Analytical Bayesian approach for the design of surveillance and control programs to assess pest-eradication success

Large invasive species eradication programs are undertaken to protect native biodiversity and agriculture. Programs are typically followed by a series of surveys to assess the likelihood of eradication success and, when residual pests are detected, small-scale control or 'mop-ups' are implemented to eliminate these infestations. Further surveys follow to confirm absence with 'freedom' declared when a target probability of absence is reached. Such biosecurity programs comprise many interacting processes - stochastic biological processes including growth, and response and control interventions - and are an important component of post-border biosecurity. Statistical frameworks formulated to contribute to the design and efficiency of these surveillance and control programs are few and, those available, rely on the simulation of the component processes. In this paper we formulate an analytical Bayesian framework for a general biosecurity program with multiple components to assess pest-eradication success. Our model incorporates stochastic growth and detection processes, and several pest control mechanisms. Survey results and economic considerations are also taken into account to support a range of biosecurity management decisions. Using a case study we demonstrate that solutions match published simulation results and extend the available analysis. Principally, we show how analytical solutions can offer a powerful tool to support the design of effective and cost-efficient biosecurity systems, and we establish some general principles that guide and contribute to robust design.

DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse

We have developed a mouse DNA methylation array that contains 296,070 probes representing the diversity of mouse DNA methylation biology. We present a mouse methylation atlas as a rich reference resource of 1,239 DNA samples encompassing distinct tissues, strains, ages, sexes, and pathologies. We describe applications for comparative epigenomics, genomic imprinting, epigenetic inhibitors, patient-derived xenograft assessment, backcross tracing, and epigenetic clocks. We dissect DNA methylation processes associated with differentiation, aging, and tumorigenesis. Notably, we find that tissue-specific methylation signatures localize to binding sites for transcription factors controlling the corresponding tissue development. Age-associated hypermethylation is enriched at regions of Polycomb repression, while hypomethylation is enhanced at regions bound by cohesin complex members. Apc ^Min/+ polyp-associated hypermethylation affects enhancers regulating intestinal differentiation, while hypomethylation targets AP-1 binding sites. This Infinium Mouse Methylation BeadChip (version MM285) is widely accessible to the research community and will accelerate high-sample-throughput studies in this important model organism.

Power on: The rapid transition of a large interdisciplinary behavioral health department to telemental health during the COVID-19 pandemic

Background

The COVID-19 pandemic necessitated a rapid transition to telemental health (TMH) for behavioral health services in the behavioral health department of a large integrated primary care organization. Although the COVID-19 pandemic was the initial trigger for rapid organizational change, systems were developed with a focus on longer term scalability and sustainability.

Methods

This paper discusses the process of organizational change within our healthcare delivery system using the Strengths, Opportunities, Aspirations, and Results (SOAR) framework. Within this framework a structured mixed methods survey of 38 clinicians representing 5 different disciplines was conducted. Internal and survey data were analyzed to evaluate and guide the iterative change process.

Results

The majority of BH clinicians reported that they were as or more effective with TMH. The transition to TMH in our organization resulted in increased access to care, with a 10.3% increase in BH visit completions. The transition to TMH may benefit clinician work-life balance, but requires resources to support clinical, technological, and communication/teamwork changes.

Implications/conclusions

TMH is a feasible treatment modality for integrated care settings. It is cost-effective and well-accepted by clinicians. The SOAR framework can be used to guide rapid organizational change and ongoing QI processes.

A mammalian methylation array for profiling methylation levels at conserved sequences

Infinium methylation arrays are not available for the vast majority of non-human mammals. Moreover, even if species-specific arrays were available, probe differences between them would confound cross-species comparisons. To address these challenges, we developed the mammalian methylation array, a single custom array that measures up to 36k CpGs per species that are well conserved across many mammalian species. We designed a set of probes that can tolerate specific cross-species mutations. We annotate the array in over 200 species and report CpG island status and chromatin states in select species. Calibration experiments demonstrate the high fidelity in humans, rats, and mice. The mammalian methylation array has several strengths: it applies to all mammalian species even those that have not yet been sequenced, it provides deep coverage of conserved cytosines facilitating the development of epigenetic biomarkers, and it increases the probability that biological insights gained in one species will translate to others.

Methods to probe DNA methylation in the majority of non-human mammals are lacking. Here the authors developed a Mammalian Methylation Array that includes 36k well-conserved CpGs in mammals which will facilitate cross-species comparisons. They annotate the conserved CpGs in > 200 species. The array allows one to measure methylation in all mammalian species including unsequenced ones.

Analytical Bayesian models to quantify pest eradication success or species absence using zero-sighting records

It is not possible to establish the absence of a population with certainty using imperfect zero-sighting records, but absence can be inferred. In this paper we use Bayesian methods to formulate analytical inferred distributions and statistics. When such formulations are available, they offer a highly efficient and powerful means of analysis. Our purpose is to provide accessible and versatile formulations to support an assessment of population absence for management decisions, using data from a series of regular and targeted surveys with zero-sightings. The stochastic processes considered here are prior population size, growth and imperfect detection, which are combined into a single distribution with sufficient flexibility to accommodate alternative distributions for each of the driving processes. Analytical solutions formulated include the inferred mean and variance for population size or number of infested survey-units, the probability of absence, the probability of a series of negative surveys conditional on presence, and the probability a population is first detected in a given survey, although we also formulate other statistics and provide explicit thresholds designed to support management decisions. Our formulation and results are straightforward to apply and provide insight into the nonlinear interactions and general characteristics of such systems. Although motivated by an assessment of population absence following a pest eradication program, results are also relevant to the status of threatened species, to 'proof-of-freedom' requirements for trade, and for inferring population size when a population is first detected.

