A map of white matter tracts in a lesser ape, the lar gibbon

The recent development of methods for constructing directly comparable white matter atlases in primate brains from diffusion MRI allows us to probe specializations unique to humans, great apes, and other primate taxa. Here, we constructed the first white matter atlas of a lesser ape using an ex vivo diffusion-weighted scan of a brain from a young adult (5.5 years) male lar gibbon. We find that white matter architecture of the gibbon temporal lobe suggests specializations that are reminiscent of those previously reported for great apes, specifically, the expansion of the arcuate fasciculus and the inferior longitudinal fasciculus in the temporal lobe. Our findings suggest these white matter expansions into the temporal lobe were present in the last common ancestor to hominoids approximately 16 million years ago and were further modified in the great ape and human lineages. White matter atlases provide a useful resource for identifying neuroanatomical differences and similarities between humans and other primate species and provide insight into the evolutionary variation and stasis of brain organization.

Variation in spatial dependencies across the cortical mantle discriminates the functional behaviour of primary and association cortex

Recent theories of cortical organisation suggest features of function emerge from the spatial arrangement of brain regions. For example, association cortex is located furthest from systems involved in action and perception. Association cortex is also 'interdigitated' with adjacent regions having different patterns of functional connectivity. It is assumed that topographic properties, such as distance between regions, constrains their functions, however, we lack a formal description of how this occurs. Here we use variograms, a quantification of spatial autocorrelation, to profile how function changes with the distance between cortical regions. We find function changes with distance more gradually within sensory-motor cortex than association cortex. Importantly, systems within the same type of cortex (e.g., fronto-parietal and default mode networks) have similar profiles. Primary and association cortex, therefore, are differentiated by how function changes over space, emphasising the value of topographical features of a region when estimating its contribution to cognition and behaviour.

Cortical Morphology and White Matter Tractography of Three Phylogenetically Distant Primates: Evidence for a Simian Elaboration

Comparative neuroimaging has been used to identify changes in white matter architecture across primate species phylogenetically close to humans, but few have compared the phylogenetically distant species. Here, we acquired postmortem diffusion imaging data from ring-tailed lemurs (Lemur catta), black-capped squirrel monkeys (Saimiri boliviensis), and rhesus macaques (Macaca mulatta). We were able to establish templates and surfaces allowing us to investigate sulcal, cortical, and white matter anatomy. The results demonstrate an expansion of the frontal projections of the superior longitudinal fasciculus complex in squirrel monkeys and rhesus macaques compared to ring-tailed lemurs, which correlates with sulcal anatomy and the lemur’s smaller prefrontal granular cortex. The connectivity of the ventral pathway in the parietal region is also comparatively reduced in ring-tailed lemurs, with the posterior projections of the inferior longitudinal fasciculus not extending toward parietal cortical areas as in the other species. In the squirrel monkeys we note a very specific occipito-parietal anatomy that is apparent in their surface anatomy and the expansion of the posterior projections of the optical radiation. Our study supports the hypothesis that the connectivity of the prefrontal-parietal regions became relatively elaborated in the simian lineage after divergence from the prosimian lineage.

U-net model for brain extraction: Trained on humans for transfer to non-human primates

Brain extraction (a.k.a. skull stripping) is a fundamental step in the neuroimaging pipeline as it can affect the accuracy of downstream preprocess such as image registration, tissue classification, etc. Most brain extraction tools have been designed for and applied to human data and are often challenged by non-human primates (NHP) data. Amongst recent attempts to improve performance on NHP data, deep learning models appear to outperform the traditional tools. However, given the minimal sample size of most NHP studies and notable variations in data quality, the deep learning models are very rarely applied to multi-site samples in NHP imaging. To overcome this challenge, we used a transfer-learning framework that leverages a large human imaging dataset to pretrain a convolutional neural network (i.e. U-Net Model), and then transferred this to NHP data using a small NHP training sample. The resulting transfer-learning model converged faster and achieved more accurate performance than a similar U-Net Model trained exclusively on NHP samples. We improved the generalizability of the model by upgrading the transfer-learned model using additional training datasets from multiple research sites in the Primate Data-Exchange (PRIME-DE) consortium. Our final model outperformed brain extraction routines from popular MRI packages (AFNI, FSL, and FreeSurfer) across a heterogeneous sample from multiple sites in the PRIME-DE with less computational cost (20 s~10 min). We also demonstrated the transfer-learning process enables the macaque model to be updated for use with scans from chimpanzees, marmosets, and other mammals (e.g. pig). Our model, code, and the skull-stripped mask repository of 136 macaque monkeys are publicly available for unrestricted use by the neuroimaging community at https://github.com/HumanBrainED/NHP-BrainExtraction.

