bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correcting dynamic distortions in 7T echo planar imaging using a jittered echo time sequence
Authors: Dymerska Barbara , Poser Benedikt A. , Bogner Wolfgang , Visser Eelke , Eckstein Korbinian , Cardoso Pedro , Barth Markus , Trattnig Siegfried , Robinson Simon D. 
Published: November 2015

PurposeTo develop a distortion correction method for echo planar imaging (EPI) that is able to measure dynamic changes in B0.Theory and MethodsThe approach we propose is based on single‐echo EPI with a jittering of the echo time between two values for alternate time points. Field maps are calculated between phase images from adjacent volumes and are used to remove distortion from corresponding magnitude images. The performance of our approach was optimized using an analytical model and by comparison with field maps from dual‐echo EPI. The method was tested in functional MRI experiments at 7T with motor tasks and compared with the conventional static approach.ResultsUnwarping using our method was accurate even for head rotations up to 8.2°, where the static approach introduced errors up to 8.2 mm. Jittering the echo time between 19 and 25 ms had no measurable effect on blood oxygenation level–dependent (BOLD) sensitivity. Our approach reduced the distortions in activated regions to <1 mm and repositioned active voxels correctly.ConclusionThis method yields accurate distortion correction in the presence of motion. No reduction in BOLD sensitivity was observed. As such, it is suitable for application in a wide range of functional MRI experiments. Magn Reson Med 76:1388–1399, 2016. © 2015 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Examining the association between musculoskeletal injuries and carpal tunnel syndrome in manual laborers
Authors: Cartwright Michael S. , Yeboah Samuel , Walker Francis O. , Rosenbaum Daryl A. , Newman Jill C. , Arcury Thomas A. , Mora Dana C. , Quandt Sara A. 
Published: November 2015

ABSTRACTIntroduction: The association between musculoskeletal injuries and carpal tunnel syndrome (CTS) has not been investigated in a large, population‐based study. Methods: Latino manual laborers were recruited as part of a study of work‐related health conditions. Each had a clinical examination, completed a hand diagram, and had nerve conduction studies. Results: A total of 512 individuals completed all testing. An association was found between rotator cuff syndrome and CTS, with an adjusted odds ratio of 2.25 (P = 0.01) for the right arm, 2.08 (P = 0.03) for the left arm, and 1.84 (P = 0.03) for all individuals. Associations between epicondylitis and CTS did not reach statistical significance. Conclusions: Individuals with rotator cuff syndrome have a higher prevalence of CTS. Further investigations will be needed to examine for causation and to determine if 1 condition typically occurs first and leads to the other. Muscle Nerve 54: 31–35, 2016
The shape of protein–polymer conjugates in dilute solution
Authors: Lam Christopher N. , Chang Dongsook , Wang Muzhou , Chen Wei‐Ren , Olsen Bradley D. 
Published: November 2015

ABSTRACTProtein–polymer conjugation can significantly affect many different aspects of protein behavior, ranging from their solution properties to their ability to form solution and bulk nanostructured materials. An underlying fundamental question is how the molecular design affects the shape of the conjugate and, consequently, its properties. This work measures the molecular configuration of model protein–polymer conjugates in dilute solution using small‐angle neutron scattering (SANS) and uses quantitative model fitting to understand the shape of the molecules. Form factor measurements of four model bioconjugates of the red fluorescent protein mCherry and the polymers poly(N‐isopropylacrylamide), poly(hydroxypropyl acrylate), poly(oligoethylene glycol acrylate), and poly(ethylene glycol) show that these protein–polymer conjugates are well described by a recently developed scattering function for colloid–polymer conjugates that explicitly incorporates excluded volume interactions in the polymer configuration. In the regime where the protein does not exhibit strong interactions with the polymer, modeling the protein–polymer interactions using a purely repulsive Weeks–Chandler–Andersen potential also leads to a coarse‐grained depiction of the conjugate that agrees well with its scattering behavior. The coarse‐grained model can additionally be used for systems with varying protein–polymer interactions, ranging from purely repulsive to strongly attractive, which may be useful for conjugates with strong electrostatic or hydrophobic attractive interactions. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 292–302
Surfactant deficiency in full‐term newborns with transient tachypnea delivered by elective C‐section
Authors: Estorgato Geovana Rhoden , Fiori Humberto Holmer , da Silva Ribeiro Manoel Antonio , de Paula Davi , Garcia Pedro Celiny Ramos , Mattiello Rita , Fiori Renato Machado 
Published: November 2015

