Molybdenum Disulfide Nanoribbons with Enhanced Edge Nonlinear Response and Photoresponsivity

MoS₂ nanoribbons have attracted an increased interest due to their properties, which can be tailored by tuning their dimensions. Herein, we demonstrate the growth of MoS₂ nanoribbons and 3D triangular crystals formed by the reaction between ultra-thin films of MoO₃ grown by Pulsed Laser Deposition and NaF in a sulfur-rich environment. The multilayer nanoribbons can reach up to 10 μm in length, and feature single-layer edges, forming a monolayer-multilayer MoS₂ junction enabled by the lateral modulation in thickness. The single-layer edges of the nanoribbons show a pronounced second harmonic generation due to the symmetry breaking, in contrast to the centrosymmetric multilayer structure, which is unsusceptible to the second-order nonlinear process. A pronounced splitting of the Raman spectra was observed in MoS₂ nanoribbons arising from distinct contributions from the monolayer edges and multilayer core. Nanoscale imaging reveals a blue-shifted exciton emission of the monolayer edge compared to the triangular MoS₂ monolayers due to built-in local strain and disorder. We further report on an ultrasensitive photodetector made of a single MoS₂ nanoribbon with a responsivity of 8.72×10² A/W at 532 nm, among the highest reported up-to-date for single-nanoribbon photodetectors. Our findings can inspire the design of MoS₂ semiconductors with tunable geometries for efficient optoelectronic devices. This article is protected by copyright. All rights reserved.

Machine-learning algorithm in acute stroke: real-world experience

AIM

To assess the clinical performance of a commercially available machine learning (ML) algorithm in acute stroke.

MATERIALS AND METHODS

CT and CT angiography (CTA) studies of 104 consecutive patients (43 females, age range 19-93, median age 62) performed for suspected acute stroke at a single tertiary institution with real-time ML software analysis (RAPID™ ASPECTS and CTA) were included. Studies were retrospectively reviewed independently by two neuroradiologists in a blinded manner.

RESULTS

The cohort included 24 acute infarcts and 16 large vessel occlusions (LVO). RAPID™ ASPECTS interpretation demonstrated high sensitivity (87.5%) and NPV (87.5%) but very poor specificity (30.9%) and PPV (30.9%) for detection of acute ischaemic parenchymal changes. There was a high percentage of false positives (51.1%). In cases of proven LVO, RAPID™ ASPECTS showed good correlation with neuroradiologists' blinded independent interpretation, Pearson correlation coefficient = 0.96 (both readers), 0.63 (RAPID™ vs reader 1), 0.69 (RAPID™ vs reader 2). RAPID™ CTA interpretation demonstrated high sensitivity (92.3%), specificity (85.3%), and negative predictive (NPV) (98.5%) with moderate positive predictive value (PPV) (52.2%) for detection of LVO (N=13). False positives accounted for 12.5% of cases, of which 27.3% were attributed to arterial stenosis.

CONCLUSION

RAPID™ CTA was robust and reliable in detection of LVO. Although demonstrating high sensitivity and NPV, RAPID™ ASPECTS interpretation was associated with a high number of false positives, which decreased clinicians' confidence in the algorithm. However, in cases of proven LVO, RAPID™ ASPECTS performed well and had good correlation with neuroradiologists' blinded interpretation.

P12.03 A Delphi survey to inform core ‘red flag’ symptoms for an electronic patient reported outcome system in glioblastoma follow up

BACKGROUND

Glioblastoma is a common and aggressive primary malignant brain tumour in adults associated with a poor prognosis and considerable symptom burden. Clinical review and serial neuroimaging remain the primary monitoring tools to assess for disease status. However, the evidence base for the existing surveillance imaging schedule is yet to be established. New models of follow up care are needed to demonstrate better patient outcomes in this patient cohort. There are indications that patient-reported outcome measures (PROMs) can contribute to improved survival and maintaining an optimal quality of life in other oncology populations.