Host methylation predicts SARS-CoV-2 infection and clinical outcome

BACKGROUND

Since the onset of the SARS-CoV-2 pandemic, most clinical testing has focused on RT-PCR1. Host epigenome manipulation post coronavirus infection2-4 suggests that DNA methylation signatures may differentiate patients with SARS-CoV-2 infection from uninfected individuals, and help predict COVID-19 disease severity, even at initial presentation.

METHODS

We customized Illumina's Infinium MethylationEPIC array to enhance immune response detection and profiled peripheral blood samples from 164 COVID-19 patients with longitudinal measurements of disease severity and 296 patient controls.

RESULTS

Epigenome-wide association analysis revealed 13,033 genome-wide significant methylation sites for case-vs-control status. Genes and pathways involved in interferon signaling and viral response were significantly enriched among differentially methylated sites. We observe highly significant associations at genes previously reported in genetic association studies (e.g. IRF7, OAS1). Using machine learning techniques, models built using sparse regression yielded highly predictive findings: cross-validated best fit AUC was 93.6% for case-vs-control status, and 79.1%, 80.8%, and 84.4% for hospitalization, ICU admission, and progression to death, respectively.

CONCLUSIONS

In summary, the strong COVID-19-specific epigenetic signature in peripheral blood driven by key immune-related pathways related to infection status, disease severity, and clinical deterioration provides insights useful for diagnosis and prognosis of patients with viral infections.

Graphite Furnace Atomic Absorption Spectrometric Determination of Lead and Cadmium Extracted from Ceramic Foodware: Collaborative Study

A modification of the official flame atomic absorption spectrometric (FAAS) method for determining lead and cadmium extracted from ceramic foodware was collaboratively studied. In the modified method, graphite furnace atomic absorption spectrometry (GFAAS) is substituted for FAAS. The modified method also includes mandatory quality control procedures to improve method performance. The extraction procedure of the official method (leaching with 4% acetic acid for 24 h at room temperature) remains unchanged. Seven laboratories analyzed blind duplicate portions of 3 ceramicware leach solutions containing Pb at concentrations of 0.0196, 0.403, and 3.73 μg/mL and Cd at concentrations of 0.00236, 0.0456, and 0.544 μg/mL. Performance of the modified method compared well with that of the official method. The repeatability relative standard deviation (RSDr) ranged from 0.87 to 6.7% for Pb and from 3.7 to 11% for Cd. The reproducibility relative standard deviation (RSDR) ranged from 4.5 to 12% for Pb and from 7.0 to 11% for Cd. Accuracy of collaborator results was 97–98% for Pb and 93–101% for Cd. Quality control results and quantitation limits were excellent. Method quantitation limits varied among laboratories from 0.005 to 0.019 μg/mL for Pb and from 0.0004 to 0.0019 μg/mL for Cd. The modified method was adopted First Action by AOAC INTERNATIONAL.

Modelling the impact of biosecurity practices on the risk of high pathogenic avian influenza outbreaks in Australian commercial chicken farms

As of 2018, Australia has experienced seven outbreaks of highly pathogenic avian influenza (HPAI) in poultry since 1976, all of which involved chickens. There is concern that increases in free-range farming could heighten HPAI outbreak risk due to the potential for greater contact between chickens and wild birds that are known to carry low pathogenic avian influenza (LPAI). We use mathematical models to assess the effect of a shift to free-range farming on the risk of HPAI outbreaks of H5 or H7 in the Australian commercial chicken industry, and the potential for intervention strategies to reduce this risk. We find that a shift of 25% of conventional indoor farms to free-range farming practices would result in a 6-7% increase in the risk of a HPAI outbreak. Current practices to treat water are highly effective, reducing the risk of outbreaks by 25-28% compared to no water treatment. Halving wild bird presence in feed storage areas could reduce risk by 16-19% while halving wild bird access of potential bridge-species to sheds could reduce outbreak risk by 23-25%, and relatively small improvements in biosecurity measures could entirely compensate for increased risks due to the increasing proportion of free-range farms in the industry. The short production cycle and cleaning practices for chicken meat sheds considerably reduce the risk that an introduced low pathogenic avian influenza virus is maintained in the flock until it is detected as HPAI through increased mortality of chickens. These findings help explain HPAI outbreak history in Australia and suggest practical changes in biosecurity practices that could reduce the risk of future outbreaks.

Targeted methylation sequencing of plasma cell-free DNA for cancer detection and classification

Background

Targeted methylation sequencing of plasma cell-free DNA (cfDNA) has a potential to expand liquid biopsies to patients with tumors without detectable oncogenic alterations, which can be potentially useful in early diagnosis.

