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OBJECTIVE The aim of this study was to describe the processes and outcomes associated with patients at five sites in the Adult Hydrocephalus Clinical Research Network (AHCRN) who had undergone evaluation and treatment for suspected idiopathic normal pressure hydrocephalus (iNPH) and had 1-year postoperative follow-up. METHODS Subjects with possible iNPH who had been prospectively enrolled in the AHCRN registry between November 19, 2014, and December 31, 2018, were evaluated by CSF drainage via either lumbar puncture or external lumbar drainage, consistent with recommendations of the international iNPH guidelines. Standardized clinical evaluations of gait, cognition, urinary symptoms, depression, and functional outcomes were conducted at baseline, before and after CSF drainage, and at 4-month intervals after shunt surgery. Complications of CSF drainage and shunt surgery were recorded. RESULTS Seventy-four percent (424/570) of patients with possible iNPH had CSF drainage, and 46% of them (193/424) underwent shunt surgery. The mean change in gait velocity with CSF drainage was 0.18 m/sec in patients who underwent shunt surgery versus 0.08 m/sec in patients who did not. For shunt surgery patients, gait velocity increased by 54% from 0.67 m/sec before CSF drainage to 0.96 m/sec 8–12 months after surgery, and 80% of patients had an increase of at least 0.1 m/sec by the first postoperative visit. Evaluation of cognition, urinary symptoms, depression, and functional outcomes also revealed improvement after shunt surgery. Of 193 patients who had undergone shunt surgery, 176 (91%) had no complications and 17 (9%) had 28 complications. Eleven patients (6%) had 14 serious complications that resulted in the need for surgery or an extended hospital stay. The 30-day reoperation rate was 3%. CONCLUSIONS Using criteria recommended by the international iNPH guidelines, the authors found that evaluation and treatment of iNPH are safe and effective. Testing with CSF drainage and treatment with shunt surgery are associated with a high rate of sustained improvement and a low rate of complications for iNPH in the 1st year after shunt surgery. Patients who had undergone shunt surgery for iNPH experienced improvement in gait, cognitive function, bladder symptoms, depression, and functional outcome measures. Gait velocity, which is an easily measured, objective, continuous variable, should be used as a standard outcome measure to test a patient’s response to CSF drainage and shunt surgery in iNPH.

BackgroundThe coastal wetland tree speciesMelaleuca quinquenervia(Cav.) S.T.Blake (Myrtaceae), commonly named the broad-leaved paperbark, is a foundation species in eastern Australia, Indonesia, Papua New Guinea, and New Caledonia. The species has been widely grown as an ornamental, becoming invasive in areas such as Florida in the United States. Long-lived trees must respond to a wide range pests and pathogens throughout their lifespan, and immune receptors encoded by the nucleotide- binding domain and leucine-rich repeat containing (NLR) gene family play a key role in plant stress responses. Expansion of this gene family is driven largely by tandem duplication, resulting in a clustering arrangement on chromosomes. Due to this clustering and their highly repetitive domain structure, comprehensive annotation of NLR encoding genes within genomes has been difficult. Additionally, as many genomes are still presented in their haploid, collapsed state, the full allelic diversity of the NLR gene family has not been widely published for outcrossing tree species.ResultsWe assembled a chromosome-level pseudo-phased genome forM.quinquenerviaand describe the full allelic diversity of plant NLRs using the novel FindPlantNLRs pipeline. Analysis reveals variation in the number of NLR genes on each haplotype, differences in clusters and in the types and numbers of novel integrated domains.ConclusionsWe anticipate that the high quality of the genome forM. quinquenerviawill provide a new framework for functional and evolutionary studies into this important tree species. Our results indicate a likely role for maintenance of NLR allelic diversity to enable response to environmental stress, and we suggest that this allelic diversity may be even more important for long-lived plants.

Rhabdias pseudosphaerocephalais a well-studied invasive nematode parasite of amphibians. However, there are several outstanding questions aboutR. pseudosphaerocephalathat are best answered using genomic data. This species differs phenotypically across its invasive range. These differences are challenging to interpret because this species is part of a complex that is diverse and cryptic in its home-range, and we do not know how many species from this complex originally colonised Australia. For this reason, it is unknown whether the phenotypic differences across the introduced range are due to intraspecific differentiation between populations or due to the presence of multiple species. In addition, there is little consensus in the placement of Rhabdiasidae family within the phylum Nematoda, making it difficult to perform comparative analyses with other nematodes. Within this paper, we assemble a reference genome forR. pseudosphaerocephala, the first assembly of any Rhabdiasidae species. We then use resequencing data to address outstanding questions about this species. Specifically, we combine population genetic and phylogenetic analyses to determine that there is likely only a singleR. pseudosphaerocephalalineage within Australia, and identify that the invasive range population is closely related to home rage isolates that infect similar host species. We present compelling evidence for a genetic bottleneck following introduction to Australia and genetic differentiation occurring between invasive range populations. We then use genome-scale phylogenomic analysis to place the Rhabdiasidae family in the suborder Rhabditina. Ultimately, this paper brings the study of Rhabdiasidae into the genomic era, and sheds light on its ancient and modern evolutionary history.

Genetic divergence is the fundamental process that drives evolution and ultimately speciation. Structural variants (SVs) are large-scale genomic differences within a species or population and can cause functionally important phenotypic differences. Characterizing SVs across invasive species will fill knowledge gaps regarding how patterns of genetic diversity and genetic architecture shape rapid adaptation under new selection regimes. Here, we seek to understand patterns in genetic diversity within the globally invasive European starling, Sturnus vulgaris. Using whole genome sequencing of eight native United Kingdom (UK), eight invasive North America (NA), and 33 invasive Australian (AU) starlings, we examine patterns in genome-wide SNPs and SVs between populations and within Australia. Our findings detail the landscape of standing genetic variation across recently diverged continental populations of this invasive avian. We demonstrate that patterns of genetic diversity estimated from SVs do not necessarily reflect relative patterns from SNP data, either when considering patterns of diversity along the length of the organism's chromosomes (owing to enrichment of SVs in subtelomeric repeat regions), or interpopulation diversity patterns (possibly a result of altered selection regimes or introduction history). Finally, we find that levels of balancing selection within the native range differ across SNP and SV of different classes and outlier classifications. Overall, our results demonstrate that the processes that shape allelic diversity within populations is complex and support the need for further investigation of SVs across a range of taxa to better understand correlations between often well-studied SNP diversity and that of SVs.

