Comparison of multiple comparison methods for identifying differential gene expression in simulated and real papillary thyroid cancer microarray data

The difficulty of detecting differential gene expression in microarray data has existed for many years. Several correction procedures try to avoid the family-wise error rate in multiple comparison process, including the Bonferroni and Sidak single-step p-value adjustments, Holm's step-down correction method, and Benjamini and Hochberg's false discovery rate (FDR) correction procedure. Each multiple comparison technique has its advantages and weaknesses. We studied each multiple comparison method through numerical studies (simulations) and applied the methods to the real exploratory DNA microarray data, which detect of molecular signatures in papillary thyroid cancer (PTC) patients. According to our results of simulation studies, Benjamini and Hochberg step-up FDR controlling procedure is the best process among these multiple comparison methods and we discovered 1277 potential biomarkers among 54675 probe sets after applying the Benjamini and Hochberg's method to PTC microarray data.^

Proceedings of the 23rd Annual Biochemical Engineering Symposium

The 23rd Annual Biochemical Engineering Symposium was held at the University of Oklahoma on April 17, 1993. The objectives of the symposium were to provide 1) a forum for informal discussion of biochemical engineering research being carried at the participating universities and 2) an opportunity for students to present and publish their work. Thirteen papers presented at the symposium are included in the proceedings. Because final publication usually takes place in refereed journals, the articles included here are typically brief and often cover work in progress. The program of the symposium and a list of participants are included in the proceedings. ContentsA Low-Cost Bioreactor Strategy for RNA Synthesis, H. Anthony Marble, Eleni Chrisikos, and Robert H. Davis Development of a CELSS Bioreactor: Oxygen Transfer and Micromixing in Parabolic Flight, P.E. Villeneuve, K.S. Wenger, B.G. Thompson, T. Kedar, and E.H. Dunlop Scale-up of Dexter Murine Bone Marrow Cultures Utilizing a Three-Dimensional Fiberglass Support Matrix, John G. Highfill, Paul Todd, Steve Haley, and Dhinaker Kompala Modeling and Estimation of States of Recombinant Fermentations Using Nonlinear Input/Output Models, Vicotr M. Saucedo and M. Nazmul Karim Deadent Microfiltration of Bovine Serum Albumin Suspension Through Yeast Cake Layers and Assymetric Polymeric Membranes, Naveen Arora and Robert H. Davis Monitoring the Fate of Toluene and Phenol in the Rhizosphere, N. Muralidharan, Lawrence C. Davis, and Larry E. Erickson Hydrodynamic Motions Associated with Bubble Coalescence and Breakup, T.Y. Yiin, L.A. Glasgow, and L.E. Erickson Expression and Purification of a-Human Atrial Natriuretic Peptide in Escherichia coli by Fusion with L-Asparaginase, Nien-Tung Ma and Roger G. Harrison High Pressure Crystallization of Proteins, Mungara V. Saikumar, Charles E. Glatz, and Maurice A. Larson Structure/Function Relationships in the Catalytic and Starch Binding Domains of Glucoamylase, Pedro M. Coutinho, Clark Ford, Peter J. Reilly Cellular Responses of Insect Cell Spodoptera frugiperda to Environmental Stresses, Paul Yeh, Grace Y. Sun, Gary A. Weisman, Rakesh Bajpai A Novel Approach to Understanding the Antimicrobial Activity of Peptides, Naveen Pathak, Marie-Helene Janna, Gael Ruche, David McCarthy, and Roger Harrison Mass Transfer in the Bioremediation of Soils Contaminated with Trapped Non-Aqueous Phase Liquids, Xiaoqing Yang, Larry E. Jacobson, and L.T. Fan

Tabacaleros y acopiadores en la colonización del Alto Paraná Misionero (1930-1946)

Durante la expansión colonizadora de las décadas de 1920-1930 en el Alto Paraná Misionero, el tabaco fue para los colonos alemanes-brasileños un cultivo destinado a la obtención de ingresos monetarios y bienes de consumo. El objetivo de este trabajo es analizar el vínculo entre productores y acopiadores de tabaco, tratando de identificar los elementos conflictivos de esta relación (disputas por la clasificación y el precio del producto). El trabajo heurístico se focalizó en la Compañía Johann, la empresa acopiadora más grande de la colonia Puerto Rico y la única que mantiene los registros desde su creación (1929). El producto que acopió por más tiempo fue el tabaco (1929-1985), y en orden de importancia decreciente también acopiaron tung, almidón de mandioca y grasa de cerdo. A través de los libros de acopio y de venta de tabaco enfardelado se da vida a las dos caras de la producción del tabaco: los productores tabacaleros y los acopiadores. Dicha información ha sido enriquecida con entrevistas a informantes clave.

