bluuebunny/crossref_metadata_2025 huggingface dataset:
Diagnostic and Prognostic Value of Cell‐cycle Regulatory Genes in Malignant Thyroid Neoplasms
Authors: Kebebew Electron , Peng Miao , Reiff Emily , Duh Quan‐Yang , Clark Orlo H. , McMillan Alex
Published: March 2006

Background

Approximately 30% of patients with thyroid nodules have indeterminate or suspicious fine‐needle aspiration (FNA) biopsy results. Because their risk of cancer is approximately 20%, these patients undergo thyroidectomy. We hypothesized that genes that regulate cell‐cycle progression would be differentially expressed in malignant versus benign thyroid nodules and could serve as diagnostic markers and markers of disease aggressiveness.

Methods

We used a cDNA array with 96 cell‐cycle regulatory genes to identify differentially expressed genes in pooled benign versus malignant thyroid neoplasms. Genes up‐ or down‐regulated by more than 2‐fold in malignant thyroid neoplasms were further evaluated by real‐time quantitative polymerase chain reaction (PCR) in 95 patients with hyperplastic nodules (n = 19), follicular adenoma (n = 19), follicular thyroid cancer (n = 19), the follicular variant of papillary thyroid cancer (n = 19), and papillary thyroid cancer (n = 19).

Results

cDNA array analysis showed that cyclin B1, MCM5, MCM7, RAD9, ubiquitin C, CDK6, SKP2, and APAF1 were up‐regulated in malignant thyroid neoplasms. Real‐time quantitative PCR showed that MCM5, MCM7, and RAD9 mRNA expression were significantly higher in malignant than in benign thyroid neoplasms (≤0.0012). The combined use of MCM5, MCM7, and RAD9 mRNA expression had a sensitivity of 98.2% and a specificity of 65.7%. The level of MCM7 mRNA expression was higher in T4 than in T1, T2, and T3 differentiated thyroid cancers (P < 0.0127).

Conclusions

MCM5, MCM7, and RAD9 are overexpressed in malignant thyroid neoplasms of follicular cell origin. These genes may be useful markers of malignant thyroid neoplasms as an adjunct to FNA biopsy. MCM7 mRNA expression is higher in locally invasive differentiated thyroid cancer.
Thyroidectomy Using Monitored Local or Conventional General Anesthesia: An Analysis of Outpatient Surgery, Outcome and Cost in 1,194 Consecutive Cases
Authors: Spanknebel Kathryn , Chabot John A. , DiGiorgi Mary , Cheung Kenneth , Curty James , Allendorf John , LoGerfo Paul
Published: March 2006

Background

Critical appraisal of safety, feasibility, and economic impact of thyroidectomy procedures using local (LA) or general anesthesia (GA) is performed.

Methods

Consecutive patients undergoing thyroidectomy procedures were selected from a prospective database from January 1996 to June 2003 of a single‐surgeon practice at a tertiary center. Statistical analyses determined differences in patient characteristics, outcomes, operative data, and length of stay (LOS) between groups. A cohort of consecutive patients treated in 2002–2003 by all endocrine surgeons at the institution was selected for cost analysis.

Results

A total of 1,194 patients underwent thyroidectomy, the majority using LA (n = 939) and outpatient surgery (65%). Female gender (76%), body mass index ≥30 kg/m2 (29%), median age (49 years), and cancer diagnosis (45%) were similar between groups. Extent of thyroidectomy (59% total) and concomitant parathyroidectomy (13%) were similarly performed. GA was more commonly utilized for patients with comorbidity [15% vs. 10%, Anesthesia Society of America (ASA) ≥3; P < 0.001], symptomatic goiter (13% vs. 7%; P = 0.004), reoperative cases (10% vs. 6%; P = 0.01), and concomitant lymphadenectomy procedures (15% vs. 3%; P < 0.001). GA was associated with significant increase in LOS ≥24 hours (17 % vs. 4%) or overnight observation (49 % vs. 14%), P < 0.001. Operative room utilization was significantly associated with type of anesthesia (180 min vs. 120 min, GA vs. LA, P <. 001) and impacted to a lesser degree by surgeon operative time (89 minutes vs. 76 minutes, GA vs. LA; P =. 089). Overall morbidity rates were similar between groups (GA 5.8 % vs. LA 3.2%). The actual total cost (ATC) per case for GA was 48% higher than for LA and 30% higher than the ATC for all procedures (P = 0.006), with the combined weighted average impacted by more LA cases (n = 217 vs. 85).

Conclusion

These data from a large, unselected group of thyroidectomy patients suggest LA results in similar outcomes and morbidity rates to GA. It is likely that associated LA costs are lower.
Benign Peritoneal Cystic Mesothelioma
Authors: Søreide Jon Arne , Søreide Kjetil , Körner Hartwig , Søiland Håvard , Greve Ole Jacob , Gudlaugsson Einar
Published: March 2006

Background

Benign peritoneal cystic mesothelioma (BPCM) is a rare tumor of unknown origin, most frequently encountered in women of reproductive age. Etiology is unknown; definitions and terminology are confusing, and preoperative diagnosis is difficult. Several differential diagnoses must be considered.

Methods

Based on our own clinical experience and a review of the relevant literature, we address clinical challenges and controversies of importance.

