bluuebunny/crossref_metadata_2025_split huggingface dataset:
Feature-based translation of CAD models with macro-parametric approach: issues of feature mapping, persistent naming, and constraint translation
Authors: Safdar Mutahar , Jauhar Tahir Abbas , Kim Youngki , Lee Hanra , Noh Chiho , Kim Hyebin , Lee Inhwan , Kim Imgyu , Kwon Soonjo , Han Soonhung 
Published: March 2020

Abstract
Feature-based translation of computer-aided design (CAD) models allows designers to preserve the modeling history as a series of modeling operations. Modeling operations or features contain information that is required to modify CAD models to create different variants. Conventional formats, including the standard for the exchange of product model data or the initial graphics exchange specification, cannot preserve design intent and only geometric models can be exchanged. As a result, it is not possible to modify these models after their exchange. Macro-parametric approach (MPA) is a method for exchanging feature-based CAD models among heterogeneous CAD systems. TransCAD, a CAD system for inter-CAD translation, is based on this approach. Translators based on MPA were implemented and tested for exchange between two commercial CAD systems. The issues found during the test rallies are reported and analyzed in this work. MPA can be further extended to remaining features and constraints for exchange between commercial CAD systems.
Relative Insect Frequency and Species Richness on Sun-Exposed and Shaded Rabbit Carrions
Authors: Mashaly Ashraf , Mahmoud Ahmed , Ebaid Hossam 
Published: March 2020

Abstract
On rabbit carcasses (Oryctolagus cuniculus L.) exposed in open and shaded habitats, the relative abundance of insects and species richness were observed. The decomposition process was classified into four stages: fresh, bloated, decayed, and dry. Except for the decayed stage, the elapsed time for each stage of decomposition was similar between open and shaded habitats, with all carcasses reaching dryness in 13 and 14 d, respectively. In total, 2009 insects were collected during the decomposition process with 1,863 flies belonging to seven families and 15 species, and 146 beetles belonging to six species and three families. Insect abundances rose between the fresh and decay stages. The dominant families of insects included Calliphoridae and Muscidae (80.9% of the collected insects) and accounting for 38.07% of the species richness, whereas Histeridae accounted for 4.3% of the collected insects and 14.29% of the species richness. The open habitat attracted 1,233 insects belonging to 18 families, including 1,142 flies and 91 beetles, whereas the shaded habitat attracted 776 insects belonging to 18 families, including 721 flies and 55 beetles. Diversity level and ratios of exclusive species are also reported for each habitat (open 61.4%; shaded 38.6%). Between habitats, there were substantially separate insect communities, however. In addition, there was a substantial difference in the insect number and species between decomposition stages. This study demonstrates that the exposure status needs to be evaluated and examined when estimating the time since death.
Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks
Authors: Madrid-Mencía Miguel , Raineri Emanuele , Cao Tran Bich Ngoc , Pancaldi Vera 
Published: March 2020

AbstractWe introduce an R package and a web-based visualization tool for the representation, analysis and integration of epigenomic data in the context of 3D chromatin interaction networks. GARDEN-NET allows for the projection of user-submitted genomic features on pre-loaded chromatin interaction networks, exploiting the functionalities of the ChAseR package to explore the features in combination with chromatin network topology properties. We demonstrate the approach using published epigenomic and chromatin structure datasets in haematopoietic cells, including a collection of gene expression, DNA methylation and histone modifications data in primary healthy myeloid cells from hundreds of individuals. These datasets allow us to test the robustness of chromatin assortativity, which highlights which epigenomic features, alone or in combination, are more strongly associated with 3D genome architecture. We find evidence for genomic regions with specific histone modifications, DNA methylation, and gene expression levels to be forming preferential contacts in 3D nuclear space, to a different extent depending on the cell type and lineage. Finally, we examine replication timing data and find it to be the genomic feature most strongly associated with overall 3D chromatin organization at multiple scales, consistent with previous results from the literature.
In-Hospital Illicit Drug Use and Patient-Directed Discharge: Barriers to Care for Patients With Injection-Related Infections
Authors: Eaton Ellen F , Westfall Andrew O , McClesky Brandi , Paddock Cayce S , Lane Peter S , Cropsey Karen L , Lee Rachael A 
Published: March 2020

Abstract

Background
Hospitalized persons who inject drugs are at a greater risk of adverse hospital outcomes including discharge against medical advice, inpatient illicit drug use, overdose, and death. However, there are limited data on the frequency and outcomes of these events in the United States.