Tabacaleros y acopiadores en la colonización del Alto Paraná Misionero (1930-1946)

Durante la expansión colonizadora de las décadas de 1920-1930 en el Alto Paraná Misionero, el tabaco fue para los colonos alemanes-brasileños un cultivo destinado a la obtención de ingresos monetarios y bienes de consumo. El objetivo de este trabajo es analizar el vínculo entre productores y acopiadores de tabaco, tratando de identificar los elementos conflictivos de esta relación (disputas por la clasificación y el precio del producto). El trabajo heurístico se focalizó en la Compañía Johann, la empresa acopiadora más grande de la colonia Puerto Rico y la única que mantiene los registros desde su creación (1929). El producto que acopió por más tiempo fue el tabaco (1929-1985), y en orden de importancia decreciente también acopiaron tung, almidón de mandioca y grasa de cerdo. A través de los libros de acopio y de venta de tabaco enfardelado se da vida a las dos caras de la producción del tabaco: los productores tabacaleros y los acopiadores. Dicha información ha sido enriquecida con entrevistas a informantes clave.

Tabacaleros y acopiadores en la colonización del Alto Paraná Misionero (1930-1946)

Durante la expansión colonizadora de las décadas de 1920-1930 en el Alto Paraná Misionero, el tabaco fue para los colonos alemanes-brasileños un cultivo destinado a la obtención de ingresos monetarios y bienes de consumo. El objetivo de este trabajo es analizar el vínculo entre productores y acopiadores de tabaco, tratando de identificar los elementos conflictivos de esta relación (disputas por la clasificación y el precio del producto). El trabajo heurístico se focalizó en la Compañía Johann, la empresa acopiadora más grande de la colonia Puerto Rico y la única que mantiene los registros desde su creación (1929). El producto que acopió por más tiempo fue el tabaco (1929-1985), y en orden de importancia decreciente también acopiaron tung, almidón de mandioca y grasa de cerdo. A través de los libros de acopio y de venta de tabaco enfardelado se da vida a las dos caras de la producción del tabaco: los productores tabacaleros y los acopiadores. Dicha información ha sido enriquecida con entrevistas a informantes clave.

Pollen and macroremains from three sediment cores from Göttingen, Germany

In a borehole in the southern outskirts of the town of Göttingen, limnic sediments of several Pleistocene warm periods occur intercalated with coarse solifluction debris and gravel of the river Leine. Pollen analysis of the limnic sediments in a borehole at Ottostrasse gave evidence of three warm periods of interglacial character, followed by three interstadial phases. The warm phases are separated one from another by stadial phases with, at least in one case, indications of periglacial solifluction. This sequence belongs to the Brunhes magnetic epoch. The pollen data allow to exclude an Eemian or Holsteinian age of the warm period sediments. Thus a Cromerian age is assumed, though the exact position of the newly described warm periods within the ''Cromerian'' remains uncertain. A section in a borehole at Akazienweg is of Holsteinian age.

Compilation of quality controlled nutrient profiles from the Mediterranean Sea

In the last decades, a striking amount of hydrographic data, covering the most part of Mediterranean basin, have been generated by the efforts made to characterize the oceanography and ecology of the basin. On the other side, the improvement in technologies, and the consequent perfecting of sampling and analytical techniques, provided data even more reliable than in the past. Nutrient data enter fully in this context, but suffer of the fact of having been produced by a large number of uncoordinated research programs and of being often deficient in quality control, with data bases lacking of intercalibration. In this study we present a computational procedure based on robust statistical parameters and on the physical dynamic properties of the Mediterranean sea and its morphological characteristics, to partially overcome the above limits in the existing data sets. Through a data pre filtering based on the outlier analysis, and thanks to the subsequent shape analysis, the procedure identifies the inconsistent data and for each basin area identifies a characteristic set of shapes (vertical profiles). Rejecting all the profiles that do not follow any of the spotted shapes, the procedure identifies all the reliable profiles and allows us to obtain a data set that can be considered more internally consistent than the existing ones.