MATERIALS AND METHODS

There are no standardised PROMs for the priority symptoms in glioblastoma patients, which can be used for evaluation in clinical care as a surrogate marker for disease progression. A broad set of symptoms were therefore initially identified in a targeted literature search and were further refined via Delphi methodology, with the aim to obtain consensus amongst a small expert panel involved in the care of glioblastoma patients. A three round Delphi email survey was conducted. Consensus was defined as 70% agreement.

RESULTS

Symptom and function constructs were assessed for relevance, relationship to disease and treatment, sensitivity to change, psychometric properties and patient acceptability. Consensus was reached on the red flag symptoms and symptom clusters to monitor, as well as the minimum severity thresholds needed to trigger an alert on an electronic symptom reporting system, which has been developed to allow patient self-reporting of symptoms during treatment.

CONCLUSION

The red flag symptoms to monitor, along with the symptom severity thresholds, informed an app-based symptom reporting system, which is currently being piloted in a feasibility study exploring triggered imaging using ePROMs. This has the potential to inform future clinical practice through development of patient reported biomarkers.

O15: DISRUPTION OF THE BLOOD-SPINAL CORD BARRIER PREDICTS PERMANENT PARAPLEGIA AFTER THORACOABDOMINAL AORTIC ANEURYSM REPAIR

Introduction

Paraplegia post-thoracoabdominal aortic aneurysm (TAAA) repair remains both a devastating and poorly understood complication. We related temporal changes in cellular and protein composition of cerebrospinal fluid (CSF) to neurological outcomes after TAAA repair to gain mechanistic insights driving paraplegia.

Method

Patients undergoing TAAA repair (open or endovascular) with a CSF drain were prospectively recruited between 2016-2018. CSF was collected pre-operatively and 24-hourly until removal. Daily neurological examinations were performed by blinded neurologists to the study. CSF cell content was characterised by flow cytometry and proteome analysed by tandem-mass-tag proteomics. An in-vivo rat model was modified using 15 minutes of aortic occlusion to produce consistent paraplegia. Rats were analysed neuro-behaviourally and histologically.

Result

CSF was analysed from 52 patients (age: 70.27+/-11.4; 66% male; open (n=9), endovascular (n=43)). 12 developed paraplegia of whom 5 remained permanently-paraplegic. Demographics were comparable between paraplegics, those who recovered and without post-op neurology. Permanent paraplegia was associated with a significant infiltration of CSF CD45+ leucocytes (P<0.0001). Levels of ADVS-1 was >3-fold higher in permanent-paraplegics CSF versus those who recovered (P=0.0008). ADVS-1 >15ng/ml predicted permanent paraplegia with 100% specificity. Pre-treatment with ADVS-1 inhibition significantly improved walking (<0.001) and increased astrocytic staining in the lateral corticospinal, reticulospinal and rubrospinal tracts versus controls (P=0.03, 0.04, 0.04 respectively).

Conclusion

Permanent paraplegia is associated with shedding of ADVS-1 from parenchymal cord into CSF and blood/spinal-cord barrier disruption leading to cord oedema/leucocyte infiltration. Pre-treatment with ADVS-1 inhibition led to neurobehavioural and histological improvements offering translational hope for this devastating complication.

Take-home message

ADVS-1 is a novel biomarker of paraplegia where accurate biomarkers have proven challenging but more importantly it has proven a therapeutic target with genuine translational potential.

Pseudoxanthomonas winnipegensis sp. nov., derived from human clinical materials and recovered from cystic fibrosis and other patient types in Canada, and emendation of Pseudoxanthomonas spadix Young et al. 2007

