bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioanalysis of acetylcarnitine in cerebrospinal fluid by HILIC–mass spectrometry
Authors: Holder Brian R. , McNaney Colleen A. , Luchetti David , Schaeffer Eric , Drexler Dieter M. 
Published: February 2015

AbstractAcetyl‐l‐carnitine (ALCAR) is a potential biomarker for the modulation of brain neurotransmitter activity, but is also present in cerebrospinal fluid (CSF). Recent studies have utilized hydrophilic interaction liquid chromatography–tandem mass spectrometry (HILIC‐MS/MS) based assays to detect and quantify ALCAR within biofluids such as urine, plasma and serum, using various sample pretreatment procedures. In order to address the need to quantify ALCAR in CSF on a high‐throughput scale, a new and simple HILIC‐MS/MS assay has been successfully developed and validated. For rapid analysis, CSF sample pretreatment was performed via ‘dilute and shoot’ directly onto an advanced HILIC column prior to MS/MS detection. This newly developed HILIC‐MS/MS assay shows good recoveries of ALCAR without the need for chemical derivatization and multistep sample extraction procedures. The employment of this assay is suitable for the high‐throughput bioanalysis and quantification of ALCAR within the CSF of various animal models and human clinical studies. Copyright © 2015 John Wiley & Sons, Ltd.
Commonly Consumed Beverages in Daily Life: Do They Cause Atrial Fibrillation?
Authors: Turagam Mohit K. , Velagapudi Poonam , Kocheril Abraham G. , Alpert Martin A. 
Published: February 2015

AbstractAtrial fibrillation (AF) is the most prevalent cardiac arrhythmia in the United States and worldwide. Caffeine, alcohol, and, more recently, energy drinks are the most commonly consumed beverages in daily living, especially by young individuals. Several questions have been raised about the implications of caffeine, alcohol, and energy drinks in cardiovascular health, especially in triggering AF. This review focuses on the role of these commonly consumed beverages as a cause of AF, with special emphasis of potential mechanisms and studies addressing this issue.
Soil pipe collapses in a loess pasture of Goodwin Creek watershed, Mississippi: role of soil properties and past land use
Authors: Wilson Glenn V. , Rigby James R. , Dabney Seth M. 
Published: February 2015

AbstractLittle is known about the association of soil pipe collapse features with soil properties or land use history. Three loess covered catchments in northern Mississippi, USA were characterized to investigate these relationships. Soil pipe collapses were characterized for their size, type feature and spatial location along with soil properties across the three catchments. Although mapped as the same soil, one of the catchments did not contain pipe collapse features while the other two had 29.4 and 15.4 pipe collapses per hectare. These loess soils contained fragipan layers that are suspected of perching water, thereby initiating the piping processes. Pipe collapses associated with subsurface flow paths were not always consistent with surface topography. The surface layer tended to be non‐erodible while layers below, even the upper fragipan layers, were susceptible to erosion by pipeflow. Soil properties of the lowest fragipan layer were highly variable but tended to prevent further downward erosion of soil pipes and thus formed a lower boundary for gullies. Middle to lower landscape positions in one of the piped catchments contained anthropic soils that were highly erodible. These anthropic soils were previously gullies that were filled‐in in the 1950s when forested areas, assumed to have been established when land was previously converted from crop to forest land, were converted to pasture. Three decades after this land use change from forest to pasture, pipe collapses became evident. In contrast, the adjacent catchment that does not exhibit pipe collapse features experienced severe sheet and rill erosion prior to the 1930s while in cotton production. The surface horizons above the lower fragipan layer were completely removed during this period, thus the top‐soil layer that tends to form a bridge above soil pipes in the more erodible subsoil layers was removed. This study showed that knowledge of soil characteristics or topography alone do not explain the distribution of soil pipe collapses as past land use can play a definitive role. Copyright © 2015 John Wiley & Sons, Ltd.
Review of polyoxymethylene passive sampling methods for quantifying freely dissolved porewater concentrations of hydrophobic organic contaminants
Authors: Arp Hans Peter H. , Hale Sarah E. , Elmquist Kruså Marie , Cornelissen Gerard , Grabanski Carol B. , Miller David J. , Hawthorne Steven B. 
Published: February 2015

