Reaction monitoring via benchtop nuclear magnetic resonance spectroscopy: A practical comparison of on-line stopped-flow and continuous-flow sampling methods

The ability for nuclear magnetic resonance (NMR) spectroscopy to provide quantitative, structurally rich information makes this spectroscopic technique an attractive reaction monitoring tool. The practicality of NMR for this type of analysis has only increased in the recent years with the influx of commercially available benchtop NMR instruments and compatible flow systems. In this study, we aim to compare 19F NMR reaction profiles acquired under both on-line continuous-flow and stopped-flow sampling methods, with modern benchtop NMR instrumentation, and two reaction systems: a homogeneous imination reaction and a biphasic activation of a carboxylic acid to acyl fluoride. Reaction trends with higher data density can be acquired with on-line continuous-flow analyses, and this work highlights that representative reaction trends can be acquired without any correction when monitoring resonances with a shorter spin-lattice relaxation time (T1), and with the used flow conditions. On-line stopped-flow analyses resulted in representative reaction trends in all cases, including the monitoring of resonances with a long T1, without the need of any correction factors. The benefit of easier data analysis, however, comes with the cost of time, as the fresh reaction solution must be flowed into the NMR system, halted, and time must be provided for spins to become polarized in the instrument's external magnetic field prior to spectral measurement. Results for one of the reactions were additionally compared with the use of a high-field NMR.

A reliable external calibration method for reaction monitoring with benchtop NMR

Nuclear magnetic resonance (NMR) spectroscopy is a powerful analytical technique with the ability to acquire both quantitative and structurally insightful data for multiple components in a test sample. This makes NMR spectroscopy a desirable tool to understand, monitor, and optimize chemical transformations. While quantitative NMR (qNMR) approaches relying on internal standards are well-established, using an absolute external calibration scheme is beneficial for reaction monitoring as resonance overlap complications from an added reference material to the sample can be avoided. Particularly, this type of qNMR technique is of interest with benchtop NMR spectrometers as the likelihood of resonance overlap is only enhanced with the lower magnetic field strengths of the used permanent magnets. The included study describes a simple yet robust methodology to determine concentration conversion factors for NMR systems using single- and multi-analyte linear regression models. This approach is leveraged to investigate a pharmaceutically relevant amide coupling batch reaction. An on-line stopped-flow (i.e., interrupted-flow or paused-flow) benchtop NMR system was used to monitor both the 1,1'-carbonyldiimidazole (CDI) promoted acid activation and the amide coupling. The results highlight how quantitative measurements in benchtop NMR systems can provide valuable information and enable analysts to make decisions in real time.

Global fine-resolution data on springtail abundance and community structure

Springtails (Collembola) inhabit soils from the Arctic to the Antarctic and comprise an estimated ~32% of all terrestrial arthropods on Earth. Here, we present a global, spatially-explicit database on springtail communities that includes 249,912 occurrences from 44,999 samples and 2,990 sites. These data are mainly raw sample-level records at the species level collected predominantly from private archives of the authors that were quality-controlled and taxonomically-standardised. Despite covering all continents, most of the sample-level data come from the European continent (82.5% of all samples) and represent four habitats: woodlands (57.4%), grasslands (14.0%), agrosystems (13.7%) and scrublands (9.0%). We included sampling by soil layers, and across seasons and years, representing temporal and spatial within-site variation in springtail communities. We also provided data use and sharing guidelines and R code to facilitate the use of the database by other researchers. This data paper describes a static version of the database at the publication date, but the database will be further expanded to include underrepresented regions and linked with trait data.

The effect of tube quality on externally calibrated quantitative nuclear magnetic resonance analysis: How bad can it be?

Externally calibrated quantitative nuclear magnetic resonance (NMR) approaches offer practical means to simultaneously evaluate chemical identity and content without the addition of calibrants to the test sample. Despite continuous advances in external calibration over the last few decades, adoption of these approaches has been slower than expected. Variations in NMR tube geometry are a commonly overlooked factor that can have a substantial effect on externally calibrated quantitation methods. In this report, we investigate the extent to which tube-to-tube volume variability can affect quantitative NMR outcomes. The results highlight the importance of considering tube quality during the development stages of externally calibrated quantitative methods. In addition, we propose a simple, yet effective volume correction strategy using the residual protonated solvent signal that, based on experiments with mixed NMR tubes of varying quality, alleviates the effect of tube-to-tube variability.

Global data on earthworm abundance, biomass, diversity and corresponding environmental properties

Earthworms are an important soil taxon as ecosystem engineers, providing a variety of crucial ecosystem functions and services. Little is known about their diversity and distribution at large spatial scales, despite the availability of considerable amounts of local-scale data. Earthworm diversity data, obtained from the primary literature or provided directly by authors, were collated with information on site locations, including coordinates, habitat cover, and soil properties. Datasets were required, at a minimum, to include abundance or biomass of earthworms at a site. Where possible, site-level species lists were included, as well as the abundance and biomass of individual species and ecological groups. This global dataset contains 10,840 sites, with 184 species, from 60 countries and all continents except Antarctica. The data were obtained from 182 published articles, published between 1973 and 2017, and 17 unpublished datasets. Amalgamating data into a single global database will assist researchers in investigating and answering a wide variety of pressing questions, for example, jointly assessing aboveground and belowground biodiversity distributions and drivers of biodiversity change.

