A hybrid method in combining treatment effects from matched and unmatched studies

In the biomedical studies, the general data structures have been the matched (paired) and unmatched designs. Recently, many researchers are interested in Meta-Analysis to obtain a better understanding from several clinical data of a medical treatment. The hybrid design, which is combined two data structures, may create the fundamental question for statistical methods and the challenges for statistical inferences. The applied methods are depending on the underlying distribution. If the outcomes are normally distributed, we would use the classic paired and two independent sample T-tests on the matched and unmatched cases. If not, we can apply Wilcoxon signed rank and rank sum test on each case. ^ To assess an overall treatment effect on a hybrid design, we can apply the inverse variance weight method used in Meta-Analysis. On the nonparametric case, we can use a test statistic which is combined on two Wilcoxon test statistics. However, these two test statistics are not in same scale. We propose the Hybrid Test Statistic based on the Hodges-Lehmann estimates of the treatment effects, which are medians in the same scale.^ To compare the proposed method, we use the classic meta-analysis T-test statistic on the combined the estimates of the treatment effects from two T-test statistics. Theoretically, the efficiency of two unbiased estimators of a parameter is the ratio of their variances. With the concept of Asymptotic Relative Efficiency (ARE) developed by Pitman, we show ARE of the hybrid test statistic relative to classic meta-analysis T-test statistic using the Hodges-Lemann estimators associated with two test statistics.^ From several simulation studies, we calculate the empirical type I error rate and power of the test statistics. The proposed statistic would provide effective tool to evaluate and understand the treatment effect in various public health studies as well as clinical trials.^

Classification of cellular malignancy associated changes in cervical cancer

Cervical cancer is the leading cause of death and disease from malignant neoplasms among women in developing countries. Even though the Pap smear has significantly decreased the number of deaths from cervical cancer in the past years, it has its limitations. Researchers have developed an automated screening machine which can potentially detect abnormal cases that are overlooked by conventional screening. The goal of quantitative cytology is to classify the patient's tissue sample based on quantitative measurements of the individual cells. It is also much cheaper and potentially can take less time. One of the major challenges of collecting cells with a cytobrush is the possibility of not sampling any existing dysplastic cells on the cervix. Being able to correctly classify patients who have disease without the presence of dysplastic cells could improve the accuracy of quantitative cytology algorithms. Subtle morphologic changes in normal-appearing tissues adjacent to or distant from malignant tumors have been shown to exist, but a comparison of various statistical methods, including many recent advances in the statistical learning field, has not previously been done. The objective of this thesis is to use different classification methods applied to quantitative cytology data for the detection of malignancy associated changes (MACs). In this thesis, Elastic Net is the best algorithm. When we applied the Elastic Net algorithm to the test set, we combined the training set and validation set as "training" set and used 5-fold cross validation to choose the parameter for Elastic Net. It has a sensitivity of 47% at 80% specificity, an AUC 0.52, and a partial AUC 0.10 (95% CI 0.09-0.11).^

