Limited Sample Set Research Articles

SEARCHING THE LONG TAIL: HIDDEN STRUCTURE IN SOCIAL TAGGING

In this paper we explore a method of decomposition of compound tags found in social tagging systems and outline several results, including improvement of search indexes, extraction of semantic information, and benefits to usability. Analysis of tagging habits demonstrates that social tagging systems such as del.icio.us and flickr include both formal metadata, such as geotags, and informally created metadata, such as annotations and descriptions. The majority of tags represent informal metadata; that is, they are not structured according to a formal model, nor do they correspond to a formal ontology. Statistical exploration of the main tag corpus demonstrates that such searches use only a subset of the available tags; for example, many tags are composed as ad hoc compounds of terms. In order to improve accuracy of searching across the data contained within these tags, a method must be employed to decompose compounds in such a way that there is a high degree of confidence in the result. An approach to decomposition of English-language compounds, designed for use within a small initial sample tagset, is described. Possible decompositions are identified from a generous wordlist, subject to selective lexicon snipping. In order to identify the most likely, a Bayesian classifier is used across term elements. To compensate for the limited sample set, a word classifier is employed and the results classified using a similar method, resulting in a successful classification rate of 88%, and a false negative rate of only 1%.

Profiling of Glycans in Serum for the Discovery of Potential Biomarkers for Ovarian Cancer

A glycomic approach is developed to identify oligosaccharide markers for ovarian cancer by rapidly profiling globally released oligosaccharides. Glycoproteins shed by cancer cells are found in the supernatant (or conditioned media) of cultured cells. In this approach, shed glycoproteins are profiled for their oligosaccharide content using beta-elimination conditions. Changes in glycosylation are monitored by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICR-MS). Because shed glycoproteins would also be found in serum, similar glycan profiling was performed to observe potential oligosaccharide markers. Oligosaccharide profiling data on a limited set of patient and normal serum samples were studied to determine potential glycan markers in ovarian cancer. We were able to demonstrate the presence of at least 15 unique serum glycan markers in all patients but absent in normal individuals. To determine the structure of the glycan biomarkers, a number of the ions were isolated and further analyzed using infrared multiphoton dissociation (IRMPD). One major advantage of this approach is that glycans are examined directly from patient sera without the need to obtain cancer biopsy specimens or to purify glycosylated proteins from these specimens.

Effect of Sex and Assay Method on Serum Concentrations of Growth Hormone in Patients with Acromegaly and in Healthy Controls

Diagnosis and follow-up of acromegaly is based on measurements of serum growth hormone (GH) concentrations during an oral glucose tolerance test (OGTT). A nadir value <1 microg/L is commonly used to define a normal response, but some authors suggest lower cutoff values. To compare the results and subsequent patient classification obtained with 3 GH assays, we obtained basal serum samples from 78 apparently healthy adult controls (43 women and 35 men; median age, 32.5 years) and from 71 treated (44 women and 27 men; median age, 55.2 years) and 7 untreated acromegaly patients (4 women and 3 men; median age, 54.6 years), and OGTT was performed on all patients and on 72 of the 78 controls. GH was determined by 2 immunometric assays-a double monoclonal (AutoDELFIA; Wallac) and a monopolyclonal (Immulite 2000; DPC) assay-and in a limited set of samples by an RIA (Spectria RIA; Orion). There was a strong correlation (r = 0.995; P < 0.001) between the 2 immunometric methods, but the results obtained with the Immulite 2000 were, on average, 1.4-fold higher than those obtained with the AutoDELFIA. At concentrations around the cutoff (1 microg/L), however, the difference was approximately 2-fold. Overall, the Orion RIA method also showed a good correlation (r = 0.951-0.959) with the other methods, but it did not measure concentrations <2 microg/L. Women had higher basal and OGTT nadir GH concentrations than men. Reference intervals should be determined separately for each method, and the need for establishing sex-specific reference values should be investigated.

