bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic Characterization of Caenorhabditis elegans Larval Development
Authors: Xia Tian , Horton Edward R. , Salcini Anna Elisabetta , Pocock Roger , Cox Thomas R. , Erler Janine T. 
Published: November 2017

AbstractThe nematode Caenorhabditis elegans is widely used as a model organism to study cell and developmental biology. Quantitative proteomics of C. elegans is still in its infancy and, so far, most studies have been performed on adult worm samples. Here, we used quantitative mass spectrometry to characterize protein level changes across the four larval developmental stages (L1–L4) of C. elegans. In total, we identified 4130 proteins, and quantified 1541 proteins that were present across all four stages in three biological replicates from independent experiments. Using hierarchical clustering and functional ontological analyses, we identified 21 clusters containing proteins with similar protein profiles across the four stages, and highlighted the most overrepresented biological functions in each of these protein clusters. In addition, we used the dataset to identify putative larval stage‐specific proteins in each individual developmental stage, as well as in the early and late developmental stages. In summary, this dataset provides system‐wide analysis of protein level changes across the four C. elegans larval developmental stages, which serves as a useful resource for the C. elegans research community. MS data were deposited in ProteomeXchange (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the primary accession identifier PXD006676.
A new parameter‐rich structure‐aware mechanistic model for amino acid substitution during evolution
Authors: Chi Peter B. , Kim Dohyup , Lai Jason K. , Bykova Nadia , Weber Claudia C. , Kubelka Jan , Liberles David A. 
Published: November 2017

AbstractImprovements in the description of amino acid substitution are required to develop better pseudo‐energy‐based protein structure‐aware models for use in phylogenetic studies. These models are used to characterize the probabilities of amino acid substitution and enable better simulation of protein sequences over a phylogeny. A better characterization of amino acid substitution probabilities in turn enables numerous downstream applications, like detecting positive selection, ancestral sequence reconstruction, and evolutionarily‐motivated protein engineering. Many existing Markov models for amino acid substitution in molecular evolution disregard molecular structure and describe the amino acid substitution process over longer evolutionary periods poorly. Here, we present a new model upgraded with a site‐specific parameterization of pseudo‐energy terms in a coarse‐grained force field, which describes local heterogeneity in physical constraints on amino acid substitution better than a previous pseudo‐energy‐based model with minimum cost in runtime. The importance of each weight term parameterization in characterizing underlying features of the site, including contact number, solvent accessibility, and secondary structural elements was evaluated, returning both expected and biologically reasonable relationships between model parameters. This results in the acceptance of proposed amino acid substitutions that more closely resemble those observed site‐specific frequencies in gene family alignments. The modular site‐specific pseudo‐energy function is made available for download through the following website: https://liberles.cst.temple.edu/Software/CASS/index.html.
Integrated fault estimation and fault‐tolerant control for stochastic systems with Brownian motions
Authors: Liu Xiaoxu , Gao Zhiwei 
Published: November 2017

SummaryThis paper presents an integrated robust fault estimation and fault‐tolerant control technique for stochastic systems subjected to Brownian parameter perturbations. The augmented system approach, unknown input observer method, and optimization technique are integrated to achieve robust simultaneous estimates of the system states and the means of faults concerned. Meanwhile, a robust fault‐tolerant control strategy is developed by using actuator and sensor signal compensation techniques. Stochastic linear time‐invariant systems, stochastic systems with Lipschitz nonlinear constraint, and stochastic systems with quadratic inner‐bounded nonlinear constraint are respectively investigated, and the corresponding fault‐tolerant control algorithms are addressed. Finally, the effectiveness of the proposed fault‐tolerant control techniques is demonstrated via the drivetrain system of a 4.8 MW benchmark wind turbine, a 3‐tank system, and a numerical nonlinear model.
All‐Inorganic Metal Halide Perovskite Nanostructures: From Photophysics to Light‐Emitting Applications
Authors: Wang Yue , Sun Handong 
Published: November 2017

