Genome sequences of 31 mycobacteriophages isolated on Mycobacterium smegmatis mc2155 at room temperature.

We report the genome sequences of 31 mycobacteriophages isolated on Mycobacterium smegmatis mc2155 at room temperature. The genomes add to the diversity of Clusters A, B, C, G, and K. Collectively, the genomes include 70 novel protein-coding genes that have no close relatives among the actinobacteriophages.

The Classification of Movement in Infants for the Autonomous Monitoring of Neurological Development.

Neurodevelopmental delay following extremely preterm birth or birth asphyxia is common but diagnosis is often delayed as early milder signs are not recognised by parents or clinicians. Early interventions have been shown to improve outcomes. Automation of diagnosis and monitoring of neurological disorders using non-invasive, cost effective methods within a patient's home could improve accessibility to testing. Furthermore, said testing could be conducted over a longer period, enabling greater confidence in diagnoses, due to increased data availability. This work proposes a new method to assess the movements in children. Twelve parent and infant participants were recruited (children aged between 3 and 12 months). Approximately 25 min 2D video recordings of the infants organically playing with toys were captured. A combination of deep learning and 2D pose estimation algorithms were used to classify the movements in relation to the children's dexterity and position when interacting with a toy. The results demonstrate the possibility of capturing and classifying children's complexity of movements when interacting with toys as well as their posture. Such classifications and the movement features could assist practitioners to accurately diagnose impaired or delayed movement development in a timely fashion as well as facilitating treatment monitoring.

Needle in a Whey-Stack: PhRACS as a Discovery Tool for Unknown Phage-Host Combinations.

The field of metagenomics has rapidly expanded to become the go-to method for complex microbial community analyses. However, there is currently no straightforward route from metagenomics to traditional culture-based methods of strain isolation, particularly in (bacterio)phage biology, leading to an investigative bottleneck. Here, we describe a method that exploits specific phage receptor binding protein (RBP)-host cell surface receptor interaction enabling isolation of phage-host combinations from an environmental sample. The method was successfully applied to two complex sample types-a dairy-derived whey sample and an infant fecal sample, enabling retrieval of specific and culturable phage hosts. IMPORTANCE PhRACS aims to bridge the current divide between in silico genetic analyses (i.e., phageomic studies) and traditional culture-based methodology. Through the labeling of specific bacterial hosts with fluorescently tagged recombinant phage receptor binding proteins and the isolation of tagged cells using flow cytometry, PhRACS allows the full potential of phageomic data to be realized in the wet laboratory.

Biomechanical differences between able-bodied and spinal cord injured individuals walking in an overground robotic exoskeleton.

BACKGROUND: Robotic assisted gait training (RAGT) uses a powered exoskeleton to support an individual's body and move their limbs, with the aim of activating latent, pre-existing movement patterns stored in the lower spinal cord called central pattern generators (CPGs) to facilitate stepping. The parameters that directly stimulate the stepping CPGs (hip extension and ipsilateral foot unloading) should be targeted to maximise the rehabilitation benefits of these devices. AIM: To compare the biomechanical profiles of individuals with a spinal cord injury (SCI) and able-bodied individuals inside the ReWalkTM powered exoskeleton and to contrast the users' profiles with the exoskeleton. METHODS: Eight able-bodied and four SCI individuals donned a ReWalkTM and walked along a 12-meter walkway, using elbow crutches. Whole-body kinematics of the users and the ReWalkTM were captured, along with GRF and temporal-spatial characteristics. Discreet kinematic values were analysed using a Kruskall-Wallis H and Dunn's post-hoc analysis. Upper-body differences, GRF and temporal-spatial characteristics were analysed using a Mann-Whitney U test (P<0.05). RESULTS: Walking speed ranged from 0.32-0.39m/s. Hip abduction, peak knee flexion and ankle dorsiflexion for both the SCI and able-bodied groups presented with significant differences to the ReWalkTM. The able-bodied group presented significant differences to the ReWalkTM for all kinematic variables except frontal plane hip ROM (P = 0.093,δ = -0.56). Sagittal plane pelvic and trunk ROM were significantly greater in the SCI vs. able-bodied (P = 0.004,δ = -1; P = 0.008,δ = -0.94, respectively). Posterior braking force was significantly greater in the SCI group (P = 0.004, δ = -1). DISCUSSION: The different trunk movements used by the SCI group and the capacity for the users' joint angles to exceed those of the device suggest that biomechanical profiles varied according to the user group. However, upright stepping with the ReWalkTM device delivered the appropriate afferent stimulus to activate CPGs as there were no differences in key biomechanical parameters between the two user groups.

