Skull base angiomatous leiomyoma: a case report and review of literature.

Leiomyomas, benign neoplasms of mesenchymal origin, are common in gastrointestinal and genitourinary tracts. They are comprised of well-differentiated smooth muscle cells with few mitotic figures. Leiomyomas should not exhibit metastatic potential, though metastasis has been reported. Primary intracranial lesions remain rare. Only 4 cases have been reported in immunocompetent patients. Here we report an intracranial leiomyoma in an immunocompetent patient. A 60 year-old woman with unremarkable past medical history presented with a right sixth nerve palsy. On examination, there was a right sixth nerve palsy with numbness over the right V2 and V3 areas. CT scan showed a well-defined lesion within the right middle cranial fossa adjacent to the cavernous sinus with bony remodelling of the lateral wall of the sphenoid sinus and greater wing of the right sphenoid. MRI showed extra axial mass lesion arising from the right Meckel´s cave/cavernous sinus. The lesion was T2 hyperintense and T1 isointense. Homogenously enhancing centrally with little enhancement peripherally. CT CAP showed no primary lesions. Differential diagnosis at that stage was between meningioma, schwannoma or metastasis. The patient underwent craniotomy and debulking of tumour. Histological analysis confirmed leiomyoma. Post-operative MRI showed residual enhancement in the region of Meckel's cave. As residual tumour was significant, the patient underwent STRS. Further MRI at 1 year showed regression of the tumour. Majority of intracranial leiomyomas are discovered in immunocompromised patients incidentally. Histology reveals spindle shaped cells with blunt ends and few mitotic figures. The best treatment option to date for primary intracranial leiomyomas remains surgical gross total resection without adjuvant radiation therapy. Intracranial leiomyoma transitioning to leiomyosarcoma post radiotherapy has been reported before and therefore follow up with serial imaging is warranted.

Long-term safety of gamma knife radiosurgery (SRS) for acromegaly.

PURPOSE: Acromegaly has high morbidity and mortality when growth hormone secretion remains uncontrolled. Stereotactic radiosurgery (SRS) may be used when pituitary surgery is not suitable or unsuccessful, but there are few very long-term safety data available, especially for significant adverse events such as stroke. METHODS: 118 patients with acromegaly were treated with SRS between 1985 and 2015, at the National Centre for Stereotactic Radiosurgery, Sheffield, UK. Data were gathered from case notes, hospital databases, and patient questionnaires. Stroke incidence in comparison to the normal population was quantified using the standardised incidence ratio (SIR), and visual complications assessed. RESULTS: 88% (104/118) had complete morbidity follow up data for analysis. The mean follow-up was 134 months, and median SRS dose was 30 Gy. 81% of tumours had cavernous sinus invasion. There was no excess stroke rate relative to that seen in two age- and sex-matched large population studies (SIR = 1.36, 95% CI 0.27-3.96; SIR = 0.52, 95% CI 0.06-1.89). In 68/104 patients who had MRI-guided SRS with no further radiation treatment (SRS or fractionated radiotherapy) there was no loss of visual acuity and 3% developed ophthalmoplegia. There was a positive correlation between > 1 radiation treatment and both ophthalmoplegia and worsening visual acuity. CONCLUSION: Stroke rate is not increased by SRS for acromegaly. Accurate MRI-based treatment planning and single SRS treatment allow the lowest complication rates. More than one radiation treatment (SRS or fractionated radiotherapy) was associated with increased visual complications.

ITTREAT (Integrated Community Test - Stage - TREAT) Hepatitis C service for people who use drugs: Real-world outcomes.