Survival in hospice patients with dementia: the effect of home hospice and nurse visits

BACKGROUND

Hospice patients with dementia are at increased risk for live discharge and long lengths of stay (>180 days), causing patient and family caregiver stress and burden. The location and timing of clinician visits are important factors influencing whether someone dies as expected, in hospice, or experiences a live discharge or long length of stay.

OBJECTIVE

Examine how home hospice and nurse visit frequency relate to dying in hospice within the Medicare-intended 6-month period.

DESIGN

Retrospective cohort study.

SETTING

Non-profit hospice agency.

PARTICIPANTS

Three thousand eight hundred and thirty seven patients with dementia who received hospice services from 2013 to 2017.

METHODS

Multivariable survival analyses examined the effects of receiving home hospice (vs. nursing home) and timing of nurse visits on death within 6 months of hospice enrollment, compared to live discharge or long length of stay. Models adjust for relevant demographic and clinical factors.

RESULTS

Thirty-nine percent (39%) of patients experienced live discharge or long length of stay. Home hospice patients were more likely to experience live discharge or long length of stays (HR for death: 0.77, 95%CI: 0.69-0.86, p < 0.001). Frequency of nurse visits was inversely associated with live discharge and long lengths of stay (HR for death: 2.87, 95%CI: 2.47-3.33, p < 0.001).

CONCLUSION

Nearly 40% of patients with dementia in our study experienced live discharge or a long length of stay. Additional research is needed to understand why home hospice may result in live discharge or a long length of stay for patients with dementia. Nurse visits were associated with death, suggesting their responsiveness to deteriorating patient health. Hospice guidelines may need to permit longer stays so community-dwelling patients with dementia, a growing segment of hospice patients, can remain continuously enrolled in hospice and avoid burden and costs associated with live discharge.

Towards an integrative understanding of soil biodiversity

Soil is one of the most biodiverse terrestrial habitats. Yet, we lack an integrative conceptual framework for understanding the patterns and mechanisms driving soil biodiversity. One of the underlying reasons for our poor understanding of soil biodiversity patterns relates to whether key biodiversity theories (historically developed for aboveground and aquatic organisms) are applicable to patterns of soil biodiversity. Here, we present a systematic literature review to investigate whether and how key biodiversity theories (species-energy relationship, theory of island biogeography, metacommunity theory, niche theory and neutral theory) can explain observed patterns of soil biodiversity. We then discuss two spatial compartments nested within soil at which biodiversity theories can be applied to acknowledge the scale-dependent nature of soil biodiversity.

Race, Ethnicity, and Other Risks for Live Discharge Among Hospice Patients with Dementia

OBJECTIVES

The end-of-life trajectory for persons with dementia is often protracted and difficult to predict, placing these individuals at heightened risk of live discharge from hospice. Risks for live discharge due to condition stabilization or failure to decline among patients with dementia are not well established. Our aim was to identify demographic, health, and hospice service factors associated with live discharge due to condition stabilization or failure to decline among hospice patients with dementia.

DESIGN

Retrospective cohort study.

SETTING

A large not-for-profit agency in New York City.

PARTICIPANTS

A total of 2629 hospice patients with dementia age 65 years and older.

MEASUREMENTS

Primary outcome was live discharge from hospice due to condition stabilization or failure to decline (vs death). Measures include demographic factors (race/ethnicity, Medicaid, sex, age, marital status, parental status), health characteristics (primary dementia diagnosis, comorbidities, functional status, prior hospitalization), and hospice service (location, length of service, number and timing of nurse visits).

RESULTS

Logistic regression models indicated that compared with white hospice patients with dementia, African American and Hispanic hospice patients with dementia experienced increased risk of live discharge (African American: adjusted odds ratio [aOR] = 2.42; 95% confidence interval [CI] = 1.34-4.38; Hispanic: aOR = 2.99; 95% CI = 1.81-4.94). Home hospice (aOR = 7.57; 95% CI = 4.04-14.18), longer length of service (aOR = 1.04; 95% CI = 1.04-1.05), and more days between nurse visits and discharge (aOR = 1.86; 95% CI = 1.56-2.21) were also associated with live discharge.

CONCLUSION

To avoid burdensome and disruptive transitions out of hospice in patients with dementia, interventions to reduce live discharge due to condition stabilization or failure to decline should be tailored to meet the needs of African American, Hispanic, and home hospice patients. Policies regarding sustained hospice eligibility should account for the variable and protracted end-of-life trajectory of patients with dementia. J Am Geriatr Soc 68:551-558, 2020.