A collaborative resource platform for non-human primate neuroimaging

Neuroimaging non-human primates (NHPs) is a growing, yet highly specialized field of neuroscience. Resources that were primarily developed for human neuroimaging often need to be significantly adapted for use with NHPs or other animals, which has led to an abundance of custom, in-house solutions. In recent years, the global NHP neuroimaging community has made significant efforts to transform the field towards more open and collaborative practices. Here we present the PRIMatE Resource Exchange (PRIME-RE), a new collaborative online platform for NHP neuroimaging. PRIME-RE is a dynamic community-driven hub for the exchange of practical knowledge, specialized analytical tools, and open data repositories, specifically related to NHP neuroimaging. PRIME-RE caters to both researchers and developers who are either new to the field, looking to stay abreast of the latest developments, or seeking to collaboratively advance the field.

An epidemiological survey of methicillin-resistant Staphylococcus aureus in a tertiary referral hospital

Over a 30-month period from July 1995 to December 1997, new detections of methicillin-resistant Staphylococcus aureus (MRSA) were prospectively studied in a tertiary referral hospital. The aims of the study were to determine the incidence of colonization of patients admitted to each of the hospital's 39 clinical units and ascertain where each patient had become colonized. Epidemiological information (time to detection, ward movement, admission to other hospitals, data on MRSA isolations in hospital wards) and phage typing were used by the hospital's infection control unit to make this determination. Routine containment procedures included cohorting, flagging and triclosan body washes. Surveillance cultures were collected infrequently. Patients known to be colonized with MRSA were excluded from orthopaedic and haematology wards. During the study period, 995 patients were found to be newly colonized. The incidence of colonization varied from nil to 72 per 1000 admissions, being highest in the main intensive care unit and in services which frequently used that unit. The incidence of colonization in elective orthopaedic surgery (< 1 per 1000) and haematology (3 per 1000) was very low. Determining the place where patients acquired MRSA was made difficult by the high frequency of endemic phage types and frequent patient transfer between wards. Epidemiological data suggested that the main intensive care unit and surgical wards nursing patients with colorectal, urological and vascular diseases were the places where most patients became colonized. MRSA was never acquired by patients nursed in wards which practised an exclusion policy towards patients known to be colonized with MRSA. Our data suggest that in tertiary referral hospitals, where MRSA is not only endemic but frequently imported from other hospitals, it is possible to establish areas where MRSA is never acquired.

A prospective survey of current methicillin-resistant Staphylococcus aureus control measures

BACKGROUND

Methicillin-resistant Staphylococcus aureus (MRSA) is now endemic in tertiary referral hospitals among the developed world. By prospective survey, the effect of two measures aimed to reduce the spread of MRSA was determined. First, a surgical ward with persistently high levels of MRSA detection was cleaned and renovated. Second, the medical records of all MRSA-colonized patients were electronically flagged, facilitating immediate application of control measures on readmission.

METHODS

Data were collected for 995 newly colonized patients admitted between 1 July 1995 and 31 December 1997. Methicillin-resistant Staphylococcus aureus detection was determined before and after implementation of the interventions, along with the likely place of MRSA acquisition and the monthly incidence of MRSA detection for all inpatients. Chi-squared testing with odds ratios and 95% confidence intervals determined associations between the effect of control measures studied and MRSA detection rates.

RESULTS

New MRSA detection was 21.6 per 1000 admissions before refurbishment compared with 20.4 per 1000 admissions to the surgical ward after refurbishment. New MRSA detection averaged 6.4 per 1000 hospital admissions before the introduction of record flagging and patient cohorting, compared with 6.2 per 1000 admissions after.

CONCLUSION

Neither ward refurbishment, nor introduction of flagging, significantly reduced rates of colonization during the study period. In hospitals that receive MRSA-colonized patients and provide intensive care facilities, spread of MRSA is a major problem. Effective containment demands separate wards for MRSA-colonized and non-colonized patients. The need for such containment should be considered in design of the modern hospital.