Raman identification of glassy silicates used in ceramics, glass and jewellery: a tentative differentiation guide

As an optical method, Raman microspectroscopy offers a great advantage over most other techniques in that it can be performed without any contact with the studied artefact, both at the laboratory using high-resolution, large spectral window instruments, and on site using medium resolution, portable instruments. Six years of experience on various materials has enabled us to propose a tentative guide to identify different types of glassy silicates and to classify them as a function of their composition. In previous papers, different families were recognised empirically using a limited set of samples and the relationship between the peak area ratio (A500/A1000) of the SiO bending (∼500 cm−1) and stretching (i.e. ∼1000 cm−1) envelopes, and the different components of the latter peak were established for porcelain glazes. In this paper, we extend the procedure to a larger set of samples (30 representative samples with known compositions selected from hundreds of spectra). Additional relationships between the origin of the material, the Raman parameters and the glass composition (fluxing oxide content, ionicity ratio, etc.) are discussed. Finally we propose different procedures with different degrees of complexity (from two to multivariate treatment) to identify the glass composition. The method is illustrated with an example, namely, the differentiation between Iznik and Kutahya productions. Copyright © 2006 John Wiley & Sons, Ltd.

Safety Comparison of New Jersey Jug Handle Intersections and Conventional Intersections

New Jersey jug handle intersections (NJJI) have been around for the past few decades. The basic design philosophy behind implementing jug handle intersections at suitable locations is to improve traffic operations by the elimination of the left-turn phase on a major road and to improve traffic safety by a reduction of the total number of potential conflict points and specific conflicting maneuvers at the intersection. This study, based on statistical analyses of intersection crash data, investigates the differences between and similarities in safety performance of NJJIs and conventional intersections for a limited sample set of 44 NJJIs and 50 conventional intersections. Results from raw data indicated that conventional intersections tended to have more head-on, left-turn, fatal-plus-injury, and property-damage-only accidents and relatively fewer rear-end accidents than NJJIs. These observations were confirmed by negative binomial crash prediction models that were developed to account for the influence of other causal factors. Models were estimated for total, fatal-plus-injury accidents, rear-end, and sideswipe accidents for both sets of intersections.

Safety Comparison of New Jersey Jug Handle Intersections and Conventional Intersections

New Jersey jug handle intersections (NJJI) have been around for the past few decades. The basic design philosophy behind implementing jug handle intersections at suitable locations is to improve traffic operations by the elimination of the left-turn phase on a major road and to improve traffic safety by a reduction of the total number of potential conflict points and specific conflicting maneuvers at the intersection. This study, based on statistical analyses of intersection crash data, investigates the differences between and similarities in safety performance of NJJIs and conventional intersections for a limited sample set of 44 NJJIs and 50 conventional intersections. Results from raw data indicated that conventional intersections tended to have more head-on, left-turn, fatal-plus-injury, and property-damage-only accidents and relatively fewer rear-end accidents than NJJIs. These observations were confirmed by negative binomial crash prediction models that were developed to account for the influence of other causal factors. Models were estimated for total, fatal-plus-injury accidents, rear-end, and sideswipe accidents for both sets of intersections.

A simplified analysis of [18F]3′-deoxy-3′-fluorothymidine metabolism and retention

[18F]3'-deoxy-3'-fluorothymidine (FLT) is a thymidine analog developed for imaging tumor proliferation with positron emission tomography (PET). To quantitatively assess images, the blood activities of FLT and its glucuronidated metabolite were measured and its kinetics analyzed. This study sought to limit the number of blood samples needed to measure FLT retention. Total FLT activity was measured from 18 venous samples obtained over the first hour and dynamic imaging performed on 33 patients (average dose 350 MBq/mmol). The 5-, 10-, 30- and 60-min samples were analyzed to measure the fraction of activity in FLT and its glucuronide. HPLC analysis was compared against a two-step column (Sep-Pak) and metabolic rates measured using full and limited sampling. Probenecid (2 g, oral) was given to two patients to determine whether imaging of the liver improved. At 60 min, 74% of the blood activity was unmetabolized (range 57-85%). HPLC and Sep-Pak gave comparable results (r=0.97; average difference 2.1%). For kinetic analysis, eight venous samples were sufficient to accurately measure total activity; for metabolite analysis, a single sample at 60 min yielded data with mean errors of 2.2%. The metabolic rate correlated with average SUV (r2=0.85; p=0.0002). An aorta input function gave kinetic results comparable to venous blood (r2=0.82). Probenecid did not improve imaging of the liver. Dynamic measurements of FLT retention can be used to calculate metabolic rates using a limited set of samples and correction for metabolites measured in a single sample obtained at 60 min.

