bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonliposuction Endoscopic Sentinel Lymph Node Biopsy Through the Periareolar Incision
Authors: Liang Yinghui , Xu Shuangta 
Published: July 2020

Background. Sentinel lymph node biopsy (SLNB) has been an alternative to axillary lymph node dissection as a standard procedure for breast cancer patients with clinically negative lymph nodes. Endoscopic technique has been developed for over 20 years but remains to be mastered by a slice of surgeons. Suction and squeezing in the liposuction endoscopic procedures may increase risk of local recurrence and metastasis. In this study, we present our method of SLNB procedure through the periareolar incision which improves the shape of the breast-conserving surgery. Patients and Procedures. Twenty-eight breast cancer patients with clinically negative lymph nodes received this procedure. Methylene blue dye and technetium-99m sulfur colloid were used to be the tracker of sentinel lymph nodes (SLNs). Periareolar incision was the main surgical technique. The STORZ HD endoscopic system and some special instruments were used during the operation. Results. SLNs can be accurately located and biopsied under an endoscope without additional incisions. The SLNs detection rate, sensitivity, and false-negative rate are 88%, 80%, and 11.1%, respectively. And, the complications such as paresthesia and upper limb lymphedema are similar compared with traditional breast-conserving surgery (10.7% vs 9.8% and 7.1% vs 7.8%). Conclusion. Endoscopic technique can be used to accurately assess the status of SLNs in patients with breast cancer. Nonliposuction endoscopic breast-conserving surgery is one of the safe and alternative surgical procedures for early breast cancer.
Improved Cartilage Quality on Delayed Gadolinium-Enhanced MRI of Hip Cartilage after Subchondral Drilling of Acetabular Cartilage Flaps in Femoroacetabular Impingement Surgery at Minimum 5-Year Follow-Up
Authors: Schmaranzer Florian , Haefeli Pascal C. , Liechti Emanuel F. , Hanke Markus S. , Tannast Moritz , Büchler Lorenz 
Published: July 2020

Objective To assess whether subchondral drilling of acetabular cartilage flaps during femoroacetabular impingement (FAI) surgery improves (1) acetabular dGEMRIC indices and (2) morphologic magnetic resonance imaging (MRI) scores, compared with hips in which no additional treatment of cartilage lesions had been performed; and (3) whether global dGEMRIC indices and MRI scores correlate. Design Prospective cohort study of consecutive patients with symptomatic FAI treated with open surgery between 2000 and 2007. Patients with subchondral drilling of acetabular cartilage flaps were allocated to the study group, those without drilling to the control group. All patients underwent indirect 3-T MR arthrography to assess cartilage quality by dGEMRIC indices and a semiquantitative morphologic MRI score at minimum 5 years after surgery. dGEMRIC indices and morphologic MRI scores were compared between and among groups using analysis of covariance/paired t tests. Results No significant difference was found between the global dGEMRIC indices of the study group (449 ± 147 ms, 95% CI 432-466 ms) and the control group (428 ± 143 ms, 95% CI 416-442 ms; P = 0.235). In regions with cartilage flaps, the study group showed higher dGEMRIC indices (472 ± 160 ms, 95% CI 433-510 ms) compared with the control group (390 ± 122 ms, 95% CI 367-413 ms; P < 0.001). No significant differences were found for the morphologic MRI scores. A strong inversely linear correlation between the dGEMRIC indices and the morphologic MRI scores ( r = −0.727, P < 0.001) was observed. Conclusions Treatment of acetabular cartilage flaps with subchondral drilling leads to better cartilage quality in regions with cartilage flaps at minimum 5 years of follow-up.
Comparison of breast density assessments according to BI-RADS 4th and 5th editions and experience level
Authors: Gemici Aysegul Akdogan , Bayram Ersoy , Hocaoglu Elif , Inci Ercan 
Published: July 2020

Background Breast density is an important variable that can change the sensitivity of mammography. It can be analyzed with using the 4th and 5th editions of the Breast Imaging and Reporting Data System (BI-RADS) recommendations from the American College of Radiology (ACR). Purpose To define the intra- and inter-reader agreement levels of breast density assignments performed by readers with different experience levels using two versions of BI-RADS. Material and Methods The breast density assessments of 330 women were conducted by two readers with different levels of experience (one breast radiologist and one resident). Each reader independently defined the breast density four times—twice using the 4th edition and twice using the 5th edition. Assessments were analyzed on four- and two-category scales. Results The intra-reader agreement of the breast radiologist for the 4th and 5th editions of BI-RADS was almost perfect (k = 0.90 and k = 0.87, respectively.) The resident had similar results (k = 0.88 and k = 0.87, respectively). The agreement between the breast radiologist and resident for the 4th and 5th edition of BI-RADS was substantial (k = 0.70 and k = 0.63, respectively). There was a statistically significant difference with the two-category scale analysis between the dense and non-dense for both readers and versions of BI-RADS (McNemar’s test, P < 0.001). Conclusion Although there were high intra- and inter-reader agreement levels when using both versions, the percentage of women having dense breasts increased when using the 5th edition, and the difference was statistically significant. There were no differences found with regard to the readers’ level of experience in all analyses.
Demographics, Treatment, and Cost of Periprosthetic Femur Fractures: Fixation Versus Revision
Authors: Ragland Katelyn , Reif Rebecca , Karim Saleema , Sexton Kevin W. , Cherney Steven M. , Stambough Jeffrey B. , Mears Simon C. 
Published: July 2020