AbstractAll‐inorganic metal halide perovskite nanostructures (IHPNs) have sparked intense research interest by virtue of their superior optical properties and their cost‐effective synthesis. Since the first report in 2015, striking development of IHPNs has been witnessed in terms of fabrication strategies, optical characterization, and optoelectronic applications. Here, a brief survey of the mainstream fabrication routes is given. The emphasis is placed on the understanding of the photophysics of IHPNs, including the electronic structures, steady‐state and transient absorption and emission, nonlinear optical properties, and representative exotic photophysical phenomena. Afterward, the light‐emitting applications of IHPNs in lasers and light‐emitting diodes are summarized. Finally, the challenges and a perspective of the future development of IHPNs are presented.
‘Blogging Sometimes Leads to Dementia, Doesn’t It?’ The Roman Catholic Church in Times of Deep Mediatization
Authors: Radde-Antweiler Kerstin , Grünenthal Hannah , Gogolok Sina 
Published: November 2017

Abstract
The chapter analyzes religious authorities in Catholicism in times of deep mediatization. Like few other organizations, the Catholic Church seems to be caught between the general tendency of deep mediatization and its own reluctance to adapt to a mediatized world and society. One topic that is directly connected to media change is the construction of religious authority. Unlike earlier perspectives on the relation of religious authority and media, the figurational perspective offers the possibility to look at changes in the construction of religious authority and their interrelation with media change on different levels. Those different levels refer to different actor constellations and different media ensembles, as well as to different levels of authority, in other words local and translocal authority. In this chapter, we will explore how official religious authorities in the Catholic Church, namely priests in different positions, deal with deep mediatization. This includes the question concerning how they use media themselves, in which situations they use or don’t use media, how and why they are reluctant; but also how they define their own and other’s authority in a mediatized society and how all of this effects the organization as a whole. We will find out that there are different scopes in which authority is constructed differently: while the degree of mediatization is relatively low on the local scope, religious authorities are expected to go with mediatization in a translocal and global scope.
Chaos Computer Club: The Communicative Construction of Media Technologies and Infrastructures as a Political Category
Authors: Kubitschko Sebastian 
Published: November 2017

Abstract
This chapter displays how hackers’ political engagement today relies on a wide range of practices related to media technologies and infrastructures and, at the same time, continues to be oriented towards larger publics as well as ‘traditional’ centres of political power. By employing the concept of communicative figuration, the chapter elaborates how one of the world’s oldest and largest hacker organizations—the Chaos Computer Club (CCC)—communicatively constructs media technologies and infrastructures as a political category in its own right. To implement this approach, the chapter will proceed in three aligned steps. First, the hacker organization itself is conceptualized as a communicative figuration, which also includes direct political action in the form of hacking. Second, the chapter explains how the CCC positions itself in the public discourse surrounding media technologies. Third, the chapter demonstrates how the Club’s internal figuration and its linkages with relevant actors, such as journalists, politicians and judges as well as the general public, creates a spiral of legitimation that enables the hacker organization to constitute media technologies and infrastructures as publicly recognized political phenomena.
SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research
Authors: Yaniv Ziv , Lowekamp Bradley C. , Johnson Hans J. , Beare Richard 
Published: November 2017

Abstract
Modern scientific endeavors increasingly require team collaborations to construct and interpret complex computational workflows. This work describes an image-analysis environment that supports the use of computational tools that facilitate reproducible research and support scientists with varying levels of software development skills. The Jupyter notebook web application is the basis of an environment that enables flexible, well-documented, and reproducible workflows via literate programming. Image-analysis software development is made accessible to scientists with varying levels of programming experience via the use of the SimpleITK toolkit, a simplified interface to the Insight Segmentation and Registration Toolkit. Additional features of the development environment include user friendly data sharing using online data repositories and a testing framework that facilitates code maintenance. SimpleITK provides a large number of examples illustrating educational and research-oriented image analysis workflows for free download from GitHub under an Apache 2.0 license: github.com/InsightSoftwareConsortium/SimpleITK-Notebooks.
Tendon Excision Following Distal Semitendinosus Injury in the Elite Athlete: A Surgical Technique
Authors: Rebolledo Brian J. , McAdams Timothy R. , Cooper Daniel E. 
Published: November 2017