AbstractIntroductionPrevious studies have suggested that full‐term newborns delivered by elective cesarean section who develop transient tachypnea have low gastric microbubble counts. In the present study, microbubble concentrations in oral fluid samples were used to evaluate pulmonary maturity.ObjectiveTo evaluate lung maturity in full‐term newborns delivered by elective caesarean section using the stable microbubble test in oral aspirates collected at birth.MethodThe study involved newborns with gestational age >37 weeks delivered by elective cesarean section. Oral fluid samples were obtained in the delivery room immediately after birth, and gastric fluid was collected within the first hour of life. Samples were frozen and analyzed by two blinded researchers.ResultsThe sample comprised 544 newborns. Twenty‐two were diagnosed with transient tachypnea of the newborn by the assisting physician, and required admission to the Neonatal Intensive or Intermediate Care Unit. The median (interquartile range) of the number of microbubbles in the oral samples of these patients was 67.5 (45–150) microbubbles/mm2. The remaining 498 newborns without respiratory difficulties had a count of 350 (150–750) microbubbles/mm2–P < 0.001. Gastric fluid tests revealed a count of 150 (82.5–700) microbubbles/mm2 for neonates with respiratory difficulties, and of 600 (216–1125) microbubbles/mm2–P < 0.05 for those without respiratory symptoms.ConclusionThe present results suggest that transient tachypnea of the newborn is associated with surfactant dysfunction. Pediatr Pulmonol. 2016;51:596–600. © 2015 Wiley Periodicals, Inc.
Metabolic and molecular regulation of dietary polyunsaturated fatty acids on prostate cancer
Authors: Zhao Heng , Pflug Beth R. , Lai Xianyin , Wang Mu 
Published: November 2015

PurposeThe aim of this study is to investigate the role of n‐3 and n‐9 fatty acids in crucial processes involved in prostate cancer cell growth through a large‐scale proteomic analysis.Experimental designWe used a label‐free protein quantification method to profile global protein expression of fish oil and oleic acid treated PCa cells and validated a panel of differentially expressed proteins by either Western blot or multiple reaction monitoring. Bioinformatic analysis was also performed to uncover the pathways involved in fatty acid metabolism.ResultsFish oil, not oleic acid, suppresses prostate cancer cell viability. Assessment of fatty acid synthesis pathway activity also shows that oleic acid is a more potent inhibitor than fish oil on de novo fatty acid synthesis. Although fatty acid synthase activity decreases with fish oil treatment, the inhibition of its activity occurs over time while reduction in viability occurs within 24 h. Bioinformatic analysis revealed the pathways altered by these fatty acid treatments.Conclusions and clinical relevanceThis study suggests that suppression of cell viability by fish oil is independent of fatty acid synthase and fish oil regulates prostate cancer cells through activation of other pathways depending upon length of exposure to fish oil.
Chemical and Textural Characterization of Iron Oxide Nanoparticles and Their Effect on the Thermal Decomposition of Ammonium Perchlorate
Authors: Campos Eunice Aparecida , Cortez Fernandes Maria Tereza , Kawachi Elizabete Yoshie , Sampaio de Oliveira José Irineu , de Cássia Lazzarini Dutra Rita 
Published: November 2015