Spontaneous regression of oesophageal squamous cell carcinoma.

Partial or complete spontaneous regression (SR) of cancer is unusual, particularly in patients with oesophageal cancer. This case report describes a patient with biopsy-proven squamous cell carcinoma of the oesophagus which spontaneously regressed without any treatment. Regression of the primary tumour was confirmed on histological examination of the resected specimen. The process of SR remains an enigma, but potential mechanisms are considered.

A biomechanical comparison of powered robotic exoskeleton gait with normal and slow walking: An investigation with able-bodied individuals.

BACKGROUND: Overground lower-limb robotic exoskeletons are assistive devices used to facilitate ambulation and gait rehabilitation. Our understanding of how closely they resemble comfortable and slow walking is limited. This information is important to maximise the effects of gait rehabilitation. The aim was to compare the 3D gait parameters of able-bodied individuals walking with and without an exoskeleton at two speeds (self-selected comfortable vs. slow, speed-matched to the exoskeleton) to understand how the user's body moved within the device. METHODS: Eight healthy, able-bodied individuals walked along a 12-m walkway with and without the exoskeleton. Three-dimensional whole-body kinematics inside the device were captured. Temporal-spatial parameters and sagittal joint kinematics were determined for normal and exoskeleton walking. One-way repeated measures ANOVAs and statistical parametric mapping were used to compare the three walking conditions (P < .05). FINDINGS: The walking speeds of the slow (0.44[0.03] m/s) and exoskeleton (0.41[0.03] m/s) conditions were significantly slower than the comfortable walking speed (1.54[0.07] m/s). However, time in swing was significantly greater (P < .001, d = -3.64) and double support was correspondingly lower (P < .001, d = 3.72) during exoskeleton gait than slow walking, more closely resembling comfortable speed walking. Ankle and knee angles were significantly reduced in the slow and exoskeleton conditions. Angles were also significantly different for the upper body. INTERPRETATION: Although the slow condition was speed-matched to exoskeleton gait, the stance:swing ratio of exoskeleton stepping more closely resembled comfortable gait than slow gait. The altered upper body kinematics suggested that overground exoskeletons may provide a training environment that would also benefit balance training.

Accuracy of the revised Vienna Classification for predicting postendoscopic resection outcomes for gastric and oesophageal neoplasms: a retrospective cohort study of patients from a UK tertiary referral centre.

AIMS: To review the effectiveness of the revised Vienna classification (rVC) at predicting histological outcome and defining the postendoscopic resection (ER) clinical management plan of gastro-oesophageal dysplasia and early neoplasia in a UK tertiary-centre population. METHODS: This was a retrospective cohort study between November 2011 and May 2018. 157 patients from Salford Royal NHS Foundation Trust in the UK were included. The primary outcome was the histological results of postsurgical resection (SR) specimens compared with their post-ER rVC. The secondary outcome was overall survival rates of patients with category 4.4 and 5 of the rVC. RESULTS: One-hundred and thirteen patients were diagnosed with category ≥4 of the rVC. 23 patients (20.4%) were referred for additional surgery, whereas 69 patients (61.1%) were on endoscopic surveillance only. 60.9% of post-SR specimens (14/23) revealed no residual neoplasia. 78.6% of these cancer-free specimens were classed as category 5 rVC. The overall 7-year survival rate of 25 patients with category ≥4.4 was 68% with causes of mortality not linked to upper gastrointestinal neoplasia. The overall 7-year and 3-year survival rates of category 4.4 and 5 were 73.6% and 50%, respectively, although age and comorbid state played a role. CONCLUSIONS: This study provides evidence of outcomes comparable to other reported cohorts for cases after ER in a single-centre UK population even at rVC 4.4/5. It suggests surgery may not be necessary in all cases due to the lack of residual disease and further refinement of the rVC category 5 may help guide management.

Staphylococcus aureus internalization in mast cells in nasal polyps: Characterization of interactions and potential mechanisms.

