bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of Laser and Ozone Pretreatment on the Shear Bond Strength of Fissure Sealants: An In Vitro Comparative Study
Authors: Çelik Neslihan , Yapar Merve Is¸can , Karalar Buket , Kılıç Münevver 
Published: September 2020

Aim: To evaluate the shear bond strength (SBS) of 3 fissure sealants used alone and with ozone and laser pretreatment. Materials and Methods: For the SBS test, the flattened enamel surfaces of 90 healthy third molars were randomly divided into nine groups ( n  =  10 for each groups), based on different sealants (BeautiSealant, Fuji Triage, and Grandio Seal) and pretreatment conditions (no pretreatment, pretreatment with ozone, and pretreatment with neodymium-doped yttrium aluminum garnet [Nd:YAG laser]). Ozone was applied for 30 s in caries superficial mode, and Nd:YAG laser was applied for 60 s. After the pretreatment procedures, sealants were placed inside a mold on the enamel surface. SBS was measured with a universal testing machine. Data were analyzed using analysis of variance. Tukey’s multiple comparison tests were applied to determine the difference between the groups (α  = 0.05). Results: The lowest SBS was observed in the Fuji triage group. Nd:YAG laser and ozone did not affect the SBS of BeautiSealant. However, significant differences were determined in the Fuji triage and Grandio Seal groups after pretreatment procedures ( P  < .05). Conclusion: Ozone and laser can be employed to disinfect fissures before BeautiSealant application.
Formalizing a Residency Mentorship Program with a “Business of Medicine” Curriculum
Authors: Sampat Ajay , Larson Danielle , Culler George , Bega Danny 
Published: September 2020

Background: Mentorship is critical for achieving success in academic medicine and is also considered one of the core professional competencies for residency training. Despite its importance, there has been a decline in the mentor-mentee relationship, largely due to time constraints and lack of clear guidelines for productive discussions. We provide a mentorship curriculum with an easily adoptable workbook which may serve as a guide for programs seeking more formalized mentorship opportunities. Methods: We created a mentorship curriculum that was divided into 4 quarterly sessions, each with topics to facilitate career guidance and development, and to provide insight into the practical aspects of business of medicine. The mentorship pilot curriculum was implemented during the 2017 to 2018 academic year. Specific questions were provided to stimulate reflection and appropriate discussion between resident mentee and faculty mentor. A post-curriculum survey was distributed to evaluate the effectiveness and satisfaction of the curriculum. Results: A total of 23 residents participated in this pilot project. A majority had not had any formal teaching related to the business aspects of medicine (82%). Upon completion of the curriculum, most residents felt several topics were sufficiently covered, and a majority were satisfied with the course and relationship developed with their mentor (87%). Conclusions: Our pilot curriculum provides a model to address a knowledge gap in the practical aspects of medicine while simultaneously enhancing residency mentorship. The one-year course was generally well-received by residents and can serve as a model to other academic residency programs with similar challenges and goals.
High D-dimer plasma concentration in systemic sclerosis patients: Prevalence and association with vascular complications
Authors: Furtado Sofia , Dunogué Bertrand , Jourdi Georges , Chaigne Benjamin , Chibah Aziza , Legendre Paul , Mouthon Luc 
Published: September 2020

