Making bioinformatics training FAIR: the EMBL-EBI training portal

EMBL-EBI provides a broad range of training in data-driven life sciences. To improve awareness and access to training course listings and to make digital learning materials findable and simple to use, the EMBL-EBI Training website, www.ebi.ac.uk/training, was redesigned and restructured. To provide a framework for the redesign of the website, the FAIR (findable, accessible, interoperable, reusable) principles were applied to both the listings of live training courses and the presentation of on-demand training content. Each of the FAIR principles guided decisions on the choice of technology used to develop the website, including the details provided about training and the way in which training was presented. Since its release the openly accessible website has been accessed by an average of 58,492 users a month. There have also been over 12,000 unique users creating accounts since the functionality was added in March 2022, allowing these users to track their learning and record completion of training. Development of the website was completed using the Agile Scrum project management methodology and a focus on user experience. This framework continues to be used now that the website is live for the maintenance and improvement of the website, as feedback continues to be collected and further ways to make training FAIR are identified. Here, we describe the process of making EMBL-EBI's training FAIR through the development of a new website and our experience of implementing Agile Scrum.

Hemihamate arthroplasties in pilon fractures: a modified approach and experience in 30 patients

Hemihamate arthroplasty is an established method of managing difficult Pilon fractures of the proximal interphalangeal (PIP) joint. We present our experience in 30 patients, whose injuries were further complicated by severe comminution and late presentations. Several modifications were utilized, including preoperative distraction, use of smaller size grafts and functional release of collaterals. The average follow-up period was 28 months (range 18 to 28). Postoperatively, the average range of flexion at the PIP joint improved from 30° (range 20° to 45°) preoperatively to 104° (90° to 110°) at the final follow-up. The average extension lag was 6° (0° to 20°). Five patients required secondary procedures and no patient had a recurrent dorsal dislocation. We propose these modifications in the use of hemihamate arthroplasty for the management of difficult PIP joint fractures.Level of evidence: IV.

Assessing the Usability of Flexor Digiti Minimi Muscle for Opponensplasty: An Anatomic Study

PURPOSE

The abductor digiti minimi (ADM) and flexor digiti minimi (FDM) muscles have a similar vascular and nerve supply. The purpose of this study was to assess the feasibility of transferring the FDM instead of ADM for thumb opposition.

METHODS

Thirty cadaver hands were dissected under loupe magnification to assess the presence of the ADM and FDM muscles as well as their blood and nerve supply. The length of these muscles and their location in relation to the radial aspect of the thumb metacarpophalangeal joint were assessed.

RESULTS

The ADM muscle was present in all cadavers whereas the FDM muscle was absent in 33% of hands. When the dimensions were suitable (53%), the more radially located FDM muscle reached the thumb metacarpophalangeal joint more easily.

CONCLUSIONS

Although the dissections revealed considerable variability in FDM anatomy, when present, it can have positional advantage over the ADM for opponensplasty.

CLINICAL RELEVANCE

In some cases with radial longitudinal deficiency, preservation of ADM function is essential. In these children, the FDM can potentially be explored and transferred if it is found to be suitable.

Release of Extensive Post Traumatic Radio-Ulnar Synostosis with Vascularized Free Flap Interposition

Radioulnar synostosis is a rare complication after a forearm or elbow injury. The severity of initial trauma, associated head injury along with timing and the type of surgical treatment have been implicated in the formation of extra bone leading to synostosis. Surgical intervention is the standard treatment and is recommended after the maturation of synostotic bone. Surgery involves resection of the extra bone with or without tissue interposition. Materials used for interposition may include synthetic materials, allografts, and vascularized and non-vascularized autologous tissue superiority of one material over the other has not been demonstrated. Reported is a case of extensive soft-tissue defect and severe type II synostosis, with a relevant review of the literature. Level of Evidence Level IV.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s43465-021-00395-5.

