Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Individual consistency of feather pecking behavior in laying hens: once a feather pecker always a feather pecker?

The pecking behavior [severe feather, gentle feather, and aggressive pecks (AP)] of individual White Shaver non-cage laying hens (n = 300) was examined at 21, 24, 27, 32, and 37 weeks. Hens were housed in 30 groups of 10 hens each and on 3 cm litter with access to a feeder, perch, and two nest boxes. The number of severe feather pecks given (SFPG) and received (SFPR) was used to categorize hens as feather peckers (P), victims (V), neutrals (N), or feather pecker-victims (PV) at each age. Hens categorized as PV exhibited pecking behaviors similar to P and received pecks similar to V. SFP given were correlated with APs given, but not with gentle feather pecks (GFP) given throughout the study. State-transition plot maps illustrated that 22.5% of P remained P, while 44% of PV remained PV throughout the duration of the study. Lifetime behavioral categories identified hens as a consistent feather pecker (5%), consistent neutral (3.9%), consistent victim (7.9%), consistent feather pecker-victim (29.4%), or inconsistent (53.8%) in their behavioral patterns throughout their life. Consistent feather peckers performed more SFP than hens of other categories, and consistent neutral hens received fewer GFP than consistent feather PV. No differences in corticosterone or whole blood serotonin levels were observed among the categories. Approximately, half of the population was classified as a feather pecker at least once during the study, while the remainder was never categorized as a feather pecker. Therefore, even if the development and cause of feather pecking may be multifactorial, once the behavior has been developed, some hens may persist in feather pecking. However, as some hens were observed to never receive or perform SFP, emphasis should be made to select for these hens in future breeding practices

Use of dynamic and rewarding environmental enrichment to alleviate feather pecking in non-cage laying hens

Feather pecking (FP) can cause feather loss, resulting in physical injuries, which may lead to cannibalism. FP appears to be a redirection of foraging behavior, which intensifies when hens have difficulty coping with stress and fear. Dynamic environmental enrichment (EE) may allow expression of natural foraging behavior thus reducing conspecific pecking behavior and alleviating hen injury. Three treatments (plastic box: BOX; hay bale: HAY; and no enrichment: CON) were randomly applied to 30 identical floor pens (10 hens/pen; 10 pens/trt). At the pen level, hen behavior, and the number of severe FP (SFP), gentle FP (GFP), aggressive pecks (AP), and enrichment pecks (EP) were recorded from video prior to (21 wk) and after (24 wk) treatment implementation, and when hens were 27, 32, and 37 wk of age. A manual restraint test (MR) was performed immediately after behavioral observations and levels of blood serotonin (5-HT) and glucocorticoids (GC) measured. Short-term (ST) and long-term (LT) analyses identified the impact of EE over the ST (21 vs. 24 wk of age) and LT (21 vs. all other ages) at the pen level. At the pen level, HAY (3.18 ± 0.33) tended to reduce GFP compared to CON (4.10 ± 0.34) over the ST (P = 0.15) and LT (P = 0.09), but did not impact the number of SFP, or AP over the ST or LT. More EP was observed in HAY (3.56 ± 0.14) than BOX (1.61 ± 0.18) throughout the study (P <0.0001). More HAY hens perched (P = 0.05) at 24 wk (0.28 ± 0.12) compared to 21 wk (0.19 ± 0.11), and more HAY hens (3.69 ± 0.25) performed dust bathing compared to CON (4.14 ± 0.22, P = 0.05) throughout the study. CON performed more struggles (1.13 ± 0.04, P = 0.04) and were quicker to vocalize (4.87 ± 0.07 s, P = 0.05) during MR than HAY (latency to vocalize(s): 5.16 ± 0.05; number of struggles: 0.96 ± 0.05), counter-intuitively suggesting CON were less fearful. Treatment did not affect 5-HT or GC. HAY appears to be a promising EE for mitigating GFP in non-cage laying hens. Future studies should examine the impact of EE on individual, rather than group-level responses. These results suggest that the presence of a hay bale is stimulating and may reduce GFP while encouraging hens to redirect pecking towards a dynamic and manipulable EE

MagellanPlus Workshop: Mission-specific platform approaches to assessing natural hazards that impact society

Oceanic natural hazards pose threats to coastal communities worldwide. These include earthquakes, tsunamis, submarine landslide, volcanic eruptions, and tropical cyclones. Scientific ocean drilling can contribute to our understanding and assessment of these hazards through rapid response measurements of hazardous events, learning from past hazard records, and sub-seafloor monitoring and observation. With the impending retirement of the D/V JOIDES Resolution and operational limitations of the D/V Chikyu, it is important to consider other options for achieving scientific ocean drilling goals. We convened a workshop in Lisbon, Portugal, in July 2022 to identify locations where natural hazards, or preferably several different hazards, can be addressed with mission-specific platform (MSP) drilling, with a consideration of further location-based workshops. Participants split into three working groups to develop hypotheses surrounding climate and tropical cyclones, slope failure, and processes at active margins that can be tested with MSP drilling and can be addressed using the unique capabilities of these platforms. We produced 13 questions or hypotheses with recommendations on specific areas or locations for drilling. Our hope is that the results of this workshop will lay the groundwork for future pre-proposals. © 2023 Copyright AuthorsOpen access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]