nils-herrmann/clean_scirepeval huggingface dataset:
Prognostic and predictive value of Ki 67 in triple negative breast cancer
Venue: Oncotarget

This study was to investigate the prognostic role of Ki 67 in further classification of triple negative breast cancer (TNBC) and to test whether high expression level of Ki67 can predict benefit from carboplatin. From January 2004 to December 2012, 363 patients operated for TNBC were identified through the institutional clinical database. After a median follow up time of 34 months (5.2 120.0 months) 62 patients (17.1% had relapses and 33 patients (9.1% died of breast cancer. In univariate analysis, high Ki 67 index as well as larger tumor size and lymph node involvement was associated with shorter disease free survival (DFS) and overall survival (OS) In multivariate analysis, high Ki 67 is an independent risk factor for DFS (Risk Ratio, RR: 2.835, 95% confidence interval, 95% CI: 1.586 5.068, P 0.001) and OS (RR: 3.180, 95% CI: 1.488 6.793, P 0.003) When analyzing the 3 year DFS by Ki 67 distribution, Subpopulation Treatment Effect Pattern Plot analysis showed a beneficial effect of carboplatin in patients with high Ki 67 index. In conclusion, TNBC is probably a heterogeneous disease with different characteristics and prognosis, and may be further subdivided according to the Ki 67 expression levels. Patients in the high Ki 67 group seem to benefit more from treatment with carboplatin, but this needs to be further verified.
Ringed Substructure and a Gap at 1 AU in the Nearest Protoplanetary Disk

We present long baseline Atacama Large Millimeter/submillimeter Array (ALMA) observations of the 870 micron continuum emission from the nearest gas rich protoplanetary disk, around TW Hya, that trace millimeter sized particles down to spatial scales as small as 1 AU (20 mas) These data reveal a series of concentric ring shaped substructures in the form of bright zones and narrow dark annuli (1 6 AU) with modest contrasts (5 30% We associate these features with concentrations of solids that have had their inward radial drift slowed or stopped, presumably at local gas pressure maxima. No significant non axisymmetric structures are detected. Some of the observed features occur near temperatures that may be associated with the condensation fronts of major volatile species, but the relatively small brightness contrasts may also be a consequence of magnetized disk evolution (the so called zonal flows) Other features, particularly a narrow dark annulus located only 1 AU from the star, could indicate interactions between the disk and young planets. These data signal that ordered substructures on ~AU scales can be common, fundamental factors in disk evolution, and that high resolution microwave imaging can help characterize them during the epoch of planet formation.
Raising Questions About Capitalist Globalization and Universalizing Views on Women: A Transnational Feminist Critique of the World Development Report: Gender Equality and Development
Venue: ANS. Advances in nursing science

Nursing in the United States has embraced global health primarily from a clinical perspective, with emphasis on care delivery to populations in underserved, resource poor settings. Less attention has been devoted to developing expertise about social, economic, and political contexts that produce ill health around the world. The purpose of this article is to offer a transnational feminist critique of the World Development Report: Gender Equality and Development and to illuminate implications such reports may have in the lives of the world's most marginalized women and girls. We examine the political economy idealized in the report, raising questions about the capitalist framework underpinning its agenda. Second, we examine the assumptive language used in the report, suggesting that it discursively constructs a problematic representation of women in low income countries. We contend that the report perpetuates a hegemonic discourse of patriarchy and inequality for women in the Global South through the use of an uncontested economic framework and universalist reasoning. We conclude the article with discussion about a transformative policy making that could be more inclusive of the wisdoms, values, and everyday experiences of women living in the Global South and about the vital role nurses can play in advancing gender equity through their active collaboration in policy critique and policy formulation.
The Transnational Capitalist Class, Social Movements, and Alternatives to Capitalist Globalization

This paper attempts to rethink and globalize the concept of the capitalist class, to suggest ways in which this class uses social movements, and to explore what might come after capitalist globalization and the hegemony of the transnational capitalist class (TCC) The first section of the paper provides evidence that there is now a flourishing community of scholars largely but not exclusively connected with the Network for Critical Studies of Global Capitalism (NCSGC) who are building a substantial foundation for research on the transnational capitalist class all over the world. The next section poses questions around the hegemony of the TCC and highlights the importance of what is conceptualized as social movements for global capitalism. Relatively little attention is paid to this compared to the vast literature on social movements against global capitalism. The paper concludes with the question: Is there a non capitalist alternative to globalization dominated by the TCC? The answer begins with the aphorism: "It is easier to imagine the end of the world, than to imagine the end of capitalism." My view is that this expresses a profound truth, forcing us to begin again to think through what we once conceptualized as democratic socialism.
Upper airway dimensions in patients undergoing orthognathic surgery: a systematic review and meta analysis.
Venue: International journal of oral and maxillofacial surgery

