bluuebunny/crossref_metadata_2025 huggingface dataset:
Promoter Methylation in Prostate Cancer and its Application for the Early Detection of Prostate Cancer Using Serum and Urine Samples
Authors: Ahmed Hafiz
Published: November 2010

Prostate cancer is the second most common cancer and the second leading cause of cancer death in men. However, prostate cancer can be effectively treated and cured, if it is diagnosed in its early stages when the tumor is still confined to the prostate. Combined with the digital rectal examination, the PSA test has been widely used to detect prostate cancer. But, the PSA screening method for early detection of prostate cancer is not reliable due to the high prevalence of false positive and false negative results. Epigenetic alterations including hypermethylation of gene promoters are believed to be the early events in neoplastic progression and thus these methylated genes can serve as biomarkers for the detection of cancer from clinical specimens. This review discusses DNA methylation of several gene promoters during prostate carcinogenesis and evaluates the usefulness of monitoring methylated DNA sequences, such as GSTP1, RASSF1A, RARβ2 and galectin-3, for early detection of prostate cancer in tissue biopsies, serum and urine.
Breast Cancer Biomarker Discovery in the Functional Genomic Age: A Systematic Review of 42 Gene Expression Signatures
Authors: Abba M.C , Lacunza E , Butti M , Aldaz C.M
Published: November 2010

In this review we provide a systematic analysis of transcriptomic signatures derived from 42 breast cancer gene expression studies, in an effort to identify the most relevant breast cancer biomarkers using a meta-analysis method. Meta-data revealed a set of 117 genes that were the most commonly affected ranging from 12% to 36% of overlap among breast cancer gene expression studies. Data mining analysis of transcripts and protein-protein interactions of these commonly modulated genes indicate three functional modules significantly affected among signatures, one module related with the response to steroid hormone stimulus, and two modules related to the cell cycle. Analysis of a publicly available gene expression data showed that the obtained meta-signature is capable of predicting overall survival ( P < 0.0001) and relapse-free survival ( P < 0.0001) in patients with early-stage breast carcinomas. In addition, the identified meta-signature improves breast cancer patient stratification independently of traditional prognostic factors in a multivariate Cox proportional-hazards analysis.
Bioremediation of Fluorophenols by Glycosylation with Immobilized Marine Microalga Amphidinium Crassum
Authors: Shimoda Kei , Hamada Hiroki
Published: November 2010

Fluorophenols are used as agrochemicals and released into environment as pollutants. Cultured marine microalga Amphidinium crassum ( Gymnodinium) glucosylated 2-fluorophenol (1), 3-fluorophenol (2), and 4-fluorophenol (3) to the corresponding β-D-glucosides, ie, 2-fluorophenyl β-D-glucoside (4, 60 μg/g cells), 3-fluorophenyl β-D-glucoside (5, 20 μg/g cells), and 4-fluorophenyl β-D-glucoside (6, 40 μg/g cells). On the other hand, 2-, 3-, and 4-fluorophenols were efficiently converted by immobilized A. crassum in sodium alginate gel to give their β-D-glucosides in higher yields (4: 140 μg/g cells; 5: 60 μg/g cells; 6: 100 μg/g cells). In repetitive batch use, the immobilized cells of A. crassum maintained the potential for the glucosylation of the substrate fluorophenol after 5 times of usage.
Radiative impact of mineral dust on monsoon precipitation variability over West Africa
Authors: Zhao C. , Liu X. , Leung L. R. , Hagos S.
Published: November 2010

Abstract. The radiative forcing of dust and its impact on precipitation over the West Africa monsoon (WAM) region is simulated using a coupled meteorology and aerosol/chemistry model (WRF-Chem). During the monsoon season, dust is a dominant contributor to aerosol optical depth (AOD) over West Africa. In the control simulation, on 24-h domain average, dust has a cooling effect (−6.11 W/m2) at the surface, a warming effect (6.94 W/m2) in the atmosphere, and a relatively small TOA forcing (0.83 W/m2). Dust modifies the surface energy budget and atmospheric diabatic heating and hence causes lower atmospheric cooling in the daytime but warming in the nighttime. As a result, atmospheric stability is increased in the daytime and reduced in the nighttime, leading to a reduction of late afternoon precipitation by up to 0.14 mm/h (25%) and an increase of nocturnal and early morning precipitation by up to 0.04 mm/h (45%) over the WAM region. Dust-induced reduction of diurnal precipitation variation improves the simulated diurnal cycle of precipitation when compared to measurements. However, daily precipitation is only changed by a relatively small amount (−0.17 mm/day or −4%). The dust-induced change of WAM precipitation is not sensitive to interannual monsoon variability. On the other hand, sensitivity simulations show that, from weaker to stronger absorbing dust representing the uncertainty in dust solar absorptivity, dust longwave warming effect in the nighttime surpasses its shortwave cooling effect in the daytime at the surface, leading to a less stable atmosphere associated with more convective precipitation in the nighttime. As a result, the dust-induced change of daily WAM precipitation varies from a significant reduction of −0.52 mm/day (−12%, weaker absorbing dust) to a small increase of 0.03 mm/day (1%, stronger absorbing dust). This variation originates from the competition between dust impact on daytime and nighttime precipitation, which depends on dust shortwave absorption. Dust reduces the diurnal variation of precipitation regardless of its absorptivity, but more reduction is associated with stronger absorbing dust.
Understanding the transport of Patagonian dust and its influence on marine biological activity in the South Atlantic Ocean
Authors: Johnson M. S. , Meskhidze N. , Kiliyanpilakkil V. P. , Gassó S.
Published: November 2010