Methods
This retrospective analysis included patients with injection-related infections receiving a protocol for injection drug use (IDU) at University of Alabama at Birmingham Hospital from 2016 to 2017. In-hospital IDU was suspected or reported drug usage plus confirmatory drug screen, and documented discharges “against medical advice” were deemed patient-directed discharges (PDD). We analyzed the frequency of and associations between in-hospital IDU, PDD, 30-day readmission, and deaths (between 2016 and 2019) using McNemar’s tests. Logistic regression models evaluated the association between PDD, in-hospital IDU, readmission, and death.

Results
Overall, 83 patients met inclusion criteria: 28 (34%) with in-hospital IDU, 12 (14%) PDD, 9 (11%) died, and 12 (14%) 30-day readmission. In-hospital IDU was significantly associated with PDD (P = .003), 30-day readmission (P = .005), and death (P = .0003). Patient-directed discharges and 30-day readmission were not significantly associated with death nor with each other.

Conclusions
In a cohort of patients receiving inpatient care for injection-related infections, illicit drug use, PDD, 30-day readmissions, and death were common. Furthermore, patients who use illicit drugs while hospitalized are significantly more likely to leave early, be readmitted, and/or die. We must design models of care that prevent adverse outcomes, including drug use and PDD, to reduce barriers to evidence-based treatment of infections.
Effect of expanding nanocellulose sponge on nasal mucosal defects in an animal model
Authors: Kim Ji Won , Woo Kyungbae , Kim Jeong Mi , Choi Mi Eun , Kim Young-Mo , Yang Su-Geun , Shim Bong Sup , Choi Jeong-Seok 
Published: March 2020

Abstract
Nanocellulose has emerged for a wide range of applications in biomedical engineering because of its water absorption capacity, appropriate elasticity. We investigated the hemostatic and regenerative abilities of an expanding polyvinyl alcohol (PVA)-nanocellulose sponge on nasal mucosal defects. A 3 mm-diameter nasal defect was made in experimental rabbits. Rabbits were divided into four groups with control, vaseline, PVA and PVA-nanocellulose packing groups. After the defect was created, bleeding times and amounts were monitored. Packing materials were removed on experimental day (ED) 2. On ED 3, 7 and 14, histological analysis and immunohistochemical study for neutrophils were performed. Inflammatory cells were counted and epithelial thicknesses were evaluated. Bleeding amounts and times in the vaseline packing group were smaller than in the PVA groups. PVA-nanocellulose group showed less neutrophils than in the other groups on ED 7. Average epithelium thickness in the PVA-nanocellulose group was significantly smaller than in the control group at ED 7, but at ED 14, there was no significant intergroup difference. PVA-nanocellulose group had a significant lower inflammatory cell count than the control group on ED 7. PVA-nanocellulose sponge applied to nasal mucosal defects can significantly enhance mucosal regeneration during early wound healing.
Investigating the microbial composition of Recurrent Vulvovaginal Candidiasis samples and biofilm formation of Candida clinical isolates
Authors: McKloud Emily , Sherry Leighann , Kean Ryan , Delaney Christopher , Metcalfe Rebecca , Ramage Gordon 
Published: March 2020