BackgroundOne difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-qualityde novolong read chromosomal assembly with epigenetic footprints and morphology to describe the Alpine dingo female named Cooinda. It was critical to establish an Alpine dingo reference because this ecotype occurs throughout coastal eastern Australia where the first drawings and descriptions were completed.FindingsWe generated a high-quality chromosome-level reference genome assembly (Canfam_ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. Compared to the previously published Desert dingo assembly, there are large structural rearrangements on Chromosomes 11, 16, 25 and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and nine previously publishedde novocanine assemblies show dingoes are monophyletic and basal to domestic dogs. Network analyses show that the mtDNA genome clusters within the southeastern lineage, as expected for an Alpine dingo. Comparison of regulatory regions identified two differentially methylated regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. Morphological data, comprising geometric morphometric assessment of cranial morphology place dingo Cooinda within population-level variation for Alpine dingoes. Magnetic resonance imaging of brain tissue show she had a larger cranial capacity than a similar-sized domestic dog.ConclusionsThese combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphological characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney.

Cerebellar mutism syndrome (CMS) is one the most disabling postoperative neurological complications after posterior fossa surgery in children. CMS is characterized by a transient mutism with a typical onset demonstrated within 2 days postoperatively accompanied by associated ataxia, hypotonia, and irritability. Several hypotheses for the anatomical basis of pathophysiology and risk factors have been suggested. However, a definitive theory and treatment protocols have not yet been determined. Animal histological and electrophysiological studies and more recent human imaging studies have demonstrated the existence of a compartmentalized representation of cerebellar function, the understanding of which might provide more information on the pathophysiology. Damage to the dentatothalamocortical pathway and cerebrocerebellar diaschisis have been described as the anatomical substrate to the CMS. The risk factors, which include tumor type, brainstem invasion, tumor localization, tumor size, and vermal splitting technique, have not yet been clearly elucidated. The efficacy of potential pharmacological and speech therapies has been studied in small trials. Long-term motor speech deficits and associated cognitive and behavioral disturbances have now been found to be common among CMS survivors, affecting their development and requiring rehabilitation, leading to significant financial effects on the healthcare system and distress to the family. The aim of the present review was to outline the cerebellar anatomy and function and its connections in relationship to the pathophysiology and to refine the risk factors and treatment strategies for CMS.

BACKGROUND: Whether revascularization by percutaneous coronary intervention (PCI) can improve event-free survival and left ventricular function in patients with severe ischemic left ventricular systolic dysfunction, as compared with optimal medical therapy (i.e., individually adjusted pharmacologic and device therapy for heart failure) alone, is unknown. METHODS: We randomly assigned patients with a left ventricular ejection fraction of 35% or less, extensive coronary artery disease amenable to PCI, and demonstrable myocardial viability to a strategy of either PCI plus optimal medical therapy (PCI group) or optimal medical therapy alone (optimal-medical-therapy group). The primary composite outcome was death from any cause or hospitalization for heart failure. Major secondary outcomes were left ventricular ejection fraction at 6 and 12 months and quality-of-life scores. RESULTS: A total of 700 patients underwent randomization - 347 were assigned to the PCI group and 353 to the optimal-medical-therapy group. Over a median of 41 months, a primary-outcome event occurred in 129 patients (37.2%) in the PCI group and in 134 patients (38.0%) in the optimal-medical-therapy group (hazard ratio, 0.99; 95% confidence interval [CI], 0.78 to 1.27; P = 0.96). The left ventricular ejection fraction was similar in the two groups at 6 months (mean difference, -1.6 percentage points; 95% CI, -3.7 to 0.5) and at 12 months (mean difference, 0.9 percentage points; 95% CI, -1.7 to 3.4). Quality-of-life scores at 6 and 12 months appeared to favor the PCI group, but the difference had diminished at 24 months. CONCLUSIONS: Among patients with severe ischemic left ventricular systolic dysfunction who received optimal medical therapy, revascularization by PCI did not result in a lower incidence of death from any cause or hospitalization for heart failure. (Funded by the National Institute for Health and Care Research Health Technology Assessment Program; REVIVED-BCIS2 ClinicalTrials.gov number, NCT01920048.).

Recurrent epidemics of coffee leaf rust, caused by the fungal pathogen Hemileia vastatrix, have constrained the sustainable production of Arabica coffee for over 150 years. The ability of H. vastatrix to overcome resistance in coffee cultivars and evolve new races is inexplicable for a -pathogen that supposedly only utilizes clonal reproduction. Understanding the evolutionary complexity between H. vastatrix and its only known host, including determining how the pathogen evolves virulence so rapidly is crucial for disease management. Achieving such goals relies on the availability of a comprehensive and high-quality genome reference assembly. To date, two reference genomes have been assembled and published for H. vastatrix that, while useful, remain fragmented and do not represent chromosomal scaffolds. Here, we present a complete scaffolded pseudochromosome-level genome resource for H. vastatrix strain 178a (Hv178a). Our initial assembly revealed an unusually high degree of gene duplication (over 50% BUSCO basidiomycota_odb10 genes). Upon inspection, this was predominantly due to a single scaffold that itself showed 91.9% BUSCO Completeness. Taxonomic analysis of predicted BUSCO genes placed this scaffold in Exobasidiomycetes and suggests it is a distinct genome, which we have named Hv178a associated fungal genome (Hv178a AFG). The high depth of coverage and close association with Hv178a raises the prospect of symbiosis, although we cannot completely rule out contamination at this time. The main Ca. 546 Mbp Hv178a genome was primarily (97.7%) localised to 11 pseudochromosomes (51.5 Mb N50), building the foundation for future advanced studies of genome structure and organization.