BACKGROUND/AIMS: Direct-acting antivirals (DAAs) provide an unprecedented opportunity for a "find-and-treat strategy." We aimed to report real-world clinical, patient reported and health economic outcomes of community-based hepatitis C virus (HCV) screening/treatment in people who use drugs (PWUDs). METHODS: Project ITTREAT (2013-2021), established at a drug and alcohol treatment centre, offered a comprehensive service. Generic (SF-12v2 and EQ-5D-5L) and liver-specific (SFLDQoL) health-related quality of life (HRQoL) were assessed before and after HCV treatment. Costs/case detected and cured were calculated. Primary outcome measure was sustained virological response (SVR) (intention to treat). RESULTS: Till March 2018, 573 individuals recruited, 462 (81%) males, mean age 40.5 ± 10.0 years. Of the 125 treated, 115 (92%) had past/current history of injecting drug use, 88 (70%) were receiving opioid agonist treatment and 50 (40%) were homeless. Twenty-six per cent received interferon-based and 74% DAA-only regimens. SVR (ITT) was 87% (90% with DAAs). Service uptake/HCV treatment completion rates were >95%, HCV reinfection being 2.63/100 person years (95% CI 0.67-10.33). HRQoL improved significantly at end of treatment (EOT) in those with SVR: SFLDQoL (symptoms, memory, distress, loneliness, hopelessness, sleep and stigma) (P

Radiosurgery as primary management for acromegaly.

OBJECTIVE: Transsphenoidal surgery (TSS) remains the recommended primary treatment for acromegaly. Long-term outcome data are not available for patients treated with gamma knife radiosurgery (STRS) as a primary treatment. DESIGN: Retrospective cohort study. DATA COLLECTION: notes review, laboratory results, general physician notes, patient questionnaire and death certification. PATIENTS: Twenty acromegaly patients underwent primary STRS at the National Centre for Radiosurgery, Sheffield, UK, between 1985 and 2015. MEASUREMENTS: Biochemical control (GH/IGF1), hypopituitarism, morbidity and mortality were all recorded. RESULTS: At 20 years of follow-up, control was seen in all on acromegaly-specific medication (n = 12) and 75% of those off medication (3/4). Time for 50% to achieve control on medication was 3 years, and 7.4 years off medication. Median marginal radiation dose was 27.5 Gy, and median follow-up was 166.5 months. 53% of patients developed new hypopituitarism at a median follow-up of 146 months, and the development of first onset of hypopituitarism occurred as late as 20 years after treatment. With MRI planning, no other complications were noted. Three patients underwent subsequent TSS due to poor biochemical control. During follow-up, 7 patients died at a median age of 65 years. There were no STRS-related deaths. CONCLUSION: This is the longest follow-up of patients who have undergone primary STRS for acromegaly. It shows low morbidity, but significant latency to biochemical control and new-onset hypopituitarism. This mandates very long-term follow-up for these patients. STRS has shown good long-term efficacy providing initial control can be afforded by optimal medical management. While TSS remains best practice, STRS offers an alternative for those in whom surgery is not an option.

Deep brain stimulation of the periaqueductal gray releases endogenous opioids in humans.

Deep brain stimulation (DBS) of the periaqueductal gray (PAG) is used in the treatment of severe refractory neuropathic pain. We tested the hypothesis that DBS releases endogenous opioids to exert its analgesic effect using [11C]diprenorphine (DPN) positron emission tomography (PET). Patients with de-afferentation pain (phantom limb pain or Anaesthesia Dolorosa (n=5)) who obtained long-lasting analgesic benefit from DBS were recruited. [11C]DPN and [15O]water PET scanning was performed in consecutive sessions; first without, and then with PAG stimulation. The regional cerebral tracer distribution and kinetics were quantified for the whole brain and brainstem. Analysis was performed on a voxel-wise basis using statistical parametric mapping (SPM) and also within brainstem regions of interest and correlated to the DBS-induced improvement in pain score and mood. Brain-wide analysis identified a single cluster of reduced [11C]DPN binding (15.5% reduction) in the caudal, dorsal PAG following DBS from effective electrodes located in rostral dorsal/lateral PAG. There was no evidence for an accompanying focal change in blood flow within the PAG. No correlation was found between the change in PAG [11C]DPN binding and the analgesic effect or the effect on mood (POMSSV) of DBS. The analgesic effect of DBS in these subjects was not altered by systemic administration of the opioid antagonist naloxone (400ug). These findings indicate that DBS of the PAG does indeed release endogenous opioid peptides focally within the midbrain of these neuropathic pain patients but we are unable to further resolve the question of whether this release is responsible for the observed analgesic benefit.

Characterising the Analgesic Effect of Different Targets for Deep Brain Stimulation in Trigeminal Anaesthesia Dolorosa.

