bluuebunny/crossref_metadata_2025 huggingface dataset:
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

Atrial 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

Little 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

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
Evolution of depositional settings in the Torrey area during the Smithian (Early Triassic, Utah, USA) and their significance for the biotic recovery
Authors: Olivier Nicolas , Brayard Arnaud , Vennin Emmanuelle , Escarguel Gilles , Fara Emmanuel , Bylund Kevin G. , Jenks James F. , Caravaca Gwénaël , Stephen Daniel A.
Published: February 2015

This work focuses on well‐exposed Lower Triassic sedimentary rocks in the area of Torrey (south‐central Utah, USA). The studied Smithian deposits record a large‐scale third‐order sea‐level cycle, which permits a detailed reconstruction of the evolution of depositional settings. During the middle Smithian, peritidal microbial limestones associated with a rather low‐diversity benthic fauna were deposited seaward of the tidal flat siliciclastic red beds. Associated with siliceous sponges, microbial limestones formed small m‐scale patch reefs. During the late middle to late Smithian interval, the sedimentary system is characterized by tidal flat dolostones of an interior platform, ooid‐bioclastic deposits of a tide‐dominated shoal complex, and mid‐shelf bioclastic limestones. Microbial deposits, corresponding to sparse stromatolites formed in the interior platform, are contemporaneous with a well‐diversified marine fauna living in a seaward shoal complex and mid‐shelf area. The nature and distribution of these Smithian microbial deposits are not related to any particular deleterious environmental condition, highlighting that observed patterns of biotic recovery after the end‐Permian mass extinction were directly influenced by depositional settings. Facies evolution and stratal stacking patterns allow us to identify large, medium and small‐scale, as well as elementary depositional sequences. Large‐ and medium‐scale sequences are consistent with sea‐level changes, whereas small‐scale and elementary sequences are better explained by autocyclic processes. Copyright © 2015 John Wiley & Sons, Ltd.
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

To 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

Red 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

Detailed 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

This 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

In 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
Graphite‐reinforced oxygen barrier conducting starch bionanocomposites
Authors: Pradhan Gopal C. , Swain Sarat K.
Published: February 2015

Starch bionanocomposites are prepared by reinforcement of chemically modified expanded graphite (EG) powder. The interaction of EG with starch is studied by Fourier transform infrared spectroscopy (FTIR) whereas; the structural behavior is investigated by X‐ray diffraction (XRD). The starch/expanded graphite (starch/EG) bionanocomposites are characterized by field emission scanning electron microscopy (FESEM), high resolution transmission electron microscopy (HRTEM), energy dispersive spectroscopy (EDS), and selected area electron diffraction (SAED) study. The thermal stability of starch is enhanced tremendously with incorporation of EG. An increase in conductivity is observed due to the increase in EG concentrations. The bionanocomposites are resistant towards acid and alkali with little sacrifice in biodegradability. A substantial reduction in permeability is observed due to dispersion of graphite platelets. The combining properties of thermal and chemical resistant along with the gas barrier behavior of starch bionanocomposites may enable the material for packaging applications. POLYM. COMPOS., 37:2083–2091, 2016. © 2015 Society of Plastics Engineers
Bond performance of fiber reinforced polymer rebars in different casting positions
Authors: Park Ji‐Sun , Lim A‐Ra , Kim Jinyoung , Lee Jung‐Yoon
Published: February 2015

In the last two decades, fiber reinforced polymer (FRP) rebars have become attractive to civil engineers, due to their corrosion resistance and high strength‐to‐weight ratio. To take advantage of such properties, many research studies have been carried out on the mechanical and physical properties of FRP rebars in concrete, and critical issues have been discovered regarding the bond behavior of FRP rebars. In this study, an effort was made to investigate the effects of FRP rebar types, locations and concrete casting positions on the bond performance of FRP rebars embedded in concrete members. Experimental investigations were conducted using a total of 63 specimens, with seven types of reinforcing bars, and three different casting positions. According to the test results, the bond performance of FRP reinforced concrete was greatly influenced by FRP type and surface condition; while vertical casting showed higher bond strength than horizontal casting. In addition, the bond strength reduction ratio of FRP rebars cast in the horizontal direction was smaller than that of steel bars. POLYM. COMPOS., 37:2098–2108, 2016. © 2015 Society of Plastics Engineers
High thermally conductive PLA based composites with tailored hybrid network of hexagonal boron nitride and graphene nanoplatelets
Authors: Mosanenzadeh Shahriar Ghaffari , Khalid Saad , Cui Yi , Naguib Hani E.
Published: February 2015

