bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the Gene Regulatory Landscape in 1,188 Human Tumors
Authors: Calabrese C , Lehmann K , Urban L , Liu F , Erkek S , Fonseca NA , Kahles A , Kilpinen H , Markowski J ,   PCAWG Group 3, Waszak SM , Korbel JO , Zhang Z , Brazma A , Rätsch G , Schwarz RF , Stegle O 
Published: November 2017

AbstractCancer is characterised by somatic genetic variation, but the effect of the majority of non-coding somatic variants and the interface with the germline genome are still unknown. We analysed the whole genome and RNA-Seq data from 1,188 human cancer patients as provided by the Pan-cancer Analysis of Whole Genomes (PCAWG) project to map cis expression quantitative trait loci of somatic and germline variation and to uncover the causes of allele-specific expression patterns in human cancers. The availability of the first large-scale dataset with both whole genome and gene expression data enabled us to uncover the effects of the non-coding variation on cancer. In addition to confirming known regulatory effects, we identified novel associations between somatic variation and expression dysregulation, in particular in distal regulatory elements. Finally, we uncovered links between somatic mutational signatures and gene expression changes, including TERT and LMO2, and we explained the inherited risk factors in APOBEC-related mutational processes. This work represents the first large-scale assessment of the effects of both germline and somatic genetic variation on gene expression in cancer and creates a valuable resource cataloguing these effects.
Collapse and rescue of cooperation in evolving dynamic networks
Authors: Akçay Erol 
Published: November 2017

AbstractThe evolutionary dynamics of social traits depend crucially on the social structure of a population, i.e., who interacts with whom. A large body of work studies the effect of social structure on behaviors such as cooperation, but relatively little is known about how social structure itself coevolves with social traits. Here, I use a simple yet realistic model of within-group social structure to study such coevolution. In this model, social connections are either inherited from a parent or made with random individuals. My model shows cooperation can evolve when individuals make few random connections, but the presence of cooperation selects for increased rates of random connections, which leads to the collapse of cooperation. Inherent costs of social connections can prevent this negative feedback, but the more beneficial cooperation is, the higher linking costs have to be maintain it, and linking costs can negate some or all of the aggregate benefits of cooperation. Exogenously maintained social inheritance can mitigate the latter problem and allow cooperation to persist and increase the average fitness of a population. These results illustrate how coevolutionary dynamics can constrain the long-term persistence of cooperation.
Foliar pathogens are unlikely to stabilize coexistence of competing species in a California grassland
Authors: Spear Erin R. , Mordecai Erin A. 
Published: November 2017

AbstractPathogen infection is common in wild plants and animals, and may regulate their populations. If pathogens have narrow host ranges and increase with the density of their favored hosts, they may promote host species diversity by suppressing common species to the benefit of rare species. Yet, because many pathogens infect multiple co-occurring hosts, they may not strongly respond to the relative abundance of a single host species. Are natural communities dominated by specialized pathogens that respond to the relative abundance of a specific host or by pathogens with broad host ranges and limited responses to the relative abundance of single host? The answer determines the potential for pathogens to promote host coexistence, as often hypothesized, or to have negligible or even negative effects on host coexistence. We lack a systematic understanding of the impacts, identities, and host ranges of pathogens in natural communities. Here we characterize a community of foliar fungal pathogens and evaluate their host specificity and fitness impacts in a California grassland community of native and exotic species. We found that most of the commonly isolated fungal pathogens were multi-host, with intermediate to low specialization. The amount of pathogen damage each host experienced was independent of host species local relative abundance. Despite pathogen sharing among the host species, fungal communities slightly differed in composition across host species. Plants with high pathogen damage tended to have lower seed production but the relationship was weak, suggesting limited fitness impacts. Moreover, seed production was not dependent on the local relative abundance of each plant species, suggesting that stabilizing coexistence mechanisms may operate at larger spatial scales in this community. Because foliar pathogens in this grassland community are multi-host and have small fitness impacts, they are unlikely to promote negative frequency-dependence or plant species coexistence in this system. Still, given that pathogen community composition differentiates across host species, some more subtle feedbacks between host relative abundance and pathogen community composition, damage, and fitness impacts are possible, which could in turn promote either coexistence or competitive exclusion.
Mean bond-length variations in crystals for ions bonded to oxygen
Authors: Gagné Olivier Charles , Hawthorne Frank Christopher 
Published: November 2017

