bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developing a data model for understanding geographical analysis models with consideration of their evolution and application processes
Authors: Chen Min , Yang Chen , Hou Tao , Lü Guonian , Wen Yongning , Yue Songshan 
Published: November 2018

AbstractGeographical analysis models are widely employed to mirror real phenomena and processes on Earth. The current geographical analysis models can provide prediction and decision support‐oriented information in various domains through analysis and simulation results. However, the complexity of models is increasing due to their continuous development and related research, and the relationships between models are becoming increasingly complicated, which severely hinders the ability to select and use suitable models. To bridge the requirements of model understanding with related abundant information, a data model for geographical analysis models is designed with consideration of their evolution and application processes. In addition to basic metadata (e.g., name, classification, and modeling approach), evolution and application information, which is often neglected in traditional model expression methods, can provide clues about model development histories and usage relationships. Thus, this information will provide scientists with a comprehensive understanding and will form an overall picture of geographic models that can be used for future research. Based on the analysis of the elements related to the evolution and application information, the data model is designed and an information abstraction strategy is proposed. The Soil and Water Assessment Tool (SWAT) is employed as a case study to show the capacity of the designed data model to contribute to both sharing of geographical analysis model knowledge and further model analysis.
Narrative review of methods and findings of recent studies on the carriage of meningococci and other Neisseria species in the African Meningitis Belt
Authors: Greenwood Brian M. , Aseffa Abraham , Caugant Dominique A. , Diallo Kanny , Kristiansen Paul A. , Maiden Martin C. J. , Stuart James M. , Trotter Caroline L. 
Published: November 2018

AbstractObjectiveTo review the findings of studies of pharyngeal carriage of Neisseria meningitidis and related species conducted in the African meningitis belt since a previous review published in 2007.MethodsPubMed and Web of Science were searched in July 2018 using the terms ‘meningococcal OR Neisseria meningitidis OR lactamica AND carriage AND Africa’, with the search limited to papers published on or after 1st January 2007. We conducted a narrative review of these publications.ResultsOne hundred and thirteen papers were identified using the search terms described above, 20 of which reported new data from surveys conducted in an African meningitis belt country. These papers described 40 surveys conducted before the introduction of the group A meningococcal conjugate vaccine (MenAfriVacR) during which 66 707 pharyngeal swabs were obtained. Carriage prevalence of N. meningitidis varied substantially by time and place, ranging from <1% to 24%. The mean pharyngeal carriage prevalence of N. meningitidis across all surveys was 4.5% [95% CI: 3.4%, 6.8%] and that of capsulated N. meningitidis was 2.8% [95% CI: 1.9%; 5.2%]. A study of households provided strong evidence for meningococcal transmission within and outside households. The introduction of MenAfriVac® led to marked reductions in carriage of the serogroup A meningococcus in Burkina Faso and Chad.ConclusionsRecent studies employing standardised methods confirm the findings of older studies that carriage of N. meningitidis in the African meningitis belt is highly variable over time and place, but generally occurs with a lower prevalence and shorter duration than reported from industrialised countries.
Lleida Bat Lyssavirus isolation in Miniopterus schreibersii in France
Authors: Picard‐Meyer Evelyne , Beven Veronique , Hirchaud Edouard , Guillaume Cédric , Larcher Gérald , Robardet Emmanuelle , Servat Alexandre , Blanchard Yannick , Cliquet Florence 
Published: November 2018

AbstractBat rabies cases are attributed in Europe to five different Lyssavirus species of 16 recognized Lyssavirus species causing rabies. One of the most genetically divergent Lyssavirus spp. has been detected in a dead Miniopterus schreibersii bat in France. Brain samples were found positive for the presence of antigen, infectious virus and viral RNA by classical virological methods and molecular methods respectively. The complete genome sequence was determined by next‐generation sequencing. The analysis of the complete genome sequence confirmed the presence of Lleida bat lyssavirus (LLEBV) in bats in France with 99.7% of nucleotide identity with the Spanish LLEBV strain (KY006983).
THE AMBIVALENCE OF SCIENTIFIC NATURALISM: A RESPONSE TO MARK HARRIS
Authors: Brooke John Hedley 
Published: November 2018