Bio‐based polymers and multifunctional polymeric composites are promising for the development of new environmentally sustainable materials and are becoming increasingly popular compared to their oil based counterparts. This research aims to develop new multifunctional bio‐based polymer composites with improved thermal conductivity and tailored electrical properties to be used as heat management materials in the electronics industry. A series of parametric studies were conducted to clarify the science behind the hybrid composites' behavior and their structure‐to‐property relationships. Using bio‐based polymers [e.g., polylactic acid (PLA)] as the matrix, heat transfer networks were developed and structured by embedding hexagonal boron nitride (hBN) and graphene nanoplatelets (GNP) in a PLA matrix. The effects of random uniform thermal hybrid networks of hBN‐GNP on improving the effective thermal conductivity (keff) of produced composites were studied and compared. Composites were characterized with respect to physical, thermal, electrical, and mechanical properties for practical application in the electronics industry. The use of high thermally conductive hybrid filler systems, with optimized filler content, was found to promote the composites' effective thermal conductivity to more than 12 times over neat PLA. The thermally conductive composite is expected to provide unique opportunities to injection mold three‐dimensional, net‐shape, lightweight, and eco‐friendly microelectronic enclosures with superior heat dissipation performance. POLYM. COMPOS., 37:2196–2205, 2016. © 2015 Society of Plastics Engineers
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

Material 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

We 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

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

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

Objective

To compare sociodemographic and pregnancy characteristics of pregnancy‐related deaths identified by the direct sisterhood and the verbal autopsy with household mortality (HHVA) methods.

Methods

Nationally 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.

Results

Overall, 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).

Conclusion

The 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.
Disulfiram (DSF) acts as a copper ionophore to induce copper‐dependent oxidative stress and mediate anti‐tumor efficacy in inflammatory breast cancer
Authors: Allensworth Jennifer L. , Evans Myron K. , Bertucci François , Aldrich Amy J. , Festa Richard A. , Finetti Pascal , Ueno Naoto T. , Safi Rachid , McDonnell Donald P. , Thiele Dennis J. , Van Laere Steven , Devi Gayathri R.
Published: February 2015

Cancer cells often have increased levels of reactive oxygen species (ROS); however, acquisition of redox adaptive mechanisms allows for evasion of ROS‐mediated death. Inflammatory breast cancer (IBC) is a distinct, advanced BC subtype characterized by high rates of residual disease and recurrence despite advances in multimodality treatment. Using a cellular model of IBC, we identified an oxidative stress response (OSR) signature in surviving IBC cells after administration of an acute dose of an ROS inducer. Metagene analysis of patient samples revealed significantly higher OSR scores in IBC tumor samples compared to normal or non‐IBC tissues, which may contribute to the poor response of IBC tumors to common treatment strategies, which often rely heavily on ROS induction. To combat this adaptation, we utilized a potent redox modulator, the FDA‐approved small molecule Disulfiram (DSF), alone and in combination with copper. DSF forms a complex with copper (DSF‐Cu) increasing intracellular copper concentration both in vitro and in vivo, bypassing the need for membrane transporters. DSF‐Cu antagonized NFκB signaling, aldehyde dehydrogenase activity and antioxidant levels, inducing oxidative stress‐mediated apoptosis in multiple IBC cellular models. In vivo, DSF‐Cu significantly inhibited tumor growth without significant toxicity, causing apoptosis only in tumor cells. These results indicate that IBC tumors are highly redox adapted, which may render them resistant to ROS‐inducing therapies. DSF, through redox modulation, may be a useful approach to enhance chemo‐ and/or radio‐sensitivity for advanced BC subtypes where therapeutic resistance is an impediment to durable responses to current standard of care.
Protection Against Cold in Prehospital Care: Wet Clothing Removal or Addition of a Vapor Barrier
Authors: Henriksson Otto , Lundgren Peter J. , Kuklane Kalev , Holmér Ingvar , Giesbrecht Gordon G. , Naredi Peter , Bjornstig Ulf
Published: February 2015

Objective

The purpose of this study was to evaluate the effect of wet clothing removal or the addition of a vapor barrier in shivering subjects exposed to a cold environment with only limited insulation available.

