The use of Bayesian Belief Networks (BBNs) to probe deeper into railway safety management systems - Two studies from Great Britain and Italy

The importance of Safety Management Systems (SMS) to the railway industry is underlined by the fact that all organisations operating on UK railways are required by law to have one. Analysing SMSs can provide a reliable systemic tool to identify hazards and weaknesses within complex systems like the railway, making it possible to significantly increase safety, reducing the odds of near misses and accidents. However, there is little empirical research evidence to determine the impact on safety of a structured SMS. The current paper describes two studies which use Bayesian Belief Networks (BBN) to conceptualise SMSs and their impact on front-line performance. The paper presents the usefulness of BBNs to compare complex systems and reconcile cultural differences within the railway industry, identifying factors that are deemed vital within Italy and Britain. The two studies allowed us to identify the most influential factors within a SMS and how they interact with each other, as well as the strength of the identified relationships. A BBN is particularly useful in estimating how changing some of the node states (e.g., by making safety leadership present) affected the other factors. The current study showed that safety leadership has an impact on the SMSs of the British and Italian railway industries.

Noncanonical DNA polymerization by aminoadenine-based siphoviruses

Bacteriophage genomes harbor the broadest chemical diversity of nucleobases across all life forms. Certain DNA viruses that infect hosts as diverse as cyanobacteria, proteobacteria, and actinobacteria exhibit wholesale substitution of aminoadenine for adenine, thereby forming three hydrogen bonds with thymine and violating Watson-Crick pairing rules. Aminoadenine-encoded DNA polymerases, homologous to the Klenow fragment of bacterial DNA polymerase I that includes 3'-exonuclease but lacks 5'-exonuclease, were found to preferentially select for aminoadenine instead of adenine in deoxynucleoside triphosphate incorporation templated by thymine. Polymerase genes occur in synteny with genes for a biosynthesis enzyme that produces aminoadenine deoxynucleotides in a wide array of Siphoviridae bacteriophages. Congruent phylogenetic clustering of the polymerases and biosynthesis enzymes suggests that aminoadenine has propagated in DNA alongside adenine since archaic stages of evolution.

A tunable magnetic metamaterial based on the dipolar four-state Potts model

Metamaterials, tunable artificial materials, are useful playgrounds to investigate magnetic systems. So far, artificial Ising spin systems have revealed features such as emergent magnetic monopoles^1,2 and charge fragmentation³. Here we present a metasystem composed of a lattice of dipolarly coupled nanomagnets. The magnetic spin of each nanomagnet is constrained to lie along a body diagonal, which yields four possible spin states. We show that the magnetic ordering of this metasystem (antiferromagnetic, ferromagnetic or spin ice like) is determined by the spin states orientation relative to the underlying lattice. The dipolar four-state Potts model explains our experimental observations and sheds light on the role of symmetry, as well as short- and long-range dipolar magnetic interactions, in such non-Ising spin systems.

Metabolic Recruitment and Directed Evolution of Nucleoside Triphosphate Uptake in Escherichia coli

We report the design and elaboration of a selection protocol for importing a canonical substrate of DNA polymerase, thymidine triphosphate (dTTP) in Escherichia coli. Bacterial strains whose growth depend on dTTP uptake, through the action of an algal plastid transporter expressed from a synthetic gene inserted in the chromosome, were constructed and shown to withstand the simultaneous loss of thymidylate synthase and thymidine kinase. Such thyA tdk dual deletant strains provide an experimental model of tight nutritional containment for preventing dissemination of microbial GMOs. Our strains transported the four canonical dNTPs, in the following order of preference: dCTP > dATP ≥ dGTP > dTTP. Prolonged cultivation under limitation of exogenous dTTP led to the enhancement of dNTP transport by adaptive evolution. We investigated the uptake of dCTP analogues with altered sugar or nucleobase moieties, which were found to cause a loss of cell viability and an increase of mutant frequency, respectively. E. coli strains equipped with nucleoside triphosphate transporters should be instrumental for evolving organisms whose DNA genome is morphed chemically by fully substituting its canonical nucleotide components.

