bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic Significance of CHEK2 Mutation in Progression of Breast Cancer
Authors: Ansari Narges , Shahrabi Saeid , Khosravi Abbas , Shirzad Reza , Rezaeean Hadi 
Published: February 2019

Abstract
Breast cancer (BC) is one of the most common cancers among women; genetic mutations reflect the development of this disease. Mutations in cell signaling factors can be the main cause of BC development. In this study, we focused on mutations in checkpoint kinase 2 (CHEK2) and their impact as a prognostic factor in the pathogenesis of BC.
CHEK2 is controlled in cell signaling pathways through the influence of upstream genes. Also, several downstream genes are regulated by CHEK2. In addition, mutations in CHEK2 lead to resistance of BC cells to chemotherapy and metastasis of cancer cells to other parts of the body.
Finally, detection of mutations in CHEK2 can be used as a prognostic factor for patient response to treatment and for targeting downstream molecules of CHEK2 that are involved in the proliferation of breast tumor cells. Mutations such as c.1100delC and I157T can distinguish which patients are susceptible to metastasis.
MTL-algebras as rotations of basic hoops
Authors: Aglianò Paolo , Ugolini Sara 
Published: February 2019

Abstract
In this paper, we use the generalize d rotation construction to lift results from the lattice of subvarieties of basic hoops to some parts of the lattice of subvarieties of monoidal t-norm based logic-algebras. In particular, we study splitting algebras for (the lattice of subvarieties of) varieties generated by generalized rotations of basic hoops and relevant subvarieties such as Wajsberg hoops, cancellative hoops and Gödel hoops. Finally, we show that the generalized rotation construction preserves the amalgamation property.
Decentralization and Policy Experimentation in Education: the Consequences of Enhancing Local Autonomy in California
Authors: Adams Brian E 
Published: February 2019

Abstract
A hypothesized benefit of decentralization is that it will promote policy experimentation, yet there have been few studies examining this link. In this article, I identify three pathways through which decentralization could plausibly lead to greater experimentation and empirically assess their presence through an analysis of California’s Local Control Funding Formula (LCFF), a policy that enhanced the fiscal autonomy of local school districts. I find mixed results; even though there was some evidence to suggest greater policy activity, most new actions taken by school districts were incremental changes. Further, there was little ideological differentiation in adopted policies despite variation in districts’ partisan composition. Small districts were slightly more likely to experiment than larger ones, supporting the hypothesis that smaller jurisdictions are more nimble and flexible and thus more likely to enact policy change. I conclude by exploring how the incentives and preferences of local officials mediate the causal connection between decentralization and policy experimentation.
Association of socioeconomic and lifestyle factors with chronic non-communicable diseases and multimorbidity among the elderly in rural southwest China
Authors: Li Xiao , Cai Le , Cui Wen-long , Wang Xu-ming , Li Hui-fang , He Jian-hui , Golden Allison Rabkin 
Published: February 2019

Abstract

Background
This study estimates the prevalence of five chronic non-communicable disease (NCDs) (hypertension, diabetes, CHD, COPD and stroke) and its multimorbidity, and examines the relationship between SES and lifestyle factors and multimorbidity among older adults in rural southwest China.

Methods
A cross-sectional survey of 4833 consenting adults aged ≥60 years was conducted in 2017. Data on the demographics, smoking, drinking, height, weight, blood pressure and fasting blood glucose were collected.

Results
Among the participants, the overall prevalence of hypertension, diabetes, stroke, COPD and CHD was 50.6, 10.2, 6.4, 5.4 and 5.5%, respectively, and of multimorbidity was 16.1%. Females had a higher prevalence of hypertension, diabetes and multimorbidity of chronic NCDs, but a lower prevalence of COPD than males (P &lt; 0.05). Older adults with good household assets and access to medical services were less likely to experience multimorbidity, whereas obese and centrally obese participants, current smokers, current drinkers and those with a family history of chronic NCDs had a greater probability of multimorbidity.

Conclusions
The findings suggest that effective strategies for prevention and control of chronic NCDs and its multimorbidity are urgently needed, especially for low-income, elderly, ethnic minority adults with poor access to medical services.
Man shall not live by bread alone: the role of perceived emotional support in low-income adults’ health outcomes
Authors: Namkoong Kang , Stanley Samantha J , Kim Jiyoun 
Published: February 2019

Abstract

Background
Adults with low income have limited access to valuable health resources thus presenting a major obstacle to improving their health. Although there are diverse health enhancement programs for low-income populations, relatively few focus on emotional support despite the positive impact of perceived emotional support on health. This study examines the interaction of perceived emotional support and income on the overall health status and psychological well-being of adults with low income.

