bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gap gene regulatory dynamics evolve along a genotype network
Authors: Crombach Anton , Wotton Karl R. , Jiménez-Guri Eva , Jaeger Johannes 
Published: August 2015

AbstractDevelopmental gene networks implement the dynamic regulatory mechanisms that pattern and shape the organism. Over evolutionary time, the wiring of these networks changes, yet the patterning outcome is often preserved, a phenomenon known as “system drift”. System drift is illustrated by the gap gene network—involved in segmental patterning—in dipteran insects. In the classic model organismDrosophila melanogasterand the non-model scuttle flyMegaselia abdita, early activation and placement of gap gene expression domains show significant quantitative differences, yet the final patterning output of the system is essentially identical in both species. In this detailed modeling analysis of system drift, we use gene circuits which are fit to quantitative gap gene expression data inM. abditaand compare them to an equivalent set of models fromD. melanogaster.The results of this comparative analysis show precisely how compensatory regulatory mechanisms achieve equivalent final patterns in both species. We discuss the larger implications of the work in terms of “genotype networks” and the ways in which the structure of regulatory networks can influence patterns of evolutionary change (evolvability).
Toward high-throughput predictive modeling of protein binding/unbinding kinetics
Authors: Chiu See Hong , Xie Lei 
Published: August 2015

AbstractOne of the unaddressed challenges in drug discovery is that drug potency determinedin vitrois not a reliable indicator of drug activity in humans. Accumulated evidences suggest thatin vivoactivity is more strongly correlated with the binding/unbinding kinetics than the equilibrium thermodynamics of protein-ligand interactions (PLI). However, existing experimental and computational techniques are insufficient in studying the molecular details of kinetics process of PLI. Consequently, we not only have limited mechanistic understanding of the kinetic process but also lack a practical platform for the high-throughput screening and optimization of drug leads based on their kinetic properties. Here we address this unmet need by integrating energetic and conformational dynamic features derived from molecular modeling with multi-task learning. To test our method, HIV-1 protease is used as a model system. Our integrated model provides us with new insights into the molecular determinants of kinetics of PLI. We find that the coherent coupling of conformational dynamics between protein and ligand may play a critical role in determining the kinetic rate constants of PLI. Furthermore, we demonstrate that the relative movement of normal nodes of amino acids upon ligand binding is an important feature to capture conformational dynamics of the binding/unbinding kinetics. Coupled with the multi-task learning, we can predict combined konand koffaccurately with an accuracy of 74.35%. Thus, it is possible to screen and optimize compounds based on their binding/unbinding kinetics. The further development of such computational tools will bridge one of the critical missing links in drug discovery.
Is Britain Facing a Crisis of Democracy?
Authors: Baldini Gianfranco 
Published: August 2015

AbstractThis article contributes to the debate in this journal about the state of British democracy. I criticise the tendency to use a ‘demand–supply’ dichotomy in interpreting the strong distrust experienced by institutions and politicians, and especially the idea that all the blame for current problems is to be attributed to the inadequateness of the British political tradition (BPT). By referring to international data on democracy and to recent British trends in both public attitudes and institutional innovations, a more nuanced picture on the state of democracy emerges. I argue that the BPT is not incompatible with incremental changes that have already introduced innovations in the way politics works in Britain today, and that the task of empowering citizens is one of the most delicate aspects in this process of innovation.
Image Analysis of Foods
Authors: Russ John C. 
Published: August 2015

AbstractThe structure of foods, both natural and processed ones, is controlled by many variables ranging from biology to chemistry and mechanical forces. The structure also controls many of the properties of the food, including consumer acceptance, taste, mouthfeel, appearance, and so on, and nutrition. Imaging provides an important tool for measuring the structure of foods. This includes 2‐dimensional (2D) images of surfaces and sections, for example, viewed in a microscope, as well as 3‐dimensional (3D) images of internal structure as may be produced by confocal microscopy, or computed tomography and magnetic resonance imaging. The use of images also guides robotics for harvesting and sorting. Processing of images may be needed to calibrate colors, reduce noise, enhance detail, and delineate structure and dimensions. Measurement of structural information such as volume fraction and internal surface areas, as well as the analysis of object size, location, and shape in both 2‐ and 3‐dimensional images is illustrated and described, with primary references and examples from a wide range of applications.
Landowner Motivations for Civic Engagement in Water Resource Protection
Authors: Pradhananga Amit K. , Davenport Mae , Olson Bjorn 
Published: August 2015

