bluuebunny/crossref_metadata_2025_split huggingface dataset:
A coupled hierarchical modeling approach to simulating the geomorphic response of river systems to anthropogenic climate change
Authors: Praskievicz Sarah 
Published: March 2015

AbstractAnthropogenic climate change is expected to change the discharge and sediment transport regime of river systems. Because rivers adjust their channels to accommodate their typical inputs of water and sediment, changes in these variables can potentially alter river morphology. In this study, a hierarchical modeling approach was developed and applied to examine potential changes in reach‐averaged bedload transport and spatial patterns of erosion and deposition for three snowmelt‐dominated gravel‐bed rivers in the interior Pacific Northwest. The modeling hierarchy was based on discharge and suspended‐sediment load from a basin‐scale hydrologic model driven by a range of downscaled climate‐change scenarios. In the field, channel morphology and sediment grain‐size data for all three rivers were collected. Changes in reach‐averaged bedload transport were estimated using the Bedload Assessment of Gravel‐bedded Streams (BAGS) software, and the Cellular Automaton Evolutionary Slope and River (CAESAR) model was used to simulate the spatial pattern of erosion and deposition within each reach to infer potential changes in channel geometry and planform. The duration of critical discharge was found to control bedload transport. Changes in channel geometry were simulated for the two higher‐energy river reaches, but no significant morphological changes were found for a lower‐energy reach with steep, cohesive banks. Changes in sediment transport and river morphology resulting from climate change could affect the management of river systems for human and ecological uses. Copyright © 2015 John Wiley & Sons, Ltd.
Influence of fire retardants on the reaction‐to‐fire properties of coextruded wood–polypropylene composites
Authors: Nikolaeva Marina , Kärki Timo 
Published: March 2015

SummaryThe reaction‐to‐fire properties of coextruded wood–plastic composites containing different fire retardants (melamine, zinc borate, ammonium polyphosphate, aluminium trihydroxide, natural flake graphite and expandable graphite) in the shell layer have been studied with the cone calorimetry technique. The effect of ammonium polyphosphate in combination with graphite has also been studied with a cone calorimeter test. A coextruded composite manufactured without any fire retardant addition has been used as a reference. The fire properties measured in the cone calorimeter are discussed, including the heat release rate, total heat release, smoke production, specific extinction area, CO yield and mass loss rate. The results show that the introduction of fire retardants in the shell layer of coextruded wood–polypropylene composites has a favourable effect on the fire resistance properties of the composite materials. The reaction‐to‐fire properties have been improved according to the fire classification of construction products based on the Euroclass system. Copyright © 2015 John Wiley & Sons, Ltd.
Differential patterns of functional and structural plasticity within and between inferior frontal gyri support training‐induced improvements in inhibitory control proficiency
Authors: Chavan Camille F. , Mouthon Michael , Draganski Bogdan , van der Zwaag Wietske , Spierer Lucas 
Published: March 2015

AbstractAmple evidence indicates that inhibitory control (IC), a key executive component referring to the ability to suppress cognitive or motor processes, relies on a right‐lateralized fronto‐basal brain network. However, whether and how IC can be improved with training and the underlying neuroplastic mechanisms remains largely unresolved. We used functional and structural magnetic resonance imaging to measure the effects of 2 weeks of training with a Go/NoGo task specifically designed to improve frontal top‐down IC mechanisms. The training‐induced behavioral improvements were accompanied by a decrease in neural activity to inhibition trials within the right pars opercularis and triangularis, and in the left pars orbitalis of the inferior frontal gyri. Analyses of changes in brain anatomy induced by the IC training revealed increases in grey matter volume in the right pars orbitalis and modulations of white matter microstructure in the right pars triangularis. The task‐specificity of the effects of training was confirmed by an absence of change in neural activity to a control working memory task. Our combined anatomical and functional findings indicate that differential patterns of functional and structural plasticity between and within inferior frontal gyri enhanced the speed of top‐down inhibition processes and in turn IC proficiency. The results suggest that training‐based interventions might help overcoming the anatomic and functional deficits of inferior frontal gyri manifesting in inhibition‐related clinical conditions. More generally, we demonstrate how multimodal neuroimaging investigations of training‐induced neuroplasticity enable revealing novel anatomo‐functional dissociations within frontal executive brain networks. Hum Brain Mapp 36:2527–2543, 2015. © 2015 Wiley Periodicals, Inc.
A limited positioning system for memory
Authors: Shapiro Matthew 
Published: March 2015

