bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficient semiparametric mixture inferences on cure rate models for competing risks
Authors: Choi Sangbum , Huang Xuelin , Cormier Janice N.
Published: July 2015

Cancer patients may die from causes other than the diagnosed cancer. In a study of patients treated for soft tissue sarcoma, the patients may die from the disease or die without experiencing disease recurrence. In addition, a substantial proportion of the patients will remain cancer‐free after surgical resection of the tumour, and therefore will not be at increased risk of any type of failure. Our goal is to describe the effect of adjuvant chemotherapy simultaneously on the probabilities of long‐term survival, death from cancer, or death from other causes. To this end, we propose a semiparametric mixture model to determine the effects of factors on the probability of occurrence, allowing the surviving fraction, and the hazard rate conditional on each of the failure types. These quantities are combined in the mixture approach using a multinomial logistic model and a class of semiparametric transformation models. Estimation of the regression and nonparametric parameters is achieved with a novel nonparametric maximum likelihood approach. Statistical inferences can be conveniently made from the inverse of the observed information matrix. Simulation studies show that the procedures work well in practical settings. The methodology is illustrated with data from the soft tissue sarcoma study. The Canadian Journal of Statistics 43: 420–435; 2015 © 2015 Statistical Society of Canada
Synthesis, Structure, and Photoluminescence Properties of Novel KBaSc2(PO4)3:Ce3+/Eu2+/Tb3+ Phosphors for White‐Light‐Emitting Diodes
Authors: Jiao Mengmeng , Lü Wei , Shao Baiqi , Zhao Lingfei , You Hongpeng
Published: July 2015

A series of novel KBaSc2(PO4)3:Ce3+/Eu2+/Tb3+phosphors are prepared using a solid‐state reaction. X‐ray diffraction analysis and Rietveld structure refinement are used to check the phase purity and crystal structure of the prepared samples. Ce3+‐ and Eu2+‐doped phosphors both have broad excitation and emission bands, owing to the spin‐ and orbital‐allowed electron transition between the 4f and 5d energy levels. By co‐doping the KBaSc2(PO4)3:Eu2+ and KBaSc2(PO4)3:Ce3+ phosphors with Tb3+ ions, tunable colors from blue to green can be obtained. The critical distance between the Eu2+ and Tb3+ ions is calculated by a concentration quenching method and the energy‐transfer mechanism for Eu2+→Tb3+ is studied by utilizing the Inokuti–Hirayama model. In addition, the quantum efficiencies of the prepared samples are measured. The results indicate that KBaSc2(PO4)3:Eu2+,Tb3+ and KBaSc2(PO4)3:Ce3+,Tb3+ phosphors might have potential applications in UV‐excited white‐light‐emitting diodes.
Different Perspectives of Clinicians and Patients with Severe Mental Illness on Motivation for Treatment
Authors: Jochems Eline C. , van Dam Arno , Duivenvoorden Hugo J. , Scheffer Sylvia C. M. , van der Feltz‐Cornelis Christina M. , Mulder Niels L.
Published: July 2015

The present study assessed motivation for engaging in treatment as rated by clinicians (n = 57) and patients with severe mental illness (SMI, n = 294) using measures based on three different motivation theories. Questionnaires were derived from self‐determination theory, the transtheoretical model and the integral model of treatment motivation. It was investigated to which extent clinicians of patients with SMI were able to estimate their patient's perspective on motivation for engaging in treatment, to which extent they agreed on the patient's motivation and which factors were associated with estimation and agreement on treatment motivation. It was found that clinicians were poorly to moderately capable of estimating their patient's type of motivation and readiness for change. Further, agreement on the level of motivation between patients and clinicians was moderate. These findings were consistent across diagnostic groups (psychotic and personality disorders). A higher quality therapeutic relationship was generally associated with higher clinician‐rated motivation. The patient's ethnicity and socially desirable responding were factors that differentiated between scales of different motivation theories. It is concluded that patients with SMI and their clinicians have different perceptions on the patient's motivation for engaging in psychiatric treatment, regardless of the theoretical framework that is used to measure motivation. The findings imply that a negotiated approach is needed where both perceptions of clinicians and patients on motivation for treatment are considered to ensure effective mental health interventions. Copyright © 2015 John Wiley & Sons, Ltd.

Key Practitioner Message

Clinicians show poor to moderate capability in estimating how patients perceive their motivation for engaging in treatment, especially so when the patient's motives revolve around feelings of shame and guilt.

Clinicians generally give higher motivation ratings for patients where they experience a higher quality therapeutic relationships with, whereas—depending on the scale that is used to measure motivation—they give lower ratings to patients who respond in socially desirable ways and to ethnic minority patients.