Twelve isolates recovered from 10 cystic fibrosis/other patient types and a variety of clinical sources, were referred to Canada's National Microbiology Laboratory over 7 years. These were assignable to the genus Pseudoxanthomonas but were unidentifiable to species level. Patients included five males and five females from two geographically separated provinces, ranging in age from 2 months to 84 years. In contrast, most Pseudoxanthomonas species described to date have been derived from water, plants or contaminated soils. By 16S rRNA gene sequencing, the patient strains had ≥99.4 % similarity to each other but only 97.73-98.29 % to their closest relatives, Pseudoxanthomonas spadix or Pseudoxanthomonas helianthi. Bacteria were studied by whole genome sequencing using average nucleotide identity by Blastn, digital DNA-DNA hybridization, average amino acid identity, core genome and single nucleotide variant analyses, MALDI-TOF, biochemical and cellular fatty acid analyses, and by antimicrobial susceptibility testing. Bacterial structures were assessed using scanning and transmission electron microscopy. Strains were strict aerobes, yellowish-pigmented, oxidative, non-motile, Gram-stain-negative bacilli and generally unable to reduce nitrate. Strains were susceptible to most of the antibiotics tested; some resistance was observed towards carbapenems, several cephems and uniformly to nitrofurantoin. The single taxon group observed by 16S rRNA gene sequencing was supported by whole genome sequencing; genomes ranged in size from 4.36 to 4.73 Mb and had an average G+C content of 69.12 mol%. Based on this study we propose the name Pseudoxanthomonas winnipegensis sp. nov. for this cluster. Pseudoxanthomonas spadix DSM 18855^T, acquired for this study, was found to be non-motile phenotypically and by electron microscopy; we therefore propose the emendation of Pseudoxanthomonas spadix Young et al. 2007 to document that observation.

Congenital nasal pyriform aperture stenosis: Analysis of twenty cases at a single institution

OBJECTIVES

Congenital nasal pyriform aperture stenosis (CNPAS) is a rare cause of neonatal respiratory distress that is difficult to treat. The primary objective of this study was to identify factors that predict the need for initial and revision surgery for CNAPS. The secondary objective is to identify risk factors in maternal history associated with the development of CNPAS.

METHODS

Infants with CNPAS between 2010 and 2017 were identified by ICD- 9 and 10 codes. Demographics, maternal history, anatomic features on imaging and medical and/or surgical management were reviewed. Frequencies, means and standard deviations were calculated. A p-value <.05 was considered significant.

RESULTS

Twenty infants were included. All underwent flexible nasal endoscopy with inability to pass the scope in either nostril in 65% of infants. Nineteen had a CT scan and 13 had a MRI with midline defects in 76.3% and 53.8%, respectively. Solitary central mega-incisor was present in 65%. Half underwent surgical intervention at a mean age of 74.8 days, with 90% requiring revision surgery. There was no difference in pyriform aperture distance in the surgical and non-surgical patient subgroups (5.4 mm and 5.2 mm, p = .6 respectively). No specific variables were predictive of need for initial or revision surgery. Maternal diabetes mellitus (MDM) was found in 55% of mothers of infants with CNPAS.

CONCLUSION

Pyriform aperture distance was not a predictor of surgical intervention. MRI should be considered in all infants with CNPAS as the rate of intracranial complications is high. MDM may be a risk factor for CNPAS.

Intracranial complications of acute sinusitis in children: The role of endoscopic sinus surgery

OBJECTIVE

To study the role of endoscopic sinus surgery (ESS) in the management of intracranial complications of children with acute rhinosinusitis METHODS: Retrospective chart review at a tertiary care pediatric hospital MAIN OUTCOMES: Demographics, intracranial complications, length of hospital stay (LOS), neurological sequelae, ESS, neurosurgical procedures RESULTS: Twenty-four children with a mean age (SD) of 12.9 years (+/-3.2) with an intracranial complication(s) of acute rhinosinusitis were identified between 2005-2016. A total of 22 were included and 15 (68%) of these were males. The most common complications were: subdural abscess (n=10), epidural abscess (n=10), meningitis (n=5), intraparenchymal abscess (n=5), and cavernous sinus thrombosis (n= 2). Neurologic symptoms included headache (n=12), hemiparesis (n=5) and aphasia (n=3). Average length of stay was 16 (+/- 9.2) days. Average follow up was 7 (+/-5.6) months. One patient had residual seizures and 1 had recurrent rhinosinusitis. Aphasia and hemiparesis resolved in all patients within 1 year. Nineteen (86%) patients had ESS within 4 days of admission. Fourteen patients (63%) had a neurosurgical procedure, 6 (27%) required more than 1 neurosurgical procedure. Six patients (27%) had concurrent neurosurgical drainage and ESS. Four patients (17%) had neurosurgical procedure followed by ESS and 3 patients (13%) were treated only by a neurosurgical procedure. Patients who underwent ESS prior to a neurosurgical procedure had significantly less risk of needing a neurosurgical intervention (OR = .02, p < .01). There was a significantly higher proportion of neurosurgical patients with positive Strep anginosus cultures compared to the ESS only group (85.7% vs 37.5%, p = .02). Studies with larger patient populations are needed to determine the role of ESS in the management of intracranial complications of children with acute rhinosinusitis.

