bluuebunny/crossref_metadata_2025 huggingface dataset:
Occupation and risk of primary Fallopian tube carcinoma in Nordic countries
Authors: Riska A. , Martinsen J.I. , Kjaerheim K. , Lynge E. , Sparen P. , Tryggvadottir L. , Weiderpass E. , Pukkala E.
Published: July 2011

The aetiology of primary Fallopian tube carcinoma (PFTC) is poorly understood. Occupational exposures may contribute to PFTC risk. We studied incidence of PFTC in occupational categories in the Nordic female population aged 30–64 years during the 1960, 1970, 1980/1981 and/or 1990 censuses in Denmark, Finland, Iceland, Norway and Sweden. Standardized incidence ratios (SIRs) for the years following inclusion in the study up to 2005 were calculated for 53 occupations; the expected numbers of cases were based on PFTC incidence in the national populations. Altogether 2,206 PFTC cases were detected during follow up via data linkages with the Nordic cancer registries. Significantly increased risks of PFTC were observed for smelting workers (SIR 3.99, 95% confidence interval 1.46–8.68, Obs = 6), artistic workers (2.64, 1.44–4.43, Obs = 14), hairdressers (2.18, 1.41–3.22, Obs = 25), packers (1.62, 1.11–2.29, Obs = 32), nurses (1.49, 1.14–1.92, Obs = 60), shop workers (1.25, 1.07–1.46, Obs = 159) and clerical workers (1.20, 1.07–1.35, Obs = 271) and these sustained over times and different Nordic countries. There was a nonsignificant increased risk for PFTC among welders, printers, painters and chemical process workers. The risk was significantly and consistently low for women working in farming (0.68, 0.47–0.95, Obs = 34) and among economically inactive women (0.88, 0.82–0.94, Obs = 833). The possible role of occupational exposures to the PFTC risks found in this study must be further evaluated in studies with a possibility to adjust for possible confounding factors, such as reproductive and life‐style factors, which was not possible in our study.
Calreticulin promotes tumor lymphocyte infiltration and enhances the antitumor effects of immunotherapy by up‐regulating the endothelial expression of adhesion molecules
Authors: Wang Hao‐Tien , Lee Hsin‐I , Guo Jih‐Huong , Chen Shih‐Hui , Liao Zhe‐Kang , Huang Kai‐Wen , Torng Pao‐Ling , Hwang Lih‐Hwa
Published: July 2011

Tumor‐induced angiogenesis has been shown to suppress immune responses. One mechanism is to suppress leukocyte–endothelial cell interaction by down‐regulating the expression of adhesion molecules, such as intercellular adhesion molecule (ICAM)‐1, vascular cell adhesion molecule (VCAM)‐1 and E‐selectin on the tumor endothelium, which enables tumor cells to escape immune surveillance. Calreticulin (CRT), a chaperone protein mainly located in the endoplasmic reticulum, has been shown to exert anti‐angiogenic activity and inhibit tumor growth. Here, we demonstrate that in addition to inhibiting angiogenesis, CRT also enhances the expression of both ICAM‐1 and VCAM‐1 on tumor endothelial cells. This expression results in enhanced leukocyte–endothelial cell interactions and increased lymphocyte infiltration into tumors. Therefore, combining intramuscular CRT gene transfer with intratumoral cytokine gene therapies significantly improves the antitumor effects of immunotherapy by markedly increasing the levels of tumor‐infiltrating lymphocytes. This combined treatment increased the levels of infiltrating lymphocytes to those achieved using four times the cytokine dosage. The combined therapy also resulted in lower levels of immunosuppressive molecules and higher levels of activated T‐cells in the tumor microenvironment than immunotherapy alone. In conclusion, this study describes a new antitumor mechanism of CRT that involves the up‐regulation of tumor endothelial adhesion molecules and the enhanced infiltration of tumor‐specific lymphocytes. Thus, CRT treatment can make tumor cells more vulnerable to immunotherapy and improve the therapeutic efficacy of immunotherapy.
RETRACTED: High‐density lipoprotein of patients with type 2 diabetes mellitus elevates the capability of promoting migration and invasion of breast cancer cells
Authors: Pan Bing , Ren Hui , Ma Yijing , Liu Donghui , Yu Baoqi , Ji Liang , Pan Ling , Li Jing , Yang Liangui , Lv Xiaofeng , Shen Xiaoli , Chen Bin , Zhang Youyi , Willard Belinda , He Yubin , Zheng Lemin
Published: July 2011