Gastric bleeding risk following spleen preserving distal pancreatectomy with excision of the splenic vessels: a long-term follow-up

BACKGROUND

Spleen-preserving distal pancreatectomy with resection of the splenic vessels (VR-SPDP) is an effective procedure. However, hemodynamic changes in splenogastric circulation may lead to the development of gastric varices (GV) with a risk of gastrointestinal (GI) bleeding. This retrospective study aimed to assess the long-term postoperative clinical follow-up of patients and review the late postoperative abdominal computed tomography (CT) or endoscopic examination.

METHODS

From 1988 to 2015, 48 consecutive VR-SPDP for benign or low-grade malignant disease were included. Late postoperative follow-up was undertaken with the use of a prospective database and assessment undertaken by CT and/or endoscopy.

RESULTS

The median follow-up was 76 months (range: 12-334 months). Two patients were lost to follow-up. Gastrointestinal hemorrhage occurred in one patient. Endoscopy and abdominal CT showed submucosal GV in five patients. Ten patients had perigastric varices (27%), but none developed clinical complications from their varices. All varices occurred within one year after distal pancreatectomy and remained stable during follow-up.

DISCUSSION

Asymptomatic varices frequently occurred in patients who underwent VR-SPDP, but bleeding risk seemed low. Abdominal CT could identify GV and distinguish submucosal varices with a higher risk of gastric bleeding.

Size distribution of magnetic charge domains in thermally activated but out-of-equilibrium artificial spin ice

A crystal of emerging magnetic charges is expected in the phase diagram of the dipolar kagomé spin ice. An observation of charge crystallites in thermally demagnetized artificial spin ice arrays has been recently reported by S. Zhang and coworkers and explained through the thermodynamics of the system as it approaches a charge-ordered state. Following a similar approach, we have generated a partial order of magnetic charges in an artificial kagomé spin ice lattice made out of ferrimagnetic material having a Curie temperature of 475 K. A statistical study of the size of the charge domains reveals an unconventional sawtooth distribution. This distribution is in disagreement with the predictions of the thermodynamic model and is shown to be a signature of the kinetic process governing the remagnetization.

Microsurgery in liver research: end-to-side portocaval microanastomoses in dogfish

BACKGROUND

The use of an operating microscope in animal liver surgery has made it possible to obtain new experimental models. The goal of this prospective animal study is to present our experience with dogfish portocaval microanastomoses.

METHODS

Nineteen portocaval microanastomoses were performed in dogfish. The end-to-side anastomoses were accomplished using continuous 11-0 sutures. The diameter of the vessels and time required for the anastomoses were measured. A patency test and its outcome were also prospectively evaluated at the time of anastomoses and then 3 and 6 months after.

RESULTS

The mean vessel diameter was 2.5 ± 0.2mm. The mean anastomosis time was 14 ± 1.5 min. The anastomoses patency rate was 100% at the time of surgery. A postoperative control performed after 3 and 6 months showed a partial stenosis in three animals.

CONCLUSION

The dogfish appears to be a reliable experimental model in liver research. Moreover, this technique could be used for microsurgical training.

Dorsalis pedis artery pseudoaneurysm: an uncommon cause of soft tissue mass of the dorsal foot in children

Pseudoaneurysm of the dorsalis pedis artery is an extremely rare entity with only 3 pediatric cases previously presented in the English literature. We describe a new case and discuss the clinical presentation and surgical management. A 6-year-old boy was referred to our clinic because of a pulsatile tumor of the right dorsal foot increasing in size. A focused history found a low grade trauma to the dorsal foot one year previously. Magnetic resonance imaging revealed a pseudoaneurysm of the DPA. Resection of the pseudoaneurysm was completed without complications. Pseudoaneurysm of the DPA is a very uncommon cause of soft tissue mass of the dorsal foot. It can appear after low grade trauma. Treatment is surgical.