BACKGROUND: Several deep brain stimulation (DBS) targets have been explored for the alleviation of trigeminal anaesthesia dolorosa. We aimed to characterise the analgesia produced from the periaqueductal grey (PAG) and centromedian-parafascicular (CmPf) nucleus using a within-subject design. METHOD: We report a case series of 3 subjects implanted with PAG and CmPf DBS systems for the treatment of anaesthesia dolorosa. At follow-up, testing of onset and offset times, magnitude, and thermal and mechanical sensitivity was performed. RESULTS: The mean pain score of the cohort was acutely reduced by 56% (p < 0.05) with PAG and 67% (p < 0.01) with CmPf stimulation at mean time intervals of 38 and 16 min, respectively. The onset time was 12.5 min (p < 0.05) for PAG stimulation and 2.5 min (p < 0.01) for CmPf. The offset time was 2.5 min (p < 0.05) for PAG and 12.5 min (p < 0.01) for CmPf. The two targets were effective at different stimulation frequencies and were not antagonistic in effect. CONCLUSION: The mechanisms by which stimulation at these two targets produces analgesia are likely to be different. Certain pain qualities may respond more favourably to specific targets. Knowledge of onset and offset times for the targets can guide optimisation of stimulation settings. The use of more than one stimulation target may be beneficial and should be considered in anaesthesia dolorosa patients.

Ventriculostomy associated haemorrhage: a complication of anti-platelet therapy during coiling.

A young man with Fisher grade IV subarachnoid haemorrhage (SAH) underwent aneurysm coiling following external ventriculostomy. Coiling was complicated by thrombus formation and parent vessel occlusion necessitating anti-platelet therapy. Several hours after anti-platelet therapy, catastrophic haemorrhage associated with the ventriculostomy tract occurred. Timing and location of haemorrhage suggest combined anti-platelet therapy and ventriculostomy may have been causal. The literature on ventriculostomy haemorrhage rates and risks with concomitant anti-platelet therapy are reviewed. Where endovascular coiling is being considered, the possibility of ventriculostomy-related haemorrhage should be considered and should influence subsequent treatment decisions.

Operative Epidemiology of the First Five Years in a New African Neurosurgery Training Center: The Experience in Rural Kenya at Tenwek Hospital 2016 to 2021.

BACKGROUND: One strategy to increase the availability of neurosurgical services in underserved regions within Sub-Saharan African countries is to create new residency training programs outside of cosmopolitan cities where programs may already exist. In 2016 Tenwek Hospital in rural western Kenya began offering full-time neurosurgical services and in 2020 inaugurated a residency training program. This review highlights the operative epidemiology of the first 5 years of the hospital's neurosurgical department. METHODS: A retrospective review of all cases performed by a neurosurgeon at Tenwek Hospital between September 2016 and February 2022 was performed. Patient demographics, surgical indications, length of stay, and in-hospital mortality rates were collected. RESULTS: A total of 1756 cases were retrievable. Of these, 1006 (57.3%) were male and mean age was 30 years (range 1 day to 97 years). Mean length of stay was 11 ± 2 days and in-hospital mortality rate was 4.4% (77 patients). The most common pathologies in children comprised hydrocephalus and spina bifida (42.5% and 21.1%, respectively); in adults, cranial trauma (28.2%), oncology (25.2%), and degenerative spine (18.5%) were most common. Trauma was the leading cause of death. CONCLUSIONS: The neurosurgical caseload of a rural hospital in an underserved area can provide not only an adequate neurosurgical volume, but a robust and varied exposure that is necessary for training safe and competent surgeons who are willing to remain in their countries of origin.

Gender differences in hepatitis C seroprevalence and suboptimal vaccination and hepatology services uptake amongst substance misusers.