Abstract. The supply of bioavailable iron to the high-nitrate low-chlorophyll (HNLC) waters of the Southern Ocean through atmospheric pathways could stimulate phytoplankton blooms and have major implications for the global carbon cycle. In this study, model results and remotely-sensed data are analyzed to examine the horizontal and vertical transport pathways of Patagonian dust and quantify the effect of iron-laden mineral dust deposition on marine biological productivity in the surface waters of the South Atlantic Ocean (SAO). Model simulations for the atmospheric transport and deposition of mineral dust and bioavailable iron are carried out for two large dust outbreaks originated at the source regions of Northern Patagonia during the austral summer of 2009. Model-simulated horizontal and vertical transport pathways of Patagonian dust plumes are in reasonable agreement with remotely-sensed data. Simulations indicate that the synoptic meteorological patterns of high and low pressure systems are largely accountable for dust transport trajectories over the SAO. According to model results and retrievals from the Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO), synoptic flows caused by opposing pressure systems (a high pressure system located to the east or north-east of a low pressure system) elevate the South American dust plumes well above the marine boundary layer. Under such conditions, the bulk concentration of mineral dust can quickly be transported around the low pressure system in a clockwise manner, follow the southeasterly advection pathway, and reach the HNLC waters of the SAO and Antarctica in ~3–4 days after emission from the source regions of Northern Patagonia. Two different mechanisms for dust-iron mobilization into a bioavailable form are considered in this study. A global 3-D chemical transport model (GEOS-Chem), implemented with an iron dissolution scheme, is employed to estimate the atmospheric fluxes of soluble iron, while a dust/biota assessment tool (Boyd et al., 2010) is applied to evaluate the amount of bioavailable iron formed through the slow and sustained leaching of dust in the ocean mixed layer. The effect of iron-laden mineral dust supply on surface ocean biomass is investigated by comparing predicted surface chlorophyll-a concentration ([Chl-a]) to remotely-sensed data. As the dust transport episodes examined here represent large summertime outflows of mineral dust from South American continental sources, this study suggests that (1) atmospheric fluxes of mineral dust from Patagonia are not likely to be the major source of bioavailable iron to ocean regions characterized by high primary productivity; (2) even if Patagonian dust plumes may not cause visible algae blooms, they could still influence background [Chl-a] in the South Atlantic sector of the Southern Ocean.
Cold and transition season cloud condensation nuclei measurements in western Colorado
Authors: Ward D. S. , Cotton W. R.
Published: November 2010

Abstract. Recent research has shown that orographic precipitation and the water resources that depend on it in the Colorado Rocky Mountains are sensitive to the variability of the region's aerosols, whether emitted locally or from distant sources. However, observations of cloud-active aerosols in western Colorado, climatologically upwind of the Colorado Rocky Mountains, have been limited to a few studies at a single, northern site. To address this knowledge gap, atmospheric aerosols were sampled at a ground site in southwestern Colorado and in low-level north to south transects of the Colorado Western Slope as part of the Inhibition of Snowfall by Pollution Aerosols (ISPA-III) field campaign. Total particle and cloud condensation nuclei (CCN) number concentration were measured for a 24-day period in Mesa Verde National Park, climatologically upwind of the San Juan Mountains, in Sept. and Oct. 2009. Regression analysis showed a positive relationship between mid-troposphere atmospheric pressure to the west of the site and the total particle count at the ground site, but no similar statistically significant relationship for the observed CCN. These data were supplemented with particle and CCN number concentration, as well as particle size distribution measurements aboard the KingAir platform during December 2009. A CCN closure attempt was performed using the size distribution information and suggested that the sampled aerosol in general had low hygroscopicity that changed slightly with the large-scale wind direction. Together, the sampled aerosols from these field programs were characteristic of a rural continental environment with a cloud active portion that varied slowly in time, and little in space along the Western Slope.
The effect of trimethylamine on atmospheric nucleation involving H2SO4
Authors: Erupe M. E. , Viggiano A. A. , Lee S.-H.
Published: November 2010

Abstract. Field observations and quantum chemical calculations have shown that organic amine compounds may be important in new particle formation processes involving H2SO4. Here, we report laboratory observations that investigate the effect of trimethylamine (TMA) on H2SO4-H2O nucleation made under aerosol precursor concentrations typically found in the lower troposphere ([H2SO4] of 106–107 cm−3; [TMA] of 180–1350 pptv). These results show that the threshold [H2SO4] needed to produce the unity nucleation rate ([H2SO4] of 106–107 cm−3) and the number of precursor molecules in the critical cluster (nH2SO4 = 4–6; nTMA = 1) are surprisingly similar to those found in the ammonia (NH3) ternary nucleation study (Benson et al., 2010a). At lower RH, however, enhancement in nucleation rates due to TMA was up to an order of magnitude greater than that due to NH3. These findings imply that both amines and NH3 are important nucleation species, but under dry atmospheric conditions, amines may have stronger effects on H2SO4 nucleation than NH3. Aerosol models should therefore take into account inorganic and organic bases together to fully understand the widespread new particle formation events in the lower troposphere.
Multi-scale modeling study of the source contributions to near-surface ozone and sulfur oxides levels over California during the ARCTAS-CARB period
Authors: Huang M. , Carmichael G. R. , Spak S. N. , Adhikary B. , Kulkarni S. , Cheng Y. F. , Wei C. , Tang Y. , D'Allura A. , Wennberg P. O. , Huey G. L. , Dibb J. E. , Jimenez J. L. , Cubison M. J. , Weinheimer A. J. , Kaduwela A. , Cai C. , Wong M. , Pierce R. B. , Al-Saadi J. A. , Streets D. G. , Zhang Q.
Published: November 2010