The objective of this systematic review was to evaluate the effect of different types of orthognathic surgery on the dimensions of the upper airways assessed using three dimensional images. An electronic search was performed in Cochrane Library, Medline, Scopus, VHL, Web of Science, and the System for Information on Grey Literature in Europe, ending January 2015. Inclusion criteria encompassed clinical studies in humans, patient age >15 years, patients submitted to maxillary or mandibular advancement or setback surgery, isolated or in combination, and presentation of airway measures, specifically volume and/or minimum cross sectional area (CSA) obtained from computed tomography or magnetic resonance imaging. Additional searches were conducted on the references of included articles and in the NLM catalogue. An assessment of the risk of bias was performed. A total of 1180 studies were retrieved, of which 28 met the eligibility criteria; one was later excluded as it presented a high risk of bias. A meta analysis was performed. There is moderate evidence to conclude that the upper airway minimum CSA increases significantly (124.13 mm(2) after maxillomandibular advancement (MMA) the total volume increases significantly after MMA (7416.10mm(3) and decreases significantly after maxillary advancement+mandibular setback 1552.90 mm(3) and isolated mandibular setback 1894.65 mm(3)
An Autophagic Flux Probe that Releases an Internal Control.
Venue: Molecular cell

Macroautophagy is an intracellular degradation system that utilizes the autophagosome to deliver cytoplasmic components to the lysosome. Measuring autophagic activity is critically important but remains complicated and challenging. Here, we have developed GFP LC3 RFP LC3DG, a fluorescent probe to evaluate autophagic flux. This probe is cleaved by endogenous ATG4 proteases into equimolar amounts of GFP LC3 and RFP LC3DG. GFP LC3 is degraded by autophagy, while RFP LC3DG remains in the cytosol, serving as an internal control. Thus, autophagic flux can be estimated by calculating the GFP/RFP signal ratio. Using this probe, we re evaluated previously reported autophagy modulating compounds, performed a high throughput screen of an approved drug library, and identified autophagy modulators. Furthermore, we succeeded in measuring both induced and basal autophagic flux in embryos and tissues of zebrafish and mice. The GFP LC3 RFP LC3DG probe is a simple and quantitative method to evaluate autophagic flux in cultured cells and whole organisms.
Damage detection on mesosurfaces using distributed sensor network and spectral diffusion maps

In this work, we develop a data driven method for the diagnosis of damage in mesoscale mechanical structures using an array of distributed sensor networks. The proposed approach relies on comparing intrinsic geometries of data sets corresponding to the undamaged and damaged states of the system. We use a spectral diffusion map approach to identify the intrinsic geometry of the data set. In particular, time series data from distributed sensors is used for the construction of diffusion maps. The low dimensional embedding of the data set corresponding to different damage levels is obtained using a singular value decomposition of the diffusion map. We construct appropriate metrics in the diffusion space to compare the different data sets corresponding to different damage cases. The developed algorithm is applied for damage diagnosis of wind turbine blades. To achieve this goal, we developed a detailed finite element based model of CX 100 blade in ANSYS using shell elements. Typical damage, such as crack or delamination, will lead to a loss of stiffness, is modeled by altering the stiffness of the laminate layer. One of the main challenges in the development of health monitoring algorithms is the ability to use sensor data with a relatively small signal to noise ratio. Our developed diffusion map based algorithm is shown to be robust to the presence of sensor noise. The proposed diffusion map based algorithm is advantageous by enabling the comparison of data from numerous sensors of similar or different types of data through data fusion, hereby making it attractive to exploit the distributed nature of sensor arrays. This distributed nature is further exploited for the purpose of damage localization. We perform extensive numerical simulations to demonstrate that the proposed method can successfully determine the extent of damage on the wind turbine blade and also localize the damage. We also present preliminary results for the application of the developed algorithm on the experimental data. These preliminary results obtained using experimental data are promising and is a topic of our ongoing investigation.
A comprehensive survey of security mechanisms in healthcare applications
Venue: 2016 International Conference on Communication and Electronics Systems (ICCES)