Injecting drug users are the principal at risk group for blood borne viruses. The aim was to assess the feasibility of screening substance misusers for blood borne viruses, and to offer appropriate vaccinations/referral to hepatology services. This was a nurse led prospective 6-month study based at a large Substance Misuse Service in south east England. Of the 196 consecutive individuals assessed, 81 were eligible for HBV immunization of whom only 33.3% completed a vaccination course. Prevalence of positive serological markers were: anti-HBc 14.4%, HBsAg 1.5%, and HCV antibody 37.9%. Compared to men, women were more likely to accept blood borne virus testing (83.3% vs. 62.3%), have ever injected (89.6% vs. 76.3%), overdose (54.2% vs. 23.6%), be anti-HBc positive (27.5% vs. 8.8%), drink alcohol above national recommended guidelines (41.7% vs. 25.7%), and have a positive HCV serology (55% vs. 30.4%) (P ≤ 0.05 for all). Of the 73 individuals identified with a positive HBsAg and or HCV antibody, only 14 (19.1%) were known to hepatology services and 8 (20%) of those eligible subsequently accepted a specialist referral. In conclusion, serological markers for blood borne viruses remain high in substance misusers (anti-HBc 14.4%, HCV antibody 37.9%), with women more likely to be positive. Overall, only 33.3% and 20%, respectively, complete HBV vaccination and accept a hepatology referral. A multidisciplinary approach is paramount to address both the blood borne viruses and the substance misuse and realignment of hepatitis services to Substance Misuse Services may offer such a strategy.

Supervised injectable heroin or injectable methadone versus optimised oral methadone as treatment for chronic heroin addicts in England after persistent failure in orthodox treatment (RIOTT): a randomised trial.

BACKGROUND: Some heroin addicts persistently fail to benefit from conventional treatments. We aimed to compare the effectiveness of supervised injectable treatment with medicinal heroin (diamorphine or diacetylmorphine) or supervised injectable methadone versus optimised oral methadone for chronic heroin addiction. METHODS: In this multisite, open-label, randomised controlled trial, we enrolled chronic heroin addicts who were receiving conventional oral treatment (>or=6 months), but continued to inject street heroin regularly (>or=50% of days in preceding 3 months). Randomisation by minimisation was used to assign patients to receive supervised injectable methadone, supervised injectable heroin, or optimised oral methadone. Treatment was provided for 26 weeks in three supervised injecting clinics in England. Primary outcome was 50% or more of negative specimens for street heroin on weekly urinalysis during weeks 14-26. Primary analysis was by intention to treat; data were adjusted for centre, regular crack use at baseline, and treatment with optimised oral methadone at baseline. Percentages were calculated with Rubin's rules and were then used to estimate numbers of patients in the multiple imputed samples. This study is registered, ISRCTN01338071. FINDINGS: Of 301 patients screened, 127 were enrolled and randomly allocated to receive injectable methadone (n=42 patients), injectable heroin (n=43), or oral methadone (n=42); all patients were included in the primary analysis. At 26 weeks, 80% (n=101) patients remained in assigned treatment: 81% (n=34) on injectable methadone, 88% (n=38) on injectable heroin, and 69% (n=29) on oral methadone. Patients on injectable heroin were significantly more likely to have achieved the primary outcome (72% [n=31]) than were those on oral methadone (27% [n=11], OR 7.42, 95% CI 2.69-20.46, p<0.0001; adjusted: 66% [n=28] vs 19% [n=8], 8.17, 2.88-23.16, p<0.0001), with number needed to treat of 2.17 (95% CI 1.60-3.97). For injectable methadone (39% [n=16]; adjusted: 30% [n=14]) versus oral methadone, the difference was not significant (OR 1.74, 95% CI 0.66-4.60, p=0.264; adjusted: 1.79, 0.67-4.82, p=0.249). For injectable heroin versus injectable methadone, a significant difference was recorded (4.26, 1.63-11.14, p=0.003; adjusted: 4.57, 1.71-12.19, p=0.002), but the study was not powered for this comparison. Differences were evident within the first 6 weeks of treatment. INTERPRETATION: Treatment with supervised injectable heroin leads to significantly lower use of street heroin than does supervised injectable methadone or optimised oral methadone. UK Government proposals should be rolled out to support the positive response that can be achieved with heroin maintenance treatment for previously unresponsive chronic heroin addicts. FUNDING: Community Fund (Big Lottery) Research section, through Action on Addiction.

The Amino Acid Changes T55A, A273P and R277C in the Beta-Lactamase CTX-M-14 Render E. coli Resistant to the Antibiotic Nitrofurantoin, a First-Line Treatment of Urinary Tract Infections.