Abstract. Chronic ozone (O3) problems and the increasing sulfur oxides (SOx=SO2+SO4) ambient concentrations over South Coast (SC) and other areas of California (CA) are affected by both local emissions and long-range transport. In this paper, multi-scale tracer and full-chemistry simulations with the STEM atmospheric chemistry model are used to assess the contribution of local emission sources to SC O3 and evaluate the impacts of transported sulfur and local emissions on the SC sulfur budget during the ARCTAS-CARB experiment period in 2008. Sensitivity simulations quantify contributions of biogenic and fire emissions to SC O3 levels. California biogenic and fire emissions contribute 3–4 ppb to near-surface O3 over SC, with larger contributions to other regions in CA. Long-range transport from Asia is estimated to enhance surface SO4 over SC by ~0.5 μg/sm3, and the higher SOx levels (up to ~0.7 ppb of SO2 and ~6 μg/sm3 of SO4) observed above ~6 km did not affect surface air quality in the study region. Enhanced near-surface SOx levels over SC during the flight week were attributed mostly to local emissions. Two anthropogenic SOx emission inventories (EIs) from the California Air Resources Board (CARB) and the US Environmental Protection Agency (EPA) are compared and applied in 60 km and 12 km chemical transport simulations, and the results are compared with observations. The CARB EI shows improvements over the National Emission Inventory (NEI) by EPA, but generally underestimates surface SC SOx by about a factor of two. Maritime (mostly shipping) emissions contribute to the high SO2 levels over the ocean and on-shore, and fine SO4 over the downwind areas is impacted by maritime sources. Maritime emissions also modify the NOx-VOC limitations over coastal areas. These suggest an important role for shipping emission controls in reducing fine particle and O3 concentrations in SC.
Calibration of atmospheric hydrogen measurements
Authors: Jordan A. , Steinberg B.
Published: November 2010

Abstract. Interest in atmospheric hydrogen (H2) has been growing in recent years with the prospect of H2 being a potential alternative to fossil fuels as an energy carrier. This has intensified research for a quantitative understanding of the atmospheric hydrogen cycle and its total budget, including the expansion of the global atmospheric measurement network. However, inconsistencies in published observational data constitute a major limitation in exploring such data sets. The discrepancies can be mainly attributed to difficulties in the calibration of the measurements. In this study various factors that may interfere with accurate quantification of atmospheric H2 were investigated including drifts of standard gases in high pressure cylinders. As an experimental basis a procedure to generate precise mixtures of H2 within the atmospheric concentration range was established. Application of this method has enabled a thorough linearity characterization of the commonly used GC-HgO reduction detector. We discovered that the detector response was sensitive to the composition of the matrix gas. Addressing these systematic errors, an accurate calibration scale has been generated defined by thirteen standards with dry air mole fractions ranging from 139–1226 nmol mol−1. The new scale has been accepted as the official World Meteorological Organisation's (WMO) Global Atmospheric Watch (GAW) H2 mole fraction scale.
Stratigraphic analysis of lake level fluctuations in Lake Ohrid: an integration of high resolution hydro-acoustic data and sediment cores
Authors: Lindhorst K. , Vogel H. , Krastel S. , Wagner B. , Hilgers A. , Zander A. , Schwenk T. , Wessels M. , Daut G.
Published: November 2010

Abstract. Ancient Lake Ohrid is a steep-sided, oligotrophic, karst lake that was tectonically formed most likely within the Pliocene and often referred to as a hotspot of endemic biodiversity. This study aims on tracing significant lake level fluctuations at Lake Ohrid using high-resolution acoustic data in combination with lithological, geochemical, and chronological information from two sediment cores recovered from sub-aquatic terrace levels at ca. 32 and 60 m water depth. According to our data, significant lake level fluctuations with prominent lowstands of ca. 60 and 35 m below the present water level occurred during Marine Isotope Stage (MIS) 6 and MIS 5, respectively. The effect of these lowstands on biodiversity in most coastal parts of the lake is negligible, due to only small changes in lake surface area, coastline, and habitat. In contrast, biodiversity in shallower areas was more severely affected due to disconnection of today sub-lacustrine springs from the main water body. Multichannel seismic data from deeper parts of the lake clearly image several clinoform structures stacked on top of each other. These stacked clinoforms indicate significantly lower lake levels prior to MIS 6 and a stepwise rise of water level with intermittent stillstands since its existence as water-filled body, which might have caused enhanced expansion of endemic species within Lake Ohrid.
Efficiency of small scale carbon mitigation by patch iron fertilization
Authors: Sarmiento J. L. , Slater R. D. , Dunne J. , Gnanadesikan A. , Hiscock M. R.
Published: November 2010