As patients with SMI and their clinicians have different perceptions on the patient's motivation for engaging in psychiatric treatment (regardless of the theoretical framework that is used to assess motivation), this implies that a negotiated approach is needed where both perceptions of clinicians and patients on motivation for treatment are considered to ensure effective mental health interventions.
Design of a ZVS PWM DC–DC converter for high gain applications
Authors: Javidan Javad
Published: July 2015

In this paper, a pulse width modulation DC‐DC converter with high step‐up voltage gain is proposed. The proposed converter achieves high step‐up voltage gain with appropriate duty ratio, coupled inductor, and voltage multiplier technique. The energy stored in the leakage inductor of the coupled inductor can be recycled in the proposed converter. Moreover, because both main and auxiliary switches can be turned on with zero‐voltage switching, switching loss can be reduced by soft‐switching technique. So the overall conversion efficiency is improved significantly. The theoretical steady‐state analyses and the operating principles of the proposed converter are discussed in detail for both continuous conduction mode and discontinuous conduction mode. Finally, a laboratory prototype circuit of the proposed converter is implemented to verify the performance of the proposed converter. Copyright © 2015 John Wiley & Sons, Ltd.
Flow cytometric measurement of respiratory burst activity and surface expression of neutrophils for septic patient prognosis
Authors: Bae Mi Hyun , Park So Hee , Park Chan‐Jeoung , Cho Eun‐Jung , Lee Bo‐Ra , Kim Young Jin , Park Sang Hyuk , Cho Young‐Uk , Jang Seongsoo , Song Dong‐Keun , Hong Sang‐Bum
Published: July 2015

Background

The hyperinflammation that begins with sepsis is essential for eradicating infection but also causes hypoperfusion and organ failure. To understand the innate immune status of septic patients, the functional and phenotypic changes of neutrophils during sepsis and their clinical implication were studied.

Methods

Seventy‐four patients who were admitted to intensive care unit due to severe sepsis or septic shock were enrolled. Surface antigens of neutrophils (CD64, CD10, and CD16) were detected by flow cytometry. Respiratory burst activity (RBA) was measured by flow cytometry using 2′,7′‐dichlorofluorescein diacetate and phorbol‐12‐myristate‐13‐acetate. The parameters were serially examined at Days 1 and 8 in septic shock patients.

Results

High CD64 and low CD10 and CD16 on Day 1 was associated with sepsis severity (P = 0.003, 0.017, and 0.007, respectively). On Day 1, RBA and CD64 were higher in survivors than in nonsurvivors of septic shock patients (P = 0.012 and 0.027, respectively), and on Day 8, CD10 and CD16 were higher in survivors than in nonsurvivors (P = 0.019 and 0.036, respectively). High RBA and high CD64 on Day 1 showed low 28‐day mortality in univariate analysis (P = 0.018 and 0.034, respectively). In multivariate analysis, RBA maintained statistical significance (P = 0.042) but CD64 revealed only a tendency (P = 0.064).

Conclusions

Neutrophil surface antigen (CD64, CD10, and CD16) could reflect sepsis severity. High CD64 expression and high RBA at early phase of sepsis might be associated with better prognosis, whereas high expression of CD10 and CD16 at late phase of sepsis might be associated with better prognosis. © 2015 International Clinical Cytometry Society
Dose‐dependent testosterone sensitivity of the steroidal passport and GC‐C‐IRMS analysis in relation to the UGT2B17 deletion polymorphism
Authors: Strahm Emmanuel , Mullen Jenny E. , Gårevik Nina , Ericsson Magnus , Schulze Jenny J. , Rane Anders , Ekström Lena
Published: July 2015

The newly implemented Steroid Module of the Athlete Biological Passport has improved doping tests for steroids. A biomarker included in this passport is the urinary testosterone glucuronide to epitestosterone glucuronide (T/E) ratio, a ratio greatly affected by a deletion polymorphism in UGT2B17. Suspect urine doping tests are further analyzed with gas chromatography‐combustion‐isotope ratio mass spectrometry (GC‐C‐IRMS) to determine the origin of the androgen. In this study, we investigated the sensitivity of the steroidal module and the IRMS analysis, in subjects administered with three doses of testosterone enanthate (500, 250, and 125 mg), in relation to the UGT2B17 polymorphism. All subjects carrying the UGT2B17 enzyme reached the traditionally used threshold, a T/E ratio of 4, after all three administered doses, whereas none of the subjects devoid of this enzyme reached a T/E of 4. On the other hand, using the athlete biological passport and IRMS analysis, all three doses could be detected to a high degree of sensitivity. The concentrations of all steroids included in the steroidal module were dose dependently increased, except for epitestosterone which decreased independent of dose. The decrease in epitestosterone was significantly associated with circulatory levels of testosterone post dose (rs=0.60 and p=0.007). In conclusion, these results demonstrate that administration of a single dose of 125–500 mg testosterone enanthate could be detected using the athlete biological passport, together with IRMS. Since IRMS is sensitive to testosterone doping independent of UGT2B17 genotype, also very small changes in the steroidal passport should be investigated with IRMS. Copyright © 2015 John Wiley & Sons, Ltd.
Investigation of the composition of anabolic tablets using near infrared spectroscopy and Raman chemical imaging
Authors: Rebiere Hervé , Ghyselinck Céline , Lempereur Laurent , Brenier Charlotte
Published: July 2015

The use of performance enhancing drugs is a widespread phenomenon in professional and leisure sports. A spectroscopic study was carried out on anabolic tablets labelled as 5 mg methandienone tablets provided by police departments. The analytical approach was based on a two‐step methodology: a fast analysis of tablets using near infrared (NIR) spectroscopy to assess sample homogeneity based on their global composition, followed by Raman chemical imaging of one sample per NIR profile to obtain information on sample formulation. NIR spectroscopy assisted by a principal components analysis (PCA) enabled fast discrimination of different profiles based on the excipient formulation. Raman hyperspectral imaging and multivariate curve resolution – alternating least square (MCR‐ALS) provided chemical images of the distribution of the active substance and excipients within tablets and facilitated identification of the active compounds. The combination of NIR spectroscopy and Raman chemical imaging highlighted dose‐to‐dose variations and succeeded in the discrimination of four different formulations out of eight similar samples of anabolic tablets. Some samples contained either methandienone or methyltestosterone whereas one sample did not contain an active substance. Other ingredients were sucrose, lactose, starch or talc. Both techniques were fast and non‐destructive and therefore can be carried out as exploratory methods prior to destructive screening methods. Copyright © 2015 John Wiley & Sons, Ltd.
The arabidopsis information resource: Making and mining the “gold standard” annotated reference plant genome
Authors: Berardini Tanya Z. , Reiser Leonore , Li Donghui , Mezheritsky Yarik , Muller Robert , Strait Emily , Huala Eva
Published: July 2015