Results

Current literature on BPCM is mostly based on small case reports. Complete surgical resection is recommended if possible. Nevertheless, recurrent disease is not uncommon. Clinical positive effects of various adjuvant medical treatments remain to be shown.

Conclusions

Lack of consistent definitions, various treatment approaches, and mostly short follow‐up times make it difficult to draw any firm conclusions from published reports. The natural history of this rare disease is less than well clarified. When possible, in an individual patient, surgical resection with curative intent seems to be the treatment of choice.
Does Resection Line Involvement Affect Prognosis in Early Gastric Cancer Patients? An Italian Multicentric Study
Authors: Morgagni Paolo , Garcea Domenico , Marrelli Daniele , de Manzoni Giovanni , Natalini Giovanni , Kurihara Hayato , Marchet Alberto , Vittimberga Giovanni , Saragoni Luca , Roviello Franco , Leo Alberto Di , De Santis Francesco , Panizza Valerio , Nitti Donato
Published: March 2006

Background

Resection line involvement has been indicated as an important prognostic factor for gastric cancer. Its late detection renders the choice of treatment difficult for surgeons.

Materials and Methods

We describe the multicenter experience of a group of 11 patients with early gastric carcinoma (EGC) and positive resection confirmed at histological examination who did not undergo surgical retreatment for reasons of associated disease, surgical considerations on duodenal stump, or patient refusal.

Results

The gastric margin was involved in 4 patients, and 7 patients had duodenal resection line involvement. No surgical complications or postoperative deaths were observed. Five and 8‐year survival was 100% and 86%, respectively. The only patient who relapsed did not have lymph node involvement and died from liver metastases, without local recurrence.

Conclusions

It is sometimes difficult to accurately define the resection line in gastric cancer surgery, especially in the early stages of disease, but because of the strongly negative prognostic value of an infiltrated margin, frozen sections are recommended if neoplastic invasion is suspected and a new resection is always recommended if possible. Nevertheless, the good prognosis of resected EGC patients with resection line involvement must be considered before submitting patients with associated diseases to radical surgical retreatment.
Parental Perspectives on the Causes of an Autism Spectrum Disorder in their Children
Authors: Mercer L. , Creighton S. , Holden J. J. A. , Lewis M. E. S.
Published: March 2006

Autism Spectrum Disorders (ASDs) are complex neurodevelopmental disorders with many biological causes, including genetic, syndromic and environmental. Such etiologic heterogeneity impacts considerably upon parents’ needs for understanding their child's diagnosis. A descriptive survey was designed to investigate parental views on the cause(s) of ASD in their child. Among the 41 parents who replied to the questionnaire, genetic influences (90.2%), perinatal factors (68.3%), diet (51.2%), prenatal factors (43.9%) and vaccines (40.0%) were considered to be the most significant contributory factors. Parents reported inaccurately high recurrence risks, misperceptions of the contribution of various putative factors, feelings of guilt and blame regarding their child's diagnosis, as well as a lack of advocacy for genetic counseling by non‐geneticist professionals. This study offers clinicians and researchers further insight into what parents believe contributed to their child's diagnosis of ASD and will help facilitate genetic counseling for these families.
Decomposing the process of species accumulation into area dependent and time dependent parts
Authors: Ulrich Werner
Published: March 2006

In 1960, Preston predicted that the process of species accumulation in time (species–time relationship, STR) should be similar to the species–area relationship (SAR) and follow a power function with a slope of about 0.26. Here these two conjectures are tested using data of the spatiotemporal species accumulation in a local community of beech forest Hymenoptera. A power function species–area–time model of the form S = S0 Az tτ gave better fits to observed species numbers than a simple power function SAR model, and was able to predict similar species turnover rates (about 9% per year) to those inferred by other methods. The STR was well fitted by a power function, although due the limited time span (8 years) a logarithmic STR pattern cannot be ruled out. STR slopes ranged between 0.01 and 0.23 and were lower than predicted by Preston. Temporal species turnover appeared to be negatively correlated to species densities and positively correlated to species body weights. Ecological guild and taxon membership did not significantly influence temporal species turnover.
Designing a “tailor‐made” ecological network using geographical information systems
Authors: Bona Francesca , Badino Guido , Isaia Marco
Published: March 2006

During the last few years, geographical information systems (GIS) have spread as powerful tools for landscape analysis. The main purpose of this work was to use GIS to display an ecological network made up of core areas, key areas and ecological corridors. As an example of the application of this method we refer to the population of deer (Cervus elaphus) and roe deer (Capreolus capreolus) in an alpine area in northwestern Italy. The method provided an overall view of the ecological network of the area, highlighting how linear infrastructures can affect animal populations and consequently, their survival probability.
Genetic differentiation of neutral markers and quantitative traits in predominantly selfing metapopulations: confronting theory and experiments with Arabidopsis thaliana
Authors: PORCHER EMMANUELLE , GIRAUD TATIANA , LAVIGNE CLAIRE
Published: March 2006

