bluuebunny/crossref_metadata_2025 huggingface dataset:
A costing model for offshore decommissioning in California
Authors: Bressler Andrew , Bernstein Brock B
Published: April 2015

California's 27 offshore oil and gas platforms will reach the end of their useful lifetimes sometime in the near future and will require decommissioning. Although existing leases require complete removal of all platforms and associated infrastructure, the underlying laws and regulations have changed in recent years to allow a number of alternative uses after decommissioning. In particular, AB 2503, signed into law in September 2010, provides for a rigs-to-reefs program that allows the state to accept ownership of decommissioned platforms in federal waters. Decisions about whether to remove platforms completely or leave them in place as artificial reefs will depend in part on the relative cost of the 2 options. In this study, we describe the design and use of a mathematical decision model that provides detailed cost estimates of complete and partial removal (to 85 feet below the water line) for California's offshore platforms. The model, PLATFORM, is loaded with Bureau of Safety and Environmental Enforcement (BSEE) and Bureau of Ocean Energy Management (BOEM) costs for complete removal, along with costs for partial removal calculated for this study and estimates of the uncertainty associated with decommissioning cost estimates. PLATFORM allows users to define a wide range of decommissioning and costing scenarios (e.g., number of platforms, choice of heavy lift vessel, shell mound removal, reef enhancement). As a benchmark cost, complete removal of all 27 offshore platforms, grouped into the 7 decommissioning projects defined by the most recent federal cost estimates produced in 2010, would cost an estimated $1.09 billion, whereas partial removal of these platforms, grouped into the same set of projects, would cost $478 million, with avoided costs of $616 million (with minor rounding). Integr Environ Assess Manag 2015;X:000–000. © 2015 SETAC

Key Points

PLATFORM is an interactive decision model that uses options and suboptions to calculate oil and gas platform decommissioning costs, for complete and partial decommissioning scenarios. PLATFORM allows users to explore a wide range of decommissioning and costing scenarios, as well as providing preprogrammed features that allow detailed examination of how uncertainty may affect analysis results. Using PLATFORM, complete removal of all 27 offshore platforms as proposed would cost an estimated $1.09 billion, while partial removal of these platforms would cost $478 million, with avoided costs of about $616 million. Using PLATFORM to estimate costs for 3 illustrative scenarios, the cost savings of the partial removal option for decommissioning was found to be substantial for larger platforms when compared to complete removal.
Evaluating alternatives for decommissioning California's offshore oil and gas platforms
Authors: Bernstein Brock B
Published: April 2015

This paper introduces a series of 6 additional papers in this issue that describe an in-depth analysis of options for decommissioning oil and gas platforms offshore southern California. Although current leases require lessees in both state and federal waters to completely remove all production facilities and restore the seafloor to its pre-platform condition, other options have emerged since these leases were signed. Laws and regulations in other jurisdictions (particularly in federal waters) have evolved to allow a number of other uses such as aquaculture, alternative energy production, and artificial reefing. In response, the California Natural Resources Agency initiated an effort to investigate the issues associated with these and other decommissioning alternatives. The papers in this series are the result of the second phase in this process, a broad investigation of the engineering, economic, and environmental costs and benefits of the most feasible and likely options. In addition to the project's final report, the authors produced an interactive mathematical decision model, PLATFORM, that enables users to explore the implications of different decommissioning projects and options, as well as the effects of different approaches to valuing the associated costs and benefits. Integr Environ Assess Manag 2015;X:000–000. © 2015 SETAC

Key Points

This article introduces the papers in this series analyzing options for decommissioning the 27 oil and gas platforms off the coast of Southern California, in both state and federal waters. Current leases require lessees in both state and federal water to completely decommission all platform facilities and restore the seafloor to preproduction conditions. Since platform leases were signed, additional decommissioning options have become available including artificial reefs, aquaculture, and alternative reefing, resulting in subsequent changes in laws and regulations.
Reading Outside the Book
Authors: Kentner Sarah
Published: April 2015

This column features essays written by current middle school and high school teachers, media specialists, librarians, literacy coaches, curriculum specialists, administrators, preservice teachers, teacher educators, and adolescent and adult learners. They highlight diverse perspectives on teaching and/or learning with literacies to inspire reader reflection.
Print‐Based Texts
Authors: Blasingame James
Published: April 2015

This column provides reviews of adolescent and adult literature and provides a valuable resource for literature selection in‐ and outside the classroom.
Visual and Digital Texts
Authors: Botzakis Stergios
Published: April 2015

This column provides reviews of adolescent and adult visual and digital texts and provides a valuable resource for visual and digital text selection in‐ and outside the classroom.
Pavlovian conditioning enhances resistance to disruption of dogs performing an odor discrimination
Authors: Hall Nathaniel J. , Smith David W. , Wynne Clive D.L.
Published: April 2015