New Combinatorial Approach for the Investigation of Kinetics and Temperature Dependence of Surface Reactions in Thin Organic Films

In this paper we present a new, simple, and reproducible method for the rapid determination of the temperature dependence of solution phase surface reactions of organic thin films on solid supports. Instead of estimating the extent of reaction for many separate samples for many different temperatures sequentially, we exploit in our new high throughput combinatorial approach surface reactions carried out under a thermal gradient followed by position-resolved contact angle (CA) measurements. The reaction kinetics, activation energies, and entropies are, thus, accessible on the basis of measurements on a very limited set of samples that differ in reaction times. The kinetics and temperature dependence of surface reactions of the previously studied alkaline hydrolysis of 11,11'-dithiobis(N-hydroxysuccinimidylundecanoate) (NHS-C10) self-assembled monolayers (SAMs) on gold, as well as the ester hydrolysis in SAMs of the novel disulfide 11,11-dithiobis(tert-butylundecanoate) (t-Bu-C10), were investigated in detail using the conventional sequential and the new combinatorial approach. The reaction kinetics, corresponding apparent rate constants k, and activation energies Ea, as well as activation entropies deltaS double dagger, determined according to both approaches agree well with each other to within the experimental error. Hence, these parameters can be quantitatively determined using the described combinatorial approach. A comparison of the reactions of the two model systems indicated that the transition state is tighter for the acid-catalyzed ester hydrolysis in SAMs of the novel disulfide t-Bu-C10 compared to the hydrolysis of the ester groups in SAMs of NHS-C10 on gold.

Detection of 5-fluorouracil in saliva using surface-enhanced Raman spectroscopy

The ability of a surface-enhanced Raman active capillary to extract and detect the chemotherapy drug 5-fluorouracil (5-FU) in saliva is presented. Several methods to isolate 5-FU from potential interfering chemical components of saliva, in particular thiocyanate, were explored. It was found that this and other anions that could potentially deactivate the Raman signal enhancing properties of silver could be removed by passing the sample through an ion retardation column. It was also found that pH adjustment of the sample and the surface-enhanced Raman active capillary yielded better results, and 50 μg of 5-FU in 1 mL saliva was easily measured with an estimated limit of detection of 2 μg/mL. The entire analysis, sample preparation and spectral acquisition, required less than 5 min. However, the success of either method is based on a very limited set of saliva samples and the requirements necessary to remove anions and other physiological chemicals in saliva have not been fully defined. Nevertheless, these measurements suggest that disposable SERS-active capillaries could be used to measure 5-FU concentrations in chemotherapy patient saliva, thereby providing metabolic data that would allow regulating dosage.

Forecasting municipal solid waste generation in a fast-growing urban region with system dynamics modeling

Both planning and design of municipal solid waste management systems require accurate prediction of solid waste generation. Yet achieving the anticipated prediction accuracy with regard to the generation trends facing many fast-growing regions is quite challenging. The lack of complete historical records of solid waste quantity and quality due to insufficient budget and unavailable management capacity has resulted in a situation that makes the long-term system planning and/or short-term expansion programs intangible. To effectively handle these problems based on limited data samples, a new analytical approach capable of addressing socioeconomic and environmental situations must be developed and applied for fulfilling the prediction analysis of solid waste generation with reasonable accuracy. This study presents a new approach – system dynamics modeling – for the prediction of solid waste generation in a fast-growing urban area based on a set of limited samples. To address the impact on sustainable development city wide, the practical implementation was assessed by a case study in the city of San Antonio, Texas (USA). This area is becoming one of the fastest-growing regions in North America due to the economic impact of the North American Free Trade Agreement (NAFTA). The analysis presents various trends of solid waste generation associated with five different solid waste generation models using a system dynamics simulation tool – Stella ®. Research findings clearly indicate that such a new forecasting approach may cover a variety of possible causative models and track inevitable uncertainties down when traditional statistical least-squares regression methods are unable to handle such issues.