The Arabidopsis Information Resource (TAIR) is a continuously updated, online database of genetic and molecular biology data for the model plant Arabidopsis thaliana that provides a global research community with centralized access to data for over 30,000 Arabidopsis genes. TAIR's biocurators systematically extract, organize, and interconnect experimental data from the literature along with computational predictions, community submissions, and high throughput datasets to present a high quality and comprehensive picture of Arabidopsis gene function. TAIR provides tools for data visualization and analysis, and enables ordering of seed and DNA stocks, protein chips, and other experimental resources. TAIR actively engages with its users who contribute expertise and data that augments the work of the curatorial staff. TAIR's focus in an extensive and evolving ecosystem of online resources for plant biology is on the critically important role of extracting experimentally based research findings from the literature and making that information computationally accessible. In response to the loss of government grant funding, the TAIR team founded a nonprofit entity, Phoenix Bioinformatics, with the aim of developing sustainable funding models for biological databases, using TAIR as a test case. Phoenix has successfully transitioned TAIR to subscription‐based funding while still keeping its data relatively open and accessible. genesis 53:474–485, 2015. © 2015 Wiley Periodicals, Inc.
The avoidance strategy of environmental constraints by an aquatic plant Potamogeton alpinus in running waters
Authors: Robionek Alicja , Banaś Krzysztof , Chmara Rafał , Szmeja Józef
Published: July 2015

Aquatic plants anchored in streams are under pressure from various constraints linked to the water flow and display strategies to prevent their damage or destruction. We assume that the responses of aquatic plants to fast‐water flow are a manifestation of a trade‐off consisting in either maximizing the resistance to damage (tolerance strategy) in minimizing the hydrodynamic forces (avoidance strategy), or both. Our main hypothesis was that Potamogeton alpinus demonstrate the avoidance strategy. We analyzed architecture traits of the modules of this clonal plant from slow‐ and fast‐flowing streams. In fast‐flowing waters, the avoidance strategy of P. alpinus is reflected by the following: (1) the presence of floating leaves that stabilize the vertical position of the stem and protect the inflorescence against immersion; (2) elongation of submerged leaves (weakens the pressure of water); and (3) shoot diameter reduction and increase in shoot density (weakens the pressure of water, increases shoot elasticity), and by contrast in slow‐water flow include the following: (4) the absence of floating leaves in high intensity of light (avoiding unnecessary outlays on a redundant organ); (5) the presence of floating leaves in low intensity of light (avoidance of stress caused by an insufficient assimilation area of submerged leaves).
DoesAcacia dealbataexpress shade tolerance inMediterranean forest ecosystems ofSouthAmerica?
Authors: Aguilera Narciso , Sanhueza Carolina , Guedes Lubia M. , Becerra José , Carrasco Sebastián , Hernández Víctor
Published: July 2015

The distribution ofAcacia dealbataLink (Fabaceae) in its non‐native range is associated with disturbed areas. However, the possibility that it can penetrate the native forest during the invasion process cannot be ruled out. This statement is supported by the fact that this species has been experimentally established successfully under the canopy of native forest. Nonetheless, it is unknown whetherA. dealbatacan express shade tolerance traits to help increase its invasive potential. We investigated the shade tolerance ofA. dealbataunder the canopy of two native forests and one non‐native for three consecutive years, as well as its early growth and photosynthetic performance at low light intensities (9, 30, and 70 μmol m−2sec−1) under controlled conditions. We found manyA. dealbataplants surviving and growing under the canopy of native and non‐native forests. The number of plants of this invasive species remained almost constant under the canopy of native forests during the years of study. However, the largest number ofA. dealbataplants was found under the canopy of non‐native forest. In every case, the distribution pattern varied with a highest density of plants in forest edges decreasing progressively toward the inside. Germination and early growth ofA. dealbatawere slow but successful at three low light intensities tested under controlled conditions. For all tested light regimes, we observed that in this species, most of the energy was dissipated by photochemical processes, in accordance with the high photosynthetic rates that this plant showed, despite the really low light intensities under which it was grown. Our study reveals thatA. dealbataexpressed shade tolerance traits under the canopy of native and non‐native forests. This behavior is supported by the efficient photosynthetic performance thatA. dealbatashowed at low light intensities. Therefore, these results suggest that Mediterranean forest ecosystems of South America can become progressively invaded byA. dealbataand provide a basis for estimating the possible impacts that this invasive species can cause in these ecosystems in a timescale.
Spatio‐temporal variation in European starling reproductive success at multiple small spatial scales
Authors: Brickhill Daisy , Evans Peter G.H. , Reid Jane M.
Published: July 2015