Recent trends and the accurate knowledge of human anatomy allow the healthcare professionals to handle the emergency scenario. Remote monitoring of patients by the healthcare professionals or doctors through the utilization of Wireless Sensor Network (WSN) offers the solution to the shortage problem. The special form of WSN used for remote monitoring called Wireless Body Area Network (WBAN) or Wireless Medical Sensor Network (WMSN) utilizes the numerous sensors that collect the data from the human body and send it to the central device for processing (raising the alarm for anomalies detection) and storage. This paper presents the survey of WMSN topologies, data sharing mechanisms, cryptography and attributes based encryption in privacy preserving in detail. The survey addresses the issues in cryptographic approaches such as storage computational overhead, the trade off between the security and elasticity, trust assurance against the attacks respectively. The detailed survey conveys that the secure data transfer from the user to the server is the major issue against the several inside and outside attackers. The processes involved in cryptography mechanisms such as key generation, encryption, and decryption introduces the storage and computational overheads and delegation issues in data preserving. To overcome these issues, the trusted authority and the hash verifier is included to generate and exchange the keys. Besides, the trade off between the security and overhead reduction is still investigating the issue in the healthcare applications.
The role of fluid structure interaction for safety and life time prediction in hydraulic machinery

Reliable assessments of dynamic phenomena in hydraulic machinery require the consideration of fluid structure interaction (FSI) if natural frequencies or damping properties of submerged structural parts clearly change due to the surrounding water or if the interaction may cause instabilities. Exemplarily, three different applications of strongly coupled FSI are presented which all have a high impact on operational safety or dynamic stresses and fatigue life. At first, flow induced damping effects at a Francis runner exhibit a strong dependency on operating condition and mode shape. Secondly, if a rotating disc is submerged, a splitting of natural frequencies is observed for mode shapes with different spinning direction. Finally, a hydroelastic instabilitiy is identified in a bypass valve at small opening.
Performance Implications of Extended Page Tables on Virtualized x86 Processors
Venue: VEE 2016

Managing virtual memory is an expensive operation, and becomes even more expensive on virtualized servers. Process ing TLB misses on a virtualized x86 server requires a two dimensional page walk that can have 6x more page table lookups, hence 6x more memory references, than a native page table walk. Thus much of the recent research on the subject starts from the assumption that TLB miss processing in virtual environments is significantly more expensive than on native servers. However, we will show that with the latest software stack on modern x86 processors, most of these page table lookups are satisfied by internal paging structure caches and the L1/L2 data caches, and the actual virtualization overhead of TLB miss processing is a modest fraction of the overall time spent processing TLB misses. In this paper, we present a detailed accounting of the TLB miss processing costs on virtualized x86 servers for an exhaustive set of workloads, in particular, two very demanding industry standard workloads. We show that an implementation of the TPC C workload that actively uses 475 GB of memory on a 72 CPU Haswell EP server spends 20% of its time processing TLB misses when the application runs in a VM. Although this is a non trivial amount, it is only 4.2% higher than the TLB miss processing costs on bare metal. The multi VM VMmark benchmark sees 12.3% in TLB miss processing, but only 4.3% of that can be attributed to virtualization overheads. We show that even for the heaviest workloads, a well tuned application that uses large pages on a recent OS release with a modern hypervisor running on the latest x86 processors sees only minimal degradation from the additional overhead of the two dimensional page walks in a virtualized server.
A Convnet for Non maximum Suppression
Venue: GCPR

Non maximum suppression (NMS) is used in virtually all state of the art object detection pipelines. While essential object detection ingredients such as features, classifiers, and proposal methods have been extensively researched surprisingly little work has aimed to systematically address NMS. The de facto standard for NMS is based on greedy clustering with a fixed distance threshold, which forces to trade off recall versus precision. We propose a convnet designed to perform NMS of a given set of detections. We report experiments on a synthetic setup, crowded pedestrian scenes, and for general person detection. Our approach overcomes the intrinsic limitations of greedy NMS, obtaining better recall and precision.
Face Detection with End to End Integration of a ConvNet and a 3D Model
Venue: ECCV

This paper presents a method for face detection in the wild, which integrates a ConvNet and a 3D mean face model in an end to end multi task discriminative learning framework. The 3D mean face model is predefined and fixed (e.g. we used the one provided in the AFLW dataset) The ConvNet consists of two components: (i) The face proposal component computes face bounding box proposals via estimating facial key points and the 3D transformation (rotation and translation) parameters for each predicted key point w.r.t. the 3D mean face model. (ii) The face verification component computes detection results by pruning and refining proposals based on facial key points based configuration pooling. The proposed method addresses two issues in adapting state of the art generic object detection ConvNets (e.g. faster R CNN) for face detection: (i) One is to eliminate the heuristic design of predefined anchor boxes in the region proposals network (RPN) by exploiting a 3D mean face model. (ii) The other is to replace the generic RoI (Region of Interest) pooling layer with a configuration pooling layer to respect underlying object structures. The multi task loss consists of three terms: the classification Softmax loss and the location smooth (l_1\ losses of both the facial key points and the face bounding boxes. In experiments, our ConvNet is trained on the AFLW dataset only and tested on the FDDB benchmark with fine tuning and on the AFW benchmark without fine tuning. The proposed method obtains very competitive state of the art performance in the two benchmarks.
Applying learning theories and instructional design models for effective instruction.
Venue: Advances in physiology education

