bluuebunny/crossref_metadata_2025 huggingface dataset:
A QSAR study for modeling of thyroid receptors β1 selective ligands by application of adaptive neuro‐fuzzy inference system and radial basis function
Authors: Azimi Gholamhassan , Afiuni‐Zadeh Somaieh , Karami Alireza
Published: April 2012

A quantitative structure–activity relationship study of thyroid hormone receptors β1 is described in this paper. We used adaptive neuro‐fuzzy inference system (ANFIS) and radial basis function (RBF) methods coupling to genetic algorithm (GA) to predict binding affinity of some ligands with β1 thyroid receptors. A set of 83 selective ligands with known affinity of thyroid receptors β1 (pIC50) were selected, and a large number of molecular descriptors were calculated for each molecule by Dragon. Seven most relevant descriptors were selected by GA‐stepwise partial least squares as variable selection tool. The best descriptors (SCBO and EEig08x) and (SCBO, EEig08x, and BEHe1) were applied to train the ANFIS and RBF models, respectively. Then the number and shape of related functions were optimized. The ability and robustness of the GA‐ANFIS, GA‐RBF, and GA‐multiple linear regression (MLR) models in predicting the pIC50 of thyroid receptors β1 are illustrated by internal validation technique of leave one out and also heuristic and randomized techniques as external validation methods. The results have indicated that the proposed models of ANFIS and RBF in this work are superior to MLR method because of generation of simpler models with only two and three descriptors, respectively. Copyright © 2012 John Wiley & Sons, Ltd.
Resolution of 2‐chloromandelic acid with (R)‐(+)‐N‐benzyl‐1‐phenylethylamine: chiral discrimination mechanism
Authors: Peng Yangfeng , He Quan , Rohani Sohrab , Jenkins Hilary
Published: April 2012

During the resolution of 2‐chloromandelic acid with (R)‐(+)‐N‐benzyl‐1‐phenylethylamine, the crystals of the less soluble salt were grown, and their structure were determined and presented. The chiral discrimination mechanism was investigated by examining the weak intermolecular interactions (such as hydrogen bond, CH/π, and van der Waals interactions) and molecular packing mode in crystal structure of the less soluble diastereomeric salt. A one‐dimensional double‐chain hydrogen‐bonding network and a “lock‐and‐key” supramolecular packing mode are disclosed. The investigation demonstrates that hydrophobic layers with corrugated surfaces can fit into the grooves of one another to realize a compact packing, when the molecular structure of resolving agent is much larger than that of the racemate. This “lock‐and‐key” assembly is recognized to be another characteristic of molecular packing contributing to the chiral discrimination, in addition to the well‐known sandwich‐like packing by hydrophobic layers with planar boundary surfaces. Chirality 24:349–355, 2012. © 2012 Wiley Periodicals, Inc.
Novel Chiral Selector Based on Mefloquine – A Comparative NMR Study to Elucidate Intermolecular Interactions with Acidic Chiral Selectands
Authors: Kohout Michal , Kählig Hanspeter , Wolrab Denise , Roller Alexander , Lindner Wolfgang
Published: April 2012

The synthesis, ab initio calculations, and a comparative nuclear magnetic resonance study of a novel chiral mefloquine‐based selector (SO) are presented. On a series of variously N‐acyl protected leucine selectands (SAs), a feasibility study of mefloquine carbamate as a basic chiral solvating agent, and potential fluorophilic high‐performance liquid chromatography selector has been undertaken and evaluated. An analogy is drawn between the new SO and tert‐butylcarbamoyl quinidine as a reference. Chirality 24:936–943, 2012. © 2012 Wiley Periodicals, Inc.
Hormone receptor status influences the locoregional benefit of trastuzumab in patients with nonmetastatic breast cancer
Authors: Kim Michelle M. , Dawood Shaheenah , Allen Pamela , Sahin Aysegul A. , Woodward Wendy A. , Smith Benjamin D. , Strom Eric A. , Hunt Kelly K. , Meric‐Bernstam Funda , Gonzalez‐Angulo Ana Maria , Buchholz Thomas A.
Published: April 2012

BACKGROUND:

Previous studies have shown that hormone receptor (HR) and human epidermal growth factor receptor 2 (HER2) status influence the outcome of locoregional treatments. However, the interrelationship of these factors with trastuzumab is unclear. In this study, the role of HR and HER2 status on the locoregional benefit of trastuzumab treatment was investigated in patients with nonmetastatic breast cancer.

METHODS:

Locoregional outcomes of 5683 women treated at The University of Texas MD Anderson Cancer Center from 2000 to 2008 for invasive breast cancer were analyzed using Kaplan‐Meier and Cox regression methods to compare 6 subgroups: HR‐positive (HR+)/HER2‐negative (HER2−), HR−/HER2− (triple‐negative), HR+/HER2+ with or without trastuzumab, and HR−/HER2+ with or without trastuzumab.

RESULTS:

Overall, locoregional recurrence (LRR) was 5% at 5 years among patients with HER2+ disease. Patients with HR+/HER2+ disease treated with trastuzumab had half the rate of LRR as patients who did not receive trastuzumab, whereas patients with HR−/HER2+ disease had similar rates of LRR regardless of trastuzumab treatment. On Cox regression analysis comparing LRR risk to the cohort with HR+/HER2− disease, only the HR+/HER2+ cohort treated with trastuzumab had similar LRR risk (hazard ratio = 1.24, 95% confidence interval = 0.56‐2.73, P = .591). All other subgroups, including the HR+/HER2+ cohort who did not receive trastuzumab, had significantly worse outcomes. LRR risk was highest among patients with triple‐negative disease (hazard ratio = 4.73, 95% confidence interval = 3.42‐6.54, P < .001).

