bluuebunny/crossref_metadata_2025 huggingface dataset:
Monitoring cytoplasmic protein complexes with blue native gel electrophoresis and stable isotope labelling with amino acids in cell culture: Analysis of changes in the 20S proteasome
Authors: Couttas Timothy A. , Raftery Mark J. , Erce Melissa A. , Wilkins Marc R.
Published: June 2011

Analysis of protein complexes is of increasing interest in the field of proteomics. A challenge is to develop methods for monitoring changes in the quantity and subunit composition of protein complexes on a proteome‐wide scale. Here, we describe the combination of 1‐D blue native polyacrylamide gel electrophoresis (BN‐PAGE) with stable isotope labelling of amino acids in cell culture (SILAC) and tandem mass spectrometry (MS/MS). Cleared lysates from normal and perturbed samples, one incorporating heavy stable isotopes and the other light isotopes, are co‐separated by blue native PAGE and then analysed and quantitated with MS/MS and appropriate software. This permits the analysis of cytoplasmic complexes. To demonstrate this technique, we explored how the 20S proteasome changes when the Pre9/α3 subunit, the only non‐essential subunit of this complex, was deleted. Our results showed that ΔPre9/α3 cells can form the 20S proteasome complex, although with reduced efficiency. This involves an increase in expression of the α4 subunit. Our findings suggest this technique as an approach for the study of quantitative and qualitative differences in protein complexes, from cleared cell lysates.
An allelic ladder based upon reference alleles for mtDNA SNP analysis using the SNaPshot technique
Authors: Köhnemann Stephan , Pennekamp Petra , Pfeiffer Heidi
Published: June 2011

The analysis of mitochondrial DNA (mtDNA) single‐nucleotide polymorphisms (SNPs) using the SNaPshot technique (Applied Biosystems) is a fast and sensitive method for the reliable identification of disease‐associated mtDNA SNPs, genetic ancestry mtDNA SNPs and forensically important mtDNA SNPs. The detection of many SNPs in one multiplex PCR and one subsequent multiplex minisequencing reaction is challenging for laboratories who want to establish this technique, due to the problem that there is no allelic ladder available for mtDNA SNP analysis via SNaPshot technique. Normally, the laboratory has to invent long‐term testing and studies. The interpretation of false and correct alleles is up to some specialists knowing the expected and the estimated size of each allele SNP. We here present a protocol to assemble up to 84 alleles of 42 different mtDNA SNPs in an allelic ladder that is based upon reference alleles. We recommend using allelic ladders/reference alleles for SNP analysis to maintain high‐quality analysis standards.
Entrapment of a Trigonopsis variabilis D‐amino acid oxidase variant F54Y for oxidative deamination of cephalosporin C
Authors: Wong Kin‐Sing , Fong Wing‐Ping , Tsang Paul Wai‐Kei
Published: June 2011

Trigonopsis variabilis D‐amino acid oxidase (TvDAAO) is an enzyme used in the industrial bioconversion of cephalosporin C (CPC) into 7‐aminocephalosporanic acid, a crucial biosynthetic nucleus for a wide spectrum of semi‐synthetic cephem antibiotics. Using homology modeling and site‐directed mutagenesis, we have previously shown that the TvDAAO variant F54Y possesses improved catalytic activity and thermostability. To further explore its industrial application, the conditions for immobilization of the enzyme were examined in the present investigation. The results showed that entrapment in a calcium alginate (Ca‐alginate) matrix using 2% alginate, 500 mM CaCl2, and 15 min stabilization appeared to be optimal for the immobilization of F54Y. The entrapped enzyme allowed complete CPC conversion. The entrapped enzyme also showed good operational stability and retained at least 90% of its original activity after 20 reaction cycles. To conclude, the entrapment of F54Y in Ca‐alginate appeared to be a simple and efficient biocatalysis system with potential application in the antibiotics industry.
Cyclic performance of large‐scale corroded reinforced concrete beams
Authors: Ou Yu‐Chen , Tsai Li‐Lan , Chen Hou‐Heng
Published: June 2011

Nine large‐scale beam specimens were constructed. Of which, one was used as the control, whereas the other eight ones were divided into four sets. Each set had two specimens and was subjected to accelerated corrosion using an imposed current for the same time interval. Following the corrosion, a specimen in each set was tested using cyclic loading to examine the seismic performance, whereas the other one was demolished to examine the extent of corrosion. Cyclic loading results indicated that with an increasing corrosion level, the ultimate drift, ductility, plastic rotation capacity, and energy dissipation of the beams initially increased and later decreased. The failure mode switched from flexural failure, largely owing to buckling of the longitudinal reinforcement to flexural‐shear failure, which is mainly caused by fracturing of the transverse reinforcement. Corrosion increased shear deformation and the spread of plasticity of the plastic hinge region. The residual flexural strength, as estimated by an empirical equation based on the maximum pit depth in the longitudinal reinforcement, closely corresponds to experimental values. Furthermore, the residual shear strength estimated based on the minimum reduced cross‐sectional area of transverse reinforcement correlates better with the experimental observations than that based on the weight loss. Copyright © 2011 John Wiley & Sons, Ltd.
The Relationship Among Compulsive Buying, Compulsive Internet Use and Temperament in a Sample of Female Patients with Eating Disorders
Authors: Claes Laurence , Müller Astrid , Norré Jan , Van Assche Leen , Wonderlich Steve , Mitchell James E.
Published: June 2011