Domestic dogs are used to aid in the detection of a variety of substances such as narcotics and explosives. Under real‐world detection situations there are many variables that may disrupt the dog's performance. Prior research on behavioral momentum theory suggests that higher rates of reinforcement produce greater resistance to disruption, and that this is heavily influenced by the stimulus‐reinforcer relationship. The present study tests the Pavlovian interpretation of resistance to change using dogs engaged in an odor discrimination task. Dogs were trained on two odor discriminations that alternated every six trials akin to a multiple schedule in which the reinforcement probability for a correct response was always 1. Dogs then received several sessions of either odor Pavlovian conditioning to the S+ of one odor discrimination (Pavlovian group) or explicitly unpaired exposure to the S+ of one odor discrimination (Unpaired group). The remaining odor discrimination pair for each dog always remained an unexposed control. Resistance to disruption was assessed under presession feeding, a food‐odor disruptor condition, and extinction, with baseline sessions intervening between disruption conditions. Equivalent baseline detection rates were observed across experimental groups and odorant pairs. Under disruption conditions, Pavlovian conditioning led to enhanced resistance to disruption of detection performance compared to the unexposed control odor discrimination. Unpaired odor conditioning did not influence resistance to disruption. These results suggest that changes in Pavlovian contingencies are sufficient to influence resistance to change.
Characterization of N,N‐dimethyl amino acids by electrospray ionization–tandem mass spectrometry
Authors: Naresh Chary V. , Sudarshana Reddy B. , Kumar Ch. Dinesh , Srinivas R. , Prabhakar S.
Published: April 2015

Methylation is an essential metabolic process for a number of critical reactions in the body. Methyl groups are involved in the healthy function of the body life processes, by conducting methylation process involving specific enzymes. In these processes, various amino acids are methylated, and the occurrence of methylated amino acids in nature is diverse. Nowadays, mass‐spectrometric‐based identification of small molecules as biomarkers for diseases is a growing research. Although all dimethyl amino acids are metabolically important molecules, mass spectral data are available only for a few of them in the literature. In this study, we report synthesis and characterization of all dimethyl amino acids, by electrospray ionization–tandem mass spectrometry (MS/MS) experiments on protonated molecules. The MS/MS spectra of all the studied dimethyl amino acids showed preliminary loss of H2O + CO to form corresponding immonium ions. The other product ions in the spectra are highly characteristic of the methyl groups on the nitrogen and side chain of the amino acids. The amino acids, which are isomeric and isobaric with the studied dimethyl amino acids, gave distinctive MS/MS spectra. The study also included MS/MS analysis of immonium ions of dimethyl amino acids that provide information on side chain structure, and it is further tested to determine the N‐terminal amino acid of the peptides. Copyright © 2015 John Wiley & Sons, Ltd.
Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure
Authors: D'Atri Valentina , Porrini Massimiliano , Rosu Frédéric , Gabelica Valérie
Published: April 2015

Ion mobility spectrometry experiments allow the mass spectrometrist to determine an ion's rotationally averaged collision cross section ΩEXP. Molecular modelling is used to visualize what ion three‐dimensional structure(s) is(are) compatible with the experiment. The collision cross sections of candidate molecular models have to be calculated, and the resulting ΩCALC are compared with the experimental data. Researchers who want to apply this strategy to a new type of molecule face many questions: (1) What experimental error is associated with ΩEXP determination, and how to estimate it (in particular when using a calibration for traveling wave ion guides)? (2) How to generate plausible 3D models in the gas phase? (3) Different collision cross section calculation models exist, which have been developed for other analytes than mine. Which one(s) can I apply to my systems? To apply ion mobility spectrometry to nucleic acid structural characterization, we explored each of these questions using a rigid structure which we know is preserved in the gas phase: the tetramolecular G‐quadruplex [dTGGGGT]4, and we will present these detailed investigation in this tutorial. © 2015 The Authors. Journal of Mass Spectrometry published by John Wiley & Sons Ltd.
Evaluation of adsorption and desorption steps in the solid‐phase extraction of explosives using carbon/silica gel nanocomposites
Authors: Tomaszewski Waldemar , Gun'ko Vladimir M.
Published: April 2015

New series of carbon/silica gel nanocomposites, carbosils, prepared by the carbonization of starch bound to silica gel, and carbosils additionally silylated with octadecyldimethylchlorosilane were synthesized. These materials were applied as adsorbents in the solid‐phase extraction of explosive nitrate esters and nitroaromatics from aqueous solutions. The adsorption and desorption steps were evaluated separately. It was found that both the molecular properties of explosives (dipole moments, orbital energies, solvation effects) and textural properties influenced by carbon deposits or octadecyl moieties have a large impact on the recovery rates. It was shown that the composites with moderate content of carbon deposits or with the highest amounts of carbon deposits and additionally silylated can be used as materials tailored for extraction of explosives from the aqueous solutions.
Molecularly imprinted polymers on a silica surface for the adsorption of tobacco‐specific nitrosamines in mainstream cigarette smoke
Authors: Li Min‐ting , Zhu Yong‐yan , Li Li , Wang Wen‐na , Yin Yong‐guan , Zhu Quan‐hong
Published: April 2015