Variations in mean bond length are examined in oxide and oxysalt crystals for 55 cation configurations bonded to O2−. Stepwise multiple regression analysis shows that mean bond length is correlated to bond-length distortion in 42 ion configurations at the 95% confidence level, with a mean coefficient of determination (〈R
2〉) of 0.35. Previously published correlations between mean bond length and mean coordination number of the bonded anions are found not to be of general applicability to inorganic oxide and oxysalt structures. For two of 11 ions tested for the 95% confidence level, mean bond lengths predicted using a fixed radius for O2− are significantly more accurate as those predicted using an O2− radius dependent on coordination number, and are statistically identical otherwise. As a result, the currently accepted ionic radii for O2− in different coordinations are not justified by experimental data. Previously reported correlation between mean bond length and the mean electronegativity of the cations bonded to the oxygen atoms of the coordination polyhedron is shown to be statistically insignificant; similar results are obtained with regard to ionization energy. It is shown that a priori bond lengths calculated for many ion configurations in a single structure-type leads to a high correlation between a priori and observed mean bond lengths, but a priori bond lengths calculated for a single ion configuration in many different structure-types leads to negligible correlation between a priori and observed mean bond lengths. This indicates that structure type has a major effect on mean bond length, the magnitude of which goes beyond that of the other variables analyzed here.
Lean leadership attributes: a systematic review of the literature
Authors: Aij Kjeld Harald , Teunissen Maurits 
Published: November 2017

Purpose
Emphasis on quality and reducing costs has led many health-care organizations to reconfigure their management, process, and quality control infrastructures. Many are lean, a management philosophy with roots in manufacturing industries that emphasizes elimination of waste. Successful lean implementation requires systemic change and strong leadership. Despite the importance of leadership to successful lean implementation, few researchers have probed the question of ideal leadership attributes to achieve lean thinking in health care. The purpose of this paper is to provide insight into applicable attributes for lean leaders in health care.

Design/methodology/approach
The authors systematically reviewed the literature on principles of leadership and, using Dombrowski and Mielke’s (2013) conceptual model of lean leadership, developed a parallel theoretical model for lean leadership in health care.

Findings
This work contributes to the development of a new framework for describing leadership attributes within lean management of health care.

Originality/value
The summary of attributes can provide a model for health-care leaders to apply lean in their organizations.
Blockchain systems for trade clearing
Authors: Tsai Wei-Tek , Luo Yong , Deng Enyan , Zhao Jing , Ding Xiaoqiang , Li Jie , Yuan Bo 
Published: November 2017

PurposeThis paper aims to apply blockchains (BCs) for trade clearing and settlement in a realistic clearinghouse. The purpose is to demonstrate the feasibility and scalability of this approach.Design/methodology/approachThe study uses account BCs and trading BCs as building blocks for trade clearing and settlement. Careful design is made to ensure that this approach is feasible and scalable.FindingsA design has been proposed that can process hundreds of thousands of trades for a clearinghouse and it addresses performance, privacy and scalability of realistic trade clearing and settlement. The design has been implemented and experimented in a clearinghouse for over two months and processes over 3B real transactions from an exchange. The first month was to experiment with the system with historical data, the second month was to experiment with real-time data during market trading hours. The system performed as designed and intended.Research limitations/implicationsThis is the first large research paper that applied BCs for clearing in the world. The authors applied the system to a clearinghouse and processed over 3 billion transactions, equivalent to 13 years of London Stock Exchange transaction volume, demonstrating that BCs can handle a large number of transactions.Practical implicationsThe design can be duplicated to many clearinghouses in the world, and this also paves the way BCs can be used in large financial institutions.Social implicationsAn implication is that other trading firms, clearinghouses and banks can apply the same technology for trade clearing, ushering the way BCs can be used in institutions. As clearing is a core function in business transactions, this has significant implications. The design can be discussed and improved in various communities.Originality/valueAs this is the first application of BCs to large clearinghouses that uses unique BC designs. This has significant value. Many studies have been performed but few have been reported in the scientific community. The system has been implemented, experimented and demonstrated in public for months.
Laser direct metal deposition process of thin-walled parts using variable spot by inside-beam powder feeding
Authors: Wang Lifang , Zhu Gangxian , Shi Tuo , Wu Jizhuo , Lu Bin , Fu Geyan , Ye Yunxia 
Published: November 2017

Purpose
The purpose of this paper is to improve the forming efficiency and quality of unequal-width parts fabricated by laser direct metal deposition technology, some experiments were designed.

Design/methodology/approach
A new method by varying laser spot was adopted to fabricate unequal-width single track using one scanning rather than multi-track overlapping in the way of the inside-beam powder feeding, and the thin-walled parts were fabricated layer by layer. The theoretical model among layer thickness of z-axis, height of single track and the section curve order of single track was established.

Findings
The top surface unevenness of the thin-walled parts could be compensated automatically within the laser defocusing ranges from −2.5 to −5 mm and from 0.5 to 2.5 mm. The growth rate with the large width/height ratio was more than the small ratio, while the set height of the single track was uniform. The problem of non-uniform growth rate could be solved based on a stepped single-track method. The thin-walled parts with the smooth top surface was fabricated layer by layer which had a continuously variable width from 1 to 3 mm by splicing the laser defocusing range.