Introduction: Periprosthetic femur fractures (PPFX) are complications of both total hip and knee arthroplasty and may be treated with open reduction and internal fixation (ORIF) or revision arthroplasty. Differences in treatment and fracture location may be related to patient demographics and lead to differences in cost. Our study examined the effects of demographics and treatment of knee and hip PPFXs on length of stay (LOS) and cost. Methods: Of all, 932 patients were identified with hip or knee PPFXs in the National Inpatient Sample from January 2013 to September 2015. Age, gender, race, mortality, comorbidity level, LOS, total cost, procedure type, geographic region, and hospital type were recorded. A generalized linear regression model was conducted to analyze the effect of fracture type on LOS and cost. Results: Differences in gender (66% vs 83.7% female, P < .01), comorbidities (fewer in hips, P < .01), and costs (US$30 979 vs US$27 944, P < .01) were found between the hip and knee groups. Knees had significantly higher rates of ORIF treatment (80.7% vs 39.1%) and lower rates of revision arthroplasties (19.3% vs 60.9%) than hip PPFXs ( P < .01). Within both groups, patients with more comorbidities, revision surgery, and blood transfusions were more likely to have a longer LOS and higher cost. Conclusion: Periprosthetic femur fractures patients are not homogenous and treatment varies between hip and knee locations. For knee patients, those treated with ORIF were younger, with fewer comorbidities than those treated with revision. Conversely, hip patients treated with ORIF were older, with more comorbidities than those treated with revision. Hips had higher costs than knees, and cost correlated with revision arthroplasty and more comorbidities. In both hip and knee groups, longer LOS was associated with more comorbidities and being treated in urban teaching hospitals. Total cost had the strongest associations with revision procedures as well as number of comorbidities and blood product use.
Evaluation of Intra-Lesional Interleukin 2 for the Treatment of In-Transit Melanoma Disease: L’évaluation de l’interleukine-2 intralésionnelle pour traiter les mélanomes en transit
Authors: Lopez-Obregon Beatriz , Barreto Marcio P. , Fyfe Allison , McKinnon Greg , Webb Carmen , Temple-Oberle Claire 
Published: July 2020

Background: Intra-lesional interleukin 2 (IL-2) therapy trials for the treatment of in-transit melanoma using different treatment protocols have been published reporting varied results. This study assesses the results of IL-2 therapy in our institution and to evaluate the reproducibility of our response rates when using the same treatment protocol as another Canadian centre. Methods: A retrospective review was undertaken of patients with in-transit melanoma who were treated with intralesional IL-2 in a single institution from 2010 to 2016. Responses were evaluated using RECIST criteria. Demographic data, tumour characteristics, follow-up data, in-transit-free interval, and survival data were collected and analysed. Results: Forty-nine patients were identified. Overall tumour response rate was 72%, including complete response in 23 patients (47%) and partial response in 12 patients (24%). Stable disease was observed in 4% of patients and progressive disease in 25%. The main side effects were minor discomfort with injections and auto-limited flu-like symptoms. The presence of tumour-infiltrating lymphocytes may be a predictor of better response. Conclusion: This study confirms prior experience with intra-lesional IL-2, demonstrating it to be an effective, safe, and well-tolerated therapy for in-transit melanoma. Tumour-infiltrating lymphocytes as a predictor of better response warrant further study.
Avoiding Difficult Conversations in the Australian Health Sector
Authors: King Christine , Edlington Tanya , Williams Brett 
Published: July 2020