Tobacco‐specific nitrosamines are one of the most important groups of carcinogens in tobacco products. Using adsorbents as filter additives is an effective way to reduce tobacco‐specific nitrosamines in cigarette smoke. Molecularly imprinted polymers (MIPs) using nicotinamide as template were grafted on the silica gel surface to obtain MIP@SiO2 and employed as filter additives to absorb tobacco‐specific nitrosamines in mainstream cigarette smoke. Four milligrams of MIP@SiO2 per cigarette was added to the interface between filter and tobacco rod to prepare a binary filter system. The mainstream smoke was collected on an industry‐standard Cambridge filter pad and extracted with ammonium acetate aqueous solution before analysis. Compared to the cigarette smoke of the control group, the levels of tobacco‐specific nitrosamines with silica gel and with MIP@SiO2 were both reduced, and the adsorption rates of N‐nitrosonornicotine, N‐nitrosoanabasine, N‐nitrosoanatabine, and 4‐(methylnitrosamino)‐1‐(3‐pyridine)‐1‐butanone with silica gel and with MIP@SiO2 were 20.76, 15.32, 18.79, and 18.01%, and 41.33, 34.04, 37.86, and 35.53%, respectively. Furthermore the content of total particle materials in cigarette smoke with silica gel was decreased evidently but showed no observable change with MIP@SiO2. It indicated MIP@SiO2 could selectively reduce tobacco‐specific nitrosamines in the mainstream cigarette smoke with no change to the cigarette flavor.
Simultaneous quantitation of six major quassinoids in Tongkat Ali dietary supplements by liquid chromatography with tandem mass spectrometry
Authors: Han Young Min , Jang Moonhee , Kim In Sook , Kim Seung Hyun , Yoo Hye Hyun
Published: April 2015

Tongkat Ali (Eurycoma longifolia) is one of the most popular traditional herbs in Southeast Asia and generally consumed as forms of dietary supplements, tea, or drink additives for coffee or energy beverages. In this study, the liquid chromatography with tandem mass spectrometry method for the simultaneous quantitation of six major quassinoids of Tongkat Ali (eurycomanone, 13,21‐dihydroeurycomanone, 13α(21)‐epoxyeurycomanone, 14,15β‐dihydroxyklaineanone, eurycomalactone, and longilactone) was developed and validated. Using the developed method, the content of the six quassinoids was measured in Tongkat Ali containing dietary supplement tablets or capsules, and the resulting data were used to confirm the presence of Tongkat Ali in those products. Among the six quassinoids, eurycomanone was the most abundant quassinoid in all samples tested. The developed method would be useful for the quality assessment of Tongkat Ali containing dietary supplements.
Development of an enzyme‐linked immunosorbent assay and immunoaffinity chromatography for glycyrrhizic acid using an anti‐glycyrrhizic acid monoclonal antibody
Authors: Zhang Yue , Qu Huihua , Zeng Wenhao , Zhao Yan , Shan Wenchao , Wang Xueqian , Wang Qingguo , Zhao Yan
Published: April 2015

In this work, a new monoclonal antibody specific for glycyrrhizic acid was prepared and characterized. A hybridoma secreting an anti‐glycyrrhizic acid monoclonal antibody was produced by fusing splenocytes from a mouse immunized against a glycyrrhizic acid–bovine serum albumin conjugate with the hypoxanthine–aminopterin–thymidine‐sensitive mouse myeloma cell line (Sp2/0‐Ag14). Subsequently, an indirect, competitive enzyme‐linked immunosorbent assay for glycyrrhizic acid was developed using the monoclonal antibody. In this assay, we detected an effective measuring range of 78.12–2500 ng/mL. Both intra‐assay and inter‐assay repeatability and precision were achieved, with relative standard deviations lower than 10%. In addition, glycyrrhizic acid levels in both formulated Chinese medicines and biological samples were determined with high sensitivity and efficiency. We then successfully developed a reliable immunoaffinity chromatography to separate glycyrrhizic acid completely from its parent medicine. These methods will contribute to further research investigations to better understand the interactions of glycyrrhizic acid with other drugs in the complex system of traditional Chinese medicine.
Rivastigmine for mild cognitive impairment in Parkinson disease: A placebo‐controlled study
Authors: Mamikonyan Eugenia , Xie Sharon X. , Melvin Emilie , Weintraub Daniel
Published: April 2015

Mild cognitive impairment (MCI) in Parkinson's disease (PD) may be associated with subtle functional impairment and worse quality of life. The objective of this study was to determine the efficacy and tolerability of rivastigmine for PD‐MCI. Patients with PD‐MCI (n = 28) were enrolled in a 24‐week, randomized, double‐blind, placebo‐controlled, crossover, single‐site study of the rivastigmine transdermal patch. The primary outcome measure was the Alzheimer's Disease Cooperative Study—Clinical Global Impression of Change (ADCS‐CGIC). Secondary outcomes included the Montreal Cognitive Assessment (MoCA), Dementia Rating Scale‐2 (DRS‐2), Neurotrax computerized cognitive battery, the Everyday Cognition Battery (ECB), and the Parkinson's Disease Questionnaire (PDQ‐8). Twenty‐six participants (92.9%) completed both study phase assessments, and 23 (82.1%) completed both phases on study medication. The CGIC response rate demonstrated a trend effect in favor of rivastigmine (regression coefficient for interaction term in linear mixed‐effects model = 0.44, F[df] = 3.01 [1, 24], P = 0.096). For secondary outcomes, a significant rivastigmine effect on the ECB (regression coefficient = –2.41, F[df] = 5.81 [1, 22.05], P = 0.03) was seen, but no treatment effect was found on any cognitive measures. Trend effects also occurred in favor of rivastigmine on the PDQ‐8 (regression coefficient = 4.55, F[df] = 3.93 [1, 14. 79], P = 0.09) and the State Anxiety Inventory (regression coefficient = –1.24, F[df] = 3.17 [1, 33], P = 0.08). Rivastigmine in PD‐MCI showed a trend effect for improvements on a global rating of cognition, disease‐related health status, and anxiety severity, and significant improvement on a performance‐based measure of cognitive abilities. © 2015 International Parkinson and Movement Disorder Society
Accurate genetic diagnosis of Finnish pulmonary arterial hypertension patients using oligonucleotide‐selective sequencing
Authors: Vattulainen Sanna , Aho Joonas , Salmenperä Pertteli , Bruce Siina , Tallila Jonna , Gentile Massimiliano , Sankelo Marja , Laitinen Tarja , Koskenvuo Juha W. , Alastalo Tero‐Pekka , Myllykangas Samuel
Published: April 2015