The antibiotic nitrofurantoin is a furan flanked by a nitro group and a hydantoin ring. It is used to treat lower urinary tract infections (UTIs) that have a lifetime incidence of 50-60% in adult women. UTIs are typically caused by uropathogenic Escherichia coli (UPEC), which are increasingly expressing extended-spectrum beta-lactamases (ESBL), rendering them multi-drug resistant. Nitrofurantoin is a first-line treatment for gram-negative ESBL-positive UTI patients, given that resistance to it is still rare (0% to 4.4%). Multiplex PCR of ß-lactamase genes of the blaCTX-M groups 1, 2, 9 and 8/25 from ESBL-positive UTI patients treated at three referral hospitals in North Wales (UK) revealed the presence of a novel CTX-M-14-like gene harbouring the missense mutations T55A, A273P and R277C. While R277 is close to the active site, T55 and A273 are both located in external loops. Recombinant expression of CTX-M-14 and the mutated CTX-M-14 in the periplasm of E. coli revealed a significant increase in the Minimum Inhibitory Concentration (MIC) for nitrofurantoin from ≥6 µg/mL (CTX-M-14) to ≥512 µg/mL (mutated CTX-M-14). Consistent with this finding, the mutated CTX-M protein hydrolysed nitrofurantoin in a cell-free assay. Detection of a novel nitrofurantoin resistance gene indicates an emerging clinical problem in the treatment of gram-negative ESBL-positive UTI patients.

Comparison of Navigated versus Fluoroscopic-Guided Pedicle Screw Placement Accuracy and Complication Rate.

OBJECTIVES: Accurate placement of the pedicle screw is requisite for any successful spinal instrumentation procedure. Screw insertion can be achieved using free-hand and fluoroscopic- or navigation-guided techniques. We sought to assess the variation in accuracy between fluoroscopic- and navigation-guided techniques, which are both used in Sheffield Teaching Hospitals National Health Service Trust, a tertiary spine referral center. METHODS: Using a retrospective study design, we assessed all the pedicle screws placed between 2013 and 2018. Radiographic and clinical assessment of all cases was performed. RESULTS: We studied 176 spinal instrumented cases, with a total of 831 screws implanted, out of which 296 (35.6%) were navigated and 535 (64.4%) were fluoroscopic guided. Pathology treated included spinal stenosis, spondylolisthesis, tumors, and trauma. Suboptimal screw position was identified in 2.03% (n = 6) of the navigation-guided series and 4.11% (n = 22) of the fluoroscopic-guided series with an overall screw misplacement rate of 3.4%. Evaluating surgeons' individual accuracy rates revealed that suboptimal screw placement registered a higher variation for the fluoroscopy-guided technique, and the misplacement rate was higher for surgeons with a lower volume of cases. CONCLUSIONS: Use of navigation during spinal instrumentation helps lower the rate of screw misplacement for spinal surgeons who are at the beginning of their learning curve or do not frequently perform this kind of procedure. Navigation-guided spinal instrumentation is more accurate compared with fluoroscopic-guided techniques and appears to have a lower complication rate.

Developing a community HCV service: project ITTREAT (integrated community-based test - stage - TREAT) service for people who inject drugs.

Background and aims Majority of the individuals with hepatitis C virus (HCV) infection in England are people who inject drugs, a vulnerable and disenfranchised cohort with poor engagement with secondary care. Our aim is to describe our experiences in setting up a successful nurse led HCV service at a substance misuse service (SMS). METHODS: We justify the need for a community HCV service and review the different community based models. Our experiences in engaging with stakeholders, obtaining funding, service set up, challenges faced and key recommendations are discussed. Finally, a summary of interim clinical outcomes is presented. RESULTS: A successful community based "one-stop" nurse led HCV service was set up in Dec 2013 at a large SMS. It provides all aspects of care (blood borne virus screening, non-invasive assessment of hepatic fibrosis, Hepatology input, HCV treatment, peer mentor, social and psychiatrist support, and opiod substitution) at one site. Interim clinical data indicate high service uptake with HCV treatment outcomes comparable to secondary care. CONCLUSIONS: The advent of direct acting antivirals provides a unique opportunity for HCV elimination in England by 2030. Our "one-stop" integrated and multidisciplinary community HCV model suggests that HCV care can be successfully delivered outside of a hospital setting and warrants national adoption.

The Initiation Factors eIF2, eIF2A, eIF2D, eIF4A, and eIF4G Are Not Involved in Translation Driven by Hepatitis C Virus IRES in Human Cells.