CONCLUSIONS:

Among patients with HR+/HER2+ disease, treatment with trastuzumab reduces LRR risk to the more favorable outcome of patients with HR+/HER2− disease. In contrast, the increased LRR risk among patients with HR−/HER2+ disease remains despite treatment with trastuzumab. Additional locoregional strategies are needed in this subgroup of patients. Cancer 2012. © 2012 American Cancer Society.
Involvement of epidermal growth factor receptor overexpression in the promotion of breast cancer brain metastasis
Authors: Nie Fang , Yang Jian , Wen Song , An Yan‐Li , Ding Jie , Ju Sheng‐Hong , Zhao Zhen , Chen Hua‐Jun , Peng Xin‐Gui , Wong Stephen T. C. , Zhao Hong , Teng Gao‐Jun
Published: April 2012

BACKGROUND:

Brain‐metastatic breast cancer (BMBC) is increasing and poses a severe clinical problem because of the lack of effective treatments and because the underlying molecular mechanisms are largely unknown. Recent work has demonstrated that deregulation of epidermal growth factor receptor (EGFR) may correlate with BMBC progression. However, the exact contribution that EGFR makes to BMBC remains unclear.

METHODS:

The role of EGFR in BMBC was explored by serial analyses in a brain‐trophic clone of human MDA‐MB‐231 breast carcinoma cells (231‐BR cells). EGFR expression was inhibited by stable short‐hairpin RNA transfection or by the kinase inhibitor erlotinib, and it was activated by heparin‐binding epidermal growth factor‐like growth factor (HB‐EGF). Cell growth and invasion activities also were analyzed in vitro and in vivo.

RESULTS:

EGFR inhibition or activation strongly affected 231‐BR cell migration/invasion activities as assessed by an adhesion assay, a wound‐healing assay, a Boyden chamber invasion assay, and cytoskeleton staining. Also, EGFR inhibition significantly decreased brain metastases of 231‐BR cells in vivo. Surprisingly, changes to EGFR expression affected cell proliferation activities less significantly as determined by a 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide (MTT) assay, an anchorage‐independent growth assay, and cell cycle analysis. Immunoblot analysis suggested that EGFR drives cells' invasiveness capability mainly through phosphoinositide 3‐kinase/protein kinase B and phospholipase C γ downstream pathways. In addition, EGFR was involved less in proliferation because of the insensitivity of the downstream mitogen‐activated protein kinase pathway.

CONCLUSIONS:

The current results indicated that EGFR plays more important roles in cell migration and invasion to the brain than in cell proliferation progression on 231‐BR cells, providing new evidence of the potential value of EGFR inhibition in treating BMBC. Cancer 2012. © 2012 American Cancer Society.
A 13 bit 10 MHz bandwidth MASH 3–2 Σ∆ modulator in 90 nm CMOS
Authors: Sohrabi Zahra , Yavari Mohammad
Published: April 2012

In this paper, a new multi loop sigma‐delta (ΣΔ) modulator is proposed which employs one order redundant noise shaping in the first stage so the effect of the quantization noise leakage is minimized. Thus, analog circuit requirements are considerably relaxed compared to the conventional Multi‐stAge‐noise‐SHaping (MASH) structures. This enhancement makes the structure appropriate for low voltage and broadband applications. The proposed architecture is compared with traditional high‐order structures, and the advantages are demonstrated by both the analysis and behavioral system level simulations. As a prototype, the proposed MASH 3–2 sigma‐delta modulator is designed, and the detailed design procedure is presented from the system level to the circuit level in a 90 nm CMOS technology. Circuit level simulation results show that the modulator achieves a peak signal‐to‐noise and distortion ratio of 79.4 dB and 79 dB dynamic range over a 10 MHz bandwidth with a sampling frequency of 160 MHz. It consumes 35.4 mW power from a single 1 V supply. Copyright © 2012 John Wiley & Sons, Ltd.
Cryptococcal lymphadenitis in HIV: A chance diagnosis by FNAC
Authors: Bhuyan Pallavi , Pattnaik Kaumudee , Kar Asaranti , Brahma Rathish Chandra , Mahapatra Smita
Published: April 2012

Cryptococcosis is a life threatening, opportunistic fungal disease in human immunodeficiency virus‐infected individual. Lymph node involvement as a presenting feature in Cryptococcosis is not a common manifestation. A prompt diagnosis is of utmost importance in this disseminated form of cryptococcosis. There are very few reports, however, of cryptococcal lymphadenitis as a presenting feature. We report here a case of cryptococcal lymphadenitis that was diagnosed by fine‐needle aspiration cytology of the involved cervical lymph node. Diagn. Cytopathol. 2013. © 2012 Wiley Periodicals, Inc.
Cytologic and histologic findings of iron pill‐induced injury of the lower respiratory tract
Authors: Cimino‐Mathews Ashley , Illei Peter B.
Published: April 2012