BACKGROUND: Chronic rhinosinusitis (CRS) with nasal polyps is a common chronic condition. The exact cause of nasal polyps remains unknown. Recently, we made the novel observation of intracellular localization of Staphylococcus aureus within mast cells in nasal polyps. OBJECTIVE: This follow-up study aimed to further characterize interactions between S aureus and mast cells in this setting and elucidate potential internalization mechanisms with particular emphasis on the role of staphylococcal enterotoxin B (SEB). METHODS: A prospective study was performed using an explant tissue model with ex vivo inferior turbinate mucosa obtained from patients with chronic rhinosinusitis with nasal polyps (n = 7) and patients without CRS (n = 5). Immunohistochemistry was used to characterize S aureus uptake into mast cells and investigate the effects of SEB on this process. An in vitro cell-culture model was used to investigate mast cell-S aureus interactions by using a combination of fluorescent in situ hybridization, confocal laser scanning microscopy, scanning electron microscopy, transmission electron microscopy, and proliferation assays. RESULTS: S aureus was captured by extracellular traps and entered mast cells through phagocytosis. Proliferating intracellular S aureus led to the expansion and eventual rupture of mast cells, resulting in release of viable S aureus into the extracellular space. The presence of SEB appeared to promote internalization of S aureus into mast cells. CONCLUSION: This study provides new insights into the interactions between S aureus and mast cells, including the internalization process, and demonstrates a prominent role for SEB in promoting uptake of the bacteria into these cells.

Ubiquitous Carbohydrate Binding Modules Decorate 936 Lactococcal Siphophage Virions.

With the availability of an increasing number of 3D structures of bacteriophage components, combined with powerful in silico predictive tools, it has become possible to decipher the structural assembly and functionality of phage adhesion devices. In the current study, we examined 113 members of the 936 group of lactococcal siphophages, and identified a number of Carbohydrate Binding Modules (CBMs) in the neck passage structure and major tail protein, on top of evolved Dit proteins, as recently reported by us. The binding ability of such CBM-containing proteins was assessed through the construction of green fluorescent protein fusion proteins and subsequent binding assays. Two CBMs, one from the phage tail and another from the neck, demonstrated definite binding to their phage-specific host. Bioinformatic analysis of the structural proteins of 936 phages reveals that they incorporate binding modules which exhibit structural homology to those found in other lactococcal phage groups and beyond, indicating that phages utilize common structural "bricks" to enhance host binding capabilities. The omnipresence of CBMs in Siphophages supports their beneficial role in the infection process, as they can be combined in various ways to form appendages with different shapes and functionalities, ensuring their success in host detection in their respective ecological niches.

The Classification of Minor Gait Alterations Using Wearable Sensors and Deep Learning.

OBJECTIVE: This paper describes how non-invasive wearable sensors can be used in combination with deep learning to classify artificially induced gait alterations without the requirement for a medical professional or gait analyst to be present. This approach is motivated by the goal of diagnosing gait abnormalities on a symptom-by-symptom basis, irrespective of other neuromuscular movement disorders the patients may be affected by. This could lead to improvements in treatment and offer a greater insight into movement disorders. METHODS: In-shoe pressure was measured for 12 able-bodied participants, each subject to eight artificially induced gait alterations, achieved by modifying the underside of the shoe. The data were recorded at 100 Hz over 2520 data channels and were analyzed using the deep learning architecture and the long term short term memory networks. Additionally, the rationale for the decision-making process of these networks was investigated. CONCLUSION: Long term short term memory networks are applicable to the classification of the gait function. The classifications can be made using only 2 s of sparse data (82.0% accuracy over 96 000 instances of test data) from participants who were not a part of the training set. SIGNIFICANCE: This paper provides potential for the gait function to be accurately classified using non-invasive techniques, and at more regular intervals, outside of a clinical setting, without the need for healthcare professionals to be present.

Evolutionary history of human colitis-associated colorectal cancer.

OBJECTIVE: IBD confers an increased lifetime risk of developing colorectal cancer (CRC), and colitis-associated CRC (CA-CRC) is molecularly distinct from sporadic CRC (S-CRC). Here we have dissected the evolutionary history of CA-CRC using multiregion sequencing. DESIGN: Exome sequencing was performed on fresh-frozen multiple regions of carcinoma, adjacent non-cancerous mucosa and blood from 12 patients with CA-CRC (n=55 exomes), and key variants were validated with orthogonal methods. Genome-wide copy number profiling was performed using single nucleotide polymorphism arrays and low-pass whole genome sequencing on archival non-dysplastic mucosa (n=9), low-grade dysplasia (LGD; n=30), high-grade dysplasia (HGD; n=13), mixed LGD/HGD (n=7) and CA-CRC (n=19). Phylogenetic trees were reconstructed, and evolutionary analysis used to reveal the temporal sequence of events leading to CA-CRC. RESULTS: 10/12 tumours were microsatellite stable with a median mutation burden of 3.0 single nucleotide alterations (SNA) per Mb, ~20% higher than S-CRC (2.5 SNAs/Mb), and consistent with elevated ageing-associated mutational processes. Non-dysplastic mucosa had considerable mutation burden (median 47 SNAs), including mutations shared with the neighbouring CA-CRC, indicating a precancer mutational field. CA-CRCs were often near triploid (40%) or near tetraploid (20%) and phylogenetic analysis revealed that copy number alterations (CNAs) began to accrue in non-dysplastic bowel, but the LGD/HGD transition often involved a punctuated 'catastrophic' CNA increase. CONCLUSIONS: Evolutionary genomic analysis revealed precancer clones bearing extensive SNAs and CNAs, with progression to cancer involving a dramatic accrual of CNAs at HGD. Detection of the cancerised field is an encouraging prospect for surveillance, but punctuated evolution may limit the window for early detection.

