LEARN: A multi-centre, cross-sectional evaluation of Urology teaching in UK medical schools

OBJECTIVE: To evaluate the status of UK undergraduate urology teaching against the British Association of Urological Surgeons (BAUS) Undergraduate Syllabus for Urology. Secondary objectives included evaluating the type and quantity of teaching provided, the reported performance rate of General Medical Council (GMC)-mandated urological procedures, and the proportion of undergraduates considering urology as a career. MATERIALS AND METHODS: LEARN was a national multicentre cross-sectional study. Year 2 to Year 5 medical students and FY1 doctors were invited to complete a survey between 3rd October and 20th December 2020, retrospectively assessing the urology teaching received to date. Results are reported according to the Checklist for Reporting Results of Internet E-Surveys (CHERRIES). RESULTS: 7,063/8,346 (84.6%) responses from all 39 UK medical schools were included; 1,127/7,063 (16.0%) were from Foundation Year (FY) 1 doctors, who reported that the most frequently taught topics in undergraduate training were on urinary tract infection (96.5%), acute kidney injury (95.9%) and haematuria (94.4%). The most infrequently taught topics were male urinary incontinence (59.4%), male infertility (52.4%) and erectile dysfunction (43.8%). Male and female catheterisation on patients as undergraduates was performed by 92.1% and 73.0% of FY1 doctors respectively, and 16.9% had considered a career in urology. Theory based teaching was mainly prevalent in the early years of medical school, with clinical skills teaching, and clinical placements in the later years of medical school. 20.1% of FY1 doctors reported no undergraduate clinical attachment in urology. CONCLUSION: LEARN is the largest ever evaluation of undergraduate urology teaching. In the UK, teaching seemed satisfactory as evaluated by the BAUS undergraduate syllabus. However, many students report having no clinical attachments in Urology and some newly qualified doctors report never having inserted a catheter, which is a GMC mandated requirement. We recommend a greater emphasis on undergraduate clinical exposure to urology and stricter adherence to GMC mandated procedures

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

TABLE 3. NISP, MNE, and MNI of Isisfordia duncani specimens from Isisford.

Summary of the Isisfordia duncani fossil elements recovered from the Isisford locality, including the number of identified specimens—where ‘specimens’ refers to the number of bone fragments—recovered per taxon (NISP), minimum number of elements (MNE) which may comprise multiple fragments each, and minimum number of individuals (MNI). We have included totals both without dermal skeletal units (as NISP and MNE), and with dermal skeletal units such as osteoderms included (as NISP inc. ost. and MNE inc. ost.). The relatively high NISP and MNE compared to MNI for I. duncani indicates that the majority of individuals comprise a multitude of articulated and/or closely associated skeletal elements. Approximate size range taken from and estimated using Salisbury et al. [66]

Data from: Taphonomy of Isisfordia duncani specimens from the Lower Cretaceous (upper Albian) portion of the Winton Formation, Isisford, central-west Queensland

Taphonomic analysis of fossil material can benefit from including the results of actualistic decay experiments. This is crucial in determining the autochthony or allochthony of fossils of juvenile and adult Isisfordia duncani, a basal eusuchian from the Lower Cretaceous (upper Albian) distal-fluvial-deltaic lower Winton Formation near Isisford. The taphonomic characteristics of the I. duncani fossils were documented using a combination of traditional taphonomic analysis alongside already published actualistic decay data from juvenile Crocodylus porosus carcasses. We found that the I. duncani holotype, paratypes, and referred specimens show little signs of weathering and no signs of abrasion. Disarticulated skeletal elements are often found in close proximity to the rest of the otherwise articulated skeleton. The isolated and disarticulated skeletal elements identified, commonly cranial, maxillary, and mandibular elements, are typical of lag deposits. The holotype QM F36211 and paratype QMF34642 were classified as autochthonous, and the remaining I. duncani paratypes and referred specimens are parautochthonous. We propose that I. duncani inhabited upper and lower delta plains near the Eromanga Sea in life. Their carcasses were buried in sediment-laden floodwaters in delta plain overbank and distributary channel deposits. Future studies should refer to I. duncani as a brackish water tolerant species

TABLE 5. Table incorporating all other taphonomic classification systems used in this study of the I. duncani specimens from Isisford [13,16,20,26–28,32,101–104,106–114] that were used in conjunction with Table IV in Dodson [19] and trends classified by Beardmore et al. [40].