Epidemiological studies suggested complicated associations between type 2 diabetes mellitus and breast cancer. There is a significant inverse association between high‐density lipoprotein (HDL) and the risk and mortality of breast cancer. However, HDL could be modified in various ways in diabetes patients, and this may lead to the altered effects on many different types of cells. In our study, we found that glycation and oxidation levels are significantly higher in HDL from type 2 diabetes mellitus patients compared to that from healthy subjects. Diabetic HDL dramatically had a stronger capability to promote cell proliferation, migration and invasion of breast cancer (as examined both on hormone‐independent cells and on hormone‐dependent cells). In addition, glycated and oxidized HDL, which were produced in vitro, acted in similar way as diabetic HDL. Diabetic HDL, glycated HDL and oxidized HDL also induced higher synthesis and secretion of VEGF‐C, MMP‐2 and MMP‐9 from malondialdehyde (MDA)‐MB‐231 cells. It was indicated that diabetic, glycated and oxidized HDL promote MDA‐MB‐231 cell migration and invasion through ERK and p38 MAPK pathways, and Akt pathway plays an important role as well in MDA‐MB‐231 cell invasion. The Akt, ERK and p38 MAPK pathways are also involved in VEGF‐C and MMP‐9 secretion induced by diabetic, glycated and oxidized HDL. Our study demonstrated that glycation and oxidation of HDL in diabetic patients could lead to abnormal actions on MDA‐MB‐231 cell proliferation, migration and invasion, thereby promoting the progression of breast cancer. This will largely draw the attention of HDL‐based treatments in diabetic patients especially those with breast cancer.
Involvement of Bid and caspase‐2 in endoplasmic reticulum stress‐ and oxidative stress‐induced retinal ganglion cell death
Authors: Uchibayashi Rumi , Tsuruma Kazuhiro , Inokuchi Yuta , Shimazawa Masamitsu , Hara Hideaki
Published: July 2011

Endoplasmic reticulum (ER) stress and oxidative stress are involved in many diseases, including retinal disorders, causing toxicity in various tissues and cells; however, intracellular signaling of ER stress and cross‐talk between ER stress and oxidative stress are unknown in retinal ganglion cells (RGC), whose degeneration is associated with glaucoma. The aim of the study was to clarify the mechanisms of ER stress‐ and oxidative stress‐induced RGC death, using cultured retinal ganglion cells (RGC‐5) in vitro and N‐methyl‐D‐aspartate (NMDA)‐ or ER stress‐induced retinal damage in mice in vivo. We focused on both BH3‐interacting domain death agonist (Bid) and caspase‐2, which work as apoptosis promotion factors. In an in vitro study, both Bid and caspase‐2 inhibitors protected against RGC‐5 death from ER stress or oxidative stress. A caspase‐2 inhibitor did not inhibit Bid cleavage, although a Bid inhibitor reduced the increase of caspase‐2 activity in ER stress‐induced RGC‐5 death. A Bid inhibitor also reduced the increase of caspase‐2 activity in oxidative stress‐induced RGC‐5 death. Moreover, both Bid and caspase‐2 inhibitors reduced the increase of caspase‐3 activity. In an in vivo study, a Bid inhibitor inhibited NMDA‐ or ER stress‐induced retinal damage. These findings indicate that a common mechanism through Bid and caspase‐2 existsin both ER stress‐ and oxidative stress‐induced RGC death and that they are activated in the order of Bid, caspase‐2, and caspase‐3. © 2011 Wiley‐Liss, Inc.
Longitudinal evaluation of cartilage after osteochondral autogenous transfer with delayed gadolinium‐enhanced MRI of the cartilage (dGEMRIC)
Authors: Shirai Takaaki , Kobayashi Masahiko , Nakamura Shinichiro , Arai Ryuzo , Nishitani Kohei , Satake Tsuyoshi , Dahlberg Leif E. , Kuroki Hiroshi , Nakagawa Yasuaki , Okada Tomohisa , Togashi Kaori , Nakamura Takashi
Published: July 2011

The aim was to use repeat delayed gadolinium‐enhanced magnetic resonance imaging of cartilage (dGEMRIC) to estimate glycosaminoglycan (GAG) content in reparative cartilage after osteochondral autogenous transfer (OAT). The study group comprised 7 knees of 7 patients that were examined three times by dGEMRIC, at 3, 6, and 12 months using a 1.5 Tesla MRI system in both OAT operated and nonoperated condyles at 90 min after the injection. The gadolinium diethylene triamine pentaacetic acid (Gd‐DTPA)2− containing contrast medium (0.2 mmols/kg) was injected intravenously. The mean T1 values of the plug cartilage at 3, 6, and 12 months after OAT was 230 ± 40, 213 ± 31, and 230 ± 23 ms (mean ± SD), respectively. There were differences between the plug and control cartilage at 3 (p < 0.01) and 12 (p < 0.05) months after OAT, but not at 6 months (p = 0.089). No T1 changes were detected between the plug cartilage at the different time points after OAT. The fact that the GAG content of the OAT plugs were maintained for 12‐month study period suggest that no major deterioration of load‐bearing properties occurs in the cartilage after the OAT. © 2011 Orthopaedic Research Society Published by Wiley Periodicals, Inc. J Orthop Res 30:221–225, 2012
Climatic control of the surge periodicity of an Icelandic outlet glacier
Authors: Striberger Johan , Björck Svante , Benediktsson Ívar Örn , Snowball Ian , Uvo Cintia B. , Ingólfsson Ólafur , Kjær Kurt H.
Published: July 2011

Surging outlet glaciers are important in draining large ice caps, but the mechanisms controlling surge periodicities are poorly known. We investigated a sediment sequence from the glacier‐fed Lake Lögurinn in eastern Iceland, and our unique annually resolved data, based on sedimentary varves, imply that Eyjabakkajökull, an outlet glacier of Vatnajökull, began surging about 2200 cal a BP (before 1950 AD). Approximately 1700 cal a BP, the glacier started to surge at a uniform 34‐ to 38‐year periodicity that prevailed until the coldest part of the Little Ice Age when the periodicity almost halved to 21–23 years. Since the late 1800 s the surge periodicity of Eyjabakkajökull has returned to a longer period of 35–40 years. We suggest that surge periodicities of Eyjabakkajökull are forced by climatically driven mass balance changes, which may be a common forcing factor for similar surge‐type outlet glaciers. Copyright © 2011 John Wiley & Sons, Ltd.
The Suitability of Yoga as a Potential Therapeutic Intervention for Rheumatoid Arthritis: A Focus Group approach
Authors: Ward Lesley , Treharne Gareth J. , Stebbings Simon
Published: July 2011

Objectives

The aim of this study was to explore the views of patients with rheumatoid arthritis (RA) regarding the suitability of yoga as a potential therapeutic intervention in the management of RA.