Methods

Volunteer subjects (n = 8) wearing wet clothing were positioned on a spineboard in a climatic chamber (–18.5°C) and subjected to an initial 20 minutes of cooling followed by 30 minutes of 4 different insulation interventions in a crossover design: 1) 1 woolen blanket; 2) vapor barrier plus 1 woolen blanket; 3) wet clothing removal plus 1 woolen blanket; or 4) 2 woolen blankets. Metabolic rate, core body temperature, skin temperature, and heart rate were continuously monitored, and cold discomfort was evaluated at 5-minute intervals.

Results

Wet clothing removal or the addition of a vapor barrier significantly reduced metabolic rate (mean difference ± SE; 14 ± 4.7 W/m2) and increased skin temperature rewarming (1.0° ± 0.2°C). Increasing the insulation rendered a similar effect. There were, however, no significant differences in core body temperature or heart rate among any of the conditions. Cold discomfort (median; interquartile range) was significantly lower with the addition of a vapor barrier (4; 2–4.75) and with 2 woolen blankets (3.5; 1.5–4) compared with 1 woolen blanket alone (5; 3.25–6).

Conclusions

In protracted rescue scenarios in cold environments with only limited insulation available, wet clothing removal or the use of a vapor barrier is advocated to limit the need for shivering thermogenesis and improve the patient’s condition on admission to the emergency department.
Presence of L-Canavanine in Hedysarum alpinum Seeds and Its Potential Role in the Death of Chris McCandless
Authors: Krakauer Jon , Long Ying , Kolbert Andrew , Thanedar Shri , Southard Jonathan
Published: February 2015

Objective

For the past 2 decades there has been vigorous disagreement over the purported toxicity of Hedysarum alpinum seeds, and whether the consumption of such seeds was a factor in the 1992 death of Chris McCandless, the subject of the book Into the Wild. Our objective was to confirm or disprove the presence of L-canavanine (a nonprotein amino acid known to induce systemic lupuslike symptoms in humans) in H alpinum seeds.

Methods

Liquid chromatography–tandem mass spectrometry analysis of H alpinum seeds was performed.

Results

Our analysis confirmed the presence of L-canavanine in H alpinum seeds and demonstrated that it is a significant component of the seeds, with a concentration of 1.2% (weight/weight), roughly half of that found in Canavalia ensiformis.

Conclusions

The data led us to conclude it is highly likely that the consumption of H alpinum seeds contributed to the death of Chris McCandless.
Gastropods from upper Pliensbachian–Toarcian (Lower Jurassic) sediments of Causses Basin, southern France and their recovery after the early Toarcian anoxic event
Authors: GATTO ROBERTO , MONARI STEFANO , NEIGE PASCAL , PINARD JEAN-DANIEL , WEIS ROBERT
Published: February 2015

A gastropod fauna has been studied from upper Pliensbachian – upper Toarcian deposits of two sections of the Causses Basin (southern France) in order to investigate the mode of recovery after the early Toarcian anoxic event. The fauna consists of 15 species, one of which is new (Bathrotomaria kronzwilmesorumsp. nov.). Their stratigraphical distribution shows two peaks of diversity – in the Bifrons Zone (Bifrons Subzone) and in the Aalensis Zone (Mactra Subzone) – which reflect brief times during which the oxygen content and bottom consistency favoured the settlement of a relatively diversified fauna. In the Variabilis–Pseudoradiosa zones, gastropods are only represented by two species. This probably indicates more severe and unstable environmental conditions, only allowing the survival of gastropod taxa with wide adaptive capacities. The very low species diversity and the discontinuous and slow faunal recovery were probably determined by physiographic factors. The Causses area was a small basin confined by exposed lands and open towards the central part of western Tethys. Gastropods described here occur exclusively in the Toarcian – early Aalenian communities of the European epicontinental seas, whereas species from the central region of western Tethys are absent. Geographic isolation and marginal location of the Causses Basin restricted faunal exchange with the western European epicontinental seas, preventing fast recovery after the anoxic event. Gastropods of the central region of the western Tethys were probably unable to settle and colonize that area due to the strongly different environment.
Saturation-power enhancement of a free-electron laser amplifier through parameters adjustment
Authors: Ji Yu-Pin , Xu Y.-G. , Wang S.-J. , Xu J.-Y. , Liu X.-X. , Zhang S.-C.
Published: February 2015