Prognostic factors and long-term results of pulmonary metastasectomy for pediatric histologies

OBJECTIVE

Pulmonary resection in metastatic pediatric solid tumors is an accepted method of treatment. The purpose of this study was to determine the clinical course, outcome and prognostic factors after surgery.

METHODS

A retrospective analysis from 1985 to 2006 of 52 patients less than 17 years old at the time of tumor diagnosis and submitted to thoracotomy for pulmonary metastatic disease was performed. Three had nodules excised which proved to be benign at histology and were excluded from further analysis. There were 28 males and 21 females with median age of 13.2 years [2-36] at the time of metastasectomy. The primaries were osteosarcoma (25), Ewing's sarcoma (6), Wilms' tumors (4), hepatoblastoma (3) and miscellaneous (11). Pulmonary metastases were encountered either at the time of initial diagnosis (18%) or occurring within 1 month to 22 years. Disease free interval (DFI) was equal or less than 2 years in 31 (63%) patients and more than 2 years in 18 (37%).

RESULTS

Patients had one (24), two (16), three (2), four or more (7) metastasectomies resulting in a total of 95 thoracotomies. Wedges (75%) were performed more frequently than anatomic resections (25%). The number of resected metastatic nodules ranged from 1 to 45, median 3. There were no perioperative deaths. There were six complications: pneumothoraces requiring chest tube drainage in two cases. Resection was incomplete in four cases. The mean drainage time and hospital length of stay were 2.7 and 5 days, respectively. Using the date of pulmonary resection as the starting point, 5-year survival rate was 25%. By univariate analysis, we found that a significantly longer survival was observed for patients with a complete resection (p=0.004), with two or less metastases (p=0.0004), with unilateral metastases (p=0.001) or when the DFI was more than 2 years (p=0.003). By multivariate analysis, we showed that the number of pulmonary metastases was an independent predictor of survival.

CONCLUSION

We conclude that resection of pulmonary metastases of pediatric solid tumors is a safe and effective treatment that offers improved survival benefit in carefully selected patients within a multidisciplinary approach for pediatric cancer. Prognosis related criteria that support patient selection for surgery are identified.

Partial splenectomy for portal hypertension in cystic fibrosis related liver disease

AIMS

To review the middle- and long-term effects of partial splenectomy (PS) on portal hypertension (PHT) and its complications in patients with cystic fibrosis (CF) related liver disease risky PHT.

METHOD

Over a 20 years period, 19 patients aged 7-23 years underwent partial PS for massive splenomegaly, hypersplenism, and/ or severe PHT.

RESULTS

In all but three cases, PHT and hypersplenism have improved for long periods. Noticeable improvement of hepatic tests occurred simultaneously. In all patients PS resolved abdominal discomfort. Fifteen patients are alive and a stabilization of the liver disease occurred with a follow-up of 1-20 years (mean 7.9). One patient died following respiratory insufficiency 10 years after PS although PHT was stable. Manifestations recurred in 2 patients 5 and 6 years after PS. In two patients, the course of the disease evolved to hepatic insufficiency without recurrence of PHT 3 and 8 years after PS. PS did not give the expected results in three cases only, in which PHT was not modified or reoccurred during the following year. No severe complication was observed. Early (three patients) or late (one patient) eventration required surgical procedure.

CONCLUSIONS

Our results show that PS is a reliable and well-tolerated technique. Therefore, it is a therapeutic option for the management of PHT in CF patients with a preserved liver function. It can prevent and significantly delay a liver transplantation and its constraints.