Objective: To determine the frequency of elevated D-dimer plasma concentration (>500 ng/mL) in patients with systemic sclerosis and evaluate its association with systemic sclerosis–specific microvascular and macrovascular complications. Methods: Retrospective observational study of patients with systemic sclerosis followed in a tertiary referral center with at least one measurement of D-dimer between 2010 and 2018. Results: A total of 214 patients were analyzed. Mean age at inclusion was 55.1 ± 14.7 years; 180 (84.1%) were female; 74 (34.6%) had diffuse cutaneous systemic sclerosis. Anti-Scl70 and anti-centromere antibodies were positive in 74 (34.6%) and 75 (35.0%) patients, respectively. D-dimer level was elevated in 93 (43.5%) patients, independently of cutaneous subtype (44.6% in diffuse cutaneous systemic sclerosis vs 42.9% in limited cutaneous systemic sclerosis, p = 0.81). At least one microvascular complication was found in 108 (50.5%) patients: 105 (49.1%) with previous or current digital ulcers, 6 (2.8%) with renal crisis, and 4 (1.9%) with pulmonary arterial hypertension. Microvascular complications were more frequent in patients with elevated D-dimer (57.0% vs 45.5%, p = 0.09), significantly so after exclusion of patients with a history of cancer and/or venous thromboembolism (60.5% vs 44.8%, p = 0.04). Macrovascular complications were detected in 15 (7.0%) patients and were associated with a high D-dimer level (11.8% vs 3.3%, p = 0.03). Over a median follow-up of 2.3 years [1.1–3.3] after D-dimer measurement, new macrovascular complications occurred only in patients with high D-dimer (n = 8). Conclusion: High D-dimer levels are frequently found in systemic sclerosis patients and seem to be associated with the occurrence of macrovascular and microvascular complications after adjustment for confounding factors.
Improving the quality of the daily ward round in a Plastic Surgery unit by adapting the SAFE Ward Round Tool of the Royal College of Surgeons of Edinburgh
Authors: Koumoullis Harry D , Shapev Martin , Wong Gabriel , Gerring Sophie , Patrinios Goerge , Depasquale Ivan , Ahmed Jamil S 
Published: September 2020

Aim Our goal was to audit the quality of the ward round documentation in our Plastic Surgery department by using the SAFE Ward Round Tool of the RCS Edinburgh’s as a reference standard, and to create an in-house pro-forma based on results and discussion. Method An initial cycle based on the SAFE Tool was undertaken with prospective audit of individual daily ward round entries. A sticker pro forma was introduced and re-audit was done using the same criteria. Based on results and discussion, the pro-forma was further improved. Re-audit was performed to assess percentage of completion of its contents. Results The first cycle showed 47% (n = 42) completion rate and re-audit after implementation of the sticker found a rise up to 70% (n = 42). The third cycle examining solely sticker completion yielded a compliance of 88% (n = 61). This improvement reflected to the enthusiastic comments received from staff working in allied specialties. Conclusions Significant lapses in daily ward round documentation were revealed by our methodology. A sticker pro-forma, which we have named the Surgical Tool for the Assessment of Rounds (STAR), was introduced and provided measurable and sustainable improvements on our daily ward round practice. That had as a result the safeguarding of patient safety in the frame of Good Medical Practice. We suggest same methodology to be followed based on the SAFE Ward Round Tool for surgical ward rounds improvement in all the surgical and interventional specialties particularly when there is a component of emergency admission in their daily practice
Osteoporosis and fracture risk associated with inhaled corticosteroid use among Swedish COPD patients: the ARCTIC study
Authors: Janson Christer , Lisspers Karin , Ställberg Björn , Johansson Gunnar , Gutzwiller Florian S. , Mezzi Karen , Mindeholm Linda , Bjerregaard Bine Kjoeller , Jorgensen Leif , Larsson Kjell 
Published: September 2020

The effect of inhaled corticosteroids (ICS) on the risk of osteoporosis and fracture in patients with chronic obstructive pulmonary disease (COPD) remains uncertain. The aim of this study was to assess this risk in patients with COPD.Electronic medical record data linked to National Health Registries were collected from COPD patients and matched reference controls at 52 Swedish primary care centres from 2000 to 2014. The outcomes analysed were the effect of ICS on all fractures, fractures typically related to osteoporosis, recorded osteoporosis diagnosis, prescriptions of drugs for osteoporosis and a combined measure of any osteoporosis-related event. The COPD patients were stratified by the level of ICS exposure.A total of 9651 patients with COPD and 59 454 matched reference controls were analysed. During the follow-up, 19.9% of COPD patients had at least one osteoporosis-related event compared with 12.9% of reference controls (p<0.0001). Multivariate analysis in the COPD population demonstrated a dose–effect relationship, with high-dose ICS being significantly associated with any osteoporosis-related event (risk ratio 1.52 (95% CI 1.24–1.62)), while the corresponding estimate for low-dose ICS was 1.27 (95% CI 1.13–1.56) compared with COPD patients not using ICS. A similar dose-related adverse effect was found for all four of the specific osteoporosis-related events: all fractures, fractures typically related to osteoporosis, prescriptions of drugs for osteoporosis and diagnosis of osteoporosis.We conclude that patients with COPD have a greater risk of bone fractures and osteoporosis, and high-dose ICS use increased this risk further.
Targeting HIF2α-ARNT hetero-dimerisation as a novel therapeutic strategy for pulmonary arterial hypertension
Authors: Macias David , Moore Stephen , Crosby Alexi , Southwood Mark , Du Xinlin , Tan Huiling , Xie Shanhai , Vassallo Arlette , Wood Alexander J.T. , Wallace Eli M. , Cowburn Andrew S. 
Published: September 2020