Application of CRAFT in two-dimensional NMR data processing

Two-dimensional (2D) data are typically truncated in both dimensions, but invariably and severely so in the indirect dimension. These truncated FIDs and/or interferograms are extensively zero filled, and Fourier transformation of such zero-filled data is always preceded by a rapidly decaying apodization function. Hence, the frequency line width in the spectrum (at least parallel to the evolution dimension) is almost always dominated by the apodization function. Such apodization-driven line broadening in the indirect (t₁ ) dimension leads to the lack of clear resolution of cross peaks in the 2D spectrum. Time-domain analysis (i.e. extraction of frequency, amplitudes, line width, and phase parameters directly from the FID, in this case via Bayesian modeling into a tabular format) of NMR data is another approach for spectral resonance characterization and quantification. The recently published complete reduction to amplitude frequency table (CRAFT) technique converts the raw FID data (i.e. time-domain data) into a table of frequencies, amplitudes, decay rate constants, and phases. CRAFT analyses of time-domain data require minimal or no apodization prior to extraction of the four parameters. We used the CRAFT processing approach for the decimation of the interferograms and compared the results from a variety of 2D spectra against conventional processing with and without linear prediction. The results show that use of the CRAFT technique to decimate the t₁ interferograms yields much narrower spectral line width of the resonances, circumventing the loss of resolution due to apodization. Copyright © 2016 John Wiley & Sons, Ltd.

Meta-Analysis of Association Between Mediastinal Radiotherapy and Long-Term Heart Failure

This investigation sought to identify and quantify any increased risk of long-term heart failure (HF) after thoracic radiotherapy (RT) for cancer and identify any population covariates that corresponded with increased risk. Electronic databases were systematically searched for studies reporting relative risk, odds ratio, and hazard ratio (HR) for symptomatic HF more than 5 years after RT administration. Clinical characteristics, study design, univariable effect sizes, and associated 95% CIs were extracted. Univariable effect size was pooled and computed in a meta-analysis using random-effects model weighted by inverse variance. Six studies (45,669 patients) with weighted median follow-up duration of 13.9 years were included, each data-linkage study that reported HRs for HF. Pooled HR for long-term HF was significant (HR 1.83 [1.09 to 3.08], p = 0.022), with significant between-study heterogeneity (Q 43.38, df = 5, p <0.001, I² 88.47%). Statistical significance was lost when excluding studies of malignancies other than breast cancer or hematological malignancies and excluding studies with Newcastle-Ottawa scores <8, but the direction of effect and magnitude remained approximately the same. Subgroup and meta-regression analyses demonstrated that study differences in age at time of RT administration and duration of follow-up explained approximately 80% of observed heterogeneity. Earlier publication date was associated with increased HF risk. Other variables, including female proportion, proportion of adjuvant chemotherapy use, and sample size did not significantly impact the conclusions. In conclusion, RT approximately doubled the long-term risk of HF. This finding was associated with younger age at time of RT and longer follow-up duration, which explained approximately 80% of interstudy heterogeneity.

Improved Efficiency of Muller’s Muscle Resection Through the Use of Locking Forceps In Lieu of Traction Sutures

Muller’s muscle resection (MMR) surgery is effective for repair of eyelid ptosis. We describe an efficient modification to the MMR surgery, as described by Putterman, which uses locking 0.5-mm forceps, in place of retraction sutures, to retract the conjunctiva and Muller’s muscle while the ptosis clamp is applied. A chart review was performed to identify 100 consecutive patients starting from January 2015 who underwent the described technique of MMR. Primary end points were need for reoperation or complications. Pathologic specimens were reviewed for similarity between the standard approach using retraction sutures and the modified technique using locking forceps. All 100 patients had satisfactory surgical outcomes. There were no complications or reoperations needed. Pathologic analysis on tissue from the standard technique and modified technique was similar. The described technique is a technically easy, cost-effective, and logistically feasible modification that ptosis surgeons could adopt immediately.

A comprehensive model for correcting RNFL readings of varying signal strengths in cirrus optical coherence tomography

PURPOSE

To develop a model for the Cirrus HD-OCT that allows for the comparison of retinal nerve fiber layer (RNFL) thickness measurements with dissimilar signal strengths (SS) and accounts for test-retest variability.

METHODS

Retinal nerve fiber layers were obtained in normals using the Cirrus optic disc cube 200 × 200 protocol during a single encounter. Five RNFL scans were obtained with a SS of 9 or 10. Diffusion lens filters were used to degrade SS to obtain five scans at each SS group of 7 or 8, 5 or 6, and 3 or 4. The relationship between average RNFL thickness and SS was established, and an equation was developed to allow for adjustment of an RNFL measurement had it been a SS of 7. Intravisit interclass correlation coefficient (ICC) and coefficient of variation (CV) parameter estimates for each SS group were calculated. Repeatability and upper tolerance limit were calculated as 1.96 × √2 × within-subject standard deviation (Sw) and 1.645 × √2 × Sw, respectively.

RESULTS

There was a linear relationship between average RNFL and SS. RNFLadj = RNFL - 1.03*SS + 7.21 allows for the adjustment of RNFL readings to the same SS. Interclass correlation coefficients and CVs were good for all measurements down to SS of 3 or 4. Repeatability and upper tolerance limit were 5.24 and 4.40 μm, respectively.

CONCLUSIONS

Our model adjusts RNFL readings based on SS and includes an upper tolerance limit of 5 μm. If validated, this model could improve the detection of real RNFL changes. Further study to validate this model should be performed before widespread use is adopted.