Proceedings of the Twenty-Sixth Annual Biochemical Engineering Symposium

This volume contains the Proceedings of the Twenty-Sixth Annual Biochemical Engineering Symposium held at Kansas State University on September 21, 1996. The program included 10 oral presentations and 14 posters. Some of the papers describe the progress of ongoing projects, and others contain the results of completed projects. Only brief summaries are given of some of the papers; many of the papers will be published in full elsewhere. A listing of those who attended is given below. ContentsForeign Protein Production from SV40 Early Promoter in Continuous Cultures of Recombinant CHO Cells - Gautam Banik, Paul Todd, and Dhinakar Kampala Enhanced Cell Recruitment Due to Cell-Cell Interactions - Brad Farlow and Matthias Nollert The Recirculation of Hybridoma Suspension Cultures: Effects on Cell Death, Metabolism and Mab Productivity - Peng Jin and Carole A. Heath The Importance of Enzyme Inactivation and Self-Recovery in Cometabolic Biodegradation of Chlorinated Solvents - Xi-Hui Zhang, Shanka Banerji, and Rakesh Bajpai Phytoremediation of VOC contaminated Groundwater using Poplar Trees - Melissa Miller, Jason Dana, L.C. Davis, Murlidharan Narayanan, and L.E. Erickson Biological Treatment of Off-Gases from Aluminum Can Production: Experimental Results and Mathematical Modeling - Adeyma Y. Arroyo, Julio Zimbron, and Kenneth F. Reardon Inertial Migration Based Separation of Chlorella Microalgae in Branched Tubes - N.M. Poflee, A.L. Rakow, D.S. Dandy, M.L. Chappell, and M.N. Pons Contribution of Electrochemical Charge to Protein Partitioning in Aqueous Two-Phase Systems - Weiyu Fan and Charles C. Glatz Biodegradation of Some Commercial Surfactants Used in Bioremediation - Jun Gu, G.W. Preckshot, S.K. Banerji, and Rakesh Bajpai Modeling the Role of Biomass in Heavy Metal Transport Ln Vadose Zone - K.V. Nedunuri, L.E. Erickson, and R.S. Govindaraju Multivariable Statistical Methods for Monitoring Process Quality: Application to Bioinsecticide Production by 73 89 Bacillus Thuringiensis - c. Puente and M.N. Karim The Use of Polymeric Flocculants in Bacterial Lysate Streams - H. Graham, A.S. Cibulskas and E.H. Dunlop Effect of Water Content on transport of Trichloroethylene in a Chamber with Alfalfa Plants - Muralidharan Narayanan, Jiang Hu, Lawrence C. Davis, and Larry E. Erickson Detection of Specific Microorganisms using the Arbitrary Primed PCR in the Bacterial Community of Vegetated Soil - X. Wu and L.C. Davis Flux Enhancement Using Backpulsing - V.T. Kuberkar and R.H. Davis Chromatographic Purification of Oligonucleotides: Comparison with Electrophoresis - Stephen P. Cape, Ching-Yuan Lee, Kevin Petrini, Sean Foree, Micheal G. Sportiello and Paul Todd Determining Singular Arc Control Policies for Bioreactor Systems Using a Modified Iterative Dynamic Programming Algorithm - Arun Tholudur and W. Fred Ramirez Pressure Effect on Subtilisins Measured via FTIR, EPR and Activity Assays, and Its Impact on Crystallizations - J.N. Webb, R.Y. Waghmare, M.G. Bindewald, T.W. Randolph, J.F. Carpenter, C.E. Glatz Intercellular Calcium Changes in Endothelial Cells Exposed to Flow - Laura Worthen and Matthias Nollert Application of Liquid-Liquid Extraction in Propionic Acid Fermentation - Zhong Gu, Bonita A. Glatz, and Charles E. Glatz Purification of Recombinant T4 Lysozyme from E. Coli: Ion-Exchange Chromatography - Weiyu Fan, Matt L. Thatcher, and Charles E. Glatz Recovery and Purification of Recombinant Beta-Glucuronidase from Transgenic Corn - Ann R. Kusnadi, Roque Evangelista, Zivko L. Nikolov, and John Howard Effects of Auxins and cytokinins on Formation of Catharanthus Roseus G. Don Multiple Shoots - Ying-Jin Yuan, Yu-Min Yang, Tsung-Ting Hu, and Jiang Hu Fate and Effect of Trichloroethylene as Nonaqueous Phase Liquid in Chambers with Alfalfa - Qizhi Zhang, Brent Goplen, Sara Vanderhoof, Lawrence c. Davis, and Larry E. Erickson Oxygen Transport and Mixing Considerations for Microcarrier Culture of Mammalian Cells in an Airlift Reactor - Sridhar Sunderam, Frederick R. Souder, and Marylee Southard Effects of Cyclic Shear Stress on Mammalian Cells under Laminar Flow Conditions: Apparatus and Methods - M.L. Rigney, M.H. Liew, and M.Z. Southard

A comparison between multi-proxy and historical data of drift-ice conditions on the East Greenland shelf