AbstractMetal oxide nanoparticles have been used as burning rate catalysts for ammonium perchlorate (AP) decomposition in composite solid propellants. Though most papers point to the efficiency of different sizes, shapes and compositions, the texture of the agglomerated particles plays an important role in the catalytic efficiency, but this aspect is not always discussed. In this paper, iron oxide and composite iron oxide/silica powders were synthesized in microemulsion systems and their effect on the decomposition of AP was investigated. X‐ray diffraction (XRD) analysis and Fourier transformed infrared spectroscopy (FT‐IR) showed that the synthesized powders have an amorphous to nanocrystalline pattern, with Fe2O3 composition. The use of different FT‐IR spectroscopic techniques – transmission, diffuse reflectance (DRIFT) and universal attenuated total reflectance (UATR) – allied to electron microscopy analysis allowed the characterization of the samples’ surface, indicating that silicon oxide forms a thick matrix that covers the iron oxide nanoparticles. Adsorption of N2, light scattering and electron microscopy pointed that all samples are formed by mesoporous agglomerated nanoparticles containing micropores indicating that silicon oxide forms a thick matrix that covers the iron oxide nanoparticles. Adsorption of N2, pointed that all samples show different microstructures and light scattering indicated results refer to agglomerated particles. Finally, the catalytic effect of the samples on the decomposition of AP was evaluated by thermogravimetric analysis coupled to differential thermal analysis (TG/DTA), showing that only the high temperature decomposition step of AP was affected by the catalyst, shifting to lower temperatures the higher the surface area of the synthesized iron oxide sample, regardless of the presence of the silica matrix.
The zero phonon line revisited
Authors: York Mark C. A. 
Published: November 2015

AbstractWe treat the exciton–thermal acoustic phonon interaction as a coupling to a (not necessarily classical) stochastic background, in turn applying a Luttinger–Ward style of resummation to self–energy diagrams and leading to a non–perturbative resolution of the exciton spectral density. Such an approach is useful in settings where higher order corrections are not small, e.g. finite temperature and certain processes involving optical phonons. Our main observations lend a promising outlook for applications with quantum wires, quantum dots and localized states as well as a similar non–perturbative description of optical phonon relaxation/emission processes. (© 2016 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A model for analyzing performance problems and root causes in the personal software process
Authors: Raza M. , Faria J. P. 
Published: November 2015

AbstractHigh‐maturity software development processes, such as the Team Software Process and the accompanying Personal Software Process (PSP), can generate significant amounts of data that can be periodically analyzed to identify performance problems, determine their root causes, and devise improvement actions. However, there is a lack of tool support for automating that type of analysis, and hence diminish the manual effort and expert knowledge required. So, we propose in this paper a comprehensive performance model, addressing time estimation accuracy, quality, and productivity, to enable the automated (tool based) analysis of performance data produced by PSP developers, namely, identify and rank performance problems and their root causes. A PSP data set referring to more than 30 000 projects was used to validate and calibrate the model. Copyright © 2015 John Wiley & Sons, Ltd.
Modeling plant–water interactions: an ecohydrological overview from the cell to the global scale
Authors: Fatichi Simone , Pappas Christoforos , Ivanov Valeriy Y. 
Published: November 2015

Vegetation and the water cycles are inherently coupled across a wide range of spatial and temporal scales. Water availability interacts with plant ecophysiology and controls vegetation functioning. Concurrently, vegetation has direct and indirect effects on energy, water, carbon, and nutrient cycles. To better understand and model plant–water interactions, highly interdisciplinary approaches are required. We present an overview of the main processes and relevant interactions between water and plants across a range of spatial scales, from the cell level of leaves, where stomatal controls occur, to drought stress at the level of a single tree, to the integrating scales of a watershed, region, and the globe. A review of process representations in models at different scales is presented. More specifically, three main model families are identified: (1) models of plant hydraulics that mechanistically simulate stomatal controls and/or water transport at the tree level; (2) ecohydrological models that simulate plot‐ to catchment‐scale water, energy, and carbon fluxes; and (3) terrestrial biosphere models that simulate carbon, water, and nutrient dynamics at the regional and global scales and address feedback between Earth's vegetation and the climate system. We identify special features and similarities across the model families. Examples of where plant–water interactions are especially important and have led to key scientific findings are also highlighted. Finally, we discuss the various data sources that are currently available to force and validate existing models, and we present perspectives on the evolution of the field. WIREs Water 2016, 3:327–368. doi: 10.1002/wat2.1125This article is categorized under:

Water and Life > Nature of Freshwater Ecosystems
Science of Water > Hydrological Processes
Culture-independent discovery of natural products from soil metagenomes
Authors: Katz Micah , Hover Bradley M , Brady Sean F 
Published: November 2015