The genetic basis of pulmonary arterial hypertension (PAH) among Finnish PAH patients is poorly understood. We adopted a novel‐targeted next‐generation sequencing (NGS) approach called Oligonucleotide‐Selective Sequencing (OS‐Seq) and developed a custom data analysis and interpretation pipeline to identify pathogenic base substitutions, insertions, and deletions in seven genes associated with PAH (BMPR2, BMPR1B, ACVRL1, ENG, SMAD9, CAV1, and KCNK3) from Finnish PAH patients. This study represents the first clinical study with OS‐Seq technology on patients suffering from a rare genetic disorder. We analyzed DNA samples from 21 Finnish PAH patients, whose BMPR2 and ACVRL1 mutation status had been previously studied using Sanger sequencing. Our sequencing panel covered 100% of the targeted base pairs with >15× sequencing depth. Pathogenic base substitutions were identified in the BMPR2 gene in 29% of the Finnish PAH cases. Two of the pathogenic variant‐positive patients had been previously tested negative using Sanger sequencing. No clinically significant variants were identified in the six other PAH genes. Our study validates the use of targeted OS‐Seq for genetic diagnostics of PAH and revealed pathogenic variants that had been previously missed using Sanger sequencing.
Free flow‐through anterolateral thigh flap for complex knee defect including the popliteal artery
Authors: Miyamoto Shimpei , Fujiki Masahide , Nakatani Fumihiko , Sakisaka Masanobu , Sakuraba Minoru
Published: April 2015

Reconstruction of complex knee defects including the popliteal artery presents a challenging problem in reconstructive microsurgery. Reconstruction of the popliteal artery and soft‐tissue coverage should be performed simultaneously for limb salvage. We present the one‐stage reconstruction of a complex knee defect including the popliteal artery using a free flow‐through anterolateral thigh (ALT) flap as a bypass flap in two patients with sarcomas. In both patients, the popliteal artery and vein were reconstructed using branches of the lateral circumflex femoral arterial system. The flaps survived without vascular compromise and the limbs were preserved successfully. Free flow‐through ALT flap enables simultaneous leg revascularization and soft‐tissue coverage with a single free flap. The lateral circumflex femoral arterial system has many branches with large diameters, making it suitable for reconstruction of multiple infrapopliteal arteries. © 2015 Wiley Periodicals, Inc. Microsurgery 35:485–488, 2015.
Comparison of the effects of five dietary fibers on mucosal transcriptional profiles, and luminal microbiota composition and SCFA concentrations in murine colon
Authors: Lange Katja , Hugenholtz Floor , Jonathan Melliana C. , Schols Henk A , Kleerebezem Michiel , Smidt Hauke , Müller Michael , Hooiveld Guido J. E. J.
Published: April 2015

Scope

The aim of our study was to investigate and compare the effects of five fibers on the mucosal transcriptome, together with alterations in the luminal microbiota composition and SCFA concentrations in the colon.

Methods and results

Mice were fed fibers that differed in carbohydrate composition or a control diet for 10 days. Colonic gene expression profiles and luminal microbiota composition were determined by microarray techniques, and integrated using multivariate statistics. Our data showed a distinct reaction of the host and microbiota to resistant starch, a fiber that was not completely fermented in the colon, whereas the other fibers induced similar responses on gene expression and microbiota. Consistent associations were revealed between fiber‐induced enrichment of Clostridium cluster IV and XIVa representatives, and changes in mucosal expression of genes related to energy metabolism. The nuclear receptor PPAR‐γ was predicted to be an important regulator of the mucosal responses.

Conclusion

Results of this exploratory study suggest that despite different sources and composition, fermentable fibers induce a highly similar mucosal response that may at least be partially governed by PPAR‐γ.
Distribution of serum transferrin, and its associations with metabolic disorders among Chinese: A nation‐wide, health and nutrition survey
Authors: Zhao Hong‐Qiang , Wu He , Meng Ran , Du Shufa , Tao Shu‐Juan
Published: April 2015

Scope

This study examined the associations of serum transferrin and metabolic disorders among Chinese population.

Methods and results

This study is based on nation‐wide, population‐based China Health and Nutrition survey including 8564 men and women aged 18 years or older. Anthropometric and fasting blood glucose, insulin, lipids, and transferrin data were collected. Elevated transferrin concentrations associated with higher body mass index, waist circumference, lipids, insulin, glucose (all p < 0.0001). Serum transferrin concentrations increased gradually with increasing numbers of metabolic syndrome (MetS) components among men and women (p = 0.0003). Elevated concentrations of transferrin were significantly related with higher risk of MetS (p = 0.0006), obesity (p = 0.0089), overweight (p < 0.0001). No associations between transferrin concentrations and risk of diabetes and high blood pressure were observed in both men and women.