Selection and evolution of NTP-specific aptamers

ATP occupies a central position in biology, for it is both an elementary building block of RNA and the most widely used cofactor in all living organisms. For this reason, it has been a recurrent target for in vitro molecular evolution techniques. The exploration of ATP-binding motifs constitutes both an important step in investigating the plausibility of the 'RNA world' hypothesis and a central starting point for the development of new enzymes. To date, only two RNA motifs that bind ATP have been characterized. The first one is targeted to the adenosine moiety, while the second one recognizes the 'Hoogsteen' face of the base. To isolate aptamers that bind ATP in different orientations, we selected RNAs on an affinity resin that presents ATP in three different orientations. We obtained five new motifs that were characterized and subsequently submitted to a secondary selection protocol designed to isolate aptamers specific for cordycepin. Interestingly, all the ATP-binding motifs selected specifically recognize the sugar-phosphate backbone region of the nucleotides. Three of the aptamers show some selectivity for adenine derivatives, while the remainder recognize any of the four nucleotides with similar efficiency. The characteristics of these aptamers are discussed along with implications for in vitro molecular evolution.

Mitomycin C as an adjunct in the treatment of localised ocular surface squamous neoplasia

AIM

To report the outcome of topical mitomycin C (MMC) used as adjunctive treatment following primary excision of ocular surface squamous neoplasia (OSSN).

METHOD

Prospective, non-comparative interventional case series of 27 primary OSSN lesions from 26 patients treated in a single ocular oncology centre over a 4 year period.

RESULT

27 cases of OSSN received a treatment regimen of surgical excision, followed by topical MMC. Mean follow up of 27 (SD 12) months (range 12-50, median 25 months) revealed zero recurrences.

CONCLUSION

MMC treatment following surgical excision decreases the recurrence rate of primary ocular surface neoplasia and should be considered as adjunctive therapy in primary treatment.

Analysis of pFQ31, a 8551-bp cryptic plasmid from the symbiotic nitrogen-fixing actinomycete Frankia

The actinomycete Frankia has never been transformed genetically. To favour the development of Frankia cloning vectors, we have fully sequenced the Frankia alni pFQ31 cryptic plasmid and performed analyses to characterise its coding and non-coding regions. This plasmid is 8551 bp-long and contains 72% G+C. Computer-assisted analyses identified 18 open reading frames (ORFs). These ORFs show a synonymous codon usage different from the one of Frankia chromosomal genes, suggesting an evolutionary bias linked to the nature of the replicon or a horizontal transfer. Three ORFs were found to encode genes likely to be involved in plasmid replication and stability: parFA (partition protein), ptrFA (transcriptional repressor of the GntR family) and repFA (initiation of replication). DNA signatures of a replication origin were identified in the ptrFA-repFA intergenic region. These structural motifs are similar to those observed among origins of iteron-containing plasmids replicating via a θ mode.

Bilateral cystic pleuropulmonary blastoma in early infancy

We report 2 cases of multifocal cystic (type 1) pleuropulmonary blastoma, diagnosed during the first 6 months of life. This rare entity must be recognized before evolution into the prognostically unfavorable type 2 or type 3 pleuropulmonary blastoma.

Cataract extraction in a major ophthalmic hospital: day-case or overnight stay?

PURPOSE

Cataract surgery is increasing in Australia and represents a significant burden on limited health resources. This study examines the frequency and outcomes of cataract surgery for patients who were hospitalized overnight compared with those treated as day surgery cases.

METHODS

Medical records of 671 consecutive admissions for cataract surgery at the Royal Victorian Eye and Ear Hospital were reviewed. Data analysed included demographic features, insurance status, length of hospitalization, ophthalmic conditions, medical conditions, social problems and planned surgical technique. Ophthalmic and anaesthetic complications, active ophthalmic and medical interventions were also studied.

RESULTS

Of the 671 patient admissions for cataract during the study period, 226 (33.4%) were hospitalized overnight. Factors significantly associated with overnight hospitalization in univariate analyses include older age, female sex, country residence, Veterans' Affairs insurance, monocular vision status, pre-existing ischaemic heart disease, pre-existing asthma/chronic obstructive lung disease, absence of carer, transportation problems, planned extra-capsular cataract extraction technique, ophthalmic complications and active ophthalmic and/or medical interventions. After adjusting for possible confounding factors using backwards stepwise multivariate logistic regression models all except pre-existing ischaemic heart disease and ophthalmic complications were significantly associated with overnight admission for cataract surgery. In total, 14 cases (2.1%) needed active ophthalmic and/or medical interventions, 13 overnight cases and one day case.