In the airways, iron pill‐induced mucosal injury is uncommon and can lead to necrosis and stricture of the respiratory tracts. The process is characterized by mucosal ulceration with deposition of crystalline iron particles, and the diagnosis is usually made on tissue biopsies. We report a case of iron‐sulfate‐induced mucosal injury in the bronchial washing and biopsy of a patient receiving therapeutic oral iron supplementation with no known aspiration event. Clinically, the patient presented with hemoptysis, and bronchoscopy detected ulcerated main stem bronchus mucosa clinically suspicious for a neoplastic process. Bronchial washings revealed reactive epithelial cells and numerous histiocytes with both intracellular and extracellular refractile brown crystalline material, which was positive on iron stain. The histologic findings on biopsy showed mucosal ulceration with deposits of extracellular crystalline iron particles. These histologic changes are similar to those seen in iron pill‐induced mucosal injury of the upper gastrointestinal tract in patients with “iron pill” gastritis. The cytologic and histologic features of iron pill‐induced airway injury clinically can mimic cancer. The presence of extracellular and intracellular crystalline iron in the airway lumen and/or mucosa with associated varying degrees of ulceration and inflammation confirms the diagnosis. Diagn. Cytopathol. 2013;41:901–903. © 2012 Wiley Periodicals, Inc.
Gynecologic cytology on conventional and liquid‐based preparations: A comprehensive review of similarities and differences
Authors: Hoda Rana S. , Loukeris Kristina , Abdul‐Karim Fadi W.
Published: April 2012

Liquid‐based preparations (LBPs) have largely replaced conventional Papanicolaou smears (CPS) for cervical samples in the United States and in many other industrialized countries. The two FDA‐approved LBP currently in use include ThinPrep (TP), (Hologic Inc., Bedford, MA) and SurePath (SP), (BD Diagnostic, Burlington, NC). Split‐sample and direct‐to‐vial studies have shown that LBPs show an overall improvement in sample collection and processing, reduce artifacts that interfere in diagnosis, are more sensitive, can be utilized for ancillary tests and are a cost‐effective replacement for CPS. Comparative analyses of diagnostic accuracy indicate that LBPs perform at least as well as CPS. However, the added advantages of standardized, automated preparations and screening, reduced unsatisfactory rate, improved specimen adequacy and ability to perform human papillomavirus (HPV) test, are enough to continue use of LBP. The cytologic features in LBP are similar to CPS with subtle differences, particularly in background information. There are also subtle differences between the two LBPs, SP and TP, which are reflective of different sampling devices, collection media, and processing techniques. Architecturally, LBP shows smaller cell clusters and sheets and more dyscohesion. Cytologically, enhanced nuclear features and smaller cell size are more prominent. Advances in liquid‐based Papanicolaou's (Pap) test have lead to well‐defined patient management guidelines by the American Society for Colposcopy and Cervical Pathology. Herein, we review these aspects of Pap test including, morphology, automation, ancillary tests (HPV and immunochemistry), pertinent QA/QC monitors, patient management guidelines, and review of pertinent literature. Diagn. Cytopathol. 2013. © 2012 Wiley Periodicals, Inc.
Technology of building an expert system based on a set of quantitative features of tumor cell nuclei for diagnosing breast cancer
Authors: Kirillov Vladimir
Published: April 2012

The technology of building an expert system for diagnosing malignant nature of invasive tumors of the mammary gland based on a set of quantitative features of the cell nuclei has been developed. Its peculiarity was the presence of weighting coefficients in all the features. Quantitative features were obtained by transforming the initial morphometric data with the help of simple (evaluation of mean values and building of histograms) and complex (regression analysis) mathematical operations. The expert system consisted of one‐dimensional X‐matrix used for investigations and two‐dimensional standard S‐matrix. The X‐matrix elements were assigned for filling with the quantitative features of the studied sample with a nonestablished diagnosis. The S‐matrix elements contained threshold values of quantitative features from the system of diagnostic decision criteria for malignant forms of diseases and their weighting coefficients. Threshold values of nuclear features (larger or smaller) were determined taking into account the range of their values in the groups of malignant and benign pathology. Significance of quantitative features in diagnosing diseases has been assessed. The presence of weighting coefficients allowed diagnosing malignant and benign pathology in a quantitative form by the diagnostic index value. Diagnostic index was calculated by the sum of weighting coefficients of features of the studied sample, which fell within the range of system of the S‐matrix diagnostic decision criteria. Clinical trials revealed high efficiency of the developed approach while diagnosis of breast cancer invasive forms at a preoperative stage. Diagn. Cytopathol. 2013. © 2012 Wiley Periodicals, Inc.
Quantification of active ingredients in suppositories by FT‐Raman spectroscopy
Authors: Szostak Roman , Mazurek Sylwester
Published: April 2012

An efficient method for the quantitative determination of acetaminophen (AAP) and diclofenac sodium (DS) in commercial suppositories based on partial least squares (PLS) treatment of FT‐Raman spectra is described. The relative standard errors of prediction (RSEP) were calculated for calibration and validation data sets to evaluate the quality of the constructed models. In the case of DS determination, RSEP error values of 1.9 % and 2.3 % for the calibration and validation data sets, respectively, were found. For AAP these errors amounted to 1.6–2.3 % and 1.8–2.8 %, respectively, for the different calibration models. Four commercial preparations containing 5, 12.5, 16.7 and 33.3 % (w/w) AAP and one containing 5 % (w/w) DS were successfully quantified using the developed models. Concentrations derived from the developed models correlated strongly with the declared values and yielded recoveries of 99.4–100.2 % and 99.6 % for AAP and DS, respectively. The proposed procedure can be used as a fast, economic and reliable method for quantification of the active pharmaceutical ingredients in suppositories. Copyright © 2012 John Wiley & Sons, Ltd.
Production of a mouse line with a conditional Crim1 mutant allele
Authors: Chiu Han Sheng , York J. Philippe , Wilkinson Lorine , Zhang Pumin , Little Melissa H. , Pennisi David J.
Published: April 2012

