bluuebunny/crossref_metadata_2025 huggingface dataset:
Myeloid leukemia in a urine specimen: A case report and review of the literature
Authors: McCroskey Zulfia , Mehta Vikas , Wojcik Eva M. , Barkan Güliz A.
Published: June 2013

Urinary tract cytology has a long history of utilization for the diagnosis and follow‐up of tumors involving the urothelial tract. As expected, the most common tumor encountered in exfoliative urine cytology is urothelial carcinoma. While the sensitivity of urinary tract cytology for the diagnosis of low‐grade urothelial carcinomas is low, its sensitivity and accuracy for high grade urothelial carcinomas is much higher. However, nonurothelial malignancies, such as hematopoietic malignancies, can also be encountered in urine specimens. Leukemic cells in urine can be diagnosed readily by cytological examination in cases where more invasive procedures are difficult to perform. Additionally, cell block sections can be utilized to determine the immunocytochemical profile of the tumor cells to confirm the diagnosis.

Herein we report a case of a 75‐year‐old man with a past medical history of acute myeloid leukemia (AML), who presented with congested heart failure and painless macroscopic hematuria. AML relapse was diagnosed. Cytological examination of the urine using a ThinPrep® smear, cytospin preparation, and immunohistochemical stains performed on the cell block sections were examined. Findings were consistent with leukemic cells of myeloid origin in the bladder washing specimen. Diagn. Cytopathol. 2014;42:700–704. © 2013 Wiley Periodicals, Inc.
The effects of prenatal stress on Alpha4 Beta2 and Alpha7 hippocampal nicotinic acetylcholine receptor levels in adult offspring
Authors: Schulz Kalynn M. , Andrud Kristin M. , Burke Maria B. , Pearson Jennifer N. , Kreisler Alison D. , Stevens Karen E. , Leonard Sherry , Adams Catherine E.
Published: June 2013

Prenatal stress in humans is associated with psychiatric problems in offspring such as anxiety, depression, and schizophrenia. These same illnesses are also associated with neuronal nicotinic acetylcholine receptor (nAChR) dysfunction. Despite the known associations between prenatal stress exposure and offspring mental illness, and between mental illness and nAChR dysfunction, it is not known whether prenatal stress exposure impacts neuronal nAChRs. Thus, we tested the hypothesis that maternal stress alters the development of hippocampal alpha4 beta2 (α4β2∗) and alpha7 (α7∗) nicotinic receptor levels in adult offspring. Female Sprague‐Dawley rats experienced unpredictable variable stressors two to three times daily during the last week of gestation. At weaning (21 days) the offspring of prenatally stressed (PS) and nonstressed (NS) dams were assigned to same‐sex PS or NS groups. In young adulthood (56 days), the brains of offspring were collected and adjacent sections processed for quantitative autoradiography using [125I]‐epibatidine (α4β2* nicotinic receptor‐selective) and [125I]‐α‐bungarotoxin (α‐BTX; α7* nicotinic receptor‐selective) ligands. We found that PS significantly increased hippocampal α4β2* nAChRs of males and females in all subfields analyzed. In contrast, only females showed a trend toward PS‐induced increases in α7* nAChRs in the dentate gyrus. Interestingly, NS females displayed a significant left‐biased lateralization of α7* nAChRs in the laconosum moleculare of area CA1, whereas PS females did not, suggesting that PS interfered with normal lateralization patterns of α7* nAChRs during development. Taken together, our results suggest that PS impacts the development of hippocampal nAChRs, which may be an important link between PS exposure and risk for neuropsychiatric illness. © 2013 Wiley Periodicals, Inc. Develop Neurobiol 73:806–814, 2013
Estimating home‐range size: when to include a third dimension?
Authors: Monterroso Pedro , Sillero Neftalí , Rosalino Luís Miguel , Loureiro Filipa , Alves Paulo Célio
Published: June 2013

Most studies dealing with home ranges consider the study areas as if they were totally flat, working only in two dimensions, when in reality they are irregular surfaces displayed in three dimensions. By disregarding the third dimension (i.e., topography), the size of home ranges underestimates the surface actually occupied by the animal, potentially leading to misinterpretations of the animals' ecological needs. We explored the influence of considering the third dimension in the estimation of home‐range size by modeling the variation between the planimetric and topographic estimates at several spatial scales. Our results revealed that planimetric approaches underestimate home‐range size estimations, which range from nearly zero up to 22%. The difference between planimetric and topographic estimates of home‐ranges sizes produced highly robust models using the average slope as the sole independent factor. Moreover, our models suggest that planimetric estimates in areas with an average slope of 16.3° (±0.4) or more will incur in errors ≥5%. Alternatively, the altitudinal range can be used as an indicator of the need to include topography in home‐range estimates. Our results confirmed that home‐range estimates could be significantly biased when topography is disregarded. We suggest that study areas where home‐range studies will be performed should firstly be scoped for its altitudinal range, which can serve as an indicator for the need for posterior use of average slope values to model the surface area used and/or available for the studied animals.
Pricing Vulnerable Options with Correlated Credit Risk Under Jump‐Diffusion Processes
Authors: Tian Lihui , Wang Guanying , Wang Xingchun , Wang Yongjin
Published: June 2013