Two pollen profiles of the middle Pleistocene at Samerberg/Upper Bavaria, Germany

Previous pollen analytical studies on sediments from the pleistocene lake basin at Samerberg, situated on the northern edge of the Bavarian Alps (47°45' N, 12°12' E, 607 m a.s.l.) had been performed on samples taken from cores and exposures close to the southern shore of the former lake. After geoelectric and refraction-seismic measurements had shown that the lake basin had been much deeper in its northern part, another core was taken where maximum depth could be expected. The corer penetrated three moraines, two of them lying above pollen-bearing sediments, and one below them, and reached the hard rock (Kössener Kalk) at a depth of 93 m. Two forest phases could be identified by pollen analysis. The pollen record begins abruptly in a forest phase at the end of a spruce-dominated period when fir started to spread (DA 1, DA = pollen zone). Following this, Abies (fir) was the main tree species at Samerberg, Picea being second, and deciduous trees were almost non-existent. First box (Buxus) was of major importance in the fir forests (DA 2), but later on beech (Fagus) and wing-nut (Pterocarya) spread (DA 3). Finally this forest gave way to a spruce forest with pine (DA 4). The beginning and the end of this interglacial cycle are not recorded. Its vegetational development is different from the eemian one known from earlier studies at Samerberg. It is characterized by the occurrence of Abies together with Buxus, Pterocarya and Fagus. A similar association of woody species is known only from the Holsteinian age deposits in an area ranging from England to Poland, though at no other place these species were such important constituents of the vegetation as at Samerberg. Therefore zone 1 to 4 are attributed to the Holsteinian interglacial period. The younger forest phase, separated from the interglacial by a stadial with open vegetation (DA 5), seems to be completely represented, though its sediments are disturbed, apparently by sliding which caused repetition of same-age-sediments in the core (DA 7a, b, c) The vegetational development is simple. A juniper phase (DA 6) was followed by reforestation with spruce, accompanied by some fir (DA 7, 9). Finally pine became the dominant species (DA 9). The simple vegetational development of this younger forest phase does not allow a safe correlation with one of the known pre-eemian interstadials, but for stratigraphical reasons it can be related best to the Dömnitz-interglacial, which among others is also known as Wacken- or Holstein-II-interglacial. Possibly another phase of reforestation is indicated at the end of the following stadial (DA 10). But due to an erosional unconformity nothing than the rise of the juniper curve can be stated. It was only after this sequence of forest phases and periods with open vegetation that glaciers reached the Samerberg area again.

Seawater carbonate chemistry and protein content, respiration, symbiodinium densities, survivorship of Pocillopora damicornis larvae in a laboratory experiment

Efforts to evaluate the response of coral larvae to global climate change (GCC) and ocean acidification (OA) typically employ short experiments of fixed length, yet it is unknown how the response is affected by exposure duration. In this study, we exposed larvae from the brooding coral Pocillopora damicornis to contrasts of temperature (24.00 °C [ambient] versus 30.49 °C) and pCO2 (49.4 Pa versus 86.2 Pa) for varying periods (1-5 days) to test the hypothesis that exposure duration had no effect on larval response as assessed by protein content, respiration, Symbiodinium density, and survivorship; exposure times were ecologically relevant compared to representative pelagic larval durations (PLD) for corals. Larvae differed among days for all response variables, and the effects of the treatment were relatively consistent regardless of exposure duration for three of the four response variables. Protein content and Symbiodinium density were unaffected by temperature and pCO2, but respiration increased with temperature (but not pCO2) with the effect intensifying as incubations lengthened. Survival, however, differed significantly among treatments at the end of the study, and by the 5th day, 78% of the larvae were alive and swimming under ambient temperature and ambient pCO2, but only 55-59% were alive in the other treatments. These results demonstrate that the physiological effects of temperature and pCO2 on coral larvae can reliably be detected within days, but effects on survival require > or = 5 days to detect. The detection of time-dependent effects on larval survivorship suggests that the influence of GCC and OA will be stronger for corals having long PLDs.