Pulmonary arterial hypertension (PAH) is a destructive disease of the pulmonary vasculature often leading to right heart failure and death. Current therapeutic intervention strategies only slow disease progression. The role of aberrant hypoxia-inducible factor (HIF)2α stability and function in the initiation and development of pulmonary hypertension (PH) has been an area of intense interest for nearly two decades.Here we determine the effect of a novel HIF2α inhibitor (PT2567) on PH disease initiation and progression, using two pre-clinical models of PH. Haemodynamic measurements were performed, followed by collection of heart, lung and blood for pathological, gene expression and biochemical analysis. Blood outgrowth endothelial cells from idiopathic PAH patients were used to determine the impact of HIF2α-inhibition on endothelial function.Global inhibition of HIF2a reduced pulmonary vascular haemodynamics and pulmonary vascular remodelling in both su5416/hypoxia prevention and intervention models. PT2567 intervention reduced the expression of PH-associated target genes in both lung and cardiac tissues and restored plasma nitrite concentration. Treatment of monocrotaline-exposed rodents with PT2567 reduced the impact on cardiovascular haemodynamics and promoted a survival advantage.In vitro, loss of HIF2α signalling in human pulmonary arterial endothelial cells suppresses target genes associated with inflammation, and PT2567 reduced the hyperproliferative phenotype and overactive arginase activity in blood outgrowth endothelial cells from idiopathic PAH patients. These data suggest that targeting HIF2α hetero-dimerisation with an orally bioavailable compound could offer a new therapeutic approach for PAH. Future studies are required to determine the role of HIF in the heterogeneous PAH population.
Veno-venous extracorporeal membrane oxygenation in coronavirus disease 2019: a case series
Authors: Zhang Joe , Merrick Blair , Correa Genex L. , Camporota Luigi , Retter Andrew , Doyle Andrew , Glover Guy W. , Sherren Peter B. , Tricklebank Stephen J. , Agarwal Sangita , Lams Boris E. , Barrett Nicholas A. , Ioannou Nicholas , Edgeworth Jonathan , Meadows Christopher I.S. 
Published: September 2020

BackgroundThe use of veno-venous extracorporeal membrane oxygenation (VV-ECMO) in severe hypoxaemic respiratory failure from coronavirus disease 2019 (COVID-19) has been described, but reported utilisation and outcomes are variable, and detailed information on patient characteristics is lacking. We aim to report clinical characteristics, management and outcomes of COVID-19 patients requiring VV-ECMO, admitted over 2 months to a high-volume centre in the UK.MethodsPatient information, including baseline characteristics and clinical parameters, was collected retrospectively from electronic health records for COVID-19 VV-ECMO admissions between 3 March and 2 May 2020. Clinical management is described. Data are reported for survivors and nonsurvivors.ResultsWe describe 43 consecutive patients with COVID-19 who received VV-ECMO. Median age was 46 years (interquartile range 35.5–52.5) and 76.7% were male. Median time from symptom onset to VV-ECMO was 14 days (interquartile range 11–17.5). All patients underwent computed tomography imaging, revealing extensive pulmonary consolidation in 95.3%, and pulmonary embolus in 27.9%. Overall, 79.1% received immunomodulation with methylprednisolone for persistent maladaptive hyperinflammatory state. Vasopressors were used in 86%, and 44.2% received renal replacement therapy. Median duration on VV-ECMO was 13 days (interquartile range 8–20). 14 patients died (32.6%) and 29 survived (67.4%) to hospital discharge. Nonsurvivors had significantly higher d-dimer (38.2versus9.5 mg·L−1, fibrinogen equivalent units; p=0.035) and creatinine (169versus73 μmol·L−1; p=0.022) at commencement of VV-ECMO.ConclusionsOur data support the use of VV-ECMO in selected COVID-19 patients. The cohort was characterised by high degree of alveolar consolidation, systemic inflammation and intravascular thrombosis.
DPDDI: a deep predictor for drug-drug interactions
Authors: Feng Yue-Hua , Zhang Shao-Wu , Shi Jian-Yu 
Published: September 2020