The reduction in sea ice along the SE Greenland coast during the last century has severely impacted ice-rafting to this area. In order to reconstruct ice-rafting and oceanographic conditions in the area of Denmark Strait during the last ~150 years, we conducted a multiproxy study on three short (20 cm) sediment cores from outer Kangerdlugssuaq Trough (~300 m water depth). The proxy-based data obtained have been compared with historical and instrumental data to gain a better understanding of the ice sheet-ocean interactions in the area. A robust chronology has been developed based on 210Pb and 137Cs measurements on core PO175GKC#9 (~66.2°N, 32°W) and expanded to the two adjacent cores based on correlations between calcite weight percent records. Our proxy records include sea-ice and phytoplankton biomarkers, and a variety of mineralogical determinations based on the <2 mm sediment fraction, including identification with quantitative x-ray diffraction, ice-rafted debris counts on the 63-150 µm sand fraction, and source identifications based on the composition of Fe oxides in the 45-250 µm fraction. A multivariate statistical analysis indicated significant correlations between our proxy records and historical data, especially with the mean annual temperature data from Stykkishólmur (Iceland) and the storis index (historical observations of sea-ice export via the East Greenland Current). In particular, the biological proxies (calcite weight percent, IP25, and total organic carbon %) showed significant linkage with the storis index. Our records show two distinct intervals in the recent history of the SE Greenland coast. The first of these (ad 1850-1910) shows predominantly perennial sea-ice conditions in the area, while the second (ad 1910-1990) shows more seasonally open water conditions.

(Table 1) Sediment descriptions and age at DSDP Legs 5 and 63 Holes

Sediments from immediately above basalt basement and from between sections of basalt recovered from Deep Sea Drilling Project Legs 5 and 63 were analyzed by atomic absorption spectroscopy for Mg, Al, Si, Ca, Mn, Fe, Co, Ni, Cu, Zn, and Ba. All of these sediments showed enrichment in Fe and Mn over values typical of detritus supplied to the northeastern Pacific Ocean. X-ray diffractometry and differential chemical leaching indicate that up to 50% of the sediment, by weight, is in amorphous phases and that these phases are rich in Mn, Co, Cu, Ni, and Zn. Multivariate statistical analysis and normative partitioning of the chemical data indicate that much of the excess Fe and other transition elements in the sediment originate from hydrothermal sources.

Reseña sobre las metodologías de campo, analíticas y estadísticas empleadas en la determinación y manejo de datos de los elementos de tierras raras en el sistema suelo-planta

El presente artículo es una revisión detallada de estudios científicos publicados que tratan el tema relacionado con la determinación de los elementos de las tierras raras (REEs) en el sistema suelo-planta. Los estudios han sido llevados a cabo principalmente en países europeos y asiáticos. Cabe señalar que la investigación en los países latinoamericanos es muy escasa; sin embargo, es creciente el interés de analizar la aportación de estos elementos al suelo y la planta, lo cual se debe a la aplicación de fertilizantes que contienen dosis elevadas de estos elementos en su composición. Diversas técnicas de muestreo, experimentación y análisis han sido empleadas para la determinación de los REEs. No obstante, se considera que el manejo de los datos ha sido incorrecto estadísticamente. El contenido del presente artículo aborda: (i) las generalidades de los REEs; (ii) el análisis de la bibliografía disponible con el fin de conocer las metodologías de muestreo y análisis más utilizadas en 37 artículos en total, señalando algunos puntos que se consideran todavía deficientes; (iii) dos ejemplos de la aplicación de técnicas estadísticas (intervalo de confianza de la media y pruebas de significancia de la relación F de Fisher y t de Student) utilizando datos reportados en dos artículos. Los resultados mostraron, con los datos del primer artículo analizado, que: a) no se aplicó una metodología estadística para evaluar la calidad de datos; b) al aplicar estadística se encontró que existen diferencias sistemáticas entre los datos determinados en el laboratorio y los certificados. En el segundo artículo analizado se demostró, mediante pruebas de significancia, que existen diferencias significativas en las medias de Ce y Eu (los dos elementos tomados como ejemplos) en las plantas de un sitio a otro.