The comparison of the genetic differentiation of quantitative traits (QST) and molecular markers (FST) can inform on the strength and spatial heterogeneity of selection in natural populations, provided that markers behave neutrally. However, selection may influence the behaviour of markers in selfing species with strong linkage disequilibria among loci, therefore invalidating this test of detection of selection. We address this issue by monitoring the genetic differentiation of five microsatellite loci (FST) and nine quantitative traits (QST) in experimental metapopulations of the predominantly selfing species Arabidopsis thaliana, that evolved during eight generations. Metapopulations differed with respect to population size and selection heterogeneity. In large populations, the genetic differentiation of neutral microsatellites was much larger under heterogeneous selection than under uniform selection. Using simulations, we show that this influence of selection heterogeneity on FST can be attributable to initial linkage disequilibria among loci, creating stronger genetic differentiation of QTL than expected under a simple additive model with no initial linkage. We found no significant differences between FST and QST regardless of selection heterogeneity, despite a demonstrated effect of selection on QST values. Additional data are required to validate the role of mating system and linkage disequilibria in the joint evolution of neutral and selected genetic differentiation, but our results suggest that FST/QST comparisons can be conservative tests to detect selection in selfing species.
A recombinational portrait of the Drosophila pseudoobscura genome
Authors: ORTIZ-BARRIENTOS DANIEL , CHANG AUDREY S. , NOOR MOHAMED A. F.
Published: March 2006

Drosophila pseudoobscura has been intensively studied by evolutionary biologists for over 70 years. The recent publication of the genome sequence not only permits studies of comparative genomics with other dipterans but also opens the door to identifying genes associated with adaptive traits or speciation or testing for the signature of natural selection across the genome. Information on regional rates of recombination, localization of inversion breakpoints distinguishing it from its sibling species D. persimilis, and known polymorphic markers may be useful in such studies. Here, we present a molecular linkage map of four of the five major chromosome arms of D. pseudoobscura. In doing so, we order and orient several sequence contig groups, localize the inversion breakpoints on chromosome 2 to intervals of 200 kilobases, and identify one error in the published sequence assembly. Our results show that regional recombination rates in D. pseudoobscura are much higher than in D. melanogaster and significantly higher even than in D. persimilis. Furthermore, we detect a non-significant positive correlation between recombination rate and published DNA sequence variation. Finally, the online Appendix presents 200 primer sequence pairs for molecular markers that can be used for mapping of quantitative trait loci, of which 125 are known to be polymorphic within or between species.
Modelling epistatic effects of embryo and endosperm QTL on seed quality traits
Authors: CUI YUEHUA , WU JIANGUO , SHI CHUNHAI , LITTELL RAMON C. , WU RONGLING
Published: March 2006

Coordinated expression of embryo and endosperm tissues is required for proper seed development. The coordination among these two tissues is controlled by the interaction between multiple genes expressed in the embryo and endosperm genomes. In this article, we present a statistical model for testing whether quantitative trait loci (QTL) active in different genomes, diploid embryo and triploid endosperm, epistatically affect a trait expressed on the endosperm tissue. The maximum likelihood approach, implemented with the EM algorithm, was derived to provide the maximum likelihood estimates of the locations of embryo- and endosperm-specific QTL and their main effects and epistatic effects. This model was used in a real example for rice in which two QTL, one from the embryo genome and the other from the endosperm genome, exert a significant interaction effect on gel consistency on the endosperm. Our model has successfully detected Waxy, a candidate gene in the embryo genome known to regulate one of the major steps of amylose biosynthesis in the endosperm. This model will have great implications for agricultural and evolutionary genetic research.
Report on the Conference: Imperialism, Art and Restitution
Authors: O'Connell Mary Ellen , DePaul Sara
Published: March 2006

March 26–27, 2004, in St. Louis, Missouri, the Washington
University School of Law's Whitney R. Harris Institute for Global
Legal Studies and the School of Art hosted the Imperialism, Art and
Restitution Conference. The conference brought together many of the
world's leading experts on art and antiquities law, museum policy,
and the larger cultural context surrounding these fields. The conference
organizers chose several particularly controversial case studies to
generate debate and discussion around the issues of whether Western states
and their museums should return major works of art and antiquities,
acquired during the Age of Imperialism, to the countries of origin. The
case studies included the Elgin/Parthenon Marbles, the Bust of
Nefertiti, and objects protected by the Native American Graves Protection
and Repatriation Act (NAGPRA). The format produced a lively,
interdisciplinary, and sometimes passionate debate that helped crystallize
issues and expose complexities but certainly produced no consensus around
a simple solution of return or retain.
A Future for Our Past: International Symposium for Redefining the
Concept of Cultural Heritage: Organized by the Istanbul Initiative at the
Istanbul Bilgi University, Dolapdere Campus, June 24–26 2004
Authors: Brodie Neil
Published: March 2006

The Istanbul Initiative was established in 2003 in response to
concerns raised by the continuing episodes of cultural destruction that
have accompanied armed conflicts in Cambodia, Lebanon, Afghanistan, the
former Yugoslavia, and Iraq. The Initiative is comprised of Turkish
academics, lawyers, and media professionals who aim to raise international
awareness of the destruction of cultural heritage during wartime. Their
first action was to organize the symposium A Future for Our Past
in Istanbul from June 24 to 26 2004. The immediate impetus for the
symposium was provided by the large-scale looting of museums, libraries,
and archaeological sites that followed the Coalition invasion of Iraq in
April 2003.
Regional Workshop on the Fight against Illicit Trafficking of
Cultural Property: Cape Town, South Africa, September 27–30,
2004
Authors: Shyllon Folarin
Published: March 2006