Abstract

Meth ods involving polyoxymethylene (POM) as a passive sampler are increasing in popularity to assess contaminant freely dissolved porewater concentrations in soils and sediments. These methods require contaminant-specific POM–water partition coefficients, KPOM. Certain methods for determining KPOM perform reproducibly (within 0.2 log units). However, other methods can give highly varying KPOM values (up to 2 log units), especially for polycyclic aromatic hydrocarbons (PAHs). To account for this variation, the authors tested the influence of key methodological components in KPOM determinations, including POM thickness, extraction procedures, and environmental temperature and salinity, as well as uptake kinetics in mixed and static systems. All inconsistencies in the peer-reviewed literature can be accounted for by the likelihood that thick POM materials (500 μm or thicker) do not achieve equilibrium (causing negative biases up to 1 log unit), or that certain POM extraction procedures do not ensure quantitative extraction (causing negative biases up to 2 log units). Temperature can also influence KPOM, although all previous literature studies were carried out at room temperature. The present study found that KPOM values at room temperature are independent (within 0.2 log units) of POM manufacture method, of thickness between 17 μm and 80 μm, and of salinity between 0% and 10%. Regarding kinetics, monochloro- to hexachloro-polychlorinated biphenyls (PCBs) were within 0.2 log units of equilibrium after 28 d in the mixed system, but only dichloro-PCBs achieved near equilibrium after 126 d in the static system. Based on these insights, recommended methods and KPOM values to facilitate interlaboratory reproducibility are presented. Environ Toxicol Chem 2015;34:710–720. © 2015 SETAC
Radial variations in xylem sap flow and their effect on whole‐tree water use estimates
Authors: Zhang Jian‐Guo , He Qiu‐Yue , Shi Wei‐Yu , Otsuki Kyoichi , Yamanaka Norikazu , Du Sheng 
Published: February 2015

AbstractTo estimate whole‐tree or stand transpiration based on sap flow measurements, sap flux density (Fd) needs to be scaled up over the entire sapwood area. We investigated radial variations in Fd in the dominant oak (Quercus liaotungensis) and a commonly occurring oriental arborvitae (Platycladus orientalis) species using Granier‐type thermal dissipation probes in a semi‐arid forest in northern China. Our results show that Fd in oak trees reached a maximum just below the cambium and decreased towards the inner sapwood. On the other hand, radial sap flow patterns in oriental arborvitae trees differed among individuals. Fd values at different depths within an individual were highly correlated with each other in both species. We assessed the error of single‐depth measurements when upscaling to whole‐tree water use using multi‐depth measurements as a reference. Omitting radial variations resulted in an overestimation of daily water use by 38% and 78% in oak trees with sapwood depths of approximately 2 and 3 cm, respectively. The outer sapwood annuli (0–1 cm) contributed 74% and 65% to the total water use in the two classes of sapwood depth. These contribution coefficients may be used as correction indices for estimating whole‐tree water use. Errors of omitting radial variations in oriental arborvitae trees ranged from −42% to 21%. Using relatively long sensors (e.g. 2 cm) may improve the estimate accuracy in this species. The results would be applicable to the estimation of tree or stand transpiration based on routine depth measurements using one set of sensors. It is suggested that radial variations should be considered for accurately upscaling locally measured sap flow data to whole‐tree water use in trees with wide sapwood and that different approaches may be applied to species with different patterns of radial variations. Copyright © 2015 John Wiley & Sons, Ltd.
Nonivamide Enhances miRNA let‐7d Expression and Decreases Adipogenesis PPARγ Expression in 3T3‐L1 Cells
Authors: Rohm Barbara , Holik Ann‐Katrin , Kretschy Nicole , Somoza Mark M. , Ley Jakob P. , Widder Sabine , Krammer Gerhard E. , Marko Doris , Somoza Veronika 
Published: February 2015

ABSTRACTRed pepper and its major pungent principle, capsaicin (CAP), have been shown to be effective anti‐obesity agents by reducing energy intake, enhancing energy metabolism, decreasing serum triacylglycerol content, and inhibiting adipogenesis via activation of the transient receptor potential cation channel subfamily V member 1 (TRPV1). However, the binding of CAP to the TRPV1 receptor is also responsible for its pungent sensation, strongly limiting its dietary intake. Here, the effects of a less pungent structural CAP‐analog, nonivamide, on adipogenesis and underlying mechanisms in 3T3‐L1 cells were studied. Nonivamide was found to reduce mean lipid accumulation, a marker of adipogenesis, to a similar extent as CAP, up to 10.4% (P < 0.001). Blockage of the TRPV1 receptor with the specific inhibitortrans‐tert‐butylcyclohexanol revealed that the anti‐adipogenic activity of nonivamide depends, as with CAP, on TRPV1 receptor activation. In addition, in cells treated with nonivamide during adipogenesis, protein levels of the pro‐adipogenic transcription factor peroxisome‐proliferator activated receptor γ (PPARγ) decreased. Results from miRNA microarrays and digital droplet PCR analysis demonstrated an increase in the expression of the miRNA mmu‐let‐7d‐5p, which has been associated with decreased PPARγ levels. J. Cell. Biochem. 116: 1153–1163, 2015. © 2015 The Authors.Journal of Cellular Biochemistrypublished by Wiley Periodicals, Inc.
Correlative 3D‐imaging of Pipistrellus penis micromorphology: Validating quantitative microCT images with undecalcified serial ground section histomorphology
Authors: Herdina Anna Nele , Plenk Hanns , Benda Petr , Lina Peter H. C. , Herzig‐Straschil Barbara , Hilgers Helge , Metscher Brian D. 
Published: February 2015