DISCUSSION

Early ESS may be associated with less need for neurosurgical procedures.

Think of the children: growing up with parents who have learning difficulties

This paper summarizes the findings of a research study that set out to explore how people who were brought up in a family headed by a parent or parents with learning difficulties managed the transition to adulthood. The authors focus on four key issues arising from their research: resilience in children, the notion of parental competence, the importance of family and the effects of social exclusion. Implications for policy and practice are also addressed.

Researching Policy Research

This article addresses the problems of exploring the use of research in the policy process. Measuring the impact or outcomes of policy research raises complex methodological and conceptual issues. How the task is approached and what measures are used depend, for example, on how the nature of the policy-making process is conceived, on what functions research is presumed to play in the making of policy, and on the way in which the relationship between research and policy is presented. Drawing on the wider literature in this field, this article describes and illustrates the three main methods that have been used for studying research use in the policy arena—impact studies, insider accounts, and case studies—and examines their strengths and weaknesses.

Tools and data services registry: a community effort to document bioinformatics resources

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.

Here we present a community-driven curation effort, supported by ELIXIR—the European infrastructure for biological information—that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.

As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform

Studying fungal biodiversity using data generated from Illumina MiSeq sequencing platforms poses a number of bioinformatic challenges with the analysis typically involving a large number of tools for each analytical step from quality filtering to generating identified operational taxonomic unit (OTU) abundance tables.Here, we introduce PIPITS, an open-source stand-alone suite of software for automated processing of Illumina MiSeq sequences for fungal community analysis. PIPITS exploits a number of state of the art applications to process paired-end reads from quality filtering to producing OTU abundance tables.We provide detailed descriptions of the pipeline and show its utility in the analysis of 9 396 092 sequences generated on the MiSeq platform from Illumina MiSeq. PIPITS is the first automated bioinformatics pipeline dedicated for fungal ITS sequences which incorporates ITSx to extract subregions of ITS and exploits the latest RDP Classifier to classify sequences against the curated UNITE fungal data set.

Higher-order mode fiber enables high energy chirped-pulse amplification

Energy scaling of femtosecond fiber lasers has been constrained by nonlinear impairments and optical fiber damage. Reducing the optical irradiance inside the fiber by increasing mode size lowers these effects. Using an erbium-doped higher-order mode fiber with 6000 µm(2) effective area and output fundamental mode re-conversion, we show a breakthrough in pulse energy from a monolithic fiber chirped pulse amplification system using higher-order mode propagation generating 300 µJ pulses with duration <500 fs (FWHM) and peak power >600 MW at 1.55 µm. The erbium-doped HOM fiber has both a record large effective mode area and excellent mode stability, even when coiled to reasonable diameter. This demonstration proves efficacy of a new path for high energy monolithic fiber-optic femtosecond laser systems.

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community

Background

A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure.

Results

Cloud BioLinux is a publicly accessible Virtual Machine (VM) that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms. Users have instant access to a range of pre-configured command line and graphical software applications, including a full-featured desktop interface, documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering, assembly, display, editing, and phylogeny. Each tool's functionality is fully described in the documentation directly accessible from the graphical interface of the VM. Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud installed at the J. Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer. Documentation for using Cloud BioLinux on EC2 is available from our project website, while a Eucalyptus cloud image and VirtualBox Appliance is also publicly available for download and use by researchers with access to private clouds.

Conclusions

Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds Virtual Machines, allowing the development of highly customized versions from a shared code base. This shared community toolkit enables application specific analysis platforms on the cloud by minimizing the effort required to prepare and maintain them.

Toward interoperable bioscience data

To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' framework to support that vision.