The fungal plant pathogen Austropuccinia psidii is spreading globally and causing myrtle rust disease symptoms on plants in the family Myrtaceae. A. psidii is dikaryotic, with two nuclei that do not exchange genetic material during the dominant phase of its life-cycle. Phased and scaffolded genome resources for rust fungi are important for understanding heterozygosity, mechanisms of pathogenicity, pathogen population structure and for determining the likelihood of disease spread. We have assembled a chromosome-level phased genome for the pandemic biotype of A. psidii and, for the first time, show that each nucleus contains 18 chromosomes, in line with other distantly related rust fungi. We show synteny between the two haplo-phased genomes and provide a new tool, ChromSyn, that enables efficient comparisons between chromosomes based on conserved genes. Our genome resource includes a fully assembled and circularised mitochondrial sequence for the pandemic biotype.

Dogs are uniquely associated with human dispersal and bring transformational insight into the domestication process. Dingoes represent an intriguing case within canine evolution being geographically isolated for thousands of years. Here, we present a high-quality de novo assembly of a pure dingo (CanFam_DDS). We identified large chromosomal differences relative to the current dog reference (CanFam3.1) and confirmed no expanded pancreatic amylase gene as found in breed dogs. Phylogenetic analyses using variant pairwise matrices show that the dingo is distinct from five breed dogs with 100% bootstrap support when using Greenland wolf as the outgroup. Functionally, we observe differences in methylation patterns between the dingo and German shepherd dog genomes and differences in serum biochemistry and microbiome makeup. Our results suggest that distinct demographic and environmental conditions have shaped the dingo genome. In contrast, artificial human selection has likely shaped the genomes of domestic breed dogs after divergence from the dingo.

Background Test balloon occlusion (TBO) is important in the management of complex cerebrovascular and skull base lesions when permanent occlusion (PO) of a parent artery may be indicated. Several adjuncts may be used to increase the sensitivity of TBO to predict whether PO will be tolerated. This is an observational study to evaluate the utility of internal carotid artery (ICA) TBO using single photon emission computed tomography (SPECT) scan in the management of complex vascular pathology and skull base tumors. Methods All TBO procedures performed over a 20-year period were analyzed. Clinical assessment and angiographic collateral flow were combined with semi-quantitative cerebral blood flow analysis using 99mTc hexamethylpropylene-amine oxime SPECT scan during ICA TBO. Evaluation of collateral circulation after TBO, and the complications of TBO and the safety of PO after successful TBO were evaluated. Results Eighty-three patients underwent TBO without complication. Of 45 patients with satisfactory TBO, 28 proceeded to PO. Three patients developed transient ischemic symptoms thought to be embolic in origin. Thirty-eight patients had unsatisfactory TBO, of whom 15 required PO accompanied by a bypass procedure. Forty patients in the series did not undergo permanent vessel occlusion. Conclusions SPECT scan–enhanced TBO is an important component of the management of complex vascular pathology and skull base tumors, permitting safe PO of the parent vessel and definitive treatment of the main pathology.

Transposable elements (TEs), also known as jumping genes, are sequences able to move or copy themselves within a genome. As TEs move throughout genomes they often act as a source of genetic novelty, hence understanding TE evolution within lineages may help in understanding environmental adaptation. Studies into the TE content of lineages of mammals such as bats have uncovered horizontal transposon transfer (HTT) into these lineages, with squamates often also containing the same TEs. Despite the repeated finding of HTT into squamates, little comparative research has examined the evolution of TEs within squamates. Here we examine a diverse family of Australo-Melanesian snakes (Hydrophiinae) to examine if the previously identified, order-wide pattern of variable TE content and activity holds true on a smaller scale. Hydrophiinae diverged from Asian elapids ~15-25 Mya and have since rapidly diversified into six amphibious, ~60 marine and ~100 terrestrial species which fill a broad range of ecological niches. We find TE diversity and expansion differs between hydrophiines and their Asian relatives and identify multiple HTTs into Hydrophiinae, including three likely transferred into the ancestral hydrophiine from fish. These HTT events provide the first tangible evidence that Hydrophiinae reached Australia from Asia via a marine route. Table S1. Genbank accession numbers, assembly names and binomial names of the 2314 metazoan genomes assemblies investigated as the potential sources of the horizontally transferred TEs. Data S1. RepeatMasker output of elapid genomes and repeat library used for said masking. Genome assemblies annotated with RepeatMasker using a custom library of curated RepeatModeler2 libraries and previously described lepidosaur TEs from the Repbase RepeatMasker library. Data S2. Filtered output of BLASTN 2.7.1+ (-task dc-megablast) searches of the 2314 metazoan genomes assemblies for HT candidates. Of the 2314 genomes searched, only 373 contained hits of significant quality (>70% pairwise identity, >50% coverage). Data S3. Nucleotide multiple sequence alignments of each HT candidate and the curated consensus sequences identified in other species. Sequences were aligned using MAFFT v7.453 (--localpair). Data S4. Phylogenies of each HT candidate and the curated consensus sequences identified in other species. Trees constructed using FastTree 2.1.1.1.

Chromosome rearrangements can result in the rapid evolution of hybrid incompatibilities. Robertsonian fusions, particularly those with monobrachial homology, can drive reproductive isolation amongst recently diverged taxa. The recent radiation of rock-wallabies (genus Petrogale) is an important model to explore the role of Robertsonian fusions in speciation. Here, we pursue that goal using an extensive sampling of populations and genomes of Petrogale from north-eastern Australia. In contrast to previous assessments using mitochondrial DNA or nuclear microsatellite loci, genomic data are able to separate the most closely related species and to resolve their divergence histories. Both phylogenetic and population genetic analyses indicate introgression between two species that differ by a single Robertsonian fusion. Based on the available data, there is also evidence for introgression between two species which share complex chromosomal rearrangements. However, the remaining results show no consistent signature of introgression amongst species pairs and where evident, indicate generally low introgression overall. X-linked loci have elevated divergence compared with autosomal loci indicating a potential role for genic evolution to produce reproductive isolation in concert with chromosome change. Our results highlight the value of genome scale data in evaluating the role of Robertsonian fusions and structural variation in divergence, speciation, and patterns of molecular evolution.