Análisis de componentes principales con datos georreferenciados : una aplicación en agricultura de precisión

La utilización de nuevas tecnologías asociadas a la agricultura de precisión permite capturar información de múltiples variables en gran cantidad de sitios georreferenciados dentro de lotes en producción. Las covariaciones espaciales de las propiedades del suelo y el rendimiento del cultivo pueden evaluarse a través del análisis de componentes principales clásico (PCA). No obstante, como otros métodos multivariados descriptivos, el PCA no ha sido desarrollado explícitamente para datos espaciales. Nuevas versiones de análisis multivariado permiten contemplar la autocorrelación espacial entre datos de sitios vecinos. En este trabajo se aplican y comparan los resultados de dos técnicas multivariadas, el PCA y MULTISPATI-PCA. Este último incorpora la información espacial a través del cálculo del índice de Moran entre los datos de un sitio y el dato promedio de sus vecinos. Los resultados mostraron que utilizando MULTISPATI-PCA se detectaron correlaciones entre variables que no fueron detectadas con el PCA. Los mapas de variabilidad espacial construidos a partir de la primera componente de ambas técnicas fueron similares; no así los de la segunda componente debido a cambios en la estructura de co-variación identificada, al corregir la variabilidad por la autocorrelación espacial de los datos. El método MULTISPATI-PCA constituye una herramienta importante para el mapeo de la variabilidad espacial y la identificación de zonas homogéneas dentro de lotes.

Características palinológicas de mieles de eucalipto (Eucalyptus sp.) y tréboles (Trifolium sp.) provenientes de la Provincia Fitogeográfica Pampeana Argentina

El objetivo de este trabajo fue estudiar el perfil polínico de mieles de tréboles y de eucalipto de la Provincia Fitogeográfica Pampeana Argentina, con el fin de contribuir a su caracterización palinológica. Se realizó un análisis polínico cualitativo y se aplicaron técnicas estadísticas descriptivas y multivariadas, para conocer la distribución de frecuencia de los pólenes y caracterizar cada origen floral, según los pólenes acompañantes y los años de cosecha. Se analizaron 81 muestras de miel, de cuatro cosechas diferentes. Se encontraron 41 tipos morfológicos de polen, cuya variación por muestra osciló entre dos y ocho. El taxón presente en más del 80% de las mieles fue Eucalyptus sp. Los principales pólenes acompañantes encontrados pertenecieron a los tipos Helianthus annuus y Carduus sp., para ambos orígenes florales estudiados, y a la familia de las Brassicaceae, para las mieles de tréboles. Los años de cosecha estudiados mostraron diferentes espectros polínicos.

Un desafío pendiente para el próximo quinquenio : Los objetivos de desarrollo del milenio

En el año 2000, los gobiernos de 189 países se comprometieron a alcanzar dieciocho metas para combatir la desigualdad y mejorar el desarrollo humano en el mundo a través del cumplimiento de los denominados Objetivos de Desarrollo del Milenio (ODM) de la Organización de las Naciones Unidas (ONU), todo ello con un horizonte para el año 2015. Los ODM deben ser monitoreados por los institutos de estadística existentes en la mayoría de los países que calculan indicadores económicos. En la Argentina, el Instituto Nacional de Estadística y Censos tiene una larga experiencia en la creación y cálculo de índices, específicamente, del índice de Precios al Consumidor el cual ha sido considerado como el mejor índice de precios de toda América Latina. Sin embargo, desde el año 2007 se ha implementado una nueva metodología para su cálculo. En esta comunicación se presentan resultados de trabajos realizados desde diferentes puntos de vista que aportan los métodos exploratorios y confirmatorios tendientes a conocer la situación de pobreza e indigencia y la distribución de los ingresos de los habitantes del Aglomerado Gran Rosario. Los análisis exploratorios y confirmatorios aplicados presentan incuestionables resultados que reflejan la coherencia de las conclusiones a que se ha arribado. Los datos primarios de calidad utilizados permitieron plasmar análisis dinámicos con la información homogénea disponible. Finalmente y a la luz de estas circunstancias, ¿se podrá saber fehacientemente si se alcanzarán los Objetivos de Desarrollo del Milenio en el año 2015?