AbstractBackgroundThe treatment of complex diseases by taking multiple drugs becomes increasingly popular. However, drug-drug interactions (DDIs) may give rise to the risk of unanticipated adverse effects and even unknown toxicity. DDI detection in the wet lab is expensive and time-consuming. Thus, it is highly desired to develop the computational methods for predicting DDIs. Generally, most of the existing computational methods predict DDIs by extracting the chemical and biological features of drugs from diverse drug-related properties, however some drug properties are costly to obtain and not available in many cases.ResultsIn this work, we presented a novel method (namely DPDDI) to predict DDIs by extracting the network structure features of drugs from DDI network with graph convolution network (GCN), and the deep neural network (DNN) model as a predictor. GCN learns the low-dimensional feature representations of drugs by capturing the topological relationship of drugs in DDI network. DNN predictor concatenates the latent feature vectors of any two drugs as the feature vector of the corresponding drug pairs to train a DNN for predicting the potential drug-drug interactions. Experiment results show that, the newly proposed DPDDI method outperforms four other state-of-the-art methods; the GCN-derived latent features include more DDI information than other features derived from chemical, biological or anatomical properties of drugs; and the concatenation feature aggregation operator is better than two other feature aggregation operators (i.e., inner product and summation). The results in case studies confirm that DPDDI achieves reasonable performance in predicting new DDIs.ConclusionWe proposed an effective and robust method DPDDI to predict the potential DDIs by utilizing the DDI network information without considering the drug properties (i.e., drug chemical and biological properties). The method should also be useful in other DDI-related scenarios, such as the detection of unexpected side effects, and the guidance of drug combination.
Analysis of G-quadruplexes upstream of herpesvirus miRNAs: evidence of G-quadruplex mediated regulation of KSHV miR-K12–1-9,11 cluster and HCMV miR-US33
Authors: Kumar Shivani , Choudhary Divya , Patra Anupam , Bhavesh Neel Sarovar , Vivekanandan Perumal 
Published: September 2020

Abstract
Background
G-quadruplexes regulate gene expression, recombination, packaging and latency in herpesviruses. Herpesvirus-encoded miRNAs have been linked to important biological functions. The presence and the biological role of G-quadruplexes have not been studied in the regulatory regions of virus miRNA. We hypothesized that herpesvirus-encoded miRNAs are regulated by G-quadruplexes in their promoters.

Results
We analyzed the 1 kb regulatory regions of all herpesvirus-encoded miRNAs for the presence of putative quadruplex-forming sequences (PQS). Over two-third (67%) of the regulatory regions of herpesvirus miRNAs had atleast 1 PQS. The 200 bp region of the promoter proximal to herpesvirus miRNA is particularly enriched for PQS. We chose to study the G-quadruplex motifs in the promoters of miR-K12 cluster in Kaposi's sarcoma-associated Herpesvirus (KSHV miR-K12–1-9,11) and the miR-US33 encoded by Human Cytomegalovirus (HCMV miR-US33). Biophysical characterization indicates that the G-quadruplex motifs in the promoters of the KSHV miR-K12 cluster and the HCMV miR-US33 form stable intramolecular G-quadruplexes in vitro. Mutations disrupting the G-quadruplex motif in the promoter of the KSHV miR-K12 cluster significantly inhibits promoter activity, while those disrupting the motif in the promoter of HCMV miR-US33 significantly enhance the promoter activity as compared to that of the respective wild-type promoter. Similarly, the addition of G-quadruplex binding ligands resulted in the modulation of promoter activity of the wild-type promoters (with intact G-quadruplex) but not the mutant promoters (containing quadruplex-disrupting mutations).

