bluuebunny/crossref_metadata_2025_split huggingface dataset:
Does the Arctic Stratospheric Polar Vortex Exhibit Signs of Preconditioning Prior to Sudden Stratospheric Warmings?
Authors: Lawrence Zachary D. , Manney Gloria L. 
Published: November 2019

Abstract
Characteristics of the Arctic stratospheric polar vortex are examined using reanalysis data with dynamic time warping (DTW) and a clustering technique to determine whether the polar vortex exhibits canonical signs of preconditioning prior to sudden stratospheric warmings (SSWs). The DTW and clustering technique is used to locate time series motifs in vortex area, vortex edge-averaged PV gradients, and vortex edge-averaged wind speeds. Composites of the motifs reveal that prior to roughly 75% of SSWs, in the middle to upper stratosphere, PV gradients and wind speeds in the vortex edge region increase, and vortex area decreases. These signs agree with prior studies that discuss potential signals of preconditioning of the vortex. However, similar motifs are also found in a majority of years without SSWs. While such non-SSW motifs are strongly associated with minor warming signals apparent only in the middle and upper stratosphere, only roughly half of these can be associated with later “significant disturbances” (SDs) that do not quite meet the threshold for major SSWs. The median lead time for sharpening vortex edge PV gradients represented in the motifs prior to SSWs and SDs is ~25 days, while the median lead time for the vortex area and edge wind speeds is ~10 days. Overall, canonical signs of preconditioning do appear to exist prior to SSWs, but their existence in years without SSWs implies that preconditioning of the vortex may be an insufficient condition for the occurrence of SSWs.
Comparison of Referral Pathways in Otolaryngology at a Public Versus Private Academic Center
Authors: Bertelsen Caitlin , Choi Janet S. , Jackanich Anna , Ge Marshall , Sun Gordon H. , Chambers Tamara 
Published: November 2019

Objective: Delayed medical care may be costly and dangerous. Examining referral pathways may provide insight into ways to reduce delays in care. We sought to compare time between initial referral and first clinic visit and referral and surgical intervention for index otolaryngologic procedures between a public safety net hospital (PSNH) and tertiary-care academic center (TAC). Methods: Retrospective cohort study of eligible adult patients undergoing one of several general otolaryngologic procedures at a PSNH (n = 216) and a TAC (n = 161) over a 2-year time period. Results: PSNH patients were younger, less likely to have comorbidities and more likely to be female, Hispanic or Asian, and to lack insurance. Time between referral and first clinic visit was shorter at the PSNH than the TAC (Mean 35.8 ± 47.7 vs 48.3 ± 60.3 days; P = .03). Time between referral and surgical intervention did not differ between groups (129 ± 90 for PSNH vs 141 ± 130 days for TAC, P = .30). On multivariate analysis, the TAC had more patient-related delays in care than the PSNH (OR: 3.75, P < .001). Time from referral to surgery at a PSNH was associated with age, source of referral, type of surgery, diagnostic workup and comorbidities, and at a TAC was associated with gender and type of surgery and comorbidities. Conclusions: Sociodemographic differences between PSNH and TAC patients, as well as differences in referral pathways between the types of institutions, influence progression of surgical care in otolaryngology. These differences may be targets for interventions to streamline care. Level of Evidence: 2c
Finding a way with words: Delphi study to develop a discussion prompt list for paediatric palliative care
Authors: Ekberg Stuart , Herbert Anthony , Johns Kristi , Tarrant Gabrielle , Sansone Holly , Yates Patsy , Danby Susan , Bradford Natalie K 
Published: November 2019

Background: Effective communication is a cornerstone of quality paediatric palliative care. Families report struggling, however, to know what to discuss, with whom, and when. Although question prompt lists exist for adult palliative care, they do not suit the unique circumstances of paediatric palliative care. Aim: To develop a prompt list suitable for paediatric palliative care. Design: Underpinned by Delphi methodology, a six-phase procedure was adopted: (1) drafting items based on the findings of a literature review, (2) condensing the list of items based on group discussion, (3) refining items based on a survey of expert healthcare professionals, (4) additional refining of items based on another survey of professionals, (5) further refining of items based on cognitive interviews with family members, and (6) final review by healthcare professional and family member groups. Participants: Three participant groups were involved during various phases: (1) members of an Australasian paediatric palliative care national reference group, (2) healthcare professionals associated with a local paediatric palliative care service, and (3) family members who were users of the same local service. Results: Through multi-phase consultation across participant groups, the draft question prompt list was refined progressively to 28 items, split across two booklets to allow end-of-life items to be provided separately, and reconceptualised as a discussion prompt list rather than a question prompt list. Conclusion: By involving representatives of major stakeholder groups, this study has facilitated the design of a prompt list suited to the circumstances of paediatric palliative care. Future research should trial the effectiveness of this resource.
Pre-clinical evaluation of surface coating performance in guidewire surrogates: Potential implications for coated interventional surgical devices
Authors: Shi Huiyu , Wang Jonathan , Vorvolakos Katherine , White Kathleen , Duraiswamy Nandini 
Published: November 2019