Abstract. While nutrient depletion scenarios have long shown that the high-latitude High Nutrient Low Chlorophyll (HNLC) regions are the most effective for sequestering atmospheric carbon dioxide, recent simulations with prognostic biogeochemical models have suggested that only a fraction of the potential drawdown can be realized. We use a global ocean biogeochemical general circulation model developed at GFDL and Princeton to examine this and related issues. We fertilize two patches in the North and Equatorial Pacific, and two additional patches in the Southern Ocean HNLC region north of the biogeochemical divide and in the Ross Sea south of the biogeochemical divide. We evaluate the simulations using observations from both artificial and natural iron fertilization experiments at nearby locations. We obtain by far the greatest response to iron fertilization at the Ross Sea site, where sea ice prevents escape of sequestered CO2 during the wintertime, and the CO2 removed from the surface ocean by the biological pump is carried into the deep ocean by the circulation. As a consequence, CO2 remains sequestered on century time-scales and the efficiency of fertilization remains almost constant no matter how frequently iron is applied as long as it is confined to the growing season. The second most efficient site is in the Southern Ocean. The North Pacific site has lower initial nutrients and thus a lower efficiency. Fertilization of the Equatorial Pacific leads to an expansion of the suboxic zone and a striking increase in denitrification that causes a sharp reduction in overall surface biological export production and CO2 uptake. The impacts on the oxygen distribution and surface biological export are less prominent at other sites, but nevertheless still a source of concern. The century time scale retention of iron in this model greatly increases the long-term biological response to iron addition as compared with simulations in which the added iron is rapidly scavenged from the ocean.
Reference crop evapotranspiration derived from geo-stationary satellite imagery: a case study for the Fogera flood plain, NW-Ethiopia and the Jordan Valley, Jordan
Authors: de Bruin H. A. R. , Trigo I. F. , Jitan M. A. , Temesgen Enku N. , van der Tol C. , Gieske A. S. M.
Published: November 2010

Abstract. First results are shown of a project aiming to estimate daily values of reference crop evapotranspiration ET0 from geo-stationary satellite imagery. In particular, for Woreta, a site in the Ethiopian highland at an elevation of about 1800 m, we tested a radiation-temperature based approximate formula proposed by Makkink (MAK), adopting ET0 evaluated with the version of the Penman-Monteith equation described in the FAO Irrigation and Drainage paper 56 as the most accurate estimate. More precisely we used the latter with measured daily solar radiation as input (denoted by PMFAO-Rs). Our data set for Woreta concerns a period where the surface was fully covered with short green non-stressed vegetation. Our project was carried out in the context of the Satellite Application Facility on Land Surface Analysis (LANDSAF) facility. Among others, the scope of LANDSAF is to increase benefit from the EUMETSAT Satellite Meteosat Second Generation (MSG). In this study we applied daily values of downward solar radiation at the surface obtained from the Spinning Enhanced Visible and Infrared Imager (SEVIRI) radiometer. In addition, air temperature at 2 m was obtained from 3-hourly forecasts provided by the European Centre for Medium-Range Weather Forecasts (ECMWF). Both MAK and PMFAO-Rs contain the psychrometric "constant", which is proportional to air pressure, which, in turn, decreases with elevation. In order to test elevation effects we tested MAK and its LANDSAF input data for 2 sites in the Jordan Valley located about 250 m b.s.l. Except for a small underestimation of air temperature at the Ethiopian site at 1800 m, the first results of our LANDSAF-ET0 project are promising. If our approach to derive ET0 proves successfully, then the LANDSAF will be able to initiate nearly real time free distribution of ET0 for the full MSG disk.
Linking Grain Boundaries and Grain Growth in Ceramics
Authors: Bäurer Michael , Störmer Heike , Gerthsen Dagmar , Hoffmann Michael J.
Published: November 2010

The macroscopic properties of most materials are strongly influenced by grain size. In ceramic materials the microstructure usually results from the sintering process. Understanding the basic mechanisms of grain growth on an atomic length scale in ceramics would be beneficial to tailor the microstructure for improved macroscopic performance of devices. A method is presented using grain growth experiments to select samples for closer examination of grain boundaries with transmission electron microscopy. The growth experiments are used to identify temperatures were changes at grain boundaries occur at high temperature. Subsequently samples of interest are investigated using transmission electron microscopy (TEM) methods. The correlation between TEM results and changes in grain growth behavior can be used to gain closer insight into the processes occurring during grain growth at an atomic length scale. Strontium titanate is used as model system to demonstrate the combination of growth experiments with TEM results. Normal grain growth shows two distinct drops in growth rate in the temperature range between 1 300 and 1 425 °C, independent of the A‐site to B‐site stoichiometry of the perovskite. In previous studies a high preference for grain boundary planes oriented parallel to the 100 direction of one of the adjacent grains was found in the high temperature regime. This study shows that the preference does not exist in the low temperature regime possibly explaining the change in grain growth rate.
Allometry and apparent paradoxes in human limb proportions: Implications for scaling factors
Authors: Auerbach Benjamin M. , Sylvester Adam D.
Published: November 2010