Metabolic costs of larval settlement and metamorphosis in the coral Seriatopora caliendrum under ambient and elevated pCO2

We tested the effects of pCO2 on Seriatopora caliendrum recruits over the first 5.3 d of post-settlement existence. In March 2011, 11-20 larvae were settled in glass vials (3.2 mL) and incubated at 24.0 °C and ~250 µmol quanta/m**2/s while supplied with seawater (at 1.4 mL/s) equilibrated with 51.6 Pa pCO2 (ambient) or 86.4 Pa pCO2. At 51.6 Pa pCO2, mean respiration 7 h post-settlement was 0.056 ± 0.007 nmol O2/recruit/min, but rose quickly to 0.095 ± 0.007 nmol O2/recruit/min at 3.3 d post-settlement, and thereafter declined to 0.075 ± 0.002 nmol O2/recruit/min at 5.3 d post-settlement (all ± SE). Elevated pCO2 depressed respiration of recruits by 19% after 3.3 d and 12% overall (i.e., integrated over 5.3 d), and while it had no effect on corallite area, elevated pCO2 was associated with weaker adhesion to the glass settlement surface and lower protein biomass. The unique costs of settlement and metamorphosis for S. caliendrum over 5.3 d are estimated to be 257 mJ/recruit at 51.6 Pa pCO2, which is less than the energy content of the larvae and recruits.

Ocean acidification has no effect on thermal bleaching in the coral Seriatopora caliendrum

The objective of this study was to test whether elevated pCO2 predicted for the year 2100 (85.1 Pa) affects bleaching in the coral Seriatopora caliendrum (Ehrenberg 1834) either independently or interactively with high temperature (30.5 °C). Response variables detected the sequence of events associated with the onset of bleaching: reduction in the photosynthetic performance of symbionts as measured by maximum photochemical efficiency (F v/F m) and effective photochemical efficiency (delta F/F m') of PSII, declines in net photosynthesis (P net) and photosynthetic efficiency (alpha), and finally, reduced chlorophyll a and symbiont concentrations. S. caliendrum was collected from Nanwan Bay, Taiwan, and subjected to combinations of temperature (27.7 vs. 30.5 °C) and pCO2 (45.1 vs. 85.1 Pa) for 14 days. High temperature reduced values of all dependent variables (i.e., bleaching occurred), but high pCO2 did not affect Symbiodinium photophysiology or productivity, and did not cause bleaching. These results suggest that short-term exposure to 81.5 Pa pCO2, alone and in combination with elevated temperature, does not cause or affect coral bleaching.

Seawater carbonate chemistry, respiration, maximum photochemical efficiency and mortality of brooded larvae of Pocillopora//damicornis in a laboratory experiment

To evaluate the effects of temperature and pCO2 on coral larvae, brooded larvae of Pocillopora damicornis from Nanwan Bay, Taiwan (21°56.179' N, 120°44.85' E), were exposed to ambient (419-470 µatm) and high (604-742 µatm) pCO2 at ~25 and ~29 °C in two experiments conducted in March 2010 and March 2012. Larvae were sampled from four consecutive lunar days (LD) synchronized with spawning following the new moon, incubated in treatments for 24 h, and measured for respiration, maximum photochemical efficiency of PSII (F v/F m), and mortality. The most striking outcome was a strong effect of time (i.e., LD) on larvae performance: respiration was affected by an LD × temperature interaction in 2010 and 2012, as well as an LD × pCO2 × temperature interaction in 2012; F v/F m was affected by LD in 2010 (but not 2012); and mortality was affected by an LD × pCO2 interaction in 2010, and an LD × temperature interaction in 2012. There were no main effects of pCO2 in 2010, but in 2012, high pCO2 depressed metabolic rate and reduced mortality. Therefore, differences in larval performance depended on day of release and resulted in varying susceptibility to future predicted environmental conditions. These results underscore the importance of considering larval brood variation across days when designing experiments. Subtle differences in experimental outcomes between years suggest that transgenerational plasticity in combination with unique histories of exposure to physical conditions can modulate the response of brooded coral larvae to climate change and ocean acidification.

Discarge compilation from The Global River Discharge (RivDIS) Project

The Global River Discharge (RivDIS) data set contains monthly discharge measurements for 1018 stations located throughout the world. The period of record varies widely from station to station, with a mean of 21.5 years. These data were digitized from published UNESCO archives by Charles Voromarty, Balaze Fekete, and B.A. Tucker of the Complex Systems Research Center (CSRC) at the University of New Hampshire. River discharge is typically measured through the use of a rating curve that relates local water level height to discharge. This rating curve is used to estimate discharge from the observed water level. The rating curves are periodically rechecked and recalibrated through on-site measurement of discharge and river stage.