This study extends the framework of Klein [Journal of Banking & Finance, 20, 1211–1229] to price vulnerable options. We provide a pricing model for vulnerable options which face not only default risk but also rare shocks encountered by the underlying asset and the assets of the counterparty. The dynamics of asset prices are governed by jump‐diffusions with two sorts of assets correlated with each other. Jumps are divided into idiosyncratic component for each asset price and systematic component affecting the prices of all assets. A closed‐form valuation formula is derived for vulnerable European options. Numerical analysis compares the results of this model with those of other pricing formulae, and illustrates jump effects on the vulnerable option prices. © 2013 Wiley Periodicals, Inc. Jrl Fut Mark 34:957–979, 2014
Future Arctic Ocean primary productivity from CMIP5 simulations: Uncertain outcome, but consistent mechanisms
Authors: Vancoppenolle Martin , Bopp Laurent , Madec Gurvan , Dunne John , Ilyina Tatiana , Halloran Paul R. , Steiner Nadja
Published: June 2013

Net Arctic Ocean primary production (PP) is expected to increase over this century, due to less perennial sea ice and more available light, but could decrease depending on changes in nitrate (NO3) supply. Here Coupled Model Intercomparison Project Phase 5 simulations performed with 11 Earth System Models are analyzed in terms of PP, surface NO3, and sea ice coverage over 1900–2100. Whereas the mean model simulates reasonably well Arctic‐integrated PP (511 TgC/yr, 1998–2005) and projects a mild 58 TgC/yr increase by 2080–2099 for the strongest climate change scenario, models do not agree on the sign of future PP change. However, similar mechanisms operate in all models. The perennial ice loss‐driven increase in PP is in most models NO3‐limited. The Arctic surface NO3 is decreasing over the 21st century (−2.3 ± 1 mmol/m3), associated with shoaling mixed layer and with decreasing NO3 in the nearby North Atlantic and Pacific waters. However, the intermodel spread in the degree of NO3 limitation is initially high, resulting from >1000 year spin‐up simulations. This initial NO3 spread, combined with the trend, causes a large variation in the timing of oligotrophy onset—which directly controls the sign of future PP change. Virtually all models agree in the open ocean zones on more spatially integrated PP and less PP per unit area. The source of model uncertainty is located in the sea ice zone, where a subtle balance between light and nutrient limitations determines the PP change. Hence, it is argued that reducing uncertainty on present Arctic NO3 in the sea ice zone would render Arctic PP projections much more consistent.
Extreme wave runup on a vertical cliff
Authors: Carbone Francesco , Dutykh Denys , Dudley John M. , Dias Frédéric
Published: June 2013

Wave impact and runup onto vertical obstacles are among the most important phenomena which must be taken into account in the design of coastal structures. From linear wave theory, we know that the wave amplitude on a vertical wall is twice the incident wave amplitude with weakly nonlinear theories bringing small corrections to this result. In this present study, however, we show that certain simple wave groups may produce much higher runups than previously predicted, with particular incident wave frequencies resulting in runup heights exceeding the initial wave amplitude by a factor of 5, suggesting that the notion of the design wave used in coastal structure design may need to be revisited. The results presented in this study can be considered as a note of caution for practitioners, on one side, and as a challenging novel material for theoreticians who work in the field of extreme wave‐coastal structure interaction.
The role of the geothermal heat flux in driving the abyssal ocean circulation
Authors: Mashayek A. , Ferrari R. , Vettoretti G. , Peltier W. R.
Published: June 2013

The results presented in this paper demonstrate that the geothermal heat flux (GHF) from the solid Earth into the ocean plays a non‐negligible role in determining both abyssal stratification and circulation strength. Based upon an ocean data set, we show that the map of upward heat flux at the ocean floor is consistent (within a factor of 2) with the ocean floor age‐dependent map of GHF. The observed buoyancy flux above the ocean floor is consistent with previous suggestions that the GHF acts to erode the abyssal stratification and thereby enhances the strength of the abyssal circulation. Idealized numerical simulations are performed using a zonally averaged single‐basin model which enables us to address the GHF impact as a function of the depth dependence of diapycnal diffusivity. We show that ignoring this vertical variation leads to an under‐prediction of the influence of the GHF on the abyssal circulation. Independent of the diffusivity profile, introduction of the GHF in the model leads to steepening of the Southern Ocean isopycnals and to strengthening of the eddy‐induced circulation and the Antarctic bottom water cell. The enhanced circulation ventilates the GHF derived heating to shallow depths, primarily in the Southern Ocean.
The Novaya Zemlya Bora and its impact on Barents Sea air‐sea interaction
Authors: Moore G. W. K.
Published: June 2013

Novaya Zemlya is a mountainous archipelago in the Eastern Arctic. Weather station data indicates that southeasterly high‐speed winds are frequent, especially during the winter. Although it has been proposed that a bora is responsible for these winds, there has been no quantitative analysis of the flow in the region. Here we present the first high‐resolution climatology of the three‐dimensional wind field near Novaya Zemlya. The high‐speed wind events are shown to share many characteristics with bora as well as models of downslope windstorms. The highest wind speeds occur where Barents Sea dense water is observed to form, and we show that there is a doubling in the turbulent heat transfer from the ocean to the atmosphere during bora. It is argued that the bora plays an important role in the transformation of the Atlantic water that passes by the archipelago en route to the central Arctic Ocean.
Volumetric analysis of medial temporal lobe subregions in developmental amnesia using high‐resolution magnetic resonance imaging
Authors: Olsen Rosanna K. , Palombo Daniela J. , Rabin Jennifer S. , Levine Brian , Ryan Jennifer D. , Rosenbaum R. Shayna
Published: June 2013