Kistimonas alittae sp. nov., a gammaproteobacterium isolated from the marine annelid Alitta succinea.

A novel Gram-stain-negative, rod-shaped, motile, non-spore-forming, facultatively anaerobic marine bacterium was isolated from the gastrointestinal tract of the sandworm Alitta succinea collected from Grice Cove, South Carolina, USA. The strain was arginine dihydrolase-positive, and oxidase- and catalase-positive. Growth occurred between 10 and 37 °C, with optimal growth occurring between 30 and 32 °C. Comparative 16S rRNA gene sequence analysis showed its nearest neighbours are members of the genus Kistimonas of the family Hahellaceae, which is found in the order Oceanospirillales, class Gammaproteobacteria. The closest related species was Kistimonas asteriae KMD 001T with 16S rRNA gene sequence similarity of 99.0 %. However, DNA-DNA hybridization between these strains revealed less than 70 % DNA-DNA relatedness, supporting the novel species status of the strain. The major fatty acids were C16 : 0, C18 : 0, C18 : 1ω7c and a summed feature that contained C16 : 1ω6c/C16 : 1ω7c. The major respiratory quinone was ubiquinone-9 and the predominant polar lipids were phosphatidylserine, phosphoethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content was 52.5 mol%. Based on the data presented, strain BGP-2T is considered to represent a novel member of the genus Kistimonas, for which the name Kistimonas alittae sp. nov. is proposed. The type strain is BGP-2T (=CCUG 65711T=JCM 30010T).

Relaxing life of the city? Allostatic load in yellow-bellied marmots along a rural-urban continuum.

Urban environments are expanding. As rural areas are urbanized, animals living in those environments must respond. Examinations of ecological responses to urbanization are abundant, but much less work has focused on the physiological responses driving those ecological patterns, particularly in mammals. Whether an animal interprets urbanized environments as stressful or not can help us understand, and even predict, the likelihood of individuals persisting in urbanized areas. Unpredictable events can cause stress and responses to such events can deplete limited stores of energy. Differences between required and available energy is termed allostatic load and is an indicator of stress. Allostatic load, and hence stress, is correlated with baseline levels of the metabolic hormones, glucocorticoids. We examined allostatic load in yellow-bellied marmots along a rural-urban gradient through analysis of fecal glucocorticoid metabolites (FGMs). We used GIS data and 'on-the-ground' measurements to quantify the degree of urbanization. We collected fecal samples from males and females of all age classes at six sites along this continuum. Female marmots had higher FGMs than males. All age groups of marmots exhibited a parabolic relationship between the degree of urbanization and FGM levels. In general, adult marmots had higher FGMs in more rural than urban environments, and both juveniles and yearlings had exhibited higher FGM levels in more urban environments.

Identification of Dual Receptor Binding Protein Systems in Lactococcal 936 Group Phages.

Siphoviridae of the lactococcal 936 group are the most commonly encountered bacteriophages in the dairy processing environment. The 936 group phages possess a discrete baseplate at the tip of their tail-a complex harbouring the Receptor Binding Protein (RBP) which is responsible for host recognition and attachment. The baseplate-encoding region is highly conserved amongst 936 phages, with 112 of 115 publicly available phages exhibiting complete synteny. Here, we detail the three exceptions (Phi4.2, Phi4R15L, and Phi4R16L), which differ from this genomic architecture in possessing an apparent second RBP-encoding gene upstream of the "classical" rbp gene. The newly identified RBP possesses an elongated neck region relative to currently defined 936 phage RBPs and is genetically distinct from defined 936 group RBPs. Through detailed characterisation of the representative phage Phi4.2 using a wide range of complementary techniques, we demonstrated that the above-mentioned three phages possess a complex and atypical baseplate structure. Furthermore, the presence of both RBPs in the tail tip of the mature virion was confirmed, while the anticipated host-binding capabilities of both proteins were also verified.