It has been consistently demonstrated that human proximal limb elements exhibit negative allometry, while distal elements scale with positive allometry. Such scaling implies that longer limbs will have higher intralimb indices, a phenomenon not borne out by empirical analyses. This, therefore, creates a paradox within the limb allometry literature. This study shows that these apparently conflicting results are the product of two separate phenomena. First, the use of the geometric mean of limb elements produces allometry coefficients that are not independent, and that when using ordinary least squares regression must yield an average slope of one. This phenomenon argues against using the geometric mean as a size variable when examining limb allometry. While the employment of relevant dimensions independent of those under analysis to calculate the geometric mean—as suggested by Coleman (Am J Phys Anthropol 135 (2008) 404–415)—may be a partial method for resolving the problem, an empirically determined, independent and biologically relevant size variable is advocated. If stature is used instead of the geometric mean as an independent size variable, all major limb elements scale with positive allometry. Second, while limb allometry coefficients do indicate differential allometry in limb elements, and thus should lead to some intralimb index allometry, this pattern appears to be attenuated by other sources of limb element length variation. Am J Phys Anthropol, 2011. © 2010 Wiley‐Liss, Inc.
Hamate‐pisiform coalition: Morphology, clinical significance, and a simplified classification scheme for carpal coalition
Authors: Burnett Scott E.
Published: November 2010

Hamate‐pisiform coalition is characterized by the abnormal union of the pisiform bone and hamulus of the hamate. Because most reported cases are isolated, and literature on the subject is sparse, relatively little is known about this condition and its clinical significance. The purpose of this report is to discuss the occurrence, morphology, and frequency of hamate‐pisiform coalition identified in a skeletal sample of native South Africans, and to conduct a metaanalysis of all known cases in order to clarify the sex distribution, laterality, form, and clinical significance of this condition. Five new cases (three male, two female) of hamate‐pisiform coalition were identified in 527 native South Africans. Results indicate that hamate‐pisiform coalition is infrequent (0.76%) but may be more likely encountered in individuals of African ancestry. Morphologically, non‐osseous examples ranged in appearance from minor expressions involving pitting of an expanded hamulus base, to a variably pitted articulation between an elongated pisiform and hamulus. Osseous union between the two bones tends to extend beyond the hamulus base to adjacent areas of the hamate. Cases involving osseous union appear predisposed to fracture while ulnar neuropathy is significantly more frequent in individuals exhibiting non‐osseous coalition. As both non‐osseous and osseous cases can have clinical significance, awareness of the variable manifestations of this condition is necessary for hand specialists. A simplified classification system is suggested to more consistently characterize carpal coalitions. Clin. Anat. 24:188–196, 2011. © 2010 Wiley‐Liss, Inc.
Stereospecific pharmacokinetics of racemic homoeriodictyol, isosakuranetin, and taxifolin in rats and their disposition in fruit
Authors: Vega‐Villa Karina R. , Remsberg Connie M. , Takemoto Jody K. , Ohgami Yusuke , Yáñez Jaime A. , Andrews Preston K. , Davies Neal M.
Published: November 2010

The chirality of flavonoids has been overlooked in the majority of pharmacokinetic studies of homoeriodictyol, isosakuranetin, and taxifolin. The stereospecific pharmacokinetic disposition of these xenobiotics in male Sprague‐Dawley rats is described for the first time. Validated HPLC methods were used to analyze serum and urine samples of rats following intravenous administration of each flavonoid via jugular vein cannulation and to determine their content in selected fruits. The characterization and interpretation of the pharmacokinetic disposition profiles of homoeriodictyol, isosakuranetin, and taxifolin are described. A discrepancy exists between half‐lives in serum and urine which may be attributed to low assay sensitivity in serum for the three compounds; thus, a more accurate estimation of the pharmacokinetic parameters was obtained from urine. The pharmacokinetics of homoeriodictyol, isosakuranetin, and taxifolin revealed distribution, metabolism, and elimination that were dependent on the stereochemistry of the stereoisomers. The (−)‐(S)‐enantiomers of homoeriodictyol and isosakuranetin and the (+)‐(2S; 3R)‐stereoisomer of taxifolin were predominant in lemon, grapefruit, and tomato. These findings were achieved using chiral methods of analysis; the utility and necessity of developing chiral methods of analysis for chiral xenobiotics are discussed. Chirality, 2011. © 2010 Wiley‐Liss, Inc.
Melanoma's deadly march to the brain
Authors: Othus Megan , Moon James , Margolin Kim
Published: November 2010

The 3 articles reviewed in this issue of Cancer add to and update previously reported experience regarding the prognosis of melanoma patients diagnosed with brain metastases, but do not answer the important question of identifying which patients diagnosed with early melanoma will go on to develop this complication that most frequently determines the outcome in metastatic melanoma and how and when to best intervene therapeutically. If clinicians wish to use retrospective databases to help improve outcomes for these patients, then better biologic discriminators, based on careful clinico‐pathologic correlational observations, need to be incorporated and then validated in large datasets to define useful prognostic subsets.
Three‐Pulse Photon‐Echo Peak Shift Spectroscopy and Its Application for the Study of Solvation and Nanoscale Excitons
Authors: Oh Megan H. J. , Salvador Mayrose R. , Wong Cathy Y. , Scholes Gregory D.
Published: November 2010