There is great interest in the cognitive consequences of hippocampal volume loss in developmental amnesia (DA). In many DA cases, volume loss occurs before the hippocampus is fully developed, and yet little is known about the locus, extent, and distribution of damage in these cases. We used high‐resolution MRI to manually segment the medial temporal lobe (MTL) subregions in H.C., an adult with DA, and a group of sex‐, age‐ and education‐matched control participants (n = 10). The hippocampus was defined and divided into anterior (head) and posterior (body and tail) segments. Within the body of the hippocampus, the subregions (CA1, DG/CA2/3, and subiculum) were defined. Finally, the entorhinal (ERC), perirhinal (PRC), and parahippocampal (PHC) cortices were segmented. Anterior hippocampus was reduced bilaterally and posterior hippocampus was significantly reduced on the right. In the body of the hippocampus, all three subregions were reduced in the left hemisphere, whereas CA1 and subiculum were reduced in the right hemisphere. No group differences were observed in the PRC and ERC, whereas left PHC volume was marginally increased in H.C. compared to controls. These results can be used to inform patterns of spared and impaired cognitive abilities in DA and perhaps in amnesia more generally. © The Authors. Hippocampus Published by Wiley Periodicals, Inc.
Patients undergoing lymphadenectomy for stage III melanomas of known or unknown primary site do not differ in outcome
Authors: Hughes Maria Celia , Wright Annaliesa , Barbour Andrew , Thomas Janine , Smithers B. Mark , Green Adele C. , Khosrotehrani Kiarash
Published: June 2013

The outcome of patients with palpable melanoma metastases in lymph nodes in the presence (metastatic melanoma of known primary site, MKP) or absence (metastatic melanoma of unknown primary site, MUP) of an identifiable primary tumour remains controversial. Some of the previous studies contained large case series that included historical patients. We aimed to compare outcomes of those with MUPs versus MKPs with palpable lymph node invasion, after staging with modern imaging technology. Aprospective study of patients from a single tertiary institution who were undergoing lymph node dissection for palpable metastatic melanoma between 2000 and 2011 was conducted. All patients were ascertained by computerised tomography scanning and most diagnosed after 2004 had positron emission tomography scanning also. Clinicopathological details about the primary melanoma and lymph node dissections were gathered. Factors associated with recurrence and melanoma‐specific mortality in those with MKP and with MUP were assessed using univariate and multivariate analyses. Out of 485 patients studied, 82 had MUP and 403 had MKP. Patients were followed up for a median of 17.4 and 19.0 months, for MKP and MUP, respectively. Five‐year adjusted melanoma‐specific survival was 58% for MUPs versus 49% for MKPs and was not significantly different between the two groups (adjusted Cox proportional Hazard ratio = 0.88 95% confidence interval [0.58, 1.33] p = 0.54). Previously established prognostic factors such as number of positive nodes and extracapsular extension were confirmed in both sets of patients. We conclude that among melanoma patients presenting with clinically detectable nodes, when accurately staged, those without an identifiable primary lesion have similar outcomes to patients with MKP.
Activation of C–H bond in methane by Pd atom from the bonding evolution theory perspective
Authors: Nizovtsev Anton S.
Published: June 2013

We report detailed study focused on the electron density redistribution during the simple oxidative addition reaction being the crucial stage of various catalytic processes. The bonding evolution theory based on the electron localization function and Thom's catastrophe theory shows that activation of methane's CH bond by Pd atom consist of six elementary steps. The important feature revealed is the pronounced reorganization of Pd's outer core maxima corresponding toN‐shell electrons of metal. Electronic rearrangements identified in this model reaction are likely to be the case in the more complex reactions of the same type involving transition metal compounds and, in principle, can be observed by modern ultrafast spectroscopy and diffraction techniques. © 2013 Wiley Periodicals, Inc.
Membrane fractionation of a β‐lactoglobulin tryptic digest: effect of the membrane characteristics
Authors: Fernández Ayoa , Zhu Yishen , FitzGerald Richard J. , Riera Francisco A.
Published: June 2013

BACKGROUND

Membrane separation technologies seem to be one of the best available techniques to fractionate protein hydrolysates containing bioactive peptides and obtain peptide fractions with increased functionality. The influence of the molecular weight cut‐off (MWCO) of the membrane and its hydrophilic/hydrophobic characteristics on the fractionation of a β‐lactoglobulin tryptic hydrolysate were studied in this research work in order to obtain more purified peptidic fractions.

RESULTS

The molecular weight of the solutes, their charge and, ultimately, their hydrophobicity influenced peptide transmission. As regards the composition of the active layer of the membrane, high permeate flux values were maintained throughout the pH working range (from pH 4.0 to pH 10.0) when an extremely hydrophilic membrane was employed, even in the presence of peptide aggregates at acidic pH values. In addition, the decrease in the MWCO of the membrane (from 5 kDa to 1 kDa) did not improve the selectivity of the fractionation process, however, it assumed a significant decrease of the permeate flux through the membrane.