Understanding population dynamics requires spatio‐temporal variation in demography to be measured across appropriate spatial and temporal scales. However, the most appropriate spatial scale(s) may not be obvious, few datasets cover sufficient time periods, and key demographic rates are often incompletely measured. Consequently, it is often assumed that demography will be spatially homogeneous within populations that lack obvious subdivision. Here, we quantify small‐scale spatial and temporal variation in a key demographic rate, reproductive success (RS), within an apparently contiguous population of European starlings. We used hierarchical cluster analysis to define spatial clusters of nest sites at multiple small spatial scales and long‐term data to test the hypothesis that small‐scale spatio‐temporal variation in RS occurred. RS was measured as the number of chicks alive ca. 12 days posthatch either per first brood or per nest site per breeding season (thereby incorporating multiple breeding attempts). First brood RS varied substantially among spatial clusters and years. Furthermore, the pattern of spatial variation was stable across years; some nest clusters consistently produced more chicks than others. Total seasonal RS also varied substantially among spatial clusters and years. However, the magnitude of variation was much larger and the pattern of spatial variation was no longer temporally consistent. Furthermore, the estimated magnitude of spatial variation in RS was greater at smaller spatial scales. We thereby demonstrate substantial spatial, temporal, and spatio‐temporal variation in RS occurring at very small spatial scales. We show that the estimated magnitude of this variation depended on spatial scale and that spatio‐temporal variation would not have been detected if season‐long RS had not been measured. Such small‐scale spatio‐temporal variation should be incorporated into empirical and theoretical treatments of population dynamics.
Deletional and regulatory mechanisms coalesce to drive transplantation tolerance through mixed chimerism
Authors: Hock Karin , Mahr Benedikt , Schwarz Christoph , Wekerle Thomas
Published: July 2015

Establishing donor‐specific immunological tolerance could improve long‐term outcome by obviating the need for immunosuppressive drug therapy, which is currently required to control alloreactivity after organ transplantation. Mixed chimerism is defined as the engraftment of donor hematopoietic stem cells in the recipient, leading to viable coexistence of both donor and recipient leukocytes. In numerous experimental models, cotransplantation of donor bone marrow (BM) into preconditioned (e.g., through irradiation or cytotoxic drugs) recipients leads to transplantation tolerance through (mixed) chimerism. Mixed chimerism offers immunological advantages for clinical translation; pilot trials have established proof of concept by deliberately inducing tolerance in humans. Widespread clinical application is prevented, however, by the harsh preconditioning currently necessary for permitting BM engraftment. Recently, the immunological mechanisms inducing and maintaining tolerance in experimental mixed chimerism have been defined, revealing a more prominent role for regulation than historically assumed. The evidence from murine models suggests that both deletional and regulatory mechanisms are critical in promoting complete tolerance, encompassing also the minor histocompatibility antigens. Here, we review the current understanding of tolerance through mixed chimerism and provide an outlook on how to realize widespread clinical translation based on mechanistic insights gained from chimerism protocols, including cell therapy with polyclonal regulatory T cells.
Adoptive T‐cell therapy for cancer: The era of engineered T cells
Authors: Bonini Chiara , Mondino Anna
Published: July 2015

Tumors originate from a number of genetic events that deregulate homeostatic mechanisms controlling normal cell behavior. The immune system, devoted to patrol the organism against pathogenic events, can identify transformed cells, and in several cases cause their elimination. It is however clear that several mechanisms encompassing both central and peripheral tolerance limit antitumor immunity, often resulting into progressive diseases. Adoptive T‐cell therapy with either allogeneic or autologous T cells can transfer therapeutic immunity. To date, genetic engineering of T cells appears to be a powerful tool for shaping tumor immunity. In this review, we discuss the most recent achievements in the areas of suicide gene therapy, and TCR‐modified T cells and chimeric antigen receptor gene‐modified T cells. We provide an overview of current strategies aimed at improving the safety and efficacy of these approaches, with an outlook on prospective developments.
Preparation of 1, 3‐dioleoyl‐2‐palmitoylglycerol‐rich structured lipids from basa catfish oil: Combination of fractionation and enzymatic acidolysis
Authors: Zou Xiaoqiang , Jin Qingzhe , Guo Zheng , Huang Jianhua , Xu Xuebing , Wang Xingguo
Published: July 2015

1,3‐dioleoyl‐2‐palmitoylglycerol (OPO)‐rich structured lipids were successfully prepared from basa catfish oil by a two‐step process, namely, fractionation to enrich triacylglycerol (TAG) fractions with high content of sn‐2 palmitic acid and Lipozyme RM IM‐catalyzed acidolysis of the fractionated products with free fatty acids from high oleic acid sunflower oil to increase the content of OPO. In the first step, the content of sn‐2 palmitic acid of solid fraction was increased from 49.34 to 60.42% after programmed temperature treatment of basa catfish oil at 60°C for 30 min followed by 30°C for 12 h. In the second step, the solid fraction was used for transesterification with the fatty acids from high oleic acid sunflower oil and the conditions selected for acidolysis reactions were as follows: substrate molar ratio, 1:6 (fatty acids/solid fat); enzyme load, 12 wt%; reaction temperature, 50°C; and reaction time, 2 h. Under these conditions, the contents of sn‐2 plamitic acid and sn‐1, 3 oleic acid were 57.80 and 79.21%, respectively, and the content of POO was increased from 20.13% in the basa catfish oil to 43.80% in the enzymatic product, which indicated high content of OPO.