Conclusion

Elevated transferrin concentrations were positively associated with risk of MetS and obesity, but not with risk of diabetes among Chinese.
Mortality in myasthenia gravis: A nationwide population–based follow‐up study in Denmark
Authors: Hansen Julie S. , Danielsen Ditte H. , Somnier Finn E. , Frøslev Trine , Jakobsen Johannes , Johnsen Søren P. , Andersen Henning
Published: April 2015

Introduction: In previous studies of myasthenia gravis (MG), increased mortality has been reported. The aim of this study was to estimate mortality in patients with acetylcholine receptor antibody–positive (AChR‐Ab–seropositive) MG in a nationwide population–based, long‐term follow‐up study. Methods: All AChR‐Ab–seropositive MG patients, diagnosed between 1985 and 2005, were identified. Defined by age at diagnosis (≤50 or >50 years), patients were classified as having early‐ or late‐onset MG. For comparison, 10 non‐MG individuals from the general population were matched with each patient. All patients and controls were followed until January 1, 2009. Mortality rates and estimated mortality rate ratios (MRRs) were calculated. Results: Of 702 AChR‐Ab–seropositive MG patients, 302 died during follow‐up. Overall mortality was higher for patients with MG (MRR = 1.41, range 1.24–1.60). In late‐onset women and men, the MRRs were 1.64 (1.36–1.99) and 1.22 (1.02–1.46), respectively. Total MRR was highest during the first 5 years after diagnosis. Conclusions: MG diagnosis is still associated with increased mortality. Muscle Nerve 53: 73–77, 2016
Musculoskeletal Symptoms in Nurses in the Early Implementation Phase of California's Safe Patient Handling Legislation
Authors: Lee Soo‐Jeong , Lee Joung Hee , Gershon Robyn R. M.
Published: April 2015

Musculoskeletal injuries and symptoms are prevalent in nurses and are largely associated with strenuous patient handling. In 2011, California enacted legislation that required acute‐care hospitals to implement safe patient handling (SPH) policies and programs. To assess the early phase of this legislation, we conducted an epidemiological assessment of organizational SPH practices, musculoskeletal symptoms, and perceptions in a random sample of 396 registered nurses. Among those who worked in hospitals and had patient handling duties (n = 220), the 12 month prevalence of work‐related musculoskeletal symptoms was 69% (lower back 54%, neck 41%, shoulders 34%, and hands/wrists 26%). Twenty‐two percent of the nurses reported that their hospitals had a “no‐lift” policy, 37% reported that their hospitals had lift teams, and 61% reported the availability of mechanical lift equipment such as floor or ceiling lifts. Nurses whose facilities employed lift teams were significantly less likely to report low back pain (OR = 0.54, 95% CI [0.30–0.97]). Nurses whose units had ceiling lifts were significantly less likely to report shoulder pain than nurses with no access to lifts (OR = 0.32, 95% CI [0.10–0.98]). Roughly 60% of respondents were aware of the SPH law, and 33% reported changes in their hospital's patient handling policies or programs since the law went into effect. Hospital SPH practices reported by the nurses in our sample were generally sub‐optimal, but our findings suggest positive effects of elements required by SPH legislation. These data will serve as the baseline for future evaluation of the impact of this law in California. © 2015 Wiley Periodicals, Inc.
Comparison of the mechanical, thermomechanical, thermal, and morphological properties of pumice and calcium carbonate‐filled poly(phenylene sulfide) composites
Authors: Sahin Alperen , Karsli Nevin Gamze , Sinmazcelik Tamer
Published: April 2015

In this study, it was aimed to investigate the mechanical, thermal, thermomechanical, and morphological properties of pumice and calcium carbonate (CaCO3)‐filled poly(phenylene sulfide) (PPS) composites and compare the effect of these filler materials on the properties of composites. Mechanical test results indicate that %1 pumice and CaCO3 addition increased the tensile strength value of PPS. With the %1 loading level of pumice, tensile strain of composites remained unchanged, but for other loading levels of both fillers, tensile strain of composites decreased. Hardness of composites increased with the addition of pumice to PPS matrix for all loading levels of pumice. The lowest damping factor peak intensity was observed for %1 pumice included composites. Morphological analyses results revealed that pumice particles are clearly embedded in the PPS matrix and covered with matrix. On the other hand, there are a number of microvioids that can be observed in the tensile fracture surfaces of CaCO3‐filled composites. POLYM. COMPOS., 37:3160–3166, 2016. © 2015 Society of Plastics Engineers
Proteomic approach to understand metastatic spread
Authors: Skvortsov Sergej , Arnold Christoph R. , Debbage Paul , Lukas Peter , Skvortsova Ira
Published: April 2015

The majority of tumor‐related deaths are due to metastasis. Despite the clinical importance of understanding metastasis, we lack knowledge of the molecular mechanisms underlying tumor cell spreading and cell survival far from the primary tumor. Elucidating the molecular characteristics of highly metastatic carcinoma cells would help identify biomarkers or therapeutic targets relevant to predicting or combatting metastasis, and for this the phenotype of metastatic cells could be much more important than their genotype. Hence, proteomic approaches have wide potential utility. This review discusses possibilities of analyzing metastasis‐specific protein patterns in a range of sample types, including in vitro and in vivo cancer models, and tissues and biological fluids from patients. Proteome approaches can identify proteins involved in regulating the metastatic capacities of tumors.
Acute phase proteins altered in the plasma of patients with congenital ventricular septal defect
Authors: Zhang Xi , Wang Kai , Yang Qin , Wang Jun , Xuan Chao , Liu Xiao‐Cheng , Liu Zhi‐Gang , He Guo‐Wei
Published: April 2015

Purpose

Ventricular septal defect (VSD) has intracardiac left‐to‐right shunt and increased pulmonary flow that may affect the acute phase response (APR). We examined the hypothesis that plasma proteins of VSD patients may be altered.