AbstractScholars and water resource professionals recognize citizens must get involved in water resource issues to protect water resources. Yet questions persist on how to motivate community members to get and stay civically involved in nonpoint source pollution issues, given that problems are often ill‐defined. To be successful, interventions intended to engage individuals in collective action must be based on an understanding of the determinants of public‐sphere behavior. The purpose of this study is to explore the psycho‐social factors which influence landowner civic engagement in water resource protection. Data were collected using a self‐administered mail survey of landowners in the Cannon River Watershed and analyzed using structural equation modeling. Study findings suggest landowners are more likely to be civically engaged in water resource issues if they feel a personal obligation to take civic action and perceive they have the ability to protect water resources. Landowners who believe water resource protection is a local responsibility, perceive important others expect them to protect water resources, and believe they have the ability to protect water resources are more likely to feel a sense of obligation to take civic action. A combination of strategies including civic engagement programs addressing barriers to landowner engagement will be most effective for promoting civic engagement in water resource protection.
A framework for detecting natural selection on traits above the species level
Authors: Hoehn Kenneth B. , Harnik Paul G. , Roth V. Louise 
Published: August 2015

Summary

To what extent can natural selection act on groupings above the species level? Despite extensive theoretical discussion and growing practical concerns over increased rates of global ecological turnover, the question has largely evaded empirical resolution. A flexible and robust hypothesis‐testing framework for detecting the phenomenon could facilitate significant progress in resolving this issue.

We introduce a permutation‐based approach, implemented in the R package perspectev, which provides an explicit test of whether empirical patterns of correlation between upper level trait values and survivorship are reducible to correlations manifested at lower levels. The package is applicable to virtually any nested set of upper‐ and lower level groupings, a wide variety of upper level traits, and both historical and contemporary occurrence data. We apply this approach to five paleontological data sets that represent different magnitudes of extinction and differ in taxonomic breadth, geological timing and geographic extent.

Using simulations, we demonstrate that this method is a robust means of detecting irreducibility in the relationship between upper level traits and survivorship, and outline circumstances in which the method is less effective. We also find evidence consistent with previous findings of selection above the species level for geographic range size in North American K‐Pg molluscs and show that this phenomenon was evident for the same molluscan genera globally.

Ultimately, we conclude that at certain points in history, some higher level taxonomic groups have survived differentially with respect to geographic range size in a manner that is not explained by the same trait at the species level, and we show that evidence for this phenomenon varies across taxa and extinction events. We release our method as a flexible and easy‐to‐use R package that will allow others to help determine the relative frequency of this macroevolutionary phenomenon, both in the fossil record and in estimates of contemporary extinction risk.
Rare disaster risk and the expected equity risk premium
Authors: Berkman Henk , Jacobsen Ben , Lee John B. 
Published: August 2015

AbstractConsistent with the predictions of rare disaster models, we find that a proxy for the time‐varying probability of rare disasters helps to explain fluctuations in expectations of the equity risk premium. Our proxy for disaster risk is a recently developed measure of global political instability, and the expected market risk premium is from Value Line analysts' expected stock returns. Consistent with long‐run risk models, uncertainty about expected GDP growth and expected consumption growth is also significantly positively related to the expected market risk premium. We obtain similar results when we use the earnings–price ratio and the dividend–price ratio as proxies for the expected market risk premium.
Ritual sounds, political echoes: Vocal agency and the sensory cultures of secularism in the Dutch Syriac diaspora
Authors: BAKKER KELLOGG SARAH 
Published: August 2015