Abstract
Bacterial natural products have proven to be invaluable starting points in the development of many currently used therapeutic agents. Unfortunately, traditional culture-based methods for natural product discovery have been deemphasized by pharmaceutical companies due in large part to high rediscovery rates. Culture-independent, or “metagenomic,” methods, which rely on the heterologous expression of DNA extracted directly from environmental samples (eDNA), have the potential to provide access to metabolites encoded by a large fraction of the earth’s microbial biosynthetic diversity. As soil is both ubiquitous and rich in bacterial diversity, it is an appealing starting point for culture-independent natural product discovery efforts. This review provides an overview of the history of soil metagenome-driven natural product discovery studies and elaborates on the recent development of new tools for sequence-based, high-throughput profiling of environmental samples used in discovering novel natural product biosynthetic gene clusters. We conclude with several examples of these new tools being employed to facilitate the recovery of novel secondary metabolite encoding gene clusters from soil metagenomes and the subsequent heterologous expression of these clusters to produce bioactive small molecules.
Anti-tuberculosis lead molecules from natural products targeting Mycobacterium tuberculosis ClpC1
Authors: Lee Hanki , Suh Joo-Won 
Published: November 2015

Abstract
Tuberculosis (TB) is a serious and potentially fatal disease caused by Mycobacterium tuberculosis (M. tb). The occurrence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) M. tb is a significant public health concern because most of the anti-TB drugs that have been in use for over 40 years are no longer effective for the treatment of these infections. Recently, new anti-TB lead compounds such as cyclomarin A, lassomycin, and ecumicin, which are cyclic peptides from actinomycetes, have shown potent anti-TB activity against MDR and XDR M. tb as well as drug-susceptible M. tb in vitro. The target molecule of these antibiotics is ClpC1, a protein that is essential for the growth of M. tb. In this review, we introduce the three anti-TB lead compounds as potential anti-TB therapeutic agents targeting ClpC1 and compare them with the existing anti-TB drugs approved by the US Food and Drug Administration.
Correlation between Physical Properties and Shear Adhesion Strength of Enzymatically Modified Soy Protein‐Based Adhesives
Authors: Kim Min Jung , Sun Xiuzhi Susan 
Published: November 2015

AbstractThis work was to correlate physical properties with adhesion properties of soy protein‐based adhesives. By building such a correlation, the adhesion properties can be predicted by measuring physical properties of soy protein‐based adhesives. In this context, three important physical properties, viscosity, tacky force, and water resistance, were selected to correlate with adhesion strength of enzymatically modified soy protein‐based adhesives (ESP). Response surface methodology, specifically central composite design, was used with three independent variables to prepare ESP: trypsin concentration (X1), incubation time (X2), and glutaraldehyde (GA) concentration (X3). The three physical properties measured were all greatly affected by our three independent variables with significance at the 95 % confidence level. The responses were then correlated with the adhesion properties of ESP. In conclusion, viscosity can be used to predict the dry adhesion strength of ESP based on the coefficient of determination (R2) of 0.8558. In addition, tacky force and water resistance can be used to represent wet adhesion strength of ESP based on R2 of 0.7082 and 0.6930, respectively (P < 0.05). This work preliminarily identified the significant physical properties that can predict the adhesion strength of the ESP system crosslinked with GA, but the results need to be further confirmed by another protein modification system to give a generic conclusion.
Where you say it matters: Why packages are a more believable source of product claims than advertisements
Authors: Fajardo Tatiana M. , Townsend Claudia 
Published: November 2015

AbstractThis research demonstrates that a marketing claim placed on a package is more believable than a marketing claim placed in an advertisement. In three studies, we show that the benefit of greater believability for packages is driven by perceptions of proximity. In general, consumers perceive packages, and thus the claims they offer, as closer to the product than ads and their respective claims. This perception of greater claim‐to‐product proximity is likely to make a claim seem more verifiable. Therefore, claim‐to‐product proximity is taken as a signal of the marketers' credibility, decreasing inferences of manipulative intent and thereby increasing claim believability and purchase likelihood.
Hepatitis B virus stimulates G6PD expression through HBx-mediated Nrf2 activation
Authors: Liu B , Fang M , He Z , Cui D , Jia S , Lin X , Xu X , Zhou T , Liu W 
Published: November 2015