Patients and methods

We developed a comprehensive methylation sequencing assay targeting 9223 CpG sites consistently hypermethylated according to The Cancer Genome Atlas. Next, we carried out a clinical validation of our method using plasma cfDNA samples from 78 patients with advanced colorectal cancer, non-small-cell lung cancer (NSCLC), breast cancer or melanoma and compared results with patients' outcomes.

Results

Median methylation scores in plasma cfDNA samples from patients on therapy were lower than from patients off therapy (4.74 versus 85.29; P = 0.001). Of 68 plasma samples from patients off therapy, methylation scores detected the presence of cancer in 57 (83.8%), and methylation-based signatures accurately classified the underlying cancer type in 45 (78.9%) of these. Methylation scores were most accurate in detecting colorectal cancer (96.3%), followed by breast cancer (91.7%), melanoma (81.8%) and NSCLC (61.1%), and most accurate in classifying the underlying cancer type in colorectal cancer (88.5%), followed by NSCLC (81.8%), breast cancer (72.7%) and melanoma (55.6%). Low methylation scores versus high were associated with longer survival (10.4 versus 4.4 months, P < 0.001) and longer time-to-treatment failure (2.8 versus 1.6 months, P = 0.016).

Conclusions

Comprehensive targeted methylation sequencing of 9223 CpG sites in plasma cfDNA from patients with common advanced cancers detects the presence of cancer and underlying cancer type with high accuracy. Methylation scores in plasma cfDNA correspond with treatment outcomes.

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

: We describe Manta, a method to discover structural variants and indels from next generation sequencing data. Manta is optimized for rapid germline and somatic analysis, calling structural variants, medium-sized indels and large insertions on standard compute hardware in less than a tenth of the time that comparable methods require to identify only subsets of these variant types: for example NA12878 at 50× genomic coverage is analyzed in less than 20 min. Manta can discover and score variants based on supporting paired and split-read evidence, with scoring models optimized for germline analysis of diploid individuals and somatic analysis of tumor-normal sample pairs. Call quality is similar to or better than comparable methods, as determined by pedigree consistency of germline calls and comparison of somatic calls to COSMIC database variants. Manta consistently assembles a higher fraction of its calls to base-pair resolution, allowing for improved downstream annotation and analysis of clinical significance. We provide Manta as a community resource to facilitate practical and routine structural variant analysis in clinical and research sequencing scenarios.

AVAILABILITY AND IMPLEMENTATION

Manta is released under the open-source GPLv3 license. Source code, documentation and Linux binaries are available from https://github.com/Illumina/manta.

CONTACT

csaunders@illumina.com

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Changes in cancer incidence attributable to tobacco smoking in Germany, 1999-2008

Tobacco smoking, a major cancer risk factor, is very common in Germany as in many other high-income countries. Few studies have assessed the burden of tobacco-associated cancer incidence in the German population. We calculated the proportion of cancers attributable to tobacco smoking to estimate the burden of tobacco-associated cancer in 1999 and 2008. Smoking prevalence was determined from national surveys of a representative sample of the German population in 1998 and 2008-2011, and data on relative risks were obtained from meta-analyses. Cancer incidence for the years 1999 and 2008 was estimated by the German Centre for Cancer Registry Data at the Robert Koch Institute. We estimate that 72,208 incident cancer cases were attributable to tobacco smoking in Germany in 2008, an increase of >6,200 cases over 1999 levels. Among the cases in 2008 were 55,057 cases among men (22.8% (95% CI, 21.3-24.1) of all new cases) and 17,151 cases among women (7.9% (95% CI, 7.21-8.68) of all new cases). The highest proportions attributable to smoking were estimated for cancer of the lung, larynx, pharynx and the lower urinary tract. Tobacco smoking is currently responsible for more than one in five cancer cases among men and nearly 1 in 12 among women. Considering the increasing trends in cancer incidence and, until very recently, rising prevalence of smoking among women, it can be expected that the number of tobacco-attributable cancer cases will rise further.

Genome-wide DNA methylation profiling using Infinium® assay

AIMS

Bisulfite sequence analysis of individual CpG sites within genomic DNA is a powerful approach for methylation analysis in the genome. The major limitation of bisulfite-based methods is parallelization. Both array and next-generation sequencing technology are capable of addressing this bottleneck. In this report, we describe the application of Infinium® genotyping technology to analyze bisulfite-converted DNA to simultaneously query the methylation state of over 27,000 CpG sites from promoters of consensus coding sequences (CCDS) genes.

MATERIALS & METHODS

We adapted the Infinium genotyping assay to readout an array of over 27,000 pairs of CpG methylation-specific query probes complementary to bisulfite-converted DNA. Two probes were designed to each CpG site: a 'methylated' and an 'unmethylated' query probe. The probe design assumed that all underlying CpG sites were 'in phase' with the queried CpG site due to their close proximity. Bisulfite conversion was performed with a modified version of the Zymo EZ DNA Methylation™ kit.

RESULTS

We applied this technology to measuring methylation levels across a panel of 14 different human tissues, four Coriell cell lines and six cancer cell lines. We observed that CpG sites within CpG islands (CGIs) were largely unmethylated across all tissues (~80% sites unmethylated, β < 0.2), whereas CpG sites in non-CGIs were moderately to highly methylated (only ~12% sites unmethylated, β < 0.2). Within CGIs, only approximately 3-6% of the loci were highly methylated; in contrast, outside of CGIs approximately 25-40% of loci were highly methylated. Moreover, tissue-specific methylation (variation in methylation across tissues) was much more prevalent in non-CGIs than within CGIs.