GramAlign: fast alignment driven by grammar-based phylogeny

Multiple sequence alignment involves identifying related subsequences among biological sequences. When matches are found, the associated pieces are shifted so that when sequences are presented as successive rows-one sequence per row-homologous residues line-up in columns. Exact alignment of more than a few sequences is known to be computationally prohibitive. Thus many heuristic algorithms have been developed to produce good alignments in an efficient amount of time by determining an order by which pairs of sequences are progressively aligned and merged. GRAMALIGN is such a progressive alignment algorithm that uses a grammar-based relative complexity distance metric to determine the alignment order. This technique allows for a computationally efficient and scalable program useful for aligning both large numbers of sequences and sets of long sequences quickly. The GRAMALIGN software is available at http://bioinfo.unl.edu/gramalign.php for both source code download and a web-based alignment server.

(1) H-NMR quantification of major saccharides in açaí raw materials: a comparison of the internal standard methodology with the absolute intensity qNMR method

INTRODUCTION

While the use of internal standard methodology for qNMR is a proven and reliable form of quantification, simplified alternative approaches are needed. Agilent's absolute intensity qNMR utility software is a valuable alternative that has not yet been subjected to validation in the peer-reviewed literature.

OBJECTIVE

To provide validation of Agilent's absolute intensity qNMR method with a specific application to natural product quantification by measuring saccharide content in açaí materials.

METHODS

In order to validate the method, calibration test samples of ibuprofen were prepared in DMSO-d6 at nine different concentrations and measured with (1) H-NMR. A minimum of 40 spectra were collected for each sample, and the absolute intensity utility was used for quantification. The same methodology was then applied to the açaí materials, creating triplicates for each of the materials and using 3-(trimethylsilyl)-1-propanesulphonic acid sodium salt in water-d2 as both the solvent and internal standard. (1) H-NMR spectra were collected, and the amounts of glucose, sucrose and fructose were determined using both the internal standard approach and the absolute intensity qNMR method.

RESULTS

Applying the absolute intensity utility to the ibuprofen samples demonstrated a linear response (R(2)  = 0.99943). For the açaí investigations, results obtained from the absolute intensity method were comparable to those obtained from the internal standard approach, with percentage differences ranging from 0.5-6.2%.

CONCLUSION

This study demonstrates the accuracy, precision and reliability of Agilent's absolute intensity qNMR method. In addition, practical information is provided for assessing the saccharide contents of açaí materials.

Development of an outcome measurement system for service planning for children and youth with special needs

AIM

This study described the process used in developing an outcome measurement framework for system planning to improve services for children and youth with special needs and their families in a Canadian province. The study reports the results of several parent-completed measures, which would be useful in service planning as well as the acceptability and utility of these measures for use by families and service centres.

METHODS/RESULTS

Development of a theoretical framework, consultation with key stakeholders, testing the utility of selected outcome measures and initial dissemination of results were critical elements in the successful development of an outcome system. Consultation with stakeholders confirmed use of the International Classification of Functioning, Disability and Health and the child-within-family-within community model as theoretical frameworks while building valuable partnerships and identifying potential barriers to implementation. Pilot testing showed three outcome measures were feasible for families to complete and the measures provided information about services for children that was valuable to families as well as service providers. Gaps in service delivery were identified and the need for better communication between service providers and communities to facilitate integrated services was highlighted.

CONCLUSION

The findings from this study can be used to implement an outcome measurement system for children with special needs and may serve as a resource for international researchers who are working to develop valid tools as well as outcome systems that are useful for system planning.

Effect of radiation therapy on intraocular pressure in patients with Graves' orbitopathy

PURPOSE

To describe the effect of radiation therapy on intraocular pressure in patients who have had orbital radiation for Graves' orbitopathy, and to provide a descriptive analysis of these patients.

DESIGN

Retrospective case series.

PARTICIPANTS

24 consecutive patients referred for orbital radiation therapy for Graves' orbitopathy from December 1st, 2001 through July 31st, 2009.

INTERVENTION

Patients received a total of 2000 cGy fractionated over 10 days.

MAIN OUTCOME MEASURES

Medical records were reviewed for: demographics, tobacco history, ocular history, history related to Graves' disease, medications, visual field tests, retinopathy, and physical exam findings. The two-tailed Student's t-test was used to determine statistically significant differences in intraocular pressure before radiation therapy and 0-3 (T1), 4-6 (T2), 7-12 (T3), and 13-18 (T4) months following radiation therapy.

RESULTS

34 eyes were available for analysis. There was no correlation between intraocular pressure and SPECS scores. Mean intraocular pressure prior to radiation therapy was 18.15 ± 3.83 mm Hg. Patients who had orbital decompression, eye muscle surgery, or glaucoma were excluded from the final analysis. There were 7, 11, 14, and 11 eyes with data at times T1, T2, T3, and T4 following radiation therapy, respectively. There was a significant decrease in mean intraocular pressure at T2, T3 and T4 of 26.00% ± 9.25%, 11.75% ± 27.58%, and 16.72% ± 13.94%, respectively.

CONCLUSIONS

There was a significant drop in mean intraocular pressure between 4 and 18 months after radiation therapy in our patient population. The mechanism by which this decrease in intraocular pressure occurs is not understood.