ABSTRACTAmong Syriac Orthodox Christian migrant communities in the Netherlands, liturgical performance is a site of controversy over where and how to draw a boundary between “religious” and “ethnic” identity. Tensions materialize in discordant singing styles and modes of performance, echoing complex historical encounters with Dutch, Syrian, and Turkish secularisms. These encounters, I argue, have refashioned the liturgical tradition's role as a central axis of ethnoreligious social life and kin relations across the diaspora. Secular state practices shape a diasporic sensory culture that is met with a distinct form of vocal agency. Syriac Orthodox liturgical experiments show how the voice can transform the sensorial interface between human subjectivity and social intelligibility, in turn transforming how categories of secular modernity—whether ritual, art, ethnicity, or politics—are distinguished and lived.
The becoming of ancestral land: Place and property in Mapuche land claims
Authors: DI GIMINIANI PIERGIORGIO 
Published: August 2015

ABSTRACTIf Mapuche land claims in southern Chile reflect the incommensurability of local notions of place and the legal principles of property, they also reveal intersections between indigenous and legal ontologies of land. Property languages and technologies allow claimants to frame knowledge about ancestral territory in ways consistent with local significations of place as a sentient agent. Yet they also serve as mechanisms for codifying indigenous geographies in terms congruent with existing property regimes and market configuration. Drawing on Deleuze and Guattari's notions of becoming, I argue that understanding ancestral land formation requires an anthropological imagination that acknowledges the conceptual antagonism of state and indigenous geographies as well as their intersections in claimants’ actions. [land, state, property, indigeneity, Latin America, Chile, deterritorialization]
Dataset of scientific inquiry learning environment
Authors: Ting Choo‐Yee , Ho Chiung Ching 
Published: August 2015

AbstractThis paper presents the dataset collected from student interactions with INQPRO, a computer‐based scientific inquiry learning environment. The dataset contains records of 100 students and is divided into two portions. The first portion comprises (1) raw log data, capturing the student's name, interfaces visited, the interface components the student interacted with, the actions performed by the students and the values asserted at a particular interface component; (2) transformed log data, a restructured and refined raw log data that take the form of an attribute‐value pair record. The second portion of the dataset consists of pretest‐posttest results. This paper begins with an overview of INQPRO and the discussion on how student–computer interactions were captured. Subsequently, the process of preprocessing and transformation of raw log data into relational database tables will be presented. In this paper, two applications of INQPRO dataset are presented; the first application discusses how students' levels of scientific inquiry skills can be extracted from the dataset while the second application demonstrates how the dataset supports the prediction of conceptual change occurrence. The paper ends with highlighting potential future research work by using this dataset, which includes techniques to elicit clusters of students as well as provision of adaptive pedagogical interventions as the student interacts with INQPRO. In conclusion, this dataset attempts to contribute to the research community through: (1) time and cost saving in acquiring field data, and (2) as a benchmark dataset to evaluate and compare different predictive models.
Determining the number of participants needed for the usability evaluation of e‐learning resources: A Monte Carlo simulation
Authors: Davids Mogamat Razeen , Harvey Justin , Halperin Mitchell L. , Chikte Usuf M. E. 
Published: August 2015

AbstractThe usability of computer interfaces has a major influence on learning. Optimising the usability of e‐learning resources is therefore essential. However, this may be neglected because of time and monetary constraints. User testing is a common approach to usability evaluation and involves studying typical end‐users interacting with the application being tested. Determining the minimum number of users that are required for such an evaluation is important as it has a direct bearing on the costs and time requirements. This issue has long been a subject of debate and the widely cited recommendation of five users being enough has been questioned. We conducted a usability evaluation of an e‐learning resource for electrolyte and acid‐base disorders by studying the interaction of medical doctors with the application. A total of 15 serious usability problems were detected, most of these related to an interactive treatment simulation. With this report, we are making available the data on the detection of serious usability problems by each of our participants. We have used these data to run a Monte Carlo simulation and examine how many users would be sufficient to test our application. The simulation revealed that we would have required 10 participants to detect 80% of the serious usability problems. The MATLAB® code for running the simulation is supplied, as are our calculations of problem discovery rates. The e‐learning resource which was evaluated is freely available, together with a revised version with all identified usability problems addressed.
Waks, Leonard J (2014) Education 2.0Paradigm Publishers (Boulder, CO, and London) isbn 978‐1‐61205‐036‐2 269 pp $32.95 https://paradigm.presswarehouse.com/books/BookDetail.aspx?productID=356922
Authors: Martin Marie 
Published: August 2015