Purpose Polymer fragments have been identified from autopsy reports of patients who had at some point undergone intravascular procedures with medical devices (such as guidewires and catheters) with lubricious coatings. Coating separation on these devices may cause a range of adverse events, the most severe being patient death associated with undesired embolization of blood vessels by coating particles. The objective of the present study is to identify bench test methods for evaluation of hydrophobic and hydrophilic coatings to better understand the relationships between coating formulation and coating behavior, which in turn helps to determine safety and effectiveness of the coating on the device. Methods Hydrophilic or hydrophobic coatings were applied on prepared 304 V stainless steel guidewire surrogates. Coating integrity was assessed after exposing the surrogates to extended periods of soaking and rotary bend fatigue testing. Additionally, coating durability was evaluated by abrasion testing. Results Soaking tests showed deionized water can cause more changes to the microscopic appearance of the coating on the guidewire surrogates as compared to 0.9% saline at both room temperature and 37°C; however, soaking tests in either medium did not alter coating integrity after 11 hours. Rotary bend fatigue, which subjects the coatings to both tension and compression, did not affect coating integrity on the guidewire surrogates after three hours. The pad material used in abrasion testing can lead to markedly different performance predictions. Conclusion Soaking, bend fatigue test, and abrasion tests can provide valuable information on coating performance. Coating integrity and durability were affected during abrasion testing, a test method that can provide more useful information for evaluating bench coating performance. It remains to correlate these findings with clinical performance, but emphasis should be placed on comprehensive characterization. Further investigation is needed by multidisciplinary stakeholders: materials scientists, engineers, and clinicians, to properly inform next steps.
Pedicle Screws Challenged: Lumbar Cortical Density and Thickness Are Greater in the Posterior Elements Than in the Pedicles
Authors: Odeh Khalid , Rosinski Alexander , Leasure Jeremi , Kondrashov Dimitriy 
Published: November 2019

Study Design: Controlled laboratory study. Objective: To measure the total bone mineral density (BMD), cortical volume, and cortical thickness in seven different anatomical regions of the lumbar spine. Methods: Using computed tomography (CT) images, 3 cadaveric spines were digitally isolated by applying filters for cortical and cancellous bone. Each spine model was separated into 5 lumbar vertebrae, followed by segmentation of each vertebra into 7 anatomical regions of interest using 3-dimensional software modeling. The average Hounsfield units (HU) was determined for each region and converted to BMD with calibration phantoms of known BMD. These BMD measurements were further analyzed by the total volume, cortical volume, and cancellous volume. The cortical thickness was also measured. A similar analysis was performed by vertebral segment. St Mary’s Medical Center’s Institutional Review Board approved this study. No external funding was received for this work. Results: The lamina and inferior articular process contained the highest total BMD, thickest cortical shell, and largest percent volumes of cortical bone. The vertebral body demonstrated the lowest BMD. The BMDs of the L4 and L5 segments were lower; however, there were no statistically significant differences in BMD between the L1-L5 vertebral segments. Conclusion: Extrapedicular regions of the lumbar vertebrae, including the lamina and inferior articular process, contain denser bone than the pedicles. Since screw pullout strength relies greatly on bone density, the lamina and inferior articular processes may offer stronger fixation of the lumbar spine.
TACITuS: transcriptomic data collector, integrator, and selector on big data platform
Authors: Alaimo Salvatore , Di Maria Antonio , Shasha Dennis , Ferro Alfredo , Pulvirenti Alfredo 
Published: November 2019

Abstract
Background
Several large public repositories of microarray datasets and RNA-seq data are available. Two prominent examples include ArrayExpress and NCBI GEO. Unfortunately, there is no easy way to import and manipulate data from such resources, because the data is stored in large files, requiring large bandwidth to download and special purpose data manipulation tools to extract subsets relevant for the specific analysis.

Results
TACITuS is a web-based system that supports rapid query access to high-throughput microarray and NGS repositories. The system is equipped with modules capable of managing large files, storing them in a cloud environment and extracting subsets of data in an easy and efficient way. The system also supports the ability to import data into Galaxy for further analysis.