Recurrent vulvovaginal candidiasis (RVVC) is a chronic and debilitating condition that is estimated to affect 138 million women annually. In spite of this high prevalence and its associated economic burden, pathogenesis of disease is poorly understood. The biofilm-forming yeast Candida albicans is reported as the causative pathogen in up to 90% of VVC cases and around 50% in RVVC disease. Despite the identification of Candidabiofilms on the vaginal mucosa, their associated therapeutic challenge in RVVC is still disputed.
A panel of 100 HVS and cervico-vaginal lavage (CVL) samples were obtained for this trial. Patient questionnaires collected data on patient’s vaginal thrush history, treatments and any contraception currently used. Microbiological screening of clinical samples was performed, and microbiome analysis was utilized to determine predominant microbes present in each cohort.
Non-C. albicans species (NCAS) such as intrinsically azole-resistant C. glabrata were found to account for 27% of RVVC cases, notably higher than historically reported. Additionally, microbiome analysis showed a reduction in Lactobacillus species associated with a healthy microbiome in RVVC compared to health.
This study supports a previous clinical trial by our group using 300 HVS to investigate the epidemiology of RVVC showing an increasing prevalence of NCAS responsible for disease. Additionally, this work strengthens the hypothesis that formation of Candida biofilms on the vaginal mucosa could negatively impact clinical treatment. Further research to identify triggers for RVVC, and the pathogenesis of the predominant microbes involved, could considerably improve prevention and treatment options for women with recurrent, azole-resistant infections.
Development of a licenced Faecal Microbiota Transplantation service for the treatment of patients in the NHS
Authors: McCune Victoria , Manzoor Susan , Shabir Sahida , Quraishi Mohammed Nabil , Sharma Naveen , Hawkey Peter , Iqbal Tariq 
Published: March 2020

Introduction: Faecal microbiota transplantation (FMT) is an effective and licensed treatment for recurrent and refractory Clostridium difficile infection (CDI) and has shown encouraging signals for treatment of ulcerative colitis (UC). Access to FMT has been limited by the introduction of new regulations in the UK. Centres producing FMT are now required to hold a manufacturing licence from the Medicines and Healthcare products Regulatory Agency (MHRA).
Methods:The first licenced FMT service in UK - University of Birmingham Microbiome Treatment Centre (UoBMTC) was launched in 2017. Policies and procedures were developed in accordance with MHRA ‘Good Manufacturing Practice’ guide.
Results: Since August 2018, 132 FMT aliquots have been supplied for recurrent and refractory CDI to 39 NHS Trusts across UK. Twenty-nine of these Trusts did not have access / perform FMT prior to this service. In all cases, FMT was delivered within 48 hours (unless delayed delivery was requested). The service is the sole supplier of FMT since 2018 via an NHS Innovation and Technology Tariff. UoBMTC has also to date supplied 360 FMT aliquots for a multi-centre trial of FMT in UC (STOP-Colitis). Furthermore, the service has provided FMT to other refractory conditions within clinical settings.
Conclusions: Development of a licenced FMT facility has greatly enhanced equality of access for this treatment across the NHS. FMT is provided at a zero-cost model for CDI and is available within 48 hours of request. UoBMTC continues to facilitate research in this field by providing FMT for clinical trials exploring its use for other indications.
UK Paediatric Antimicrobial Stewardship: a call for action
Authors: Vergnano Stefania , Chappell Faye , Bamford Alasdair , Demirjian Alicia , Doerholt Katja , Emonts Marieke , Goenka Anu , Jones Laura , Herberg Jethro Herberg , Hinds Lucy Hinds , McGarrity Orlagh , Moriarty Paul , Patel Mitul , Paulus Stephane , Porter David , Stock Kate , Patel Sanjay 
Published: March 2020

Background:
Paediatric antimicrobial stewardship (PAS) networks exist in the USA and Australia but not in the UK. We sought to capture a snapshot of the current PAS landscape across UK children’s hospitals.

Methods:
A survey of PAS activities was conducted in tertiary children’s hospitals.

Results:
Infectious disease or microbiology consultants responded to the survey (n=15). All hospitals had neonatal, paediatric intensive care and surgical patients.All centres provided a PAS education programme for doctors, 7 for nurses and 9 for pharmacists as well. All centres had empirical antimicrobial prescribing guidelines. All centres with a paediatric infectious diseases (PID) team (11/15) used “audit and feedback” rounds, although their frequency and coverage varied. The PAS teams mostly included a PID consultant and/or microbiology consultants and a pharmacist. Three centres also had a nurse covering also the paediatric out-patient antibiotic treatment programme. Funding for PAS were inconsistent: Great Ormond Street Hospital had secured a dedicated full-time paediatric microbiologist, antimicrobial pharmacist and PID consultant with a ratio of 1/453 in-patient beds. 9 centres did not have dedicated funding for a paediatric antimicrobial pharmacist, 7 did not have funding for a paediatric infectious disease consultant. Only 2 hospitals had microbiology consultant time for paediatric audit and feedback.