SummaryThis stimulating book offers a radical vision of education for our networked digital age. It challenges us to make the paradigm shift from the entrenched factory school model to Education 2.0, a “Learningweb revolution” made possible by the internet. It urges its target readers—who are all the stakeholders in education—to accelerate this shift by pressing for change at local level. Does this book seem likely to be relevant to you? If so, I recommend that you arrange to borrow a copy for a while.Marie Martin
Society for Endocrinology UK guidance on the initial evaluation of an infant or an adolescent with a suspected disorder of sex development (Revised 2015)
Authors: Ahmed S. Faisal , Achermann John C. , Arlt Wiebke , Balen Adam , Conway Gerry , Edwards Zoe , Elford Sue , Hughes Ieuan A. , Izatt Louise , Krone Nils , Miles Harriet , O'Toole Stuart , Perry Les , Sanders Caroline , Simmonds Margaret , Watt Andrew , Willis Debbie 
Published: August 2015

SummaryIt is paramount that any child or adolescent with a suspected disorder of sex development (DSD) is assessed by an experienced clinician with adequate knowledge about the range of conditions associated with DSD. If there is any doubt, the case should be discussed with the regional DSD team. In most cases, particularly in the case of the newborn, the paediatric endocrinologist within the regional team acts commonly as the first point of contact. This clinician should be part of a multidisciplinary team experienced in management of DSD and should ensure that the affected person and parents have access to specialist psychological support and that their information needs are comprehensively addressed. The underlying pathophysiology of DSD and the strengths and weaknesses of the tests that can be performed should be discussed with the parents and affected young person and tests undertaken in a timely fashion. Finally, in the field of rare conditions, it is imperative that the clinician shares the experience with others through national and international clinical and research collaboration.
Angiotensin II prevents calcification in vascular smooth muscle cells by enhancing magnesium influx
Authors: Herencia Carmen , Rodríguez‐Ortiz M Encarnacion , Muñoz‐Castañeda Juan R. , Martinez‐Moreno Julio Manuel , Canalejo Rocío , Montes de Oca Addy , Díaz‐Tocados Juan M. , Peralbo‐Santaella Esther , Marín Carmen , Canalejo Antonio , Rodriguez Mariano , Almaden Yolanda 
Published: August 2015

AbstractBackgroundVascular calcification (VC) is highly prevalent in patients with chronic kidney disease (CKD). Low magnesium levels are associated with VC, and recent in vitro studies confirm a protective role of magnesium, which is mediated by its entry into the VSMCs through the Transient Receptor Potential Melastatin 7 (TRPM7) channel. The role of Angiotensin II (Ang II) on VC is still unclear. As Ang II is able to stimulate TRPM7 activity, we hypothesize that it might prevent VC. Thus, the aim of this study was to dissect the direct effect of Ang II on VC.Materials and methodsWe worked with a model of high phosphate (HP)‐induced calcification in human aortic smooth muscle cells, which resembles the CKD‐related VC.ResultsAddition of Ang II to cells growing in HP decreased calcification, which was associated with the upregulation of the osteogenic factors BMP2, Runx2/Cbfa1, Osterix and ALP. A reduction of magnesium entry into the HP‐calcifying cells was found. The treatment with Ang II avoided this reduction, which was reversed by the cotreatment with the TRPM7‐inhibitor 2‐APB. The protective effect of Ang II was related to AT1R‐induced ERK1/2 MAPKinase activation. HP‐induced calcification was also associated with the upregulation of the canonical Wnt/beta‐catenin pathway, while its downregulation was related to attenuation of calcification by Ang II.ConclusionAs hypothesized, Ang II prevented phosphate‐induced calcification in VSMCs, which appears mediated by the increase of magnesium influx and by the activation of the ERK1/2 and the inhibition of the canonical Wnt/beta‐catenin signalling pathways.
Prognostic significance of WNT and hedgehog pathway activation markers in cancer of unknown primary
Authors: Fotopoulos George , Gousia Anna , Bareta Eleni , Koumpis Epameinondas , Chrisafi Sofia , Bobos Matthaios , Malamou‐Mitsi Vassiliki , Fountzilas George , Pavlidis Nicholas , Pentheroudakis George 
Published: August 2015