The aim of the present study was to investigate the association among compulsive buying (CB), compulsive internet use (CIU) and reactive/regulative temperament in a sample of 60 female patients with eating disorders. All patients were assessed by means of the Compulsive Buying Scale, the CIU scale, the Eating Disorder Inventory—2, the Behavioral Inhibition System/Behavioral Activation System scales, the Dimensional Assessment of Personality Pathology and the effortful control scale of the Adult Temperament Questionnaire. The results showed a positive association between CB and CIU, both categorized as impulse control disorders, not otherwise specified. Both CB and CIU showed significantly positive correlations with emotional lability, excitement seeking and lack of effortful control (more specifically lack of inhibitory and lack of activation control). The implication of these findings for the treatment of both disorders will be discussed. Copyright © 2011 John Wiley & Sons, Ltd and Eating Disorders Association.
Coupling of methylmercury uptake with respiration and water pumping in freshwater tilapia Oreochromis niloticus
Authors: Wang Rui , Wong Ming-Hung , Wang Wen-Xiong
Published: June 2011

The relationships among the uptake of toxic methylmercury (MeHg) and two important fish physiological processes—respiration and water pumping—in the Nile tilapia (Oreochromis niloticus) were explored in the present study. Coupled radiotracer and respirometric techniques were applied to measure simultaneously the uptake rates of MeHg, water, and oxygen under various environmental conditions (temperature, dissolved oxygen level, and water flow). A higher temperature enhanced MeHg influx and the oxygen consumption rate but had no effect on the water uptake, indicating the influence of metabolism on MeHg uptake. The fish showed a high tolerance to hypoxia, and the oxygen consumption rate was not affected until the dissolved oxygen concentration decreased to extremely low levels (below 1 mg/L). The MeHg and water uptake rates increased simultaneously as the dissolved oxygen level decreased, suggesting the coupling of water flux and MeHg uptake. The influence of fish swimming performance on MeHg uptake was also investigated for the first time. Rapidly swimming fish showed significantly higher uptake rates of MeHg, water, and oxygen, confirming the coupling relationships among respiration, water pumping, and metal uptake. Moreover, these results support that MeHg uptake is a rate-limiting process involving energy. Our study demonstrates the importance of physiological processes in understanding mercury bioaccumulation in fluctuating aquatic environments. Environ. Toxicol. Chem. 2011;30:2142–2147. © 2011 SETAC
A linear solvation energy relationship model of organic chemical partitioning to particulate organic carbon in soils and sediments
Authors: Kipka Undine , Di Toro Dominic M
Published: June 2011

Predicting the association of contaminants with particulate organic matter in the environment is critical in determining the fate and bioavailability of chemicals. A ubiquitous measure of contaminant association with soil and sediment particulate organic matter is the organic carbon partition coefficient KOC. Chemical class-specific models relating the KOC to the octanol–water partition coefficient KOW have been used to predict the partitioning to organic carbon in the water column and sediment for nonpolar hydrophobic pollutants and some polar pollutants. A single linear solvation energy relationship (LSER) is proposed as a simpler and chemically based alternative for predicting KOC for a more diverse set of compounds. A chemically diverse set of KOC data is used to obtain a more robust and more universally representative model of organic carbon partitioning than previously available LSER models. The resulting model has a root mean square error (RMSE) of prediction for log KOC of RMSE = 0.48 for the fitted data set and RMSE = 0.55 for an independent data set. An analysis of LSER coefficients highlights the relative importance of hydrogen bonding interactions. Environ. Toxicol. Chem. 2011;30:2013–2022. © 2011 SETAC
Effect of zinc on diversity of riverine benthic macroinvertebrates: Estimation of safe concentrations from field data
Authors: Iwasaki Yuichi , Kagaya Takashi , Miyamoto Ken-ichi , Matsuda Hiroyuki , Sakakibara Mayu
Published: June 2011

We conducted field surveys at 25 sites in three Japanese catchments to provide conservative estimates of the safe concentration of zinc (Zn) for the protection of riverine macroinvertebrate diversity. The relationships between the Zn concentration and six macroinvertebrate metrics for taxon richness were determined by using regression analysis; this included a piecewise regression model, where two lines are joined at an unknown point. For each metric the piecewise regression model with a zero slope below a threshold concentration was selected as the best model to explain the influence of Zn. Under the assumption that macroinvertebrate diversity reductions of <10% are acceptable, the safe concentrations of Zn were estimated to be 84, 115, 84, 80, 85, and 70 µg/L for total taxon richness, Ephemeroptera, Plecoptera, and Trichoptera (EPT) richness, mayfly richness, caddisfly richness, chironomid richness, and estimated total taxon richness at the riffle scale, respectively. These concentrations are more than twice the water quality standard for Zn in Japan (30 µg/L), suggesting that the standard is likely overprotective for macroinvertebrate diversity. Field studies are useful for evaluating the level of protectiveness of safe concentrations (water quality standards) based on individual-level effects from laboratory toxicity tests, and this evaluation process will have a crucial role in implementing more purpose-driven ecological risk managements that aim to protect natural populations and communities. Environ. Toxicol. Chem. 2011;30:2237–2243. © 2011 SETAC
Extended homotopy perturbation method and the axisymmetric flow past a porous stretching sheet
Authors: Al‐Mdallal Qasem M. , Syam Muhammed I. , Donald Ariel P.
Published: June 2011