CONCLUSION

Our results demonstrate a genome-wide scalable array-based methylation readout platform that is both highly reproducible and quantitative. In the near future, this platform should enable the analysis of hundreds of thousands to millions of CpG sites per sample.

[The (German) Center for Cancer Registry Data (ZfKD) at the Robert Koch Institute (RKI) in Berlin]

Cancer represents the second most common cause of death in Germany. The country's federal states operate regional population-based cancer registries that collect and analyze data on cancer patients. This provides an essential basis for describing the cancer burden in the German population. In order to obtain valid and reliable information on cancer incidence at the national level, the Robert Koch Institute (RKI) set up the Federal Cancer Surveillance Unit in 1983 as a central institution for evaluating this cancer registry data. In August 2009, when the Federal Cancer Registry Data Act (BKRG) came into force, the Center for Cancer Registry Data (ZfKD) at the RKI took over the work of the Cancer Surveillance Unit with a broader remit. In the future, it will also regularly publish findings on survival, prevalence, and tumor stage distribution. A newly established record linkage process will help identify multiple submissions from the federal states. Further innovations and new tasks of the ZfKD include expanding an interactive Internet platform and encouraging a more intensive use of cancer registry data for epidemiological research by providing datasets to external scientists. The range of information available to the interested public is also to be expanded.

Abstract LB-176: A novel high density DNA methylation array with single CpG site resolution

Aberrations in DNA methylation patterns are widely recognized as a hallmark of the cancer cell. DNA methylation has emerged as a promising biomarker for the detection and classification of various types of cancer, and ability to accurately assess the DNA methylation changes plays an important role in understanding of disease onset and progression.

We developed a new generation of genome-wide DNA methylation BeadChip which allows high-throughput methylation profiling of human genome. The new high density BeadChip can assay over 480K CpG sites and analyze twelve samples in parallel. The innovative content includes coverage of 99% of RefSeq genes with multiple probes per gene, 96% of CpG islands from the UCSC database, CpG island shores and additional content selected from whole-genome bisulfite sequencing data and input from DNA methylation experts. The well-characterized Infinium® assay is used for analysis of CpG methylation using bisulfite-converted genomic DNA. In this assay, unmethylated cytosines (C) are converted to uracil (U) when treated with bisulfite, while methylated cytosines remain unchanged. The assay design is using single probe assays for CpG loci with up to two underlying CpG dinucleotides, and two-probe assays for CpG loci with multiple underlying CpG sites, with one probe querying the “unmethylated” allele and the other probe querying the “methylated” allele. The assays are designed under the assumption that methylation is regionally correlated (within 50 base pairs) and that all CpG sites underlying the probe are assumed to be “in phase” with the queried CpG site.

For the BeadChip development, we used methylation standards created by de-methylating gDNA with Phi29 whole genome amplification, methylating the amplified DNA with SssI methylase and mixing the unmethylated and methylated DNA in a 1:1 ratio to create a 50% methylation state. 500 ng gDNA input is used for bisulfite conversion and is sufficient for two assays. Reproducible DNA methylation profiles were obtained between replicates (an average R2 of 0.98).

We applied this technology to DNA methylation analyses in cancer cell lines of different tissue of origin and normal DNA samples derived from multiple tissues. Highly specific methylation signatures were obtained for each sample type.

The ability to determine genome-wide methylation patterns will rapidly advance methylation research and ultimately lead to the development of powerful tools for diagnosis, prognosis, and treatment of human diseases.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-176. doi:10.1158/1538-7445.AM2011-LB-176

Corrosion Behaviour of British Magnox Waste Glass in Pure Water

The corrosion behaviour of Magnox Waste (MW) glass in deionized water has been investigated under the aegis of the Japanese-Swedish-Swiss (JSS) project. The studies carried out at PSI and BNFL included static leaching and corrosion layer characterization. The results were used by HMI to derive the modelling parameters for the MW glass with the PHREEQE/GLASSOL codes. The silica concentration was found to strongly influence the corrosion rate of the glass. The MW glass selectively retains Cs due to the formation of a Cs-Mg-Al-Si-O-rich layer on its surface.

Identification of Interferon Regulatory Factor (IRF)-5 Tumor Suppressor Function in Human Breast Cancer

