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

Clinical findings and treatment in 63 cows with haemorrhagic bowel syndrome

The clinical, haematological and biochemical findings, treatment and outcome of 63 cows with haemorrhagic bowel syndrome are described. The general condition and demeanor were moderately to severely abnormal in all the cows. Signs of colic occurred in 27 cows, decreased rectal temperature in 46 and tachycardia in 44. With the exception of one cow, intestinal motility was decreased or absent. Transrectal palpation revealed dilatation of the rumen in 47 cows and dilatation of the small intestine in 18. Faecal output was markedly reduced or absent, and the faeces were dark brown to black and contained blood. Nine cows were euthanized immediately after physical examination. Conservative medical therapy was instituted in two cows; however, both were euthanized a few days later because of deterioration in condition. Exploratory right flank laparotomy was carried out in 52 cows. Of these, 22 were euthanized intraoperatively because of severe lesions. In 27 cows, intestinal massage to reduce the size of blood clots was carried out; 11 were euthanized several days postoperatively because of deterioration in condition. In three other cows, intestinal resection was carried out and all survived. Of the 63 cows, 19 (30.2%) survived and were healthy at the time of discharge from the clinic

Herniation of the gravid uterus through a mesoduodenal defect an concurrent omental hernia in a cow

OBJECTIVES: To describe surgical treatment of herniation of the gravid uterus through the mesoduodenum, displacement of the descending duodenum around the gravid uterus, and concurrent herniation of the small and large intestines into the omental bursa in a cow. STUDY DESIGN: Clinical report. ANIMAL: Three-year-old, five-month-pregnant Swiss Braunvieh cow. METHODS: Repositioning of the displaced uterus and descending duodenum without transection and anastomosis of the duodenum was performed through a right flank laparotomy. Concurrent displacement of a large portion of the small and large intestines into the omental bursa was not associated with intestinal strangulation and was corrected manually. The defects in the omentum and mesoduodenum were sutured. RESULTS: There were no postoperative complications, and the cow was healthy at discharge from the clinic 1 week after surgery. Telephone follow-up revealed that the cow had delivered a live calf and was producing a normal amount of milk. The cow was slaughtered 14 months after the surgery because of an udder problem. CONCLUSIONS: Herniation of the gravid uterus through a tear in the mesoduodenum with subsequent displacement of the descending duodenum around the uterus combined with internal omental herniation caused nonspecific clinical signs and no ileus. Exploratory laparotomy in an early stage of pregnancy facilitated reduction of the displaced uterus without transection of the descending duodenum

Splenectomy for treatment of suppurative splenitis caused by a reticular foreign body in a heifer

OBJECTIVE: To report the clinical findings and treatment of a heifer with suppurative splenitis. STUDY DESIGN: Clinical report. ANIMALS: A 30-month-old heifer. METHODS: Splenectomy in the standing calf after local anesthesia and 13th rib resection. RESULTS: The heifer had an uneventful recovery but was culled because of septic tarsitis 3 months later. CONCLUSIONS: Splenectomy is a useful treatment for cattle with traumatic splenitis if diagnosed early. Partial splenectomy may have prevented the late complication of septic tarsitis. CLINICAL RELEVANCE: Suppurative splenitis is usually a complication of hardware disease and has a grave prognosis unless splenectomy is carried out

A new TADA-inspired decision algorithm for training primary care practitioners in dermoscopy.

DEAR EDITOR, Dermoscopy has proven to be an effective tool for triaging suspicious skin lesions when performed by properly trained primary care practitioners (PCPs). In this regard, several dermoscopic training programs have been developed and demonstrated to improve the PCPs' skills for skin tumour triage in the short term. However, the skills acquired tended to regress rapidly after most trainings. […

Clinical findings and treatment in cattle with caecal dilatation

BACKGROUND: This retrospective study describes the clinical and laboratory findings, treatment and outcome of 461 cattle with caecal dilatation. RESULTS: The general condition and demeanor were abnormal in 93.1% of cases, and 32.1% of the patients had colic. Ruminal motility was reduced or absent in 78.3% of cattle. In 82.6% of cases, swinging and/or percussion auscultation were positive on the right side, and 82.4% had little or no faeces in the rectum. Caecal dilatation could be diagnosed via rectal palpation in 405 (88.0%) cattle. There was caudal displacement of the dilated caecum in 291 patients, torsion around the longitudinal axis in 20 and retroflexion in 94. The most important laboratory finding was hypocalcaemia, which occurred in 85.1% of cases. Of the 461 cattle, 122 (26.5%) initially received conservative therapy (intravenous fluids, neostigmine, calcium borogluconate) and 329 (71.4%) underwent surgical treatment. Ten patients were slaughtered or euthanased after the initial physical examination. Of the 122 cattle that received conservative treatment, 42 did not respond after one to two days of therapy and required surgical treatment. The final number of cattle that were operated was 371 (80.5%). Because of a grave prognosis, 24 cases were euthanased or slaughtered intraoperatively. Another 24 cattle did not respond to one or more operations and were euthanased or slaughtered. Of the 461 patients, 403 (87.4%) responded to either conservative or surgical treatment and were cured, and 58 were euthanased or slaughtered. CONCLUSIONS: Caecal dilatation can usually be diagnosed based on clinical findings and treated conservatively or surgically. Swinging and percussion auscultation as well as rectal examination are important diagnostic tools. Conservative treatment is not rewarding in cattle considered surgical candidates with suspected caecal torsion or retroflexion and surgery should not be delayed in these patients

Internal herniation of the small and large intestines in 18 cattle

Internal intestinal hernia was diagnosed during laparotomy in 18 cattle with a tentative diagnosis of ileus; the diagnosis was made during a second laparotomy in two cases. In 14 cattle, the hernial orifice was in the visceral layer of the greater omentum and the intestines had herniated into the caudal recess of the omental bursa. In two animals both the visceral and parietal layers had an opening; in one, the orifice was in the mesoduodenum, and in the other in the mesojejunum. The length of the hernial orifice ranged from 3 to >25cm and the length of the herniated intestine ranged from 30cm to the entire length of the small and large intestines. The omental rents were located near the caudal flexure of the duodenum (n=9), ventrally near the rumen (n=6) or in both of these locations (n=1). Seven cattle were euthanased intraoperatively because of incarceration of the jejunum; three of these had ruptured intestines and localised peritonitis; another animal was euthanased following a second laparotomy because of peritonitis. Ten animals, two of which underwent jejunal resection-anastomosis, recovered and were discharged. Nine of these survived a 6-month-postoperative period (mean±SD: 27±18months) and remained free of colic, and one was slaughtered 3months postoperatively because of rupture of the mammary suspensory ligament