Animal viruses have evolved a variety of strategies to ensure the efficient translation of their mRNAs. One such strategy is the use of internal ribosome entry site (IRES) elements, which circumvent the requirement for some eukaryotic initiation factors (eIFs). Much effort has been directed to unravel the precise mechanism of translation initiation by hepatitis C virus (HCV) mRNA. In the present study, we examined the involvement of several eIFs in HCV IRES-driven translation in human cells in a comparative analysis with mRNAs bearing the encephalomyocarditis virus or the Cricket paralysis virus IRES element. Consistent with previous findings, several inhibitors of eIF2 activity, including sodium arsenite, thapsigargin, tunicamycin, and salubrinal, had no inhibitory effect on the translation of an mRNA bearing the HCV IRES, and all induced the phosphorylation of eIF2α. In addition, hippuristanol and pateamine A, two known inhibitors of eIF4A, failed to block HCV IRES-directed translation. To test the release of nuclear proteins to the cytoplasm and to analyze the formation of stress granules, the location of the nuclear protein TIA1 was tested by immunocytochemistry. Both arsenite and pateamine A could efficiently induce the formation of stress granules containing TIA1 and eIF4G, whereas eIF3 and eIF2 failed to localize to these cytoplasmic bodies. The finding of eIF4A and eIF4G in stress granules suggests that they do not participate in mRNA translation. Human HAP1 cells depleted for eIF2A, eIF2D, or both factors, were able to synthesize luciferase from an mRNA bearing the HCV IRES even when eIF2α was phosphorylated. Overall, these results demonstrate that neither eIF2A nor eIF2D does not participate in the translation directed by HCV IRES. We conclude that eIF2, eIF4A, eIF2A, and eIF2D do not participate in the initiation of translation of HCV mRNA.

Renal Outcomes in Children with Operated Spina Bifida in Uganda.

BACKGROUND: To describe the extent of renal disease in Ugandan children surviving at least ten years after spina bifida repair and to investigate risk factors for renal deterioration in this cohort. PATIENTS AND METHODS: Children who had undergone spina bifida repair at CURE Children's Hospital of Uganda between 2000 and 2004 were invited to attend interview, physical examination, renal tract ultrasound, and a blood test (creatinine). Medical records were retrospectively reviewed. The following were considered evidence of renal damage: elevated creatinine, hypertension, and ultrasound findings of hydronephrosis, scarring, and discrepancy in renal size >1cm. Female sex, previous UTI, neurological level, mobility, detrusor leak point pressure, and adherence with clean intermittent catheterisation (CIC) were investigated for association with evidence of renal damage. RESULTS: 65 of 68 children aged 10-14 completed the assessment. The majority (83%) reported incontinence. 17 children (26%) were performing CIC. One child had elevated creatinine. 25 children (38%) were hypertensive. There was a high prevalence of ultrasound abnormalities: hydronephrosis in 10 children (15%), scarring in 42 (64%), and >1cm size discrepancy in 28 (43%). No children with lesions at S1 or below had hydronephrosis (p = 0.025), but this group had comparable prevalence of renal size discrepancy, scarring, and hypertension to those children with higher lesions. CONCLUSIONS: Incontinence, ultrasound abnormalities, and hypertension are highly prevalent in a cohort of Ugandan children with spina bifida, including those with low neurological lesions. These findings support the early and universal initiation of CIC with anticholinergic therapy in a low-income setting.

Clustered sequence representation for fast homology search.

We present a novel approach to managing redundancy in sequence databanks such as GenBank. We store clusters of near-identical sequences as a representative union-sequence and a set of corresponding edits to that sequence. During search, the query is compared to only the union-sequences representing each cluster; cluster members are then only reconstructed and aligned if the union-sequence achieves a sufficiently high score. Using this approach with BLAST results in a 27% reduction in collection size and a corresponding 22% decrease in search time with no significant change in accuracy. We also describe our method for clustering that uses fingerprinting, an approach that has been successfully applied to collections of text and web documents in Information Retrieval. Our clustering approach is ten times faster on the GenBank nonredundant protein database than the fastest existing approach, CD-HIT. We have integrated our approach into FSA-BLAST, our new Open Source version of BLAST (available from http://www.fsa-blast.org/). As a result, FSA-BLAST is twice as fast as NCBI-BLAST with no significant change in accuracy.