Methods

Twenty‐two participants with RA were recruited from outpatient clinics at a regional hospital in New Zealand and divided into four focus groups. Heterogeneity between groups in terms of age, gender, duration of RA and functional ability provided opinions from a cross‐section of RA patients. Transcripts were analysed using thematic analysis, with four themes predominating.

Results

Firstly, participants described their experience of symptoms related to their RA in three independent but linked categories of physical, mental and social well‐being. Secondly, participants perceived the management of their RA to be prescriptive, medicalized and failing to address their wider health concerns. Thirdly, participants perceived yoga as a safe, adaptable therapy that may allow self‐management of their RA. However, there was some concern that functional limitations may inhibit ability to practise the physical aspects of yoga. Fourthly, requirements for a yoga intervention that would be feasible for people with RA were presented by participants.

Conclusions

Patients with RA perceive a disparity between their personal experience of living with RA and their current medical management. Yoga is perceived as a potential therapy to address this disparity. Based on opinions expressed by participants, future research regarding a yoga intervention as an adjunctive therapy for managing RA should meet patients’ views on feasibility and test outcome measures reflecting the domains of physical, mental and social well‐being. Copyright © 2011 John Wiley & Sons, Ltd.
Sampling of closely‐spaced ordered set of uniformly distributed random variables
Authors: Tadinada Sashi Kanth , Gupta Abhinav
Published: July 2011

When the individual PDFs of closely‐spaced random variables such as natural frequencies of a structure overlap, generation of sample sets by assuming the frequencies to be independent random variables can lead to incorrect sets of frequencies in the sense that the frequencies do not remain as ordered sets. Rejection of such disordered sample sets results in individual density functions that are significantly different from the distributions initially assumed for sampling each random variable. One way to overcome this constraint in the simulation of an ordered set of random variables is to consider them in an implicit manner using a joint PDF. In this paper, we present a formulation for a joint density function that is developed using fundamental probability approaches. The formulation ensures that the sampled random variables always remain as ordered sets and maintain the individual density functions for each variable. Application of the proposed formulation is illustrated for cases with not just two closely‐spaced variables but also for a case with multiple closely‐spaced variables such that the PDFs of more than two random variables overlap with each other. An expression is presented to determine the exact number of terms needed in the formulation. However, it is also illustrated that only two terms are sufficient in most applications even when the exact number of terms needed is very high. Copyright © 2011 John Wiley & Sons, Ltd.
A geometric nonlinear rotation‐free triangle and its application to drape simulation
Authors: Zhou Y.X. , Sze K.Y.
Published: July 2011

In this paper, a rotation‐free triangle is formulated. Unlike the thin and degenerated shell finite element models, rotation‐free triangles employ translational displacements as the only nodal DOFs. Compared with the existing rotation‐free triangles, the present triangle is simple and physical yet its accuracy remains competitive. Using a corotational approach and the small strain assumption, the tangential bending stiffness matrix of the present triangle can be approximated by a constant matrix that does not have to be updated regardless of the displacement magnitude. This unique feature suggests that the triangle is a good candidate for fabric drape simulation in which fabric sheets are often flat initially and the displacement is much larger than those in conventional shell problems. Nonlinear shell and fabric drape examples are examined to demonstrate the efficacy of the formulation. Copyright © 2011 John Wiley & Sons, Ltd.
Topology optimization of compliant circular path mechanisms based on an aggregated linear system and singular value decomposition
Authors: Takezawa A. , Kitamura M.
Published: July 2011

This paper proposes a topology optimization method for the design of compliant circular path mechanisms, or compliant mechanisms having a set of output displacement vectors with a constant norm, which is induced by a given set of input forces. To perform the optimization, a simple linear system composed of an input force vector, an output displacement vector and a matrix connecting them is constructed in the context of a discretized linear elasticity problem using FEM. By adding two constraints: 1, the dimensions of the input and the output vectors are equal; 2, the Euclidean norms of all local input force vectors are constant; from the singular value decomposition of the matrix connecting the input force vector and the output displacement vector, the optimization problem, which specifies and equalizes the norms of all output vectors, is formulated. It is a minimization problem of the weighted summation of the condition number of the matrix and the least square error of the second singular value and the specified value. This methodology is implemented as a topology optimization problem using the solid isotropic material with penalization method, sensitivity analysis and method of moving asymptotes. The numerical examples illustrate mechanically reasonable compliant circular path mechanisms and other mechanisms having multiple outputs with a constant norm. Copyright © 2011 John Wiley & Sons, Ltd.
Raw Material Availability and Technological Choice: Modified Metapodia from an Early Bronze Age Site in Central Israel
Authors: Allentuck A.
Published: July 2011