Detection of persistent vegetative bacteria and amplified viral nucleic acid from in-use testing of gastrointestinal endoscopes

Hospital-acquired infection attributed to inadequate decontamination of gastrointestinal endoscopes prompted an in use evaluation of recommended procedures. Specimens were obtained from the internal channels of 123 endoscopes before, during and after decontamination by flushing with saline and brushing with a sterile brush, and examined for vegetative bacteria by broth and plate culture. Four endoscopy units were tested; the chemical disinfectants used were: 2% glutaraldehyde in Centres 1 and 2 (automated) and Centre 3 (manual); peracetic acid in Centre 4 (automated). Samples from patients in Centre 1 with known chronic hepatitis B virus (HBV), hepatitis C virus (HCV) and human immunodeficiency virus (HIV-1) infection were also examined for viral nucleic acid by ultracentrifugation, nucleic acid extraction, reverse transcription (for RNA) and polymerase chain reaction (PCR). No persistent vegetative bacteria were found following standard manual cleaning and disinfection for 20 min in 2% glutaraldehyde in Centres 2 and 3 (N = 37). At Centre 1, while plate culture yielded no growth, 34% of samples (10/29) grew vegetative bacteria in broth culture after cleaning and disinfection for 20 min in 2% glutaraldehyde. Investigation revealed an error in manual cleaning; no bacteria were detected in 37 samples taken after this was corrected. At Centre 4, despite the use of peracetic acid as a sterilant, three out of 20 (15%) of post decontamination samples grew bacteria; one contained persistent bacteria. HBV and HCV PCR analysis detected viral nucleic acid in three out of four and four out of six samples from viraemic patients undergoing endoscopy in Centre 1 during the period of improper manual washing. After proper cleaning was instituted, samples from nine out of nine HCV viraemic patients were negative. HIV RNA was detected in five of 14 samples taken from endoscopes after use on HIV positive patients but all post decontamination samples were negative. Detection of bacteria in washes from endoscope channels is a useful warning of a breakdown in decontamination practice. Inadequate brushing of internal channels may result in persistent HCV and HBV viral nucleic acid, the significance of which is not clear. These results reinforce the importance of adequate manual cleaning of endoscopes before chemical disinfection.

Molecular epidemiology of Burkholderia cepacia in two Australian cystic fibrosis centres

Forty individual patient sputum isolates of Burkholderia cepacia from two Australian cystic fibrosis (CF) centres more than 100 km apart were genotyped using pulsed-field gel electrophoresis (PFGE) with XbaI restriction enzyme digestion. Hospital 1 had an endemic strain with 19 of 20 isolates being closely related. This centre does not implement an inpatient segregation policy for its paediatric patients who constitute the majority of those colonized with B. cepacia. Hospital 2 did not have a single endemic strain; there were two different sibling clusters and a third cluster involving a cohabiting couple, but all other patients had unique isolates. One patient at Hospital 2 carried an organism closely related to the endemic strain from Hospital 1. Hospital 2 practises segregation of colonized inpatients and also segregation external to the hospital. It would appear that no nosocomial spread of infection is occurring with this policy.

A national collaborative study of the in vitro activity of oral cephalosporins and loracarbef (LY 163892). Australian Group for the Study of Antimicrobial Resistance (AGAR)

A national collaborative study involving the laboratories of 17 Australian hospitals examined the in vitro activity of loracarbef, cefaclor, cephalexin, amoxycillin and amoxycillin/clavulanate against 2661 recently isolated common bacterial pathogens. Loracarbef was the most active agent against Escherichia coli (MIC90 = 1 mg/l) and had activity comparable to other agents against Klebsiella pneumoniae and Proteus mirabilis. Like the oral cephalosporins, it had no activity against species of Enterobacter and Serratia. beta-lactamase-producing Staphylococcus aureus and Haemophilus influenzae were moderately sensitive to loracarbef (MIC90 = 8 mg/l for both species). Streptococcus pneumoniae was moderately sensitive to loracarbef (MIC90 = 2 mg/l) but strains which were insensitive to penicillin were often highly resistant.

Multi-centre collaborative study for the in vitro evaluation of new macrolides dirithromycin and erythromycylamine. Australian Group for Antimicrobial Resistance (AGAR)

A national study was conducted to determine the in vitro activity of 2 newer macrolides, dirithromycin and erythromycylamine compared with that of erythromycin, tetracycline and penicillin. Nineteen major teaching hospitals participated in the study. Minimal Inhibitory Concentrations (MICs) were determined by agar dilution, mostly using Iso-Sensitest Agar and an inoculum of 10(4) cells per spot. 2284 clinically significant strains were isolated in late 1991 and early 1992, comprising 1736 Gram-positive cocci, 355 Haemophilus influenzae, 97 Moraxella catarrhalis, 32 Listeria monocytogenes, 25 Neisseria meningitidis and 39 Neisseria gonorrhoeae were tested. The study indicates that dirithromycin and erythromycylamine possess antibacterial activity equivalent to that of erythromycin against most Gram-positive cocci and M. catarrhalis. Strains resistant to erythromycin were also resistant to dirithromycin and to erythromycylamine. Tetracycline was as active as the macrolides against both penicillin-resistant and penicillin-susceptible strains of Staphylococcus aureus. Coagulase-negative penicillin-resistant staphylococci, compared with tetracycline, were relatively resistant to the macrolides. H. influenzae was less susceptible than the Gram-positive cocci.