Background: Transcription factors of the IRF family participate in the early host response to pathogens, hematopoietic differentiation and immunomodulation. IRFs can regulate cell growth and apoptosis thereby affecting the susceptibility to and progression of cancer. IRF-1 was recently identified as a tumor suppressor in breast cancer. Early evidence from our lab and others suggests that IRF-5 may also have tumor suppressor activities. Although loss of IRF-5 expression has recently been shown to enhance transformation by Ha-ras, very little is known of IRF-5 tumor suppressor function(s).Material and Methods: Using paraffin-embedded formalin-fixed human breast tissue specimens from 64 patients with varying stages of ductal carcinoma, we analyzed and compared the expression of IRF-1 and IRF-5 by immunofluorescence (IF). Clinical data, such as histological subtype, stage, and receptor expression (ER, PR Her-2) were available for clinicopathological correlations. Protein levels were also determined in normal human breast epithelial MCF-10A, and -12A cells, and in cancer cell lines MCF-7, MDA-MB-231, -468, and T47D by immunoblot and IF. By retroviral infection, we overexpressed IRF-5 in breast cancer cell lines or knocked-down IRF-5 in normal MCF-10A and -12A cells and examined cell growth, apoptosis, metastasis and sensitivity to cytotoxic stress. In vivo tumor suppressor function was determined in NCr nu/nu mice inoculated with MCF-7 or MDA-MB-231 cells expressing or lacking IRF-5.Results: We confirmed recent data on IRF-1 revealing that it is expressed less frequently in tumor tissue of high-grade ductal carcinoma in situ (DCIS) or invasive DC compared with normal breast tissue. Data from patient samples indicate a significant difference between IRF-1 and IRF-5 expression that was distinctly associated with breast cancer disease stages, including early-to-late stage DCIS, suggesting their utilization as prognostic indicators.Similar findings were made in breast cancer cell lines. We demonstrate that forced expression of IRF-5 in breast cancer cells inhibits colony formation, sensitizes cells to cytotoxic stress-induced apoptosis, inhibits metastasis, and tumor formation in nude mice. Conversely, knockdown of IRF-5 in MCF-10A and -12A cells resulted in resistance to stress-induced cell death.Discussion: Data from this study strongly support a tumor suppressor function for IRF-5 in breast cancer. Ultimately, the study is expected to lead us to the identification of new prognostic indicators and therapeutic approaches for the treatment of breast cancer.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3160.

Highly sensitive and specific microRNA expression profiling using BeadArray technology

We have developed a highly sensitive, specific and reproducible method for microRNA (miRNA) expression profiling, using the BeadArray™ technology. This method incorporates an enzyme-assisted specificity step, a solid-phase primer extension to distinguish between members of miRNA families. In addition, a universal PCR is used to amplify all targets prior to array hybridization. Currently, assay probes are designed to simultaneously analyse 735 well-annotated human miRNAs. Using this method, highly reproducible miRNA expression profiles were generated with 100–200 ng total RNA input. Furthermore, very similar expression profiles were obtained with total RNA and enriched small RNA species (R² ≥ 0.97). The method has a 3.5–4 log (10⁵–10⁹ molecules) dynamic range and is able to detect 1.2- to 1.3-fold-differences between samples. Expression profiles generated by this method are highly comparable to those obtained with RT–PCR (R² = 0.85–0.90) and direct sequencing (R = 0.87–0.89). This method, in conjunction with the 96-sample array matrix should prove useful for high-throughput expression profiling of miRNAs in large numbers of tissue samples.

SAM-T04: what is new in protein-structure prediction for CASP6

The SAM-T04 method for predicting protein structures uses a single protocol across the entire range of targets, from comparative modeling to new folds. This protocol is similar to the SAM-T02 protocol used in CASP5, but has improvements in the iterative search for similar sequences in finding and aligning templates, in creating fragment libraries, in generating protein conformations, and in scoring the conformations. The automatic procedure made some improvements over simply selecting an alignment to the highest-scoring template, and human intervention made substantial improvements over the automatic procedure. The main improvements made by human intervention were from adding constraints to build (or retain) beta-sheets and from splitting multidomain proteins into separate domains. The uniform protocol was moderately successful across the entire range of target difficulty, but was somewhat less successful than other approaches in CASP6 on the comparative modeling targets.

Modelling the isotope enrichment of leaf water

Farquhar and Gan have proposed a model for the spatial variation in the isotopic enrichment of H(2)(18)O across a leaf, which is specifically formulated for monocotyledoneous leaves. The model is based on the interaction between mass fluxes longitudinally within the xylem, and fluxes laterally through veinlets into the lamina mesophyll, where moisture leaves the leaf through transpiration. The lighter, more abundant, molecule H(2)(16)O escapes preferentially with the evaporating water, resulting in the enrichment of H(2)(18)O at these sites. Enriched water diffuses throughout the leaf, and it is this spatial distribution of enriched water which the model seeks to capture. In this paper we present a general formulation of the model in terms of mass flux, extending it to include variable transpiration rates across the leaf surface, as well as a tapering xylem. Solutions are developed for the general case and, since the solutions present in the form of Kummer functions, properties are established as well as methods for estimating the solutions under certain conditions relevant to the biology. The model output is compared with Gan's data collected from maize plants.