Crim1 is a developmentally expressed, transmembrane protein essential for normal embryonic development. We generated mice engineered to contain a Crim1 conditional null allele by flanking exons three and four of Crim1 with unidirectional LoxP sites. After crossing Crim1+/FLOX mice with a CMV‐Cre line, a Crim1+/Δflox colony was established after germline transmission of the deleted allele. We then analyzed genomic DNA, mRNA transcripts, and protein expression from Crim1Δflox/Δflox null mice to confirm the nature of the genomic lesion. Crim1Δflox/Δflox mice displayed phenotypes similar to those previously described for a Crim1 gene‐trap mutant, Crim1KST264/KST264, including perinatal lethality, digit syndactyly, eye, and kidney abnormalities, with varying penetrance and severity. The production of a conditional mutant allele represents a valuable resource for the study of the tissue‐specific roles for Crim1, and for understanding the pleimorphic phenotypes associated with Crim1 mutation. genesis 50:711–716, 2012. © 2012 Wiley Periodicals, Inc.
Sulfur Oxygenation of [Ni(btdt)2]2– by Aerial Oxidation under Ambient Conditions – Syntheses, Crystal Structures, and Properties of [Bu4N]2[Ni(btdt)2] and [Bu4N]2­[Ni(btdtO2)2]·H2O ({btdt}2– = 2,1,3‐Benzenethiadiazole‐5,6‐dithiolate)
Authors: Bolligarla Ramababu , Das Samar K.
Published: April 2012

[Bu4N]2[Ni(btdt)2] (1) ({btdt}2– = 2,1,3‐benzenethiadiazole‐5,6‐dithiolate) was synthesized by treating one equivalent of NiCl2·6H2O with two equivalents of H2btdt in MeOH in the presence of NaOH under nitrogen, and then obtaining a precipitate by adding tetrabutylammonium bromide. When the same reaction is carried out under ambient conditions, it yields the trans‐disulfinate complex [Bu4N]2[Ni(btdtO2)2]·H2O (2) along with complex 1. Complex 1 crystallizes in the triclinic space group P$\bar {1}$, whereas complex 2 crystallizes in the monoclinic space group C2/c. The NiII ion, coordinated with four sulfur atoms present in complex 1, shows almost square‐planar geometry, but trans‐disulfinate complex 2 shows distorted square‐planar geometry around the NiII ion with a nonplanar molecular structure. Oxygen atoms of the sulfinates are involved in C–H···O and O–H···O hydrogen‐bonding interactions, which might be important factors for the nonplanarity of complex 2. Complex 1 undergoes a reversible oxidation (ΔE = 0.09 V) at E1/2 = +0.22 V vs. Ag/AgCl and an irreversible oxidation at +0.77 V, whereas complex 2 shows quasi‐reversible oxidation at E1/2 = +0.50 V vs. Ag/AgCl in acetonitrile solution.
Diels–Alder Reactions for the Construction of Cyclopropylarenes
Authors: Arndt Marion , Hilt Gerhard , Khlebnikov Alexander F. , Kozhushkov Sergei I. , de Meijere Armin
Published: April 2012

The straightforward synthesis of new bicyclopropyl‐substituted alkynes and 1,3‐dienes and their application in cobalt‐catalyzed Diels–Alder reactions are described. The cycloaddition processes generated the desired bicyclopropyl‐substituted arene derivatives in moderate to good yields, depending on the steric congestion of the reaction partners. The regioselectivity of the cycloaddition was controlled by the ligand coordinated to the cobalt center. The cyclopropyl moiety remained unchanged over the course of the Diels–Alder reaction, indicating that no radical type intermediates were formed. Only in a single case did the DDQ oxidation of the primarily formed dihydroaromatic product lead to ring opening of a cyclopropyl subunit. In all of the other cases, cyclopropyl‐modified arenes with various functionalities were obtained.
Beyond the myth of venting: Social sharing modes determine the benefits of emotional disclosure
Authors: Nils Frédéric , Rimé Bernard
Published: April 2012

When individuals experience an emotion, they talk about it afterwards. A popular ‘emotional venting’ belief claims that doing so dissolves the emotional impact. This study tested a model of when and how sharing emotions is beneficial. It predicts that benefits vary according to the listener's response mode. A socio‐affective (empathic) mode was expected to buffer emotional distress temporarily. A cognitive (reframing) mode was anticipated to grant emotional recovery. Participants viewed an aversive film and then talked about it with an intimate. The latter was instructed to adopt either cognitive or socio‐affective response modes in a 2 × 2 design (cognitive/non‐cognitive; socio‐affective/neutral). Emotional, cognitive and social benefits were assessed immediately afterwards and again 2 days later following re‐exposure to the film. As predicted, emotional recovery occurred exclusively when the listener stimulated the participant's cognitive work. Cognitive variables (basic assumptions) were also positively modified by these conditions. Listeners' socio‐affective responses entailed enhanced social integration (i.e. greater proximity to the listener; less loneliness) and an impression of feeling better. These results demonstrated that sharing emotions can lead to multiple benefits depending upon the listeners' response modes: emotional recovery, consolidation of shattered assumptions, social integration and temporary distress reduction. Copyright © 2012 John Wiley & Sons, Ltd.
Gender differences in implicit gender self‐categorization lead to stronger gender self‐stereotyping by women than by men
Authors: Cadinu Mara , Galdi Silvia
Published: April 2012