Faculty members in higher education are involved in many instructional design activities without formal training in learning theories and the science of instruction. Learning theories provide the foundation for the selection of instructional strategies and allow for reliable prediction of their effectiveness. To achieve effective learning outcomes, the science of instruction and instructional design models are used to guide the development of instructional design strategies that elicit appropriate cognitive processes. Here, the major learning theories are discussed and selected examples of instructional design models are explained. The main objective of this article is to present the science of learning and instruction as theoretical evidence for the design and delivery of instructional materials. In addition, this article provides a practical framework for implementing those theories in the classroom and laboratory.
Learning theories 101: application to everyday teaching and scholarship.
Venue: Advances in physiology education

Shifts in educational research, in how scholarship in higher education is defined, and in how funding is appropriated suggest that educators within basic science fields can benefit from increased understanding of learning theory and how it applies to classroom practice. This article uses a mock curriculum design scenario as a framework for the introduction of five major learning theories. Foundational constructs and principles from each theory and how they apply to the proposed curriculum designs are described. A summative table that includes basic principles, constructs, and classroom applications as well as the role of the teacher and learner is also provided for each theory.
Sexual Safety Planning as an HIV Prevention Strategy for Survivors of Domestic Violence.
Venue: Journal of women's health

Victims of domestic violence (DV) are not only subject to physical and emotional abuse but may also be at increased risk for less recognized dangers from infection with human immunodeficiency virus (HIV) and other sexually transmitted pathogens. Because of the close link between DV and sexual risk, women need to be educated about the consequences of acquiring a life threatening sexually transmitted infection, risk reduction measures, and how to access appropriate HIV services for diagnosis and treatment. It is therefore critical for DV workers to receive sufficient training about the link between DV and HIV risk so that sexual safety planning can be incorporated into activities with their clients in the same way as physical safety plans. In this article, we discuss how the Many Hands Working Together project provides interactive training for workers in DV and DV affiliated agencies to increase their knowledge about HIV and teach sexual safety planning skills to achieve HIV risk reduction.
Role of Lean, Environmental and Social Practices to Increasing Firm's Overall Performance

The companies face a competition increasingly sharp. In this context, the adoption of Lean practices is highly demanded. It aims to accelerate the flow, to reduce non value added, as part of a continuous improvement process. Furthermore, since the 90s, sustainable development is a growing interest. Corporate social responsibility (CSR) is the firms contribution to sustainable development issues. This approach is for companies to take into account the social and environmental impacts of their activity to adopt the best possible practices and contribute to the betterment of society and the protection of the environment. Literature suggests that selected stand alone practices of lean, environmental and social have a positive impact on firm sustainability performance. Our goal in this study is to show the impact of deferent combinations of lean, environmental and social practices on firm financial, environmental, social, and overall performance.
Virtual reality and augmented reality for education: panel
Venue: SIGGRAPH ASIA Symposium on Education: Talks

Since the last few decades, virtual reality (VR) and augmented reality (AR) interfaces have shown the potential to enhance teaching and learning, by combining physical and virtual worlds and leveraging the advantages of both [Yannier et al. 2015] Educators from different countries have been experimenting this technology in their education systems. In 2007, Hougang Elementary school in Singapore applied an AR prototype in a typical primary (11 years old) class to facilitate the learning of seed germination and plant growth, and indicated significant engagement and motivation encouraged by the use of the technology [Pang et al. 2007] More recently, the advanced development of the VR devices has make VR an affordable and suitable interface for educations in different levels, including primary schools, secondary schools, colleges, and universities. In particular, virtual sandbox environment [min 2015] as defined as the VR environments that allow users to freely move through a virtual world, choose how/when to approach objectives, and create domain specific mods, serve as a good candidate for teachers to design VR based teaching and learning environment, and for students to explore the new knowledge freely. Motivated by the rapid development of AR and VR, this panel invites representatives from Hong Kong, Australia, and UK. The discussion will focus on the application of AR and VR technologies in different levels of education.