This paper explores the incongruous relationship between bone raw material availability and technological choice at the Early Bronze Age site of Horvat 'Illin Tahtit (HIT) in central Israel. At HIT, the worked bone assemblage is mostly comprised of minimally modified sheep and goat metapodia whose function(s) are enigmatic. Most specimens have longitudinally oriented scraping abrasions on at least one face, and of these, some have bilaterally symmetrical drilled perforations on the distal–posterior face. Furthermore, the distal epiphyseal plates of almost all worked metapodia are unfused, whereas unfused epiphyses are nearly absent from the general faunal assemblage. Worked goat metacarpals are significantly more common than sheep metacarpals or metatarsals of either species, despite the greater abundance of sheep over goat in the general faunal assemblage. This paper proposes that the desire to express specific visible attributes of the bone raw material was the key motivation in choosing unfused goat metacarpals over similar, more abundant choices. The analysis considers material properties such as bone mineral density and natural morphology and concludes that material properties between various choices were equivocal. This result suggests that social meanings attributed to specific animals and specific skeletal elements structured bone raw material procurement decisions. Copyright © 2011 John Wiley & Sons, Ltd.
High‐risk pregnancy and neonatal complications in the DNA repair and transcription disorder trichothiodystrophy: report of 27 affected pregnancies
Authors: Tamura Deborah , Merideth Melissa , DiGiovanna John J. , Zhou Xiaolong , Tucker Margaret A. , Goldstein Alisa M. , Brooks Brian P. , Khan Sikandar G. , Oh Kyu‐Seon , Ueda Takahiro , Boyle Jennifer , Moslehi Roxana , Kraemer Kenneth H.
Published: July 2011

Objective

To identify the frequency of pregnancy and neonatal complications in pregnancies carrying fetuses affected with trichothiodystrophy (TTD).

Methods

We identified pregnancy and neonatal complications and serum screening results from mothers of TTD patients in a DNA repair diseases study from 2001 to 2011.

Results

Pregnancy reports of 27 TTD patients and their 23 mothers were evaluated and 81% of the pregnancies had complications: 56% had preterm delivery, 30% had preeclampsia, 19% had placental abnormalities, 11% had HELLP syndrome, and 4% had an emergency c‐section for fetal distress, while 44% had two or more complications. Only 19% of the pregnancies delivered at term without complications. Eight of the ten pregnancies tested had abnormal multiple marker results including elevated levels of human chorionic gonadotrophin. Eighty‐five percent of the neonates had complications: 70% were low birth weight (<2500 g), 35% had birth weight < 10 centile for gestational age, 70% had NICU admission, 67% had a collodion membrane, and 31% of the 16 males had cryptorchidism. Cataracts were present in 54% of the TTD patients examined.

Conclusion

TTD is a multisystem disease that predisposes mothers of affected patients to substantial risks for pregnancy complications and TTD neonates have a high incidence of multiple abnormalities. Published 2011. This article is a U.S. Government work and is in the public domain in the USA
Ultrasonographic findings of placenta lacunae and a lack of a clear zone in cases with placenta previa and normal placenta
Authors: Hamada Shoko , Hasegawa Junichi , Nakamura Masamitsu , Matsuoka Ryu , Ichizuka Kiyotake , Sekizawa Akihiko , Okai Takashi
Published: July 2011

Objectives

To evaluate whether the frequencies of placenta lacunae and lack of a clear zone are higher in cases of placenta previa compared with those without it.

Methods

Ultrasonographic findings just before delivery, including placenta lacunae and lack of a clear zone were prospectively evaluated in consecutive subjects. After collection, a case‐control study with 1:5 matched pairs was conducted. The frequencies of ultrasonographic findings were analyzed in cases with placenta previa and normal placenta.

Results

Seventy cases with placenta previa and 350 cases with normal placentas were observed. Five and zero cases with abnormal placental adherence were observed in cases with placenta previa and normal placenta, respectively. Lack of a clear zone was observed in 60 and 1.5% of cases with and without the placental adherence (p = 0.001). Placenta lacunae and lack of a clear zone were observed in 31.4 and 9.7% of cases with and without placenta previa [odds ratio (OR) 4.2]. Lack of a clear zone was observed in 5.7 and 0.9% of cases with and without placenta previa (OR 7.0).

Conclusions

Placenta lacunae and lack of a clear zone are frequently observed in placenta previa even when there is no adherence of the placenta. Copyright © 2011 John Wiley & Sons, Ltd.
Measuring balance and model selection in propensity score methods
Authors: Belitser Svetlana V. , Martens Edwin P. , Pestman Wiebe R. , Groenwold Rolf H.H. , de Boer Anthonius , Klungel Olaf H.
Published: July 2011

Purpose

Propensity score (PS) methods focus on balancing confounders between groups to estimate an unbiased treatment or exposure effect. However, there is lack of attention in actually measuring, reporting and using the information on balance, for instance for model selection. We propose to use a measure for balance in PS methods and describe several of such measures: the overlapping coefficient, the Kolmogorov‐Smirnov distance, and the Lévy distance.

Methods

We performed simulation studies to estimate the association between these three and several mean based measures for balance and bias (i.e., discrepancy between the true and the estimated treatment effect).

Results

For large sample sizes (n = 2000) the average Pearson's correlation coefficients between bias and Kolmogorov‐Smirnov distance (r = 0.89), the Lévy distance (r = 0.89) and the absolute standardized mean difference (r = 0.90) were similar, whereas this was lower for the overlapping coefficient (r = −0.42). When sample size decreased to 400, mean based measures of balance had stronger correlations with bias. Models including all confounding variables, their squares and interaction terms resulted in smaller bias than models that included only main terms for confounding variables.