An unusual case of pneumocephalus

The authors present an unusual cause of pneumocephalus in a previously fit and well female octogenarian who presented with acute onset altered level of consciousness and generalised weakness. Radiological imaging demonstrated widespread cerebritis with pneumocephalus and gas within the superior sagittal sinus. Blood culture grew Clostridium septicum, a virulent but rare organism that can infect normal tissues. The close association between C septicum and both haematological and bowel malignancies must be considered if this organism is cultured.

Data shopping in an open marketplace: Introducing the Ontogrator web application for marking up data using ontologies and browsing using facets

In the future, we hope to see an open and thriving data market in which users can find and select data from a wide range of data providers. In such an open access market, data are products that must be packaged accordingly. Increasingly, eCommerce sellers present heterogeneous product lines to buyers using faceted browsing. Using this approach we have developed the Ontogrator platform, which allows for rapid retrieval of data in a way that would be familiar to any online shopper. Using Knowledge Organization Systems (KOS), especially ontologies, Ontogrator uses text mining to mark up data and faceted browsing to help users navigate, query and retrieve data. Ontogrator offers the potential to impact scientific research in two major ways: 1) by significantly improving the retrieval of relevant information; and 2) by significantly reducing the time required to compose standard database queries and assemble information for further research. Here we present a pilot implementation developed in collaboration with the Genomic Standards Consortium (GSC) that includes content from the StrainInfo, GOLD, CAMERA, Silva and Pubmed databases. This implementation demonstrates the power of ontogration and highlights that the usefulness of this approach is fully dependent on both the quality of data and the KOS (ontologies) used. Ideally, the use and further expansion of this collaborative system will help to surface issues associated with the underlying quality of annotation and could lead to a systematic means for accessing integrated data resources.

Megascience. 'Omics data sharing

Data sharing, and the good annotation practices it depends on, must become part of the fabric of daily research for researchers and funders.

Potential for phosphonoacetate utilization by marine bacteria in temperate coastal waters

Phosphonates are organic compounds that contain a C-P bond and are a poorly characterized component of the marine phosphorus cycle. They may represent a potential source of bioavailable phosphorus, particularly in oligotrophic conditions. This study has investigated the distribution of the phnA gene which encodes phosphonoacetate hydrolase, the enzyme that mineralizes phosphonoacetate. Using newly designed degenerate primers targeting the phnA gene we analysed the potential for phosphonoacetate utilization in DNA and cDNA libraries constructed from a phytoplankton bloom in the Western English Channel during July 2006. Total RNA was isolated and reverse transcribed and phosphonoacetate hydrolase (phnA) transcripts were PCR amplified from the cDNA with the degenerate primers, cloned and sequenced. Phylogenetic analysis demonstrated considerable diversity with 14 sequence types yielding five unique phnA protein groups. We also identified 28 phnA homologues in a 454-pyrosequencing metagenomic and metatranscriptomic study from a coastal marine mesocosm, indicating that > 3% of marine bacteria in this study contained phnA. phnA homologues were also present in a metagenomic fosmid library from this experiment. Finally, cultures of four isolates of potential coral pathogens belonging to the Vibrionaceae contained the phnA gene. In the laboratory, these isolates were able to grow with phosphonoacetate as sole P and C source. The fact that the capacity to utilize phosphonoacetate was evident in each of the three coastal environments suggests the potential for widespread utilization of this bioavailable P source.

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

The Minimum Information for Biological and Biomedical Investigations (MIBBI) project provides a resource for those exploring the range of extant minimum information checklists and fosters coordinated development of such checklists.

Data capture in bioinformatics: requirements and experiences with Pedro

BACKGROUND

The systematic capture of appropriately annotated experimental data is a prerequisite for most bioinformatics analyses. Data capture is required not only for submission of data to public repositories, but also to underpin integrated analysis, archiving, and sharing - both within laboratories and in collaborative projects. The widespread requirement to capture data means that data capture and annotation are taking place at many sites, but the small scale of the literature on tools, techniques and experiences suggests that there is work to be done to identify good practice and reduce duplication of effort.

RESULTS

This paper reports on experience gained in the deployment of the Pedro data capture tool in a range of representative bioinformatics applications. The paper makes explicit the requirements that have recurred when capturing data in different contexts, indicates how these requirements are addressed in Pedro, and describes case studies that illustrate where the requirements have arisen in practice.