Saturation-power enhancement of a free-electron laser (FEL) amplifier by using tapered wiggler amplitude is based on the postponement of the saturation length of the uniform wiggler. In this paper, we qualitatively and quantitatively demonstrate that the saturation-power enhancement can be approached by means of the parameters adjustment, which is comparable to that by using a tapered wiggler. Compared to the method by tapering the wiggler amplitude, the method of parameters adjustment substantially shortens the saturation length, which is favorable to cutting down the manufacture and operation costs of the device.
Preparation and application of a carbon nanotube reinforced polyamide-based stir bar for sorptive extraction of naproxen from biological samples prior to its spectrofluorometric determination
Authors: Ayazi Zahra , Rafighi Parvin
Published: February 2015

A novel stir bar sorptive extraction method based on CNT/polyamide coating was developed and was successfully applied for microextraction of naproxen from biological samples. Response surface methodology was used for the optimization of extraction and desorption processes.
Effect of the orientation and fluid flow on the accumulation of organotin compounds to Chemcatcher passive samplers
Authors: Ahkola H. , Juntunen J. , Laitinen M. , Krogerus K. , Huttula T. , Herve S. , Witick A.
Published: February 2015

The effect of environmental conditions on the passive sampling process should be understood to estimate the concentration of chemical required by environmental legislation.
Topology analysis of metal–organic frameworks based on metal–organic polyhedra as secondary or tertiary building units
Authors: Kim Dongwook , Liu Xinfang , Lah Myoung Soo
Published: February 2015

MOFs of complicated topologies can be analyzed as networks having simple underlying topologies when the MOPs are considered as TBUs.
Amazing selectivity for Am(iii) uptake by composite graphene oxide-PES polymeric beads prepared by phase inversion
Authors: Gujar Rajesh Bhikaji , Mohapatra Prasanta Kumar
Published: February 2015

Novel polyethersulphone (PES) based polymeric beads containing graphene oxide (GO), prepared by a phase inversion technique for the first time, were evaluated for actinide ion uptake from acidic feed solutions.
Crystal structure and physical properties of new transition metal based pnictide compounds: LaTM2AsN (TM = Fe, Co, and Ni)
Authors: Jeong Sehoon , Matsuishi Satoru , Bang Joonho , Hosono Hideo
Published: February 2015

New 3d transition metal-based mixed-pnictide compounds, LaTM2AsN (TM = Fe, Co, and Ni) are synthesized by solid state reactions under a high pressure of 2.5 GPa. These compounds crystallize with an orthorhombic structure (space group Cmcm) containing four formula units per unit cell. The crystal structure consists of an anisotropic network of TMAs3N tetrahedra sharing As-As edges along the in-plane ac direction and N corners along the b-direction, forming a TM honeycomb lattice with a boat-shape conformation bridged by TM-N-TM linear bonds. The temperature dependences of the electrical resistivity and magnetic susceptibility indicate that these crystals are itinerant antiferromagnets exhibiting parasitic ferromagnetism with transition temperatures of 560, 260, and 410 K for TM = Fe, Co, and Ni, respectively. These compounds are expected to be parent materials for new superconductors.
Adhesion and separation models for direct hydrophilic bonding
Authors: Navarro E. , Bréchet Y. , Barthelemy A. , Radu I. , Raskin J.-P. , Pardoen T.
Published: February 2015