Functional variation of HIV-1 Rev response element in a longitudinally studied cohort

We showed previously that HIV-1 Rev Response Element (RRE) contains a certain degree of structural variation, and in a set of limited samples, RRE from HIV-1 natural isolates were found to have functional variability. The significance of the RRE heterogeneity is addressed further by analyzing the functional variation of RREs in a longitudinal cohort. While the RRE activity at early time points was not a good predictor of disease outcome, the RRE activity at late time points was correlated with rates of CD4+ count decline. These data suggest that RRE heterogeneity may be important in viral pathogenesis and disease progression.

Combined Measurement of Ferritin, Soluble Transferrin Receptor, Retinol Binding Protein, and C-Reactive Protein by an Inexpensive, Sensitive, and Simple Sandwich Enzyme-Linked Immunosorbent Assay Technique

The measurement of vitamin A (VA) and iron status is very important in the assessment of nutritional deficiencies. The objective of this research was to develop a sandwich ELISA technique for the simultaneous measurement of ferritin, soluble transferrin receptor, retinol binding protein, and C-reactive protein (CRP) as indicators for VA and iron status. The inclusion of CRP as marker of infection allows for more accurate interpretation of VA and iron status. This is accomplished in a 30-microL serum or plasma sample using an ELISA with different capture and detection antibodies and different dilutions of the sample. Commercially available clinical serum controls were used for calibration purposes. The developed assays were compared to commercially available traditional tests. Regression coefficients comparing both assays were better than 0.84 (P < 0.001). Using a limited sample set, the sandwich ELISA assay produced very similar specificity and sensitivity compared to traditional methods when common cutoff values were applied. Intra- and interassay variability was between 5 and 14% for all tests. The cost of the materials for all 5 measurements decreases to less than $1/sample if a large number of samples is analyzed. Due to the low cost, high throughput, and comparability to traditional tests, this procedure has several advantages for assessing VA and iron status in population surveys.

Cancer risk according to type and location of ATM mutation in ataxia-telangiectasia families.

Epidemiological studies have indicated that ataxia-telangiectasia (AT) heterozygotes in AT families have an increased risk of cancer, particularly of breast cancer (BC). However, in BC case-control studies, no significant differences were found in the frequency of ATM mutations between patients and controls. In such studies missense mutations were found more frequently than truncating mutations, suggesting that the cancer risk depends on mutation type. To investigate this possibility, we assessed the risk of BC according to the type and position of the ATM truncating mutation in extended AT families. DNA or RNA that had been isolated from blood or buccal cells of AT children and their relatives was screened for ATM germ-line mutations using restriction endonuclease fingerprinting, the protein truncation test, fluorescence-assisted mismatch analysis, and direct sequencing. The standardized incidence ratio of cancer associated with ATM heterozygosity status and type of mutation was estimated. We tested for genotype-phenotype correlations by simulations, permuting mutations among parental branches. No significant difference was found in the relative risk of breast cancer or any other type of cancer based on mutation type. However, the occurrence of BC may be associated with truncating mutations in certain binding domains of the ATM protein (e.g., P53/BRCA1, beta-adaptin, and FAT domains; P = 0.006). In this limited sample set, the presence of missense or truncating ATM mutations was not associated with different cancer risks. The risk of BC appeared to be associated with the alteration of binding domains rather than with the length of the predicted ATM protein.