Conclusion:
PAS programmes in the UK are limited, funding is inconsistent and their set up is variable, even in tertiary children’s hospitals with a strong interest in infectious diseases. We propose a national PAS network to advocate for more consistency and research into the implementation of PAS programmes.
A qualitative study on factors influencing the implementation of a Clostridium difficile risk prediction tool in the Scottish secondary care setting
Authors: A. Ansu Joseph , Kurdi Amanj , Bennie Marion 
Published: March 2020

Introduction: Clostridium difficile is the leading cause of hospital-acquired diarrhoea, driven mainly by the consumption of 4C antibiotics (co-amoxiclav, clindamycin, cephalosporins and ciprofloxacin). In order to support secondary care clinicians in prescribing antibiotics, an algorithm helping to identify patients at high risk of contracting Clostridium difficile infections (CDI) has been created. The aim of this study was to identify factors that are influencing the implementation of a risk predictive tool in secondary care, focusing on podiatrist as potential users.
Methods: Four podiatrists from NHS Fife were interviewed to gather their perception of CDI, the antibiotic prescription process, and the usefulness of a CDI tool in supporting their antibiotic prescribing decisions. The interviews were thematically analysed in NVivo using the consolidated framework for implementation research.
Result: A facilitator emerged during the interviews suggested that, although podiatrists tend to not prescribe 4C antibiotics, they comprehend the risks involved with CDI. Therefore, for patient’s safety netting purposes, the use of the CDI tool during consultations was considered useful. However, a barrier emerged suggested that, although implementing the tool into their electronic system was deemed favourable, this isn't feasible, due to patient data in secondary care being allocated in different systems. Therefore, standalone app or website platforms were perceived as more appropriate to develop the CDI tool.
Conclusion: In general it was understood that podiatrists are supportive in having a CDI tool, however, due to the impossibility of implementation of the tool into their system, a website or app will be developed.
Co-Amoxiclav Prescribing in Renal Impairment
Authors: Nicolson Andrew , Baggott Amy 
Published: March 2020

Intro:
Co-amoxiclav use in Forth Valley Royal Hospital is significantly higher than any other acute hospital site in Scotland. The drug is metabolised and excreted renally and its dosage is dependent on renal function.

Methods:
An online questionnaire was sent to clinicans to ascertain their prescribing knowledge in renal impairment. Following this a review of all prescriptions of Co-Amoxiclav over a one month (19/02/19-19/03/19) period was reviewed and cross matched with patients renal function to determine those with a degree of kidney injury. Standard of dosing was compared against the BNF as most clinicians replied that this was their main prescribing resource.

Results:
774 patients were prescribed Co-Amoxiclav; 11.8 % (92) of these with a degree of renal impairment. Only 54% (50) of these patients were prescribed the correct dose of Co-Amoxiclav. 78 patients had an acute kidney injury (AKI) with 58% (45) prescribed the correct dose. In comparison 51% (47) of patients had a Chronic Kidney Injury (CKD) with only 33% (15) prescribed the correct dosage. This number is equally low in patients with an acute on chronic kidney injury; 35.8 % (33) patients with 30% (9) on the correct dose.

Conclusion:
46% of patients with a degree of kidney injury are being prescribed the wrong dosage of Co-Amoxiclav which may potentially result in patient harm or under treatment of their condition. Further education is required within the trust to ensure prescribers use correct sources including the Renal Handbook and consider alternative antibiotics in patients with renal impairment.
Easy to get, but not always easy to treat - Clinical and serological failure with Azithromycin in Syphilis: Time to adapt national guidelines?
Authors: Ogbonmwan Daisy , Schwab Uli 
Published: March 2020

Background
Data since 2014 has shown a rise in the incidence of Syphilis especially amongst heterosexuals. In national guidelines, Macrolides remain an alternative treatment option although their efficacy has been long disputed.
We describe a case of a patient with clinical and serological failure with Azithromycin treatment.
Methods
A 46 year old female presented with painful genital ulceration confirmed as primary syphilis. Sexual transmission infection testing was negative. She described an allergy (rash) to Amoxicillin and was given Doxycycline 100mg twice daily for 14 days. On day 5 she developed an urticarial rash and was changed to Azithromycin, 2g stat and 500mg daily for 10 days.