Assessment of environmental factors in disabled children 2-12 years: development and reliability of the Craig Hospital Inventory of Environmental Factors (CHIEF) for Children-Parent Version

BACKGROUND

Children with disabilities and their families experience environmental barriers in the school and community environments. There is a need to understand and appropriately measure environmental factors that influence activity and participation for disabled children. The purpose of this paper is to describe the adaptation process of the Craig Hospital Inventory of Environmental Factors (CHIEF) to make it suitable as a parent proxy measure for disabled children aged 2-12 years.

METHODS

The adaptation process consisted of four steps using data from previous research conducted at CanChild: (i) analysis of item-total correlations from all items on the CHIEF; (ii) frequency of endorsement; (iii) determination of the representativeness of the questions; and (iv) correlations on selected items. Once the items were selected, a test-retest reliability study was conducted.

RESULTS

The internal consistencies (α) for the time 1 and time 2 administrations were 0.76 and 0.78, respectively. Test-retest reliability of the questionnaire was ICC = 0.73 for the total product score.

CONCLUSION

The 10-item CHIEF for Children-Parent Version is an acceptable, easy-to-complete and reliable measure of perceived environmental barriers for disabled children 2-12 years of age.

Age and growth of two newly established invasive populations of Tilapia mariae in northern Australia

Sagittal otoliths were used to age the samples of Tilapia mariae collected from a coastal river and an impoundment. Validation of sagittae checks was achieved using both quantitative marginal increment analysis and by tetracycline marking of the otoliths of fish kept in tanks and in a farm dam. The annulus pattern on the otoliths was generally clear and their formation appeared to be temperature related and largely completed in the Austral spring around September and October. Male T. mariae grow faster and larger than females and the maximum ages of fish from the coastal river and impoundment was 9+ and 4+ years, respectively. Past fish surveys and the absence of older age classes in the impoundment population would suggest that this population was only very recently established.

Reproductive strategies of two invasive tilapia species Oreochromis mossambicus and Tilapia mariae in northern Australia

The reproductive biology of two invasive tilapia species, Oreochromis mossambicus and Tilapia mariae, resident in freshwater habitats in north-eastern Australia was investigated. Oreochromis mossambicus exhibited plasticity in some of its life-history characteristics that enhanced its ability to occupy a range of habitats. These included a shallow, weed-choked, freshwater coastal drain that was subject to temperature and dissolved oxygen extremes and water-level fluctuations to cooler, relatively high-altitude impoundments. Adaptations to harsher conditions included a decreased total length (L(T) ) and age (A) at 50% maturity (m50), short somatic growth intervals, early maturation and higher relative fecundities. Potential fecundity in both species was relatively low, but parental care ensured high survival rates of both eggs and larvae. No significant difference in the relative fecundity of T. mariae populations in a large impoundment and a coastal river was found, but there were significant differences in relative fecundities between several of the O. mossambicus populations sampled. Total length (L(T) ) and age at 50% maturity of O. mossambicus populations varied considerably depending on habitat. The L(Tm50) and A(m50) values for male and female O. mossambicus in a large impoundment were considerably greater than for those resident in a small coastal drain. Monthly gonad developmental stages and gonado-somatic indices suggested that in coastal areas, spawning of O. mossambicus and T. mariae occurred throughout most of the year while in cooler, high-altitude impoundments, spawning peaked in the warmer, summer months. The contribution these reproductive characteristics make to the success of both species as colonizers is discussed in the context of future control and management options for tilapia incursions in Australia.

Amphidromy links a newly documented fish community of continental Australian streams, to oceanic islands of the west Pacific

BACKGROUND

Indo-Pacific high island streams experience extreme hydrological variation, and are characterised by freshwater fish species with an amphidromous life history. Amphidromy is a likely adaptation for colonisation of island streams following stochastic events that lead to local extirpation. In the Wet Tropics of north-eastern Australia, steep coastal mountain streams share similar physical characteristics to island systems. These streams are poorly surveyed, but may provide suitable habitat for amphidromous species. However, due to their ephemeral nature, common non-diadromous freshwater species of continental Australia are unlikely to persist. Consequently, we hypothesise that coastal Wet Tropics streams are faunally more similar, to distant Pacific island communities, than to nearby faunas of large continental rivers.

METHODS/PRINCIPAL FINDINGS

Surveys of coastal Wet Tropics streams recorded 26 species, 10 of which are first records for Australia, with three species undescribed. This fish community is unique in an Australian context in that it contains mostly amphidromous species, including sicydiine gobies of the genera Sicyopterus, Sicyopus, Smilosicyopus and Stiphodon. Species presence/absence data of coastal Wet Tropics streams were compared to both Wet Tropics river networks and Pacific island faunas. ANOSIM indicated the fish fauna of north-eastern Australian coastal streams were more similar to distant Pacific islands (R = 0.76), than to nearby continental rivers (R = 0.98).

MAIN CONCLUSIONS/SIGNIFICANCE

Coastal Wet Tropics streams are faunally more similar to distant Pacific islands (79% of species shared), than to nearby continental fauna due to two factors. First, coastal Wet Tropics streams lack many non-diadromous freshwater fish which are common in nearby large rivers. Second, many amphidromous species found in coastal Wet Tropics streams and Indo-Pacific islands remain absent from large rivers of the Wet Tropics. The evolutionary and conservation significance of this newly discovered Australian fauna requires clarification in the context of the wider amphidromous fish community of the Pacific.