CONCLUSION

The low efficiency of the process in terms of peptide recovery and the poor separation observed between bioactive and non‐bioactive peptides work against the use of extremely hydrophilic membranes to fractionate peptide hydrolysates. © 2013 Society of Chemical Industry
Gold nanorods as probes in two‐photon fluorescence correlation spectroscopy: Emerging applications and potential artifacts
Authors: Wang Da‐Shin , Wei Shih‐Chung , Liao Shih‐Chu , Lin Chii‐Wann
Published: June 2013

Owing to the highly efficient two‐photon fluorescence of gold nanorods and very short fluorescence lifetime compared with the rotational correlation time, the rotation and diffusion of a single gold nanorod can be easily observed by two‐photon fluorescence correlation spectroscopy (TP‐FCS). This property, along with the previous successful use as a contrast agent in two‐photon fluorescence imaging, suggests a potential application in TP‐FCS as well. Although the FCS measurement becomes highly efficient with gold nanorods as probes, the amplitude and temporal decay of the measured correlation functions depend critically on excitation power. Here, we investigate various photophysical processes of gold nanorods to determine the cause of such a sensitive power dependency. This understanding provides a basis for choosing appropriate FCS models to recover reasonable physical parameters. Although the correlation function amplitude G(0) is 32 times lower when the excitation power increases from 20 µW to 1.12 mW, the application of a saturation‐modified FCS model yields very good fit to each data set and the fitted concentration of 0.64 nM is comparable to the 0.7 nM given by the inductively coupled plasma mass spectrometry measurement. The FCS assay appears to be an efficient method for the quantification of gold nanorods when correctly interpreted. However, even with the saturation considered in the fitting model, the fitted rotational and translational diffusion rates are getting faster as the power increases. This indicates that other effects such as photothermal effects may raise the local temperature, and thus increasing the rotational and translational diffusion rate. Microsc. Res. Tech. 76:882–889, 2013. © 2013 Wiley Periodicals, Inc.
Distinction between auroral substorm onset and traditional ground magnetic onset signatures
Authors: Lyons L. R. , Nishimura Y. , Donovan E. , Angelopoulos V.
Published: June 2013

To evaluate whether ground magnetic responses traditionally viewed as signatures of substorm onset may be related to postonset auroral streamers rather than to substorm onset seen in aurora, we have analyzed ground magnetic and all‐sky image responses for 14 substorm onsets selected solely on imager coverage. We find evidence supporting this possibility, the response being approximately coincident for midlatitude positive bay and Pi2 pulsation enhancements and for abrupt auroral zone H decreases at stations near a streamer. These are all signatures of current wedge formation, indicating that substorm current wedge formation may be more of a response to plasma sheet flow channels associated with postonset streamers than to the process leading to auroral onset and that the current wedge may develop via a series of distinctly narrower wedge‐like structures. We also find evidence that periods of streamers can occur more than once during a substorm expansion phase and can give magnetic signatures of multiple onsets even if there are no additional auroral onsets. Furthermore, the peak auroral zone H decreases are seen in association with streamers and at times varying from just a few minutes to well over a half hour after substorm auroral onset if there is a prolonged period of streamers. This indicates that peak substorm AE and AL values are likely related to features of postonset streamers and their locations relative to observing stations and are not a measure of the strength of the substorm auroral onset processes. We discuss possible additional implications on substorm expansion phase development.
The radar tropopause at 78°N, 16°E: Characteristics of diurnal variation
Authors: Hall C. M.
Published: June 2013

A continuous 5 year time series of tropopause altitude made by the SOUSY VHF radar on Svalbard (78°N, 16°E) is examined for diurnal variation. The data have a nominal time resolution of 1 h, allowing for investigation of intraday timescales not normally possible using radiosonde observations. Periodicities identified in tropopause altitude are found to vary with season. Surface air temperature measurements naturally exhibit diurnal variations which depend on season: however, it is demonstrated that, using a simple scenario of constant adiabatic lapse rate in the troposphere, the tropopause altitude variation that might be anticipated from that of the surface air temperature is not in agreement with the radar observation. Of several mechanisms that could be postulated for this discrepancy, it is demonstrated that a likely candidate is intraday top‐down forcing from the stratosphere.
Speciation of “brown” carbon in cloud water impacted by agricultural biomass burning in eastern China
Authors: Desyaterik Yury , Sun Yele , Shen Xinhua , Lee Taehyoung , Wang Xinfeng , Wang Tao , Collett Jeffrey L.
Published: June 2013

Despite growing interest in the visible light‐absorbing organic component of atmospheric aerosols, referred to as “brown” carbon, our knowledge of its chemical composition remains limited. It is well accepted that biomass burning is one important source of “brown” carbon in the atmosphere. In this study, cloud water samples heavily affected by biomass burning were collected at Mount Tai (1534 m, ASL), located in Shandong province in the North China Plain in summer 2008. The samples were analyzed with high performance liquid chromatography equipped with a UV/Vis absorbance detector immediately followed by electrospray ionization and analysis using a time‐of‐flight (ToF) mass spectrometer. The high mass resolution and accuracy provided by the ToF mass spectrometer allow determination of the elemental composition of detected ions. Using this approach, the elemental compositions of 16 major light‐absorbing compounds, which together accounted for approximately half of measured sample absorption between 300 and 400 nm, were determined. The most important classes of light‐absorbing compounds were found to be nitrophenols and aromatic carbonyls. Light absorption over this wavelength range by reduced nitrogen compounds was insignificant in these samples.
Non‐negligible effects of cloud vertical overlapping assumptions on longwave spectral fingerprinting studies
Authors: Chen Xiuhong , Huang Xianglei , Liu Xu
Published: June 2013