Conclusions

We conclude that measures for balance are useful for reporting the amount of balance reached in propensity score analysis and can be helpful in selecting the final PS model. Copyright © 2011 John Wiley & Sons, Ltd.
Retribution and Restoration as General Orientations towards Justice
Authors: Okimoto Tyler G. , Wenzel Michael , Feather N. T.
Published: July 2011

We proposed two distinct understandings of what justice means to victims and what its restoration entails that are reflected in individual–level justice orientations. Individuals with a retributive orientation conceptualize justice as the unilateral imposition of just deserts against the offender. In contrast, individuals with a restorative orientation conceptualize justice as achieving a renewed consensus about the shared values violated by the offence. Three studies showed differential relations between these two justice orientations and various individual–level values/ideologies and predicted unique variance in preferences for concrete justice–restoring interventions, judicial processes and abstract justice restoration goals. The pattern of results lends validity to the understanding of justice as two distinct conceptualizations, a distinction that provides much needed explanation for divergent preferences for injustice responses. Copyright © 2011 John Wiley & Sons, Ltd.
Soluble alkyl substituted poly(3,4‐propylenedioxyselenophene)s: A new platform for optoelectronic materials
Authors: Atak Samed , İçli‐Özkut Merve , Önal Ahmet M. , Cihaner Atilla
Published: July 2011

Optical and electrochemical properties of regiosymmetric and soluble alkylenedioxyselenophene‐based electrochromic polymers, namely poly(3,3‐dibutyl‐3,4‐dihydro‐2H‐selenopheno[3,4‐b][1,4]dioxephine) (PProDOS‐C4), poly(3,3‐dihexyl‐3,4‐dihydro‐2H‐selenopheno[3,4‐b][1,4]dioxephine) (PProDOS‐C6), and poly(3,3‐didecyl‐3,4‐dihydro‐2H‐selenopheno[3,4‐b][1,4]dioxephine) (PProDOS‐C10), are highlighted. It is noted that these unique polymers have low bandgaps (1.57–1.65 eV), and they are exceptionally stable under ambient atmospheric conditions. Polymer films retained 82–97% of their electroactivity after 5000 cycles. The percent transmittance of PProDOS‐Cn (n = 4, 6, 10) films found to be between 55 and 59%. Furthermore, these novel soluble PProDOS‐Cn polymers showed electrochromic behavior: a color change form pure blue to highly transparent state in a low switching time (1.0 s) during oxidation with high coloration efficiencies (328–864 cm2 C−1) when compared to their thiophene analogues. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Influence of branching architecture on polymer properties
Authors: Zhu Xinyuan , Zhou Yongfeng , Yan Deyue
Published: July 2011

Hyperbranched polymers (HBPs), invented at the end of 1980s, are one important subclass of the fourth generation macromolecular architectures following the linear, branched, and crosslinking polymers. Due to their unique topological structure and interesting physical/chemical properties, HBPs have attracted wide attention from both academia and industry. HBPs are composed of linear units, dendritic units, and terminal units. The degree of branching (DB), a term to describe the composition of these three structure units and thus the branching architecture of polymers, is one of the most important intrinsic parameters for HBPs. This review has summarized the effect of the DB on the physical and chemical properties of HBPs, including the rheological property, crystallization and melting behaviors, glass transition, thermal and hydrolytic degradations, phase characteristics, lower critical solution temperature phase transition, optoelectronic properties, encapsulation capability, self‐assembly behavior, biomedical applications, and so on. Such a structure and property relationship will build a bridge between the syntheses and applications of HBPs, especially in the application areas of functional materials, biomedical materials, and nanotechnology. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 1277–1286, 2011
Protein expression profiles distinguish between experimental invasive pulmonary aspergillosis and Pseudomonas pneumonia
Authors: Gonzales Denise A. , De Torre Carlos , Wang Honghui , Devor Christopher B. , Munson Peter J. , Ying Sai‐Xia , Kern Steven J. , Petraitiene Ruta , Levens David L. , Walsh Thomas J. , Suffredini Anthony F.
Published: July 2011

This article was originally published in Proteomics 2010, 10, 4270–4280, DOI 10.1002/pmic.200900768
Plasma proteome analysis in diet‐induced obesity‐prone and obesity‐resistant rats
Authors: Choi Jung‐Won , Wang Xia , Joo Jeong In , Kim Dong Hyun , Oh Tae Seok , Choi Duk Kwon , Yun Jong Won
Published: July 2011

This article was originally published in Proteomics 2010, 10, 4386–4400, DOI 10.1002/pmic.201000391
Plasma profiles in active systemic juvenile idiopathic arthritis: Biomarkers and biological implications
Authors: Ling Xuefeng B. , Park Jane L. , Carroll Tanya , Nguyen Khoa D. , Lau Kenneth , Macaubas Claudia , Chen Edward , Lee Tzielan , Sandborg Christy , Milojevic Diana , Kanegaye John T. , Gao Susanna , Burns Jane , Schilling James , Mellins Elizabeth D.
Published: July 2011

This article was originally published in Proteomics 2010, 10, 4415–4430, DOI 10.1002/pmic.201000298
Proteomic analysis of the anti‐inflammatory action of minocycline
Authors: Dunston Christopher R. , Griffiths Helen R. , Lambert Peter A. , Staddon Susan , Vernallis Ann B.
Published: July 2011