Functional Outcome Following Hand and Wrist Level Replantation: A Retrospective Review

Objective: Amputations of fingers and significant parts of upper limbs are common following industrial injuries. This study was aimed at assessing the functional outcome in patients with hand replantation following amputation at the level of distal forearm or wrist. Methods: Patients presenting with amputation at the level of wrist and forearm between Jan 2015 and December 1018, with adequate follow up were included. The function in terms of total active motion at the fingers and wrist, sensory recovery, and patient satisfaction and DASH scores at the final follow up were noted. Results: Four cases of replantation at the level of wrist and one replantation at distal forearm level were included in the study. A total of 3 patients were excluded for various reasons. The average follow-up period was 38 months. The average total active motion of fingers achieved was 212○ . All patients recovered protective sensations. Conclusion: Replantation of amputated major upper limb parts restores useful function and should be attempted. Minimizing ischaemia time, secure fixation, primary repair of structures and early motion are determinants of reasonable functional outcome. Level of evidence: IV.

Replantation of Nine Fingers in a Patient: A case report

Amputation of multiple fingers of both hands is a rare and serious injury. We report a case of a 41-year-old male patient who presented to Khoula Hospital, Muscat, Oman, in 2015 with the amputation of nine fingers due to a workplace injury. With two teams working in tandem, all the amputated fingers were re-attached. A total of seven fingers survived and the patient regained reasonable functionality of his hands. To the best of the authors' knowledge, this is the first case of several finger amputations in Oman.

Effective use of simple computer programmes and clay models to demonstrate the planning and operative steps for teaching and presentations

Background:

Presenting and demonstrating a surgical procedure in the current era is difficult without good intraoperative pictures and videos. A long, complex, multi-staged surgery is better illustrated by detailed intraoperative images at various stages. Although desirable, it may be difficult due to various reasons.

Material and Methods:

A simple method of preparing illustrations with pictures/diagrams created on PowerPoint and clay models to recreate the missing links in clinical photographs has been proposed.

Results:

It is a simple technique with a moderate learning curve. Once familiar with technique, one can effectively use the technique to convey the details in much more clear manner.

Conclusion:

It is a simple and effective way of communicating through digital images, and gives the audience a 3 dimensional idea about the concept.

Modified serial extraction in a case with missing mandibular second premolars and a brief review of related treatment modalities

This article discusses a case of an 8-year-old female child who presented with severe lower anterior crowding and congenitally missing lower second premolars. A conventional serial extraction procedure could not be performed due to the congenital absence of teeth. Instead, planned extraction of a few primary teeth was done to relieve the lower anterior crowding, the results of which were near satisfactory.

An uncommon presentation of giant cell tumor

Giant Cell Tumors commonly occur at the ends of long bones. However in rare cases, they can occur in the bones of the hands and feet. Tumors in these locations occur in younger patients; in addition, these tumors are more commonly multifocal and are associated with a higher risk for local recurrence than tumors at the ends of long bones. Since lesions in the small bones may be multifocal, a patient with a giant cell tumor of the small bones should undergo a skeletal survey to exclude similar lesions elsewhere. Primary surgical treatment ranges from curettage or excision with or without bone grafting to amputation. The success of surgical treatment depends on the completeness with which the tumor was removed. We are presenting a case report of a 34 year old female, who presented with a swelling in the right hand, following trauma. X-ray of the hand showed an osteolytic expansile lesion at the base of the 1(st) metacarpal bone. The lesion was initially curetted and then treated by local resection with bone grafting. Histological examination revealed a typical benign giant cell tumor composed of closely packed stromal cells with a variable admixture of giant cells. Follow up at the end of one year did not reveal any recurrence of the tumor.