In order to monitor and attribute secular changes from outgoing spectral radiances, spectral fingerprints need to be constructed first. Large‐scale model outputs are usually used to derive such spectral fingerprints. Different models make different assumptions on vertical overlapping of subgrid clouds. We explore the extent to which the spectral fingerprints constructed under different cloud vertical overlapping assumptions can affect such spectral fingerprinting studies. Utilizing a principal component‐based radiative transfer model with high computational efficiency, we build an OSSE (Observing System Simulation Experiment) with full treatment of subgrid cloud variability to study this issue. We first show that the OLR (outgoing longwave radiation) computed from this OSSE is consistent with the OLR directly output from the parent large‐scale models. We then examine the differences in spectral fingerprints due to cloud overlapping assumptions alone. Different cloud overlapping assumptions have little effect on the spectral fingerprints of temperature and humidity. However, the amplitude of the spectral fingerprints due to the same amount of cloud fraction change can differ as much as a factor of two between maximum random versus random overlap assumptions, especially for middle and low clouds. We further examine the impact of cloud overlapping assumptions on the results of linear regression of spectral differences with respect to predefined spectral fingerprints. Cloud‐relevant regression coefficients are affected more by different cloud overlapping assumptions than regression coefficients of other geophysical variables. These findings highlight the challenges in constructing realistic longwave spectral fingerprints and in detecting climate change using all‐sky observations.
Alternative ways of using field‐based estimates to calibrate ecosystem models and their implications for carbon cycle studies
Authors: He Yujie , Zhuang Qianlai , David McGuire A. , Liu Yaling , Chen Min
Published: June 2013

Model‐data fusion is a process in which field observations are used to constrain model parameters. How observations are used to constrain parameters has a direct impact on the carbon cycle dynamics simulated by ecosystem models. In this study, we present an evaluation of several options for the use of observations in modeling regional carbon dynamics and explore the implications of those options. We calibrated the Terrestrial Ecosystem Model on a hierarchy of three vegetation classification levels for the Alaskan boreal forest: species level, plant‐functional‐type level (PFT level), and biome level, and we examined the differences in simulated carbon dynamics. Species‐specific field‐based estimates were directly used to parameterize the model for species‐level simulations, while weighted averages based on species percent cover were used to generate estimates for PFT‐ and biome‐level model parameterization. We found that calibrated key ecosystem process parameters differed substantially among species and overlapped for species that are categorized into different PFTs. Our analysis of parameter sets suggests that the PFT‐level parameterizations primarily reflected the dominant species and that functional information of some species were lost from the PFT‐level parameterizations. The biome‐level parameterization was primarily representative of the needleleaf PFT and lost information on broadleaf species or PFT function. Our results indicate that PFT‐level simulations may be potentially representative of the performance of species‐level simulations while biome‐level simulations may result in biased estimates. Improved theoretical and empirical justifications for grouping species into PFTs or biomes are needed to adequately represent the dynamics of ecosystem functioning and structure.
CHOP‐mediated hepcidin suppression modulates hepatic iron load
Authors: Mueller Katrin , Sunami Yoshiaki , Stuetzle Michael , Guldiken Nurdan , Kucukoglu Ozlem , Mueller Sebastian , Kulaksiz Hasan , Schwarz Peggy , Strnad Pavel
Published: June 2013

The liver is the central regulator of iron metabolism and accordingly, chronic liver diseases often lead to systemic iron overload due to diminished expression of the iron‐regulatory hormone hepcidin. To study the largely unknown regulation of iron metabolism in the context of hepatic disease, we used two established models of chronic liver injury, ie repeated carbon tetrachloride (CCl4) or thioacetamide (TAA) injections. To determine the impact of CCAAT/enhancer‐binding protein (C/EBP)‐homologous protein (CHOP) on hepcidin production, the effect of a single TAA injection was determined in wild‐type and CHOP knockout mice. Furthermore, CHOP and hepcidin expression was assessed in control subjects and patients with alcoholic liver disease. Both chronic injury models developed a distinct iron overload in macrophages. TAA‐, but not CCl4‐ injected mice displayed additional iron accumulation in hepatocytes, resulting in a significant hepatic and systemic iron overload which was due to suppressed hepcidin levels. C/EBPα signalling, a known hepcidin inducer, was markedly inhibited in TAA mice, due to lower C/EBPα levels and overexpression of CHOP, a C/EBPα inhibitor. A single TAA injection resulted in a long‐lasting (> 6 days) suppression of hepcidin levels and CHOP knockouts (compared to wild‐types) displayed significantly attenuated hepcidin down‐regulation in response to acute TAA administration. CHOP mRNA levels increased 5‐fold in alcoholic liver disease patients versus controls (p < 0.005) and negatively correlated with hepcidin expression. Our results establish CHOP as an important regulator of hepatic hepcidin expression in chronic liver disease. The differences in iron metabolism between the two widely used fibrosis models likely reflect the differential regulation of hepcidin expression in human liver disease. Copyright © 2013 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Seasonal impact in the frequency of isolated spina bifida
Authors: Giardini Valentina , Russo Francesca Maria , Ornaghi Sara , Todyrenchuk Lyudmyla , Vergani Patrizia
Published: June 2013

Objectives

To evaluate whether a relationship exists between season at conception and occurrence of isolated spina bifida (ISB).