Practical applications: Basa catfish oil is a type of newly discovered oil occurring in nature with similar fatty acid composition and distribution to human milk fat. Preparation of OPO‐rich structured lipids from basa catfish oil is a new method which is important for development of human milk fat substitutes. This process for OPO‐rich structured lipid preparation practically developed by combination of dry fractionation and enzymatic acidolysis has great potential for use in infant formula industry.

Basa catfish oil was found to have similar triacylglycerol (TAG) structure to that of human milk fat. The oil was used to produce OPO‐rich structured lipids via a two‐step approach. The first step is to enrich TAG fractions with palmitic acid (PA) at sn‐2 position by low‐temperature fractionation, and the second step is to incorporate more oleic acid (OA) in sn‐1, 3 positions of triacylglycerols by Lipozyme RM IM‐catalyzed acidolysis. The final product had 22.29% total PA, 58.43% PA at sn‐2 position, 80.16% OA at sn‐1, 3 positions, and the content of POO was 43.80%, which indicated high content of OPO.
Group‐based task‐oriented exercises aimed at managing kinesiophobia improved disability in chronic low back pain
Authors: Monticone M. , Ambrosini E. , Rocca B. , Cazzaniga D. , Liquori V. , Foti C.
Published: July 2015

Background

There are still doubts concerning the clinical impact of multidisciplinary cognitive behavioural rehabilitation programmes conducted in group‐based settings and about their long‐term effects on subjects with chronic low back pain (CLBP). This randomized, parallel‐group superiority‐controlled trial aimed at evaluating the effect of such a programme on disability, kinesiophobia, catastrophizing, pain and quality of life in CLBP.

Methods

One hundred and fifty patients were randomly assigned to a 5‐week group‐based multidisciplinary programme of task‐oriented exercises integrated with cognitive behavioural therapy mainly aimed at managing kinesiophobia (experimental group, 75 subjects) or group‐based traditional exercises (control group, 75 subjects). Before treatment, 5 weeks later (post‐treatment), 12 and 24 months after the end of treatment, the Oswestry Disability Index, the Tampa Scale for Kinesiophobia, the Pain Catastrophizing Scale, a pain Numerical Rating Scale and the Short Form Health Survey were assessed. A linear mixed model for repeated measures was used for each outcome measure.

Results

Significant group (p < 0.001), time (p < 0.001) and time‐by‐group interaction (p < 0.001) effects were found on disability, with a between‐group difference (95% confidence interval) after training in favour of the experimental group of −10 (−12; −8). Also kinesiophobia, catastrophizing, pain, and quality of life improved to a significantly greater extent in the experimental group. The improvements of the experimental group were maintained at follow‐ups.

Conclusion

This light group‐based multidisciplinary cognitive behavioural rehabilitation programme was superior to traditional exercises in reducing disability, kinesiophobia, catastrophizing, and enhancing the quality of life of subjects with CLBP. The effects lasted for at least 2 years after the end of the intervention.
Cross-species comparison of relative potencies and relative sensitivities of fishes to dibenzo-p-dioxins, dibenzofurans, and polychlorinated biphenyls in vitro
Authors: Eisner Bryanna K. , Doering Jon A. , Beitel Shawn C. , Wiseman Steve , Raine Jason C. , Hecker Markus
Published: July 2015

Dioxin-like compounds of varying toxicities are found in complex mixtures. The toxic equivalency factor (TEF) approach was developed based on the potency of a dioxin-like compound relative to the potency of 2,3,7,8-tetrachloro-dibenzo-p-dioxin (TCDD) to streamline risk assessment. One limitation of the TEF approach is uncertainty regarding differences in the relative potency of dioxin-like compounds among different species. Relative potencies among fishes are limited, relative to relative potencies among birds and mammals, and TEFs for fishes are based entirely on the model species, rainbow trout (Oncorhynchus mykiss). An in vitro liver explant assay was used to characterize species-specific responses with regard to up-regulation of CYP1A transcript after exposure to 6 dioxin-like compounds in rainbow trout, white sturgeon (Acipenser transmontanus), lake sturgeon (Acipenser fulvescens), and northern pike (Esox lucius). Differences in sensitivities were observed among species after exposure to dioxin-like compounds. The relative potencies developed from liver explants of rainbow trout were comparable to relative potencies developed from embryo toxicity assays. Differences in relative potencies between species with the least and greatest relative potencies were up to 40-fold. To compare relative potencies among species, concentrations of dioxin-like compounds in fish eggs in the Fraser River and in Lake Ontario were used to calculate toxic equivalency quotients (TEQs) determined from TEFs or TCDD equivalents determined from relative potencies. The TEQs underestimated TCDD equivalents for white sturgeon, lake sturgeon, and northern pike, indicating uncertainty in application of TEFs to diverse fishes. Environ Toxicol Chem 2016;35:173–181. © 2015 SETAC
Preventing numerical oscillations in the flux‐split based finite difference method for compressible flows with discontinuities, II
Authors: He Zhiwei , Zhang Yousheng , Li Xinliang , Tian Baolin
Published: July 2015