The extended homotopy perturbation method, which is an extension of the celebrated homotopy perturbation method (HPM), is applied to obtain a solution to the problem of the steady, laminar, axisymmetric flow of a viscous, incompressible fluid past a porous stretching sheet. The solution so obtained is totally analytical and is expressible in terms of the cross‐flow velocity of the fluid past the stretching sheet. Its hallmark is that it does not depend upon computation of any auxiliary parameter for enlarging the convergence region of the solution. Rather, it calculates the solution automatically adjusting the scaling factor of the independent similarity variable normal to the sheet. The results obtained by the extended HPM are in excellent agreement with the exact numerical solution. Also, an asymptotic solution valid for large suction parameter is developed, which matches well with the exact solution even for moderate values of the suction parameter. Copyright © 2011 John Wiley & Sons, Ltd.
Consistent t(1;10) with rearrangements of TGFBR3 and MGEA5 in both myxoinflammatory fibroblastic sarcoma and hemosiderotic fibrolipomatous tumor
Authors: Antonescu Cristina R. , Zhang Lei , Nielsen G.Petur , Rosenberg Andrew E. , Cin Paola Dal , Fletcher Christopher D. M.
Published: June 2011

Despite their shared predilection for superficial soft tissue of distal extremities and frequent local recurrences, myxoinflammatory fibroblastic sarcoma (MIFS) and hemosiderotic fibrolipomatous tumor (HFLT) have distinct morphologic appearances. Recent studies have identified an identical t(1;10)(p22;q24) in five cases of MIFS and two of HFLT, as well as common amplifications on 3p11‐12. To investigate further their potential relationship and to determine the incidence of t(1;10) in a larger cohort, we subjected seven MIFS, 14 HFLT, and three cases with mixed morphology, to molecular and cytogenetic analysis. Fluorescence in situ hybridization (FISH) analysis for rearrangements of TGFBR3 on 1p22 and of MGEA5 on 10q24 was performed in all cases, whereas the status of VGLL3 gene amplification on 3p12.1 was investigated in 12 cases. Conventional karyotyping was performed in one HFLT and two cases with mixed MIFS/HFLT histology. Overall 83% of cases showed rearrangements in both TGFBR3 and MGEA5. All three cases with mixed features of MIFS and HFLT were positive. Cytogenetic analysis performed in three cases confirmed an unbalanced der(10)t(1;10)(p22;q24). VGLL3 gene amplification was noted in 10/12 cases of both histologies. The high incidence of t(1;10) in MIFS and HFLT reinforces a shared pathogenetic relationship. Furthermore, the co‐existence of both components either synchronously or metachronously in a primary or subsequent recurrence, suggest either different morphologic variants or different levels of tumor progression of a single biologic entity. FISH analysis for TGFBR3 and MGEA5 rearrangements can be applied as a reliable diagnostic molecular test when confronted with limited material or a challenging diagnosis. © 2011 Wiley‐Liss, Inc.
Parafibromin immunohistochemical staining to differentiate parathyroid carcinoma from parathyroid adenoma
Authors: Kim Hee Kyung , Oh Young Lyun , Kim Seok‐Hyung , Lee Dong Youn , Kang Ho‐Cheol , Lee Ji In , Jang Hye Won , Hur Kyu Yeon , Kim Jae Hyeon , Min Yong Ki , Chung Jae Hoon , Kim Sun Wook
Published: June 2011

Background

Parafibromin is a protein encoded by the HRPT2 oncosuppressor gene, and the expression is reported to be decreased or absent in parathyroid carcinomas.

Methods

A total of 26 tumor specimens from 18 patients with adenoma and 8 patients with carcinoma were immune‐stained with an antibody against parafibromin.

Results

Parafibromin immunostaining showed strong positivity in 17 of 18 adenomas. Negative staining was noted in 3 of 8 carcinomas, and weak positivity was found in 3 of 8 carcinomas. The remaining 2 cases of carcinoma showed strong positivity. The loss of parafibromin expression (negative or weak positivity) demonstrated 94.4% specificity in the diagnosis of parathyroid carcinomas. Relapses or distant metastases of carcinoma occurred only in cases in which there was a loss of parafibromin immunostaining.

Conclusions

Loss of parafibromin immunostating showed promising results in the differential diagnosis of parathyroid carcinoma from adenoma and may also serve as a prognostic marker. © 2011 Wiley Periodicals, Inc. Head Neck, 2012
Presubiculum layer III conveys retrosplenial input to the medial entorhinal cortex
Authors: Kononenko Natalia L. , Witter Menno P.
Published: June 2011

Navigation is mediated by a network of brain areas, and research has focused on the head‐direction system in the presubiculum (PrS), the grid cell containing medial entorhinal cortex (EC) (MEC) and place cells in the hippocampus. Less research addressed the interactions of the retrosplenial cortex (RSC) and the navigational system, although it is well established that damage to the RSC leads to navigational deficits. We previously showed that RSC provides a dense input to deep layers of MEC and to superficial layers of PrS. In this study we use confocal microscopical analysis and show that the dense projection from the caudal part of the ventral retrosplenial granular cortex targets neurons in Layer III of PrS, which provide input to superficial layers of MEC. Our high resolution anatomical data indicate that sparsely spiny pyramidal neurons in Layer III of PrS that originate projections to Layer III of MEC are the main target of these retrosplenial projections. Retrosplenial axonal boutons were found to equally contact spines and shafts of basal dendrites in Layer III, but contacts on shafts are more prominent close to the soma, indicating the potential for efficient synaptic transfer. These observations suggest that neurons in Layer III of PrS have an important role in mediating RSC contributions to navigation. © 2011 Wiley‐Liss, Inc
Tumour lysis syndrome in children: experience of last decade
Authors: Ahn Yo Han , Kang Hyoung Jin , Shin Hee Young , Ahn Hyo Seop , Choi Yong , Kang Hee Gyung
Published: June 2011