A simple model describing the hydrophilic adhesion between solid surfaces, with low roughness is proposed to explain both the influence of the interface roughness and quantity of water present at the interface on the work of adhesion and work of separation. The observed hysteresis between adhesion and separation is explained by the evolving distribution of water along the bonding interface. This model is based on earlier molecular dynamics simulations of hydrophilic direct bonding previously obtained by Cole et al. An experimental validation is presented showing good agreement with model predictions.
Piles of scats for piles of DNA: deriving DNA of lizards from their faeces
Authors: Pearson S. K. , Tobe S. S. , Fusco D. A. , Bull C. M. , Gardner M. G.
Published: February 2015

Non-invasive genetic sampling using scats has a well established role in conservation biology, but has rarely been applied to reptiles. Using scats from captive and wild Egernia stokesii (Squamata, Scincidae) we evaluated two storage and six DNA-extraction methods and the reliability of subsequent genotype and sequence data. Accurate genotype and sequence data were obtained from frozen and dried captive lizard scat DNA extracted using a QIAamp® DNA Stool Mini Kit and a modified Gentra® Puregene® method, but success rates were reduced for wild lizard scats. Wild E. stokesii eat more plants than their captive counterparts, possibly resulting in scat DNA extracts containing plant compounds that inhibit PCR-amplifications. Notably, reliable genotypes and sequences were obtained from wild E. stokesii scat DNA extracted using a Qiagen DNeasy® Plant Mini Kit, a method designed to remove plant inhibitory compounds. Results highlight the opportunity for using scat-derived DNA in lizard studies, particularly for species that deposit scats in piles.
Conjugate-like immunogens produced as protein capsular matrix vaccines
Authors: Thanawastien Ann , Cartee Robert T. , Griffin Thomas J. , Killeen Kevin P. , Mekalanos John J.
Published: February 2015

Significance

Conjugate vaccines have dramatically reduced the incidence of disease in infants and young children caused by encapsulated bacterial pathogens. These vaccines, however, are difficult and expensive to manufacture, deterring their widespread use. We present an alternative technology for the production of conjugate-like vaccines whereby capsular antigens are entrapped in a cross-linked protein matrix. The versatility and ease of protein capsular matrix vaccine production compared with conjugates will likely render the manufacture of these vaccines simpler and more cost effective than conjugate vaccines. This in turn would improve the availability of such vaccines to the developing world, which has shown a limited capacity to afford the cost of conventional conjugate vaccines.
Assessment of Finfish Aquaculture Effect on Newfoundland Epibenthic Communities through Video Monitoring
Authors: Hamoutene Dounia , Salvo Flora , Bungay Terrence , Mabrouk Gehan , Couturier Cyr , Ratsimandresy Andry , Dufour Suzanne C
Published: February 2015

In Newfoundland fjords, evaluating changes to benthic communities resulting from finfish aquaculture is difficult because the depth (>30 m) and presence of patches of hard substrates at production sites hinder grab sampling. In this study, we used video surveys to characterize benthic assemblages at sites with no aquaculture, with varying amounts of finfish production, and undergoing fallowing periods. Video analyses revealed a patchy distribution of benthic organisms (identifiable at a high taxonomic level), characterized by low natural abundances and richness. Benthic communities at aquaculture sites showed evidence of organic matter enrichment through the presence of Beggiatoa sp. or opportunistic polychaete-dominated assemblages (or both), bare stations, flocculent matter, and lower abundances and richness near aquaculture cages. Maps of sites in production showed that the area of aquaculture impact was influenced by bathymetry, located underneath cages and in some instances up to 145 m away from net-pens, and often directed away from the coastline. However, correlations of abundances and richness with distance from cage were weak, and stations close to cages were not always statistically different from stations further away or at the nonproduction site. At the fallow site, a large percentage (∼70%) of stations was barren, suggesting potentially hypoxic or anoxic conditions and warranting further investigations of fallow periods. Our analysis confirms that video-based assessments can detect major aquaculture-related changes in benthic communities but cannot, at present, identify lower levels of disturbance.
Apparent Phosphorus Availabilities of Selected Traditional and Alternative Feedstuffs for Channel Catfish
Authors: Li Menghe H , Robinson Edwin H , Lucas Penelope M
Published: February 2015

