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

Vitellogenin is not an appropriate biomarker of feminisation in a Crustacean

The expression of the yolk protein vitellogenin (Vtg) has been used as a biomarker of feminisation in multiple fish species throughout the world. Since the late 1990s, researchers have attempted to develop similar biomarkers to address whether reproductive endocrine disruption also occurs in the males of invertebrate groups such as the Crustacea. To date, the vast majority of studies investigating Vtg induction in male Crustacea have resulted in negative or inconclusive results, leading researchers to question the utility of Vtg expression as a biomarker in this taxon. This study measured the expression of Vtg genes in two intersex phenotypes (termed internal and external) found in the male amphipod, Echinogammarus marinus, and compared them with those of normal males and females. Males presenting the external intersex phenotype are infected with known feminising parasites and display a variety of feminised traits including oviduct structures on their testes and external female brood plates (oostegites). The internal intersex male phenotype, that displays a pronounced oviduct structure on the testes without the external intersex characteristics, is not parasite infected and it is thought to be a result of environmental contamination. Given their morphology, these phenotypes might be considered highly ‘feminised’ or ‘de-masculinised’ and can be utilised to test the suitability of feminisation biomarkers. The E. marinus transcriptome was searched for genes resembling Vtg and two sequences were revealed, that we subsequently refer to as Vtg1 and Vtg2. Results from a high-throughput transcriptomic sequencing screen of gonadal cDNA libraries suggested that very low expression (in this manuscript gene transcription is taken to represent gene expression, although it is acknowledged that in addition to transcription, translation, transcript processing, mRNA stability and protein stability can regulate gene expression) of Vtg1 and Vtg2 in normal males (ESTs = 1 and 0 for Vtg1 and Vtg2, respectively), internal intersex males (ESTs = 0 for both Vtg sequences) and external intersex males (ESTs = 5 and 0 for Vtg1 and Vtg2, respectively). In contrast, the sequencing suggested notable levels of expression of both Vtg genes in females (ESTs = 1133 and 84 for Vtg1 and Vtg2, respectively). Subsequent qPCR analysis validates these expression levels, with the signal for Vtg1 and Vtg2 transcripts in all male phenotypes being indistinguishable from that caused by contamination of trace levels of genomic DNA or the low-level amplification non-target sequences. These findings suggest that Vtg expression is not notably induced in highly feminised amphipods and is therefore not an appropriate biomarker of feminisation/de-masculination in crustaceans. We discuss our findings in the context of previous attempts to measure Vtg in male crustaceans and suggest a requirement for more appropriate taxon-specific biomarkers to monitor feminisation in these groups

Population screening and transmission experiments indicate paramyxid-microsporidian co-infection in Echinogammarus marinus represents a non-hyperparasitic relationship between specific parasite strains

Phylogenetically distant parasites often infect the same host. Indeed, co-infections can occur at levels greater than expected by chance and are sometimes hyperparasitic. The amphipod Echinogammarus marinus presents high levels of co-infection by two intracellular and vertically transmitted parasites, a paramyxid (Paramarteilia sp. Em) and a microsporidian strain (Dictyocoela duebenum Em). This co-infection may be hyperparasitic and result from an exploitative ‘hitchhiking’ or a symbiotic relationship between the parasites. However, the best-studied amphipod species are often collected from contaminated environments and may be immune-compromised. Immune-challenged animals frequently present co-infections and contaminant-exposed amphipods present significantly higher levels of microsporidian infection. This suggests the co-infections in E. marinus may result from contaminant-associated compromised immunity. Inconsistent with hyperparasitism, we find that artificial infections transmit Paramarteilia without microsporidian. Our population surveys reveal the co-infection relationship is geographically widespread but find only chance co-infection between the Paramarteilia and another species of microsporidian, Dictyocoela berillonum. Furthermore, we identify a haplotype of the Paramarteilia that presents no co-infection, even in populations with otherwise high co-infection levels. Overall, our results do not support the compromised-immunity hypothesis but rather that the co-infection of E. marinus, although non-hyperparasitic, results from a relationship between specific Paramarteilia and Dictyocoela duebenum strains

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

Idomaar : a framework for multi-dimensional benchmarking of recommender algorithms

In real-world scenarios, recommenders face non-functional requirements of technical nature and must handle dynamic data in the form of sequential streams. Evaluation of recommender systems must take these issues into account in order to be maximally informative. In this paper, we present Idomaar—a framework that enables the efficient multi-dimensional benchmarking of recommender algorithms. Idomaar goes beyond current academic research practices by creating a realistic evaluation environment and computing both effectiveness and technical metrics for stream-based as well as set-based evaluation. A scenario focussing on “research to prototyping to productization” cycle at a company illustrates Idomaar’s potential. We show that Idomaar simplifies testing with varying configurations and supports flexible integration of different data

The price of persistence: Assessing the drivers and health implications of metal levels in indicator carnivores inhabiting an agriculturally fragmented landscape

Patterns and practices of agricultural expansion threaten the persistence of global biodiversity. Wildlife species surviving large-scale land use changes can be exposed to a suite of contaminants that may deleteriously impact their health. There is a paucity of data concerning the ecotoxicological impacts associated with the global palm oil (Elaeis guineensis) industry. We sampled wild Malay civets (Viverra tangalunga) across a patchwork landscape degraded by oil palm agriculture in Sabah, Malaysian Borneo. Using a non-lethal methodology, we quantified the levels of 13 essential and non-essential metals within the hair of this adaptable small carnivore. We robustly assessed the biological and environmental drivers of intrapopulation variation in measured levels. Metal concentrations were associated with civet age, weight, proximity to a tributary, and access to oxbow lakes. In a targeted case study, the hair metal profiles of 16 GPS-collared male civets with differing space use patterns were contrasted. Civets that entered oil palm plantations expressed elevated aluminium, cadmium, and lead, and lower mercury hair concentrations compared to civets that remained exclusively within the forest. Finally, we paired hair metal concentrations with 34 blood-based health markers to evaluate the possible sub-lethal physiological effects associated with varied hair metal levels. Our multi-facetted approach establishes these adaptable carnivores as indicator species within an extensively altered ecosystem, and provides critical and timely evidence for future studies