Experimental design

2DE and MS were used to detect differential plasma proteins in VSD patients (n = 55) and controls (n = 70). Candidate APR proteins were confirmed by ELISA in new samples.

Results

Among three differentially expressed APR proteins from 322 protein spots detected, haptoglobin (0.4 ± 0.04 versus 0.6 ± 0.07 mg/mL; p = 0.016) and serum amyloid P‐component (SAP) (3.8 ± 0.2 versus 6.3 ± 0.8 ng/mL; p = 0.003) were significantly lower and orosomucoid 2 (3.1 ± 0.1 mg/mL versus 2.3 ± 0.1 mg/mL; p < 0.001) was significantly higher in VSD patients than in normal controls.

Conclusions and clinical relevance

The plasma concentration of three acute phase proteins, haptoglobin, SAP, and orosomucoid 2 are altered that may reflect inflammation, be associated with decreased innate immune system function, and predispose the VSD patients to vulnerability to infections and pulmonary disease. These three proteins in plasma may also be developed as biomarkers for the function of innate immune system in patients with congenital heart disease.
Using fibers for rapid extraction of proteins from urine
Authors: Gao Youhe
Published: April 2015

The method for rapid extraction of proteins from urine published in this special issue (Manard, B. T. et al., Proteomics Clin. Appl. 2015, 9, 522–530) may have more profound implications than the authors have claimed, simply because urine is more important than most biomarker researchers realized. Unlike blood that is tightly controlled by homeostatic mechanisms of the body, urine tolerates, and accumulates a much larger degree of changes in its components, making it a more important biomarker source than blood.
Identifying migration corridors of mule deer threatened by highway development
Authors: Coe Priscilla K. , Nielson Ryan M. , Jackson Dewaine H. , Cupples Jacqueline B. , Seidel Nigel E. , Johnson Bruce K. , Gregory Sara C. , Bjornstrom Greg A. , Larkins Autumn N. , Speten David A.
Published: April 2015

Highways are hazardous to migratory ungulates world‐wide, causing direct and indirect impacts to ungulate survival. Moreover, significant financial costs are incurred in damage from wildlife–vehicle collisions and in building and maintaining wildlife passage structures. Information is needed to link ungulate movements to collision occurrence to prioritize needed construction of wildlife crossings on highways. We simultaneously documented mule deer (Odocoileus hemionus) migration corridors and mule deer–vehicle collisions (DVCs) in South‐central Oregon, USA, over 6 years (2005–2011). We calculated Brownian Bridge Movement Models for 359 migrating mule deer equipped with Global Positioning System technology. We modeled DVC counts as functions of probability of use during migration, annual average daily traffic (AADT), and habitat characteristics. Probability of use during migration was the strongest predictor of where DVCs occurred (r = 0.93). Predicted DVCs also increased with AADT but peaked at approximately 8,000 and then decreased. Where AADT was above approximately 8,000, fewer deer attempted to cross the highway and DVCs decreased because, over time, deer either abandoned the migration route or were killed trying to cross this busy highway. Our results suggest that managers should focus on migration corridors or high‐density DVC locations to identify where fencing and under/overpasses could be most effective for maintaining migratory corridors when confronting increasing traffic and development that bisect seasonal ranges of mule deer. © 2015 The Wildlife Society.
Assessing chemical control of earthworms at airports
Authors: Seamans Thomas W. , Blackwell Bradley F. , Bernhardt Glen E. , Potter Daniel A.
Published: April 2015

Earthworms originating from Europe (e.g., Lumbricus spp., Aporrectodea spp.), which are common in the United States and southern Canada can create hazardous conditions at airports by attracting birds that pose a threat to aircraft. These nonnative earthworms are also considered pests on golf courses and sports fields, as well as having detrimental effects on temperate boreal forests. No toxicants or repellents are currently registered for earthworm control in the United States. Our purpose was to identify products that could be used to repel or suppress nonnative earthworms on airports or other managed sites where they pose a hazard or nuisance. We conducted experiments on the National Aeronautics and Space Administration's Plum Brook Station, Ohio, USA, and at an area about 15 km south of this site, during 2007–2013. We hypothesized that either abrasiveness or extreme low or high pH levels would be characteristic of an efficacious repellent. Ammonium sulfate fertilizer (an acidic treatment) repelled Lumbricus terrestris in choice tests. However, 6 applications of ammonium sulfate over 2 years only reduced the field density of Aporrectodea spp., and not Lumbricus spp. Application of tea‐seed cake pellets (TSP), a saponin‐rich byproduct of tea oil (Camellia oleifera) manufacture that causes earthworms to come to the surface and desiccate, temporarily reduced densities of both Lumbricus and Aporrectodea spp. in field plots. However, several applications per year would probably be needed for sustained control. Ring‐billed gulls (Larus delawarensis) showed no apparent adverse effects over a 48 hour period from feeding on TSP‐killed earthworms. We discuss potential value and limitations of TSP and other methods for managing earthworms to reduce airport bird‐strike hazards. © 2015 The Wildlife Society.
Consolidating the State of Knowledge: A Synoptical Review of Wind Energy’s Wildlife Effects
Authors: Schuster Eva , Bulling Lea , Köppel Johann
Published: April 2015