A digestibility trial with Channel Catfish Ictalurus punctatus was conducted to determine apparent availability coefficients (AACs) of phosphorus for selected common feedstuffs: soybean meal, cottonseed meal, wheat middlings, corn gluten feed (CGF), and corn distillers dried grains with solubles (DDGS). A 32% protein diet containing mostly chemically defined ingredients was used as a reference diet. Test diets were formulated to contain 70% of the reference diet mix and 30% of the test ingredient. Chromic oxide was used at 0.75% of the diet as a marker. Fifteen Channel Catfish of a mean weight of 316 g/fish (SD, 5) were placed into 110-L flow-through aquaria. Water temperature and dissolved oxygen were maintained at approximately 30°C and ≥ 5 mg/L, respectively. Each diet had three replicated tanks. Apparent availability coefficients of phosphorus were 36, 22, 20, 75, and 77% for soybean meal, cottonseed meal, wheat middlings, CGF, and DDGS, respectively. Corn by-products CGF and DDGS had considerably greater phosphorus AACs than soybean meal, cottonseed meal, and wheat middlings, likely because the wet milling and fermentation processes that result in these by-products degrade the phytate form of phosphorus making it more available to the fish. It appears that phosphorus AACs of these ingredients for Channel Catfish are generally correlated to their nonphytate phosphorus levels. Phosphorus AACs obtained from the present study can be used in formulating commercial Channel Catfish feeds to optimize available phosphorus levels.
CycleFreeFlux: efficient removal of thermodynamically infeasible loops from flux distributions
Authors: Desouki Abdelmoneim Amer , Jarre Florian , Gelius-Dietrich Gabriel , Lercher Martin J.
Published: February 2015

Motivation: Constraint-based metabolic modeling methods such as Flux Balance Analysis (FBA) are routinely used to predict metabolic phenotypes, e.g. growth rates, ATP yield or the fitness of gene knockouts. One frequent difficulty of constraint-based solutions is the inclusion of thermodynamically infeasible loops (or internal cycles), which add nonbiological fluxes to the predictions.

Results: We propose a simple postprocessing of constraint-based solutions, which removes internal cycles from any given flux distribution v(0) without disturbing other fluxes not involved in the loops. This new algorithm, termed CycleFreeFlux, works by minimizing the sum of absolute fluxes ||v||1 while (i) conserving the exchange fluxes and (ii) using the fluxes of the original solution to bound the new flux distribution. This strategy reduces internal fluxes until at least one reaction of every possible internal cycle is inactive, a necessary and sufficient condition for the thermodynamic feasibility of a flux distribution. If alternative representations of the input flux distribution in terms of elementary flux modes exist that differ in their inclusion of internal cycles, then CycleFreeFlux is biased towards solutions that maintain the direction given by v(0) and towards solutions with lower total flux ||v||1. Our method requires only one additional linear optimization, making it computationally very efficient compared to alternative strategies.

Availability and implementation: We provide freely available R implementations for the enumeration of thermodynamically infeasible cycles as well as for cycle-free FBA solutions, flux variability calculations and random sampling of solution spaces.

Contact: lercher@cs.uni-duesseldorf.de
Annocript: a flexible pipeline for the annotation of transcriptomes able to identify putative long noncoding RNAs
Authors: Musacchia Francesco , Basu Swaraj , Petrosino Giuseppe , Salvemini Marco , Sanges Remo
Published: February 2015

Summary: The eukaryotic transcriptome is composed of thousands of coding and long non-coding RNAs (lncRNAs). However, we lack a software platform to identify both RNA classes in a given transcriptome. Here we introduce Annocript, a pipeline that combines the annotation of protein coding transcripts with the prediction of putative lncRNAs in whole transcriptomes. It downloads and indexes the needed databases, runs the analysis and produces human readable and standard outputs together with summary statistics of the whole analysis.

Availability and implementation: Annocript is distributed under the GNU General Public License (version 3 or later) and is freely available at https://github.com/frankMusacchia/Annocript.

Contact:  remo.sanges@szn.it