CLEF 2017 NewsREEL Overview: Offline and Online Evaluation of Stream-based News Recommender Systems

The CLEF NewsREEL challenge allows researchers to evaluate news recommendation algorithms both online (NewsREEL Live) and offline (News- REEL Replay). Compared with the previous year NewsREEL challenged participants with a higher volume of messages and new news portals. In the 2017 edition of the CLEF NewsREEL challenge a wide variety of new approaches have been implemented ranging from the use of existing machine learning frameworks, to ensemble methods to the use of deep neural networks. This paper gives an overview over the implemented approaches and discusses the evaluation results. In addition, the main results of Living Lab and the Replay task are explained

CLEF 2017 NewsREEL overview: A stream-based recommender task for evaluation and education

News recommender systems provide users with access to news stories that they find interesting and relevant. As other online, stream-based recommender systems, they face particular challenges, including limited information on users’ preferences and also rapidly fluctuating item collections. In addition, technical aspects, such as response time and scalability, must be considered. Both algorithmic and technical considerations shape working requirements for real-world recommender systems in businesses. NewsREEL represents a unique opportunity to evaluate recommendation algorithms and for students to experience realistic conditions and to enlarge their skill sets. The NewsREEL Challenge requires participants to conduct data-driven experiments in NewsREEL Replay as well as deploy their best models into NewsREEL Live’s ‘living lab’. This paper presents NewsREEL 2017 and also provides insights into the effectiveness of NewsREEL to support the goals of instructors teaching recommender systems to students. We discuss the experiences of NewsREEL participants as well as those of instructors teaching recommender systems to students, and in this way, we showcase NewsREEL’s ability to support the education of future data scientists

Transient peak-strain matching partially recovers the age-impaired mechanoadaptive cortical bone response

Mechanoadaptation maintains bone mass and architecture; its failure underlies age-related decline in bone strength. It is unclear whether this is due to failure of osteocytes to sense strain, osteoblasts to form bone or insufficient mechanical stimulus. Mechanoadaptation can be restored to aged bone by surgical neurectomy, suggesting that changes in loading history can rescue mechanoadaptation. We use non-biased, whole-bone tibial analyses, along with characterisation of surface strains and ensuing mechanoadaptive responses in mice at a range of ages, to explore whether sufficient load magnitude can activate mechanoadaptation in aged bone. We find that younger mice adapt when imposed strains are lower than in mature and aged bone. Intriguingly, imposition of short-term, high magnitude loading effectively primes cortical but not trabecular bone of aged mice to respond. This response was regionally-matched to highest strains measured by digital image correlation and to osteocytic mechanoactivation. These data indicate that aged bone’s loading response can be partially recovered, non-invasively by transient, focal high strain regions. Our results indicate that old murine bone does respond to load when the loading is of sufficient magnitude, and bones’ age-related adaptation failure may be due to insufficient mechanical stimulus to trigger mechanoadaptation

In vivo axial loading of the mouse tibia

Noninvasive methods to apply controlled, cyclic loads to the living skeleton are used as anabolic procedures to stimulate new bone formation in adults and enhance bone mass accrual in growing animals. These methods are also invaluable for understanding bone signaling pathways. Our focus here is on a particular loading model: in vivo axial compression of the mouse tibia. An advantage of loading the tibia is that changes are present in both the cancellous envelope of the proximal tibia and the cortical bone of the tibial diaphysis. To load the tibia of the mouse axially in vivo, a cyclic compressive load is applied up to five times a week to a single tibia per mouse for a duration lasting from 1 day to 6 weeks. With the contralateral limb as an internal control, the anabolic response of the skeleton to mechanical stimuli can be studied in a pairwise experimental design. Here, we describe the key parameters that must be considered before beginning an in vivo mouse tibial loading experiment, including methods for in vivo strain gauging of the tibial midshaft, and then we describe general methods for loading the mouse tibia for an experiment lasting multiple days

Overview of NewsREEL’16: Multi-dimensional evaluation of real-time stream-recommendation algorithms