The strategy against tumour lysis syndrome (TLS) had been hyperhydration, urine alkalinization, and allopurinol. Recently, rasburicase was added to the armament against this life‐threatening condition. In Korea, rasburicase is used as a rescue therapy for cases with allopurinol‐resistant hyperuricemia, because of the restriction by the National Health Insurance. We reviewed our experiences to re‐assess the risk factors of TLS and the efficacy of rasburicase. Medical records were retrospectively reviewed for 396 children who were diagnosed as positive with acute leukemia and non‐Hodgkin lymphoma between the years 2000 and 2009. The risk factors for TLS were analyzed statistically, and those before and after the availability of rasburicase were compared. Sixty eight patients (17.2%) had TLS. Multivariate analysis showed that pre‐chemotherapy hypophosphatemia was a risk factor for TLS, in addition to the known risk factors of hyperuricemia and high lactate dehydrogenase concentration. The availability of rasburicase as a rescue therapy did not negate the importance of uric acid as a risk factor of TLS. Rasburicase as a second line treatment for intractable hyperuricemia was not effective in reducing the incidence of TLS. Pre‐chemotherapy hypophosphatemia was a significant independent risk factor for TLS. Copyright © 2011 John Wiley & Sons, Ltd.
Bioinformatic analyses to select phenotype affecting polymorphisms in HTR2C gene
Authors: Piva Francesco , Giulietti Matteo , Baldelli Luisa , Nardi Bernardo , Bellantuono Cesario , Armeni Tatiana , Saccucci Franca , Principato Giovanni
Published: June 2011

Objective

Single nucleotide polymorphisms (SNPs) in serotonin related genes influence mental disorders, responses to pharmacological and psychotherapeutic treatments. In planning association studies, researchers that want to investigate new SNPs have to select some among a large number of candidates. Our aim is to guide researchers in the selection of the most likely phenotype affecting polymorphisms. Here, we studied serotonin receptor 2C (HTR2C) SNPs because, till now, only relatively few of about 2000 are investigated.

Methods

We used the most updated and assessed bioinformatic tools to predict which variations can give rise to biological effects among 2450 HTR2C SNPs.

Results

We suggest 48 SNPs that are worth considering in future association studies in the field of psychiatry, psychology and pharmacogenomics. Moreover, our analyses point out the biological level probably affected, such as transcription, splicing, miRNA regulation and protein structure, thus allowing to suggest future molecular investigations.

Conclusions

Although few association studies are available in literature, their results are in agreement with our predictions, showing that our selection methods can help to guide future association studies. Copyright © 2011 John Wiley & Sons, Ltd.
Effect of forest recovery on summer streamflow in small forested watersheds, Northeastern China
Authors: Yao Yuefeng , Cai Tijiu , Wei Xiaohua , Zhang Mingfang , Ju Cunyong
Published: June 2011

The hydrological effect of forest recovery is receiving renewed interest globally because information on forest carbon–water relationship is critically needed to support carbon management through reforestation and sustainable water management. In Northeastern China, summer (June to August) streamflow accounts for about 50% of total annual streamflow and is vital to water supply and management in the region. Understanding how forest recovery may affect streamflow is important to both reforestation campaign and long‐term water sustainability. In this study, we analysed 33 years of summer hydrologic data (1970–2002) from two comparable small‐scale watersheds located in the Xiaoxing'anling, Northeastern China. Time series analysis and two graphic methods (double mass curve and flow duration curve) with statistical testing as well as long‐term data on forest cover changes and climate were used. Our results show that the significant streamflow reduction as a result of reforestation occurred when forest cover reached 70% or 10 years after planting. After forest cover reached 85%, water reduction became stabilized. The accumulative streamflow reduction in 2002 reached 8·61% of the total accumulative streamflow. Among those water reduced, high flows (from 5 to 25 percentiles) were mostly affected, demonstrating that northeastern forests have an important role in reducing high flows. Implications of these results are discussed in the context of climate change, reforestation and water resource management. Copyright © 2011 John Wiley & Sons, Ltd.
Spatiotemporal variations and abrupt changes of potential evapotranspiration and its sensitivity to key meteorological variables in the Wei River basin, China
Authors: Zuo Depeng , Xu Zongxue , Yang Hong , Liu Xingcai
Published: June 2011