CONCLUSION

Data capture is a fundamental activity for bioinformatics; all biological data resources build on some form of data capture activity, and many require a blend of import, analysis and annotation. Recurring requirements in data capture suggest that model-driven architectures can be used to construct data capture infrastructures that can be rapidly configured to meet the needs of individual use cases. We have described how one such model-driven infrastructure, namely Pedro, has been deployed in representative case studies, and discussed the extent to which the model-driven approach has been effective in practice.

Longitudinal analysis of genotype distribution of influenza A virus from 2003 to 2005

Influenza A viruses cause yearly epidemics, in part, due to their ability to overcome immunity from previous infections through acquisition of mutations. Amino acid sequences encoded by genes 4 (HA), 6 (NA), 7 (M), and 8 (NS) from 77 H3N2 influenza A isolates, collected between November 2003 and March 2005, were analyzed to determine the extent to which the viruses mutated within epidemic periods and between the epidemics. Nucleotide and amino acid sequences were stable throughout the epidemics but experienced substantial changes between epidemics. Major changes occurred in the HA gene in 5 to 7 amino acids and the NA gene in 11 to 13 amino acids and changes of 5 amino acids occurred in the M and NS genes. In the HA gene, changes occurred in sites known to be epitopes that determine the hemagglutination inhibition reactivity, and these were shown to be associated with a change of strain from A/Fujian/411/2002-like to A/California/7/2004-like viruses. Our findings indicate that genotype determination promises to be a rapid approach for detecting new strains of influenza A viruses in a population.

Open software for biologists: from famine to feast

Developing and deploying specialized computing systems for specific research communities is achievable, cost effective and has wide-ranging benefits.

Parents with learning difficulties in the child protection system: experiences and perspectives

The article documents the views and feelings of parents with learning difficulties as they reflect on their first-hand experience of going through care proceedings. Drawing on interviews conducted as part of a wider study of how cases involving mothers and fathers with learning difficulties are handled by the child protection system and the family courts, the authors provide a parental perspective on assessments, support, case conferences and the court process as well as the after-effects on the families themselves.

Novel avian influenza H7N3 strain outbreak, British Columbia

Genome sequences of chicken (low pathogenic avian influenza [LPAI] and highly pathogenic avian influenza [HPAI]) and human isolates from a 2004 outbreak of H7N3 avian influenza in Canada showed a novel insertion in the HA0 cleavage site of the human and HPAI isolate. This insertion likely occurred by recombination between the hemagglutination and matrix genes in the LPAI virus.

Automated variance reduction for MCNP using deterministic methods

In order to reduce the user's time and the computer time needed to solve deep penetration problems, an automated variance reduction capability has been developed for the MCNP Monte Carlo transport code. This new variance reduction capability developed for MCNP5 employs the PARTISN multigroup discrete ordinates code to generate mesh-based weight windows. The technique of using deterministic methods to generate importance maps has been widely used to increase the efficiency of deep penetration Monte Carlo calculations. The application of this method in MCNP uses the existing mesh-based weight window feature to translate the MCNP geometry into geometry suitable for PARTISN. The adjoint flux, which is calculated with PARTISN, is used to generate mesh-based weight windows for MCNP. Additionally, the MCNP source energy spectrum can be biased based on the adjoint energy spectrum at the source location. This method can also use angle-dependent weight windows.

Thermodynamic law for adaptation of plants to environmental temperatures

A thermodynamic law of adaptation of plants to temperature is developed. Plant growth rate is proportional to the product of the metabolic rate and the metabolic efficiency for production of anabolic products. Over much of the growth temperature range, metabolic rate is proportional to mean temperature and efficiency is proportional to the reciprocal of temperature variability. The mean temperature and short-term (hours to weeks) variability of temperature during the growth season at a particular location thus determine the optimum energy and growth strategy for plants. Because they can grow and reproduce most vigorously, plants with a growth rate vs. temperature curve that matches the time-at-temperature vs. temperature curve during the growth season are favored by natural selection. The law of temperature adaptation explains many recent and long-standing observations of plant growth and survival, including latitudinal gradients of plant diversity and species range.