ABSTRACTThe 2014 Nobel Prize for Physiology or Medicine is an enormous triumph for John O'Keefe and May‐Britt and Edvard Moser and an historic event for cognitive and behavioral neuroscience. Neuronal representations decoded from action potentials form a mechanistic bridge between brain and mind and demonstrate the continuity of psychology with biology and physical science. The cognitive map theory powered an ongoing, international research program inspired by Hebb ( The Organization of Behavior. New York, NY: Wiley) that showed the way toward linking specific patterns of neuronal activity to high level representation and processing. The prize celebrates a path that led from fundamental, philosophical questions about psychological space to enduring, scientific facts: place, head direction, grid, and boundary fields in the hippocampus, presubiculum, entorhinal cortex, and other brain circuits provide a cellular basis for spatial behavior, learning, and memory. By awarding this prize, the Nobel committee affirmed neuroethology and comparative psychology, marked the end of a chapter in one debate about the existence of animal cognition, and recognized cognitive neurophysiology. The “inner GPS” in the brain” demonstrates “a cellular basis for higher cognitive function.” Animals represent, process, and use information defined by abstract relationships among items (O'Keefe and Conway, ) to guide flexible, goal‐directed actions. Beyond raising the ontological status of “animal mind,” the committee agreed that abstract mental representations can be investigated rigorously by recording single unit activity in the brain of behaving animals. © 2015 Wiley Periodicals, Inc.
Presence of a high‐flow‐mediated constriction phenomenon prior to flow‐mediated dilation in normal weight, overweight, and obese children and adolescents
Authors: Ostrem Joseph D. , Evanoff Nicholas , Kelly Aaron S. , Dengel Donald R. 
Published: March 2015

ABSTRACTPurposeWhen assessing vasomotor endothelial function by reactive hyperemia, the brachial artery, in some individuals, constricts immediately before beginning to dilate following cuff release. We call this response high‐flow‐mediated constriction (H‐FMC). The aim of this study was to describe the rate of the H‐FMC during reactive hyperemia in children and adolescents throughout a range of body mass index (BMI) values, and to investigate differences in flow‐mediated dilation (FMD), cardiovascular, and anthropometric measures between subjects with and without H‐FMC.MethodsFMD was assessed in 136 children and adolescents (61 male, 75 female; 13 ± 3 years) by sonographic imaging of the brachial artery. H‐FMC was characterized as the lowest point from the baseline brachial artery diameter immediately following reactive cuff release. Independent t tests were used to compare subjects with and without H‐FMC.ResultsH‐FMC was observed in 91 of the 136 participants (66.9%). No significant difference was found between H‐FMC and non‐H‐FMC subjects for age (p = 0.602), gender (p = 0.767), height (p = 0.227), or weight (p = 0.171). BMI percentile was nonsignificantly higher (91.8 ± 14.9th versus 84.6 ± 22.8th percentile, p = 0.057) and FMD was significantly lower (5.43 ± 3.41% versus 8.05 ± 3.97%, p < 0.001) in H‐FMC than in non‐H‐FMC subjects. Adding H‐FMC to FMD produced no significant difference between H‐FMC and non‐H‐FMC individuals (8.03 ± 3.27% versus 8.05 ± 3.97%, p = 0.977).ConclusionsApproximately 67% of participants demonstrated an H‐FMC during reactive hyperemia. BMI percentile was nonsignificantly higher and FMD was significantly lower in children and adolescents who displayed this phenomenon. © 2015 Wiley Periodicals, Inc. J Clin Ultrasound 43:495–501 2015
Short‐day aggression is independent of changes in cortisol or glucocorticoid receptors in male Siberian hamsters (Phodopus sungorus)
Authors: Scotti Melissa‐Ann L. , Rendon Nikki M. , Greives Timothy J. , Romeo Russell D. , Demas Gregory E. 
Published: March 2015