Bacteremia and bacterascites after endoscopic sclerotherapy for bleeding esophageal varices and prevention by intravenous cefotaxime: a randomized trial

Thirty-one patients were randomized during 39 episodes of bleeding to receive either 1 g of intravenous cefotaxime (19 patients) or no antibiotic (20 patients) immediately before emergency endoscopic sclerotherapy. Blood was obtained for culture before and at 5 minutes, 4 hours, and 24 hours after the procedure. Specimens for culture were taken from the endoscope tip and channel, water bottle, and injection needle after sclerotherapy. When ascites was present (5 patients in the antibiotic group, 7 in the control group), fluid was obtained by paracentesis before endoscopy and at 4 and 24 hours. Bacteremia occurred in 1 of 19 patients in the antibiotic group (5.3%), compared with 6 of 19 in the control group (31.6%; p = .04). The cultured organisms were oral flora and usually also contaminated the endoscope and needle. No bacteria were cultured from ascitic fluid in any patient nor was the ascitic fluid white cell count elevated. Clinical infection attributable to sclerotherapy did not develop in any patient. In conclusion, the frequency of bacteremia after endoscopic sclerotherapy for bleeding esophageal varices can be reduced by prophylactic administration of intravenous cefotaxime. However, this may not be clinically relevant, given the absence of bacterascites and infection in this study. These findings do not support the routine use of antibiotics before sclerotherapy.

Allergic fungal sinusitis presenting as a paranasal sinus tumour

Allergic fungal rhinosinusitis is a rare complication of atopic upper airways disease which may present initially as an expansive tumour of the paranasal sinuses. This reported case was caused by the rare fungal pathogen Bipolaris hawiiensis and illustrates typical clinical and laboratory features of this disorder. Although the optimum management of allergic fungal sinusitis is controversial, combined therapy with surgical clearance, antifungal agents and corticosteroids produced a favourable outcome.

Treatment of tuberculosis in Australia

The combination of isoniazid and rifampicin, initially accompanied by a third drug such as ethambutol, has become the standard treatment for pulmonary tuberculosis in Australia. Not all patients need admission to hospital but careful follow-up and encouragement of compliance with the regimen is important during the year of therapy which follows the diagnosis of the disease. Because of the higher incidence of drug resistance in disease acquired in Southeast Asia, a fourth drug, usually pyrazinamide, is added until the results of sensitivity testing are known. Pulmonary disease caused by environmental ("atypical") mycobacteria presents special problems in treatment because the infection usually complicates pre-existing lung disease; drug resistance is the rule; and there are no well controlled prospective trials to provide a rational basis for therapy.

Effect of antibiotic use on the incidence of cephalosporin resistance in two Australian hospitals

The incidence of resistance of Gram-negative bacteria to three generations of cephalosporins was surveyed in two large hospitals with widely differing rates of cephalosporin usage. Overall resistance (MIC greater than 5 mg/l) of Enterobacteriaceae to cefotaxime in the hospital using large amounts of cephalosporins was 4% compared with 0.7% in the other. Enterobacter species accounted for most resistant isolates and resistant Enterobacter cloacae replaced sensitive strains in four patients given cefotaxime in 1983. The distribution of species colonizing intensive care areas was similar in both hospitals with cephalosporin-resistant Pseudomonas aeruginosa and Acinetobacter calcoaceticus predominating.

Measurement of IgM antibodies in the diagnosis of mycoplasma pneumonia

The sera of 30 patients with complement-fixing antibodies to Mycoplasma pneumoniae (titres larger than or equal to 32) were treated with staphylococcal protein A. This procedure effectively removed 90 to 95% of the IgG antibodies. The Mycoplasma-specific antibodies in the treated sera could then be measured by a complement fixation test. This provides a useful test for distinguishing serological responses to recent Mycoplasma pneumoniae infections from anamnestic responses due to past exposure to Mycoplasma pneumoniae.