Methods
Secondary data were collected from the Health Information National Trends Survey (Cycle 4). A total of 3677 respondents completed the survey, including 889 adults with low income, as determined by their eligibility for the Supplemental Nutrition Assistance Program (SNAP). Ordinary-least square hierarchical regression analysis was conducted to test main and interaction effects.

Results
Perceived emotional support moderated the relationship between SNAP eligibility and health outcomes. Lacking an emotional support network has greater detrimental effects on the overall health and psychological well-being of people with low income compared to similar persons with higher income.

Conclusion
These findings suggest the need for health programs that enhance access to emotional support for adults with low income.
Racial Differences in Anticipated Satisfaction With Life during Retirement
Authors: Tsotsoros Cindy E , Hershey Douglas A , Kiso Helen , Koposko Janet L 
Published: February 2019

Abstract
The ability of individuals to think about their goals and imagine themselves in the future is one of the keys to developing a strategic life plan (Beach, 1998). This is a particularly important task in the context of developing a satisfying plan for retirement. In this investigation, image theory (Beach & Mitchell, 1987) was used as a foundation for exploring racial differences in individuals’ perceptions of the post-employment period. Specifically, Blacks, Whites, and Asians (n = 301, 300, 269, respectively) were asked to report perceptions of their future life satisfaction during retirement using a scale developed by Gutierrez and Hershey (2014). Mean score comparisons revealed that Blacks and Asians had significantly larger mean perceived future satisfaction levels than Whites. To explore the psychological mechanisms that underlie respondents’ perceptions, 3 separate race-based path analysis models were calculated using anticipated satisfaction scores as the criterion. Predictors in the models included: engagement in financial planning activities, retirement-related financial knowledge, retirement goal clarity, future time perspective, and a set of sociodemographic indicators. Substantial differences were observed in the amount of variance captured in the criterion, with the most variability accounted for among Asians, and the least variability accounted for among Whites. From a theoretical perspective, the findings contribute to the growing literature on race and retirement processes, and from an applied perspective, the results have implications for practitioners who seek to take race into account when developing psychologically based intervention programs.
Description and phylogenetic placement of a new marine species of phytosaur (Archosauriformes: Phytosauria) from the Late Triassic of Austria
Authors: Butler Richard J , Jones Andrew S , Buffetaut Eric , Mandl Gerhard W , Scheyer Torsten M , Schultz Ortwin 
Published: February 2019

AbstractPhytosaurs are a group of carnivorous, semi-aquatic archosaurian reptiles that attained an almost global distribution during the Late Triassic. We here describe a new species of the phytosaur genus Mystriosuchus from the Norian Dachstein Limestone of Austria, from a marine lagoonal depositional environment. The new Austrian material comprises remains of at least four individuals of similar size (c. 4 m in total length) found in association but disarticulated, and includes one complete and two partial skulls and postcrania. All of these specimens apparently represent a single taxon, which is distinguished by numerous anatomical features from the two previously named Mystriosuchus species. Maximum parsimony analysis of a comprehensive morphological dataset provides strong statistical support for the phylogenetic position of the new Austrian taxon in Mystriosuchus, as the sister taxon to a clade comprising M. planirostris and M. westphali. Histological analysis suggests that the Austrian phytosaur specimens represent individuals that were at least eight years old at time of death, but which had not yet reached skeletal maturity. Taphonomic and palaeoenvironmental data suggest that these phytosaurs were living in the marine lagoon in which they were preserved, providing the strongest evidence to date of marine adaptations in phytosaurs.
Exploring the effects of character construction and choice, outgroups and analytical method on phylogenetic inference from discrete characters in extant crocodilians
Authors: Sookias Roland B 
Published: February 2019

Abstract
Phylogenies for fossil taxa must be inferred from morphology, but accuracy of inference is questionable. Here, morphological characters for extant crocodilians are investigated to assess how to improve inference accuracy. The homoplasy of characters is assessed against a DNA-based phylogenetic tree. Cranial characters are significantly less homoplastic, but this result is perhaps confounded by research effort. Meristic characters are significantly more homoplastic and should be used with caution. Characters were reassessed first hand and documented. Those characters passing tests of robust construction are significantly less homoplastic. Suggestions are made for means to improve coding of discrete characters. Phylogenies inferred using only robust characters and a reassessed matrix, including corrected scorings, were not overall closer to the DNA tree, but did often place the gharial (Gavialis) in a position agreeing with or closer to it. The effects of the choice of analytical method were modest, but Bayesian analysis of the reassessed matrix placed Gavialis and Mecistops (slender-snouted crocodile) in DNA-concordant positions. Use of extant rather than extinct outgroups, even with the original matrix, placed Gavialis in a more DNA-concordant position, as did factoring out 3D skull shape. The morphological case for placement of Gavialis outside other extant crocodilians is arguably overstated, with many characters linked to skull shape.
Mastering the scales: a survey on the benefits of multiscale computing software
Authors: Groen Derek , Knap Jaroslaw , Neumann Philipp , Suleimenova Diana , Veen Lourens , Leiter Kenneth 
Published: February 2019