This article was originally published in Proteomics 2011, 11, 42–51, DOI 10.1002/pmic.201000273
A large set of estrogen receptor β‐interacting proteins identified by tandem affinity purification in hormone‐responsive human breast cancer cell nuclei
Authors: Nassa Giovanni , Tarallo Roberta , Ambrosino Concetta , Bamundo Angela , Ferraro Lorenzo , Paris Ornella , Ravo Maria , Guzzi Pietro H. , Cannataro Mario , Baumann Marc , Nyman Tuula A. , Nola Ernesto , Weisz Alessandro
Published: July 2011

This article was originally published in Proteomics 2011, 11, 159–165, DOI 10.1002/pmic.201000344
Resurrection of a clinical antibody: Template proteogenomic de novo proteomic sequencing and reverse engineering of an anti‐lymphotoxin‐α antibody
Authors: Castellana Natalie E. , McCutcheon Krista , Pham Victoria C. , Harden Kristin , Nguyen Allen , Young Judy , Adams Camellia , Schroeder Kurt , Arnott David , Bafna Vineet , Grogan Jane L. , Lill Jennie R.
Published: July 2011

This article was originally published in Proteomics 2011, 11, 395–405, DOI 10.1002/pmic.201000487
Proteomics of human embryonic stem cells
Authors: Hughes Chris S. , Nuhn Amelia A. , Postovit Lynne M. , Lajoie Gilles A.
Published: July 2011

This article was originally published in Proteomics 2011, 11, 675–690, DOI 10.1002/pmic.201000407
Detection of immunogenic parasite and host‐specific proteins in the sera of active and chronic individuals infected with Toxoplasma gondii
Authors: Yeng Chen , Osman Emelia , Mohamed Zeehaida , Noordin Rahmah
Published: July 2011

This article was originally published in Electrophoresis 2010, 31, 3843–3849, DOI 10.1002/elps.201000038
Proteomic approaches in myeloid leukemia
Authors: Kanaujiya Jitendra Kumar , Lochab Savita , Pal Pooja , Christopeit Maximilian , Singh Sheo Mohan , Sanyal Sabyasachi , Behre Gerhard , Trivedi Arun Kumar
Published: July 2011

This article was originally published in Electrophoresis 2011, 32, 357–367, DOI 10.1002/elps.201000428
A human sterile alpha motif domain polymerizome
Authors: Knight Mary Jane , Leettola Catherine , Gingery Mari , Li Hao , Bowie James U.
Published: July 2011

The sterile alpha motif (SAM) domain is one of the most common protein modules found in eukaryotic genomes. Many SAM domains have been shown to form helical polymer structures suggesting that SAM modules can be used to create large protein complexes in the cell. Because many polymeric SAM domains form heterogenous and insoluble aggregates that are experimentally intractable when isolated, it is likely that many polymeric SAM domains have gone uncharacterized. We, therefore, developed a method to maintain polymeric SAM domains in a soluble form that allowed rapid screening for potential SAM polymers. SAM domains were expressed as fusions to a super‐negatively charged green fluorescent protein (negGFP). The negGFP imparts three useful properties to the SAM domains: (1) the charge helps to maintain solubility; (2) the charge leads to reliable migration toward the cathode on native gels; and (3) the fluorescence emission allows visualization in crude extracts. Using the negGFP‐SAM fusions, we screened a large library of human SAM domains for polymerization using a native gel screen. A selected set of hSAM domains were then purified and examined for true polymer formation by electron microscopy. In this manner, we identified a set of new potential SAM polymers: ANKS3, Atherin, BicaudalC1, Caskin1, Caskin2, Kazrin, L3MBTL3, L3MBTL4, LBP, LiprinB1, LiprinB2, SAMD8, SAMD9, and STIM2. While further characterization will be necessary to verify that the SAM domains identified here truly form polymers, our results provide a much stronger working hypothesis for a large number of proteins that was possible from sequence analysis alone.
Crystal structure of the read‐through domain from bacteriophage Qβ A1 protein
Authors: Rumnieks Janis , Tars Kaspars
Published: July 2011

Bacteriophage Qβ is a small RNA virus that infects Escherichia coli. The virus particle contains a few copies of the minor coat protein A1, a C‐terminally prolonged version of the coat protein, which is formed when ribosomes occasionally read‐through the leaky stop codon of the coat protein. The crystal structure of the read‐through domain from bacteriophage Qβ A1 protein was determined at a resolution of 1.8 Å. The domain consists of a heavily deformed five‐stranded β‐barrel on one side of the protein and a β‐hairpin and a three‐stranded β‐sheet on the other. Several short helices and well‐ordered loops are also present throughout the protein. The N‐terminal part of the read‐through domain contains a prominent polyproline type II helix. The overall fold of the domain is not similar to any published structure in the Protein Data Bank.
Propensity for C‐terminal domain swapping correlates with increased regional flexibility in the C‐terminus of RNase A
Authors: Miller Katherine H. , Marqusee Susan
Published: July 2011