A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences

Background

We propose a sequence clustering algorithm and compare the partition quality and execution time of the proposed algorithm with those of a popular existing algorithm. The proposed clustering algorithm uses a grammar-based distance metric to determine partitioning for a set of biological sequences. The algorithm performs clustering in which new sequences are compared with cluster-representative sequences to determine membership. If comparison fails to identify a suitable cluster, a new cluster is created.

Results

The performance of the proposed algorithm is validated via comparison to the popular DNA/RNA sequence clustering approach, CD-HIT-EST, and to the recently developed algorithm, UCLUST, using two different sets of 16S rDNA sequences from 2,255 genera. The proposed algorithm maintains a comparable CPU execution time with that of CD-HIT-EST which is much slower than UCLUST, and has successfully generated clusters with higher statistical accuracy than both CD-HIT-EST and UCLUST. The validation results are especially striking for large datasets.

Conclusions

We introduce a fast and accurate clustering algorithm that relies on a grammar-based sequence distance. Its statistical clustering quality is validated by clustering large datasets containing 16S rDNA sequences.

Grammar-based distance in progressive multiple sequence alignment

BACKGROUND

We propose a multiple sequence alignment (MSA) algorithm and compare the alignment-quality and execution-time of the proposed algorithm with that of existing algorithms. The proposed progressive alignment algorithm uses a grammar-based distance metric to determine the order in which biological sequences are to be pairwise aligned. The progressive alignment occurs via pairwise aligning new sequences with an ensemble of the sequences previously aligned.

RESULTS

The performance of the proposed algorithm is validated via comparison to popular progressive multiple alignment approaches, ClustalW and T-Coffee, and to the more recently developed algorithms MAFFT, MUSCLE, Kalign, and PSAlign using the BAliBASE 3.0 database of amino acid alignment files and a set of longer sequences generated by Rose software. The proposed algorithm has successfully built multiple alignments comparable to other programs with significant improvements in running time. The results are especially striking for large datasets.

CONCLUSION

We introduce a computationally efficient progressive alignment algorithm using a grammar based sequence distance particularly useful in aligning large datasets.

Characterization of flavonols in cranberry (Vaccinium macrocarpon) powder

Flavonoids were extracted from cranberry powder with acetone and ethyl acetate and subsequently fractionated with Sephadex LH-20 column chromatography. The fraction eluted with a 60% methanol solution was composed primarily of phenolic constituents with maximum absorbance at 340 nm. A high-performance liquid chromatography procedure was developed, which resolved 22 distinct peaks with UV/vis and mass spectra corresponding to flavonol glycoside conjugates. Six new constituents not previously reported in cranberry or in cranberry products were determined through NMR spectroscopy to be myricetin-3-beta-xylopyranoside, quercetin-3-beta-glucoside, quercetin-3-alpha-arabinopyranoside, 3'-methoxyquercetin-3-alpha-xylopyranoside, quercetin-3-O-(6' '-p-coumaroyl)-beta-galactoside, and quercetin-3-O-(6' '-benzoyl)-beta-galactoside. Quercetin-3-O-(6' '-p-coumaroyl)-beta-galactoside and quercetin-3-O-(6' '-benzoyl)-beta-galactoside represent a new class of cranberry flavonol compounds with three conjugated components consisting of a flavonol, sugar, and carboxylic acid (benzoic or hydroxycinnamic acids). This is also the first report identifying quercetin-3-arabinoside in both furanose and pyranose forms in cranberry. Elucidation of specific flavonol glycosides in cranberry is significant since the specificity of the sugar moiety may play a role in the bioavailability of the flavonol glycosides in vivo.

Nutrient balance in the diet of spring-calving, pasture-fed dairy cows

AIMS

To report the nutrient composition of pastures fed to spring-calving dairy cows in the Manawatu region of New Zealand, and describe changes in the nutrient composition of these pastures over a 12-month period. Having done this we sought to: (1) compare the nutrient composition of the pasture offered with the nutrient requirements of spring-calving dairy cows; (2) identify periods when individual nutrient surpluses and deficits are likely; and, (3) identify nutrients that demonstrate a high level of variability between sampling occasions.

METHODS

Seven farms took part in the study. Each farm was visited monthly from August 1996 to July 1997. Samples of pasture were taken at each visit and submitted for estimation of dry matter (DM), metabolisable energy (ME), crude protein (CP), non-structural carbohydrate (NSC), neutral detergent fibre (NDF), acid detergent fibre (ADF), calcium (Ca), phosphorus (P), magnesium (Mg), sodium (Na), potassium (K), chlorine (Cl), sulphur (S), iron (Fe), copper (Cu) and zinc (Zn), and dietary cation-anion differences (DCAD).

RESULTS

Sampled pastures were characterised by low to marginal ME, NSC, Ca, Mg, and Zn concentrations when compared with recommended dietary nutrient concentrations for lactating and non-lactating dairy cattle in New Zealand. Analyses revealed relatively high CP, NDF and K concentrations, and DCAD.