It was hypothesized that, in natural group contexts, low‐status in‐group membership would be highly accessible, whereas membership to high‐status groups would not. Therefore, gender group membership was predicted to be more accessible for women than for men. It was further hypothesized that the high accessibility of gender group membership would lead to stronger self‐stereotyping for women than for men. To measure the accessibility of gender group membership, participants performed a Gender Self‐Categorization Implicit Association Test (Studies 1 and 2), measuring the strength of automatic associations between the self and the gender in‐group. Participants also performed a Self‐Stereotyping Implicit Association Test (Study 2), assessing the strength of automatic associations between the self and the stereotypical traits of the in‐group. As expected, implicit gender self‐categorization and implicit gender self‐stereotyping were stronger for women than for men. Importantly, implicit gender self‐categorization mediated the relation between gender and self‐stereotyping. Therefore, implicit gender self‐categorization was the mechanism underlying stronger implicit self‐stereotyping by women. Copyright © 2012 John Wiley & Sons, Ltd.
Protective role of dietary N-acetylcysteine on the oxidative stress induced by cylindrospermopsin in tilapia (Oreochromis niloticus)
Authors: Gutiérrez-Praena Daniel , Puerto María , Prieto Ana Isabel , Jos Ángeles , Pichardo Silvia , Vasconcelos Vitor , Cameán Ana M.
Published: April 2012

Cylindrospermopsin (CYN) is a toxin produced by various cyanobacteria species. Fish can be exposed to this cyanotoxin in their natural environments and in aquaculture ponds, and toxic effects can be derived. The present study investigated the effects of dietary N-acetylcysteine (NAC) on the oxidative stress induced by pure CYN and CYN from lyophilized cells of Aphanizomenon ovalisporum in tilapia (Oreochromis niloticus). Fish were pretreated with 0, 22, and 45 mg NAC/fish/d for a week, and on day seven, they received a single dose of 200 µg/kg CYN and were killed after 24 h. Oxidative biomarkers evaluated included lipid peroxidation, protein oxidation, glutathione (GSH)/oxidized glutathione (GSSG) ratio, activity of the enzyme γ-glutamylcysteine synthetase, and activity and gene expression of glutathione-S-transferase and glutathione peroxidase. Results showed that CYN induced oxidative stress as evidenced by the increase of lipid peroxidation and protein oxidation, the decrease in GSH/GSSG, and the alteration of the enzymatic activities assayed. Moreover, exposure to cyanobacterial cells containing CYN induced higher toxic effects in comparison to pure CYN. N-acetylcysteine supplementation was effective at reducing the toxicity induced by CYN, particularly at the highest dose employed, with a recovery of some of the biomarkers assayed to basal levels. Therefore, NAC can be considered a useful chemoprotectant that reduces hepatic and renal oxidative stress in the prophylaxis and treatment of CYN-related intoxication in fish. Environ. Toxicol. Chem. 2012; 31: 1548–1555. © 2012 SETAC
Mechanisms regulating bioavailability of phenanthrene sorbed on a peat soil-origin humic substance
Authors: Yang Yu , Shu Liang , Wang Xilong , Xing Baoshan , Tao Shu
Published: April 2012

The organic matter–mineral complex plays an important role in regulating the fate of hydrophobic organic compounds (HOCs) in the environment. In the present study, the authors investigated the microbial bioavailability of phenanthrene (PHE) sorbed on the original and demineralized humic acids (HAs) and humin (HM) that were sequentially extracted from a peat soil. Demineralization treatment dramatically decreased the 720-h mineralized percentage of HM-sorbed PHE from 42.5 ± 2.6% to 3.4 ± 1.3%, whereas the influence of this treatment on the biodegradability of HA-associated PHE was much lower. Degradation kinetics of HA- and HM-sorbed PHE showed that its initial degradation rate was negatively correlated with the aromatic carbon content of humic substances (p < 0.05). This was attributed to the strong interactions between PHE and the aromatic components of humic substances, which hampered its release and subsequent biodegradation. The 720-h mineralized percentage of PHE was inversely correlated with the estimated thickness of the organic matter layer at the surfaces of HAs and HMs. Therefore, in a relatively long term, diffusion of PHE within the organic matter layer could be an important factor that may limit the bioavailability of PHE to bacteria. Results of the present study highlight the molecular-scaled mechanisms governing bioavailability of PHE sorbed on humic substances. Environ. Toxicol. Chem. 2012; 31: 1431–1437. © 2012 SETAC
Salinity acclimation modulates copper toxicity in the sheepshead minnow, Cyprinodon variegatus
Authors: Adeyemi Joseph A. , Klerks Paul L.
Published: April 2012