Telopea speciosissima, the New South Wales waratah, is an Australian endemic woody shrub in the family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, and are significant from a horticultural perspective. Here, we report the first chromosome-level genome for T. speciosissima. Combining Oxford Nanopore long-reads, 10x Genomics Chromium linked-reads and Hi-C data, the assembly spans 823 Mb (scaffold N50 of 69.0 Mb) with 97.8% of Embryophyta BUSCOs "Complete". We present a new method in Diploidocus (https://github.com/slimsuite/diploidocus) for classifying, curating and QC-filtering scaffolds, which combines read depths, k-mer frequencies and BUSCO predictions. We also present a new tool, DepthSizer (https://github.com/slimsuite/depthsizer), for genome size estimation from the read depth of single-copy orthologues and estimate the genome size to be approximately 900 Mb. The largest 11 scaffolds contained 94.1% of the assembly, conforming to the expected number of chromosomes (2n = 22). Genome annotation predicted 40,158 protein-coding genes, 351 rRNAs and 728 tRNAs. We investigated CYCLOIDEA (CYC) genes, which have a role in determination of floral symmetry, and confirm the presence of two copies in the genome. Read depth analysis of 180 "Duplicated" BUSCO genes using a new tool, DepthKopy (https://github.com/slimsuite/depthkopy), suggests almost all are real duplications, increasing confidence in the annotation and highlighting a possible need to revise the BUSCO set for this lineage. The chromosome-level T. speciosissima reference genome (Tspe_v1) provides an important new genomic resource of Proteaceae to support the conservation of flora in Australia and further afield.

Background: Selective dorsal rhizotomy (SDR) is an irreversible surgical procedure involving the division of selected sensory nerve roots, followed by intensive physiotherapy. The aim is to improve function and quality of life in children with cerebral palsy and a Gross Motor Function Classification System (GMFCS) level of II or III (walks with or without assistive devices, respectively). We assessed gross motor function before and after SDR and postoperative quality of life in a study commissioned by NHS England. Methods: We did a prospective observational study in five hospitals in England who were commissioned to perform SDR on children aged 3–9 years with spastic diplegic cerebral palsy. The primary outcome was score changes in the 66-item Gross Motor Function Measure (GMFM-66) and seven domains of the Cerebral Palsy Quality of Life Questionnaire ([CP-QoL] social wellbeing and acceptance, feelings about functioning, participation and physical health, emotional wellbeing and self-esteem, access to services, family health, and pain and impact of disability) from before to 24 months after SDR. Findings: From Sept 4, 2014, to March 21, 2016, 137 children underwent SDR. The mean age was 6·0 years (SD 1·8). The mean GMFM-66 score increased after SDR with an annual change of 3·2 units (95% CI 2·9 to 3·5, n=137). Of the seven CP-QoL domains, five showed significant improvements over time: feelings about functioning mean annual change 3·0 units (95% CI 2·0 to 4·0, n=133), participation and physical health 3·9 units (2·5 to 5·3, n=133), emotional wellbeing and self-esteem 1·3 units (0·2 to 2·3, n=133), family health 2·0 units (0·7 to 3·3, n=132), and pain and impact of disability −2·5 units (−3·9 to −1·2, n=133). 17 adverse events were reported in 15 children, of which none were severe and 15 (88%) resolved. Interpretation: SDR improved function and quality of life in the 24 months after surgery in children with cerebral palsy classified as GMFCS levels II and III. On the basis of these findings, an interim national policy decision was made that SDR would be funded for eligible children in England from 2018. Funding: National Institute for Health and Care Excellence, National Institute for Health Research Biomedical Research Centre, NHS England.

Objectives Selective dorsal rhizotomy (SDR) is used to improve spasticity, gait, and pain in children with spastic diplegia. There is growing evidence supporting its long-term benefits in terms of functional outcomes, independence, and quality of life. There is, however, little contemporary work describing the surgical morbidity of this irreversible procedure. The purpose of this study is to evaluate the surgical outcomes and complications of SDR at a single United Kingdom center. Methods Demographics, surgical, postoperative, and follow-up data for all patients undergoing SDR between 2011 and 2016 were collected from medical records. Results Preoperative Gross Motor Function Classification System levels in 150 consecutive patients were II (35%), III (65%), and IV (1%). Median age was 6 years and 58% were male patients. There were no deaths, cerebrospinal fluid leaks, returns to theater, or readmissions within 30 days. There were no new motor or sphincter deficits. Postoperative neuropathic pain was reported by 5.3% and sensory symptoms by 8.7%. Other complications included: postoperative nausea and vomiting (19.3%), superficial wound infection (3.3%), urinary retention (1.3%), headache (6.7%), and urine or chest infection (4.7%). Follow-up data were available for all patients (93% to 12 months, 72% to 24 months). Persistent neuropathic symptoms were reported in 6.5% at 24 months. Conclusions SDR using a single-level approach is a safe procedure with low surgical morbidity. This study complements the growing evidence base in support of SDR for spastic diplegia and should help inform decisions when considering treatment options.