In the last decade of the twentieth century three UNESCO/ICOM
regional workshops were held in Africa (Arusha, Tanzania in 1993, Bamako,
Mali in 1994 and Kinshasa, Democratic Republic of Congo in 1996) on the
fight against illicit trafficking of cultural property. In the first
decade of this century already two UNESCO regional workshops have been
held in Africa on the same theme. The first was held in Abuja, Nigeria in
2003, and the second, which is the focus of this report, in Cape Town,
South Africa in September 2004.
Information, Transparency and Justice: International Provenance
Research Colloquium: (Washington, DC, November 2004)
Authors: Franz Dr. Michael , Gatzky Renate
Published: March 2006

Even now in 2006, sixty years after the end of World War II, the
subject of cultural assets seized under Nazi persecution (“looted
art”) and displaced during the war (“trophy art”),
continues to be of interest to politicians, historians, legal experts, and
many others. Thus, at a meeting in January 2005, Germany's Advisory
Commission for the return of cultural assets seized as a result of Nazi
persecution, particularly those cultural assets removed from Jewish
ownership, recommended the return of four paintings presently in the
possession of the Federal Republic of Germany to the community of heirs of
Julius Freund. Also in January 2005, Germany's government, all
federal states and central organizations of municipalities called on
German public bodies not to slow down in their search for cultural assets
seized as a result of Nazi persecution and to report any items found to
the Koordinierungsstelle für Kulturgutverluste (Coordination Office
for Lost Cultural Assets) for display as part of its Internet database
www.lostart.de. Furthermore, in February 2005,
Franz von Lenbach's painting “Prinzessin zu
Sayn-Wittgenstein-Sayn” which had been seized by the Nazis was
identified through www.lostart.de and returned to
the heirs of Bernhard Altmann. The painting was part of the Remaining
Stock CCP (“Linzer Liste”) within www.lostart.de enlisting cultural objects with
provenance gaps in the administration of Germany's Bundesamt zur
Regelung offener Vermögensfragen (Federal Office for the settlement
of ownership issues). The object was on loan from the Bundesamt and in
possession of the Wallraf-Richartz-Museum in Köln (Germany).
Ab initio study of the phase separation of argon in molten iron at high pressures
Authors: Ostanin S. , Alfè D. , Dobson D. , Vočadlo L. , Brodholt J. P. , Price G. D.
Published: March 2006

Using first‐principles molecular dynamics (MD) simulations, we study the solubility of argon in molten iron at high pressures and temperatures. In particular we explore whether the low pressure immiscibility of liquid Fe and Ar persists to high pressure (130 GPa) and temperature (4500K), or whether they mix. Starting from a variety of Fe/Ar mixtures we find that they always separate rapidly into two liquids. We conclude that there is no evidence for a significant increase in the solubility of Ar in Fe at these conditions. We cannot, therefore, attribute the lower melting temperatures of Fe obtained from DAC experiments compared to those obtained from ab initio calculations and shock experiments, to eutectic melting between Fe and the Ar pressure medium.
Effective real refractive index of dry aerosols in the Antarctic boundary layer
Authors: Virkkula A. , Koponen I. K. , Teinilä K. , Hillamo R. , Kerminen V‐M. , Kulmala M.
Published: March 2006

The real refractive index (nr) of dry aerosols measured at an Antarctic site was calculated using two methods. Number size distributions were applied in a Mie model where nr was varied until the measured and modeled scattering coefficients matched. Ion concentrations analyzed from impactor samples were used for calculating size‐dependent nr. Generally the two methods were consistent with each other. The average iteration‐derived nr varied mainly between ∼1.4 and ∼1.5 but also unreasonably low values, nr < 1.3, were obtained in air masses from the ocean. Possible explanations, such as inaccuracies in the method, water in the particles, non‐analyzed biogenic particles, or non‐spherical particles being responsible for the low values are discussed.
Predicting the percent live cover of corals: An in situ remote sensing approach
Authors: Mishra Deepak R. , Narumalani Sunil , Bahl Ronald , Rundquist Donald , Lawson Merlin
Published: March 2006

Percent reflectance of corals is perhaps the most important remotely sensed data that can be related to their biophysical properties. Because most of the biophysical variables of corals (i.e., pigment content, live cover and algal overgrowth) are related to their reflectance spectra, the analysis and inversion of the spectra may provide an account of these variables. Our research was aimed at determining the relationship between the percent live cover and reflectance of corals. Two wavelength bands (405–425 nm, and 590–600 nm) were identified to establish the relationship. A linear relationship was observed, which showed higher correlation (R2 = 0.886) at 405–425 nm when compared to 590–600 nm (R2 = 0.602). Validation methods revealed that 405–425 nm wavelength range provided a better relationship than 590–600 nm in predicting percent live cover of corals.
Waves and climate change in the north‐east Atlantic
Authors: Wolf Judith , Woolf David K.
Published: March 2006

Wave height in the North Atlantic has been observed to increase over the last quarter‐century, based on monthly‐mean data derived from observations. Empirical models have linked a large part of this increase in wave height with the North Atlantic Oscillation. Wave models provide a tool to study impacts of various climate change scenarios and investigate physical explanations of statistical results. In this case we use a wave model of the NE Atlantic. Model tests were carried out, using synthetic wind fields, varying the strength of the prevailing westerly winds and the frequency and intensity of storms, the location of storm tracks and the storm propagation speed. The strength of the westerly winds is most effective at increasing mean and maximum monthly wave height. The frequency, intensity, track and speed of storms have little effect on the mean wave height but intensity, track and speed significantly affect maximum wave height.
Accuracy of GRACE mass estimates
Authors: Wahr John , Swenson Sean , Velicogna Isabella
Published: March 2006