Conclusions
TACITuS automates most of the pre-processing needed to analyze high-throughput microarray and NGS data from large publicly-available repositories. The system implements several modules to manage large files in an easy and efficient way. Furthermore, it is capable deal with Galaxy environment allowing users to analyze data through a user-friendly interface.
ImaGene: a convolutional neural network to quantify natural selection from genomic data
Authors: Torada Luis , Lorenzon Lucrezia , Beddis Alice , Isildak Ulas , Pattini Linda , Mathieson Sara , Fumagalli Matteo 
Published: November 2019

AbstractBackgroundThe genetic bases of many complex phenotypes are still largely unknown, mostly due to the polygenic nature of the traits and the small effect of each associated mutation. An alternative approach to classic association studies to determining such genetic bases is an evolutionary framework. As sites targeted by natural selection are likely to harbor important functionalities for the carrier, the identification of selection signatures in the genome has the potential to unveil the genetic mechanisms underpinning human phenotypes. Popular methods of detecting such signals rely on compressing genomic information into summary statistics, resulting in the loss of information. Furthermore, few methods are able to quantify the strength of selection. Here we explored the use of deep learning in evolutionary biology and implemented a program, called , to apply convolutional neural networks on population genomic data for the detection and quantification of natural selection.Resultsenables genomic information from multiple individuals to be represented as abstract images. Each image is created by stacking aligned genomic data and encoding distinct alleles into separate colors. To detect and quantify signatures of positive selection, implements a convolutional neural network which is trained using simulations. We show how the method implemented in can be affected by data manipulation and learning strategies. In particular, we show how sorting images by row and column leads to accurate predictions. We also demonstrate how the misspecification of the correct demographic model for producing training data can influence the quantification of positive selection. We finally illustrate an approach to estimate the selection coefficient, a continuous variable, using multiclass classification techniques.ConclusionsWhile the use of deep learning in evolutionary genomics is in its infancy, here we demonstrated its potential to detect informative patterns from large-scale genomic data. We implemented methods to process genomic data for deep learning in a user-friendly program called . The joint inference of the evolutionary history of mutations and their functional impact will facilitate mapping studies and provide novel insights into the molecular mechanisms associated with human phenotypes.
Exploratory analysis of transposable elements expression in the C. elegans early embryo
Authors: Ansaloni Federico , Scarpato Margherita , Di Schiavi Elia , Gustincich Stefano , Sanges Remo 
Published: November 2019

Abstract
Background
Transposable Elements (TE) are mobile sequences that make up large portions of eukaryote genomes. The functions they play within the complex cellular architecture are still not clearly understood, but it is becoming evident that TE have a role in several physiological and pathological processes. In particular, it has been shown that TE transcription is necessary for the correct development of mice embryos and that their expression is able to finely modulate transcription of coding and non-coding genes. Moreover, their activity in the central nervous system (CNS) and other tissues has been correlated with the creation of somatic mosaicisms and with pathologies such as neurodevelopmental and neurodegenerative diseases as well as cancers.

Results
We analyzed TE expression among different cell types of the Caenorhabditis elegans (C. elegans) early embryo asking if, where and when TE are expressed and whether their expression is correlated with genes playing a role in early embryo development. To answer these questions, we took advantage of a public C. elegans embryonic single-cell RNA-seq (sc-RNAseq) dataset and developed a bioinformatics pipeline able to quantify reads mapping specifically against TE, avoiding counting reads mapping on TE fragments embedded in coding/non-coding transcripts. Our results suggest that i) canonical TE expression analysis tools, which do not discard reads mapping on TE fragments embedded in annotated transcripts, may over-estimate TE expression levels, ii) Long Terminal Repeats (LTR) elements are mostly expressed in undifferentiated cells and might play a role in pluripotency maintenance and activation of the innate immune response, iii) non-LTR are expressed in differentiated cells, in particular in neurons and nervous system-associated tissues, and iv) DNA TE are homogenously expressed throughout the C. elegans early embryo development.

Conclusions
TE expression appears finely modulated in the C. elegans early embryo and different TE classes are expressed in different cell types and stages, suggesting that TE might play diverse functions during early embryo development.
Doxapram alleviates low SpO2 induced by the combination of propofol and fentanyl during painless gastrointestinal endoscopy
Authors: Gu Zhengfeng , Xin Lian , Wang Haoxing , Hu Chunxiao , Wang Zhiping , Lu Shunmei , Xu Jingjing , Qian Yiling , Wang Jun 
Published: November 2019

Abstract
Background
Painless gastrointestinal endoscopy under intravenous propofol anesthesia is widely applied in the clinical scenario. Despite the good sedation and elimination of anxiety that propofol provides, low SpO2 may also result. Doxapram is a respiratory stimulant with a short half-life. The primary aim of this study was to investigate the effects of doxapram on alleviating low SpO2 induced by the combination of propofol and fentanyl during painless gastrointestinal endoscopy.

Methods
In this prospective study, patients scheduled for painless gastrointestinal endoscopy were randomly assigned to group D or S with 55 patients per group. Initially, both groups received a combination of propofol and fentanyl. Patients in group D received 50 mg doxapram after propofol injection, while patients in group S received an equal volume of saline. Vital signs of the patients, propofol dose, examination duration, and incidences of low SpO2 were recorded.