The Norwegian founder mutations in BRCA1: high penetrance confirmed in an incident cancer series and differences observed in the risk of ovarian cancer

We aimed to describe the penetrances of the four Norwegian founder mutations in BRCA1 (816delGT, 1135insA, 1675delA and 3347delAG) with regard to breast and ovarian cancers in families ascertained through cancer family clinics or a consecutive series of women with breast or ovarian cancer. We have extended the families as far as possible and tested all family members that asked for genetic testing. Penetrance is based upon counting the mutation carriers. The series contains sufficient numbers of mutation carriers to minimise variation in the estimates due to a limited sample set. The penetrances for all four mutations were high, both with respect to breast and ovarian cancers. This is in accordance with other reports from cancer family clinics, but contrasts with reports from population-based series of mutation carriers. Risks of first cancer (breast or ovarian), breast cancer, and ovarian cancer at age 50 years were 43, 30 and 17%, respectively. Corresponding risks at age 70 years were 84, 58 and 58%. Risks for breast cancer before age 30 years and for ovarian cancer before 35 years were low. Penetrances with regard to ovarian cancer were different for the four mutations. The risk of ovarian cancer was doubled in carriers of the 1675delA mutation when compared with the 816delGT mutation (24 versus 12% at age 50 years, P=0.004). The mutations analysed are high penetrance alleles. No differences in penetrance between the series ascertained through the cancer family clinic or the series of consecutive cancer patients was observed. There are discrepancies between our findings and the low penetrances reported for other mutations in other populations. This may be due to methodological differences, but may reflect differences between mutations and/or modifying factors in different populations.

Effects of Composition and Annealing on the Electrical Properties of CoSb3

A series of CoSb3 samples was synthesized at low temperature (∼150 °C) using modulated elemental reactants, with composition varying between Co-rich and Sb-rich, resulting in lattice parameters ranging from 9.023 to 9.090 Å. The samples were annealed in 100 °C increments from 200 to 600 °C, with lattice parameter, electrical resistivity, and Seebeck coefficient measured after each annealing. The spread of lattice parameters decreased with annealing (9.045 to 9.062 Å). The electrical resistivity of the samples changed from being nominally temperature independent, characteristic of a heavily doped semiconductor, to an exponential temperature dependence expected for a semiconductor, with band gaps of ∼0.1 eV. Seebeck measurements confirm the reduction in electrically active defect concentration with increasing annealing temperature. The nonequilibrium defect concentration trapped by low-temperature crystallization and varying composition, combined with the annealing studies, allowed a wide range of structural and electrical properties to manifest within a limited sample set.

Variation in composition of fine particulate emissions from heavy‐duty diesel vehicles

Samples of fine particle emissions from four heavy‐duty diesel vehicles were analyzed for chemical and molecular composition. Significant variation was found for the composition of particle emissions from vehicles under load, with the fraction of carbonaceous particles emitted as elemental carbon (i.e., soot) varying between 19 and 94%. The emissions from vehicles idling shows little compositional variation with low soot formation and elemental carbon representing between 12 and 21% of total carbon emitted. This variation is important to consider when performing source apportionment calculations as the difference in fraction carbon emitted as elemental carbon is used to separate diesel emissions from gasoline‐powered vehicle emissions and other sources. The molecular composition of the organic particulate matter was quantified for samples collected from each of the four vehicles under load plus a composite sample of all four vehicles while idling. The variation of the molecular composition of organic particulate matter was highest for polycyclic aromatic hydrocarbons and least for petroleum biomarkers, supporting the use of petroleum biomarkers as tracers for diesel vehicle emissions when the compositional information from sources is based on a limited sample set.

Statistics for Environmental Engineers

Statistics for Environmental Engineers covers a wide range of subject areas, some of which are not typically found in textbooks on statistics. The book contains 54 chapters, which are typically 6 to 10 pages in length. The intention was to make each chapter independent of the others and able to stand alone. Books on statistics for non-statisticians can be terse and still cover the necessary material well—an example is Halstead (1966), the text used for the sophomore-level statistics class I took in 1970. However, the result in the present instance is chapters that are unnecessarily limited in scope, so that a complete discussion of some topics, such as prediction of upper confidence limits for a data set based on a limited set of samples, often takes several chapters. The reader would be better served if the chapters were longer and of greater scope. The intended audience for the book is `environmental engineers' in the sense used by civil engineers—that is, water and wastewater treatment engineers. Hence, most of the examples and end-of-chapter exercises concern problems and data types typical of situations encountered in water and wastewater treatment rather than those encountered in environmental engineering in the more generic …