Background Hamstring injuries can present in numerous forms, some of which can lead to persistent pain, loss of function, and delay in return to sport. Although most are treated conservatively, proximal and distal tendon avulsion injuries have become more commonly treated with surgery. Distal semitendinosus avulsion injuries have been largely reported in the elite athlete population. While conservative management has been utilized, failure in this group can significantly impact a future career. Purpose The purpose of the manuscript is to describe our approach of surgical tendon excision for distal semitendinosus injury in an elite athlete. Methods We highlight a two-incision technique to isolate the avulsed tendon, followed by exteriorization and tendon excision. In addition, we provide insight on clinical and imaging findings to help guide management. Results This technique provides a reliable and effective surgical option for managing these rare injuries of the distal semitendinosus, along with outlining rehabilitation goals in the postoperative period. Conclusion In this setting, we present a detailed surgical technique to excise the injured distal semitendinosus tendon to promote recovery and potentially allow for earlier return to play.
Implant Removal and Spacer Placement for Infected Shoulder Arthroplasty: Risk Factors for Repeat Procedures, Spacer Retention, and Mortality
Authors: Cancienne J. M. , Brockmeier Stephen F. , Carr James C. , Werner Brian C. 
Published: November 2017

Background Current studies reporting on patients following prosthesis removal and spacer placement for periprosthetic joint infection (PJI) of the shoulder have largely been descriptive and insufficiently powered to determine risk factors for outcomes other than reimplantation. Purpose The objective of the present study is to provide a national perspective on the 1-year outcomes following prosthesis removal and spacer placement and risk factors for outcomes other than reimplantation for treatment of PJI following shoulder arthroplasty. Methods A national database was queried for Medicare patients who underwent prosthesis removal and spacer placement for PJI between 2005 and 2012. These patients were then evaluated for 5 major study endpoints including: (1) replantation of a shoulder prosthesis within 1 year postoperatively, (2) a repeat irrigation and debridement with second antibiotic spacer placement procedure within 1 year postoperatively, (3) in-hospital death within 1 year postoperatively, (4) a shoulder Girdlestone-type procedure within 1 year postoperatively, and (5) the remaining patients, who were considered to have a retained spacer. Patients with a study endpoint within 1 year postoperatively were included in the study: (1) mortality, (2) repeat debridement, (3) resection arthroplasty, and (4) reimplantation. While it is possible that some patients were not captured due to errors in coding, it is unlikely that patients were lost to follow-up due to change in location of services, given that the database captures all episodes of care that are coded throughout the USA. Independent risk factors were evaluated using logistic regression analysis. Results Nine hundred seventy-five patients who underwent prosthesis removal and spacer placement were included. Within 1 year postoperatively, 21 patients died (2.2%), 70 patients had a repeat debridement procedure (7.2%), 55 patients had a resection arthroplasty procedure (5.6%), 349 patients retained their spacers (35.8%), and the remaining 480 patients had a shoulder arthroplasty reimplanted (49.2%). Numerous independent risk factors exist for all outcomes studied. Conclusion The fate of antibiotic spacers placed for PJI of the shoulder at 1 year is variable, with numerous independent risk factors for outcomes other than reimplantation. Patients with PJI following total shoulder arthroplasty should be counseled on the risk factors that influence the outcomes of staged revision for shoulder PJI.
SWI/SNF-Komplex-assoziierte Tumordispositions-Syndrome
Authors: Bens Susanne , Kehrer-Sawatzki Hildegard , Hasselblatt Martin , Frühwald Michael C. , Siebert Reiner 
Published: November 2017