The GRACE satellite mission is mapping the Earth's gravity field at monthly intervals. The solutions can be used to determine monthly changes in the distribution of water on land and in the ocean. Most GRACE studies to‐date have focussed on producing maps of mass variability, with little discussion of the errors in those maps. Error estimates, though, are necessary if GRACE is to be used as a diagnostic tool for assessing and improving hydrology and ocean models. Furthermore, only with error estimates can it be decided whether some feature of the data is real, and how accurately that feature is determined by GRACE. Here, we describe a method of constructing error estimates for GRACE mass values. The errors depend on latitude and smoothing radius. Once the errors are adjusted for these factors, we find they are normally‐distributed. This allows us to assign confidence levels to GRACE mass estimates.
An analytical model for fracture nucleation in collapsible stratifications
Authors: Heierli J. , Zaiser M.
Published: March 2006

In collapsible stratifications a particular type of fracture can develop for which nucleation and propagation are governed by the transformation of gravitational energy into fracture energy. The associated nucleation problem is studied for a stratification consisting of an elastic surface layer, a collapsible intermediate layer and a rigid basal layer. An analytical model for fracture nucleation is obtained by calculating the energy (‘crack energy’) associated with a localized collapse of the intermediate layer. The size and energy of a critical crack are evaluated as functions of continuum properties of the strata. The theory is illustrated by an application to the case of whumpfs in collapsible snow stratifications.
Magnetospheric convection and thermal ions in the dayside outer magnetosphere
Authors: Chen S.‐H. , Moore T. E.
Published: March 2006

We have surveyed 3.5 years of Polar Thermal Ion Dynamics Experiment (TIDE) data between 1 January 2000 and 30 June 2003, when Polar apogee paths (sections of orbits with geocentric distances r > 5 RE) were in the dayside outer magnetosphere, to study the spatial distribution of thermal ions and the magnetospheric convection paths of the thermal ions, as a function of interplanetary magnetic field (IMF) orientation. We have found a dawn‐dusk asymmetry in the occurrence of detectable thermal ions above the instrument threshold. The occurrence rate was significantly higher at the duskside. The probability of observing thermal ions, particularly at 1300–1600 local time (LT) near the magnetopause, was >50%, compared with <30% at the dawnside. We interpret the thermal ion events as the result of plasmaspheric drainage plumes, as observed by IMAGE spacecraft or geosynchronous orbiters. The episodic appearance of the thermal ions in the outer magnetosphere could be a significant factor for the dynamo process of global magnetospheric convection. The variation of the convection pattern due to the IMF orientation is consistent with equatorward and poleward reconnection scenarios that superimpose dayside convection driven by reconnection on top of the background convection driven by a viscous interaction at the magnetopause, together with the corotation of the magnetospheric plasma with the ionosphere.
Factors affecting the performance of the optical plankton counter in large lakes: Insights from Lake Michigan and laboratory studies
Authors: Liebig James R. , Vanderploeg Henry A. , Ruberg Steven A.
Published: March 2006

There has been a question as to whether the optical plankton counter (OPC) accurately measures zooplankton density and biomass in large lakes, oceans, and estuaries. Results from our Lake Michigan surveys in 1998–2000 often revealed poor agreement between the OPC‐2T and 153‐μm mesh plankton net samples. The most serious common problem was overestimation of zooplankton biomass by the OPC relative to net tows. Such overestimates have been attributed to the orientation of zooplankton assuming that their maximal silhouette area is detected by the OPC, coincidence, and the presence of nonzooplankton particles. Experiments using an OPC‐1L with polymer microspheres, nylon rods, or live zooplankton confirmed that the OPC accurately counts and sizes zooplankton at low zooplankton concentrations typically found in Lake Michigan and that a shape factor correction often used need not be applied. Most overestimation of biomass was associated with the presence of nonzooplankton particles. Worst agreement was seen in shallow nearshore zones during periods of high total suspended matter (TSM), which consisted of fine sediments and large resuspended particles such as sediment‐phytoplankton aggregates, and benthic plant and animal debris. Best agreement was found under low TSM conditions associated with offshore waters during the stratified period.
Testing a glacial erosion rule using hang heights of hanging valleys, Jasper National Park, Alberta, Canada
Authors: Amundson J. M. , Iverson N. R.
Published: March 2006

In most models of glacial erosion, glacier sliding velocity is hypothesized to control rates of bedrock erosion. If this hypothesis is correct, then the elevation difference between hanging and trunk valley floors, the hang height, should be dictated by the relative sliding velocities of the glaciers that occupied these valleys. By considering sliding velocity to be proportional to balance velocity and using mass continuity, hang height is expressed in terms of glacier catchment areas, slopes, and widths, which can be estimated for past glaciers from the morphology of glacial valleys. These parameters were estimated for 46 hanging valleys and their trunk valleys in three adjacent regions of Jasper National Park. The variability in valley morphology can account for 55–85% of the hang height variability if erosion rate scales with balance velocity raised to a power of 1/3. This correspondence is in spite of spatial variations in glaciation duration, snow accumulation rates, and other variables that likely affected hang heights but cannot be readily estimated and so are not included in our formulation. Thus it appears that balance velocity, and by extension, sliding velocity if the two are proportional, may be a reasonable control variable for assessing erosion rate.
Modeling polar ionospheric effects during the October–November 2003 solar proton events
Authors: Clilverd Mark A. , Seppälä Annika , Rodger Craig J. , Thomson Neil R. , Verronen Pekka T. , Turunen Esa , Ulich Thomas , Lichtenberger János , Steinbach Péter
Published: March 2006