Problems in the characteristic‐wise flux‐split based finite difference method when compressible flows with contact discontinuities or material interfaces are computed were presented and analyzed. The current analysis showed the following: (i) Even with the local characteristic decomposition technique, numerical errors could be caused by point‐wise flux vector splitting (FVS) methods, such as the Steger–Warming FVS or the van Leer FVS. Therefore, the Lax–Friedrichs type FVS method is required. (ii) If the isobars of a material are vertical lines, the combination of using the local characteristic decomposition and the global Lax–Friedrichs FVS can avoid velocity and pressure oscillations of contact discontinuities in this material for weighted essentially non‐oscillatory (WENO) schemes. (iii) For problems with material interfaces, the quasi‐conservative approach can be realized using characteristic‐wise flux‐split based finite difference WENO schemes if nonlinear WENO schemes in genuinely nonlinear characteristic fields can be guaranteed to be the same and the decomposition equation representing material interfaces is discretized properly. Copyright © 2015 John Wiley & Sons, Ltd.
Solution of the incompressible Navier–Stokes equations by the method of lines
Authors: Strumendo Matteo
Published: July 2015

The numerical method of lines (NUMOL) is a numerical technique used to solve efficiently partial differential equations. In this paper, the NUMOL is applied to the solution of the two‐dimensional unsteady Navier–Stokes equations for incompressible laminar flows in Cartesian coordinates. The Navier–Stokes equations are first discretized (in space) on a staggered grid as in the Marker and Cell scheme. The discretized Navier–Stokes equations form an index 2 system of differential algebraic equations, which are afterwards reduced to a system of ordinary differential equations (ODEs), using the discretized form of the continuity equation. The pressure field is computed solving a discrete pressure Poisson equation. Finally, the resulting ODEs are solved using the backward differentiation formulas.

The proposed method is illustrated with Dirichlet boundary conditions through applications to the driven cavity flow and to the backward facing step flow. Copyright © 2015 John Wiley & Sons, Ltd.
Computing a Synthetic Chronic Psychosocial Stress Measurement in Multiple Datasets and its Application in the Replication of G × E Interactions of the EBF1 Gene
Authors: Singh Abanish , Babyak Michael A. , Brummett Beverly H. , Jiang Rong , Watkins Lana L. , Barefoot John C. , Kraus William E. , Shah Svati H. , Siegler Ilene C. , Hauser Elizabeth R. , Williams Redford B.
Published: July 2015

Chronic psychosocial stress adversely affects health and is associated with the development of disease [Williams, ]. Systematic epidemiological and genetic studies are needed to uncover genetic variants that interact with stress to modify metabolic responses across the life cycle that are the proximal contributors to the development of cardiovascular disease and precipitation of acute clinical events. Among the central challenges in the field are to perform and replicate gene‐by‐environment (G × E) studies. The challenge of measurement of individual experience of psychosocial stress is magnified in this context. Although many research datasets exist that contain genotyping and disease‐related data, measures of psychosocial stress are often either absent or vary substantially across studies. In this paper, we provide an algorithm to create a synthetic measure of chronic psychosocial stress across multiple datasets, applying a consistent criterion that uses proxy indicators of stress components. We validated the computed scores of chronic psychosocial stress by observing moderately strong and significant correlations with the self‐rated chronic psychosocial stress in the Multi‐Ethnic Study of Atherosclerosis Cohort (Rho = 0.23, P < 0.0001) and with the measures of depressive symptoms in five datasets (Rho = 0.15–0.42, Ps = 0.005 to <0.0001) and by comparing the distributions of the self‐rated and computed measures. Finally, we demonstrate the utility of this computed chronic psychosocial stress variable by providing three additional replications of our previous finding of gene‐by‐stress interaction with central obesity traits [Singh et al., ].
Contemporary Considerations for Constructing a Genetic Risk Score: An Empirical Approach
Authors: Goldstein Benjamin A. , Yang Lingyao , Salfati Elias , Assimes Themistoclies L.
Published: July 2015

Genetic risk scores are an increasingly popular tool for summarizing the cumulative risk of a set of Single Nucleotide Polymorphisms (SNPs) with disease. Typically only the set of the SNPs that have reached genome‐wide significance compose these scores. However recent work suggests that including additional SNPs may aid risk assessment. In this paper, we used the Atherosclerosis Risk in Communities (ARIC) Study cohort to illustrate how one can choose the optimal set of SNPs for a genetic risk score (GRS). In addition to P‐value threshold, we also examined linkage disequilibrium, imputation quality, and imputation type. We provide a variety of evaluation metrics. Results suggest that P‐value threshold had the greatest impact on GRS quality for the outcome of coronary heart disease, with an optimal threshold around 0.001. However, GRSs are relatively robust to both linkage disequilibrium and imputation quality. We also show that the optimal GRS partially depends on the evaluation metric and consequently the way one intends to use the GRS. Overall the implications highlight both the robustness of GRS and a means to empirically choose the best set of GRSs.
Storm runoff response to rainfall pattern, magnitude and urbanization in a developing urban catchment
Authors: Guan Mingfu , Sillanpää Nora , Koivusalo Harri
Published: July 2015