ABSTRACTDetailed knowledge of histomorphology is a prerequisite for the understanding of function, variation, and development. In bats, as in other mammals, penis and baculum morphology are important in species discrimination and phylogenetic studies. In this study, nondestructive 3D‐microtomographic (microCT, µCT) images of bacula and iodine‐stained penes of Pipistrellus pipistrellus were correlated with light microscopic images from undecalcified surface‐stained ground sections of three of these penes of P. pipistrellus (1 juvenile). The results were then compared with µCT‐images of bacula of P. pygmaeus, P. hanaki, and P. nathusii. The Y‐shaped baculum in all studied Pipistrellus species has a proximal base with two club‐shaped branches, a long slender shaft, and a forked distal tip. The branches contain a medullary cavity of variable size, which tapers into a central canal of variable length in the proximal baculum shaft. Both are surrounded by a lamellar and a woven bone layer and contain fatty marrow and blood vessels. The distal shaft consists of woven bone only, without a vascular canal. The proximal ends of the branches are connected with the tunica albuginea of the corpora cavernosa via entheses. In the penis shaft, the corpus spongiosum‐surrounded urethra lies in a ventral grove of the corpora cavernosa, and continues in the glans under the baculum. The glans penis predominantly comprises an enlarged corpus spongiosum, which surrounds urethra and baculum. In the 12 studied juvenile and subadult P. pipistrellus specimens the proximal branches of the baculum were shorter and without marrow cavity, while shaft and distal tip appeared already fully developed. The present combination with light microscopic images from one species enabled a more reliable interpretation of histomorphological structures in the µCT‐images from all four Pipistrellus species. J. Morphol. 276:695–706, 2015. © 2015 Wiley Periodicals, Inc.
Peculiar salivary glands in a silk‐producing miteBakericheyla chanayi(Cheyletidae)
Authors: Filimonova Svetlana A. , Amosova Ludmila I. 
Published: February 2015

ABSTRACTThis is the first ultrastructural investigation of salivary glands in the family Cheyletidae. In both sexes ofBakericheyla chanayi, paired acinous salivary glands and tubular coxal glands were shown to be united into the common podocephalic system. The secretory portion of the salivary gland includes medial and lateral lobes composed of the five and two cells, respectively, with clearly distinct ultrastructure. The cytoplasm of the cells is occupied by the secretory granules containing fine fibrous material. The fine structure of both cell types suggest a proteinaceous nature of their secretions. A single central process extending from the apical face of each secretory cell passes through the common acinar cavity to enter the conducting duct. A pair of intercalary cells at the base of the conducting duct links it with the secretory portion of the gland. Extending towards the acinar cavity, protrusions of intercalary cells alternate the apical regions of the secretory cells and form with them highly‐specialized contacts characterized by the apical network of microtubules and microfilaments. Two possible ways of secretion are suggested: 1) exocytosis into the acinar cavity and 2) direct passage via the central processes. The detection of axon profiles in the gland body suggests a neural control for the glandular cell function. In tritonymphs, neither secretion nor large lateral lobe cells were observed up to the pharate stage when the lateral lobe undergoes rapid differentiation. The arrangement of the acinous gland is compared to that of other arthropods. Its composition appears to be close to the class three of insect glands. The involvement of the lateral lobe cells in silk production is discussed. J. Morphol. 276:772–786, 2015. © 2015 Wiley Periodicals, Inc.
A switched‐beam microstrip antenna array with miniaturized butler matrix network
Authors: Nie Wei , Fan Yong , Luo Sha , Guo Yongxin 
Published: February 2015

ABSTRACTIn this article, a switched‐beam microstrip antenna array with miniaturized butler matrix network is proposed and experimentally verified. The miniaturized butler matrix network is implemented with the stub‐loaded transmission lines (SLTLs). By adopting the proposed SLTLs to equivalently substitute the quarter‐wavelength transmission lines of the couplers and crossovers in the traditional butler matrix network, the circuit area is immediately reduced without loss of performance. To prove the effectiveness of this substitution, the theoretical analysis is given. The proposed butler matrix only takes 45% of the area of a conventional one. Finally, a microstrip antenna array with the miniaturized butler matrix is fabricated, and the proposed design is validated by the measurement results. © 2015 Wiley Periodicals, Inc. Microwave Opt Technol Lett 57:841–845, 2015
Influence of the interface material layers and semiconductor energetic disorder on the open circuit voltage in polymer solar cells
Authors: Zampetti Andrea , Fallahpour Amir Hossein , Dianetti Martina , Salamandra Luigi , Santoni Francesco , Gagliardi Alessio , Auf der Maur Matthias , Brunetti Francesca , Reale Andrea , Brown Thomas M. , Di Carlo Aldo 
Published: February 2015