Un desafío pendiente para el próximo quinquenio : Los objetivos de desarrollo del milenio

En el año 2000, los gobiernos de 189 países se comprometieron a alcanzar dieciocho metas para combatir la desigualdad y mejorar el desarrollo humano en el mundo a través del cumplimiento de los denominados Objetivos de Desarrollo del Milenio (ODM) de la Organización de las Naciones Unidas (ONU), todo ello con un horizonte para el año 2015. Los ODM deben ser monitoreados por los institutos de estadística existentes en la mayoría de los países que calculan indicadores económicos. En la Argentina, el Instituto Nacional de Estadística y Censos tiene una larga experiencia en la creación y cálculo de índices, específicamente, del índice de Precios al Consumidor el cual ha sido considerado como el mejor índice de precios de toda América Latina. Sin embargo, desde el año 2007 se ha implementado una nueva metodología para su cálculo. En esta comunicación se presentan resultados de trabajos realizados desde diferentes puntos de vista que aportan los métodos exploratorios y confirmatorios tendientes a conocer la situación de pobreza e indigencia y la distribución de los ingresos de los habitantes del Aglomerado Gran Rosario. Los análisis exploratorios y confirmatorios aplicados presentan incuestionables resultados que reflejan la coherencia de las conclusiones a que se ha arribado. Los datos primarios de calidad utilizados permitieron plasmar análisis dinámicos con la información homogénea disponible. Finalmente y a la luz de estas circunstancias, ¿se podrá saber fehacientemente si se alcanzarán los Objetivos de Desarrollo del Milenio en el año 2015?

Un desafío pendiente para el próximo quinquenio : Los objetivos de desarrollo del milenio

En el año 2000, los gobiernos de 189 países se comprometieron a alcanzar dieciocho metas para combatir la desigualdad y mejorar el desarrollo humano en el mundo a través del cumplimiento de los denominados Objetivos de Desarrollo del Milenio (ODM) de la Organización de las Naciones Unidas (ONU), todo ello con un horizonte para el año 2015. Los ODM deben ser monitoreados por los institutos de estadística existentes en la mayoría de los países que calculan indicadores económicos. En la Argentina, el Instituto Nacional de Estadística y Censos tiene una larga experiencia en la creación y cálculo de índices, específicamente, del índice de Precios al Consumidor el cual ha sido considerado como el mejor índice de precios de toda América Latina. Sin embargo, desde el año 2007 se ha implementado una nueva metodología para su cálculo. En esta comunicación se presentan resultados de trabajos realizados desde diferentes puntos de vista que aportan los métodos exploratorios y confirmatorios tendientes a conocer la situación de pobreza e indigencia y la distribución de los ingresos de los habitantes del Aglomerado Gran Rosario. Los análisis exploratorios y confirmatorios aplicados presentan incuestionables resultados que reflejan la coherencia de las conclusiones a que se ha arribado. Los datos primarios de calidad utilizados permitieron plasmar análisis dinámicos con la información homogénea disponible. Finalmente y a la luz de estas circunstancias, ¿se podrá saber fehacientemente si se alcanzarán los Objetivos de Desarrollo del Milenio en el año 2015?

Geochemistry and isotopes at DSDP Leg 80 Holes

Thirty-eight samples from DSDP Sites 549 to 551 were analyzed for major and minor components and trace element abundances. Multivariate statistical analysis of geochemical data groups the samples into two major classes: an organic-carbon- rich group (> 1% TOC) containing high levels of marine organic matter and certain trace elements (Cu, Zn, V, Ni, Co, Ba, and Cr) and an organic-carbon-lean group depleted in these components. The greatest organic and trace metal enrichments occur in the uppermost Albian to Turanian sections of Sites 549 to 551. Carbon-isotopic values of bulk carbonate for the middle Cenomanian section of Site 550 (2.35 to 2.70 per mil) and the upper Cenomanian-Turonian sections of Sites 549 (3.35 to 4.47 per mil) and 551 (3.13 to 3.72 per mil) are similar to coeval values reported elsewhere in the region. The relatively heavy d13C values from Sites 549 and 551 indicate that this interval was deposited during the global "oceanic anoxic event" that occurred at the Cenomanian/Turonian boundary. Variation in the d18O of bulk carbonate for Section 550B-18-1 of middle Cenomanian age suggests that paleosalinity and/or paleotemperature variations may have occurred concurrently with periodic anoxia at this site. Climatically controlled increases in surface-water runoff may have caused surface waters to periodically freshen, resulting in stable salinity stratification