This study explored the hydrological impacts of urbanization, rainfall pattern and magnitude in a developing catchment. The Stormwater Management Model was parameterized, calibrated and validated in three development phases, which had the same catchment area (12.3 ha) but different land use intensities. The model calibration and validation by using sub‐hourly hydro‐meteorological data demonstrated a good performance of the model in predicting stormwater runoff in the different development phases. Based on the results, a threshold between minor and major rainfall events was identified and conservatively determined to be about 17.5 mm in depth. Direct runoff for minor storm events has a linear relationship with rainfall; however, events with a rainfall depth greater than the threshold yield a rainfall–runoff regression line with a clearly steeper slope. The difference in urban runoff generation between minor and major rainfall events diminishes with the increase of imperviousness. Urbanization leads to an increase in the production of stormwater runoff, but during infrequent major storms, the runoff contribution from pervious surfaces reduces the runoff changes owing to urbanization. Rainfall pattern exerts an important effect on urban runoff, which is reflected in pervious runoff. With the same magnitude, prolonged rainfall events with unvarying low intensity yield the smallest peak flow and the smallest total runoff, yet rainfall events with high peak intensity produce the largest runoff volume. These results demonstrate the different roles of impervious and pervious surfaces in runoff generation, and how runoff responds to rainstorms in urban catchments depends on hyetograph and event magnitude. Furthermore, the study provides a scientific basis of the design guideline sustainable urban drainage systems, which are still arbitrary in many countries. Copyright © 2015 John Wiley & Sons, Ltd.
Selective Life‐Long Skeletal Myofiber—Targeted VEGF Gene Ablation Impairs Exercise Capacity in Adult Mice
Authors: Tang Kechun , Gu Yusu , Dalton Nancy D. , Wagner Harrieth , Peterson Kirk L. , Wagner Peter D. , Breen Ellen C.
Published: July 2015

Exercise is dependent on adequate oxygen supply for mitochondrial respiration in both cardiac and locomotor muscle. To determine whether skeletal myofiber VEGF is critical for regulating exercise capacity, independent of VEGF function in the heart, ablation of the VEGF gene was targeted to skeletal myofibers (skmVEGF−/−) during embryogenesis (∼ E9.5), leaving intact VEGF expression by all other cells in muscle. In adult mice, VEGF levels were decreased in the soleus (by 65%), plantaris (94%), gastrocnemius (74%), EDL (99%) and diaphragm (64%) (P < 0.0001, each muscle). VEGF levels were unchanged in the heart. Treadmill speed (WT 86 ± 4 cm/sec, skmVEGF−/− 70 ± 5 cm/sec, P = 0.006) and endurance (WT 78 ± 24 min, skmVEGF−/− 18 ± 4 min, P = 0.0004) were severely limited in skmVEGF−/− mice in contrast to minor effect of conditional skmVEGF gene deletion in the adult. Body weight was also reduced (WT 22.8 ± 1.6 g, skmVEGF−/−, 21.1 ± 1.5, P = 0.02), but the muscle mass/body weight ratio was unchanged. The capillary/fiber ratio was lower in skmVEGF−/− plantaris (WT 1.51 ± 0.12, skmVEGF−/− 1.16 ± 0.20, P = 0.01), gastrocnemius (WT 1.61 ± 0.08, skmVEGF−/− 1.39 ± 0.08, P = 0.01), EDL (WT 1.36 ± 0.07, skmVEGF−/− 1.14 ± 0.13, P = 0.03) and diaphragm (WT 1.39 ±  0.18, skmVEGF−/− 0.79 ± 0.16, P = 0.0001) but, not in soleus. Cardiac function (heart rate, maximal pressure, maximal dP/dt, minimal dP/dt,) in response to dobutamine was not impaired in anesthetized skmVEGF−/− mice. Isolated soleus and EDL fatigue times were 16% and 20% (P < 0.02) longer, respectively, in skmVEGF−/− mice than the WT group. These data suggest that skeletal myofiber VEGF expressed during development is necessary to establish capillary networks that allow maximal exercise capacity. J. Cell. Physiol. 231: 505–511, 2016. © 2015 Wiley Periodicals, Inc.
Linguistic Cues of Deception Across Multiple Language Groups in a Mock Crime Context
Authors: Hwang Hyisung C. , Matsumoto David , Sandoval Vincent
Published: July 2015

A recent study showed that specific linguistic and grammatical features of a technique commonly referred to as statement analysis are applicable across different language groups. One limitation of that study was that it used an eyewitness crime video paradigm, which might be different from writing a statement after committing an actual criminal act. We remedied that limitation by using a mock crime paradigm. In this study, three language groups (English, Spanish, and Chinese) produced statements after committing a mock crime, taking a check, in an experimental context. Certain linguistic features significantly discriminated truths from lies similarly across the different language groups, suggesting that statement analysis might be applicable as a reliable indicator of deception across languages. Copyright © 2015 John Wiley & Sons, Ltd.
Neurovascular uncoupling in resting state fMRI demonstrated in patients with primary brain gliomas
Authors: Agarwal Shruti , Sair Haris I. , Yahyavi‐Firouz‐Abadi Noushin , Airan Raag , Pillai Jay J.
Published: July 2015

Background

To demonstrate that the problem of brain tumor‐related neurovascular uncoupling (NVU) is a significant issue with respect to resting state blood oxygen level dependent (BOLD) functional MRI (rsfMRI) similar to task‐based BOLD fMRI, in which signal detectability can be compromised by breakdown of normal neurovascular coupling.

Methods

We evaluated seven de novo brain tumor patients who underwent resting state fMRI as part of comprehensive clinical fMRI exams at 3 Tesla. For each of the seven patients who demonstrated evidence of NVU on task‐based motor fMRI, we performed both an independent component analysis (ICA) and an atlas‐based parcellation‐based seed correlation analysis (SCA) of the resting state fMRI data. For each patient, ipsilesional (IL) and contralesional (CL) regions of interest (ROIs) comprising primary motor and somatosensory cortices were used to evaluate BOLD signal changes on Z score maps derived from both ICA and SCA analysis for evidence of NVU. A subsequent two‐tailed t‐test was performed to determine whether statistically significant differences between the two sides were present that were consistent with NVU.