Schizophrenia spectrum disorders: an autosomal-wide scan in multiplex pedigrees

Genome-wide linkage studies, examining the relationship between the schizophrenia syndrome(s) and possible susceptibility regions within the human genome have identified multiple regions within which linkage to the syndrome may be explored. No regions have been found to provide supportive evidence for linkage in all cohorts. These findings are consistent with the schizophrenia syndrome being genetically heterogeneous, with genetic susceptibility arising from multiple sites which are differentially distributed in from pedigree to pedigree. The authors present data from an autosomal-wide scan of 30 multiplex pedigrees, each with a mean of 4.1 members affected with a schizophrenia spectrum disorder with respect to regions of interest for linkage with the schizophrenia spectrum disease(s). Partial, though not significant replications of susceptibility sites at D1S518 (P=0.029) described by Shaw et al. (1998: Shaw, S.H., Kelly, M., Smith, A.B., Shields, G., Hopkins, P.J., Loftus, J., Laval, S.H., Vita, A., DeHert, M., Cardon, L.R., Crow, T.J., Sherrington, R., DeLisi, L.E., 1998. A Genome-wide search for schizophrenia susceptibility genes. Am. J. Med. Genet. (Neuropsychiatric Genet.) 81, 364-376.), and at D5S426 (P=0.015) described by : Silverman, J.M., Greenberg, D.A., Altstiel, L.D., Siever, L.J., Mohs, R.C., Smith, C.J., Zhou, G., Hollander, T.Y., Yang, X.-P., Kedache, M., Li, G., Zaccario, M.L., Davis, K.L., 1996. Evidence of a locus for schizophrenia and related disorders on the short arm of chromosome 5 in a large pedigree. Am. J. Med. Genet. 67, 162-171.) were documented using multipoint non-parametric (NPL) statistics. Two additional novel regions worthy of further investigation were identified at D1S1150 (P=0.004) and at D20S171 (P=0.009). Previously reported genomic regions of interest for the schizophrenias are reviewed in the context of the same/flanking markers utilized with the present cohort of pedigrees. The data further suggests that only a fraction of pedigrees multiplex for schizophrenia link at any single susceptibility region.

A phase I-II trial of topotecan and gemcitabine in patients with previously treated, advanced non-small cell lung cancer (LOA-3)

The purposes of this study were to determine the maximum tolerated dose (MTD), dose-limiting toxicity (DLT), toxicity profile, and antitumor activity of topotecan (TOP) and gemcitabine (GEM) combination therapy when administered to patients with previously treated, advanced, non-small cell lung cancer. Both compounds were administered intravenously over 30 min, with TOP on days 1-5 and GEM on days 1 and 5 only. Nineteen patients were treated with 75 courses at three dose levels. The MTD was 0.75 and 400 mg/m2 for TOP and GEM, respectively, with thrombocytopenia and neutropenia as the DLTs. Partial responses were achieved in 3 of 17 patients (18%) with measurable disease. Six patients (32%) had disease stabilization for at least four courses of treatment. The median survival was 10 months from the initiation of TOP and GEM. This combination was relatively well tolerated and exhibited promising antitumor activity in patients with advanced, previously treated, non-small cell lung cancer.

Threaded cortical bone dowels for lumbar interbody fusion: over 1-year mean follow up in 28 patients

OBJECT

The authors retrospectively reviewed a series of 35 patients with mechanical low-back or one- to two-level discogenic pain; the patients underwent lumbar interbody fusion in which threaded cortical bone dowels (TCBDs) were placed to treat degenerative disc disease. The purpose of the study was to delineate fusion rates and outcome data in this series of patients.

METHODS

The series was composed of 18 women and 17 men whose mean age was 46 years (range 17-76 years). There were nine active cigarette smokers. All patients presented with symptoms consistent with mechanical low-back or discogenic pain, and magnetic resonance imaging revealed degenerative changes related to disc collapse at one or two vertebral levels. For placement of the TCBDs, 23 patients underwent posterior lumbar interbody fusion (PLIF), whereas 12 patients underwent anterior lumbar interbody fusion (ALIF). In all except one patient undergoing PLIF, pedicle screw and rod constructs were used without posterolateral fusion. In all patients undergoing ALIF except one, TCBDs were used as stand-alone devices without supplemental fixation. At follow up the success of fusion was determined by static lumbar radiography and/or computerized tomography scanning. The degree of lumbar lordosis at the diseased level was measured immediately postoperatively and compared with that documented on follow-up radiological studies. Outcomes were assessed using a modified Prolo Scale. Excellent and good outcomes were considered satisfactory, and fair or poor outcomes were considered unsatisfactory. In 28 patients (eight ALIF and 20 PLIF) radiological and clinical follow-up data were considered adequate. The mean follow-up duration was 12.3 months. Overall satisfactory outcome was 60%; 70% satisfactory outcome was noted in PLIF patients and 38% in ALIF patients. Osseous fusion was present in 95% of the patients in the PLIF group and in 13% of those in the ALIF group. Complications included one L-5 nerve root injury and two postoperative wound infections, all in patients who underwent PLIF; in an ALIF patient lateral breakout of one implant occurred at 8 months postoperatively.

CONCLUSIONS

Analysis of the mean 12.3 month follow-up data indicates that there is a dramatically higher fusion rate in PLIF compared with ALIF procedures when TCBDs are used. The authors believe that it is important to note that in all the PLIF procedures except one, supplemental pedicle screw/rod constructs were used, whereas in ALIF procedures no supplemental fixation was performed. The results thus suggest that TCBDs are best used in PLIF in conjunction with pedicle screw and rod constructs.

Epidemiology of invasive Streptococcus pneumoniae infections in the United States, 1995-1998: Opportunities for prevention in the conjugate vaccine era

CONTEXT

Pneumococcal polysaccharide vaccine is recommended for elderly persons and adults with certain chronic illnesses. Additionally, a recently licensed pneumococcal 7-valent conjugate vaccine has been recommended for use in young children and could dramatically change the epidemiology of pneumococcal disease.