An understanding of chemical reactivity begins with an understanding of the dynamics involved regarding system–bath interactions. Spectroscopic studies of these interactions in condensed‐phase multichromophoric systems are intricate and contain much information. Photon‐echo spectroscopy has proven to be a useful tool for probing these interactions. A description of three‐pulse photon‐echo peak shift spectroscopy (3PEPS)—theory, experiment, and application—for the study of solvation and dynamics of nanoscale excitons is presented. Also, we discuss how two‐dimensional photon‐echo spectroscopy (2DPE) relates to 3PEPS and show how 3PEPS data can be extracted from 2D photon‐echo data.
External quality assurance of circulating tumor cell enumeration using the CellSearch® system: A feasibility study
Authors: Kraan Jaco , Sleijfer Stefan , Strijbos Michiel H. , Ignatiadis Michail , Peeters Dieter , Pierga Jean‐Yves , Farace Francoise , Riethdorf Sabine , Fehm Tanja , Zorzino Laura , Tibbe Arjan G. J. , Maestro Marisa , Gisbert‐Criado Rafael , Denton Graeme , de Bono Johann S. , Dive Caroline , Foekens John A. , Gratama Jan W.
Published: November 2010

Background:

Circulating tumor cells (CTCs) are cells that have detached from solid tumors and entered the blood. CTCs can be detected, among others, by semi‐automated immunomagnetic enrichment and image cytometry using CellSearch® (Veridex, Raritan, NJ). We studied the feasibility of external quality assurance (EQA) of the entire CellSearch procedure from blood draw to interpretation of results in multiple laboratories.

Methods:

Blood samples from six cancer patients and controls were distributed to 14 independent laboratories to test between‐laboratory, between‐assay, and between‐instrument variation. Additionally, between‐operator variability was assessed through the interpretation of blinded images of all blood samples on a website.

Results:

Shipment and storage of samples had no influence on CTC values. Between‐instrument (coefficient of variation (CV) < 12%) and between‐assay variation was low (CV ≤ 20%), indicating high reproducibility. However, between‐laboratory CV ranged from 45 to 64%. Although inter‐operator agreement on image interpretation (Fleiss' κ statistics) ranged from “substantial” to “almost perfect,” image interpretation, particularly of samples containing high numbers of apoptotic cells, was the main contributor to between‐laboratory variation.

Conclusions:

This multicenter study shows the feasibility of an EQA program for CTC detection in patient samples, and the importance of continuation of such a program for the harmonization of CTC enumeration. © 2010 International International Clinical Cytometry Society
Orbital aspergillus infection diagnosed by FNAC
Authors: Kuruba Sree Lakshmi , Prabhakaran Venkatesh C. , Nagarajappa A. H. , Biligi Dayanand S.
Published: November 2010

Fungal infections of the orbit represent a small minority of orbital infections. However, due to the virulent nature of some of the fungal species, they can have a devastating effect on ocular functions. Most of these fungi are saprophytes, which cause opportunistic infections. Aspergillus is one such fungus that can cause infection at various sites in an immunosuppressed individual. Sinonasal aspergillus infection with orbital extension and orbital aspergillus infection progress relentlessly. They can have a precipitous clinical course resulting in total loss of vision. Fine needle aspiration cytology (FNAC) is rarely used as a preoperative diagnostic tool in the investigation of orbital mass lesions. Further, fungal infections of orbit are seldom diagnosed on FNAC. Two cases of fungal infection of the orbital and periorbital tissue diagnosed on FNAC are presented. A 50‐year‐old diabetic male presented with diminishing vision, pain, and forward protrusion of the left eye. On examination, he had upper eye lid fullness. A 55‐year‐old diabetic male presented with a swelling on the right upper eye lid. The patients were evaluated radiologically and then subjected to FNAC. The smears showed giant cells, histiocytes, epithelioid granulomas, and fungal hyphae. A diagnosis of fungal infection was arrived at which was subsequently confirmed by culture and biopsy. Orbital aspergillus infection can have a precipitous course. Computerized tomography and magnetic resonance imaging of the orbit provide crucial information. However, FNAC can help in making an early definitive diagnosis of fungal infection and thus obviate the need for a biopsy. Diagn. Cytopathol. 2010. © 2010 Wiley‐Liss, Inc.
Rinse fluid and imprint smear cytology of bronchial biopsies in diagnosis of lung tumors
Authors: Goyal Shilpa , Mohan Harsh , Uma Handa  , Saini Varinder
Published: November 2010

The usefulness of rinse fluid and imprint smear cytology of the bronchial biopsy has been studied in diagnosis of lung cancer. However, scarce data is available regarding rinse fluid cytology of biopsy. The aim of this study was to evaluate these cytologic techniques for their diagnostic accuracy. Bronchial biopsy was taken in 52 patients clinically/radiologically suspected to have lung carcinoma. Imprint smears of the biopsy were prepared, following which it was put in balanced saline solution to collect rinse fluid of biopsy before transferring it to formalin for fixation. Cytological diagnosis from imprint and rinse fluid smears was compared with histopathological diagnosis. Malignancy was detected in 45 cases of 52 patients on histopathology. Positive result was given by rinse fluid cytology in 34 (65.4%) cases while diagnostic accuracy was 78.8%. The imprint smears were positive for malignancy in 44 (84.6%) cases with diagnostic accuracy of 98.08%. There were no false–positive results, but one case was incorrectly typed by both the techniques. Imprint smear cytology has a better diagnostic accuracy and efficacy over rinse fluid while the two cytologic techniques can be used in combination routinely with biopsy to provide an early and reliable diagnosis in lung cancer. Diagn. Cytopathol. 2011. © 2010 Wiley Periodicals, Inc.
Calcinosis cutis: Diagnosis by fine needle aspiration cytology—A rare case report
Authors: Agrawal Pallavi , Banik Tarak , Dey Pranab
Published: November 2010