Conclusion
Our findings highlight previously unknown mechanisms of regulation of virus-encoded miRNA and also shed light on new roles for G-quadruplexes in herpesvirus biology.
GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure
Authors: Wan Yu , Wick Ryan R. , Zobel Justin , Ingle Danielle J. , Inouye Michael , Holt Kathryn E. 
Published: September 2020

Abstract
Background
Horizontal gene transfer contributes to bacterial evolution through mobilising genes across various taxonomical boundaries. It is frequently mediated by mobile genetic elements (MGEs), which may capture, maintain, and rearrange mobile genes and co-mobilise them between bacteria, causing horizontal gene co-transfer (HGcoT). This physical linkage between mobile genes poses a great threat to public health as it facilitates dissemination and co-selection of clinically important genes amongst bacteria. Although rapid accumulation of bacterial whole-genome sequencing data since the 2000s enables study of HGcoT at the population level, results based on genetic co-occurrence counts and simple association tests are usually confounded by bacterial population structure when sampled bacteria belong to the same species, leading to spurious conclusions.

Results
We have developed a network approach to explore WGS data for evidence of intraspecies HGcoT and have implemented it in R package GeneMates (github.com/wanyuac/GeneMates). The package takes as input an allelic presence-absence matrix of interested genes and a matrix of core-genome single-nucleotide polymorphisms, performs association tests with linear mixed models controlled for population structure, produces a network of significantly associated alleles, and identifies clusters within the network as plausible co-transferred alleles. GeneMates users may choose to score consistency of allelic physical distances measured in genome assemblies using a novel approach we have developed and overlay scores to the network for further evidence of HGcoT. Validation studies of GeneMates on known acquired antimicrobial resistance genes in Escherichia coli and Salmonella Typhimurium show advantages of our network approach over simple association analysis: (1) distinguishing between allelic co-occurrence driven by HGcoT and that driven by clonal reproduction, (2) evaluating effects of population structure on allelic co-occurrence, and (3) direct links between allele clusters in the network and MGEs when physical distances are incorporated.

Conclusion
GeneMates offers an effective approach to detection of intraspecies HGcoT using WGS data.
Molecular identification and evolutionary relationships between the subspecies of Musa by DNA barcodes
Authors: Dhivya S. , Ashutosh S. , Gowtham I. , Baskar V. , Harini A. Baala , Mukunthakumar S. , Sathishkumar R. 
Published: September 2020

Abstract
Background
The banana (Musa sp., AAA) genome is constantly increasing due to high-frequency of somaclonal variations. Due to its large diversity, a conventional numerical and morphological based taxonomic identification of banana cultivars is laborious, difficult and often leads to subject of disagreements.

Results
Hence, in the present study, we used universal DNA barcode ITS2 region to identify and to find the genetic relationship between the cultivars and varieties of banana. Herein, a total of 16 banana cultivars were PCR amplified using ITS2 primer pair. In addition, 321 sequences which were retrieved from GenBank, USA, were used in this study. The sequences were then aligned using Clustal W and genetic distances were computed using MEGA V5.1. The study showed significant divergence between the intra- and inter-specific genetic distances in ITS2 region. BLAST1 and Distance methods proved that ITS2 DNA barcode region successfully identified and distinguished the cultivar and varieties of banana.

Conclusion
Thus, from the results of the present study, it is clear that ITS2 is not only an efficient DNA barcode to identify the banana species but also a potential candidate for enumerating the phylogenetic relationships between the subspecies and cultivars. This is the first comprehensive study to categorically distinguish the economically important banana subspecies and varieties using DNA barcodes and to understand its evolutionary relationship.