CONCLUSIONS

These analyses identify broad trends in the nutrient balance of a pasture-only feeding regime and provide a useful reference for planning feed strategies for spring-calving, pasture-fed dairy herds in this region. Recommended changes to on-farm practice should be made after considering the whole farm system, rather than being made solely on the basis of perceived deficiencies or excesses of individual nutrients.

Gross motor function of children with down syndrome: creation of motor growth curves

OBJECTIVE

To create gross motor function growth curves for children with Down syndrome (DS) and to estimate the probability that motor functions are achieved by different ages.

DESIGN

Nonlinear growth curve analysis by using a 2-parameter (rate, upper limit) model.

SETTING

Early intervention programs, schools, and children's homes.

PARTICIPANTS

One hundred twenty-one children with DS, ages 1 month to 6 years.

MAIN OUTCOME MEASURES

Gross Motor Function Measure (GMFM) and severity of motor impairment.

RESULTS

The curves for children with mild (n = 51) and moderate/severe (n = 70) impairment were characterized by a greater increase in GMFM scores during infancy and smaller increases as the children approached the predicted maximum score of 85.9 or 87.9. The estimated probability that a child would roll by 6 months was 51%; sit by 12 months, 78%; crawl by 18 months, 34%; walk by 24 months, 40%; and run, walk up stairs, and jump by 5 years, 45% to 52%.

CONCLUSIONS

Children with DS require more time to learn movements as movement complexity increases. Impairment severity affected the rate but not the upper limit of motor function. The results have implications for counseling parents, making decisions about motor interventions, and anticipating the time frame for achievement of motor functions.

Validation of a model of gross motor function for children with cerebral palsy

BACKGROUND AND PURPOSE

Development of gross motor function in children with cerebral palsy (CP) has not been documented. The purposes of this study were to examine a model of gross motor function in children with CP and to apply the model to construct gross motor function curves for each of the 5 levels of the Gross Motor Function Classification System (GMFCS).

SUBJECTS

A stratified sample of 586 children with CP, 1 to 12 years of age, who reside in Ontario, Canada, and are known to rehabilitation centers participated.

METHODS

Subjects were classified using the GMFCS, and gross motor function was measured with the Gross Motor Function Measure (GMFM). Four models were examined to construct curves that described the nonlinear relationship between age and gross motor function.

RESULTS

The model in which both the limit parameter (maximum GMFM score) and the rate parameter (rate at which the maximum GMFM score is approached) vary for each GMFCS level explained 83% of the variation in GMFM scores. The predicted maximum GMFM scores differed among the 5 curves (level I=96.8, level II=89.3, level III=61.3, level IV=36.1, and level V=12.9). The rate at which children at level II approached their maximum GMFM score was slower than the rates for levels I and III. The correlation between GMFCS levels and GMFM scores was (.91. Logistic regression, used to estimate the probability that children with CP are able to achieve gross motor milestones based on their GMFM total scores, suggests that distinctions between GMFCS levels are clinically meaningful.

CONCLUSION AND DISCUSSION

Classification of children with CP based on functional abilities and limitations is predictive of gross motor function, whereas age alone is a poor predictor. Evaluation of gross motor function of children with CP by comparison with children of the same age and GMFCS level has implications for decision making and interpretation of intervention outcomes.

2J,(3)J-HMBC: A new long-range heteronuclear shift correlation technique capable of differentiating (2)J(CH) from (3)J(CH) correlations to protonated carbons

The development of a series of new, accordion-optimized long-range heteronuclear shift correlation techniques has been reported. A further derivative of the constant time variable delay introduced in the IMPEACH-MBC experiment, a STAR (Selectively Tailored Accordion F(1) Refocusing) operator is described in the present report. Incorporation of the STAR operator with the capability of user-selected homonuclear modulation scaling as in the CIGAR-HMBC experiment, into a long-range heteronuclear shift correlation pulse sequence, (2)J,(3)J-HMBC, affords for the first time in a proton-detected experiment the means of unequivocally differentiating two-bond ((2)J(CH)) from three-bond ((3)J(CH)) long-range correlations to protonated carbons. Copyright 2000 Academic Press.

A comparison of inverse-detected heteronuclear NMR performance: conventional vs cryogenic microprobe performance

We report a comparison of the results obtained at 500 MHz for heteronuclear shift correlation (HSQC) experiments with very small natural product samples using conventional and cryogenically cooled 3 mm NMR probes. The cryo probe affords a 12- to 16-fold reduction in data acquisition time for a comparable signal-to-noise ratio.

A prospective randomized evaluation of a hygroscopic cervical dilator, Dilapan, in the preinduction ripening of patients undergoing induction of labor

OBJECTIVE

Our purpose was to investigate the safety and efficacy of a synthetic intracervical hygroscopic dilator, Dilapan (Gynotech, Inc., Middlesex, N.J.), on ripening the cervix before medically indicated induction of labor.

STUDY DESIGN

Two hundred forty patients with a Bishop score of < or = 4 were prospectively randomized to receive either preinduction synthetic hygroscopic dilators (n = 112) or no pretreatment (n = 128) before oxytocin induction.