Diversion of cerebrospinal fluid (CSF) has been used for decades as a treatment for children with severe traumatic brain injury (TBI) and is recommended by evidenced-based guidelines. However, these recommendations are based on limited studies.To determine whether CSF diversion is associated with improved Glasgow Outcome Score-Extended for Pediatrics (GOS-EP) and decreased intracranial pressure (ICP) in children with severe TBI.This observational comparative effectiveness study was performed at 51 clinical centers that routinely care for children with severe TBI in 8 countries (US, United Kingdom, Spain, the Netherlands, Australia, New Zealand, South Africa, and India) from February 2014 to September 2017, with follow-up at 6 months after injury (final follow-up, October 22, 2021). Children with severe TBI were included if they had Glasgow Coma Scale (GCS) scores of 8 or lower, had intracranial pressure (ICP) monitor placed on-site, and were aged younger than 18 years. Children were excluded if they were pregnant or an ICP monitor was not placed at the study site. Consecutive children were screened and enrolled, data regarding treatments were collected, and at discharge, consent was obtained for outcomes testing. Propensity matching for pretreatment characteristics was performed to develop matched pairs for primary analysis. Data analyses were completed on April 18, 2022.Clinical care followed local standards, including the use of CSF diversion (or not), with patients stratified at the time of ICP monitor placement (CSF group vs no CSF group).The primary outcome was GOS-EP at 6 months, while ICP was considered as a secondary outcome. CSF vs no CSF was treated as an intention-to-treat analysis, and a sensitivity analysis was performed for children who received delayed CSF diversion.A total of 1000 children with TBI were enrolled, including 314 who received CSF diversion (mean [SD] age, 7.18 [5.45] years; 208 [66.2%] boys) and 686 who did not (mean [SD] age, 7.79 [5.33] years; 437 [63.7%] boys). The propensity-matched analysis included 98 pairs. In propensity score-matched analyses, there was no difference between groups in GOS-EP (median [IQR] difference, 0 [-3 to 1]; P = .08), but there was a decrease in overall ICP in the CSF group (mean [SD] difference, 3.97 [0.12] mm Hg; P .001).In this comparative effectiveness study, CSF diversion was not associated with improved outcome at 6 months after TBI, but a decrease in ICP was observed. Given the higher quality of evidence generated by this study, current evidence-based guidelines related to CSF diversion should be reconsidered.

Damage to the cerebellum during posterior fossa surgery can lead to ataxia and in paediatric cases, the risk of cerebellar mutism syndrome. Animal electrophysiological and human imaging studies have shown compartmentalisation of sensorimotor and cognitive functions within the cerebellum. In the present study, electrophysiological monitoring of sensory and motor pathways was carried out to assess the location of limb sensorimotor representation within the human cerebellum, as a potential approach for real time assessment of neurophysiological integrity to reduce the incidence of cerebellar surgical morbidities.Thirteen adult and paediatric patients undergoing posterior fossa surgery were recruited. For sensory mapping (n=8), electrical stimulation was applied to the median nerves, the posterior tibial nerves, or proximal and distal limb muscles and evoked field potential responses were sought on the cerebellar surface. For motor mapping (n=5), electrical stimulation was applied to the surface of the cerebellum and evoked EMG responses were sought in facial and limb muscles.Evoked potentials on the cerebellar surface were found in two patients (25% of cases). In one patient, the evoked response was located on the surface of the right inferior posterior cerebellum in response to stimulation of the right leg. In the second patient, stimulation of the extensor digitorum muscle in the left forearm evoked a response on the surface of the left inferior posterior lobe. In the motor mapping cases no evoked EMG responses could be found.Intraoperative electrophysiological mapping, therefore, indicates it is possible to record evoked potentials on the surface of the human cerebellum in response to peripheral stimulation.

OBJECTIVE The object of this study was to determine the short- and long-term efficacy of primary endoscopic third ventriculostomy (ETV) on cognition and gait in adults with chronic obstructive hydrocephalus. METHODS Patients were prospectively accrued through the Adult Hydrocephalus Clinical Research Network patient registry. Patients with previously untreated congenital or acquired obstructive hydrocephalus were included in this study. Gait velocity was assessed using a 10-m walk test. Global cognition was assessed with the Montreal Cognitive Assessment (MoCA). Only patients with documented pre- and post-ETV gait analysis and/or pre- and post-ETV MoCA were included. RESULTS A total of 74 patients had undergone primary ETV, 42 of whom were analyzed. The remaining 32 patients were excluded, as they could not complete both pre- and post-ETV assessments. The mean age of the 42 patients, 19 (45.2%) of whom were female, was 51.9 ± 17.1 years (range 19–79 years). Most patients were White (37 [88.1%]), and the remainder were Asian. Surgical complications were minor. Congenital etiologies occurred in 31 patients (73.8%), with aqueductal stenosis in 23 of those patients (54.8%). The remaining 11 patients (26.2%) had acquired cases. The gait short-term follow-up cohort (mean 4.7 ± 4.1 months, 35 patients) had a baseline median gait velocity of 0.9 m/sec (IQR 0.7–1.3 m/sec) and a post-ETV median velocity of 1.3 m/sec (IQR 1.1–1.4 m/sec). Gait velocity significantly improved post-ETV with a median within-patient change of 0.3 m/sec (IQR 0.0–0.6 m/sec, p < 0.001). Gait velocity improvements were sustained in the long term (mean 14 ± 2.8 months, 12 patients) with a baseline median velocity of 0.7 m/sec (IQR 0.6–1.3 m/sec), post-ETV median of 1.3 m/sec (IQR 1.1–1.7 m/sec), and median within-patient change of 0.4 m/sec (IQR 0.2–0.6 m/sec, p < 0.001). The cognitive short-term follow-up cohort (mean 4.6 ± 4.0 months, 38 patients) had a baseline median MoCA total score (MoCA TS) of 24/30 (IQR 23–27) that improved to 26/30 (IQR 24–28) post-ETV. The median within-patient change was +1 point (IQR 0–2 points, p < 0.001). However, this change is not clinically significant. The cognitive long-term follow-up cohort (mean 14 ± 3.1 months, 15 patients) had a baseline median MoCA TS of 23/30 (IQR 22–27), which improved to 26/30 (IQR 25–28) post-ETV. The median within-patient change was +2 points (IQR 1–3 points, p = 0.007), which is both statistically and clinically significant. CONCLUSIONS Primary ETV can safely improve symptoms of gait and cognitive dysfunction in adults with chronic obstructive hydrocephalus. Gait velocity and global cognition were significantly improved, and the worsening of either was rare following ETV.