AbstractResponding to Mark Harris, I reflect on his tantalizing question whether the provision of naturalistic explanations for biblical miracles renders the narratives more, or less, credible. I address his “reversal,” in which professional scientists now feature among defenders of a literalistic reading, while professional biblical scholars are often skeptical. I suggest this underlines the ambivalence of scientific naturalism from the standpoint of Christian theology. Historical examples are adduced to show that, until the mid‐nineteenth century, naturalistic and theistic explanations were commonly regarded as complementary. Accordingly, the primacy often accorded to scientific progress in accounts of secularization is questionable. Two concluding questions are raised. If a methodological naturalism inheres in biblical scholarship, as in the sciences, how do biblical scholars decide whether the historical trajectories they construct for the composition of biblical texts are destructive or affirmative of faith? Second, when the miracle is the Resurrection of the dead Christ, does not the scientific impossibility of this foundational event remain sacrosanct?
ON “THE NATURAL NATURE OF NATURALISM”: ANSWERS TO JOHN HEDLEY BROOKE'S QUESTIONS
Authors: Harris Mark 
Published: November 2018

AbstractIn John Hedley Brooke's response to my 2018 Boyle Lecture he provided some helpful prompts to sharpen my position on naturalism, and posed two further questions to me. This article takes up his prompts, and offers some answers to his questions, especially concerning the Resurrection of Jesus.
THE “CONFLICT THESIS” AND POSITIVIST HISTORY OF SCIENCE: A VIEW FROM THE PERIPHERY
Authors: de Asúa Miguel 
Published: November 2018

AbstractThe historiographic tradition of the history of science that originated with Auguste Comte bears all the marks of narratives with roots in the Enlightenment, such as a view of religion as an underdeveloped stage in the ascending road in humanity's quest for a more mature understanding. This article explores the development of the peripheral branch of a tradition that developed in Argentina by the mid‐twentieth century with authors such as the Italians Aldo Mieli, José Babini, and the Hungarian Desiderius Papp. It is argued that, contrary to the historiographic program of the conflict thesis developed in English‐speaking countries, those scholars who cultivated the kind of “positivist” history of science that thrived in continental Europe were inclined to see science as a social and epistemological replacement of a fossilized religious outlook. In the final section, I suggest a way to relate the more or less strong versions of the conflict thesis to different patterns of secularization.
REMEMBRANCE AND RESILIENCE: HOW THE BODYSELF RESPONDS TO TRAUMA
Authors: Pederson Ann , Nuetzman Erin , Gubbels Jennifer , Hummel Leonard 
Published: November 2018

AbstractHow do the experiences of people who undergo extreme suffering and trauma in one generation get passed on to the next generation? And how do these experiences affect religious–spiritual beliefs and practices? Can we help to create resilience in these later generations through these religious–spiritual beliefs? In order to answer these questions, one must remember and understand not only how trauma is embodied and inherited, but also the role that religious beliefs and practices play in facing and overcoming the trauma. People who have experienced trauma can pass on the effects to subsequent generations biologically through epigenetic changes to their DNA, but also through their religious and spiritual beliefs and practices. The ways people remember and recover from trauma involve complex biological, psychosocial, and spiritual processes. We use the sciences of embodied cognition and epigenetics to analyze the heritability of trauma and its spiritual–religious manifestations in the next generations. Having done so, our hope is that we can understand how spiritual and religious practices can be developed to help people who undergo trauma so that they can become resilient and thrive.
Simulation of P2X‐mediated calcium signalling in microglia
Authors: Chun Byeong Jae , Stewart Bradley D. , Vaughan Darin D. , Bachstetter Adam D. , Kekenes‐Huskey Peter M. 
Published: November 2018