ABSTRACTTestosterone mediates aggression in many vertebrates. In some species, aggression remains high during the non‐breeding season (e.g., winter), when testosterone levels are low. In Siberian hamsters (Phodopus sungorus), we have demonstrated photoperiodic changes in aggression with hamsters housed in short, “winter‐like” days displaying significantly more territorial aggression than long‐day animals, despite low levels of testosterone. The mechanisms by which photoperiod regulates aggression, however, remain largely unknown. Adrenocortical hormones (e.g., glucocorticoids) have been implicated in mediating seasonal aggression; circulating concentrations of these hormones have been correlated with aggression in some species. The goal of this study was to examine the role of cortisol and glucocorticoid receptors in mediating photoperiodic changes in aggression in male Siberian hamsters. Males were housed in long or short days and treated with either exogenous cortisol or vehicle. Circulating levels of cortisol, adrenal cortisol content, and aggression were quantified. Lastly, photoperiodic effects on glucocorticoid receptor (GR) protein levels were quantified in limbic brain regions associated with aggression, including medial prefrontal cortex, amygdala, and hippocampus. Short‐day hamsters were more aggressive than long‐day hamsters, however cortisol treatment did not affect aggression. Photoperiod had no effect on serum or adrenal cortisol or GR levels in the brain regions examined. Taken together, these data suggest that increases in cortisol levels do not cause increases associated with short‐day aggression, and further that GR protein levels are not associated with photoperiodic changes in aggression. The results of this study contribute to our understanding of the role of adrenocortical steroids in mediating seasonal aggression. J. Exp. Zool. 323A: 331–342, 2015. © 2015 Wiley Periodicals, Inc.
Spatial distribution of marine airborne bacterial communities
Authors: Seifried Jasmin S. , Wichels Antje , Gerdts Gunnar 
Published: March 2015

AbstractThe spatial distribution of bacterial populations in marine bioaerosol samples was investigated during a cruise from the North Sea to the Baltic Sea via Skagerrak and Kattegat. The analysis of the sampled bacterial communities with a pyrosequencing approach revealed that the most abundant phyla were represented by the Proteobacteria (49.3%), Bacteroidetes (22.9%), Actinobacteria (16.3%), and Firmicutes (8.3%). Cyanobacteria were assigned to 1.5% of all bacterial reads. A core of 37 bacterial OTUs made up more than 75% of all bacterial sequences. The most abundant OTU was Sphingomonas sp. which comprised 17% of all bacterial sequences. The most abundant bacterial genera were attributed to distinctly different areas of origin, suggesting highly heterogeneous sources for bioaerosols of marine and coastal environments. Furthermore, the bacterial community was clearly affected by two environmental parameters – temperature as a function of wind direction and the sampling location itself. However, a comparison of the wind directions during the sampling and calculated backward trajectories underlined the need for more detailed information on environmental parameters for bioaerosol investigations. The current findings support the assumption of a bacterial core community in the atmosphere. They may be emitted from strong aerosolizing sources, probably being mixed and dispersed over long distances.
Prediction of PARP Inhibition with Proteochemometric Modelling and Conformal Prediction
Authors: Cortés‐Ciriano Isidro , Bender Andreas , Malliavin Thérèse 
Published: March 2015

AbstractPoly(ADP‐ribose) polymerases (PARPs) play a key role in DNA damage repair. PARP inhibitors act as chemo‐ and radio‐ sensitizers and thus potentiate the cytotoxicity of DNA damaging agents. Although PARP inhibitors are currently investigated as chemotherapeutic agents, their cross‐reactivity with other members of the PARP family remains unclear. Here, we apply Proteochemometric Modelling (PCM) to model the activity of 181 compounds on 12 human PARPs. We demonstrate that PCM (R02test=0.65–0.69; RMSEtest=0.95–1.01 °C) displays higher performance on the test set (interpolation) than Family QSAR and Family QSAM (Tukey’s HSD, α 0.05), and outperforms Inductive Transfer knowledge among targets (Tukey’s HSD, α 0.05). We benchmark the predictive signal of 8 amino acid and 11 full‐protein sequence descriptors, obtaining that all of them (except for SOCN) perform at the same level of statistical significance (Tukey’s HSD, α 0.05). The extrapolation power of PCM to new compounds (RMSE=1.02±0.80 °C) and targets (RMSE=1.03±0.50 °C) is comparable to interpolation, although the extrapolation ability is not uniform across the chemical and the target space. For this reason, we also provide confidence intervals calculated with conformal prediction. In addition, we present the R package conformal, which permits the calculation of confidence intervals for regression and classification caret models.
SCD5‐induced oleic acid production reduces melanoma malignancy by intracellular retention of SPARC and cathepsin B
Authors: Bellenghi Maria , Puglisi Rossella , Pedini Francesca , De Feo Alessandra , Felicetti Federica , Bottero Lisabianca , Sangaletti Sabina , Errico Maria Cristina , Petrini Marina , Gesumundo Cinzia , Denaro Massimo , Felli Nadia , Pasquini Luca , Tripodo Claudio , Colombo Mario Paolo , Carè Alessandra , Mattia Gianfranco 
Published: March 2015