Wind energy development contributes substantially to achieve climate protection goals. Unintended side effects, especially on wildlife, have long been discussed and substantial research has evolved over the last decade. At this stage, it is important to identify what we have learnt so far, as well as which predominant uncertainties and gaps remain. This review article aims to consolidate the state of knowledge, providing a qualitative analysis of the main effects of wind energy development on- and offshore, focusing on frequently studied species groups (bats, breeding and resting birds, raptors, migratory birds, marine mammals). We reviewed over 220 publications from which we identified predominant hypotheses that were summarized and displayed in tables. Journal publications, conference contributions, and further studies have been considered. We found that research focusing on offshore wind energy within the last couple of years has increased significantly as well, catching up with the vast amount of onshore studies. Some hypotheses have been verified by numerous publications and a consensus has been reached (e.g., correlation between bat activity and weather factors), while others are still being debated more (e.g., determination of migratory corridors) or remain unknown (e.g., effect on population level). Factors influencing potential effects were mainly related to species characteristics (morphology, phenology, abundance, behavior, and response to turbines) or site characteristics (landscape features, weather, and habitat quality). Consolidating the state of research provides the groundwork for the identification of mitigation measures and advanced planning approaches. However, the quantification of effects remains challenging and uncertainties will always persist.
From comte to carnap. marcel bolland the introduction of the vienna circle in france
Authors: Srnöttler Peter
Published: April 2015

The issue of the introduction of viennese "scientific philosophy" in France appears to be resolved. However, the rediscovery of the positivist physicist Marcel Boil (1886-1971), who was the first - well before Louis Rougier - to draw the French public 's attention to the works of Schlick, Frank. and Carnap, obliges us to rethink the passage from traditional positivism to neo-positivism during the l920s and l930s. The French reception of the Vienna circ le can be dated earlier than accepted and is more profound than usualy assumed.
Clinical factors associated with the survival of patients with intrahepatic cholangiocarcinoma
Authors: Ting Chun‐Fu , Huang Wen‐Hsin , Feng Chun‐Lung , Yu Cheng‐Ju , Peng Cheng‐Yuan , Su Wen‐Pang , Lai Hsueh‐Chou , Cheng Ken‐Sheng , Chuang Po‐Heng , Kao Jung‐Ta
Published: April 2015

Background and aim

Intrahepatic cholangiocellular carcinoma (ICC) is an uncommon but lethal cancer. The aim of this study is to assess the factors affecting the survival of ICC patients and to evaluate the benefit of these factors when various therapeutic modalities are used.

Methods

Between October 2007 and June 2012, 66 ICC cases among 2255 liver cancer patients were identified by pathology and divided into two groups: Group I (surgery group; n = 17) and Group II (nonsurgery group; n = 49). Group II was further divided into Group IIa (those receiving palliative treatment; n = 19) and Group IIb (no treatment received; n = 30). Factors affecting patient survival over the study period were assessed (3‐ and 6‐month results were reported) and therapeutic benefits identified within each of the groups were evaluated.

Results

Of the 66 patients identified (male/female = 36/30), 10.6% (7/66) were in the early stages of illness. Overall, the mean patient survival duration was 3.50 ± 0.92 months (1.69–5.31 months). The mean survival duration of Group I patients was 10.50 ± 2.84 months (4.94–16.06 months). The mean survival duration of Group II patients was 3.50 ± 0.65 months (2.24–4.76 months) with Group IIa patients surviving on average 9.50 ± 3.27 months (3.10–15.90 months) and Group IIb patients surviving on average 1.50 ± 0.12 months (1.26–1.74 months). Better survival outcomes were observed in the groups receiving treatment, Group I and Group IIa, than in Group Iib, which did not receive treatment [9.50 ± 1.73 months (6.12–12.89 months) vs. 1.50 ± 0.12 months (1.26–1.74 months), p < 0.001]. Lower albumin, higher bilirubin, higher CA19‐9, advanced tumor stage, and no treatment were identified as important predictors of patient mortality at the 3‐ and 6‐month time‐points. These factors remained relevant throughout the entire study period (p = 0.002, 0.029, 0.027, 0.028, < 0.001, respectively).

Conclusion

This study identified surgery as the treatment that provided the best survival prognosis for patients with ICC. Treatment involving either chemotherapy or radiotherapy could also prolong ICC patient survival. Better liver preservation, lower CA19‐9, and less aggressive tumor conditions were identified as factors which play crucial roles in enhancing patient survival.
Structural organization of human replication timing domains
Authors: Boulos Rasha E. , Drillon Guénola , Argoul Françoise , Arneodo Alain , Audit Benjamin
Published: April 2015

Recent analysis of genome‐wide epigenetic modification data, mean replication timing (MRT) profiles and chromosome conformation data in mammals have provided increasing evidence that flexibility in replication origin usage is regulated locally by the epigenetic landscape and over larger genomic distances by the 3D chromatin architecture. Here, we review the recent results establishing some link between replication domains and chromatin structural domains in pluripotent and various differentiated cell types in human. We reconcile the originally proposed dichotomic picture of early and late constant timing regions that replicate by multiple rather synchronous origins in separated nuclear compartments of open and closed chromatins, with the U‐shaped MRT domains bordered by “master” replication origins specified by a localized (∼200–300 kb) zone of open and transcriptionally active chromatin from which a replication wave likely initiates and propagates toward the domain center via a cascade of origin firing. We discuss the relationships between these MRT domains, topologically associated domains and lamina‐associated domains. This review sheds a new light on the epigenetically regulated global chromatin reorganization that underlies the loss of pluripotency and the determination of differentiation properties.
The role of loops on the order of eukaryotes and prokaryotes
Authors: Hofmann Andreas , Heermann Dieter W.
Published: April 2015