Calcinosis cutis is characterized by deposition of calcium salts in the subcutaneous tissues in the body. In this study, we described a case of calcinosis cutis that was diagnosed by fine needle aspiration (FNA) in a 15‐year‐old male. The patient presented with multiple nodules over right forearm and right knee. FNA smears showed flakes of amorphous material indicating calcium along with few macrophages. The presence of amorphous calcium salts along with histiocytes in the appropriate clinical settings is diagnostic of calcinosis cutis. Diagn. Cytopathol. 2011. © 2010 Wiley Periodicals, Inc.
Microarray identification of novel downstream targets of FoxD4L1/D5, a critical component of the neural ectodermal transcriptional network
Authors: Yan Bo , Neilson Karen M. , Moody Sally A.
Published: November 2010

FoxD4L1/D5 is a forkhead transcription factor that functions as both a transcriptional activator and repressor. FoxD4L1/D5 acts upstream of several other neural transcription factors to maintain neural fate, regulate neural plate patterning, and delay the expression of neural differentiation factors. To identify a more complete list of downstream genes that participate in these earliest steps of neural ectodermal development, we carried out a microarray analysis comparing gene expression in control animal cap ectodermal explants (ACs), which will form epidermis, to that in FoxD4L1/D5‐expressing ACs. Forty‐four genes were tested for validation by RT‐PCR of ACs and/or in situ hybridization assays in embryos; 86% of those genes up‐regulated and 100% of those genes down‐regulated in the microarray were altered accordingly in one of these independent assays. Eleven of these 44 genes are of unknown function, and we provide herein their developmental expression patterns to begin to reveal their roles in ectodermal development. Developmental Dynamics 239:3467–3480, 2010. © 2010 Wiley‐Liss, Inc.
The long‐term efficacy of three psychotherapies for anorexia nervosa: A randomized, controlled trial
Authors: Carter Frances A. , Jordan Jennifer , McIntosh Virginia V.W. , Luty Suzanne E. , McKenzie Janice M. , Frampton Christopher M.A. , Bulik Cynthia M. , Joyce Peter R.
Published: November 2010

Objective:

To evaluate the long‐term efficacy of three psychotherapies for anorexia nervosa.

Method:

Participants were women with broadly defined anorexia nervosa who had participated in a RCT comparing specialized psychotherapies (cognitive behavior therapy, CBT, and interpersonal psychotherapy, IPT) with a control condition (specialist supportive clinical management, SSCM), and attended long‐term follow‐up assessment (mean 6.7 years ± 1.2).

Results:

Forty three of the original sample of 56 women participated in long‐term follow‐up assessment (77%). No significant differences were found on any pre‐selected primary, secondary or tertiary outcome measures among the three psychotherapies at long‐term follow‐up assessment. Significantly different patterns of recovery were identified for the psychotherapies across time on the primary global outcome measure. Although SSCM was associated with a more rapid response than IPT, by follow‐up all three treatments were indistinguishable.

Discussion:

Potential implications for the timing of interventions to improve treatment response in anorexia nervosa are critically examined. © 2010 by Wiley Periodicals, Inc. Int J Eat Disord 2010
Computationally efficient bootstrap prediction intervals for returns and volatilities in ARCH and GARCH processes
Authors: Chen Bei , Gel Yulia R. , Balakrishna N. , Abraham Bovas
Published: November 2010

We propose a novel, simple, efficient and distribution‐free re‐sampling technique for developing prediction intervals for returns and volatilities following ARCH/GARCH models. In particular, our key idea is to employ a Box–Jenkins linear representation of an ARCH/GARCH equation and then to adapt a sieve bootstrap procedure to the nonlinear GARCH framework. Our simulation studies indicate that the new re‐sampling method provides sharp and well calibrated prediction intervals for both returns and volatilities while reducing computational costs by up to 100 times, compared to other available re‐sampling techniques for ARCH/GARCH models. The proposed procedure is illustrated by an application to Yen/U.S. dollar daily exchange rate data. Copyright © 2010 John Wiley & Sons, Ltd.
Characteristics of the 2000 fissure eruption and lava flow fields at Mount Cameroon volcano, West Africa: a combined field mapping and remote sensing approach
Authors: Wantim M.N. , Suh C.E. , Ernst G.G.J. , Kervyn M. , Jacobs P.
Published: November 2010