Evapotranspiration is an important component of hydrological cycle and a key input to hydrological models. Therefore, analysis of the spatiotemporal variation of potential evapotranspiration (PET) will help a better understanding of climate change and its effect on hydrological cycle and water resources. In this study, the Penman–Monteith method was used to estimate PET in the Wei River basin (WRB) in China based on daily data at 21 meteorological stations during 1959–2008. Spatial distribution and temporal trends of annual and seasonal PET were analysed by using the Spline interpolation method and the Mann–Kendall test method. Abrupt changes were detected by using the Pettitt test method. In order to explore the contribution of key meteorological variables to the variation of PET, the sensitivity coefficients method was employed in this study. The results showed that: (1) mean annual and seasonal PET in the WRB was generally decreasing from northeast to southwest. Summer and spring made the major contributions to the annual values; (2) annual and seasonal PET series in most part of the WRB exhibited increasing trends; (3) abrupt changes appeared in 1993 for annual and spring PET series for the entire basin, while summer value series was detected in the late 1970s. (4) Relative humidity was the most sensitive variable for PET in general for the WRB, followed by wind speed, air temperature and solar radiation. In the headwater and outlet of the WRB, relative humidity and air temperature were the most sensitive variables to PET, while relative humidity and wind speed were more influential in most part of the middle‐lower region. Copyright © 2011 John Wiley & Sons, Ltd.
Evapotranspiration of a drip‐irrigated, film‐mulched cotton field in northern Xinjiang, China
Authors: Zhou Shiqiao , Wang Jin , Liu Jingxian , Yang Jinghui , Xu Yan , Li Jihui
Published: June 2011

Eddy covariance flux measurements were performed at a cotton crop site of an oasis in northern Xinjiang, northwest China from 2008 to 2010 in order to study ecosystem evapotranspiration (ET). The soil surface area was approximately 80% covered by plastic film mulch and a cotton crop was grown with a mean population density of around 24 plants m−2 under drip irrigation. The total annual ET was measured to be 560 mm, which was 350 mm more than the average annual mean precipitation for the time period 1963–2006. Due to the low vapor pressure deficit associated with low temperatures, the ET was low from November to March. The ET totaled 538 mm during the cotton crop growing season, generally from early‐April through mid‐October. Mean daily ecosystem ET was 1·4–1·6 mm day−1 in April and May, 3·4–4·7 mm day−1 from June through August, 1·8–2·3 mm day−1 in September and 0·7–0·8 mm day−1 in October. The diurnal variations of ET in all months were consistent with those of net radiation, although the leaf area index (LAI) and climate conditions changed substantially. Soil water content was not a limiting factor for ET during the period from April through September, as the crop was regularly irrigated. Therefore, ET was mainly controlled by the available energy in April and May, and by leaf area from June through September. Due to a complete lack of irrigation, ET was constrained by soil water in October. These results of ET variability are helpful for improved allocation of water resources and agricultural water use practices in the region. Copyright © 2011 John Wiley & Sons, Ltd.
Temporal fluctuations of water repellency in forest soils of Galicia, NW Spain. Do soil samples dried at laboratory reflect the potential soil water repellency?
Authors: Rodríguez‐Alleres M. , Benito E.
Published: June 2011

Water repellency is a widespread property of Pinus pinaster and Eucalyptus globulus forest soils in NW Spain and is particularly severe during the summer dry conditions. The aim of this work was to compare actual water repellency at field‐moist samples with potential water repellency after drying at 25 and 105 °C in samples collected at different times of year under four forest soils. Also, we investigated whether drying at 25 or 105 °C led to repellency values comparable to the highest levels reached under field conditions in the summer with a view to developing an appropriate sampling protocol towards estimating the maximum possible water repellency of a given soil as a key to establishing its environmental effects. The actual and potential water repellency was determined by using the water drop penetration time (WDPT) and molarity of an ethanol drop (MED) tests.

Clear seasonal patterns of water repellency were observed from the results for the four forest soils, peaking in the dry period and disappearing after prolonged wet periods. Water repellency lasts longer in sandy loam soils than in more finely textured soils, and also under eucalyptus than under pine forests. Drying soil samples at 25 or 105 °C increased water repellency, as measured with the WDPT method, in the four soils, but especially in the non‐repellent samples collected during the wet period. The increase was more marked in the sandy loam soils than in the more finely textured soils, and also after drying at 105 °C than at 25 °C. MED measurements exposed a common trait in the four soils; thus, the water repellency values obtained under field conditions in summer invariably exceeded those obtained after drying at 25 or 105 °C. In addition, the repellency values for dried samples collected in the wet period were never comparable to the maximum levels observed under field conditions in the summer. Copyright © 2011 John Wiley & Sons, Ltd.
Daily variability of river concentrations and fluxes: indicators based on the segmentation of the rating curve
Authors: Meybeck Michel , Moatar Florentina
Published: June 2011

The variability of water chemistry on a daily scale is rarely addressed due to the lack of records. Appropriate tools, such as typologies and dimensionless indicators, which permit comparisons between stations and between river materials, are missing. Such tools are developed here for daily concentrations (C), specific fluxes or yields (Y) and specific river flow (q). The data set includes 128 long‐term daily records, for suspended particulate matter (SPM), total dissolved solids (TDS), dissolved and total nutrients, totalling 1236 years of records. These 86 river basins (103–106 km2) cover a wide range of environmental conditions in semi‐arid and temperate regions. The segmentation—truncation of C–q rating curves into two parts at median flows (q50) generates two exponents (b50inf and b50sup) that are different for 66% of the analysed rating curves. After segmentation, the analysis of records results in the definition of nine major C–q types combining concentrating, diluting or stable patterns, showing inflexions, chevron and U shapes. SPM and TDS are preferentially distributed among a few types, while dissolved and total nutrients are more widely distributed. Four dimensionless indicators of daily variability combine median (C50, Y50), extreme (C99, Y99) and flow‐weighted (C*, Y*) concentrations and yields (e.g. C99/C50, Y*/Y50). They vary over two to four orders of magnitude in the analysed records, discriminating stations and river material. A second set of four indicators of relative variability [e.g. (Y*/Y50)/(q*/q50)], takes into account the daily flow variability, as expressed by q*/q50 and q99/q50, which also vary over multiple orders of magnitude. The truncated exponent b50sup is used to describe fluxes at higher flows accounting for 75% (TDS) to 97% (SPM) of interannual fluxes. It ranges from − 0·61 to + 1·86 in the database. It can be regarded as the key amplificator (positive b50sup) or reductor (negative b50sup) of concentrations or yields variability. C50, Y50, b50sup can also be estimated in discrete surveys, which provides a new perspective for quantifying and mapping water quality variability at daily scale. Copyright © 2011 John Wiley & Sons, Ltd.
A conceptual–numerical model to simulate hydraulic head in aquifers that are hydraulically connected to surface water bodies
Authors: Pulido‐Velazquez David , Sahuquillo Andrés , Andreu Joaquín
Published: June 2011