The sheepshead minnow (Cyprinodon variegatus) is able to withstand a wide range of salinities. Salinity acclimation involves physiological and biochemical changes, which may influence how organisms respond to a stressor. The present study investigated effects of salinity acclimation on subsequent Cu toxicity. In experiment 1, fish were acclimated to a hyposmotic, isosmotic, or hyperosmotic salinity for 14 d and then exposed at these salinities to 16.6 µM Cu2+ for 12 h. Survival differed during this Cu challenge; fish acclimated to 2.5 ppt salinity were much more sensitive to Cu than those acclimated to 10.5 or 18.5 ppt seawater. In experiment 2, fish were exposed to 14.6 µM Cu2+ for 6 h after the 14-d salinity acclimation. Whole-body Cu, whole-body Na, liver lipid peroxidation (LPO), liver catalase activity, and liver glucose levels were determined before and after Cu exposure. Prior to Cu exposure, the acclimation groups differed only for liver glucose levels, which were higher in the 2.5 ppt acclimated fish than in the others. These same 2.5 ppt acclimated fish were markedly affected by Cu, having increased whole-body Cu and liver LPO and decreased whole-body Na levels. Copper exposure had generally insignificant effects for the 10.5 ppt and the 18.5 ppt acclimated fish. This study showed that even in euryhaline fish, salinity acclimation can have a drastic effect on Cu toxicity. Environ. Toxicol. Chem. 2012; 31: 1573–1578. © 2012 SETAC
Building generalized open boundary conditions for fluid dynamics problems
Authors: Blayo Eric , Martin Véronique
Published: April 2012

This paper deals with the design of an efficient open boundary condition (OBC) for fluid dynamics problems. Such problematics arise, for instance, when one solves a local model on a fine grid that is nested in a coarser one of greater extent. Usually, the local solution Uloc is computed from the coarse solution Uext, thanks to an OBC formulated as , where Bh and BH are discretizations of the same differential operator (Bh being defined on the fine grid and BH on the coarse grid). In this paper, we show that such an OBC cannot lead to the exact solution, and we propose a generalized formulation , where g is a correction term. When Bh and BH are discretizations of a transparent operator, g can be computed analytically, at least for simple equations. Otherwise, we propose to approximate g by a Richardson extrapolation procedure. Numerical test cases on a 1D Laplace equation and on a 1D shallow water system illustrate the improved efficiency of such a generalized OBC compared with usual ones. Copyright © 2012 John Wiley & Sons, Ltd.
Towards simulation of flapping wings using immersed boundary method
Authors: Zhang X. Q. , Theissen P. , Schlüter J. U.
Published: April 2012

In this work the immersed boundary method is applied to simulate incompressible turbulent flows around stationary and moving objects. The goal is to demonstrate that the immersed boundary technique along with a large eddy simulation approach is capable of simulating the effect of the so‐called leading edge vortex (LEV), which can be found in flapping wing aerodynamics. A Lagrangian method is used to approximate the solutions in the freshly cleared cells that lay within solid objects at one time step and emerge into fluid domain at the next time step. Flow around a stationary cylinder at ReD = 20, 40, and 3900 (based on cylinder diameter D) is first studied to validate the immersed boundary solver based on the finite volume scheme using a staggered grid. Then, a harmonically oscillating cylinder at ReD = 10 000 is considered to test the solver after the Lagrangian method is implemented to interpolate the solution in the freshly cleared cells. Finally, this approach is used to study flows around a stationary flat‐plate at several angles of attack and fast pitching flat‐plate. The rapidly pitching plate creates a dynamic LEV that can be used to improve the efficiency of flapping wings of micro air vehicle and to determine the optimum flapping frequency. Copyright © 2012 John Wiley & Sons, Ltd.
Integrated modeling as a decision‐aiding tool for groundwater management in a Mediterranean agricultural watershed
Authors: Pisinaras V. , Petalas C. , Tsihrintzis V. A. , Karatzas G. P.
Published: April 2012

A decision‐aiding methodology for agricultural groundwater management is presented; it is based on the combination of a watershed model, a groundwater flow model, and an optimization model. This methodology was applied to an agricultural watershed in northeastern Greece. The watershed model used was the Soil and Water Assessment Tool (SWAT), which provided recharge rates for the aquifers. These recharge rates were imported in the well‐known MODFLOW groundwater flow model. Both models were calibrated and verified using field data. Then, the nonlinear optimization problem was solved by a piecewise linearization process, in which the Simplex algorithm was applied sequentially. Apart from several pumping and climate change sensitivity scenarios, a land use change scenario and a climate change scenario, combining the three models, were tested, showing the ability of this methodology to be used in the decision‐making process. Copyright © 2012 John Wiley & Sons, Ltd.
Catchment scale controls the temporal connection of transpiration and diel fluctuations in streamflow
Authors: Graham Chris B. , Barnard Holly R. , Kavanagh Kathleen L. , McNamara James P.
Published: April 2012

Diel fluctuations can comprise a significant portion of summer discharge in small to medium catchments. The source of these signals and the manner in which they are propagated to stream gauging sites is poorly understood. In this work, we analysed stream discharge from 15 subcatchments in Dry Creek, Idaho, Reynolds Creek, Idaho, and HJ Andrews, Oregon. We identified diel signals in summer low flow, determined the lag between diel signals and evapotranspiration demand and identified seasonal trends in the evolution of the lag at each site. The lag between vegetation water use and streamflow response increases throughout summer at each subcatchment, with the rate of increase as a function of catchment stream length and other catchment characteristics such as geology, vegetation and stream geomorphology. These findings support the hypothesis that variations in stream velocity are the key control on the seasonal evolution of the observed lags. Copyright © 2012 John Wiley & Sons, Ltd.
Evaluating the effectiveness of road‐crossing drainage culverts in ephemeral streams
Authors: Conesa‐García C. , García‐Lorenzo R.
Published: April 2012