AbstractMetabolic reprogramming is a hallmark of physiological changes in cancer. Cancer cells primarily apply glycolysis for cell metabolism, which enables the cells to use glycolytic intermediates for macromolecular biosynthesis in order to meet the needs of cell proliferation. Here, we show that glucose-6-phosphate dehydrogenase (G6PD), the first and rate-limiting enzyme of the pentose phosphate pathway, is highly expressed in chronic hepatitis B virus (HBV)-infected human liver and HBV-associated liver cancer, together with an elevated activity of the transcription factor Nrf2. In hepatocytes, HBV stimulates by its X protein (HBx) the expression of G6PD in an Nrf2 activation-dependent pathway. HBx associates with the UBA and PB1 domains of the adaptor protein p62 and augments the interaction between p62 and the Nrf2 repressor Keap1 to form HBx–p62–Keap1 complex in the cytoplasm. The aggregation of HBx–p62–Keap1 complexes hijacks Keap1 from Nrf2 leading to the activation of Nrf2 and consequently G6PD transcription. Our data suggest that HBV upregulates G6PD expression by HBx-mediated activation of Nrf2. This implies a potential effect of HBV on the reprogramming of the glucose metabolism in hepatocytes, which may be of importance in the development of HBV-associated hepatocarcinoma.
Palmitate induces ER calcium depletion and apoptosis in mouse podocytes subsequent to mitochondrial oxidative stress
Authors: Xu S , Nam S M , Kim J-H , Das R , Choi S-K , Nguyen T T , Quan X , Choi S J , Chung C H , Lee E Y , Lee I-K , Wiederkehr A , Wollheim C B , Cha S-K , Park K-S 
Published: November 2015

AbstractPathologic alterations in podocytes lead to failure of an essential component of the glomerular filtration barrier and proteinuria in chronic kidney diseases. Elevated levels of saturated free fatty acid (FFA) are harmful to various tissues, implemented in the progression of diabetes and its complications such as proteinuria in diabetic nephropathy. Here, we investigated the molecular mechanism of palmitate cytotoxicity in cultured mouse podocytes. Incubation with palmitate dose-dependently increased cytosolic and mitochondrial reactive oxygen species, depolarized the mitochondrial membrane potential, impaired ATP synthesis and elicited apoptotic cell death. Palmitate not only evoked mitochondrial fragmentation but also caused marked dilation of the endoplasmic reticulum (ER). Consistently, palmitate upregulated ER stress proteins, oligomerized stromal interaction molecule 1 (STIM1) in the subplasmalemmal ER membrane, abolished the cyclopiazonic acid-induced cytosolic Ca2+ increase due to depletion of luminal ER Ca2+. Palmitate-induced ER Ca2+ depletion and cytotoxicity were blocked by a selective inhibitor of the fatty-acid transporter FAT/CD36. Loss of the ER Ca2+ pool induced by palmitate was reverted by the phospholipase C (PLC) inhibitor edelfosine. Palmitate-dependent activation of PLC was further demonstrated by following cytosolic translocation of the pleckstrin homology domain of PLC in palmitate-treated podocytes. An inhibitor of diacylglycerol (DAG) kinase, which elevates cytosolic DAG, strongly promoted ER Ca2+ depletion by low-dose palmitate. GF109203X, a PKC inhibitor, partially prevented palmitate-induced ER Ca2+ loss. Remarkably, the mitochondrial antioxidant mitoTEMPO inhibited palmitate-induced PLC activation, ER Ca2+ depletion and cytotoxicity. Palmitate elicited cytoskeletal changes in podocytes and increased albumin permeability, which was also blocked by mitoTEMPO. These data suggest that oxidative stress caused by saturated FFA leads to mitochondrial dysfunction and ER Ca2+ depletion through FAT/CD36 and PLC signaling, possibly contributing to podocyte injury.