OBJECTIVES

To assess pneumococcal disease burden in the United States, estimate the potential impact of new vaccines, and identify gaps in vaccine recommendations.

DESIGN AND SETTING

Analysis of data from the Active Bacterial Core Surveillance (ABCs)/Emerging Infections Program Network, an active, population-based system in 9 states.

PATIENTS

A total of 15 860 cases of invasive pneumococcal disease occurring between January 1, 1995, and December 31, 1998.

MAIN OUTCOME MEASURES

Age- and race-specific pneumoccocal disease incidence rates per 100 000 persons, case-fatality rates, and vaccine preventability.

RESULTS

In 1998, overall incidence was 23.2 cases per 100 000, corresponding to an estimated 62 840 cases in the United States. Incidence was highest among children younger than 2 years (166.9) and adults aged 65 years or older (59.7). Incidence among blacks was 2.6 times higher than among whites (95% confidence interval [CI], 2.4-2.8). Overall, 28.6% of case-patients were at least 65 years old and 85.9% of cases in this age group were due to serotypes included in the 23-valent polysaccharide vaccine; 19.3% of case-patients were younger than 2 years and 82.2% of cases in this age group were due to serotypes included in the 7-valent conjugate vaccine. Among patients aged 2 to 64 years, 50.6% had a vaccine indication as defined by the Advisory Committee on Immunization Practices (ACIP). The case-fatality rate among patients aged 18 to 64 years with an ACIP indication was 12.1% compared with 5.4% for those without an indication (relative risk, 2.2; 95% CI, 1.7-2.9).

CONCLUSIONS

Young children, elderly persons, and black persons of all ages are disproportionately affected by invasive pneumococcal disease. Current ACIP recommendations do not address a subset of persons aged 18 to 64 years but do include those at highest risk for death from invasive pneumococcal disease.

Herniated lumbar disc material as a source of free glutamate available to affect pain signals through the dorsal root ganglion

STUDY DESIGN

Combined prospective human cohort and prospective controlled animal model.

OBJECTIVES

To determine whether free glutamate is available in herniated disc material in concentrations sufficient to diffuse to glutamate receptors and affect the activity of neurons in the dorsal root ganglion that may transmit pain information.

SUMMARY OF BACKGROUND DATA

The severity of lumbar radicular pain cannot be fully explained by physical pressure on nerve roots or ganglions. In experimental models, inflammatory processes are relatively modest under conditions of disc herniation. The hypothesis for the current study was that the proteoglycan link and core proteins, which contain high fractions of acidic amino acids, may be a source of glutamate when enzymatically degraded in an environment without glutamate reuptake systems. Glutamate would be free to diffuse to the dorsal root ganglion to affect glutamate receptors.

METHODS

Disc material was harvested during surgery from herniated and nonherniated portions in patients undergoing elective lumbar disc surgery and subjected to immunohistochemistry and high-performance liquid chromatography for assessment of the presence of extracellular disc matrix glutamate. Miniosmotic pumps with differing concentrations of radiolabeled glutamate based on human data were implanted in the rat epidural space for 72 hours and dorsal root ganglion (DRG) in the region were harvested.

RESULTS

Densitometry of disc matrix demonstrated immunohistochemical evidence for significant extracellular glutamate (P < 0.002). High performance liquid chromatography showed significant concentrations of glutamate in disc material and significantly more in herniated than in nonherniated disc material (P < 0.05). Significant radiolabeling of the dorsal root ganglion after epidural glutamate infusion was found at concentrations two orders of magnitude below measured disc glutamate levels. Autoradiography demonstrated radiolabeling of adjacent DRG.

CONCLUSIONS

Glutamate originating from degenerated disc proteoglycan may diffuse to the dorsal root ganglion and effect glutamate receptors. Consideration may be given to treating disc radiculopathy with epidural glutamate receptor antagonists.

A developmental evaluation process for nurses: enhancing professional excellence

Healthcare organizations are challenged to provide an environment that enhances professional growth. Miami Valley Hospital responded by examining its evaluation system for clinical nurses and designing a developmental evaluation process. The result is an objective position description outlining global responsibilities of a nurse and a comprehensive, unit-specific assessment of performance. As nurses are guided and nurtured in their development, the opportunities for them to excel are unlimited.

Work production and work absorption in muscle strips from vertebrate cardiac and insect flight muscle fibers

Stretch activation, which underlies the ability of all striated muscles to do oscillatory work, is a prominent feature of both insect flight and vertebrate cardiac muscle. We have examined and compared work-producing and work-absorbing processes in skinned fibers of Drosophila flight muscle, mouse papillary muscle, and human ventricular strips. Using small amplitude sinusoidal length perturbation analysis, we distinguished viscoelastic properties attributable to crossbridge processes from those attributable to other structures of the sarcomere. Work-producing and work-absorbing processes were identified in Ca(2+)-activated fibers by deconvolving complex stiffness data. An 'active' work-producing process ("B"), attributed to crossbridge action, was identified, as were two work-absorbing processes, one attributable to crossbridge action ("C") and the other primarily to viscoelastic properties of parallel passive structures ("A"). At maximal Ca(2+)-activation (pCa 5, 27 degrees C), maximum net power output (processes A, B and C combined) occurs at a frequency of: 1.3 +/- 0.1 Hz for human, 10.9 +/- 2.2 Hz for mouse, and 226 +/- 9 Hz for fly, comparable to the resting heart rate of the human (1 Hz, 37 degrees C) and mouse (10 Hz, 37 degrees C) and to the wing beat frequency of the fruit fly (200 Hz, 22 degrees C). Process B maximal work production per myosin head is 7-11 x 10(-21) J per perturbation cycle, equivalent to approximately 2 kT of energy. Process C maximal work absorption is about the same magnitude. The equivalence suggests the possibility that a thermal ratchet type mechanism operates during small amplitude length perturbations. We speculate that there may be a survival advantage in having a mechanical energy dissipater (i.e., the C process) at work in muscles if they can be injuriously stretched by the system in which they operate.