A novel metered dose transdermal spray formulation for oxybutynin

The objective of the present work was to develop a metered dose spray formulation for transdermal delivery of oxybutynin and to carry out the in vitro characterization of the optimized formulation. Oxybutynin release from a series of ethanol/acetone/methylal based formulations was assessed in vitro and the developed formulation was used for delivery from a metered dose spray. Various qualitative and quantitative parameters like spray pattern, particle size distribution, pH, evaporation time, pump seal efficiency test, average weight per metered dose, content per spray and content uniformity were evaluated. The different film forming agents were assessed and carbopol (0.5%) and lutrol (0.1%) were found to give good clarity of solution, evaporation rate, spray pattern and tackiness of the film. Diffusion studies of the optimized formulations through the semipermeable membrane showed the release of drug to the extent of almost 50% over a period of 24 h. Stability studies were conducted as per ICH guidelines and indicated that formulations were stable. Skin irritation studies were performed using rabbit as an animal model. The results obtained show that the metered dose transdermal spray formulation can be a promising and innovative therapeutic system for the transdermal administration of oxybutynin.

Actions and comparative efficacy of phosphatidylcholine formulation and isolated sodium deoxycholate for different cell types

BACKGROUND

Phosphatidylcholine formulation has been used to dissolve local fat deposits. This study aimed to evaluate and compare the effects of phosphatidylcholine formulation and its vehicle sodium deoxycholate alone on different cell lines to understand better its mechanism of action.

METHODS

Cells and media including 3T3-L1 preadipocytes, normal foreskin fibroblasts, neonatal human dermal microvascular endothelial cells (CADMEC), and fetal human skeletal muscle cells (HSkMC) were used. After 24 h, cells were exposed in 3-4, 5-dimethylthiazol-2-yl-2, 3-diphenyl tetrazolium bromide reagent (MTT assays) to increasing dosages of phosphatidylcholine formulation (0.0156-0.5 mg/ml) or an equivalent vehicle, sodium deoxycholate solution, pH 9.0 (0.0066-0.210 mg/ml). Viability was assessed after 1, 2, and 3 days of treatment. Fat tissue (4 x 4 cm) obtained ex vivo from the dorsal fat pads of five rabbits was injected with 2 ml of phosphatidylcholine formulation (50 mg/ml), sodium deoxycholate (21 mg/ml), or normal saline and incubated for 24 h. These were examined histologically to identify cell lysis and morphologic changes.

RESULTS

At 0.125- and 0.25-mg/ml doses of phosphatidylcholine solution, CADMEC and HSkMC were more sensitive (P < 0.001, one-way ANOVA) than adipocytes at all time points examined. Phosphatidylcholine formulation at a dose of 0.5 mg/ml and the equivalent vehicle, sodium deoxycholate, at a dose of 0.21-mg/ml both induced nearly 100% fat cell lysis after 24 h, and evidence of cell lysis as early as 6 h after exposure. After incubation of fat tissue for 24 h with phosphatidylcholine formulation, loss of intracellular lipid staining with an increase in extracellular lipids was seen.

CONCLUSIONS

Isolated sodium deoxycholate was almost as effective as the phosphatidylcholine formulation, at clinical concentrations, in reducing the viability of mature adipocytes over time. Similar cytotoxic effects of phosphatidylcholine formulation on normal foreskin fibroblasts, endothelial cells, and human skeletal muscle cells also were observed. The data prove that the formulation acts in a nonspecific manner and that its unintentional administration to other tissues causes cell death.

Pacinian neuroma

Neural tumors composed of Pacinian corpuscles are rare and have only occasionally been reported in the literature. All such lesions, which have been reported to date, have been benign. One such lesion described here presented as a painful lesion on the right hand in a 17-year-old Omani female. There was history of trap door injury 7 years back involving the wrist, thumb and index finger. The patient gradually developed multiple bosselated nodules near the first web space with gradually increasing pain. This case is being reported for the first time in the Sultanate of Oman. We herein report this case due to its rarity.

Massive subfascial hematoma after alteplase therapy for acute myocardial infarction

The authors report a case of a patient who received alteplase for acute myocardial infarction and developed spontaneous subfascial hematoma without any evidence of direct trauma. Subfascial hematoma remains a rare and self-limited complication of thrombolytic therapy. The development of cutaneous ecchymosis associated with a sudden fall in hemoglobin after the administration of alteplase should strongly suggest the possibility of diffuse subfascial hematoma. Physicians should be aware of the possible association between the use of alteplase and the development of subfascial hemorrhage.