In this paper, we present a conceptual‐numerical model that can be deduced from a calibrated finite difference groundwater‐flow model, which provides a parsimonious approach to simulate and analyze hydraulic heads and surface water body–aquifer interaction for linear aquifers (linear response of head to stresses). The solution of linear groundwater‐flow problems using eigenvalue techniques can be formulated with a simple explicit state equation whose structure shows that the surface water body–aquifer interaction phenomenon can be approached as the drainage of a number of independent linear reservoirs. The hydraulic head field could be also approached by the summation of the head fields, estimated for those reservoirs, defined over the same domain set by the aquifer limits, where the hydraulic head field in each reservoir is proportional to a specific surface (an eigenfunction of an eigenproblem, or an eigenvector in discrete cases). All the parameters and initial conditions of each linear reservoir can be mathematically defined in a univocal way from the calibrated finite difference model, preserving its characteristics (geometry, boundary conditions, hydrodynamic parameters (heterogeneity), and spatial distribution of the stresses). We also demonstrated that, in practical cases, an accurate solution can be obtained with a reduced number of linear reservoirs. The reduced computational cost of these solutions can help to integrate the groundwater component within conjunctive use management models. Conceptual approximation also facilitates understanding of the physical phenomenon and analysis of the factors that influence it. A simple synthetic aquifer has been employed to show how the conceptual model can be built for different spatial discretizations, the parameters required, and their influence on the simulation of hydraulic head fields and stream–aquifer flow exchange variables. A real‐world case was also solved to test the accuracy of the proposed approaches, by comparing its solution with that obtained using finite‐difference MODFLOW code. Copyright © 2011 John Wiley & Sons, Ltd.
Skykomish River, Washington: Impact of ongoing glacier retreat on streamflow
Authors: Pelto M. S.
Published: June 2011

Glacier retreat and changes in summer runoff have been pronounced in the Skykomish River Basin, North Cascades, Washington from 1950 to 2009. An analysis comparing USGS streamflow records for the 1950–1985 to the 1985–2009 period indicates that during the recent period the Skykomish River summer streamflow (July–September) has declined 26% in the watershed, spring runoff (April–June) has declined 6%, while winter runoff (November–March) has increased 10%. The minimum mean monthly August discharge from 1928 to 2010 occurred in 2003 and 2005 when streamflow was 15·1 and 15·2 m3s−1, respectively. From 1929 to 1985, streamflow was less than 14 m3s−1 during the glacier melt season on a single day in 1951. From 1986 to 2007 there were 217 days with discharge below 14 m3s−1 with 9 periods lasting for 10 consecutive days. In the Skykomish River watershed from 1958 to 2009, glacier area declined from 3·8 to 2·1 km2. Columbia, Foss, Hinman and Lynch Glacier, the primary glaciers in the basin, declined in area by 10, 60, 90 and 35%, respectively, since 1958. Annual mass balance measurements completed from 1984 to 2009 on Columbia, Foss and Lynch Glacier indicate a mass loss of 13·1 m w.e. Despite 15% higher ablation rates during the 1985–2009 period, the 45% reduction in glacier area led to a 38% reduction in glacier runoff between 1958 and 2009. The 38% reduction in glacier runoff did not lead to a significant decline in the percentage summer runoff contributed by glaciers under average conditions; the contribution has remained in the range of 1–3% from July to September. The glacier runoff decline impacted river discharge only during low flow periods in August and September. In August 2003 and 2005, glacier ablation contributed 1·5–1·6 m3s−1 to total discharge, or 10–11% of August discharge. While declining glacier area in the region has and will lead to reduced glacier runoff and reduced late summer streamflow, it has limited impact on the Skykomish River except during periods of critically low flow, below 14 m3s−1 when glaciers currently contribute more than 10% of the streamflow. Copyright © 2011 John Wiley & Sons, Ltd.
3‐Deazaneplanocin A is a promising therapeutic agent for the eradication of tumor‐initiating hepatocellular carcinoma cells
Authors: Chiba Tetsuhiro , Suzuki Eiichiro , Negishi Masamitsu , Saraya Atsunori , Miyagi Satoru , Konuma Takaaki , Tanaka Satomi , Tada Motohisa , Kanai Fumihiko , Imazeki Fumio , Iwama Atsushi , Yokosuka Osamu
Published: June 2011