Table incorporating all other taphonomic classification systems used in this study of the I. duncani specimens from Isisford [13,16,20,26–28,32,101–104,106–114] that were used in conjunction with Table IV in Dodson [19] and trends classified by Beardmore et al. [40]. We also chose to include counts of number of individual specimens (NISP) and minimum number of elements (MNE) with and without osteoderms, for ease of comparison in future with other tetrapods lacking dermal skeletons. The maximum number of skeletal elements in I. duncani, both excluding and including osteoderms, are listed next to MNE. Specimens QM F58793 and QM F58794 were found in close proximity, therefore NISP, MNE, and MNI are listed both grouped together (MNI = 2), and separately, to demonstrate the variation in NISP and MNE per individual. Where possible, life stage was determined by identifying closure neurocentral sutures in vertebrae (closure proceeds caudally to cranially throughout ontogeny, with ‘adult’ defined as possessing closed neurocentral sutures in all vertebrae) and size comparison to the holotype that has been identified as an adult (see Salisbury et al. [66]). By comparing across specimen numbers, we determined whether disarticulated elements showed greater degrees of bone surface modifications. Degrees of articulation and completeness are the sum total of scores for each skeletal unit. The Dodson [19] classification scheme assumes absences are true absences; we selected the most likely class per specimen based on other taphonomic indicators (such as truncation with block, articulation versus completeness, and so on)

Data from: Taphonomy of Isisfordia duncani specimens from the Lower Cretaceous (upper Albian) portion of the Winton Formation, Isisford, central-west Queensland

Taphonomic analysis of fossil material can benefit from including the results of actualistic decay experiments. This is crucial in determining the autochthony or allochthony of fossils of juvenile and adult Isisfordia duncani, a basal eusuchian from the Lower Cretaceous (upper Albian) distal-fluvial-deltaic lower Winton Formation near Isisford. The taphonomic characteristics of the I. duncani fossils were documented using a combination of traditional taphonomic analysis alongside already published actualistic decay data from juvenile Crocodylus porosus carcasses. We found that the I. duncani holotype, paratypes, and referred specimens show little signs of weathering and no signs of abrasion. Disarticulated skeletal elements are often found in close proximity to the rest of the otherwise articulated skeleton. The isolated and disarticulated skeletal elements identified, commonly cranial, maxillary, and mandibular elements, are typical of lag deposits. The holotype QM F36211 and paratype QMF34642 were classified as autochthonous, and the remaining I. duncani paratypes and referred specimens are parautochthonous. We propose that I. duncani inhabited upper and lower delta plains near the Eromanga Sea in life. Their carcasses were buried in sediment-laden floodwaters in delta plain overbank and distributary channel deposits. Future studies should refer to I. duncani as a brackish water tolerant species

Patterns of aquatic decay and disarticulation in juvenile Indo-Pacific crocodiles (Crocodylus porosus), and implications for the taphonomic interpretation of fossil crocodyliform material