Key points
A computational model of P2X channel activation in microglia was developed that includes downfield Ca2+‐dependent signalling pathways.
This model provides quantitative insights into how diverse signalling pathways in microglia converge to control microglial function.
AbstractMicroglia function is orchestrated through highly coupled signalling pathways that depend on calcium (Ca2+). In response to extracellular ATP, transient increases in intracellular Ca2+ driven through the activation of purinergic receptors, P2X and P2Y, are sufficient to promote cytokine synthesis. Although the steps comprising the pathways bridging purinergic receptor activation with transcriptional responses have been probed in great detail, a quantitative model for how these steps collectively control cytokine production has not been established. Here we developed a minimal computational model that quantitatively links extracellular stimulation of two prominent ionotropic purinergic receptors, P2X4 and P2X7, with the graded production of a gene product, namely the tumour necrosis factor α (TNFα) cytokine. In addition to Ca2+ handling mechanisms common to eukaryotic cells, our model includes microglia‐specific processes including ATP‐dependent P2X4 and P2X7 activation, activation of nuclear factor of activated T‐cells (NFAT) transcription factors, and TNFα production. Parameters for this model were optimized to reproduce published data for these processes, where available. With this model, we determined the propensity for TNFα production in microglia, subject to a wide range of ATP exposure amplitudes, frequencies and durations that the cells could encounter in vivo. Furthermore, we have investigated the extent to which modulation of the signal transduction pathways influence TNFα production. Our results suggest that pulsatile stimulation of P2X4 via micromolar ATP may be sufficient to promote TNFα production, whereas high‐amplitude ATP exposure is necessary for production via P2X7. Furthermore, under conditions that increase P2X4 expression, for instance, following activation by pathogen‐associated molecular factors, P2X4‐associated TNFα production is greatly enhanced. Given that Ca2+ homeostasis in microglia is profoundly important to its function, this computational model provides a quantitative framework to explore hypotheses pertaining to microglial physiology.
Using a 10-step framework to support the implementation of an evidence-based clinical pathways programme
Authors: Flores Emilia J , Mull Nikhil K , Lavenberg Julia G , Mitchell Matthew D , Leas Brian F , Williams Austin , Brennan Patrick J , Umscheid Craig A 
Published: November 2018

BackgroundIntegration of evidence into practice is suboptimal. Clinical pathways, defined as multidisciplinary care plans, are a method for translating evidence into local settings and have been shown to improve the value of patient care.ObjectiveTo describe the development of a clinical pathways programme across a large academic healthcare system.MethodsWe use a 10-step framework (grounded in the Knowledge-to-Action framework and ADAPTE Collaboration methodology for guideline adaptation) to support pathway development and dissemination, including facilitating clinical owner and stakeholder engagement, developing pathway prototypes based on rapid reviews of the existing literature, developing tools for dissemination and impact assessment. We use a cloud-based technology platform (Dorsata, Washington, DC) to assist with development and dissemination across our geographically distributed care settings and providers. Content is viewable through desktop and mobile applications. We measured programme adoption and penetration by examining number of pathways developed as well as mobile application use and pathway views.ResultsFrom 1 February 2016 to 30 April 2018, a total of 202 pathways were disseminated. The three most common clinical domains represented were oncology (46.5%, n=94), pulmonary/critical care (8.9%, n=18) and cardiovascular medicine (7.4%, n=15). Users opting to register for a personal account totalled 1257; the three largest groups were physicians (45.1%, n=567), advanced practice providers (19.5%, n=245) and nurses (19.1%, n=240). Pathway views reached an average of 2150 monthly views during the last 3 months of the period. The majority of pathways reference at least one evidence-based source (93.6%, n=180).ConclusionsA healthcare system can successfully use a framework and technology platform to support the development and dissemination of pathways across a multisite institution.
Water inflow into tunnels: assessment of the Gerede water transmission tunnel (Turkey) with complex hydrogeology
Authors: Apaydin Ahmet , Korkmaz Nur , Ciftci Donmez 
Published: November 2018