At Ny Ålesund, Svalbard (78°54′N, 11°53′E, L ∼ 18), a narrowband VLF receiver was used to monitor the behavior of the amplitude of several high‐power transmitters located in the Northern Hemisphere under the influence of the solar proton events (SPE) of October/November 2003. We have used Sodankylä ion chemistry (SIC) atmospheric model profiles calculated at the midpoint location of the propagation paths in the northern wintertime polar region to investigate the radio propagation properties of several high‐latitude paths. Different paths showed different responses to the proton precipitation, but propagation modeling was broadly able to account for most of the positive and negative responses observed. Using the SIC‐based electron density profiles, we have been able to develop models of ionospheric effective height (h′) and sharpness (β) in order to describe the D region behavior as a function of proton flux, extending previous work which reported β and h′ values as functions of the X‐ray flux from solar flares. As a result of these models, our understanding of VLF propagation influenced by SPEs is such that VLF observations might be used to predict changes in the ionospheric D region electron density profiles during other particle precipitation events.
From seamount accretion to tectonic erosion: Formation of Osa Mélange and the effects of Cocos Ridge subduction in southern Costa Rica
Authors: Vannucchi Paola , Fisher Donald M. , Bier Sara , Gardner Thomas W.
Published: March 2006

The Costa Rica portion of the Middle America Trench (MAT) is characterized by active tectonic erosion, a process that causes the removal of material from the base of the upper plate as the plate boundary migrates upward. Offshore studies demonstrate accelerated subduction erosion starting at the Miocene‐Pliocene boundary, as the result of subduction of thickened Galapagos related crust, as presently represented by the Cocos Ridge. The subduction of the Cocos Ridge also caused uplift and exposure of the outer forearc on the Osa Peninsula, which offers a window to explore the tectonic evolution of the area. The rocks outcropping on Osa Peninsula are a middle Eocene–middle Miocene mélange dominated by basalt, chert, and limestone resulting from accretion of seamounts. The accretion‐dominated period of the MAT evolution ended at the Miocene‐Pliocene boundary, when thickened crust, a paleo‐Cocos Ridge, produced at the Galapagos hot spot arrived at the trench. The thick crust caused uplift and severe tectonic erosion of the accretionary edifice allowing exhumation of the Osa Mélange. The change from accretion to erosion caused the outer forearc to be offset along subvertical faults that define small (kilometer to tens of kilometers size) blocks that are going through differential vertical movements in response to the morphology of the subducting ridge. Subduction accretion and erosion are two processes that can alternate in time and space or coexist along the same margin, so that mass removal can develop on a previously growing margin and completely remove an accretionary prism.
A fractional dispersion model for overland solute transport
Authors: Deng Zhi‐Qiang , de Lima João L. M. P. , de Lima M. Isabel P. , Singh Vijay P.
Published: March 2006

Using the kinematic‐wave overland flow equation and a fractional dispersion‐advection equation, a process‐oriented, physically‐based model is developed for overland solute transport. Two scenarios, one consisting of downslope and the other of upslope rainstorm movements, are considered for numerical computations. Under these conditions, the hydrograph displays a long‐tailed distribution due to the variation in flow velocity in both time and distance. The solute transport exhibits a complex behavior. Pollutographs are characterized by a steep rising limb, with a peak, and a long, stretched receding limb; whereas the solute concentration distributions feature a rapid receding limb followed by a long stretched rising limb. Downslope moving storms cause much higher peak in both hydrographs and pollutographs than do upslope moving storms. Both hydrographs and the pollutographs predicted by the fractional dispersion model are in good agreement with the data measured experimentally using a soil flume and a moving rainfall simulator.
Reservoir management to balance ecosystem and human needs: Incorporating the paradigm of the ecological flow regime
Authors: Suen Jian‐Ping , Eheart J. Wayland
Published: March 2006

The history of environmental flow analysis shows a shift from an emphasis on a flat line minimum flow requirement to the development of a holistic, regime‐based, approach to flow management. The ecological flow regime determines environmental flow by embracing the multitude of species within an ecosystem rather than emphasizing a single species. Moreover, this paradigm recognizes that flow magnitude, duration, frequency, timing, and predictability must be incorporated into any flow management strategy. In this study, the ecological flow regime paradigm is used to establish such comprehensive and complex management targets for operating a reservoir to satisfy a downstream aquatic ecosystem. The new paradigm incorporates the intermediate disturbance hypothesis, which holds that ecosystems are healthier under disturbances that are neither too small nor too large. The nondominated sorting genetic algorithm is used to find the Pareto set of operating rules that provides decision makers with the optimal trade‐off between human needs and ecological flow regime maintenance.
Getting the right answers for the right reasons: Linking measurements, analyses, and models to advance the science of hydrology
Authors: Kirchner James W.
Published: March 2006

