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

Small animal anesthesia and analgesia

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Watershed assessment plan for Franklin County and the City of Carnesville, Georgia: Biological assessment

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Behavioral, physiologic, and stress-related hormonal and metabolic responses to intravenous and epidural morphine in goats

Objective: To establish the effects of epidural and intravenous (IV) morphine on stress-related hormones, metabolites, and behavior in goats. Animals: Six 6-year-old neutered goats (3 males, 3 females) weighing 62.5 +/- 16.5 kg (mean +/- SD). Material and Methods: Study was a prospective cross-over design in which morphine (0.1 mg/kg, epidural and IV) was administered in 2 trials I week apart. Epidural catheters were placed 24 hours before study. Blood samples were collected, physiologic variables were measured, and behavior was scored (0 to 3; 0 = normal, 3 = fractious) at 0, 15, and 30 minutes and 1, 2, 4, 6, and 8 hours (IV trial) and at 0, 1, 2, 4, 6, 8, 12, and 24 hours (epidural trial). Analysis included repeated measures analysis of variance and Tukey-Kramer multiple comparisons test. A P value <0.05 was considered significant. Results: For IV morphine, differences were found for respiratory rate (17 +/- 10 to 27 +/- 11 breaths/min) and temperature. Temperature (38.6 +/- 0.1 degrees C increased at 8 hours (3 9.0 +/- 0.2 degrees C. After epidural morphine, heart rate (96 24 beats/min) decreased at 8 (73 +/- 15 beats/min), 12 (74 +/- 13 beats/min), and 24 (74 +/- 19 beats/min) hours; systolic blood pressure (indirect) (106 +/- 31 mmHg) increased at 6 (157 +/- 18 mmHg), 8 (151 +/- 18 mmHg), and 24 (142 +/- 10 mmHg) hours; diastolic blood pressure (indirect) (71 +/- 23 mmHg) increased at 6 (120 +/- 23 mmHg) and 8 (111 +/- 28 mmHg) hours; and mean blood pressure (indirect) (84 +/- 25 mmHg) increased at 6 (134 +/- 20 mmHg) and 8 (125 +/- 24 mmHg) hours. Glucose concentrations increased from 0 minutes (55.6 +/- 4.6 mg/dL) to 60 minutes (73.1 +/- 15.2 mg/dL) and 120 minutes (70.7 +/- 13.4 mg/dL) before returning to baseline at 720 minutes (55.9 +/- 6.0 mg/dL). Temperature ranged from 38.8 +/- 0.1 degrees C to 39.3 +/- 0.2 degrees C; and cortisol increased from baseline (1.15 +/- 0.91 mu g/dL) to 60 minutes (2.23 +/- 0.78 mu g/dL), which was higher than subsequent cortisol concentrations. Free fatty acids were maximal at 60 minutes (317 +/- 183 mmol/L) and decreased after 480 minutes (145 +/- 28 mmol/L). During the epidural trial, all goats vocalized and changed posture upon injection of the morphine. Conclusions and Clinical Relevance: Behavioral, physiologic, and stress-related hormonal and metabolic responses are minor after IV morphine in goats. Physiologic changes after epidural morphine may interfere with the postoperative evaluation of pain in goats that received epidural morphine. However, it is possible that epidural injection of any substance may initiate the stress-related changes seen in this study

Effect of medetomidine and its antagonism with atipamezole on stress-related hormones, metabolites, physiologic responses, sedation, and mechanical threshold in goats

To evaluate the effects of medetomidine and its antagonism with atipamezole in goats. Prospective randomized crossover study with 1 week between treatments. Six healthy 3-year-old neutered goats (three male and three female) weighing 39.1–90.9 kg (60.0 ± 18 kg, mean ± SD). Goats were given medetomidine (20 μg kg−1, IV) followed, 25 minutes later, by either atipamezole (100 μg kg−1, IV) or saline. Heart and respiratory rate, rectal temperature, indirect blood pressure, and mechanical threshold were measured, and sedation and posture were scored and blood samples obtained to measure epinephrine, norepinephrine, free fatty acids, glucose, and cortisol concentrations at baseline (immediately before medetomidine), 5 and 25 minutes after medetomidine administration, and at 5, 30, 60, and 120 minutes after the administration of antagonist or saline. Parametric and nonparametric tests were used to evaluate data; p < 0.05 was considered significant. Medetomidine decreased body temperature, heart rate, and respiratory rate and increased mean arterial blood pressure, cortisol, and glucose. Recumbency occurred 89 ± 50 seconds after medetomidine administration. All goats were standing 86 ± 24 seconds after atipamezole administration whereas all goats administered saline were sedate and recumbent at 2 hours. Tolerance to compression of the withers and metacarpus increased with medetomidine. From 5 to 120 minutes after saline or atipamezole administration, there were differences in body temperature, glucose, and cortisol but none in heart rate or blood pressure. Three of the six goats receiving saline developed bloat; five of six urinated. After atipamezole, four of six goats developed piloerection and all goats were agitated and vocalized. At the doses used, atipamezole antagonized the effects of medetomidine on recumbency, sedation, mechanical threshold, and the increase in glucose. Atipamezole increased the rate of return of cortisol toward baseline, and prevented further decline in rectal body temperature. Atipamezole may be used to antagonize some, but not all effects of medetomidine