The Gerede is the longest and most problematic water transmission tunnel in Turkey, at 31.6 km long with an overburden of 600 m. The tunnel will transmit water from the Ulusu river to the Camlidere reservoir. High-pressure water ingress and collapses have resulted in many delays. Although construction began in 2012, and was intended to be completed in 2014, completion is now estimated to be in 2019. The tunnel passes through permeable Tertiary sedimentary and volcano-sedimentary rocks, and Jurassic–Cretaceous limestone. Water ingress has occurred on 45 occasions along the 26 km excavated. The initial total discharge was 1.7 m
3
s
−1
and decreased to 0.5 m
3
s
−1
over time. The recharge conditions, tectonic structure, progress of the excavation and sealing by grouting affect the quantity, locations and temporal changes of the inflow of water. The major faults and formation contacts are the most problematic sites to be considered.

With the many delays in the tunnel, the driving plan and tunnel boring machine (TBM) were changed while the construction continued. The tunnel shows that hydrogeological conditions, in particular, should be taken into consideration when choosing the TBM and driving course. However, the problems we encountered provided valuable experience for future projects.
Reconstructing the Himalayan margin prior to collision with Asia: Proterozoic and lower Paleozoic geology and its implications for Cenozoic tectonics
Authors: Myrow P. M. , Hughes N. C. , McKenzie N. R. 
Published: November 2018

Abstract
Reconstructing the stratigraphic architecture of deposits prior to Cenozoic Himalayan uplift is critical for unravelling the structural, metamorphic, depositional and erosional history of the orogen. The nature and distribution of Proterozoic and lower Paleozoic strata have helped elucidate the relationship between lithotectonic zones, as well as the geometries of major bounding faults. Stratigraphic and geochronological work has revealed a uniform and widespread pattern of Paleoproterozoic strata >1.6 Ga that are unconformably overlain by <1.1 Ga rocks. The overlying Neoproterozoic strata record marine sedimentation, including a Cryogenian diamictite, a well-developed carbonate platform succession and condensed fossiliferous Precambrian–Cambrian boundary strata. Palaeontological study of Cambrian units permits correlation from the Indian craton through three Himalayan lithotectonic zones to a precision of within a few million years. Detailed sedimentological and stratigraphic analysis shows the differentiation of a proximal realm of relatively condensed, nearshore, evaporite-rich units to the south and a distal realm of thick, deltaic deposits to the north. Thus, Neoproterozoic and Cambrian strata blanketed the northern Indian craton with an extensive, northward-deepening, succession. Today, these rocks are absent from parts of the inner Lesser Himalaya, and the uplift and erosion of these proximal facies explains a marked change in global seawater isotopic chemistry at 16 Ma.
Securing agent 111, and the job of software architect
Authors: Arquilla John , Bugayenko Yegor 
Published: November 2018

The
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John Arquilla describes the new state of cyberspying, while Yegor Bugayenko considers the importance of a software architect to development projects.
Na+/Ca2+ exchanger overexpression in smooth muscle augments cytosolic Ca2+ in femoral arteries of living mice
Authors: Zhang Jin , Wang Youhua , Chen Ling , Wier W. Gil , Blaustein Mordecai P. 
Published: November 2018