Successful news recommendation requires facing the challenges of dynamic item sets, contextual item relevance, and of fulfilling non-functional requirements, such as response time. The CLEF NewsREEL challenge is a campaign-style evaluation lab allowing participants to tackle news recommendation and to optimize and evaluate their recommender algorithms both online and offline. In this paper, we summarize the objectives and challenges of NewsREEL 2016. We cover two contrasting perspectives on the challenge: that of the operator (the business providing recommendations) and that of the challenge participant (the researchers developing recommender algorithms). In the intersection of these perspectives, new insights can be gained on how to effectively evaluate real-time stream recommendation algorithms

Nuclear pore complex proteins mark the implantation window in human endometrium

Nucleolar channel systems (NCSs) are membranous organelles appearing transiently in the epithelial cell nuclei of postovulatory human endometrium. Their characterization and use as markers for a healthy receptive endometrium have been limited because they are only identifiable by electron microscopy. Here we describe the light microscopic detection of NCSs using immunofluorescence. Specifically, the monoclonal nuclear pore complex antibody 414 shows that NCSs are present in about half of all human endometrial epithelial cells but not in any other cell type, tissue or species. Most nuclei contain only a single NCS of uniform 1 μm diameter indicating a tightly controlled organelle. The composition of NCSs is as unique as their structure; they contain only a subset each of the proteins of nuclear pore complexes, inner nuclear membrane, nuclear lamina and endoplasmic reticulum. Validation of our robust NCS detection method on 95 endometrial biopsies defines a 6-day window, days 19-24 (±1) of an idealized 28 day cycle, wherein NCSs occur. Therefore, NCSs precede and overlap with the implantation window and serve as potential markers of uterine receptivity. The immunodetection assay, combined with the hitherto underappreciated prevalence of NCSs, now enables simple screening and further molecular and functional dissection

Mediastinal lymph node metastasis model by orthotopic intrapulmonary implantation of Lewis lung carcinoma cells in mice

This study is designed to establish a pulmonary tumour model to investigate the biology and therapy of lung cancer in mice. Current methods for forming a solitary intrapulmonary nodule and subsequent metastasis to mediastinal lymph nodes are not well defined. Lewis lung carcinoma (LLC) cell suspensions were orthotopically introduced into the lung parenchyma of C57/BL6 mice via a limited skin incision without thoracotomy followed by direct puncture through the intercostal space. The implantation process was performed within approximately 50 s per mouse, and the operative mortality was less than 5%. Single pulmonary nodules developed at the implanted site in 93% of animals and subsequent mediastinal lymph node metastasis was observed in all mice that formed a lung nodule after intrapulmonary implantation. The size of tumour nodule and the weight of mediastinal lymph node increased in a time-dependent manner. The mean survival time of mice implanted successfully with LLC cells was 21 ± 2 days (range 19–24 days). Histopathological analysis revealed that no metastatic tumour was detectable in the mediastinal lymph nodes on day 11, but metastatic foci at mediastinal lymph nodes were clearly observed on days 17 and 21 after implantation. Other metastases in distant organs or lymph nodes were not observed at 21 days after the implantation. Comparative studies with intrapleural and intravenous injections of LLC cells suggest that the mediastinal lymph node metastasis by intrapulmonary impantation is due to the release of tumour cells from the primary nodule, and not due to extrapulmonary leakage of cells. An intravenous administration of cis-diamine dichrolo platinum on day 1 after tumour implantation tended to suppress the primary tumour nodule and significantly inhibited lymph node metastasis. Thus, a solitary pulmonary tumour nodule model with lymph node metastasis approximates clinical lung cancer and may provide a useful basis for lung cancer research. © 1999 Cancer Research Campaig

Tibial Loading Increases Osteogenic Gene Expression and Cortical Bone Volume in Mature and Middle-Aged Mice