Study design

All fetuses with prenatal diagnosis of ISB were analyzed according to date of conception. We compared the seasonal rates of conception between ISB fetuses and a control group consisting of a cohort of fetuses delivered during the same period from 1992 to 2009.

Results

In the control group, conceptions were equally distributed among the four seasons. Chi‐square analysis showed a significantly higher rate of ISB conceptions in the fall compared with the control group (16/36, 44% vs 12467/50533, 25%, Odds Ratio (OR) 2.44, 95% confidence interval 1.21–4.92). Not a single woman with a fetus affected by ISB took preconceptional supplement of folic acid.

Conclusions

Seasonality affects the frequency of ISB. We hypothesize that the seasonal differences may reflect dietary and climate changes with reduced intake of folic acid in the fall. © 2013 John Wiley & Sons, Ltd.
Factors associated with adherence to physical activity guidelines in patients with prostate cancer
Authors: Chipperfield Kelly , Fletcher Jane , Millar Jeremy , Brooker Joanne , Smith Robin , Frydenberg Mark , Oh Tracy , Burney Sue
Published: June 2013

Objective

This study aimed to estimate the proportion of patients with prostate cancer (PCa) meeting the National Physical Activity Guidelines of Australia (NPAGA) and determine sociodemographic and medical factors associated with meeting these guidelines. Secondary aims included examining physical activity (PA) levels by treatment type and domain (leisure, work, transport and domestic) and establishing a predictive model of the likelihood that men with PCa would meet NPAGA.

Methods

A questionnaire was mailed to 638 men with PCa attending for treatment at the Alfred, Cabrini or Latrobe Regional Hospitals during 2010 and 2011, with a response rate of 59%. Measures included International Physical Activity Questionnaire, Hospital Anxiety and Depression Scale, Functional Assessment of Cancer Therapy – Prostate and sociodemographic items. Inclusion criteria were English speaking men aged 40 to 80 years, who had undergone radiotherapy (RT) between 9 and 30 months prior to the survey.

Results

Of 356 men with PCa, less than half were meeting NPAGA (41.9%). Lower education and quality of life (QoL), a higher number of comorbid conditions and symptoms of depression and anxiety were associated with decreased leisure‐time PA. Patients treated with androgen deprivation therapy were significantly less active than patients treated with RT only. Logistic regression analyses indicated that the likelihood of meeting NPAGA was significantly lower with higher levels of depressive symptoms and lower levels of education.

Conclusions

Meeting NPAGA is associated with higher QoL and psychosocial well‐being in men with PCa. These findings contribute important information for targeting PA interventions to PCa survivors. Copyright © 2013 John Wiley & Sons, Ltd.
Young breast cancer patients' involvement in treatment decisions: the major role played by decision‐making about surgery
Authors: Seror Valérie , Cortaredona Sébastien , Bouhnik Anne‐Deborah , Meresse Mégane , Cluze Camille , Viens Patrice , Rey Dominique , Peretti‐Watel Patrick
Published: June 2013

Objective

The objective of this study is to investigate young breast cancer patients' preferred and actual involvement in decision‐making about surgery, chemotherapy, and adjuvant endocrine therapy (AET).

Methods

A total of 442 women aged 18–40 years at the time of the diagnosis participated in the region‐wide ELIPPSE40 cohort study (southeastern France). Logistic regression analyses were performed on various factors possibly affecting patients' preferred and perceived involvement in the decisions about their cancer treatment.

Results

The women's mean age was 36.8 years at enrolment. Preference for a fully passive role in decision‐making was stated by 20.7% of them. It was favored by regular breast surveillance (p = 0.04) and positive experience of being informed about cancer diagnosis (p = 0.02). Patients' preferences were independently associated with their reported involvement in decision‐making about surgery (p = 0.01). A fully passive role in decision‐making about chemotherapy and AET was more likely to be reported by patients who perceived their involvement in decision‐making about surgery as having been fully passive (adjusted odds ratio = 4.8, CI95% [2.7–8.7], and adjusted odds ratio = 9.8, CI95% [3.3–29.2], respectively). This study shows a significant relationship between the use of antidepressants and involvement in decision‐making about surgery, and confirms the relationship between impaired quality of life (in the psychological domain) and a fully passive role in decisions about cancer treatment.

Conclusions

Patients' involvement in decision‐making about chemotherapy and AET was strongly influenced by their experience of decision‐making about surgery, regardless of their tumor stage and history of breast or ovarian cancer. When decisions are being made about surgery, special attention should be paid to facilitating breast cancer patients' involvement in the decision‐making. Copyright © 2013 John Wiley & Sons, Ltd.
Spiritual well‐being in long‐term colorectal cancer survivors with ostomies
Authors: Bulkley Joanna , McMullen Carmit K. , Hornbrook Mark C. , Grant Marcia , Altschuler Andrea , Wendel Christopher S. , Krouse Robert S.
Published: June 2013

Objective

Spiritual well‐being (SpWB) is integral to health‐related quality of life. The challenges of colorectal cancer (CRC) and subsequent bodily changes can affect SpWB. We analyzed the SpWB of CRC survivors with ostomies.