Short linear motifs (SLiMs) are important mediators of interactions between intrinsically disordered regions of proteins and their interaction partners. Here, we detail instructions for the computational prediction of SLiMs in disordered protein regions, using the main tools of the SLiMSuite package: (1) SLiMProb identifies and calculates enrichment of predefined motifs in a set of proteins; (2) SLiMFinder predicts SLiMs de novo in a set of proteins, accounting for evolutionary relationships; (3) QSLiMFinder increases SLiMFinder sensitivity by focusing SLiM prediction on a specific query protein/region; (4) CompariMotif compares predicted SLiMs to known SLiMs or other SLiM predictions to identify common patterns. For each tool, command-line and online server examples are provided. Detailed notes provide additional advice on different applications of SLiMSuite, including batch running of multiple datasets and conservation masking using alignments of predicted orthologues.

Background: When appropriately selected, a high proportion of patients with suspected idiopathic normal pressure hydrocephalus (iNPH) will respond to cerebrospinal fluid diversion with a shunt. Extended lumbar drainage (ELD) is regarded as the most accurate test for this condition, however, varying estimates of its accuracy are found in the current literature. Here, we review the literature in order to provide summary estimates of sensitivity, specificity, positive- and negative predictive value for this test through meta-analysis of suitably rigorous studies. Methods: Studies involving a population of NPH patients with predominantly idiopathic aetiology (>80%) in which the intention of the study was to shunt patients regardless of the outcome of ELD were included in the review. Various literature databases were searched to identify diagnostic test accuracy studies addressing ELD in the diagnosis of iNPH. Those studies passing screening and eligibility were assessed using the QUADAS-2 tool and data extracted for bivariate random effects meta-analysis. Results: Four small studies were identified. They showed disparate results concerning diagnostic test accuracy. The summary estimates for sensitivity and specificity were 94% (CI 41-100%) and 85% (CI 33-100%), respectively. The summary estimates of positive and negative predictive value were both 90% (CIs 65-100% and 48-100%, respectively). Conclusion: Large, rigorous studies addressing the diagnostic accuracy of ELD are lacking, and little robust evidence exists to support the use of ELD in diagnostic algorithms for iNPH. Therefore, a large cohort study, or ideally an RCT, is needed to determine best practice in selecting patients for shunt surgery.

Central nervous system germ cell tumors (GCTs) are a relatively rare and heterogeneous group of tumors. In general, they are more commonly seen in the Asian population, have a male preponderance, and commonly occur in the pineal or suprasellar regions. They are a unique group of tumors in which the combination of imaging characteristics and serum or cerebrospinal fluid tumor markers allows for presumptive treatment by radiation and chemotherapy without a confirmatory tissue diagnosis. Cases with negative markers require further investigation via biopsy. Excluding mature teratoma, the mainstay of treatment for this group of tumors is radiation therapy and neoadjuvant chemotherapy. Neurosurgical interventions are reserved for treatment of hydrocephalus, negative-marker tumor biopsy, resection of mature teratoma, and second-look surgery when residual tumor is present after completion of chemoradiation. This chapter discusses the epidemiology, diagnosis, and treatment of intracranial GCTs.

The cerebellum is involved in a wide range of behaviours. A key organisational principle from animal studies is that somatotopically corresponding sensory input and motor output reside in the same cerebellar cortical areas. However, compelling evidence for a similar arrangement in humans and whether it extends to cognitive functions is lacking. To address this, we applied cerebellar optimised whole‐brain functional MRI in 20 healthy subjects. To assess spatial overlap within the sensorimotor and cognitive domains, we recorded activity to a sensory stimulus (vibrotactile) and a motor task; the Sternberg verbal working memory (VWM) task; and a verb generation paradigm. Consistent with animal data, sensory and motor activity overlapped with a somatotopic arrangement in ipsilateral areas of the anterior and posterior cerebellum. During the maintenance phase of the Sternberg task, a positive linear relationship between VWM load and activity was observed in right Lobule VI, extending into Crus I bilaterally. Articulatory movement gave rise to bilateral activity in medial Lobule VI. A conjunction of two independent language tasks localised activity during verb generation in right Lobule VI‐Crus I, which overlapped with activity during VWM. These results demonstrate spatial compartmentalisation of sensorimotor and cognitive function in the human cerebellum, with each area involved in more than one aspect of a given behaviour, consistent with an integrative function. Sensorimotor localisation was uniform across individuals, but the representation of cognitive tasks was more variable, highlighting the importance of individual scans for mapping higher order functions within the cerebellum.

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Inadequate penetration of the blood-brain barrier (BBB) by systemically administered chemotherapies including carboplatin is implicated in their failure to improve prognosis for patients with glioblastoma. Convection-enhanced delivery (CED) of carboplatin has the potential to improve outcomes by facilitating bypass of the BBB.We report the first use of an implantable CED system incorporating a novel transcutaneous bone-anchored port (TBAP) for intermittent CED of carboplatin in a patient with recurrent glioblastoma.The CED catheter system was implanted using a robot-assisted surgical method. Catheter targeting accuracy was verified by performing intra-operative O-arm imaging. The TBAP was implanted using a skin-flap dermatome technique modeled on bone-anchored hearing aid surgery. Repeated infusions were performed by attaching a needle administration set to the TBAP. Drug distribution was monitored with serial real-time T2-weighted magnetic resonance imaging (MRI).All catheters were implanted to within 1.5 mm of their planned target. Intermittent infusions of carboplatin were performed on three consecutive days and repeated after one month without the need for further surgical intervention. Infused volumes of 27.9 ml per day were well tolerated, with the exception of a single seizure episode. Follow-up MRI at eight weeks demonstrated a significant reduction in the volume of tumor enhancement from 42.6 ml to 24.6 ml, and was associated with stability of the patient's clinical condition.Reduction in the volume of tumor enhancement indicates that intermittent CED of carboplatin has the potential to improve outcomes in glioblastoma. The novel technology described in this report make intermittent CED infusion regimes an achievable treatment strategy.