Practical implications
The shapes of the to-be-fabricated parts affect variable laser spot process in practical applications. For example, it will be difficult to apply variable laser spot process on the parts with the hole features.

Originality/value
This paper provided a guidance for forming unequal-width parts by laser direct metal deposition based on the inside-beam powder feeding.
Adhesion of 3D printed material on textile substrates
Authors: Grimmelsmann Nils , Kreuziger Mirja , Korger Michael , Meissner Hubert , Ehrmann Andrea 
Published: November 2017

Purpose
Composites combining two or more different materials with different physical and chemical properties allow for tailoring mechanical and other characteristics of the resulting multi-material system. In relation to fiber-reinforced plastic composites, combinations of textile materials with 3D printed polymers result in different mechanical properties. While the tensile strength of the multi-material system is increased compared to the pure 3D printed material, the elasticity of the polymer layer can be retained to a certain degree, as the textile material is not completely immersed in the polymer. Instead, an interface layer is built in which both materials interpenetrate to a certain degree. The purpose of this study is to investigate the adhesion between both materials at this interface.

Design/methodology/approach
This paper gives an overview of the parameters affecting the interface layer. It shows that both the printing material and the textile substrate influence the adhesion between both materials due to viscosity during printing, thickness and pore sizes, respectively. While some material combinations build strong form-locking connections, others can easily be delaminated.

Findings
Depending on both materials, significantly different adhesion values can be found in such 3D printed composites.

Practical implications
This makes some combinations very well suitable for building composites with novel mechanical properties, while other suffer of insufficient connections.

Originality/value
For the first time, the dependence of the polymer-textile adhesion force was evaluated according to the distance between both compound partners. It was shown that this value is of crucial interest and must thus be taken into account when producing printed polymer-textile composites.
Rapid prototyping eddy current sensors using 3D printing
Authors: Li Bo , Meng Lifan , Wang Hongyu , Li Jing , Liu Chunmei 
Published: November 2017

Purpose
The purpose of this paper is to investigate the process of rapid prototyping eddy current sensors using 3D printing technology. Making full use of the advantages of 3D printing, the authors study on a new method for fabrication of an eddy current sensor.

Design/methodology/approach
In this paper, the authors establish a 3D model using SolidWorks. And the eddy current sensor is printed by the fused deposition modeling method.

Findings
Measurement results show that the 3D printing eddy current sensor has a wider linear measurement range and better linearity than the traditional manufacturing sensor. Compared to traditional eddy current sensor fabrication method, this 3D printed sensor can be fabricated at a lower cost, and the fabrication process is more convenient and faster.

Practical implications
This demonstrated 3D printing process can be applied to the 3D printing of sensors of more sophisticated structures that are difficult to fabricate using conventional techniques.

Originality/value
In this work, the process of rapid prototyping eddy current sensors using 3D printing is presented. Sensors fabricated with the 3D printing possess lots of merits than traditional manufactures. 3D printed sensors can be customized according to the configuration of the overall system, thus reducing the demand of sensor's rigid mounting interfaces. The 3D printing also reduce design costs as well as shortens the development cycle. This allows for quick translation of a design from concept to a useful device.
A distinct mechanism of senescence activation in amnion epithelial cells by infection, inflammation, and oxidative stress
Authors: Dixon Christopher Luke , Richardson Lauren , Sheller‐Miller Samantha , Saade George , Menon Ramkumar 
Published: November 2017

ProblemWe investigated p38MAPK activation‐induced fetal membrane cell senescence in response to inflammation (tumour necrosis factor‐alpha [TNF‐α]) and infection (lipopolysaccharide [LPS]), factors associated with spontaneous preterm birth.Method of studyPrimary amnion epithelial cells (AECs) were exposed to TNF‐α, 50 ng/mL and LPS, 100 ng/mL. Cigarette smoke extract (CSE), a known OS inducer, was used as positive control. AECs were cotreated with the antioxidant N‐acetyl cysteine (NAC) and p38MAPK inhibitor SB203580 to determine the effect of OS and p38MAPK. Western blot analysis was performed for active (Phospho‐p38MAPK) and total p38MAPK. Senescence was determined by flow cytometry, and culture supernatants were tested for IL‐6 using ELISA.ResultsTNF‐α, but not LPS, increased p38MAPK activation compared to untreated cells (P = .01). The number of senescent cells and senescence‐associated IL‐6 was higher in both TNF‐α and LPS‐treated cells compared to control (P = .001, P = .01, respectively). Antioxidant NAC inhibited p38MAPK activation by TNF‐α. p38MAPK inhibitor SB203580 reduced the development of senescence and IL‐6 by TNF‐α and LPS. CSE treatment validated our current data.ConclusionTNF‐α caused OS‐mediated p38MAPK induction, senescence, and IL‐6 increase from AECs. LPS also induced senescence and IL‐6 increase. Inflammatory and infectious factors may cause premature fetal cell senescence contributing to preterm birth pathophysiology.
Effectiveness and tolerability of therapy with exenatide once weekly vs basal insulin among injectable‐drug‐naïve elderly or renal impaired patients with type 2 diabetes in the United States
Authors: Loughlin Anita M. , Qiao Qing , Nunes Anthony P. , Öhman Peter , Ezzy Stephen , Yochum Laura , Clifford C. Robin , Gately Robert , Dore David D. , Seeger John D. 
Published: November 2017