CONCLUSIONS

These data suggest that many patients who are hospitalized overnight for cataract surgery could be safely treated as day cases. Such a shift in the pattern of care for cataract surgery could provide a significant potential for health care savings.

[Pulmonary cystic images as a presentation of a pleuropulmonary blastoma]

A five-month-old infant presented with a sudden choking cough and mild dyspnea. Bilateral cystic pulmonary images were found on a chest X-ray, leading to exploratory surgery. A pleuropulmonary blastoma, a rare malignant embryonic tumor of childhood, was diagnosed on histologic examination. This case illustrates the necessity of performing surgical resection and histologic evaluation of any pulmonary cystic malformations, particularly when bilateral.

Use of a 49-peptide library for a qualitative and quantitative determination of pseudomonal serralysin specificity

The Pseudomonas aeruginosa serralysin (E.C. 3.4.24.40.), which is a zinc-dependent metalloprotease from the metzincin superfamily, has quite a broad specificity, which has not yet been clearly identified. We have studied it with an original approach, using a 49-peptide library of the type Z-AXXA (amide) (X = A, L, V, F, S, R, E). The library was analyzed by LC-MS before and after enzymatic hydrolysis. A great number of hydrolyzed peptides were screened and the preferential hydrolysis was the X-X peptide bond, even if in some cases, A-X and X-A bond could be hydrolyzed. No amino acids with a ionized side chain could be found in the P1' position. The results obtained suggest that the specificity in the P1' position, where an hydrophobic residue was preferentially found, seems more selective that in the Pn position. The P1 position was not very specific, but, on a quantitative point of view, the enzymatic activity was particularly increased when R, F or A were in this position. The results allow us to define the P1' and P1 residues for an optimal substrate of pseudomonal serralysin and usable for the design and the synthesis of a specific inhibitor.

Use of liquid chromatography-mass spectrometry coupling for monitoring the serralysin-catalyzed hydrolysis of a peptide library

The use of a peptide library of limited size, is considered to be more appropriate for studying a protease with a complex specificity, but very sensitive and efficient analytical techniques must be used. We have designed and synthesized a 49-peptide library of the type Z-AlaXXAla(amide) (X=Ala, Leu, Val, Phe, Ser, Arg, Glu) for studying the Pseudomonas aeruginosa serralysin specificity. All compounds of the peptide library could be identified by a LC-MS procedure. After hydrolysis of the library by pseudomonal serralysin, the LC-MS procedure also allowed the identification of the hydrolysis products and the different cleavage sites of the substrates.

Specificity of Pseudomonas aeruginosa serralysin revisited, using biologically active peptides as substrates

The characterization of the specificity of alkaline protease from Pseudomonas aeruginosa has not yet been clearly defined. Some previous results suggested that its specificity was influenced more by amino acids far from the hydrolyzed peptide bond, than by amino acids in P1 or P'1 position. From other data, it was a C-(COOH)-type endoprotease where the preferential amino acid in P1 position was an arginine residue. We have studied the hydrolysis of several biologically active peptides. Many various sites of cleavage have been characterized but no arginine in P1 position was found, despite the presence of arginine in the peptide sequence. In fact P1 and P'1 position could be occupied by various amino acids. It seems unlikely that Pseudomonas alkaline protease may only be considered as a protease specific to arginine in P1 position. On the other hand, we have observed that increase of the peptide chain length led to an important increase of the hydrolysis rate, suggesting an extended number of subsites.