Objectives The indications for surgery and outcomes of patients who underwent surgical removal of subependymal giant cell astrocytomas (SEGAs) in our institution between 2000 and 2011 were reviewed. Methods We reviewed the clinical details of 16 patients with a diagnosis of Tuberous Sclerosis Complex (TSC) who underwent surgery for SEGA in Bristol since 2000. We collected information on age, sex, epilepsy history and cognitive status. We reviewed the indications for surgery, age at surgery, surgical approach, and the size and location of the lesions. We analysed mortality, completeness of tumour resection, intraoperative blood transfusion, shunt placements, and surgical complications. Results 13 patients had surgery due to hydrocephalus. Increasing size of SEGA without hydrocephalus was an indication for surgery in two patients, and in one patient, the SEGA was removed because of its size and location at initial scan. 13 patients had complete tumour resection. One patient had tumour recurrence. Hydrocephalus failed to resolve or reoccurred in four patients post operatively necessitating shunt insertion. The surgical approach was transcortical in 14 patients and transcallosal in two. There was zero mortality in this series. There were no reports of cognitive decline or worsening epilepsy following surgery. Conclusion Surgery is a safe and effective treatment for SEGA. It is the authors' view that surgery remains the most appropriate treatment strategy for SEGAs that are amenable to surgery. More work needs to be undertaken to assess prospectively the neurocognitive impact of surgery, and the relative advantages of different surgical approaches.

ObjectiveIndicators for head CT scan defined by the 2007 National Institute for Health and Care Excellence (NICE) guidelines were analysed to identify CT uptake, influential variables and yield.DesignCross-sectional study.SettingHospital inpatient units: England, Wales, Northern Ireland and the Channel Islands.PatientsChildren (InterventionsCT scan.Main outcome measuresNumber of children who had CT, extent to which NICE guidelines were followed and diagnostic yield.ResultsData on 5700 children were returned by 90% of eligible hospitals, 84% of whom were admitted to a general hospital. CT scans were performed on 30.4% of children (1734), with a higher diagnostic yield in infants (56.5% (144/255)) than children aged 1 to 14 years (26.5% (391/1476)). Overall, only 40.4% (984 of 2437 children) fulfilling at least one of the four NICE criteria for CT actually underwent one. These children were much less likely to receive CT if admitted to a general hospital than to a specialist centre (OR 0.52 (95% CI 0.45 to 0.59)); there was considerable variation between healthcare regions. When indicated, children >3 years were much more likely to have CT than those ConclusionCompliance with guidelines and diagnostic yield was variable across age groups, the type of hospital and region where children were admitted. With this pattern of clinical practice the risks of both missing intracranial injury and overuse of CT are considerable.

Streptococcus pneumoniae is a commensal human pathogen and the causative agent of various invasive and noninvasive diseases. Carriage of the pneumococcus in the nasopharynx is thought to be mediated by biofilm formation, an environment where isogenic populations frequently give rise to morphological colony variants, including small colony variant (SCV) phenotypes. We employed metabolic characterization and whole-genome sequencing of biofilm-derived S. pneumoniae serotype 22F pneumococcal SCVs to investigate diversification during biofilm formation. Phenotypic profiling revealed that SCVs exhibit reduced growth rates, reduced capsule expression, altered metabolic profiles, and increased biofilm formation compared to the ancestral strain. Whole-genome sequencing of 12 SCVs from independent biofilm experiments revealed that all SCVs studied had mutations within the DNA-directed RNA polymerase delta subunit (RpoE). Mutations included four large-scale deletions ranging from 51 to 264 bp, one insertion resulting in a coding frameshift, and seven nonsense single-nucleotide substitutions that result in a truncated gene product. This work links mutations in the rpoE gene to SCV formation and enhanced biofilm development in S. pneumoniae and therefore may have important implications for colonization, carriage, and persistence of the organism. Furthermore, recurrent mutation of the pneumococcal rpoE gene presents an unprecedented level of parallel evolution in pneumococcal biofilm development.

Object The evaluation of third ventriculostomy function in hydrocephalic patients is challenging. The utility of the constant flow infusion test in predicting response to shunt insertion in normal-pressure hydrocephalus, as well as in identifying shunt malfunction, has been previously demonstrated. The object of this study was to evaluate its usefulness in determining whether a revision CSF diversion procedure was indicated in patients presenting with recurring symptoms and persisting ventriculomegaly after endoscopic third ventriculostomy (ETV). Methods The authors conducted a prospective study of all patients who, after undergoing ETV at their institution, presented postoperatively with recurring symptoms and persisting ventriculomegaly. Results Forty-six patients (mean age 40.7 years, including 11 patients younger than 18 years) underwent 56 constant flow ventricular infusion tests (VITs) at a mean of 24.7 months post-ETV. Thirty-three patients with resistance to CSF outflow (Rout) less than 13 mm Hg/ml/min underwent follow-up (median 17 months) and experienced resolution of symptoms. In 10 episodes Rout was greater than 13 mm Hg/ml/min; the patients in these cases underwent revisional CSF diversion. Two patients demonstrated high and frequent B (slow) waves despite a low Rout; these patients also underwent successful revisions. Patients who improved after surgery had increased B wave activity in the plateau phase of the VIT (p = 0.01). Thirty-four patients underwent MR imaging at the same time; 4 had high Rout despite evidence of flow across the stoma. These 4 patients underwent surgery and experienced resolution of symptoms. Of 9 patients without flow, Rout was less than 13 mm Hg/ml/min in 4; these patients were successfully treated conservatively. Conclusions The VIT is a useful and safe adjunct to clinical and MR imaging evaluation when ETV failure is suspected.