This study focuses on the compound pahoehoe lava flow fields of the 2000 eruption on Mount Cameroon volcano, West Africa and it comprehensively documents their morphology. The 2000 eruption of Mount Cameroon took place at three different sites (sites 1, 2 and 3), on the southwest flank and near the summit that built three different lava flow fields. These lava flow fields were formed during a long‐duration (28th May–mid September) summit and flank eruption involving predominantly pahoehoe flows (sites 2 and 3) and aa flows (site 1). Field observations of flows from a total of four cross‐sections made at the proximal end, midway and at the flow front, have been supplemented with data from satellite imagery (SRTM DEM, Landsat TM and ETM+) and are used to offer some clues into their emplacement. Detailed mapping of these lava flows revealed that site 1 flows were typically channel‐fed simple aa flows that evolved as a single flow unit, while sites 2 and 3 lava flow fields were fed by master tubes within fissures producing principally tube‐fed compound pahoehoe flows. Sites 2 and 3 flows issued from ∼ 33 ephemeral vents along four NE–SW‐trending faults/fissures. Pahoehoe morphologies at sites 2 and 3 include smooth, folded and channelled lobes emplaced via a continuum of different mechanisms with the principal mechanism being inflation. The dominant structural features observed on these flow fields included: fissures/faults, vents, levees, channels, tubes and pressure ridges. Other structural features present were pahoehoe toes/lobes, breakouts and squeeze‐ups. Slabby pahoehoe resulting from slab‐crusted lava was the transitionary lava type from pahoehoe to aa observed at all the sites. Transition zones correspond to slopes of > 10°. Variations in flow morphology and textures across profiles and downstream were repetitive, suggesting a cyclical nature for the responsible processes. Copyright © 2010 John Wiley & Sons, Ltd.
Indications for radiotherapy after neck dissection
Authors: Strojan Primož , Ferlito Alfio , Langendijk Johannes A. , Silver Carl E.
Published: November 2010

Up‐front surgery and postoperative radiotherapy constitute a well‐recognized treatment concept for locally or regionally advanced squamous cell carcinoma of the head and neck. This “treatment package” is further intensified with the concomitant application of chemotherapy during irradiation when high‐risk features (ie, microscopically involved resection margins, extracapsular extension of the tumor from neck nodes, the presence of soft tissue deposits) are found on histopathologic examination of a resected specimen. With regard to neck disease, however, the demarcation line between low‐ and higher‐risk clinical situations, which would differ with respect to the need for postoperative radiotherapy, is not clear. In an attempt to define the low‐risk characteristics of disease in the neck that do not require adjuvant irradiation, we reviewed the available literature reports for any direct or indirect evidence on the value of postoperative radiotherapy in various clinical scenarios. The number of positive lymph nodes found in a dissected tissue specimen that should be used as a “cut‐off” point for introduction of postoperative radiotherapy was evaluated in the context of both primary tumor characteristics and type of neck dissection. © 2010 Wiley Periodicals, Inc. Head Neck, 2012
Complete resolution of laryngeal amyloidosis with radiation treatment
Authors: Neuner Geoffrey A. , Badros Ashraf A. , Meyer Tanya K. , Nanaji Nahid M. , Regine William F.
Published: November 2010

Background.

Localized amyloidosis of the larynx is a rare entity of unclear etiology. Surgical debulking is the primary treatment modality but often is not curative.

Methods and Results.

A 41‐year‐old woman presenting with increasing hoarseness, dysphagia, dyspnea, and weight loss was found to have a submucosal mass in the left false vocal fold. Biopsy of the specimen revealed amyloid. After negative work‐up for systemic disease, the patient underwent surgical debulking. Specimens revealed a population of clonal plasma cells demonstrating lambda restriction. The patient was treated with adjuvant external beam radiation to a dose of 45 Gy. At 11 months, the patient's voice, breathing, and swallowing have all improved substantially.

Conclusions.

Recent pathologic studies suggest that localized amyloidosis of the larynx is caused by a localized, nonmalignant plasma cell disorder. Because full resection is difficult, we recommend a combination of surgery and radiation therapy to cure this disease. © 2010 Wiley Periodicals, Inc. Head Neck, 2012
Soil water movement under a bottomland hedgerow during contrasting meteorological conditions
Authors: Ghazavi R. , Thomas Z. , Hamon Y. , Merot Ph.
Published: November 2010

Linear vegetation structures such as hedge tree networks (hedgerows), shelterbelts, and isolated trees play a major role on soil water transfer. Our objective is to evaluate the influence of a bottomland hedgerow on water flux in the saturated and unsaturated zones. Soil water movement was investigated in a hillslope crossed by a hedgerow using total water‐potential gradients and shallow groundwater dynamics. Results of a dry year were presented by Ghazavi et al. (2008). In this study, we analyse a wet year and then compare the two contrasting years (dry and wet). During the 2 years, the soil located at the vicinity of the hedgerow developed a drier status than the surrounding soils. Water flux in the unsaturated zone was directed towards the hedgerow for a longer period during the dry year than the wet year. The duration of delayed rewetting of the soil decreased from 3 months for the dry year to 1 month for the wet year. Variation in water storage calculated over the study period was highest near the hedgerow and lowest far from the hedgerow.

In the hillslope studied, hedgerow and stream proximity controlled water transfer. It is clear that the hedgerow controlled water transfer in the unsaturated zone throughout the year, except for the period when the soil profile was fully saturated. First, hedgerows control water transfer by increasing lateral transfer, which is related to high soil water potential gradients in its vicinity. These processes may increase capillary rise and decrease groundwater recharge near the hedgerow. Second, reverse hydraulic gradient (upward flux of water) occurred during the period of lowest groundwater level, mainly because of groundwater and stream connectivity. Processes related to hedgerow presence, such as delayed soil rewetting and flow towards the hedgerow need to be considered to quantify the impact of linear vegetation structures on water flux. Copyright © 2010 John Wiley & Sons, Ltd.