There are conflicting data on whether age reduces the response of the skeleton to mechanical stimuli. We examined this question in female BALB/c mice of different ages, ranging from young to middle-aged (2, 4, 7, 12 months). We first assessed markers of bone turnover in control (non-loaded) mice. Serum osteocalcin and CTX declined significantly from 2 to 4 months (p<0.001). There were similar age-related declines in tibial mRNA expression of osteoblast- and osteoclast-related genes, most notably in late osteoblast/matrix genes. For example, Col1a1 expression declined 90% from 2 to 7 months (p<0.001). We then assessed tibial responses to mechanical loading using age-specific forces to produce similar peak strains (−1300 µε endocortical; −2350 µε periosteal). Axial tibial compression was applied to the right leg for 60 cycles/day on alternate days for 1 or 6 weeks. qPCR after 1 week revealed no effect of loading in young (2-month) mice, but significant increases in osteoblast/matrix genes in older mice. For example, in 12-month old mice Col1a1 was increased 6-fold in loaded tibias vs. controls (p = 0.001). In vivo microCT after 6 weeks revealed that loaded tibias in each age group had greater cortical bone volume (BV) than contralateral control tibias (p<0.05), due to relative periosteal expansion. The loading-induced increase in cortical BV was greatest in 4-month old mice (+13%; p<0.05 vs. other ages). In summary, non-loaded female BALB/c mice exhibit an age-related decline in measures related to bone formation. Yet when subjected to tibial compression, mice from 2–12 months have an increase in cortical bone volume. Older mice respond with an upregulation of osteoblast/matrix genes, which increase to levels comparable to young mice. We conclude that mechanical loading of the tibia is anabolic for cortical bone in young and middle-aged female BALB/c mice

Cohort Profile: Antiretroviral Therapy Cohort Collaboration (ART-CC)

The advent of effective combination antiretroviral therapy (ART) in 1996 resulted in fewer patients experiencing clinical events, so that some prognostic analyses of individual cohort studies of human immunodeficiency virus-infected individuals had low statistical power. Because of this, the Antiretroviral Therapy Cohort Collaboration (ART-CC) of HIV cohort studies in Europe and North America was established in 2000, with the aim of studying the prognosis for clinical events in acquired immune deficiency syndrome (AIDS) and the mortality of adult patients treated for HIV-1 infection. In 2002, the ART-CC collected data on more than 12,000 patients in 13 cohorts who had begun combination ART between 1995 and 2001. Subsequent updates took place in 2004, 2006, 2008, and 2010. The ART-CC data base now includes data on more than 70 000 patients participating in 19 cohorts who began treatment before the end of 2009. Data are collected on patient demographics (e.g. sex, age, assumed transmission group, race/ethnicity, geographical origin), HIV biomarkers (e.g. CD4 cell count, plasma viral load of HIV-1), ART regimen, dates and types of AIDS events, and dates and causes of death. In recent years, additional data on co-infections such as hepatitis C; risk factors such as smoking, alcohol and drug use; non-HIV biomarkers such as haemoglobin and liver enzymes; and adherence to ART have been collected whenever available. The data remain the property of the contributing cohorts, whose representatives manage the ART-CC via the steering committee of the Collaboration. External collaboration is welcomed. Details of contacts are given on the ART-CC website (www.art-cohort-collaboration.org

Evaluation-as-a-service for the computational sciences: overview and outlook

Evaluation in empirical computer science is essential to show progress and assess technologies developed. Several research domains such as information retrieval have long relied on systematic evaluation to measure progress: here, the Cranfield paradigm of creating shared test collections, defining search tasks, and collecting ground truth for these tasks has persisted up until now. In recent years, however, several new challenges have emerged that do not fit this paradigm very well: extremely large data sets, confidential data sets as found in the medical domain, and rapidly changing data sets as often encountered in industry. Crowdsourcing has also changed the way in which industry approaches problem-solving with companies now organizing challenges and handing out monetary awards to incentivize people to work on their challenges, particularly in the field of machine learning. This article is based on discussions at a workshop on Evaluation-as-a-Service (EaaS). EaaS is the paradigm of not providing data sets to participants and have them work on the data locally, but keeping the data central and allowing access via Application Programming Interfaces (API), Virtual Machines (VM), or other possibilities to ship executables. The objectives of this article are to summarize and compare the current approaches and consolidate the experiences of these approaches to outline the next steps of EaaS, particularly toward sustainable research infrastructures. The article summarizes several existing approaches to EaaS and analyzes their usage scenarios and also the advantages and disadvantages. The many factors influencing EaaS are summarized, and the environment in terms of motivations for the various stakeholders, from funding agencies to challenge organizers, researchers and participants, to industry interested in supplying real-world problems for which they require solutions. EaaS solves many problems of the current research environment, where data sets are often not accessible to many researchers. Executables of published tools are equally often not available making the reproducibility of results impossible. EaaS, however, creates reusable/citable data sets as well as available executables. Many challenges remain, but such a framework for research can also foster more collaboration between researchers, potentially increasing the speed of obtaining research results