP-43 may mediate neurodegeneration.