High levels of skeletal articulation and completeness in fossil crocodyliforms are commonly attributed to rapid burial, with decreasing articulation and completeness thought to result from prolonged decay of soft tissue and the loss of skeletal connectivity during 'bloat and float. These interpretations are based largely on patterns of decay in modern mammalian and avian dinosaur carcasses. To address this issue, we assessed the decay of buried and unburied juvenile Crocodylus porosus carcasses in a controlled freshwater setting. The carcasses progressed through typical vertebrate decay stages (fresh, bloated, active decay, and advanced decay), reaching the final skeletal stage on average 55 days after death. Unburied carcasses commenced floating five days postmortem during the bloated stage, and one buried carcass only commenced floating 12 days post-mortem. While floating, skeletal elements remained articulated within the still coherent dermis, except for thoracic ribs, ischia and pubic bones. The majority of disarticulation occurred at the sediment-water interface after the carcasses sank during the advanced decay stage, -36 days post-mortem. Based on these results we conclude that fossil crocodyliform specimens displaying high levels of articulation are not the result of prolonged subaerial and subaqueous decay in a low-energy, aqueous environment. Using extant juvenile C porosus as a proxy for fossil crocodyliforms, rapid burial in an aquatic setting would have to occur prior to the carcass floating, and would also have to continually negate the positive buoyancy associated with bloating. Rapid burial does not have to be the only avenue to preservation of articulation, as other mechanisms such as physical barriers and internal physiological chemistry could prevent carcasses from floating and subsequently disarticulating upon sinking. The inference that a large proportion of skeletal elements could drift from floating carcasses in a low energy setting with minimal scavenging, thereby causing a loss of completeness, seems unlikely. (c) 2014 Elsevier B.V. All rights reserved

TABLE 4. Completeness (Cp.) and articulation (Art.) scores for I. duncani specimens from Isisford (following Beardmore et al. (2012); Syme and Salisbury (2014)).

Completeness (Cp.) and articulation (Art.) scores for I. duncani specimens from Isisford. As per Beardmore et al. [40], Xp denotes skeletal units that are not visible due to truncation with the edge of the block or blocks missing, and Xh denotes skeletal obscured by matrix or overlying skeletal elements. Beardmore et al. [40] propose that specimens with 3 instances of either Xp or Xh in the dataset should be omitted from further analysis: in this instance, all specimens except the holotype QM F36211 were excluded from further analyses (denoted by ‘--’). The average completeness and articulation for QM F36211 was calculated both with and without the dermal skeletal units: with the dermal skeletal units, compared to a maximum total score of 36 (4 for each of the 9 of 11 units omitting Xp/Xh data); without the dermal skeletal units, compared to a maximum total score of 28 (4 for each of the 7 of 9 units omitting Xp/Xh data). The data was then compared with the trend lines proposed by Beardmore et al. [40] where possible

Depositional environment of the lower cretaceous (upper Albian) Winton Formation at Isisford, central-west Queensland, Australia, inferred from sandstone concretions

Numerous vertebrate and plant fossils have been found in ex-situ sandstone concretions near Isisford in central-west Queensland since the mid-1990s. These concretions are found in the Lower Cretaceous portion (upper Albian, 100.5-102.2 Ma) of the Winton Formation. The lower most Winton Formation is thought to have formed in a fluvial channel or flood-basin setting proximal to the Eromanga Sea, but due to the scarcity of good exposures, the local depositional environment at Isisford has not been ascertained. Minimal compression of vertebrate and plant fossils, a lack of grain suturing, predominantly cement-supported fabric, and fractures running through calcite cement, as well as fossil bone and framework grains, indicates that concretions formed during early diagenesis (pre-compactional or syndepositional). Calcite stable-isotope δ¹⁸O(VPDB) values range from -12.25 to -4%₀, indicating mixed marine and meteoric pore waters, and δ¹³C(VPDB) values range from -5.3 to 4.1%₀, indicative of both sulfate reduction and methanogenesis of organic material (including decaying vertebrate soft tissues) in the burial environment. The mixed marine and freshwater signature suggests a marginal marine setting, possibly deltaic or estuarine, connected to the regressive epicontinental Eromanga Seaway at around 102-100 Ma. This is not inconsistent with the lithology from nearby cores, coupled with Isisford fossil-vertebrate ecology (personal observation). Our research demonstrates the utility of investigating ex-situ concretions to refine paleoenvironments at localities where little or no outcrop is available and traditional facies analysis is impractical