Results
There were no statistical differences in propofol consumption and examination duration between the two groups. Twenty-six patients in group S experienced low SpO2 versus 10 in group D (P = 0.001). Nineteen patients in group S underwent oxygenation with a face mask in contrast to 8 in group D (P = 0.015). Eighteen patients in group S were treated with jaw lifting compared to 5 in group D (P = 0.002). Four patients in group S underwent assisted respiration compared to 2 in group D (without statistical difference). The average oxygen saturation in group S was significantly lower than that in group D at 1, 2 and 3 min after propofol injection (P < 0.001, P = 0.001 and P = 0.020, respectively). There were no statistical differences in oxygen saturation at other time points. There were no statistical differences in MAP and HR (except for the time point of 1 min after the induction) between the two groups.

Conclusions
Low dose of doxapram can effectively alleviate low SpO2 in painless gastrointestinal endoscopy with intravenous propofol, without affecting propofol consumption, examination duration, MAP, or HR.

Trail registration
The study was approved by the Institutional Ethics Committee of Clinical and New Technology of Wuxi People’s Hospital on 20th July, 2018 (KYLLH2018029) and registered in the Chinese Clinical Trial Register on 16th August, 2018 (ChiCTR1800017832).
Can risk modelling improve treatment decisions in asymptomatic carotid stenosis?
Authors: Burke James F. , Morgenstern Lewis B. , Hayward Rodney A. 
Published: November 2019

Abstract
Background
Carotid endarterectomy (CEA) is routinely performed for asymptomatic carotid stenosis, yet its average net benefit is small. Risk stratification may identify high risk patients that would clearly benefit from treatment.

Methods
Retrospective cohort study using data from the Asymptomatic Carotid Atherosclerosis Study (ACAS). Risk factors for poor outcomes were included in backward and forward selection procedures to develop baseline risk models estimating the risk of non-perioperative ipsilateral stroke/TIA. Baseline risk was estimated for all ACAS participants and externally validated using data from the Atherosclerosis Risk in Communities (ARIC) study. Baseline risk was then included in a treatment risk model that explored the interaction of baseline risk and treatment status (CEA vs. medical management) on the patient-centered outcome of any stroke or death, including peri-operative events.

Results
Three baseline risk factors (BMI, creatinine and degree of contralateral stenosis) were selected into our baseline risk model (c-statistic 0.59 [95% CI 0.54–0.65]). The model stratified absolute risk between the lowest and highest risk quintiles (5.1% vs. 12.5%). External validation in ARIC found similar predictiveness (c-statistic 0.58 [0.49–0.67]), but poor calibration across the risk spectrum. In the treatment risk model, CEA was superior to medical management across the spectrum of baseline risk and the magnitude of the treatment effect varied widely between the lowest and highest absolute risk quintiles (3.2% vs. 10.7%).

Conclusion
Even modestly predictive risk stratification tools have the potential to meaningfully influence clinical decision making in asymptomatic carotid disease. However, our ACAS model requires target population recalibration prior to clinical application.
Profiling Mycobacterium tuberculosis transmission and the resulting disease burden in the five highest tuberculosis burden countries
Authors: Ragonnet Romain , Trauer James M. , Geard Nicholas , Scott Nick , McBryde Emma S. 
Published: November 2019

Abstract
Background
Tuberculosis (TB) control efforts are hampered by an imperfect understanding of TB epidemiology. The true age distribution of disease is unknown because a large proportion of individuals with active TB remain undetected. Understanding of transmission is limited by the asymptomatic nature of latent infection and the pathogen’s capacity for late reactivation. A better understanding of TB epidemiology is critically needed to ensure effective use of existing and future control tools.

Methods
We use an agent-based model to simulate TB epidemiology in the five highest TB burden countries—India, Indonesia, China, the Philippines and Pakistan—providing unique insights into patterns of transmission and disease. Our model replicates demographically realistic populations, explicitly capturing social contacts between individuals based on local estimates of age-specific contact in household, school and workplace settings. Time-varying programmatic parameters are incorporated to account for the local history of TB control.

Results
We estimate that the 15–19-year-old age group is involved in more than 20% of transmission events in India, Indonesia, the Philippines and Pakistan, despite representing only 5% of the local TB incidence. According to our model, childhood TB represents around one fifth of the incident TB cases in these four countries. In China, three quarters of incident TB were estimated to occur in the ≥ 45-year-old population. The calibrated per-contact transmission risk was found to be similar in each of the five countries despite their very different TB burdens.

Conclusions
Adolescents and young adults are a major driver of TB in high-incidence settings. Relying only on the observed distribution of disease to understand the age profile of transmission is potentially misleading.