Recent advances in stem cell biology have identified tumor‐initiating cells (TICs) in a variety of cancers including hepatocellular carcinoma (HCC). Polycomb group gene products such as BMI1 and EZH2 have been characterized as general self‐renewal regulators in a wide range of normal stem cells and TICs. We previously reported that Ezh2 tightly regulates the self‐renewal and differentiation of murine hepatic stem/progenitor cells. However, the role of EZH2 in tumor‐initiating HCC cells remains unclear. In this study, we conducted loss‐of‐function assay of EZH2 using short‐hairpin RNA and pharmacological inhibition of EZH2 by an S‐adenosylhomocysteine hydrolase inhibitor, 3‐deazaneplanocin A (DZNep). Both EZH2‐knockdown and DZNep treatment impaired cell growth and anchorage‐independent sphere formation of HCC cells in culture. Flow cytometric analyses revealed that the two approaches decreased the number of epithelial cell adhesion molecule (EpCAM)+ tumor‐initiating cells. Administration of 5‐fluorouracil (5‐FU) or DZNep suppressed the tumors by implanted HCC cells in non‐obese diabetic/severe combined immunodeficient mice. Of note, however, DZNep but not 5‐FU predominantly reduced the number of EpCAM+ cells and diminished the self‐renewal capability of these cells as judged by sphere formation assays. Our findings reveal that tumor‐initiating HCC cells are highly dependent on EZH2 for their tumorigenic activity. Although further analyses of TICs from primary HCC would be necessary, pharmacological interference with EZH2 might be a promising therapeutic approach to targeting tumor‐initiating HCC cells.
Milk, dairy intake and risk of endometrial cancer: A 26‐year follow‐up
Authors: Ganmaa Davaasambuu , Cui Xiaohui , Feskanich Diane , Hankinson Susan E. , Willett Walter C.
Published: June 2011

Estrogens have a central role in the etiology of endometrial cancer. Milk and dairy products are a source of steroid hormones and growth factors that might have physiological effects in humans. We hypothesized that high intakes of milk and dairy products are associated with an increased risk of endometrial cancer, particularly among postmenopausal women not using hormone therapy. This was a prospective cohort study with 68,019 female participants in the Nurses' Health Study aged 34–59 in 1980. Milk and dairy consumption were assessed in 1980, 1984, 1986, 1990, 1994, 1998 and 2002 as servings per day and the follow‐up continued through 2006. The multivariate relative risks (RRs) of adenocarcinoma of the endometrium across categories of cumulatively averaged total dairy consumption compared with < 1 svg/day were: 0.94 (95% CI = 0.71–1.25) for 1–1.4 svg/day, 1.14 (0.87–1.49) for 1.5–1.9 svg/day, 1.10 (0.84–1.44) for 2–2.9 svg/day, 1.26 (0.94–1.70) for ≥ 3 svg/day (p for trend = 0.06). The association between total dairy intake and endometrial cancer was significant only among the postmenopausal women (for ≥ 3 svg/day RR = 1.41, 95% CI = 1.01–1.98, p for trend = 0.02) and was evident only among those who were not currently using hormone therapy (RR = 1.58, 95% CI = 1.05–2.36, p for trend = 0.003). Total dairy intake was not significantly associated with risk of preinvasive endometrial cancer. In conclusion, we observed a marginally significant overall association between dairy intake and endometrial cancer and a stronger association among postmenopausal women who were not using estrogen‐containing hormones.
HTLV‐1 positive and negative T cells cloned from infected individuals display telomerase and telomere genes deregulation that predominate in activated but untransformed CD4+ T cells
Authors: Zane Linda , Sibon David , Capraro Valérie , Galia Perrine , Karam Maroun , Delfau‐Larue Marie‐Hélène , Gilson Eric , Gessain Antoine , Gout Olivier , Hermine Olivier , Mortreux Franck , Wattel Eric
Published: June 2011

Untransformed HTLV‐1 positive CD4+ cells from infected individuals are selected for expressing tax and displaying morphological features consistent with telomere dysfunctions. We show that in resting HTLV‐1 positive CD4+ cells cloned from patients, hTERT expression parallels tax expression and cell cycling. Upon activation, these cells dramatically augment tax expression, whereas their increase in telomerase activity is about 20 times lower than that of their uninfected counterpart. Activated HTLV‐1 positive CD4+ but not uninfected CD4+ or CD8+ clones also repress the transcription of TRF1, TPP1, TANK1, POT1, DNA‐PKc and Ku80. Both infected and uninfected lymphocytes from infected individuals shared common telomere gene deregulations toward a pattern consistent with premature senescence. ATLL cells displayed the highest telomerase activity (TA) whereas recovered a telomere gene transcriptome close to that of normal CD4+ cells. In conclusion HTLV‐1‐dependent telomere modulations seem involved in clonal expansion, immunosuppression, tumor initiation and progression.
Loss of p16 expression is associated with the stem cell characteristics of surface markers and therapeutic resistance in estrogen receptor‐negative breast cancer
Authors: Arima Yoshimi , Hayashi Naoki , Hayashi Hidemi , Sasaki Mikako , Kai Kazuharu , Sugihara Eiji , Abe Eriko , Yoshida Atsushi , Mikami Shuji , Nakamura Seigo , Saya Hideyuki
Published: June 2011