Operator and replicability bias in comparative taphonomic studies

The operator effect is a well-known methodological bias already quantified in some taphonomic studies. However, the replicability effect, i.e., the use of taphonomic attributes as a replicable scientific method, has not been taken into account to the present. Here, we quantified for the first time this replicability bias using different multivariate statistical techniques, testing if the operator effect is related to the replicability effect. We analyzed the results reported by 15 operators working on the same dataset. Each operator analyzed 30 biological remains (bivalve shells) from five different sites, considering the attributes fragmentation, edge rounding, corrasion, bioerosion and secondary color. The operator effect followed the same pattern reported in previous studies, characterized by a worse correspondence for those attributes having more than two levels of damage categories. However, the effect did not appear to have relation with the replicability effect, because nearly all operators found differences among sites. Despite the binary attribute bioerosion exhibited 83% of correspondence among operators it was the taphonomic attributes that showed the highest dispersion among operators (28%). Therefore, we conclude that binary attributes (despite showing a reduction of the operator effect) diminish replicability, resulting in different interpretations of concordant data. We found that a variance value of nearly 8% among operators, was enough to generate a different taphonomic interpretation, in a Q-mode cluster analysis. The results reported here showed that the statistical method employed influences the level of replicability and comparability of a study and that the availability of results may be a valid alternative to reduce bias.

Seasonal production patterns of planktonic foraminifera in the NE Atlantic Ocean

Sediment trap samples from OMEX 2 (49°N, 13°W) provide a continuous record of the seasonal succession of planktonic foraminifera in the midlatitude North Atlantic and reveal a complex relationship between periods of production and specific hydrographic conditions. Neogloboquadrina pachyderma dextral coiling (d.), Globigerina bulloides, and Globorotalia inflata are found in great numbers during both the spring and summer seasons, whereas Globigerina quinqueloba, Globorotalia hirsuta, Globorotalia scitula, and Globigerinita glutinata are associated predominantly with the increase in productivity during the spring bloom. Globigerinella aequilateralis, Orbulina universa, and Globigerinoides sacculifer are restricted to late summer conditions following the establishment of a warm, well-stratified surface ocean. An annually integrated fauna from the sediment trap, comprising ~13,000 individuals, is used to evaluate the accuracy of five faunal-based statistical methods of paleotemperature estimation. All of the temperature reconstruction techniques produce estimates of ~16°C and ~11°C for summer and winter surface temperature, respectively, which are in excellent agreement with regional hydrographic data and suggest that the sediment trap assemblage is well represented in the core top faunas. Analysis of the key species that dominate the OMEX 2 sediment trap fauna, G. bulloides, G. inflata, and N. pachyderma d., based on d18O derived temperatures from North Atlantic core top samples, suggests that seasonal variations in planktonic foraminiferal production are nonuniform across the midlatitudes and that this is likely to complicate reconstructing past seasonal hydrographic dynamics using these taxa.

Geochemistry of terrigenous material in deep-sea sediments of the equatorial Pacific

Biological productivity in the modern equatorial Pacific Ocean, a region with high nutrients and low chlorophyll, is currently limited by the micronutrient Fe. In order to test whether Fe was limiting in the past and to identify potential pathways of Fe delivery that could drive Fe fertilization (i.e., dust delivery from eolian inputs vs. Fe supplied by the Equatorial Undercurrent), we chemically isolated the terrigenous material from sediment along a cross-equatorial transect in the central equatorial Pacific at 140°W and at Ocean Drilling Program Site 850 in the eastern equatorial Pacific. We quantified the contribution from each potential Fe-bearing terrigenous source using a suite of chemical- and isotopic discrimination strategies as well as multivariate statistical techniques. We find that the distribution of the terrigenous sources (i.e., Asian loess, South American ash, Papua New Guinea, and ocean island basalt) varies through time, latitude, and climate. Regardless of which method is used to determine accumulation rate, there also is no relationship between flux of any particular Fe source and climate. Moreover, there is no connection between a particular Fe source or pathway (eolian vs. Undercurrent) to total productivity during the Last Glacial Maximum, Pleistocene glacial episodes, and the Miocene "Biogenic Bloom". This would suggest an alternative process, such as an interoceanic reorganization of nutrient inventories, may be responsible for past changes in total export in the open ocean, rather than simply Fe supply from dust and/or Equatorial Undercurrent processes. Additionally, perhaps a change in Fe source or flux is related to a change in a particular component of the total productivity (e.g., the production of organic matter, calcium carbonate, or biogenic opal).