The Effect of Detomidine and its Antagonism With Tolazoline on Stress‐Related Hormones, Metabolites, Physiologic Responses, and Behavior in Awake Ponies

Six ponies were used to investigate the effect of tolazoline antagonism of detomidine on physiological responses, behavior, epinephrine, norepinephrine, Cortisol, glucose, and free fatty acids in awake ponies. Each pony had a catheter inserted into a jugular vein 1 hour before beginning the study. Awake ponies were administered detomidine (0.04 mg/kg intravenously [IV]) followed 20 minutes later by either tolazoline (4.0 mg/kg IV) or saline. Blood samples were drawn from the catheter 5 minutes before detomidine administration (baseline), 5 minutes after detomidine administration, 20 minutes after detomidine administration which was immediately before the administration of tolazoline or saline (time [T] = 0), and at 5, 30, and 60 minutes after injections of tolazoline or saline (T = 5, 30, and 60 minutes, respectively). Compared with heart rate at T = 0, tolazoline antagonism increased heart rate 45% at 5 minutes. There was no difference in heart rate between treatments at 30 minutes. Blood pressure remained stable after tolazoline, while it decreased over time after saline. Compared with concentrations at T = 0, tolazoline antagonism of detomidine in awake ponies resulted in a 55% increase in Cortisol at 30 minutes and a 52% increase in glucose at 5 minutes. The change in free fatty acids was different for tolazoline and saline over time. Free fatty acids decreased after detomidine administration. Free fatty acids did not change after saline administration. After tolazoline administration, free fatty acids increased transiently. Tolazoline tended to decrease sedation and analgesia at 15 and 60 minutes postantagonism. Antagonism of detomidine‐induced physiological and behavioral effects with tolazoline in awake ponies that were not experiencing pain appears to precipitate a stress response as measured by Cortisol, glucose, and free fatty acids. If antagonism of an α‐agonist is contemplated, the potential effect on hormones and metabolites should be considered

Involving patients in understanding hospital infection control using visual methods

Aims and Objectives. This paper explores patients' perspectives on infection prevention and control. Background. Healthcare-associated infections are the most frequent adverse event experienced by patients. Reduction strategies have predominantly addressed frontline clinicians' practices; patients' roles have been less explored. Design. Video-reflexive ethnography. Methods. Fieldwork undertaken at a large metropolitan hospital in Australia involved 300 hours of ethnographic observations, including 11 hours of video footage. This paper focuses on eight occasions, where video footage was shown back to patients in one-on-one reflexive sessions. Findings. Viewing and discussing video footage of clinical care enabled patients to become articulate about infection risks, and to identify their own roles in reducing transmission. Barriers to detailed understandings of preventative practices and their roles included lack of conversation between patients and clinicians about infection prevention and control, and being ignored or contradicted when challenging perceived suboptimal practice. It became evident that to compensate for clinicians' lack of engagement around infection control, participants had developed a range of strategies, of variable effectiveness, to protect themselves and others. Finally, the reflexive process engendered closer scrutiny and a more critical attitude to infection control that increased patients' sense of agency. Conclusion. This study found that patients actively contribute to their own safety. Their success, however, depends on the quality of patient-provider relationships and conversations. Rather than treating patients as passive recipients of infection control practices, clinicians can support and engage with patients' contributions towards achieving safer care. Relevance to clinical practice. This study suggests that if clinicians seek to reduce infection rates, they must start to consider patients as active contributors to infection control. Clinicians can engage patients in conversations about practices and pay attention to patient feedback about infection risk. This will broaden clinicians' understandings of infection control risks and behaviours, and assist them to support appropriate patient self-care behaviour