The present study proposes a method for evaluating the effectiveness of road‐crossing drainage culverts in ephemeral streams. This approach is focused on estimating the culvert capacity in road–stream crossings and the probable runoff generated on the road from hydrological thresholds associated with hydromorphological criteria. In particular, discharges at bankfull and flood‐prone stages have been used in combination with 2.5 and 100‐year peak discharges. Different hydraulic variables have been considered for calculating the discharge through culverts under these conditions (e.g. tailwater and headwater depth, inlet control, pipe roughness, pipe cross‐area and slope, pipe outlet velocity, critical water depth, and flow rate over the road). Geomorphological factors such as bed stability, bed load transport, and channel roughness have also been considered because of their potential for obstructing the drains in this type of channel. In addition, a potential obstruction index (PIOBSTR) has been calculated, as a dependent parameter of the obstacle index (IOBST) and the potential build‐up of coarse sediments (PBCS). The study has been carried out on the Mediterranean coast in the region of Murcia (Spain), where there are numerous examples of road–stream crossings equipped with culverts in ephemeral channels that could cause highly dangerous situations for road traffic. Copyright © 2012 John Wiley & Sons, Ltd.
Effects of patterned Artemisia capillaris on overland flow velocity under simulated rainfall
Authors: Zhang Guanhua , Liu Guobin , Wang Guoliang , Wang Yuxia
Published: April 2012

Vegetation cover is an important factor for erosion control. Laboratory‐simulated rainfall experiments were conducted to quantify the effectiveness of patchy distributed Artemisia capillaris in retarding overland flow velocity. Simulated storms (60, 90, 120, and 150 mm h−1) were applied on a bare plot (CK) and four different plant patterns, a banded pattern perpendicular to the slope direction (BP), a single long strip parallel to slope direction (LP), small patches distributed like a checkerboard (SP1), and small patches distributed like a letter “X” (SP2). All treatments had three replicates. Each plot underwent two sets of experiments, intact plant plots and root plots (the above‐ground parts were removed, only roots were reserved), respectively. Results showed that flow velocity increased with rainfall intensity, and the lower slope velocity (Vl) was higher than the upper slope velocity (Vu). The removal of grass shoots increased flow velocity. Compared with bare soil plot, intact plants reduced mean flow velocity by 14%–60%, whereas the reduction declined to <40% for the root plots. BP and both SP treatments performed more effectively than LP in retarding flow velocity, whereas no significant differences were identified between BP and SP. The contributions of A. capillaris shoots and roots to the reductions in flow velocity under different rainfall intensities were different. The shoots made greater contribution of 53%–97% at 60 and 90 mm h–1, and the roots contributed more (51%–81%) at 120 and 150 mm h–1. Runoff and sediment rate had significant (p < 0.05) linear correlations with mean flow velocity. Copyright © 2012 John Wiley & Sons, Ltd.
Spatial distribution and temporal trends of mean precipitation and extremes in the arid region, northwest of China, during 1960–2010
Authors: Wang Huaijun , Chen Yaning , Chen Zhongsheng
Published: April 2012

On the basis of daily precipitation records at 76 meteorological stations in the arid region, northwest of China, the spatial and temporal distribution of mean precipitation and extremes were analysed during 1960–2010. The Mann–Kendall trend test and linear least square method were utilized to detect monotonic trends and magnitudes in annual and seasonal mean precipitation and extremes. The results obtained indicate that both the mean precipitation and the extremes have increased except in consecutive dry days, which showed the opposite trend. The changes in amplitude of both mean precipitation and extremes show seasonal variability. On an annual basis, the number of rain days (R0.1) has significantly increased. Meanwhile, the precipitation intensity as reflected by simple daily intensity index (SDII), number of heavy precipitation days (R10), very wet days (R95p), max 1‐day precipitation amount (RX1day) and max 5‐day precipitation amount (RX5day) has also significantly increased. This suggests that the precipitation increase in the arid region is due to the increase in both precipitation frequency and intensity. Trends in extremes are very highly correlated with mean trends of precipitation. The spatial correlation between trends in extremes and trends in the mean is stronger for winter (DJF) than for annual and other seasons. The regional annual and seasonal precipitation and extremes are observed the step jump in mean in the late 1980s. Overall, the results of this study are good indicators of local climate change, which will definitely enhance human mitigation to natural hazards caused by precipitation extremes. Copyright © 2012 John Wiley & Sons, Ltd.
Studies of a regulated dryland river: surface–groundwater interactions
Authors: McDonald Alyson K. , Sheng Zhuping , Hart Charles R. , Wilcox Bradford P.
Published: April 2012

Unlike rivers in humid regions, dryland rivers typically exhibit reduced flow in the downstream direction as a result of transmission losses, which include seepage of streamflow into the aquifer, evaporation, and transpiration. However, much remains to be learned about the nature of the exchange between surface water and groundwater in these landscapes, especially in terms of spatial and temporal variability. Our study focused on streambank seepage and groundwater flow in the alluvial aquifer, specifically on answering questions such as: Is there seasonal variability in seepage losses? Is seepage permanently lost? Can losses be reduced by killing riparian vegetation? To better understand the magnitude, variability, and fate of streambank seepage, we assessed river stages, groundwater hydraulic gradients, and groundwater flow paths at two sites along a reach of the Pecos River, a dryland perennial river in West Texas. We found that along this reach the river was losing water to the aquifer even under low‐flow conditions; but seepage was controlled by a number of different mechanisms. Seepage increased not only during high‐flow events but also when the groundwater level was declining owing to long periods of no irrigation release. Tamarix (saltcedar) control did not affect hydraulic gradients nor reduce streambank seepage and given that this reach of the Pecos River is a losing one, streamflow will not be enhanced by controlling saltcedar. These findings can be used to improve basic conceptual models of dryland river systems and to predict hydrologic responses to changes in the timing and magnitude of streamflows and to riparian vegetation management. Copyright © 2012 John Wiley & Sons, Ltd.
Susceptibility variants for obesity and colorectal cancer risk: The multiethnic cohort and PAGE studies
Authors: Lim Unhee , Wilkens Lynne R. , Monroe Kristine R. , Caberto Christian , Tiirikainen Maarit , Cheng Iona , Park Sungshim Lani , Stram Daniel O. , Henderson Brian E. , Kolonel Laurence N. , Haiman Christopher A. , Le Marchand Loïc
Published: April 2012