Intravenous Antibiotic Therapy for Deep Neck Abscesses Defined by Computed Tomography

OBJECTIVE

To determine the effectiveness of using intravenous antibiotics alone to treat clinically stable children with clearly defined deep neck abscesses diagnosed by contrast-enhanced computed tomography (CT).

DESIGN

Retrospective chart and CT scan review.

SETTING

Tertiary care children's hospital.

PATIENTS

The study comprised clinically stable pediatric patients who presented with signs and symptoms of a deep neck infection and who had CT scans demonstrating an abscess in the parapharyngeal space, retropharyngeal space, or both that included (1) a well-formed ring enhancement around a nonenhancing density consistent with fluid and (2) a size greater than 1 cm in every dimension.

MAIN OUTCOME MEASURES

Clinical resolution of the signs and symptoms of the deep neck abscess after treatment with intravenous antibiotics.

RESULTS

Over a 22-month period (May 1999 to March 2001), 11 children ranging in age from 4 months to 16(1/2) years who had contrast-enhanced CT evidence of deep neck abscess and no clinical evidence of severe symptoms or significant airway compromise were initially treated with intravenous antibiotics. Ten (91%) of the 11 children responded to intravenous antibiotic therapy as their only treatment. All 10 responders began to improve clinically by 48 hours. The symptoms resolved in 5 children by treatment day 3. Five to 8 days of treatment were required to completely resolve the symptoms in the other 5 patients. The 1 child who did not respond to intravenous antibiotic therapy underwent surgical drainage of her deep neck abscess within 12 hours of admission, with purulence discovered at the time of surgery.

CONCLUSION

In a select number of clinically stable children, deep neck abscesses diagnosed on contrast-enhanced CT scans using strict radiographic criteria can be effectively treated with intravenous antibiotics alone.

Late onset seizures, hemiparesis and blindness in hemolytic uremic syndrome

Neurologic complications of hemolytic uremic syndrome, including seizures, usually occur early during the acute phase of the illness. We report a3-year-old girl with classic diarrhea-associated hemolytic uremic syndrome who developed late onset seizures, hemiparesis and transient blindness on the 17th hospital day, at which time her recovery was characterized by improvement in her blood pressure, serum electrolytes, renal function, hematocrit and platelet count. A CT and MR revealed brainstem and posterior parietal and occipital infarct/edema. The association of these radiologic findings within the posterior distribution along with visual loss and seizures are unique to posterior reversible encephalopathy syndrome. Within 7 days, she regained motor function and vision and had no further seizure activity. At 6 months follow-up, physical examination revealed normal motor function and vision and a repeat MR showed near resolution of the previous findings with minimal occipital lobe gliosis. This case report describes the uncommon finding of late onset seizures occurring during the recovery phase of hemolytic uremic syndrome with MR findings consistent with posterior reversible encephalopathy syndrome.

Clinical presentation of allergic fungal sinusitis in children

OBJECTIVE

To compare the differences in the clinical and radiographic presentation of allergic fungal sinusitis in children and adults.

STUDY DESIGN

Retrospective chart and computed tomography review.

METHODS

The settings included a tertiary care children's hospital, adult academic private hospital, and academic affiliated county hospital. All patients with documented allergic fungal sinusitis who underwent computed tomography evaluation and had surgical treatment of their disease from 1988 to 1999 were included in the study. In total, 151 patients aged 5 to 75 years; 44 of these patients were less than or equal to 17 years of age (children) and 107 were greater than 17 years of age (adults). Main outcome measures included 1) the presence of obvious bony facial abnormalities on presentation, 2) bilateral or unilateral sinus disease on presentation, 3) the presence of asymmetrical disease on presentation, 4) the presence of bony extension on computed tomography scan, and 5) type of fungus present.