RESULTS

Compared with controls, the dilator group exhibited a significant change in median Bishop score, but there was no significant difference in length of labor (dilator 18.8 +/- 12.8 hours vs control 21.7 +/- 14.8 hours) or in the cesarean section rate (dilator 41/112 [36.6%] vs control 49/128 [38.3%]). Relative proportions of nulliparous and multiparous patients, infant weights, and cervical dilation at the time of cesarean section were not significantly different between groups. No adverse maternal or fetal effects could be attributed to use of the device.

CONCLUSIONS

Preinduction cervical ripening with hygroscopic dilators does not shorten the length of labor or lower the cesarean section rate in patients undergoing induction of labor.

The female pelvic mass. Diagnosis and management

When a pelvic mass is encountered in a female patient, there are several tools available to the physician as diagnostic aids. The patient's age, history, and physical examination; diagnostic imaging studies; and laboratory tests can contribute valuable information to the diagnosis and management of the case. It is essential for today's physician to become familiar with these tools and to be able to direct management appropriately.

The Gross Motor Performance Measure: validity and responsiveness of a measure of quality of movement

BACKGROUND AND PURPOSE

This article presents the results of a study to validate a measure of gross motor performance for its capacity to detect changes in the quality of movement in children with cerebral palsy aged 0 to 12 years.

SUBJECTS AND METHODS

On two occasions, 4 to 6 months apart, physical therapists from three children's treatment centers assessed 106 children with cerebral palsy, 18 children who had sustained an acute head injury, and 29 nondisabled children. Validity was demonstrated by comparing changes on the measure across diagnoses, severity, and age groups.

RESULTS

Several a priori hypotheses were supported; however, relationships with parent and therapist ratings were not clearly demonstrated.

CONCLUSION AND DISCUSSION

The measure was found to be differentially responsive to changes in "stable" and "responsive" groups.

Reliability of the Gross Motor Performance Measure

BACKGROUND AND PURPOSE

The reporting of reliability coefficients and the method of their determination is expected of test developers. The purpose of this study was to estimate the interrater, intrarater, and test-retest reliability of the Gross Motor Performance Measure, a measure of quality of movement designed to accompany the Gross Motor Function Measure.

SUBJECTS

Subjects were 28 children (25 with cerebral palsy, 2 nondisabled, 1 with head injury) between the ages of 1 and 10 years.

METHODS

Reliability data were obtained from assessments of 19 therapists.

RESULTS

Intraclass correlation coefficients for reliability varied from .92 to .96 for the total scores and from .84 to .94 for the five attribute scores.

CONCLUSION AND DISCUSSION

When the Gross Motor Performance Measure was administered by therapists who are familiar with the Gross Motor Function Measure and had a 1-day training workshop, reliability of the total scores was above recommended minimums. Scores of single attributes were less reproducible.

Training users in the gross motor function measure: methodological and practical issues

BACKGROUND AND PURPOSE

The Gross Motor Function Measure (GMFM) is a criterion-referenced observational measure for assessing change in gross motor function for children with cerebral palsy (CP). The purposes of this report are to present data on the effects of training pediatric developmental therapists to administer and score the GMFM and to discuss some practical and methodological issues associated with training.

SUBJECTS AND METHODS

A weighted kappa estimate pretraining and posttraining workshop was used to determine participants' agreement of scoring a videotaped GMFM assessment against experts' scoring of the same videotaped assessment. Several children with CP, representing a spectrum of ages, severities, and levels of function, were shown on the videotape.

RESULTS

There was a significant improvement in agreement from a mean kappa of .58 to .82 (t = 15.38, df = 75, P < .001) for the first group and from .81 to .92 (t = 10.91, df = 72, P < .001) for the second group following training.

CONCLUSION AND DISCUSSION

Although there are a number of advantages to using videotapes to train test users and to assess scoring reliability, this method does not evaluate participants' ability to administer the measure. Further work is needed to determine whether reliability is maintained in a clinical situation in which it is necessary to both administer and score the GMFM.

Fiber gene and genomic origin of human adenovirus type 4

The origin of human adenovirus type 4 (Ad4), an important pathogen and candidate vaccine vector, has been the subject of speculation. Ad4 is unusual among adenoviruses, because it is the single known serotype of subgroup E. Some biological and biochemical properties of Ad4 resemble those of serotypes from subgroups B and C. The length of Ad4 fiber is intermediate between that of subgroup B and C fibers. We sequenced the Ad4 fiber gene, locus of the determinant(s) of adenovirus serotype. The number of repeating DNA sequence motifs in the shaft domain of the Ad4 fiber gene is consistent with its reported length. Regional phylogenetic analysis of Ad4 was undertaken, comparing DNA sequences of early genes and fiber genes from representative adenoviruses. The Ad4 fiber gene has close phylogenetic relationship to subgroup C fiber genes. This is in distinct contrast to the closer relationship of Ad4 to subgroup B adenoviruses in early gene sequences, distributed across the left 70% of the viral genome. We propose that Ad4 originated by recombination of genomes resembling contemporary subgroup B and subgroup C adenoviruses. This event may have occurred so recently that divergence of subgroup E serological determinants has yet to be observed.