Obesity is a leading contributor to colorectal cancer risk. We investigated whether the risk variants identified in genome‐wide association studies of body mass index (BMI) and waist size are associated with colorectal cancer risk, independently of the effect of obesity phenotype due to a shared etiology. Twenty‐four single nucleotide polymorphisms (SNPs) in 15 loci (BDNF, FAIM2, FTO, GNPDA2, KCTD15, LYPLAL1, MC4R, MSRA, MTCH2, NEGR1, NRXN3, SEC16B, SH2B1, TFAP2B and TMEM18) were genotyped in a case–control study of 2,033 colorectal cancer cases and 9,640 controls nested within the multiethnic cohort study, as part of the population architecture using genomics and epidemiology consortium. Risk alleles for two obesity SNPs were associated with colorectal cancer risk—KCTD15 rs29941 [odds ratio (OR) for C allele = 0.90, 95% confidence interval (CI) 0.83–0.98; p = 0.01] and MC4R rs17782313 (OR for C allele = 1.12, 95% CI 1.02–1.22; p = 0.02). These associations were independent of the effect of BMI. However, none of the results remained significant after adjustment for multiple comparisons. No heterogeneity was observed across race/ethnic groups. Our findings suggest that the obesity risk variants are not likely to affect the risk of colorectal cancer substantially.
Association of time since last birth, age at first birth and parity with breast cancer survival among parous women: A register‐based study from Norway
Authors: Alsaker Mirjam D.K. , Opdahl Signe , Romundstad Pål R. , Vatten Lars J.
Published: April 2012

Reproductive factors that have a well‐documented effect on breast cancer risk may also influence the prognosis of the disease, but previous studies on breast cancer survival have yielded conflicting results. We combined information from two population‐based registries and obtained information on 16,970 parous women with invasive breast cancer. Cox regression analysis was used to assess breast cancer survival in relation to age at diagnosis, age at first birth, time since last birth and parity. We stratified the analyses by age at diagnosis (<50 and ≥50 years) as an approximation for menopausal age. In women diagnosed before 50 years of age, breast cancer survival was reduced with younger age at diagnosis (p for trend <0.001), whereas in women diagnosed at 50 years or later, survival was reduced with older age at diagnosis (p for trend 0.011). For breast cancer diagnosed before 50 years, survival was poorer in women with four or more births compared to women with one or two births (hazard ratio 1.3, 95% confidence interval 1.1–1.6). A short time since last birth was associated with reduced survival (p for trend 0.05), but adjustment for stage and grade attenuated the association. Among women diagnosed at 50 years or later, we found no association with survival for any of the reproductive factors. In summary, reproductive factors were associated with survival from breast cancer diagnosed before but not after age 50 years. Young women had a particularly poor prognosis throughout the study period.
The circadian clock gene BMAL1 is a novel therapeutic target for malignant pleural mesothelioma
Authors: Elshazley Momen , Sato Mitsuo , Hase Tetsunari , Yamashita Ryo , Yoshida Kenya , Toyokuni Shinya , Ishiguro Futoshi , Osada Hirotaka , Sekido Yoshitaka , Yokoi Kohei , Usami Noriyasu , Shames David S. , Kondo Masashi , Gazdar Adi F. , Minna John D. , Hasegawa Yoshinori
Published: April 2012

Malignant pleural mesothelioma (MPM) is a highly aggressive neoplasm arising from the mesothelial cells lining the parietal pleura and it exhibits poor prognosis. Although there has been significant progress in MPM treatment, development of more efficient therapeutic approaches is needed. BMAL1 is a core component of the circadian clock machinery and its constitutive overexpression in MPM has been reported. Here, we demonstrate that BMAL1 may serve as a molecular target for MPM. The majority of MPM cell lines and a subset of MPM clinical specimens expressed higher levels of BMAL1 compared to a nontumorigenic mesothelial cell line (MeT‐5A) and normal parietal pleural specimens, respectively. A serum shock induced a rhythmical BMAL1 expression change in MeT‐5A but not in ACC‐MESO‐1, suggesting that the circadian rhythm pathway is deregulated in MPM cells. BMAL1 knockdown suppressed proliferation and anchorage‐dependent and independent clonal growth in two MPM cell lines (ACC‐MESO‐1 and H290) but not in MeT‐5A. Notably, BMAL1 depletion resulted in cell cycle disruption with a substantial increase in apoptotic and polyploidy cell population in association with downregulation of Wee1, cyclin B and p21WAF1/CIP1 and upregulation of cyclin E expression. BMAL1 knockdown induced mitotic catastrophe as denoted by disruption of cell cycle regulators and induction of drastic morphological changes including micronucleation and multiple nuclei in ACC‐MESO‐1 cells that expressed the highest level of BMAL1. Taken together, these findings indicate that BMAL1 has a critical role in MPM and could serve as an attractive therapeutic target for MPM.