Domain swapping is a type of oligomerization in which monomeric proteins exchange a structural element, resulting in oligomers whose subunits recapitulate the native, monomeric fold. It has been implicated as a potential mechanism for protein aggregation, which provides a strong impetus to understand the structural determinants and folding mechanisms that trigger domain swapping. Bovine pancreatic ribonuclease A (RNase A) is a well‐studied protein known to domain swap under extreme conditions, such as lyophilization from acetic acid. The major domain‐swapped dimer form of RNase A exchanges a β‐strand at its C‐terminus to form a C‐terminal domain‐swapped dimer. To study the mechanism by which C‐terminal swapping occurs, we used a variant of RNase A containing a P114G mutation that readily domain swaps under physiological conditions. Using NMR and hydrogen–deuterium exchange, we find that the P114G variant has decreased protection from hydrogen exchange compared to the wild‐type protein near the C‐terminal hinge region. Our results suggest that domain swapping occurs via a local high‐energy fluctuation at the C‐terminus.
Light particles coupled to photons
Authors: Massó E.
Published: July 2011

The motivation and physics of light particles coupled to photons is reviewed.
Effects of Packaging Liners on Cooling Rate and Quality Attributes of Table Grape (cv. Regal Seedless)
Authors: Ngcobo M. E. K. , Opara U. L. , Thiart G. D.
Published: July 2011

Table grapes are commonly packed in multi‐layered packages consisting of cardboard carton, plastic liners and carry bag/pouch to maintain product quality along the cold chain. Each liner is characterized by the number and the size of perforations, which influence the environmental conditions around the produce inside the package. This study investigated the effects of different carton liners on the cooling rate and quality attributes of ‘Regal Seedless’ table grapes. Fruit quality attributes measured include weight loss, stem dehydration and browning, SO2 injury, decay, berry firmness and colour. Non‐perforated liners maintained relative humidity (RH) close to 100% during cold storage and during a 7 day shelf life period, which resulted in delaying the loss of stem quality but significantly (p ≤ 0.05) increasing the incidence of SO2 injury and berry drop during storage, as compared with perforated liners. Perforated liners improved fruit cooling rates but significantly (p ≤ 0.05) reduced RH. Low RH in perforated liners resulted in significant (p ≤ 0.05) increase in stem dehydration and browning as compared with non‐perforated liners. Berry firmness decreased by 78% after 42 days of storage at −0.5°C. Significant (p ≤ 0.05) differences in berry firmness between the different packages were observed only during the first 7 days of storage. Berry colour changed from greenish‐yellow to yellowish‐green in all types of plastic liner during the storage period. Fruit decay occurred in all packages after a 7 day shelf life, with the highest incidence of decay occurring in liners with less perforation. Copyright © 2011 John Wiley & Sons, Ltd.
Collaborative service evaluation with the TwoHop trust framework
Authors: Glynos Dimitris , Argyroudis Patroklos , Douligeris Christos
Published: July 2011

The TwoHop trust framework is a collaborative system for computing trust towards service providers in a peer‐to‐peer network. TwoHop participants share their trust information so that peers without prior interaction may establish indirect trust relationships. TwoHop imposes a limit of two hops on trust delegation chains, which allows for increased efficiency in the trust calculation process. In addition, it provides multiple edges between nodes in the trust graph, allowing for the existence of both service evaluations and recommendations for service evaluators. In this paper, we present an improved version of the TwoHop trust calculation algorithm along with a formal description of its model of trust. We evaluate its key characteristics against those of other trust frameworks and compare it with the EigenTrust algorithm and to an improved version of the PeerTrust algorithm in terms of performance. Our simulation results indicate the robustness of our design against dishonest participants and its ability to scale to accommodate the needs of large peer‐to‐peer networks. Copyright © 2011 John Wiley & Sons, Ltd.
Optimality, sample size, and power calculations for the sequential parallel comparison design
Authors: Ivanova Anastasia , Qaqish Bahjat , Schoenfeld David A.
Published: July 2011

The sequential parallel comparison design (SPCD) has been proposed to increase the likelihood of success of clinical trials in therapeutic areas where high‐placebo response is a concern. The trial is run in two stages, and subjects are randomized into three groups: (i) placebo in both stages; (ii) placebo in the first stage and drug in the second stage; and (iii) drug in both stages. We consider the case of binary response data (response/no response). In the SPCD, all first‐stage and second‐stage data from placebo subjects who failed to respond in the first stage of the trial are utilized in the efficacy analysis. We develop 1 and 2 degree of freedom score tests for treatment effect in the SPCD. We give formulae for asymptotic power and for sample size computations and evaluate their accuracy via simulation studies. We compute the optimal allocation ratio between drug and placebo in stage 1 for the SPCD to determine from a theoretical viewpoint whether a single‐stage design, a two‐stage design with placebo only in the first stage, or a two‐stage design is the best design for a given set of response rates. As response rates are not known before the trial, a two‐stage approach with allocation to active drug in both stages is a robust design choice. Copyright © 2011 John Wiley & Sons, Ltd.
Bayesian information criterion for longitudinal and clustered data
Authors: Jones Richard H.
Published: July 2011