Sexual and AIDS-Related Knowledge, Attitudes and Behaviors of Adolescents in Sierra Leone, West Africa

A survey of 307 Sierra Leonean adolescents between the ages of thirteen and nineteen was assessed to determine their sexual and AIDS-related knowledge, attitudes, and behaviors. Results indicate high sexual activity rates among the sampled group; 89 percent of the males and 68 percent of the females had engaged in sexual intercourse. The mean age at first sexual intercourse was found to be 14.4 years for males and 15.1 years for females. Sixty-five percent of the males and 35 percent of the females reported having three or more sexual partners over their lifetime. Other findings included high rates of STDs and HIV/AIDS, low reported condom use, low reported use of other birth control methods, and low knowledge scores concerning pregnancy prevention, HIV/AIDS and STDs. Implications of these findings are discussed.

A starch-hemoglobin resuscitative compound

A resuscitative compound in freeze-dried form has been synthesized between a modified starch and a tetremerically stabilized hemoglobin. In order to complex the hemoglobin, the starch has been prepared in mono-, di-, tri-, and tetra-aldehyde moieties. The hemoglobin was stabilized with low molecular weight diacids. Electrophoretic densitometric patterns indicate compound formation. The resulting polymers were characterized with respect to oxygen transport (biotonometry), Hill constant and P50. The in vivo evaluation indicates that these compounds are effective in exchange-transfusion experiments with rats to a level of about 85% replacement of whole blood. The final product is a cost-effective acellular resuscitative compound which can be stored in freeze-dried form at room temperature for extended periods of time. This artificial blood substitute can be reconstituted upon the addition of water.

Mixtures of erythrocytes and acellular fluids: an in vitro evaluation

To evaluate the biophysical properties of two acellular resuscitative fluids, experiments were performed using mixtures of these with suspensions of red blood cells. Two acellular resuscitative fluids were synthesized using a diacid to tetramerically stabilized hemoglobin and then complexing it with either a hydroxyethyl starch or a Tetronic Polyol. The new polymers were characterized with respect to the molecular weight, second virial coefficient and intrinsic viscosity. These fluids were then combined with red cells and the following measurements were made: non-Newtonian flow properties, malonamide induced hemolytic kinetics, sedimentation rates and oxygen transport. The in vitro evaluation indicates that these compounds are effective hemodiluents, offer protection to the red cell membrane and do not cause erythrocyte aggregation. The oxygen transport was satisfactory.

Homotypic antibody responses to fresh clinical isolates of human immunodeficiency virus

Human immunodeficiency virus type 1 (HIV-1) exhibits extensive genomic and antigenic diversity, which is thought to contribute to the failure of the host's immune response to control infection and prevent clinical progression. Part of this failure may be due to utilization by the virus of antigenic variation as a means to escape protective immune responses. Antibody-escape variants of HIV-1 were studied here using fresh clinical isolates and autologous plasmas. HIV-1 was isolated from the plasma of seven people who were all seropositive for at least 2 years, and symptomatic sometime during that period. Isolated viruses were confirmed as HIV-1 by the presence of reverse transcriptase activity in infected culture supernatants, and by positive immunofluorescence using human monoclonal antibody to HIV-1 core protein. Plasma from these people were positive by Western immunoblot (DuPont) for most major HIV-1 (strain IIIB) antigens. These plasmas neutralized three laboratory strains of HIV-1 (i.e., IIIB, RF, and MN) but did not neutralize the homotypic strain in five cases, and had greatly reduced neutralizing titers against the homotypic strain in two cases. Homotypic neutralizing antibodies were absent in autologous plasma obtained 3 months later. When antibody titers were measured by fixed-cell indirect immunofluorescence assays (IFAs), high titers of IgG (1:6400 to 1:25,600) were detected against HIV-1 IIIB, while low titers of only 1:20 to 1:160 were detected against homotypic viral antigens at the time of virus isolation, and remained low 12 and 16 weeks later. No class IgA, IgD, IgE, or IgM antibodies to homotypic viral antigens, as possible IgG-blocking antibodies, were detected by fixed-cell IFAs. Cross-reactions with heterologous donor's plasmas were observed in some cases, and in these cases the cross-reactions were unidirectional. Live-cell IFAs detected IgG in patient's plasma to HIV-1 IIIB-infected cells but not to cells infected with homotypic isolates. These results suggest that it is common for neutralization-resistant HIV-1 variants to appear during the course of infection, and that all or most antigens of these variants are capable of escaping antibody recognition.