The science of hydrology is on the threshold of major advances, driven by new hydrologic measurements, new methods for analyzing hydrologic data, and new approaches to modeling hydrologic systems. Here I suggest several promising directions forward, including (1) designing new data networks, field observations, and field experiments, with explicit recognition of the spatial and temporal heterogeneity of hydrologic processes, (2) replacing linear, additive “black box” models with “gray box” approaches that better capture the nonlinear and non‐additive character of hydrologic systems, (3) developing physically based governing equations for hydrologic behavior at the catchment or hillslope scale, recognizing that they may look different from the equations that describe the small‐scale physics, (4) developing models that are minimally parameterized and therefore stand some chance of failing the tests that they are subjected to, and (5) developing ways to test models more comprehensively and incisively. I argue that scientific progress will mostly be achieved through the collision of theory and data, rather than through increasingly elaborate and parameter‐rich models that may succeed as mathematical marionettes, dancing to match the calibration data even if their underlying premises are unrealistic. Thus advancing the science of hydrology will require not only developing theories that get the right answers but also testing whether they get the right answers for the right reasons.
X‐chromosome targeting and dosage compensation are mediated by distinct domains in MSL‐3
Authors: Buscaino Alessia , Legube Gaëlle , Akhtar Asifa
Published: March 2006

In Drosophila, dosage compensation of X‐linked genes is achieved by transcriptional upregulation of the male X chromosome. Genetic and biochemical studies have demonstrated that male‐specific lethal (MSL) proteins together with roX RNAs regulate this process. Here, we show that MSL‐3 is essential for cell viability and that three domains in the protein have distinct roles in dosage compensation. The chromo‐barrel domain (CBD) is not necessary for MSL targeting to the male X chromosome but is important for male viability and equalization of X‐linked gene transcription. The polar region cooperates with the CBD in MSL‐3 function, whereas the MRG domain is responsible for targeting the protein to the X chromosome. Our results demonstrate that MSL‐3 localization to the male X chromosome and transcriptional upregulation of X‐linked genes are two separable functions of the MSL‐3 protein.
Structure and oligomeric state of human transcription factor TFIIE
Authors: Jawhari Anass , Uhring Muriel , De Carlo Sacha , Crucifix Corinne , Tocchini‐Valentini Guiseppe , Moras Dino , Schultz Patrick , Poterszman Arnaud
Published: March 2006

The general RNA polymerase II transcription factor TFIIE, which is composed of two subunits, has essential roles in both transcription initiation and promoter escape. Electron microscopy analysis of negatively stained human TFIIE showed a large proportion of α/β heterodimers as well as a small proportion of tetramers. Analytical ultracentrifugation, chemical crosslinking, pulldown experiments and cryo‐electron microscopy confirmed that TFIIE is a α/β heterodimer in solution. Three‐dimensional envelopes of the α/β particles showed an elongated structure composed of three distinct modules. Finally, a model for the quaternary architecture of the complex is proposed that provides a structural framework to discuss the function of TFIIE in the context of RNA polymerase II transcription initiation.
Responses of Alnus glutinosa to Anaerobic Conditions ‐ Mechanisms and Rate of Oxygen Flux into the Roots
Authors: Dittert K. , Wätzel J. , Sattelmacher B.
Published: March 2006

Abstract: Upon exposure to waterlogged growing conditions two‐year‐old alder trees reduced total root mass. Roots were concentrated in the uppermost soil horizon, and only few coarse roots penetrated into deeper soil layers. Root porosity was only slightly affected and did not exceed 8 % in fine roots. Porosity of coarse roots was higher (27 %) but unaffected by growing conditions. The stem base area covered by lenticels increased strongly and so did the cross section diameter of the stem base. The latter showed a highly significant correlation with O2 transport into the roots, measured by a Clark type oxygen electrode. Exposure of the lower 5 cm of the stem base, where lenticels were concentrated, to pure N2 led to a cessation of O2 transport, confirming that lenticels were the major site of air entry into the stem. In alder plants grown under waterlogged conditions, temperature had a pronounced effect on O2 gas exchange of the root system. The temperature compensation point, i.e., the temperature where O2 transport equals O2 consumption by respiration, was 10.5 °C for the entire root system, when measured in a range of 0.15 ‐ 0.20 mmol dissolved O2 L‐1, which is typical for an open water surface equilibrated with air. O2 net flow was inversely related to O2 concentration in the rooting media, indicating that higher root and microbial respiration induced higher net fluxes of O2 into the root system. With 0.04 mmol dissolved O2 L‐1 nutrient solution, the temperature compensation point increased to 20 °C. Measurement of O2 gradients in the rhizosphere of agar‐embedded roots using O2 microelectrodes showed a preference for O2 release in the tip region of coarse roots. Increasing stem temperature over air temperature by 5 °C stimulated O2 flux into the roots as suggested by the model of thermo‐osmotic gas transport. However determination of stem and air temperature in a natural alder swamp in northern Germany revealed that within the experimental period of almost one year, temperature gradients required for thermo‐osmotic gas transport were very seldom. From this it is concluded that under natural conditions in northern Germany, oxygen diffusion along the stem into the root system is driven by O2 concentration gradients rather than by thermo‐osmosis.
Natural Hybridization in Saxifraga callosa Sm.
Authors: Grassi F. , Labra M. , Minuto L. , Casazza G. , Sala F.
Published: March 2006