Localization of Staphylococcus aureus in infected airways of patients with cystic fibrosis and in a cell culture model of S. aureus adherence

Staphylococcus aureus causes chronic respiratory tract infections in patients with cystic fibrosis (CF). Using immunofluorescence and scanning and transmission electron microscopy we located S. aureus in lung specimens of three infected CF patients, in a nasal polyp of one CF patient, and in a suspension cell culture system of primary nasal epithelial cells in vitro. Very little of S. aureus was attached to the lung epithelium, whereas abundant S. aureus was detectable in the mucus of obstructed airways. Similarly, S. aureus adhered to components of secreted mucus on primary nasal epithelial cells of CF patients and healthy control subjects, grown as cell balls in vitro (bacteria/cell +/- SD: CF: 21.9 +/- 1.5; controls: 22. 0 +/- 5.8). Mucus depletion of cell balls prior to incubation with S. aureus resulted in a significantly reduced binding (bacteria/cell +/- SD: CF: 4.2 +/- 0.3; P < 0.001; controls: 5.0 +/- 1.3; P < 0. 007). Binding of S. aureus to cell balls from CF patients or control subjects did not differ significantly. When cell balls were treated with human neutrophil elastase, hypersecretion caused removal of S. aureus from cell-associated mucus. The results suggest that S. aureus adheres primarily to mucus components of the respiratory epithelium and that significant differences do not exist in binding of S. aureus to CF or non-CF cells.

Quantitation and enzymatic activity of the alkaline protease from Pseudomonas aeruginosa in culture supernatants from clinical strains

Alkaline protease from Pseudomonas aeruginosa (E.C. 3.4.24.40), also called pseudomonal serralysin, plays an important role in the infection bacterial process. The alkaline protease concentration and activity in the culture supernatants of 23 Pseudomonas aeruginosa strains from patients suffering from cystic fibrosis were determined by using an ELISA procedure and a specific enzymatic activity test. No correlation was demonstrated between the activity and the concentration of alkaline protease. This could be explained by the presence of an inactive precursor and a partial hydrolysis of the enzyme, confirmed by SDS-PAGE and Western blotting in the supernatants. The activity test is the only one allowing a quantification of the presence of an active form of alkaline protease.

False positive MIBG scan

The fortuitous discovery of a left posterior cervico-mediastinal mass during hospitalization for hemolytic anemia in an 18 month old baby is reported. Metaiodobenzylguanidine (MIBG) uptake suggested a sympathetic tissue origin of the mass despite negative catecholamines excretion, but histopathologic examination revealed a juvenile capillary angioma within a normal sympathic ganglion.

LasA, alkaline protease and elastase in clinical strains of Pseudomonas aeruginosa: quantification by immunochemical methods

Thirty Pseudomonas aeruginosa strains were isolated from the sputa of cystic fibrosis patients. In each culture supernatant, the amount of three exoproteases (LasA, alkaline protease and elastase) was determined using immunochemical procedures. These assays used selected peptide-MAP (multiple antigen peptide) strategy as antigen for animal immunisation. The method appeared to be reproducible, simple, sensitive and specific without cross-reactivity between the antisera. The resulting values differed from one strain to another mostly for elastase production. Despite the fact that four genes (lasA, lasB, lasR and rhlR) were shown to be necessary for full elastolytic activity, it was obvious that if LasA was not secreted in a naturally non-elastase-producing strain, in return in an elastase-producing strain, there were no apparent relationships between LasA and elastase production and between LasA and alkaline protease secretion. Furthermore, in vitro, the secretion of the three exoproteases seemed to be independent of the mucoid or non-mucoid phenotype of the bacteria.

[Intrathoracic volvulus of the spleen revealing left posterolateral diaphragmatic hernia]

BACKGROUND

Late-recognized congenital left diaphragmatic hernia may have a bad prognosis when it is revealed by perforation or volvulus of the herniated viscera.

CASE REPORT

A 20 month-old boy was admitted for vomiting and abdominal pain. X-rays showed left diaphragmatic hernia and the patient was operated on with the diagnosis of volvulus of the stomach. Surgery showed hernia through the posterolateral segments of the diaphragm with spleen volvulus into the sac, requiring splenectomy before reduction of the hernia and closure of the diaphragmatic defect.

CONCLUSION

This is the fifth report of ectopic intrathoracic spleen with volvulus revealing congenital left diaphragmatic hernia.