Results
There was initial serological response in her rapid plasma reagin (RPR) to 1:2 from 1:8 at 1 month, but at 5 months an RPR of 1:64 was seen with signs of secondary syphilis - a rash and a sore mouth. Re-infection was ruled out, she was re-treated with Azithromycin and her RPR reduced to 1:2, but she had a persistent macular rash.
Following review by Infectious Diseases, 14 days of intravenous Ceftriaxone 1g daily was given. On day 10, her RPR rose to 1:64 but 3 months after fell to 1:4 and has been serofast since without further signs of Syphilis.

Conclusion
Patients treated with Macrolides should be closely monitored. Consideration should be given for desensitisation in patients with reported Penicillin allergy. As with pregnancy, consideration should be given to the removal of Azithromycin as an alternative treatment in national guidelines.
A 1 year Tertiary Centre experience of Clostridium difficile infection
Authors: Walker Ieuan , Beinortas Tumas , Enoch David , Gouliouris Theodore 
Published: March 2020

Background

Clostridium difficile infection (CDI) adversely affects patient outcomes. CDI 30-day mortality is 15.2% nationally with some regional variation, but data on recurrence is limited. We assessed outcomes of CDI, in particular recurrence and mortality at Addenbrooke’s Hospital.
Methods
We performed a retrospective analysis of all patients who developed CDI between April 2017 and March 2018. All-cause mortality was assessed at 30 days and 1 year. Recurrence was defined as recurrence of symptoms withC. difficiletoxin positive stool or initiationof C. difficile treatment within 1-year after onset of first/previous episode. First-line therapy was metronidazole or vancomycin according to severity.
Clinical data was collected using a standardised proforma. Risk of recurrence was calculated using Cox’s Hazard method in R.

Results
143 cases of CDI in 103 patients were identified. The median age was 70 years (range 2-98). Recurrence rate was 24.6% at 12-weeks and 30.3% at 1-year. 30-day and 1-year mortality was 14.4% and 39.8%, respectively. Recurrences had longer mean length of stay compared to 1stepisodes (40.3 vs. 18 days, respectively, p<0.05). On univariate analysis, no factors predicted recurrence; acute kidney injury, C-reactive protein, toxic megacolon, Charlson comorbidity score and age predicted mortality.
Conclusions
CDI carries a significant mortality and recurrence rate placing a large burden on hospital resources. The majority of recurrences occur within 12 weeks of 1stepisode, and patients’ risk could not be accurately defined in this sample. Newer therapies with reported lower recurrence rates should be considered as 1stline therapy within our Trust.
Influenza Testing in the Emergency Department (ED): A Quality improvement project (QIP)
Authors: Patterson Charlotte , Sturdy Ann , Irish Dianne , Connor Hilary 
Published: March 2020

Background
Respiratory illness contributes significantly to higher ED attendance during winter months. Polymerase chain reaction (PCR) testing of nasopharyngeal swabs (NPS) for respiratory viruses is a key investigation, with positive influenza results having both clinical and infection control implications. In response to ED colleagues requesting clear and concise guidance, we undertook a QIP to improve management of seasonal influenza.
Methods
A survey of 10 questions was sent to all Doctors and Advanced Care Practitioners (ACPs) working in the ED, and the results collated.

Results
There were 21 survey respondents, the majority were registrars. 81% correctly identified how to request influenza testing and 95% knew the symptoms. 90% identified which risk groups should be treated, which personal protective equipment (PPE) should be donned, and suggested Oseltamavir as their treatment of choice. However only 29% of respondents knew where to find the trust guidelines and only 10% correctly prescribed prophylaxis to contacts. 95% would review a discharged case found to have influenza on testing and 67% would treat this case if they were in an at risk group.
Discussion and Conclusions
The results show that the majority of staff surveyed correctly identified the symptoms of flu, infection control precautions and those requiring treatment. However, knowledge regarding the location of guidelines, management of contacts and the use of agents other than oseltamivir was low. Based on these results we developed a single-page influenza testing algorithm aiming to improve management in A&E, and will reassess staff knowledge following the introduction of this.