Background Health professionals avoiding difficult conversations with each other can lead to serious negative consequences for patients. Clinical supervisors are in the unique position of interacting both with students as well as colleagues and peers. This study explores the avoidance of difficult conversations from the perspective of clinical supervisors in order to better understand why health professionals avoid difficult conversations. Objective This study aimed to identify the reasons why difficult conversations are avoided between health-care professionals and to gain deeper insight into the phenomenon of avoiding difficult conversations in general. Methods Convergent interviewing was used with 20 clinical supervisors to explore the following question: Why do you think that people in your workplace avoid difficult conversations? Results Major reasons for avoiding difficult conversations included the fear of negative consequences, a general distaste for confrontation, and a lack of confidence in their skills to have such conversations. Additional factors included individual qualities such as personality type and communication style, available time, size of the workplace, and a range of perceived cultural barriers standing in the way of having difficult conversations. Conclusion There is a need to encourage clinical supervisors and other health professionals to embrace difficult conversations to reduce adverse events and enhance patient outcomes. This requires additional training and educational opportunities to enhance knowledge, skills, and confidence to plan and engage in difficult conversations. Some types of difficult conversations require more skills than others.
Elastomeric respirators are safer and more sustainable alternatives to disposable N95 masks during the coronavirus outbreak
Authors: Chiang James , Hanna Andrew , Lebowitz David , Ganti Latha 
Published: July 2020

Abstract
Background
In this paper, the authors review the safety and practicality of elastomeric respirators for protecting themselves and others from the novel coronavirus or COVID-19. They also describe the safe donning and doffing procedures for this protective gear.

Main text
Due to the shortage of personal protective equipment (PPE), the CDC has recommended ways to conserve disposable N95 masks, including re-use and extended use, and reserving N95 masks for aerosol-generating procedures. However, these were never made to be re-used.
Although the modes of transmission of COVID-19 are not fully understood, based on what we know about severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), droplets and aerosolized droplets contribute to the spread of this virus. More evidence from Wuhan, China, has demonstrated that COVID-19 viral particles are aerosolized and found in higher concentrations in rooms where PPE is being removed. Thus, it is best for all healthcare providers to have full aerosol protection.

Conclusion
Given the shortage of PPE for aerosols, it is logical to utilize reusable elastomeric respirators with filter efficiency of 95% or higher. A single elastomeric respirator may replace hundreds to thousands of new disposable N95 masks.
Enhancer prediction in the human genome by probabilistic modelling of the chromatin feature patterns
Authors: Osmala Maria , Lähdesmäki Harri 
Published: July 2020

Abstract
Background
The binding sites of transcription factors (TFs) and the localisation of histone modifications in the human genome can be quantified by the chromatin immunoprecipitation assay coupled with next-generation sequencing (ChIP-seq). The resulting chromatin feature data has been successfully adopted for genome-wide enhancer identification by several unsupervised and supervised machine learning methods. However, the current methods predict different numbers and different sets of enhancers for the same cell type and do not utilise the pattern of the ChIP-seq coverage profiles efficiently.

Results
In this work, we propose a PRobabilistic Enhancer PRedictIoN Tool (PREPRINT) that assumes characteristic coverage patterns of chromatin features at enhancers and employs a statistical model to account for their variability. PREPRINT defines probabilistic distance measures to quantify the similarity of the genomic query regions and the characteristic coverage patterns. The probabilistic scores of the enhancer and non-enhancer samples are utilised to train a kernel-based classifier. The performance of the method is demonstrated on ENCODE data for two cell lines. The predicted enhancers are computationally validated based on the transcriptional regulatory protein binding sites and compared to the predictions obtained by state-of-the-art methods.

Conclusion
PREPRINT performs favorably to the state-of-the-art methods, especially when requiring the methods to predict a larger set of enhancers. PREPRINT generalises successfully to data from cell type not utilised for training, and often the PREPRINT performs better than the previous methods. The PREPRINT enhancers are less sensitive to the choice of prediction threshold. PREPRINT identifies biologically validated enhancers not predicted by the competing methods. The enhancers predicted by PREPRINT can aid the genome interpretation in functional genomics and clinical studies.
Performance evaluation of lossy quality compression algorithms for RNA-seq data
Authors: Yu Rongshan , Yang Wenxian , Wang Shun 
Published: July 2020

Abstract
Background
Recent advancements in high-throughput sequencing technologies have generated an unprecedented amount of genomic data that must be stored, processed, and transmitted over the network for sharing. Lossy genomic data compression, especially of the base quality values of sequencing data, is emerging as an efficient way to handle this challenge due to its superior compression performance compared to lossless compression methods. Many lossy compression algorithms have been developed for and evaluated using DNA sequencing data. However, whether these algorithms can be used on RNA sequencing (RNA-seq) data remains unclear.

Results
In this study, we evaluated the impacts of lossy quality value compression on common RNA-seq data analysis pipelines including expression quantification, transcriptome assembly, and short variants detection using RNA-seq data from different species and sequencing platforms. Our study shows that lossy quality value compression could effectively improve RNA-seq data compression. In some cases, lossy algorithms achieved up to 1.2-3 times further reduction on the overall RNA-seq data size compared to existing lossless algorithms. However, lossy quality value compression could affect the results of some RNA-seq data processing pipelines, and hence its impacts to RNA-seq studies cannot be ignored in some cases. Pipelines using HISAT2 for alignment were most significantly affected by lossy quality value compression, while the effects of lossy compression on pipelines that do not depend on quality values, e.g., STAR-based expression quantification and transcriptome assembly pipelines, were not observed. Moreover, regardless of using either STAR or HISAT2 as the aligner, variant detection results were affected by lossy quality value compression, albeit to a lesser extent when STAR-based pipeline was used. Our results also show that the impacts of lossy quality value compression depend on the compression algorithms being used and the compression levels if the algorithm supports setting of multiple compression levels.