Abstract: Saxifraga callosa Sm. is an evergreen perennial species distributed from Eastern Spain, through the Western Alps and the Apennines, to southern Italy. The existence of high morphological variation within different subspecies indicates that phenotypic characters are useful but not sufficient taxonomic tools. Indeed, available morphological data already suggested that S. callosa subentity lantoscana may be an outcross between S. callosa and S. cochlearis. In this work, by analyzing ITS (Internal Transcribed Sequences), AFLP (Amplified Fragment Length Polymorphisms), and cpDNA (chloroplast DNA) markers, a comprehensive study of the genomic relationships among S. callosa and related species has been carried out. The sequence of the ITS region of S. callosa subentity lantoscana gave no conclusive results on the taxonomy status of S. callosa subentity lantoscana. On the other hand, the use of the “NewHybrids” software to analyze an AFLP data‐set (208 polymorphic amplified fragments) supported a significant posterior probability that S. callosa subentity lantoscana individuals are natural hybrids between S. callosa and S. cochlearis. The level of introgression of genes from alien genomes was confirmed by a simpler and quick methodology that analyze length variation in cpDNA sequences.
Evidence from Photosynthetic Characteristics for the Hybrid Origin of Diplotaxis muralis from a C3‐C4 Intermediate and a C3 Species
Authors: Ueno O. , Wada Y. , Wakai M. , Bang S. W.
Published: March 2006

Abstract: Artificial hybridization studies have been carried out between plants with different photosynthetic types to study the genetic mechanism of photosynthetic types. However, there are only few reports describing the possibility of natural hybridization between plants with different photosynthetic types. A previous cytological and morphological study suggested that a cruciferous allotetraploid species, Diplotaxis muralis (L.) DC. (2n = 42), originated from natural hybridization between D. tenuifolia (L.) DC. (2n = 22) and D. viminea (L.) DC. (2n = 20). These putative parents have recently been reported to be a C3‐C4 intermediate and a C3 species, respectively. If this hybridization occurred, D. muralis should have characteristics intermediate between those of the C3‐C4 intermediate and C3 types. We compared leaf structures and photosynthetic characteristics of the three species. The bundle sheath (BS) cells in D. tenuifolia included many centripetally located chloroplasts and mitochondria, but those of D. viminea had only a few organelles. The BS cells in D. muralis displayed intermediate features between the putative parents. Glycine decarboxylase P protein was confined to the BS mitochondria in D. tenuifolia, but accumulated mainly in the mesophyll mitochondria in D. viminea. In D. muralis, it accumulated in both the BS and the mesophyll mitochondria. Values of CO2 compensation point and its response to changing light intensity were also intermediate between the putative parents. These data support the theory that D. muralis was created by natural hybridization between species with different photosynthetic types.
Growth Rings in the Roots of Temperate Forbs are Robust Annual Markers
Authors: von Arx G. , Dietz H.
Published: March 2006

Abstract: There is increasing interest in the analysis of annual growth rings in the secondary root xylem of perennial forbs (herb‐chronology). Therefore, we need to verify whether these growth rings are always formed annually. To investigate the formation of root rings we performed common garden experiments at two distinct sites in Switzerland. We grew nine unrelated forb species from seed and subjected them to competition and clipping treatments. Anatomical developments in the roots of the individuals were tracked during five growing seasons. Across all species and treatments at least 94 % of the expected growth rings associated with full growing seasons were identifiable and the development of the anatomical patterns was consistently seasonal. While the distinctness of annual rings varied somewhat between species and sites, the treatments had no effect on the presence of annual rings. In no case were false rings developed. The results of this study demonstrate that the growth rings in the roots of northern temperate forbs represent robust annual growth increments and, hence, can reliably be used in herb‐chronological studies of age‐ and growth‐related questions in plant ecology.
Differential Regulation of Five Pht1 Phosphate Transporters from Maize (Zea mays L.)
Authors: Nagy R. , Vasconcelos M. J. V. , Zhao S. , McElver J. , Bruce W. , Amrhein N. , Raghothama K. G. , Bucher M.
Published: March 2006

Abstract: Maize is one of the most important crops in the developing world, where adverse soil conditions and low fertilizer input are the two main constraints for stable food supply. Understanding the molecular and biochemical mechanisms involved in nutrient uptake is expected to support the development of future breeding strategies aimed at improving maize productivity on infertile soils. Phosphorus is the least mobile macronutrient in the soils and it is often limiting plant growth. In this work, five genes encoding Pht1 phosphate transporters which contribute to phosphate uptake and allocation in maize were identified. In phosphate‐starved plants, transcripts of most of the five transporters were present in roots and leaves. Independent of the phosphate supply, expression of two genes was predominant in pollen or in roots colonized by symbiotic mycorrhizal fungi, respectively. Interestingly, high transcript levels of the mycorrhiza‐inducible gene were also detectable in leaves of phosphate‐starved plants. Thus, differential expression of Pht1 phosphate transporters in maize suggests involvement of the encoded proteins in diverse processes, including phosphate uptake from soil and transport at the symbiotic interface in mycorrhizas, phosphate (re)translocation in the shoot, and phosphate uptake during pollen tube growth.