Triple‐negative breast cancer [TNBC, which is negative for the estrogen receptor (ER), progesterone receptor, and human epidermal growth factor receptor 2] is a high‐risk form of the disease without a specific therapy. DNA microarray and immunohistochemical analyses have shown that most TNBCs fall within the basal‐like histological subset of breast cancers, which frequently exhibit inactivation of the retinoblastoma tumor suppressor (Rb) and upregulation of the cyclin‐dependent kinase inhibitor p16INK4a (p16). However, downregulation of p16 expression has been observed in some basal‐like breast cancer cell lines, suggesting that such cells can be divided into two groups according to Rb and p16 status. We now show that cells that are CD44+ and CD24−, a phenotype associated with stem‐like breast cancer cells, are more abundant in ER−/p16− breast cancer cell lines than in ER−/p16+ lines. It was also found that p16 expression was downregulated in mammospheres from an ER‐negative breast cancer cell line. Depletion of p16 by RNA interference in ER‐negative breast cancer cells increased the percentage of CD44+/CD24− cells and increased the expression of mRNA of the ES‐like genes Nanog, Oct4, and Sox2 through an Rb‐independent pathway. Furthermore, such depletion of p16 reduced chemosensitivity. The loss of p16 expression may thus reduce the response of ER‐negative breast cancer cells to chemotherapy by conferring cancer stem cell‐like properties. Consistent with this conclusion, immunohistochemical analysis of the clinical samples suggests that low p16 expression in TNBC is associated with resistance to preoperative chemotherapy.
DIAGNOSTIC ANALYSIS AND FINE TUNING OF SKIMMING WELL DESIGN AND OPERATIONAL STRATEGIES FOR SUSTAINABLE GROUNDWATER MANAGEMENT ‐ INDUS BASIN OF PAKISTAN
Authors: Ashraf M. , Zeeshan A. Bhatti , Zakaullah
Published: June 2011

A survey was conducted in the Chaj Doab (the area between the rivers Chenab and Jhelum) to characterize the skimming wells used to extract freshwater layer. The survey revealed a drastic increase in the number of skimming wells installed during the drought period from 2000 to 2002. About 36% of skimming wells were found to pump water of EC greater than 2.0 dS/m. The number of strainers varied from 2 to 20 and the size varied from 5 to15 cm. The prevailing depth to the water table in the area ranged from 2 to 10 m, whereas the strainers of the wells were usually at 18 m depth.

The spatial and temporal variability of groundwater quality was very high. Based on pumping test results and analysis, it is suggested that skimming wells of about 28 lps discharge should not be installed within a radius of 350 m. Six strainers of 7.5 cm diameter are recommended for installation within a depth of 20 m to pump about 28 lps of water. The skimming wells may be operated continuously for 4 to 12 hours/day, depending on the source of recharge, without having adverse effect on groundwater and pumped water quality. Copyright © 2011 John Wiley & Sons, Ltd.
BAFFLE MODULES: IMPROVED DESIGN BASED ON THE VARIABLE HYDRAULIC SENSITIVITY CONCEPT
Authors: Bijankhan Mohammad , Kouchakzadeh Salah
Published: June 2011

A baffle sluice module minimizes water delivery deviation for relatively large upstream flow depth variations; further studies are required to establish sound design criteria. A constant relative hydraulic sensitivity was assumed for the structure when previous design methods were developed. This paper highlights the invalidity of the assumption, and based on a variable equivalent sensitivity index, two design schemes for three‐ and two‐baffle modules were proposed. In the first scheme, the criteria of previous design methods were adopted but variable relative hydraulic sensitivity is applied. The results indicated that such a scheme would facilitate the structure design procedure; however, it does not resolve the theoretical drawback of other design methods, which deliver a smaller amount of water than the design discharge. Consequently, the second design scheme was proposed to overcome the problem. Comparing the results of the best available design method with that of the proposed second scheme indicated a significant improvement in the performance of the three‐baffle module, i.e. it decreased the discharge deviation range and theoretically provided both negative and positive deviations in the discharge delivery. Copyright © 2011 John Wiley & Sons, Ltd.
Targeted therapeutics and nanodevices for vascular drug delivery: Quo vadis?
Authors: Muzykantov Vladimir R.
Published: June 2011

This issue of the journal is dedicated to targeted delivery of therapeutics in the vasculature, an approach that holds promise to optimize treatment of diverse pathological conditions ranging from ischemia and tumor growth to metabolic and genetic diseases. From the standpoint of drug delivery, circulation system represents the natural route to the targets, whereas its components (blood and vascular cells) represent targets, carriers or barriers for drug delivery. Diverse nanodevices and targeted therapeutic agents that are designed and tested in animal and early clinical studies to achieve optimal and precise spatiotemporal control of the pharmacokinetics, destination, metabolism and effect of pharmacological agents will be discussed in this introductory essay and subsequent critical reviews in this series. © 2011 IUBMB IUBMB Life, 2011
Lung vascular targeting through inhalation delivery: Insight from filamentous viruses and other shapes
Authors: Mahmud Abdullah , Discher Dennis E.
Published: June 2011

Systemic delivery of therapeutic agents via inhalation of particulates remains an attractive, noninvasive means of administration due to the possibilities of high bioavailability and high patient compliance. Optimization of particle shapes and particle properties for deep lung deposition after inhalation continues to be one of the key challenges. Here, we review several aspects of nanoparticle design for deep lung deposition as well as the nature and extent of translocation through the air–blood barrier for local or systemic vascular targeting. We describe filamentous influenza virus in comparison to worm‐like “filomicelle” polymers as one example of a nature inspired design. © 2011 IUBMB IUBMB Life, 2011