AbstractBackgroundCancer of unknown primary (CUP) possesses distinct biology and peculiar natural history, in which the roles of the winged and hedgehog signalling pathways are unclear.Materials and methodsWe constructed tissue microarrays and studied the immunohistochemical (IHC) expression of β‐catenin, smoothened (SMO) and the transcription factors TCF, LEF, GLI1 in 87 CUP cases for prognostic significance.ResultsA low rate of IHC expression of proteins was seen, the cut‐off used being any expression in ≥ 1% of tumour cells. At univariate analysis, only nuclear IHC SMO expression displayed a statistically significant association with favourable outcome [median Overall survival (OS) of 19 months in SMO‐positive vs. 12 months in SMO‐negative cases, P = 0·01]. An activated Wnt pathway, defined as IHC expression of any of nuclear β‐catenin, TCF and LEF, was significantly associated with favourable progression free survival (median 9 vs. 5 months, P = 0·037) and OS (median 19 vs. 13 months, P = 0·04). This prognostic impact on OS was mainly driven by nuclear expression of TCF and/or LEF (P = 0·03). No prognostic significance of the hedgehog pathway activation status, defined as IHC expression of SMO or nuclear GLI1, could be established. A favourable prognostic impact of the concurrent activation of both pathways was observed. A trend for association of activated Wnt with response to chemotherapy (responders 67% among activated Wnt cases vs. 35% among nonactivated Wnt cases, P = 0·07) was observed in CUP adenocarcinomas.ConclusionsActivation of the Wnt pathway was a positive prognostic factor in a small CUP series, possibly via enhanced chemosensitivity. Independent validation is warranted.
Magnetic resonance imaging as a tool to image neuroinflammation in a rat model of Parkinson's disease – phagocyte influx to the brain is promoted by bilberry‐enriched diet
Authors: Virel Ana , Rehnmark Anna , Orädd Greger , Olmedo‐Díaz Sonia , Faergemann Erik , Strömberg Ingrid 
Published: August 2015

AbstractNeuroinflammation is a chronic event in neurodegenerative disorders. In the rat model of Parkinson's disease, including a striatal injection of the neurotoxin 6‐hydroxydopamine (6‐OHDA), antioxidant treatment affects the inflammatory process. Despite a heavy accumulation of microglia early after the injury, dopamine nerve fibre regeneration occurs. It remains unclear why this heavy accumulation of microglia is found early after the lesion in antioxidant‐treated animals, or even more, what is the origin of these microglia. In this study magnetic resonance imaging (MRI) was used to elucidate whether the inflammatory response was generated from the blood or from activated brain microglia. Superparamagnetic iron oxide (SPIO) nanoparticles were injected intravenously prior to a striatal 6‐OHDA injection to tag phagocytes in the blood. Rats were fed either with bilberry‐enriched or control diet. T2*‐weighted MRI scans were performed 1 week after the lesion, and hypointense areas were calculated from T2*‐weighted images, to monitor the presence of SPIO particles. The results revealed that feeding the animals with bilberries significantly promoted accumulation of blood‐derived immune cells. Gadolinium‐enhanced MRI demonstrated no difference in leakage of the blood–brain barrier independent of diets. To conclude, bilberry‐enriched diet promotes an influx of periphery‐derived immune cells to the brain early after injury.