When a number of models are fit to the same data set, one method of choosing the ‘best’ model is to select the model for which Akaike's information criterion (AIC) is lowest. AIC applies when maximum likelihood is used to estimate the unknown parameters in the model. The value of −2 log likelihood for each model fit is penalized by adding twice the number of estimated parameters. The number of estimated parameters includes both the linear parameters and parameters in the covariance structure. Another criterion for model selection is the Bayesian information criterion (BIC). BIC penalizes −2 log likelihood by adding the number of estimated parameters multiplied by the log of the sample size. For large sample sizes, BIC penalizes −2 log likelihood much more than AIC making it harder to enter new parameters into the model. An assumption in BIC is that the observations are independent. In mixed models, the observations are not independent. This paper develops a method for calculating the ‘effective sample size’ for mixed models based on Fisher's information. The effective sample size replaces the sample size in BIC and can vary from the number of subjects to the number of observations. A number of error models are considered based on a general mixed model including unstructured, compound symmetry (random intercept), first‐order autoregression with observational error and random intercept and slope. Copyright © 2011 John Wiley & Sons, Ltd.
Analyzing direct and indirect effects of treatment using dynamic path analysis applied to data from the Swiss HIV Cohort Study
Authors: Røysland Kjetil , Gran Jon Michael , Ledergerber Bruno , von Wyl Viktor , Young James , Aalen Odd O.
Published: July 2011

When applying survival analysis, such as Cox regression, to data from major clinical trials or other studies, often only baseline covariates are used. This is typically the case even if updated covariates are available throughout the observation period, which leaves large amounts of information unused. The main reason for this is that such time‐dependent covariates often are internal to the disease process, as they are influenced by treatment, and therefore lead to confounded estimates of the treatment effect. There are, however, methods to exploit such covariate information in a useful way. We study the method of dynamic path analysis applied to data from the Swiss HIV Cohort Study. To adjust for time‐dependent confounding between treatment and the outcome ‘AIDS or death’, we carried out the analysis on a sequence of mimicked randomized trials constructed from the original cohort data. To analyze these trials together, regular dynamic path analysis is extended to a composite analysis of weighted dynamic path models. Results using a simple path model, with one indirect effect mediated through current HIV‐1 RNA level, show that most or all of the total effect go through HIV‐1 RNA for the first 4 years. A similar model, but with CD4 level as mediating variable, shows a weaker indirect effect, but the results are in the same direction. There are many reasons to be cautious when drawing conclusions from estimates of direct and indirect effects. Dynamic path analysis is however a useful tool to explore underlying processes, which are ignored in regular analyses. Copyright © 2011 John Wiley & Sons, Ltd.
The influence of prior industry affiliation on framing in nascent industries: the evolution of digital cameras
Authors: Benner Mary J. , Tripsas Mary
Published: July 2011

New industries sparked by technological change are characterized by high uncertainty. In this paper, we explore how a firm's conceptualization of products in this context, as reflected by product feature choices, is influenced by prior industry affiliation. We study digital cameras introduced from 1991–2006 by firms from three prior industries. We hypothesize and find that: (1) prior industry experience shapes a set of shared beliefs that results in similar and concurrent firm behavior; (2) firms notice and imitate the behaviors of firms from the same prior industry; and, (3) as firms gain experience with particular features, the influence of prior industry decreases. This study extends previous research on firm entry into new domains by examining heterogeneity in firms' framing and feature‐level entry choices. Copyright © 2011 John Wiley & Sons, Ltd.
Transcriptome Analysis of Neural Progenitor Cells by a Genetic Dual Reporter Strategy
Authors: Wang Jun , Zhang Heying , Young Amanda G. , Qiu Runxiang , Argalian Siranush , Li Xuejun , Wu Xiwei , Lemke Greg , Lu Qiang
Published: July 2011

Global analysis of stem/progenitor cells promises new insight into mechanisms that govern self-renewal and cellular potential, an unresolved question of stem/progenitor cell biology. Despite rapid advance of genome-wide profiling methods, the difficulty in cell purification remains a major challenge for global analysis of somatic stem/progenitor cells. Genetic tagging with a reporter provides a powerful tool for identification and isolation of a specific mature cell type; however, for stem/progenitor cells, reporter retention by progeny may be a concern for impurity. Here, we describe a genetic system combining a progenitor cell specific label with a second tag for marking differentiation. We present evidence that differential labeling of neural progenitor cells and their progeny enables prospective purification of these two cell types, whereas isolation based on a single marker compromises the purity of the intended progenitor population. Comparative expression profiling between the purified progenitors and progeny documents a neural progenitor cell transcriptome and uncovers an important role of Tyro3/Axl/Mer receptor tyrosine kinases in the maintenance of neural progenitor cells. This study establishes a general strategy for isolation of somatic stem/progenitor cells and provides a transcriptome database of neural progenitor cells useful for identification of causal factors of neural progenitor cell state, global dissection of epigenetic control of cellular potential, as well as for developing biomarkers or targets of brain cancer stem/initiating cells for therapeutic interventions.
How can urban centers adapt to climate change with ineffective or unrepresentative local governments?
Authors: Satterthwaite David
Published: July 2011

This article considers the prospects for urban areas in the Global South to adapt to climate change. It describes how most of the needed adaptations in the next few decades can be integrated into existing government functions, investments, regulations, and agencies. It also considers why most such measures are unlikely to be implemented—because of either the lack of capacity within urban governments or their unwillingness to address the infrastructure and service needs of their low‐income populations. Most urban centers in the Global South also have very large deficits in the basic infrastructure and services that are needed for resilience to climate change impacts. The article also considers how the policies and practices of higher levels of government and international agencies need to change if the much needed adaptive capacity is to be built in urban areas.WIREs Clim Change2011 2 767–776 DOI: 10.1002/wcc.136

This article is categorized under:

Vulnerability and Adaptation to Climate Change > Institutions for Adaptation

Climate and Development > Urbanization, Development, and Climate Change

Policy and Governance > Governing Climate Change in Communities, Cities, and Regions