AbstractA proper balance between saturated and unsaturated fatty acids (FAs) is required for maintaining cell homeostasis. The increased demand of FAs to assemble the plasma membranes of continuously dividing cancer cells might unbalance this ratio and critically affect tumour outgrowth. We unveiled the role of the stearoyl‐CoA desaturase SCD5 in converting saturated FAs into mono‐unsaturated FAs during melanoma progression. SCD5 is down‐regulated in advanced melanoma and its restored expression significantly reduced melanoma malignancy, both in vitro and in vivo, through a mechanism governing the secretion of extracellular matrix proteins, such as secreted protein acidic and rich in cysteine (SPARC) and collagen IV and of their proteases, such as cathepsin B. Enforced expression of SCD5 or supplementation of its enzymatic product, oleic acid, reduced the intracellular pH (pHe > pHi) and, in turn, vesicular trafficking across plasma membranes as well as melanoma dissemination. This intracellular acidification appears also to depend on SCD5‐induced reduction of the C2 subunit of the vacuolar H+‐ATPase, a proton pump whose inhibition changes the secretion profile of cancer cells. Our data support a role for SCD5 and its enzymatic product, oleic acid, in protection against malignancy, offering an explanation for the beneficial Mediterranean diet. Furthermore, SCD5 appears to functionally connect tumour cells and the surrounding stroma toward modification of the tumour microenvironment, with consequences on tumour spread and resistance to treatment. Copyright © 2015 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Retrospective analysis of prenatal ultrasound of children with Hirschsprung disease
Authors: Jakobson‐Setton Ariella , Weissmann‐Brenner Alina , Achiron Reuven , Kuint Jacob , Gindes Liat 
Published: March 2015

AbstractObjectiveHirschsprung disease (HD) is a rare gastrointestinal disorder. Our aim was to study the prenatal ultrasound findings of children who were diagnosed with HD after birth.MethodsThe study population included children who suffered from HD between 1990 and 2008. Data of anomaly scan findings in prenatal ultrasound, demographic and post‐natal physical abnormalities and treatment were retrieved from medical files and interviews with the parents.ResultsTwenty‐two patients confirmed histopathological diagnosis of HD at age of 1 day to 15 months. Nineteen fetuses had anomaly scan during pregnancy, which revealed minor sonographic abnormalities in three fetuses; two of them had hyperechogenic bowel. One fetus with hyperechogenic bowel had polyhydramnion, and another had a family history of three brothers with HD. A third fetus had dilated pelvic kidney. None of them had sonographic evidence of bowel dilatation. After birth, six patients (31%) were found to have other structural anomalies: ventriculoseptal defect, atriseptal defect, atrio‐ventricular septal defect, and pyloric stenosis.ConclusionsAbnormal sonographic findings of fetal bowel are absent in the vast majority of fetuses who are diagnosed with HD after birth. In women with a family history of HD, a third trimester anomaly scan may be warranted. © 2015 John Wiley & Sons, Ltd.
Eliminating antibody polyreactivity through addition of N‐linked glycosylation
Authors: Chuang Gwo‐Yu , Zhang Baoshan , McKee Krisha , O'Dell Sijy , Kwon Young Do , Zhou Tongqing , Blinn Julie , Lloyd Krissey , Parks Robert , Von Holle Tarra , Ko Sung‐Youl , Kong Wing‐Pui , Pegu Amarendra , Wang Keyun , Baruah Kavitha , Crispin Max , Mascola John R. , Moody M. Anthony , Haynes Barton F. , Georgiev Ivelin S. , Kwong Peter D. 
Published: March 2015