Pooling of samples for seroepidemiological surveillance of human T-cell lymphotropic virus types I and II

We evaluated a straight forward pooling strategy for antibody screening of HTLV-I/II, using panels of sera from various parts of the world including a total of 43 HTLV-I and 54 HTLV-II positive specimens. Four antibody screening assays were included in the evaluation: the HTLV-I/II GE 80/81 (Murex Diagnostics), the HTLV-I/HTLV-II Ab Capture ELISA (Ortho Diagnostics), the HTLV-I/II ELISA 3.0 (Genelabs Diagnostics) and the Serodia HTLV-I (Fujirebio). The Murex and Ortho assays represent a new generation of HTLV screening tests with a sandwich format incorporating both HTLV-I and HTLV-II synthetic and/or recombinant peptide antigens. The Genelabs assay is an indirect ELISA with recombinant HTLV-I and -II antigens and Serodia is a particle agglutionation assay with HTLV-I whole viral lysate. Each HTLV-positive sample was included in pools of 1/1 up to 1/16, in two-fold steps made in normal HTLV-negative blood donor serum from one up to nine donors. For HTLV-I, with the exception of one false negative sample in dilution 1/16 with Genelabs ELISA, all assays were positive at all dilutions. The Murex assay had absorbance values at maximum levels for all samples at all dilutions. The other assays had gradually decreasing absorbance values although clearly above cut-off. For HTLV-II, the Murex assay correctly detected all samples to dilution 1/16 despite gradually decreasing signals. The Serodia assay had 100% sensitivity to dilution 1/4 while at 1/8 and 1/16 it decreased 82 and 80%, respectively. The Genelabs ELISA had gradually decreasing sensitivity for HTLV-II from 98 (1/1) to 33% (1/16) while the Ortho assay detected all specimens at all dilutions in a limited set of samples tested. Taken together, this evaluation has shown that pooling of samples may be an appropriate strategy for serosurveillance of HTLV. It is, however, crucial to limit the number of samples and to choose assays that allow the dilution caused by the pooling. Using the best performing assays in this evaluation for pools of e.g. five samples would leave a reasonable safety margin.

Characterization of hepatitis B virus genotypes among Yucpa Indians in Venezuela.

The complete genome sequences of hepatitis B virus (HBV) from 12 HBV-infected Yucpa Indians of Venezuela, a group with highly endemic HBV, were amplified and sequenced. The 12 isolates were closely related to each other, with 98.6-100% nucleotide identity. A phylogenetic tree based on the complete genome indicated clearly that they were genotype F. Three individuals had evidence of infection with two different HBV deletion mutants. In two individuals, a three amino acid deletion was identified just prior to the 'a' determinant loop of the S region. A third individual was infected with virus that contained a complete core reading frame and a population that contained a deletion in the middle of the core region. These results indicate that genotype F HBV is present in the Venezuelan Yucpa Amerindians and the complete genome sequence allowed the identification of two unique deletion mutants in a limited set of samples.

Prediction analysis of solid waste generation based on grey fuzzy dynamic modeling

Abstract Successful planning of a solid waste management system depends critically on the prediction accuracy of solid waste generation. But the prediction condition of generation trend in many developing countries is quite different from those in developed countries. The lack of sampling and analysis in many developing countries due to insufficient budget and unavailable management task force has resulted in a situation where the historical record of solid waste generation and composition can never be completed in the long term. To effectively handle these problems with only limited samples and fulfil the prediction analysis of solid waste generation with reasonable accuracy, a special analytical technique must be developed and applied before the subsequent system planning for urban solid waste management is carried out. This study presents a new theory — grey fuzzy dynamic modeling — for the prediction of solid waste generation in the urban area based on a set of limited samples. The practical implementation has been accessed by a case study in the city of Tainan in Taiwan. It shows that such a new forecasting technique may achieve better prediction accuracy than those of the conventional grey dynamic model, least-squares regression method, and the fuzzy goal regression technique.