In the last few decades, multiscale modelling has emerged as one of the dominant modelling paradigms in many areas of science and engineering. Its rise to dominance is primarily driven by advancements in computing power and the need to model systems of increasing complexity. The multiscale modelling paradigm is now accompanied by a vibrant ecosystem of multiscale computing software (MCS) which promises to address many challenges in the development of multiscale applications. In this paper, we define the common steps in the multiscale application development process and investigate to what degree a set of 21 representative MCS tools enhance each development step. We observe several gaps in the features provided by MCS tools, especially for application deployment and the preparation and management of production runs. In addition, we find that many MCS tools are tailored to a particular multiscale computing pattern, even though they are otherwise application agnostic. We conclude that the gaps we identify are characteristic of a field that is still maturing and features that enhance the deployment and production steps of multiscale application development are desirable for the long-term success of MCS in its application fields.This article is part of the theme issue ‘Multiscale modelling, simulation and computing: from the desktop to the exascale’.
Assessing the scales in numerical weather and climate predictions: will exascale be the rescue?
Authors: Neumann Philipp , Düben Peter , Adamidis Panagiotis , Bauer Peter , Brück Matthias , Kornblueh Luis , Klocke Daniel , Stevens Bjorn , Wedi Nils , Biercamp Joachim 
Published: February 2019

We discuss scientific features and computational performance of kilometre-scale global weather and climate simulations, considering the Icosahedral Non-hydrostatic (ICON) model and the Integrated Forecast System (IFS). Scalability measurements and a performance modelling approach are used to derive performance estimates for these models on upcoming exascale supercomputers. This is complemented by preliminary analyses of the model data that illustrate the importance of high-resolution models to gain improvements in the accuracy of convective processes, a better understanding of physics dynamics interactions and poorly resolved or parametrized processes, such as gravity waves, convection and boundary layer.
This article is part of the theme issue ‘Multiscale modelling, simulation and computing: from the desktop to the exascale’.
Application of the extreme scaling computing pattern on multiscale fusion plasma modelling
Authors: Luk O. O. , Hoenen O. , Perks O. , Brabazon K. , Piontek T. , Kopta P. , Bosak B. , Bottino A. , Scott B. D. , Coster D. P. 
Published: February 2019

The extreme scaling pattern of the ComPat project is applied to a multi-scale workflow relevant to the magnetically confined fusion problem. This workflow combines transport, turbulence and equilibrium codes (together with additional auxiliaries such as initial conditions and numerical module), which aims at calculating the behaviour of a fusion plasma on long (transport) time scales based on information from much faster (turbulence) time scales. Initial findings of profile measurements are reported in this paper and indicate that, depending on the chosen performance metric for defining ‘cost’, such as time to completion, efficiency and total energy consumption of the mutliscale workflow, different choices on the number of cores would be made when determining the optimal execution configuration. A variant of the workflow which increases the inherent parallelism is presented, and shown to produce equivalent results at (typically) lower cost compared with the original workflow.
This article is part of the theme issue ‘Multiscale modelling, simulation and computing: from the desktop to the exascale’.
Semi-intrusive multiscale metamodelling uncertainty quantification with application to a model of in-stent restenosis
Authors: Nikishova A. , Veen L. , Zun P. , Hoekstra A. G. 
Published: February 2019

We explore the efficiency of a semi-intrusive uncertainty quantification (UQ) method for multiscale models as proposed by us in an earlier publication. We applied the multiscale metamodelling UQ method to a two-dimensional multiscale model for the wound healing response in a coronary artery after stenting (in-stent restenosis). The results obtained by the semi-intrusive method show a good match to those obtained by a black-box quasi-Monte Carlo method. Moreover, we significantly reduce the computational cost of the UQ. We conclude that the semi-intrusive metamodelling method is reliable and efficient, and can be applied to such complex models as the in-stent restenosis ISR2D model.This article is part of the theme issue ‘Multiscale modelling, simulation and computing: from the desktop to the exascale’.
Bolt: A new age peptide search engine for comprehensive MS/MS sequencing through vast protein databases in minutes
Authors: Prakash Amol , Ahmad Shadab , Majumder Swetaketu , Jenkins Conor , Orsburn Ben 
Published: February 2019