Conclusions
Lossy quality value compression can be incorporated into existing RNA-seq analysis pipelines to alleviate the data storage and transmission burdens. However, care should be taken on the selection of compression tools and levels based on the requirements of the downstream analysis pipelines to avoid introducing undesirable adverse effects on the analysis results.
Differential contribution of p300 and CBP to regulatory element acetylation in mESCs
Authors: Martire Sara , Nguyen Jennifer , Sundaresan Aishwarya , Banaszynski Laura A. 
Published: July 2020

Abstract
Background
The transcription coactivators CREB binding protein (CBP) and p300 are highly homologous acetyltransferases that mediate histone 3 lysine 27 acetylation (H3K27ac) at regulatory elements such as enhancers and promoters. Although in most cases, CBP and p300 are considered to be functionally identical, both proteins are indispensable for development and there is evidence of tissue-specific nonredundancy. However, characterization of chromatin and transcription states regulated by each protein is lacking.

Results
In this study we analyze the individual contribution of p300 and CBP to the H3K27ac landscape, chromatin accessibility, and transcription in mouse embryonic stem cells (mESC). We demonstrate that p300 is the predominant H3K27 acetyltransferase in mESCs and that loss of acetylation in p300KD mESCs is more pronounced at enhancers compared to promoters. While loss of either CBP or p300 has little effect on the open state of chromatin, we observe that distinct gene sets are transcriptionally dysregulated upon depletion of p300 or CBP. Transcriptional dysregulation is generally correlated with dysregulation of promoter acetylation upon depletion of p300 (but not CBP) and appears to be relatively independent of dysregulated enhancer acetylation. Interestingly, both our transcriptional and genomic analyses demonstrate that targets of the p53 pathway are stabilized upon depletion of p300, suggesting an unappreciated view of the relationship between p300 and p53 in mESCs.

Conclusions
This genomic study sheds light on distinct functions of two important transcriptional regulators in the context of a developmentally relevant cell type. Given the links to both developmental disorders and cancer, we believe that our study may promote new ways of thinking about how these proteins function in settings that lead to disease.
DNA methylation and its effects on gene expression during primary to secondary growth in poplar stems
Authors: Zhang Yang , Liu Cong , Cheng He , Tian Shuanghui , Liu Yingying , Wang Shuang , Zhang Huaxin , Saqib Muhammad , Wei Hairong , Wei Zhigang 
Published: July 2020

Abstract
Background
As an important epigenetic mark, 5-methylcytosine (5mC) methylation is involved in many DNA-dependent biological processes and plays a role during development and differentiation of multicellular organisms. However, there is still a lack of knowledge about the dynamic aspects and the roles of global 5mC methylation in wood formation in tree trunks. In this study, we not only scrutinized single-base resolution methylomes of primary stems (PS), transitional stems (TS), and secondary stems (SS) of Populus trichocarpa using a high-throughput bisulfite sequencing technique, but also analyzed the effects of 5mC methylation on the expression of genes involved in wood formation.

Results
The overall average percentages of CG, CHG, and CHH methylation in poplar stems were ~ 53.6%, ~ 37.7%, and ~ 8.5%, respectively, and the differences of 5mC in genome-wide CG/CHG/CHH contexts among PS, TS, and SS were statistically significant (p < 0.05). The evident differences in CG, CHG, and CHH methylation contexts among 2 kb proximal promoters, gene bodies, and 2 kb downstream regions were observed among PS, TS, and SS. Further analysis revealed a perceptible global correlation between 5mC methylation levels of gene bodies and transcript levels but failed to reveal a correlation between 5mC methylation levels of proximal promoter regions and transcript levels. We identified 653 and 858 DMGs and 4978 and 4780 DEGs in PS vs TS and TS vs SS comparisons, respectively. Only 113 genes of 653 DMGs and 4978 DEGs, and 114 genes of 858 DMGs and 4780 DEG were common. Counterparts of some of these common genes in other species, including Arabidopsis thaliana, are known to be involved in secondary cell wall biosynthesis and hormone signaling. This indicates that methylation may directly modulate wood formation genes and indirectly attune hormone signaling genes, which in turn impact wood formation.

Conclusions
DNA methylation only marginally affects pathway genes or regulators involved in wood formation, suggesting that further studies of wood formation should lean towards the indirect effects of methylation. The information and data we provide here will be instrumental for understanding the roles of methylation in wood formation in tree species.