AimTo evaluate the effectiveness and tolerability of exenatide once weekly (EQW) compared with basal insulin (BI) among injectable‐drug‐naïve patients with type 2 diabetes mellitus (T2DM) who are elderly or have renal impairment (RI).Materials and methodsInitiators of EQW and BI with T2DM were identified for the period 2012 to 2015 within a US electronic health record database and matched by propensity score. Matched EQW and BI initiators aged ≥65 years or who had RI were compared. Data on weight, glycated haemoglobin (HbA1c), estimated glomerular filtration rate (eGFR), blood pressure and lipids were obtained at baseline and quarterly (Q1–Q4) or semi‐annually for 1 year after drug initiation. Hypoglycaemia and gastrointestinal symptoms were identified using diagnosis codes and data abstracted from clinical notes.ResultsAmong patients aged ≥65 years, HbA1c changed by −0.50 and −0.31 percentage points from baseline to Q4 for EQW and BI initiators, respectively. Weight changed by −1.6 kg among EQW initiators compared with 0.2 kg among BI initiators. Compared with BI initiators, EQW initiators had a 1.45‐fold increased risk of nausea and vomiting. Among patients with RI, HbA1c changed by −0.58 and −0.33 percentage points from baseline to Q4 for EQW and BI initiators, respectively. Weight changed by −1.9 kg for EQW initiators while BI initiators had no change in weight. EQW initiators had a 1.28‐fold increased risk of constipation and diarrhoea compared with BI initiators.ConclusionRegardless of age or renal function, the benefits of EQW relative to BI treatment are improved glycaemic control and increased weight loss, which should be weighed against the increased risk of gastrointestinal symptoms.
Management effectiveness of large pelagic fisheries in the high seas
Authors: Pons Maite , Melnychuk Michael C , Hilborn Ray 
Published: November 2017

AbstractLarge pelagic fishes are assessed and managed by tuna Regional Fisheries Management Organizations (tRFMOs). These organizations have been criticized for not meeting conservation objectives, which may relate to aspects of governance and management. No previous studies have systematically evaluated why management performance differs among tRFMOs and among stocks within each tRFMO. In this study, we collected data on the nature of research, management, enforcement and socioeconomics of management systems in the five principal tRFMOs of the world's oceans. We quantified influences of economic and fishery‐related factors on these management characteristics and examined how these factors vary among tRFMOs. We found that tRFMOs with a greater number of member countries, a greater economic dependency on tuna resources, a lower mean per capita gross domestic product, a greater number of fishing vessels and smaller vessels were associated with less intensive research, management and enforcement in these tuna fisheries. We also quantified the influence of specific management attributes and of biological, economic and fishery‐related factors on the trends and current status of large pelagic fish stocks in these regions. The most important factors correlated with trends and current stock status were external to the management systems, and included stock size, age at maturity, ex‐vessel price and economic dependency of countries on tuna fisheries. To improve the overall status of large pelagic fish stocks in the global high seas, more intensive data collection, research and management are needed in certain areas, especially in the Indian Ocean, and for certain stocks, especially non‐target species.
Fabrication and morphological characterization of glass‐ceramic orbital implants
Authors: Baino Francesco , di Confiengo Giovanna Gautier , Faga Maria Giulia 
Published: November 2017

AbstractPorous glass‐ceramics were produced by sponge replication for possible use as orbital implant materials, characterized from a morphological viewpoint, and compared to commonly used devices. Favorable characteristics of these new materials for ocular applications include total porosity above 50 vol.%, presence of open and large macropores (>200 μm) that could potentially allow fibrovascular tissue ingrowth, and submicronic surface roughness which is significantly lower than that of commercial “gold standard” alumina implants. The last feature is key to limit the risk of postoperative conjunctival abrasion and to achieve clinical success. Therefore, these glass‐ceramic porous materials are highly promising alternatives to existing ceramic orbital implants.