ABSTRACTMaterial layers at electrode/semiconductor interfaces are fundamental for the photovoltaic properties of polymer solar cells. The relationship between open‐circuit voltage (VOC) and the work function (φ) of these interface layers is still a matter of debate. Simulations, together with experiments on over more than 20 cell architectures based on P3HT:PC60BM, enabled us to analyze the physical dependence of VOC on φ. In particular, when the work function of the contacts is well inside the gap we observe that performance depends strongly on even small variations of φ. On the other hand, when it approaches the energy levels of the semiconducting polymers, device operation becomes the most efficient and less sensitive to variations in φ. Furthermore, by varying the Gaussian density of states (DOS) of the active blend we were able to show that VOC performance depends significantly also on the DOS. Our study based on the simultaneous variation of transport layers represents a promising method to optimize the design and performance of polymer solar cells. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015, 53, 690–699
Bayes procedures for adaptive inference in inverse problems for the white noise model
Authors: Knapik B. T. , Szabó B. T. , van der  Vaart A. W. , van  Zanten J. H. 
Published: February 2015

AbstractWe study empirical and hierarchical Bayes approaches to the problem of estimating an infinite-dimensional parameter in mildly ill-posed inverse problems. We consider a class of prior distributions indexed by a hyperparameter that quantifies regularity. We prove that both methods we consider succeed in automatically selecting this parameter optimally, resulting in optimal convergence rates for truths with Sobolev or analytic “smoothness”, without using knowledge about this regularity. Both methods are illustrated by simulation examples.
YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-Based Proteomics Research
Authors: Colangelo Christopher M. , Shifman Mark , Cheung Kei-Hoi , Stone Kathryn L. , Carriero Nicholas J. , Gulcicek Erol E. , Lam TuKiet T. , Wu Terence , Bjornson Robert D. , Bruce Can , Nairn Angus C. , Rinehart Jesse , Miller Perry L. , Williams Kenneth R. 
Published: February 2015

Abstract
We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database (YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a single laboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry (LC–MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring (MRM)/selective reaction monitoring (SRM) assay development. We have linked YPED’s database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results.
Biological Databases for Human Research
Authors: Zou Dong , Ma Lina , Yu Jun , Zhang Zhang 
Published: February 2015

Abstract
The completion of the Human Genome Project lays a foundation for systematically studying the human genome from evolutionary history to precision medicine against diseases. With the explosive growth of biological data, there is an increasing number of biological databases that have been developed in aid of human-related research. Here we present a collection of human-related biological databases and provide a mini-review by classifying them into different categories according to their data types. As human-related databases continue to grow not only in count but also in volume, challenges are ahead in big data storage, processing, exchange and curation.
Comparability of sociodemographic and pregnancy characteristics of pregnancy‐related deaths identified via the sisterhood method versus the household/verbal autopsy method
Authors: El Ayadi Alison M. , Hill Kenneth , Langer Ana , Subramanian S.V. , McCormick Marie 
Published: February 2015

AbstractObjectiveTo compare sociodemographic and pregnancy characteristics of pregnancy‐related deaths identified by the direct sisterhood and the verbal autopsy with household mortality (HHVA) methods.MethodsNationally representative data for 1997–2001 were obtained from the household, verbal autopsy, and women's questionnaires of the Bangladesh Maternal Health Services and Maternal Mortality Services Survey, 2001. Sociodemographic and pregnancy characteristics were compared for maternal deaths identified by the two methods. Characteristics of deceased women were reported directly with HHVA, but extrapolated in the direct sisterhood method using the reporting sister as proxy.ResultsOverall, 201 pregnancy‐related deaths were identified via HHVA and 388 through DS reporting. There were no significant differences between reporting sister characteristics and deceased women's characteristics in educational attainment, working status, husband's educational attainment, and spouse educational parity. However, timing of death relative to pregnancy phase, number of previous live births, and years since death did differ (P < 0.05).ConclusionThe sociodemographic characteristics of women with pregnancy‐related deaths identified via the two methods were similar. However, some pregnancy characteristics differed significantly, suggesting that different policy interventions are required. Before considering using sister proxy characteristics to target services, issues responsible for these differences should be resolved, and generalizability of evaluated indicators must be considered.