Zusammenfassung
Die SWI/SNF(SWItch/Sucrose Non-fermentable)-Komplexe sind aus mehreren, je nach Geweben unterschiedlichen Untereinheiten zusammengesetzt und regulieren im Sinne von „Chromatin-(Re)Modeling“ ATP-abhängig die Zugänglichkeit von funktionellen DNA Elementen, wie Promotoren und Enhancern, für z. B. Transkriptionsfaktoren.
Keimbahnmutationen in den kodierenden Genen für die Untereinheiten SMARCB1, SMARCA4, SMARCE1 und PBRM1 des SWI/SNF-Komplexes sind mit einer Veranlagung für Tumorerkrankungen assoziiert. Keimbahnmutationen in SMARCB1 und SMARCA4 führen zu den Rhabdoidtumor-Prädispositions-Syndromen (RTPS) 1 bzw. RTPS2. Dies sind einem autosomal-dominanten Erbgang folgende Dispositionen für maligne Rhabdoidtumoren (RT) des Gehirns (AT/RT), der Nieren (RTK) und der Weichgewebe (MRT). Hinweise für ein RTPS sind eine frühe, z. T. schon pränatale Manifestation von RT, ein synchrones Auftreten mehrerer RT und eine positive Familienanamnese. Sporadisch auftretende RT weisen eine somatische Inaktivierung von SMARCB1 (oder selten SMARCA4) auf und sind im Vergleich zu auf einem RTPS beruhenden RT mit einer günstigeren Prognose assoziiert.
Keimbahnmutationen in SMARCB1 und SMARCA4 können unabhängig von einem RTPS auch zu anderen Tumoren führen. Keimbahnmutationen in SMARCA4 wurden bei Patienten mit der hyperkalzämischen Form von kleinzelligen Ovarialkarzinomen (small cell carcinoma of the ovary, hypercalcemic type; SCCOHT) nachgewiesen. SMARCB1-Keimbahnmutationen wurden neben RT z. B. mit einer Schwannomatose assoziiert. Im Unterschied zu RT und SCCOHT ist für die Manifestation einer Schwannomatose ein Funktionsverlust von SMARCB1 in Kombination mit einem somatischen Verlust von NF2 erforderlich.
Die phänotypische Breite von SMARCB1-assoziierten Neoplasien geht auf Art und Lokalisation der Mutation zurück. Weiterhin spielt vermutlich der Zeitpunkt des „second hit“ eine Rolle, da die Empfindlichkeit für die Entwicklung eines RT bei biallelischer Inaktivierung von SMARCB1 in RT-Progenitorzellen wohl nur in einem kurzen Entwicklungszeitfenster gegeben ist.
Mineralogy of Secondary Olivine-hosted Inclusions in Calcite Carbonatites of the Belaya Zima Alkaline Complex, Eastern Sayan, Russia: Evidence for Late-magmatic Na-Ca-rich Carbonate Composition
Authors: Sharygin Victor V. , Doroshkevich Anna G. 
Published: November 2017

ABSTRACT
Secondary multiphase inclusions were studied in olivine from olivine-pyrochlore varieties of calcite carbonatites of the Belaya Zima alkaline complex, Eastern Sayan, Siberia, Russia. The inclusions form trails cross-cutting the host olivine. Their composition varies from carbonate to silicate-carbonate species. Multiphase silicate-carbonate inclusions contain Na-Ca-carbonates (shortite, nyerereite), Na-Mg-carbonates (northupite, eitelite, bradleyite), common carbonates (calcite, dolomite), Ba-Sr-rich carbonates (olekminskite, burbankite, strontianite), tetraferriphlogopite, magnetite, humite-clinohumite and other mineral phases. Na-Ca-carbonates, tetraferriphlogopite, humite-clinohumite and magnetite are omnipresent and dominant phases within the inclusions. The phase composition of secondary olivine-hosted inclusions seems to reflect evolutionary features for the Belaya Zima carbonatites at their late stages of formation. During crystallization calciocarbonatite melt gradually evolved toward enrichment in alkalis (mainly, in sodium) and volatile components (Cl, F and H2O).
The Relevance of Fluid Inclusions to Mineral Systems and Ore Deposit Exploration
Authors: Mernagh Terrence P. , Wygralak A. S. , Bastrakov E. N. 
Published: November 2017