Functional carbohydrate binding modules identified in evolved dits from siphophages infecting various Gram-positive bacteria.

With increasing numbers of 3D structures of bacteriophage components, combined with powerful in silico predictive tools, it has become possible to decipher the structural assembly and associated functionality of phage adhesion devices. Recently, decorations have been reported in the tail and neck passage structures of members of the so-called 936 group of lactococcal siphophages. In the current report, using bioinformatic analysis we identified a conserved carbohydrate binding module (CBM) among many of the virion baseplate Dit components, in addition to the CBM present in the 'classical' receptor binding proteins (RBPs). We observed that, within these so-called 'evolved' Dit proteins, the identified CBMs have structurally conserved folds, yet can be grouped into four distinct classes. We expressed such modules in fusion with GFP, and demonstrated their binding capability to their specific host using fluorescent binding assays with confocal microscopy. We detected evolved Dits in several phages infecting various Gram-positive bacterial species, including mycobacteria. The omnipresence of CBM domains in siphophages indicates their auxiliary role in infection, as they can assist in the specific recognition of and attachment to their host, thus ensuring a highly efficient and specific phage-host adhesion process as a prelude to DNA injection.

The effects of robot assisted gait training on temporal-spatial characteristics of people with spinal cord injuries: A systematic review.

CONTEXT: Robotic assisted gait training (RAGT) technology can be used as a rehabilitation tool or as an assistive device for spinal cord injured (SCI) individuals. Its impact on upright stepping characteristics of SCI individuals using treadmill or overground robotic exoskeleton systems has yet to be established. OBJECTIVE: To systematically review the literature and identify if overground or treadmill based RAGT use in SCI individuals elicited differences in temporal-spatial characteristics and functional outcome measures. METHODS: A systematic search of the literature investigating overground and treadmill RAGT in SCIs was undertaken excluding case-studies and case-series. Studies were included if the primary outcomes were temporal-spatial gait parameters. Study inclusion and methodological quality were assessed and determined independently by two reviewers. Methodological quality was assessed using a validated scoring system for randomized and non-randomized trials. RESULTS: Twelve studies met all inclusion criteria. Participant numbers ranged from 5-130 with injury levels from C2 to T12, American Spinal Injuries Association A-D. Three studies used overground RAGT systems and the remaining nine focused on treadmill based RAGT systems. Primary outcome measures were walking speed and walking distance. The use of treadmill or overground based RAGT did not result in an increase in walking speed beyond that of conventional gait training and no studies reviewed enabled a large enough improvement to facilitate community ambulation. CONCLUSION: The use of RAGT in SCI individuals has the potential to benefit upright locomotion of SCI individuals. Its use should not replace other therapies but be incorporated into a multi-modality rehabilitation approach.

The relevance and implications of signet-ring cell adenocarcinoma of the oesophagus.

AIM: To review the current understanding of signet-ring type oesophageal adenocarcinoma including evidence for prognosis. METHODS: We conducted a literature search of nine healthcare literature databases for articles detailing the biology and clinical outcomes of signet-ring cell adenocarcinoma of the oesophagus. The impact of signet-ring cell morphology was analysed and detailed in written text and tabular format. Current understanding of the biology of signet-ring cell adenocarcinoma of the oesophagus was summarised. RESULTS: Signet-ring cell carcinoma was represented in 7.61% of the 18 989 cases of oesophageal carcinoma reviewed in multiple studies. The presence of signet-ring cells conferred a worse prognosis and these tumours responded differently to conventional treatments as compared with typical adenocarcinoma. Little is known about the biological features of signet-ring cell adenocarcinoma of the oesophagus. Work in gastric lesions has identified potential targets for future treatments such as CDH1 and RHOA genes. Categorisation of signet-ring cell carcinomas by the proportion of signet-ring cells within tumours differs among clinicians despite WHO criteria for classification. The current UK guidelines for histopathological reporting of oesophageal tumours do not emphasise the importance of identifying signet-ring cells. CONCLUSION: The presence of signet-ring cells in oesophageal adenocarcinomas leads to poorer clinical outcomes. Current understanding of signet-ring cell biology in oesophageal cancer is limited.