ABSTRACTAntibody polyreactivity can be an obstacle to translating a candidate antibody into a clinical product. Standard tests such as antibody binding to cardiolipin, HEp‐2 cells, or nuclear antigens provide measures of polyreactivity, but its causes and the means to resolve are often unclear. Here we present a method for eliminating antibody polyreactivity through the computational design and genetic addition of N‐linked glycosylation near known sites of polyreactivity. We used the HIV‐1‐neutralizing antibody, VRC07, as a test case, since efforts to increase VRC07 potency at three spatially distinct sites resulted in enhanced polyreactivity. The addition of N‐linked glycans proximal to the polyreactivity‐enhancing mutations at each of the spatially distinct sites resulted in reduced antibody polyreactivity as measured by (i) anti‐cardiolipin ELISA, (ii) Luminex AtheNA Multi‐Lyte ANA binding, and (iii) HEp‐2 cell staining. The reduced polyreactivity trended with increased antibody concentration over time in mice, but not with improved overall protein stability as measured by differential scanning calorimetry. Moreover, glycan proximity to the site of polyreactivity appeared to be a critical factor. The results provide evidence that antibody polyreactivity can result from local, rather than global, features of an antibody and that addition of N‐linked glycosylation can be an effective approach to reducing antibody polyreactivity.
Supporting requirements update during software evolution
Authors: Ben Charrada Eya , Koziolek Anne , Glinz Martin 
Published: March 2015

SummaryUpdating the requirements specification when software systems evolve is a manual task that is expensive and time consuming. Therefore, maintainers usually apply the changes to the code directly and leave the requirements unchanged. This results in the requirements rapidly becoming obsolete and useless. In this paper, we propose an approach that supports the maintainer in keeping the requirements specification consistent with the implementation, by identifying the requirements that are impacted whenever the code is changed. Our approach works as follows. First, we analyze the changes that have been applied to the source code and detect if they are likely to impact the requirements or not. Second, we trace the requirements‐impacting changes back to the requirements specification to identify the parts that might need to be modified. The output of the tracing is a list of requirements that are sorted according to their likelihood of being impacted. Automatically identifying the parts of the requirements specification that are likely to need maintenance reduces the effort needed for keeping the requirements up‐to‐date and thus makes the task of the maintainer easier. When applying our approach in three cases studies, 70% to 100% of the impacted requirements were identified within a list that includes less than 20% of the total number of requirements in the specification. Copyright © 2015 John Wiley & Sons, Ltd.
Actl6a Protects Embryonic Stem Cells From Differentiating Into Primitive Endoderm
Authors: Lu Weisi , Fang Lekun , Ouyang Bin , Zhang Xiya , Zhan Shaoquan , Feng Xuyang , Bai Yaofu , Han Xin , Kim Hyeung , He Quanyuan , Wan Ma , Shi Feng-Tao , Feng Xin-Hua , Liu Dan , Huang Junjiu , Songyang Zhou 
Published: March 2015

Abstract
Actl6a (actin-like protein 6A, also known as Baf53a or Arp4) is a subunit shared by multiple complexes including esBAF, INO80, and Tip60-p400, whose main components (Brg1, Ino80, and p400, respectively) are crucial for the maintenance of embryonic stem cells (ESCs). However, whether and how Actl6a functions in ESCs has not been investigated. ESCs originate from the epiblast (EPI) that is derived from the inner cell mass (ICM) in blastocysts, which also give rise to primitive endoderm (PrE). The molecular mechanisms for EPI/PrE specification remain unclear. In this study, we provide the first evidence that Actl6a can protect mouse ESCs (mESCs) from differentiating into PrE. While RNAi knockdown of Actl6a, which appeared highly expressed in mESCs and downregulated during differentiation, induced mESCs to differentiate towards the PrE lineage, ectopic expression of Actl6a was able to repress PrE differentiation. Our work also revealed that Actl6a could interact with Nanog and Sox2 and promote Nanog binding to pluripotency genes such as Oct4 and Sox2. Interestingly, cells depleted of p400, but not of Brg1 or Ino80, displayed similar PrE differentiation patterns. Mutant Actl6a with impaired ability to bind Tip60 and p400 failed to block PrE differentiation induced by Actl6a dysfunction. Finally, we showed that Actl6a could target to the promoters of key PrE regulators (e.g., Sall4 and Fgf4), repressing their expression and inhibiting PrE differentiation. Our findings uncover a novel function of Actl6a in mESCs, where it acts as a gatekeeper to prevent mESCs from entering into the PrE lineage through a Yin/Yang regulating pattern. Stem Cells 2015;33:1782–1793