ABSTRACT
Fluid inclusions provide the only direct samples of palaeofluids that may be related to mineralisation processes. In order to apply fluid inclusion data to study fluid flow on a larger scale, we have used a mineral systems approach, which regards a mineral deposit as part of a much larger system and considers all the processes that are involved in mobilising ore components from a source, transporting and accumulating them in a more concentrated form and then preserving them throughout the subsequent geological history. This not only enables a better understanding of fluid flow processes but also enables fluid inclusions to provide an exploration target that is much larger than the ore deposit itself.
As an example, a study of fluid inclusions associated with gold mineralisation in the Tanami Region of Northern Australia was used to determine the temperatures and compositions of the ore fluids. Once the parameters of the mineralising fluids were established, the study was then expanded to a region of central Australia covering almost 100,000 km2. It was concluded that a high temperature (320 – 360 °C), low salinity fluid containing CO2 and other gases was circulating in the northern part of this region at around 1720 Ma. This suggests the circulation of an orogenic gold style fluid and indicates that this region has potential for other orogenic gold deposits. In the southern part of this region, a lower temperature (120 to 190 °C), high salinity fluid with no detectable gases was present and appears to represent circulation of a basinal brine.
In the second example, fluid inclusion data from Cu-U-Au-Ag-REE prospects in the Olympic Copper-Gold Province in South Australia were used to constrain geochemical modelling of the mineralisation processes. By combining the inversion-generated, 3-D geophysical maps with geochemical and magnetic susceptibility values derived from the modelling, it has been possible to divide the range of observed magnetic susceptibilities into divisions that represent the various alteration assemblages within this region. This approach allows us to use geochemical modelling to relate alteration assemblages, and hence, the predicted sites of mineralisation, to the geophysical expressions of the mineral deposit.
An Analysis of the Database of Earth Science Projects Sponsored by the Department of Science and Technology, Government of India
Authors: Sinha-Roy S. , Mohanty M. 
Published: November 2017

ABSTRACT
Earth Science research in India evolved over the years in tune with the trends in the global scenario from studying the geologic attributes and assessing the natural resources to addressing issues related to fundamental processes involving, for example, crustal evolution, geodynamics and other aspects of contemporary Earth Science problems. Apart from various Earth Science institutions the Department of Science and Technology (DST), Govt. of India, through the SERC (now SERB) has been sponsoring Earth Science research projects in the country, and thus playing a catalytic role by providing extra-mural funding. Although the DST started funding Earth Science projects since 1985, the extent of such support increased in the 1990s and thereafter with sponsoring of a number of specialized thematic Earth Science programmes. As a result of these initiatives a prodigious amount of data has been generated that are contained in the Project Completion Reports (PCR). An analysis of the database prepared from 440 PCRs for the period 1993-2015 indicated that the projects dealing mainly with 17 themes increased almost steadily in number from 1993 to 2012 with a slight decreasing trend till 2015. A similar trend is exhibited by the yearly total project funding and the average cost per project. These aspects and the relation between the number of projects under different themes, papers published, PhDs produced and scientific and technical personnel trained are discussed here.
Pyroxene-sövite in Amba Dongar Carbonatite-alkalic Complex, Gujarat
Authors: Viladkar Shrinivas G. 
Published: November 2017

ABSTRACT
The present paper for the first times gives details of pyroxene-sövites of Amba Dongar and discusses significance of these pyroxenes in evolution of carbonatite magma in Amba Dongar. Calciocarbonatite (sövite) forms the major mass of carbonatite in Amba Dongar complex. It shows large variation in texture and mineral composition and has complex evolutionary history. Three types of compositional variations are observed in sövite samples, (1) monomineralic sövites are coarse grained with 99% calcite, (2) sövites with abundant apatite, barite, pyrochlore, magnetite and zirconolite and (3) silico-sövite with of clinopyroxene and phlogopite. In the crystallization history of various sövite types, silico-sövite seems to have crystallized as an earlier phase and was later caught up in major sövite mass. Both, phlogopite-sövite and pyroxene-sövite are coarse grained and exhibit hypidiomorphic texture. Phlogopite is strongly zoned with Mg-rich core to Fe-rich rims. Pyroxenes also exhibit zoning with decrease in Ca and Mg and increase in Fe and Na from core to rim. In general composition of clinopyroxene varies from diopsidic to aegirine-augite. Pyroxene-sövites show good concentration of Ba, Sr, Nb and LREE. Elevated concentrations of LREE are found in two aegirine-sövites.