AbstractThe standard platform for proteomics experiments today is mass spectrometry, particularly for samples derived from complex matrices. Recent increases in mass spectrometry sequencing speed, sensitivity and resolution now permit comprehensive coverage of even the most precious and limited samples, particularly when coupled with improvements in protein extraction techniques and chromatographic separation.However, the results obtained from laborious sample extraction and expensive instrumentation are often hindered by a sub optimal data processing pipelines. One critical data processing piece is peptide sequencing which is most commonly done through database search engines. In almost all MS/MS search engines users must limit their search space due to time constraints and q-value considerations. In nearly all experiments, the search is limited to a canonical database that typically does not reflect the individual genetic variations of the organism being studied. Searching for posttranslational modifications can exponentially increase the search space thus careful consideration must be used during the selection process. In addition, engines will nearly always assume the presence of only fully tryptic peptides. Despite these stringent parameters, proteomic data searches may take hours or even days to complete and opening even one of these criteria to more realistic biological settings will lead to detrimental increases in search time on expensive and custom data processing towers. Even on high performance servers, these search engines are computationally expensive, and most users decide to dial back their search parameters. We present Bolt, a new search engine that can search more than nine hundred thousand protein sequences (canonical, isoform, mutations, and contaminants) with 31 post translation modifications and N-terminal and C-terminal partial tryptic search in a matter of minutes on a standard configuration laptop. Along with increases in speed, Bolt provides an additional benefit of improvement in high confidence identifications, as demonstrated by manual validation of unique peptides identified by Bolt that were missed with parallel searching using standard engines. When in disagreement, 67% of peptides identified by Bolt may be manually validated by strong fragmentation patterns, compared to 14% of peptides uniquely identified by SEQUEST. Bolt represents, to the best of our knowledge, the first fully scalable, cloud based quantitative proteomic solution that can be operated within a user-friendly GUI interface. Data are available via ProteomeXchange with identifier PXD012700.Abstract Graphic
Experimental evidence that belowground competition can influence the evolution of root traits in two closely related morning glory species
Authors: Colom Sara M. , Baucom Regina S. 
Published: February 2019

AbstractAlthough root traits play a critical role in mediating plant-plant interactions and resource acquisition from the soil environment, research examining if and how belowground competition can influence the evolution of root traits remains largely unexplored. Here we examine the potential that root traits may evolve as a target of selection from interspecific competition using Ipomoea purpurea and I. hederacea, two closely related morning glory species that commonly co-occur in the United States. We show that belowground competitive interactions between the two species can alter the pattern of selection on root traits in each species. Specifically, competition with I. purpurea changes the pattern of selection on root angle in I. hederacea, and competitive interactions with I. hederacea changes the pattern of selection on root size in I. purpurea. However, we did not uncover evidence that intraspecific competition altered the pattern of selection on any root traits within I. hederacea. Overall, our results suggest that belowground competition between closely related species can influence the phenotypic evolution of root traits in natural populations. Our findings provide a microevolutionary perspective of how competitive belowground interactions may impact plant fitness, potentially leading to patterns of plant community structure.
RecV recombinase system for spatiotemporally controlled light-inducible genomic modifications
Authors: Cetin Ali , Yao Shenqin , Ouellette Ben , Balaram Pooja , Zhou Thomas , Mortrud Marty , Chatterjee Soumya , Wang Yun , Daigle Tanya L. , Tasic Bosiljka , Kuang Xiuli , Gong Hui , Luo Qingming , Zeng Shaoqun , Kahan Anat , Gradinaru Viviana , Zeng Hongkui 
Published: February 2019

AbstractBrain circuits are composed of vast numbers of intricately interconnected neurons with diverse molecular, anatomical and physiological properties. To allow highly specific targeting of individual neurons for structural and functional studies, we modified three site-specific DNA recombinases, Cre, Dre and Flp, by combining them with a fungal light-inducible protein, Vivid, so that their recombinase activities can be driven by blue light. We generated viral vectors to express these light-inducible recombinases and demonstrated that they can induce genomic modifications in dense or sparse populations of neurons in live mouse brains controlled by one-photon or two-photon light induction. As an important application, we showed that light-inducible recombinases can produce highly targeted, sparse and strong labeling of individual neurons thereby enabling whole-brain morphological reconstruction to identify their axonal projection specificity. In addition to targeting cortical brain areas, we applied the method in deep targets, with a demonstration of functional calcium imaging. These molecular tools enable spatiotemporally-precise, targeted genomic modifications that will greatly facilitate detailed analysis of neural circuits and linking genetic identity, morphology, connectivity and function.
A paper-filter system to investigate the real micro-environment circuiting plant roots
Authors: Huang Chao 
Published: February 2019

AbstractThe micro-environment circling the plant root is an interesting topic for many researchers. Until now there is not an approach to investigate the exact density of chemicals surrounding the plant roots. here we use a simple paper filter system and gas chromatography to quantify the exact density of chemicals surrounding the plant roots. this can help solve a long-existing doubt about the ‘real micro-environment’ surrounding the plant roots.