Methods

Two‐hundred‐eighty‐three long‐term (≥5 years) CRC survivors with permanent ostomies completed the modified City of Hope Quality of Life‐Ostomy (mCOH‐QOL‐O) questionnaire. An open‐ended question elicited respondents' greatest challenge in living with an ostomy. We used content analysis to identify SpWB responses and develop themes. We analyzed responses on the three‐item SpWB sub‐scale.

Results

Open‐ended responses from 52% of participants contained SpWB content. Fifteen unique SpWB themes were identified. Sixty percent of individuals expressed positive themes such as “positive attitude”, “I am fortunate”, “appreciate life more”, and “strength through religious faith”. Negative themes, expressed by only 29% of respondents, included “struggling to cope”, “not feeling ‘normal’ ”, and “loss”. Fifty‐five percent of respondents expressed ambivalent themes including “learning acceptance”, “an ostomy is the price for survival”, “reason to be around despite suffering”, and “continuing to cope despite challenges”. The majority (64%) had a high SpWB sub‐scale score.

Conclusions

Although CRC survivors with ostomies infrequently mentioned negative SpWB themes as a major challenge, ambivalent themes were common. SpWB themes were often mentioned as a source of resilience or part of the struggle to adapt to an altered body after cancer surgery. Interventions to improve the quality of life of cancer survivors should contain program elements designed to address SpWB that support personal meaning, inner peace, inter connectedness, and belonging. Copyright © 2013 John Wiley & Sons, Ltd.
Electronic confinement effects on the reaction field type calculations of solvent effects
Authors: García Victor , Zorrilla David , Fernández Manuel
Published: June 2013

We analyze some procedures to introduce the effect of confining the electrons of the hydrogen atoms in cavitation spheres like those used in the self‐consistent reaction field models for studying the solvent influence on molecular properties [as polarizable continuum model (PCM), or conductor screening model (COSMO)]. We have found that the boundary conditions to be applied have an important effect on the system energy that by no means should be neglected in this type of calculations. We have found as well that “‐nG” expansion technique could be applicable in this kind of calculations (even at the very simple “‐3G” level) and lead us to a relatively simple form of applying the theory. Moreover, we have found a way to define the cavitation radius of PCM calculations, by minimizing the system energy with respect to this parameter, which could be a more satisfactory procedure—at least from a theoretical point of view—than the use of empirical values characteristic of most of the PCM or COSMO standard calculations. © 2013 Wiley Periodicals, Inc.
Statistical modeling of daily and subdaily stream temperatures: Application to the Methow River Basin, Washington
Authors: Caldwell R. J. , Gangopadhyay S. , Bountry J. , Lai Y. , Elsner M. M.
Published: June 2013

Management of water temperatures in the Columbia River Basin (Washington) is critical because water projects have substantially altered the habitat of Endangered Species Act listed species, such as salmon, throughout the basin. This is most important in tributaries to the Columbia, such as the Methow River, where the spawning and rearing life stages of these cold water fishes occurs. Climate change projections generally predict increasing air temperatures across the western United States, with less confidence regarding shifts in precipitation. As air temperatures rise, we anticipate a corresponding increase in water temperatures, which may alter the timing and availability of habitat for fish reproduction and growth. To assess the impact of future climate change in the Methow River, we couple historical climate and future climate projections with a statistical modeling framework to predict daily mean stream temperatures. A K‐nearest neighbor algorithm is also employed to: (i) adjust the climate projections for biases compared to the observed record and (ii) provide a reference for performing spatiotemporal disaggregation in future hydraulic modeling of stream habitat. The statistical models indicate the primary drivers of stream temperature are maximum and minimum air temperature and stream flow and show reasonable skill in predictability. When compared to the historical reference time period of 1916–2006, we conclude that increases in stream temperature are expected to occur at each subsequent time horizon representative of the year 2020, 2040, and 2080, with an increase of 0.8 ± 1.9°C by the year 2080.
Perceived Versus Predicted Risks of Colorectal Cancer and Self‐Reported Colonoscopies by Members of Mismatch Repair Gene Mutation‐Carrying Families Who Have Declined Genetic Testing
Authors: Flander Louisa , Speirs‐Bridge Andrew , Rutstein Alison , Niven Heather , Win Aung Ko , Ait Ouakrim Driss , Hopper John L. , Macrae Finlay , Keogh Louise , Gaff Clara , Jenkins Mark
Published: June 2013