RESULTS

Fifteen of 36 (42%) pediatric patients and 10 of 103 (10%) adult patients had obvious alteration of their facial skeleton (proptosis, telecanthus, or malar flattening) on presentation (P <.05). Proptosis was the most common facial abnormality in both groups and was seen more often in children (8 of 36 [22%]) than in adults (9 of 103 [9%]) (P <.05). Twenty-eight of 40 (70%) pediatric patients and 37 of 100 (37%) adult patients presented with unilateral sinus disease (P <.05). Thirty-five of 40 (88%) pediatric patients and 58 of 100 (58%) adults presented with asymmetrical disease (P <.05). Computed tomography scans showed that 10 of 40 (25%) pediatric patients and 23 of 100 (23%) adult patients had bony erosion with extension of disease into surrounding structures (P >.05). Cultures from both adults and children showed mainly Bipolaris and Curvilaria species in equal amounts (P >.05). Adults had a greater incidence of Aspergillus species.

CONCLUSIONS

Presentation in pediatric patients with allergic fungal sinusitis is different from that in adults, with children having obvious abnormalities of their facial skeleton, unilateral sinus disease, and asymmetrical disease more often. Findings on computed tomography scan show an equal amount of bony erosion with extension of disease. The types of fungus cultured in the sinus cavities are similar in both groups.

Is first trimester exposure to the combination of antiretroviral therapy and folate antagonists a risk factor for congenital abnormalities?

OBJECTIVES

To assess use of antiretroviral therapy (ART) by HIV positive pregnant women in London since 1994 and the risk of congenital abnormalities associated with multidrug exposure during the first trimester of pregnancy.

METHODS

Retrospective multicentre study of medical, obstetric, and paediatric notes of all mother-infant pairs, where the mother was known to be HIV infected before delivery, using a standardised proforma.

RESULTS

In this study of 195 mother-infant pairs, use of ART during any stage of pregnancy increased from 33.3% in 1994 to 92.5% in 1999 (p=0.01, trend). First trimester exposure increased from 0% in 1994 to 27.5% in 1999 (p=0.00045, trend). Congenital malformations were observed in nine infants (4.6%). Compared with infants not exposed to ART or folate antagonists during the first trimester (n=148), exposure to both ART and folate antagonists during the first trimester (n=13) was associated with an increased risk of congenital abnormalities (4% v 23.1%; OR 7.10, 95% CI 1.5, 34.2). No malformations were observed in the 34 children exposed to either ART or folate antagonists alone during the first trimester.

CONCLUSION

An increasing number of HIV infected women conceived while on ART. Although there is no evidence of teratogenicity caused by ART if given alone during the first trimester, exposure to the combination of ART and folate antagonists was associated with a significantly higher risk of congenital abnormalities in this cohort.

Congenital foregut duplication cysts of the anterior tongue

OBJECTIVE

To review our experience with foregut duplication cysts of the anterior tongue, an unusual and rarely encountered mass in this location.

DESIGN

A retrospective review of patients with anterior tongue foregut duplication cysts identified between 1990 and 2000.

SETTING

Academic, tertiary care children's medical center.

PATIENTS

Six pediatric patients (5 boys and 1 girl) ranging in age from birth to 8 months at diagnosis.

INTERVENTION

Three patients underwent preoperative magnetic resonance imaging (MRI). All 6 patients underwent excisional biopsy.

MAIN OUTCOME MEASURES

Clinical description of foregut duplication cysts, ability to make the diagnosis preoperatively, and recurrence rates.

RESULTS

No patient presented with respiratory compromise, despite the large size of the anterior tongue masses (range, 1.5-2.4 cm). An MRI study was performed in 3 patients, all given a presumptive diagnosis of dermoid cyst based on the radiographic findings. No patient was diagnosed correctly prior to surgical excision. All patients underwent surgical excision, and the average time from birth to surgical excision was 11 months (range, 3 days to 3.7 years). Surgical pathologic findings were reported as a foregut duplication cyst (enterocystoma) in all patients, with 3 specimens containing foci of gastric mucosa. No recurrence has occurred at 1-month follow-up.

CONCLUSIONS

Foregut duplication cysts rarely present in the anterior tongue and are easily misdiagnosed preoperatively. An MRI study is helpful in preoperative planning, although all lesions were radiologically indistinguishable from dermoid cysts. These masses may be an underappreciated entity in the differential diagnosis of congenital anterior tongue masses.