Plasma membrane Na+/Ca2+ exchanger-1 (NCX1) helps regulate the cytosolic Ca2+ concentration ([Ca2+]CYT) in arterial myocytes. NCX1 mediates both Ca2+ entry and exit and tends to promote net Ca2+ entry in partially constricted arteries. Mean blood pressure (telemetry) is elevated by ≈10 mmHg in transgenic (TG) mice that overexpress NCX1 specifically in smooth muscle. We tested the hypothesis that NCX1 overexpression mediates Ca2+ gain and elevated [Ca2+]CYT in exposed femoral arteries that also express the Ca2+ biosensor exogenous myosin light chain kinase. [Ca2+]CYT and the NCX1-dependent (SEA0400-sensitive) component, ≈15% of total basal constriction in controls, were increased in TG arteries, but constrictions to phenylephrine and ANG II were comparable in TG and control arteries. Normalized phenylephrine dose-response curves and constriction to 30 and 300 ng/kg iv ANG II were virtually identical in control and TG arteries. ANG II-evoked constrictions, superimposed on elevated basal tone, accounted for the larger blood pressure responses to ANG II in TG arteries. TG and control mouse arteries fit the same pCa-constriction relationship over a wide range of pCa (≈125–500 nM). Vasodilation to acetylcholine, normalized to passive diameter, was also comparable in TG and control arteries, implying normal endothelial function. TG artery Na+ nitroprusside (nitric oxide donor)-induced dilations were, however, shifted to lower Na+ nitroprusside concentrations, indicating that TG myocyte vasodilator mechanisms were augmented. Maximum arterial dilation was comparable in TG and control mice, although passive diameter was ≈6–7% smaller in TG mice. The changes in TG arteries were apparently largely functional rather than structural, despite the congenital hypertension. NEW & NOTEWORTHY Smooth muscle Na+/Ca2+ exchanger-1 transgene overexpression (TG mice) increases femoral artery basal cytosolic Ca2+ concentration ([Ca2+]CYT) and tone in vivo and raises blood pressure. Arterial constriction to phenylephrine and angiotensin II are normal but superimposed on the augmented basal [Ca2+]CYT and tone (constriction) in TG mouse arteries. Similar effects in resistance arteries would explain the elevated blood pressure. Acetylcholine-induced vasodilation is unimpaired, implying a normal endothelium, but TG arteries are hypersensitive to sodium nitroprusside.
Disruption of cardiac Med1 inhibits RNA polymerase II promoter occupancy and promotes chromatin remodeling
Authors: Hall Duane D. , Spitler Kathryn M. , Grueter Chad E. 
Published: November 2018

The Mediator coactivator complex directs gene-specific expression by binding distal enhancer-bound transcription factors through its Med1 subunit while bridging to RNA polymerase II (Pol II) at gene promoters. In addition, Mediator scaffolds epigenetic modifying enzymes that determine local DNA accessibility. Previously, we found that deletion of Med1 in cardiomyocytes deregulates more than 5,000 genes and promotes acute heart failure. Therefore, we hypothesized that Med1 deficiency disrupts enhancer-promoter coupling. Using chromatin immunoprecipitation-coupled deep sequencing (ChIP-seq; n = 3/ChIP assay), we found that the Pol II pausing index is increased in Med1 knockout versus floxed control mouse hearts primarily due to a decrease in Pol II occupancy at the majority of transcriptional start sites without a corresponding increase in elongating species. Parallel ChIP-seq assays reveal that Med1-dependent gene expression correlates strongly with histone H3 K27 acetylation, which is indicative of open and active chromatin at transcriptional start sites, whereas H3 K27 trimethylated levels, representing condensed and repressed DNA, are broadly increased and inversely correlate with absolute expression levels. Furthermore, Med1 deletion leads to dynamic changes in acetyl-K27 associated superenhancer regions and their enriched transcription factor-binding motifs that are consistent with altered gene expression. Our findings suggest that Med1 is important in establishing enhancer-promoter coupling in the heart and supports the proposed role of Mediator in establishing preinitiation complex formation. We also found that Med1 determines chromatin accessibility within genes and enhancer regions and propose that the composition of transcription factors associated with superenhancer changes to direct gene-specific expression. NEW & NOTEWORTHY Based on our previous findings that transcriptional homeostasis and cardiac function are disturbed by cardiomyocyte deletion of the Mediator coactivator Med1 subunit, we investigated potential underlying changes in RNA polymerase II localization and global chromatin accessibility. Using chromatin immunoprecipitation sequencing, we found that disrupted transcription arises from a deficit in RNA polymerase II recruitment to gene promoters. Furthermore, active versus repressive chromatin marks are redistributed within gene loci and at enhancer regions correlated with gene expression changes.