People carrying germline mutations in mismatch repair genes are at high risk of colorectal cancer (CRC), yet about half of people from mutation‐carrying families decline genetic counselling and/or testing to identify mutation status. We studied the association of quantitative measures of risk perception, risk prediction and self‐reported screening colonoscopy in this elusive yet high‐risk group. The sample of 26 participants (mean age 43.1 years, 14 women) in the Australasian Colorectal Cancer Family Registry were relatives of mutation carriers; had not been diagnosed with any cancer at the time of recruitment and had declined an invitation to attend genetic counselling and/or testing. A structured elicitation protocol captured perceived CRC risk over the next 10 years. Self‐reported colonoscopy screening was elicited during a 45‐minute semi‐structured interview. Predicted 10‐year CRC risk based on age, gender, known mutation status and family history was calculated using “MMRpro.” Mean perceived 10‐year risk of CRC was 31 % [95 % CI 21, 40], compared with mean predicted risk of 4 % [2, 7] (p < 0.001); this was independent of age and sex (p = 0.9). Among those reporting any medical advice and any screening colonoscopy (n = 18), those with higher risk perception had less frequent colonoscopy (Pearson's r = 0.49 [0.02, 0.79]). People who decline genetic testing for CRC susceptibility mutations perceive themselves to be at substantially higher risk than they really are. Those with high perceived risk do not undertake screening colonoscopy more often than those who perceive themselves to be at average risk.
Knowledge of and Interest in Genetic Results Among Parkinson Disease Patients and Caregivers
Authors: Sakanaka Karina , Waters Cheryl H. , Levy Oren A. , Louis Elan D. , Chung Wendy K. , Marder Karen S. , Alcalay Roy N.
Published: June 2013

The purpose of the study is to investigate Parkinson disease (PD) patients’ and caregivers’ knowledge of and interest in genetic testing. Gaucher disease (GD) results from recessive mutations in glucocerebrosidase (GBA). Both heterozygote GBA carriers and GD patients are at greater risk for PD. Studies regarding knowledge of and interest in genetic testing have been limited and have not offered genetic results to participants. In this study, 353 PD patients and 180 caregivers were recruited to a PD genetic study. The association between GD, GBA mutations and PD was described to participants who reported their familiarity with genetic terms, answered questions on genetic concepts, and indicated their interest in knowing if they may have GD (two GBA mutations) and other genetic information that could impact their health. Ninety‐three‐percent of participants were interested in receiving GBA results; however, only 51.6 % of PD participants and 55.6 % of caregivers knew that “scientists have identified genes associated with a higher risk of developing PD.” PD patients may benefit from education and genetic counseling on the implications of genetic testing.
Crystal structure of a putative aspartic proteinase domain of the Mycobacterium tuberculosis cell surface antigen PE_PGRS16
Authors: Barathy Deivanayaga V. , Suguna Kaza
Published: June 2013

We report the crystal structure of the first prokaryotic aspartic proteinase‐like domain identified in the genome of Mycobacterium tuberculosis. A search in the genomes of Mycobacterium species showed that the C‐terminal domains of some of the PE family proteins contain two classic DT/SG motifs of aspartic proteinases with a low overall sequence similarity to HIV proteinase. The three‐dimensional structure of one of them, Rv0977 (PE_PGRS16) of M. tuberculosis revealed the characteristic pepsin‐fold and catalytic site architecture. However, the active site was completely blocked by the N‐terminal His‐tag. Surprisingly, the enzyme was found to be inactive even after the removal of the N‐terminal His‐tag. A comparison of the structure with pepsins showed significant differences in the critical substrate binding residues and in the flap tyrosine conformation that could contribute to the lack of proteolytic activity of Rv0977.
A method of determining RNA conformational ensembles using structure-based calculations of residual dipolar couplings
Authors: Borkar Aditi N. , De Simone Alfonso , Montalvao Rinaldo W. , Vendruscolo Michele
Published: June 2013

We describe a method of determining the conformational fluctuations of RNA based on the incorporation of nuclear magnetic resonance (NMR) residual dipolar couplings (RDCs) as replica-averaged structural restraints in molecular dynamics simulations. In this approach, the alignment tensor required to calculate the RDCs corresponding to a given conformation is estimated from its shape, and multiple replicas of the RNA molecule are simulated simultaneously to reproduce in silico the ensemble-averaging procedure performed in the NMR measurements. We provide initial evidence that with this approach it is possible to determine accurately structural ensembles representing the conformational fluctuations of RNA by applying the reference ensemble test to the trans-activation response element of the human immunodeficiency virus type 1.
Analyzing luminescent solar concentrators with front-facing photovoltaic cells using weighted Monte Carlo ray tracing
Authors: Woei Leow Shin , Corrado Carley , Osborn Melissa , Isaacson Michael , Alers Glenn , Carter Sue A.
Published: June 2013

Luminescent solar concentrators (LSC) collect ambient light from a broad range of angles and concentrate the captured light onto photovoltaic (PV) cells. LSCs with front-facing cells collect direct and indirect sunlight ensuring a gain factor greater than one. The flexible placement and percentage coverage of PV cells on the LSC panel allow for layout adjustments to be made in order to balance re-absorption losses and the level of light concentration desired. A weighted Monte Carlo ray tracing program was developed to study the transport of photons and loss mechanisms in the LSC to aid in design optimization. The program imports measured absorption/emission spectra of an organic luminescent dye (LR305), the transmission coefficient, and refractive index of acrylic as parameters that describe the system. Simulations suggest that for LR305, 8–10 cm of luminescent material surrounding the PV cell yields the highest increase in power gain per unit area of LSC added, thereby determining the ideal spacing between PV cells in the panel. For rectangular PV cells, results indicate that for each centimeter of PV cell width, an additional increase of 0.15 mm to the waveguide thickness is required to efficiently transport photon collected by the LSC to the PV cell with minimal loss.