The study of the three‐dimensional organization of chromatin has recently gained much focus in the context of novel techniques for detecting genome‐wide contacts using next‐generation sequencing. These chromosome conformation capture‐based methods give a deep topological insight into the architecture of the genome inside the nucleus. Several recent studies observe a compartmentalization of chromatin interactions into spatially confined domains. This structural feature of interphase chromosomes is not only supported by conventional studies assessing the interaction data of millions of cells, but also by analysis on the level of a single cell. We first present and examine the different models that have been proposed to elucidate these topological domains in eukaryotes. Then we show that a model which relies on the dynamic formation of loops within domains can account for the experimentally observed contact maps. Interestingly, the topological domain structure is not only found in mammalian genomes, but also in bacterial chromosomes.
Structure and organization of chromatin fiber in the nucleus
Authors: Li Guohong , Zhu Ping
Published: April 2015

Eukaryotic genomes are organized hierarchically into chromatin structures by histones. Despite extensive research for over 30 years, not only the fundamental structure of the 30‐nm chromatin fiber is being debated, but the actual existence of such fiber remains hotly contested. In this review, we focus on the most recent progress in elucidating the structure of the 30‐nm fiber upon in vitro reconstitution, and its possible organization inside the nucleus. In addition, we discuss the roles of linker histone H1 as well as the importance of specific nucleosome‐nucleosome interactions in the formation of the 30‐nm fiber. Finally, we discuss the involvement of structural variations and epigenetic mechanisms available for the regulation of this chromatin form.
Structure, function and evolution of topologically associating domains (TADs) atHOX loci
Authors: Lonfat Nicolas , Duboule Denis
Published: April 2015

Hox genes encode transcription factors necessary for patterning the major developing anterior to posterior embryonic axis. In addition, during vertebrate evolution, various subsets of this gene family were co‐opted along with the emergence of novel body structures, such as the limbs or the external genitalia. The morphogenesis of these axial structures thus relies in part upon the precisely controlled transcription of specificHox genes, a mechanism involving multiple long‐range enhancers. Recently, it was reported that such regulatory mechanisms were largely shared between different developing tissues, though with some specificities, suggesting the recruitment of ancestral regulatory modalities from one tissue to another. The analysis of chromatin architectures atHoxD andHoxA loci revealed the existence of two flanking topologically associating domains (TADs), precisely encompassing the adjacent regulatory landscapes. Here, we discuss the function of these TADs in the control ofHox gene regulation and we speculate about their capacity to serve as structural frameworks for the emergence of novel enhancers. In this view, TADs may have been used as genomic niches to evolve pleiotropic regulations found at many developmental loci.
Hypothalamic ER stress: A bridge between leptin resistance and obesity
Authors: Ramírez Sara , Claret Marc
Published: April 2015

The prevalence of obesity has increased worldwide at an alarming rate. However, non‐invasive pharmacological treatments remain elusive. Leptin resistance is a general feature of obesity, thus strategies aimed at enhancing the sensitivity to this hormone may constitute an excellent therapeutical approach to counteract current obesity epidemics. Nevertheless, the etiology and neuronal basis of leptin resistance remains an enigma. A recent hypothesis gaining substantial experimental support is that hypothalamic endoplasmic reticulum (ER) stress plays a causal role in the development of leptin resistance and obesity. The objective of this review article is to provide an updated view on current evidence connecting hypothalamic ER stress with leptin resistance. We discuss the experimental findings supporting this hypothesis, as well as the potential causes and underlying mechanisms leading to this metabolic disorder. Understanding these mechanisms may provide key insights into the development of novel intervention approaches.
Methods for protein complex prediction and their contributions towards understanding the organisation, function and dynamics of complexes
Authors: Srihari Sriganesh , Yong Chern Han , Patil Ashwini , Wong Limsoon
Published: April 2015

Complexes of physically interacting proteins constitute fundamental functional units responsible for driving biological processes within cells. A faithful reconstruction of the entire set of complexes is therefore essential to understand the functional organisation of cells. In this review, we discuss the key contributions of computational methods developed till date (approximately between 2003 and 2015) for identifying complexes from the network of interacting proteins (PPI network). We evaluate in depth the performance of these methods on PPI datasets from yeast, and highlight their limitations and challenges, in particular at detecting sparse and small or sub‐complexes and discerning overlapping complexes. We describe methods for integrating diverse information including expression profiles and 3D structures of proteins with PPI networks to understand the dynamics of complex formation, for instance, of time‐based assembly of complex subunits and formation of fuzzy complexes from intrinsically disordered proteins. Finally, we discuss methods for identifying dysfunctional complexes in human diseases, an application that is proving invaluable to understand disease mechanisms and to discover novel therapeutic targets. We hope this review aptly commemorates a decade of research on computational prediction of complexes and constitutes a valuable reference for further advancements in this exciting area.