Atmospheric carbon dioxide (CO

Object Intracranial pressure (ICP) monitors are currently based on fluid-filled, strain gauge, or fiberoptic technology. Capacitive sensors have minimal zero drift and energy requirements, allowing long-term implantation and telemetric interrogation; their application to neurosurgery has only occasionally been reported. The aim of this study was to undertake a preliminary in vitro and in vivo evaluation of a capacitive telemetric implantable ICP monitor. Methods Four devices were tested in air- and saline-filled pressure chambers; long-term capacitance-pressure curves were obtained. Devices implanted in a gel phantom and in a piglet were placed in a 3-T MR unit to evaluate MR compatibility. Four devices were implanted in a piglet neonatal hydrocephalus model; output was compared with ICP obtained through fluid-filled transduction and a strain-gauge ICP monitor. Results The capacitance-pressure relationship was constant over 4 weeks, suggesting minimal zero drift during this period. There were no temperature changes around the monitor. Signal loss at the sensor was minimal in both the phantom and the piglet. Over 114,000 measurements were obtained; the difference between mean capacitive ICP and fluid-transduced ICP was 1.8 ± 1.42 mm Hg. The correlation between ICP from the capacitive sensor and fluid-filled transducer (r = 0.97, p < 0.0001) or strain-gauge monitor (r = 0.99, p < 0.0001) was excellent. In vivo monitoring was restricted to 48 hours due to problems with robustness in the clinical environment. Conclusions This preliminary study demonstrates minimal long-term zero drift in vitro, good MR compatibility, and good correlation with other methods of ICP monitoring in vivo in the short term. Further long-term in vivo study is required.

Many important cellular processes involve protein–protein interactions (PPIs) mediated by a Short Linear Motif (SLiM) in one protein interacting with a globular domain in another. Despite their significance, these domain-motif interactions (DMIs) are typically low affinity, which makes them challenging to identify by classical experimental approaches, such as affinity pulldown mass spectrometry (AP-MS) and yeast two-hybrid (Y2H). DMIs are generally underrepresented in PPI networks as a result. A number of computational methods now exist to predict SLiMs and/or DMIs from experimental interaction data but it is yet to be established how effective different PPI detection methods are for capturing these low affinity SLiM-mediated interactions. Here, we introduce a new computational pipeline (SLiM-Enrich) to assess how well a given source of PPI data captures DMIs and thus, by inference, how useful that data should be for SLiM discovery. SLiM-Enrich interrogates a PPI network for pairs of interacting proteins in which the first protein is known or predicted to interact with the second protein via a DMI. Permutation tests compare the number of known/predicted DMIs to the expected distribution if the two sets of proteins are randomly associated. This provides an estimate of DMI enrichment within the data and the false positive rate for individual DMIs. As a case study, we detect significant DMI enrichment in a high-throughput Y2H human PPI study. SLiM-Enrich analysis supports Y2H data as a source of DMIs and highlights the high false positive rates associated with naïve DMI prediction. SLiM-Enrich is available as an R Shiny app. The code is open source and available via a GNU GPL v3 license at: https://github.com/slimsuite/SLiMEnrich. A web server is available at: http://shiny.slimsuite.unsw.edu.au/SLiMEnrich/.

STUDY DESIGN.: Observational study. Retrospective analysis of prospectively collected data. OBJECTIVE.: The purpose of this article was to report long-term (minimum 7 years) clinical and radiologic outcome of our series of patients with Rheumatoid Arthritis who underwent transarticular screw fixation to treat atlantoaxial subluxation. SUMMARY OF BACKGROUND DATA.: The indications for intervention in patients with atlantoaxial instability are pain, myelopathy, and progressive neurologic deficit. The various treatment options available for these patients are isolated C1-C2 fusion, occipitocervical fusion with or without transoral surgery. Review of current literature suggests that C1-C2 transarticular screw fixation has significant functional benefits, although there is discrepancy in this literature regarding improvement in function following surgery. METHODS.: Myelopathy was assessed using Ranawat myelopathy score and Myelopathy Disability Index. Pain scores were assessed using Visual Analogue Scale. The radiologic imaging was assessed and the following data were extracted; atlanto-dens interval, space available for cord, presence of signal change on T2 weighted image, and fusion rates. RESULTS.: Thirty-seven patients, median age 56, were included in the study. Average duration of neck symptoms was 15.8 months. Average duration of rheumatoid arthritis before surgery was 20.6 years. Preoperative symptoms: suboccipital pain in 26 patients; neck pain, 32; myelopathy, 22; and 5 were asymptomatic. After surgery: suboccipital pain, 2; neck pain, 3; and myelopathy, 10. Ninety percent patients with neck and suboccipital pain improved after surgery in their Visual Analogue pain scores, with all of them having >50% improvement in VAS scores (6.94-2.12 [P < 0.05]).Preoperative Ranawat grade was as follows: grade 1 in 15 patients, grade 2 in 7, and grade 3a in 14, grade 3b in 1.After surgery: grade 1 in 27 patients, grade 2 in 7, grade 3a in 1, and grade 3b in 2. The mean myelopathy score improved after surgery (59.62-32.75, P < 0.05).The space available for the cord was improved in 63%, unchanged in 33%, and worse in 4%.Twenty-seven percent had T2 signal change and 18% had cervicomedullary compression; 97% had bony fusion. BILATERAL SCREWS WERE USED IN 33 PATIENTS AND UNILATERAL SCREWS IN 4 PATIENTS (ABERRANT VERTEBRAL ARTERY).: Computer image guidance was used in 73%. CONCLUSION.: C1-C2 transarticular screw fixation is a safe technique for atlantoaxial subluxation for patients with rheumatoid arthritis. This study clearly demonstrates improvement in Visual Analogue Scale, Ranawat grading and the Myelopathy Disability Index even at long-term follow up.

BackgroundThe National Confidential Enquiry describes the epidemiology of children admitted to hospital with head injury.MethodChildren (4 h with head injury were identified from 216 UK hospitals (1 September 2009 to 28 February 2010). Data were collected using standard proformas and entered on to a database. A descriptive analysis of the causal mechanisms, child demographics, neurological impairment, CT findings, and outcome at 72 h are provided.ResultsDetails of 5700 children, median age 4 years (range 0–14.9 years), were analysed; 1093 (19.2%) were ConclusionsThe data described highlight priorities for targeted age-specific head injury prevention and have the potential to provide a baseline to evaluate the effects of regional trauma networks (2012) and National Institute of Health and Care Excellence (NICE) head injury guidelines (2014), which were revised after the study was completed.