Comparing compressed sequences for faster nucleotide BLAST searches.

Molecular biologists, geneticists, and other life scientists use the BLAST homology search package as their first step for discovery of information about unknown or poorly annotated genomic sequences. There are two main variants of BLAST: BLASTP for searching protein collections and BLASTN for nucleotide collections. Surprisingly, BLASTN has had very little attention; for example, the algorithms it uses do not follow those described in the 1997 BLAST paper and no exact description has been published. It is important that BLASTN is state-of-the-art: Nucleotide collections such as GenBank dwarf the protein collections in size, they double in size almost yearly, and they take many minutes to search on modern general purpose workstations. This paper proposes significant improvements to the BLASTN algorithms. Each of our schemes is based on compressed bytepacked formats that allow queries and collection sequences to be compared four bases at a time, permitting very fast query evaluation using lookup tables and numeric comparisons. Our most significant innovations are two new, fast gapped alignment schemes that allow accurate sequence alignment without decompression of the collection sequences. Overall, our innovations more than double the speed of BLASTN with no effect on accuracy and have been integrated into our new version of BLAST that is freely available for download from http://www.fsa-blast.org/.

Using Intraoperative Ultrasonography for Spinal Cord Tumor Surgery.

BACKGROUND: Our aim was to evaluate the usefulness of modern intraoperative ultrasonography (iUS) in the resection of a wide variety of spinal intradural pathologic entities. METHODS: We evaluated patients with spinal cord disease treated between January 2006 and September 2015. Intraoperative standard B-mode images were acquired using a 3.5-MHz to 12-MHz ultrasonographic probes (linear and curvilinear) on various ultrasound machines. The benefits and disadvantages of iUS were assessed for each case. RESULTS: A total number of 158 intradural spinal lesions were operated on using iUS. Of these, 107 lesions (68%) were intradural extramedullary and 51 (32%) were intramedullary. All lesions were clearly visible using the ultrasound probe. The high-frequency linear probes (10-12 MHz) provided a better image quality compared with lower-frequency probes. Color and power-angiography modes were helpful in assessing the vascularization of the tumors and location of the major vessels in the vascular lesions. DISCUSSION: We document how iUS was used to facilitate safe and efficient spinal tumor resection at each stage of the operation. iUS was beneficial in confirmation of tumor location and extension, planning myelotomy, and estimation of degree of resection of the intramedullary tumors. It was particularly helpful in guiding the approach in redo surgeries for recurrent spinal cord tumors. CONCLUSIONS: iUS has a fast learning curve and offers additional intraoperative information that can help improve surgical accuracy and therefore may reduce procedure-related morbidity.

Quality of life among children with spina bifida in Uganda.

BACKGROUND: Children surviving after spina bifida repair often have significant disability, the consequences of which may be more profound in low-income countries. The aim of this cross-sectional study was to measure quality of life (QOL) reported by children with spina bifida in Uganda, and to define factors associated with QOL. METHODS: QOL was measured using both the Health Utilities Index (HUI3) Tool and a visual analogue scale (VAS) marked from 0 to 10. In keeping with the WHO definition of QOL, further analysis was conducted using subjective QOL scores (using the VAS). Multivariate regression was used to investigate the association between VAS scores and prespecified variables: age, sex, hydrocephalus, mobility, urinary continence, school attendance and family size. RESULTS: Sixty two of 68 surviving children aged 10-14 were able to complete all aspects of the assessment. There was poor correlation between the VAS and HUI3 Tool (Pearson correlation 0.488). On multivariate regression, the following variables were associated with a significant change in the 10-point VAS (change in score; 95% CI): male sex (-1.45; -2.436 to -0.465), urinary continence (1.681; 0.190 to 3.172), large family size (-1.775; -2.773 to -0.777) and hydrocephalus (-1.382; -2.374 to -0.465). CONCLUSIONS: Urinary continence and family size are potentially modifiable, the former by simple and inexpensive medical management. Enhanced investment in community-based rehabilitation and support is urgently needed. Delivery of family planning services is a national priority in Uganda, and should be discussed with families as part of holistic care.