Results

In seven patients, overall decreased BOLD signal (based on suprathreshold voxels in ICA and SCA‐derived Z‐score maps) was noted in IL compared with CL ROIs (P < 0.01), consistent with NVU.

Conclusion

We have demonstrated that NVU can result in false negative BOLD signal changes on rsfMRI comparable to previously published findings on standard motor task‐based fMRI. J. MAGN. RESON. IMAGING 2016;43:620–626.
The effect of spray drying on sucrose–glycine caramel powder preparation
Authors: Huang Kai , Zhang Ping‐Jun , Hu Biao , Yu Shu‐Juan
Published: July 2015

BACKGROUND

Caramel is used as food colorant in many parts of the world. However, there have been no studies investigating the effects of spray drying on sucrose and glycine solutions. In this study, model sucrose and glycine solutions at different pH levels (pH 4, 3, 2 and 1) were treated with different inlet air temperatures (160, 180, 200, 220 and 240 °C) for durations of 50 s in the spray drying process.

RESULTS

With increasing inlet temperatures and decreasing pH, the morphology of the caramel agglomerates tended to be more scattered; however, the solubility of the caramel decreased. With increasing inlet temperature, the glycine and sucrose contents decreased but the fructose and glucose contents increased.

CONCLUSION

The content of the intermediate products, browning intensity and amount of 5‐hydroxymethyl‐2‐furaldehyde (HMF) increased with increasing inlet temperature and decreasing pH. Therefore, the amount of sucrose degradation and the change in pH can be used to evaluate caramel properties in the spray drying process. © 2015 Society of Chemical Industry
Fiber‐based laser speckle imaging for the detection of pulsatile flow
Authors: Regan Caitlin , Yang Bruce Y. , Mayzel Kent C. , Ramirez‐San‐Juan Julio C. , Wilder‐Smith Petra , Choi Bernard
Published: July 2015

Background and Objective

In endodontics, a major diagnostic challenge is the accurate assessment of pulp status. In this study, we designed and characterized a fiber‐based laser speckle imaging system to study pulsatile blood flow in the tooth.

Study Design/Materials and Methods

To take transilluminated laser speckle images of the teeth, we built a custom fiber‐based probe. To assess our ability to detect changes in pulsatile flow, we performed in vitro and preliminary in vivo tests on tissue‐simulating phantoms and human teeth. We imaged flow of intralipid in a glass microchannel at simulated heart rates ranging from 40 beats/minute (bpm) to 120 bpm (0.67–2.00 Hz). We also collected in vivo data from the upper front incisors of healthy subjects. From the measured raw speckle data, we calculated temporal speckle contrast versus time. With frequency‐domain analysis, we identified the frequency components of the contrast waveforms.

Results

With our approach, we observed in vitro the presence of pulsatile flow at different simulated heart rates. We characterized simulated heart rate with an accuracy of and >98%. In the in vivo proof‐of‐principle experiment, we measured heart rates of 69, 90, and 57 bpm, which agreed with measurements of subject heart rate taken with a wearable, commercial pulse oximeter.

Conclusions

We designed, built, and tested the performance of a dental imaging probe. Data from in vitro and in ­vivo tests strongly suggest that this probe can detect the presence of pulsatile flow. LSI may enable endodontists to noninvasively assess pulpal vitality via direct measurement of blood flow. Lasers Surg. Med. 47:520–525, 2015. © 2015 Wiley Periodicals, Inc.
Long‐term outcome of endovascular intervention in hepatic venous outflow obstruction following pediatric liver transplantation
Authors: Choi Jin Woo , Jae Hwan Jun , Kim Hyo‐Cheol , Yi Nam‐Joon , Lee Kwang‐Woong , Suh Kyung‐Suk , Chung Jin Wook
Published: July 2015

The purpose of our study was to address the long‐term outcome of angioplasty and stent placement for hepatic venous outflow obstruction following pediatric liver transplantation. From October 1999 to December 2011, 20 stenotic lesions were confirmed to constitute hepatic venous outflow obstruction in 18 pediatric patients (13 boys, 5 girls) among 152 pediatric patients following liver transplantation and were managed with endovascular intervention. Stent placement was favored over additional angioplasty in patients of preadolescent or adolescent age (>8 years old), after 1 or 2 sessions of balloon angioplasty. The primary patency and assisted primary patency were estimated using the Kaplan‐Meier method. A total of 32 procedures (24 balloon angioplasties, 8 stent placements) were conducted. The technical success rate was 90.6% (29/32). Clinical success was achieved in 15 of 18 patients (clinical success rate of 83.3%). Major complications did not occur in our study. Median follow‐up was 91.5 months (interquartile range, 54.7‐137.3 months) for the 18 patients. The 1‐year, 3‐year, 5‐year, and 10‐year primary patencies of the 20 treated lesions were 63.5%, 57.8%, 57.8%, and 57.8%, respectively. The 1‐year, 3‐year, 5‐year, and 10‐year assisted‐primary patencies of the lesions were 100%, 100%, 100%, and 100%, respectively. Of the 6 patients of preadolescent or adolescent age, 5 patients underwent stent placement procedures, and the stents were patent during the follow‐up period of 57.3‐162.5 months (median, 72.7 months). In conclusion, endovascular intervention is very effective in hepatic venous outflow obstruction following pediatric liver transplantation. In addition, early stent placement in patients of preadolescent or adolescent age can provide a safe and favorable long‐term outcome. Liver Transpl 21:1219‐1226, 2015. © 2015 AASLD.