bluuebunny/crossref_metadata_2025_split huggingface dataset:
Usefulness of self‐expandable metal stents for malignant biliary obstruction using a short‐type single‐balloon enteroscope in patients with surgically altered anatomy
Authors: Tanisaka Yuki , Ryozawa Shomei , Mizuide Masafumi , Fujita Akashi , Ogawa Tomoya , Tashima Tomoaki , Noguchi Tatsuya , Suzuki Masahiro , Katsuda Hiromune , Araki Ryuichiro 
Published: January 2021

AbstractObjectivesTo evaluate the efficacy and safety of self‐expandable metal stent (SEMS) placement for unresectable malignant biliary obstruction (MBO) using a short‐type single‐balloon enteroscopy (short SBE) in patients with surgically altered anatomy (SAA).MethodsThe technical success rate, clinical success rate, recurrent biliary obstruction (RBO), time to RBO (TRBO), procedure related adverse events, and reintervention after RBO were evaluated from September 2011 to June 2020.ResultsThirty‐seven patients (11 patients with distal MBO and 26 with hilar MBO) who underwent SEMS placement were included in the analysis. The technical and clinical success rates were 100% and 94.6%. Seven patients underwent bilateral stenting (partial stent‐in‐stent placement) for hilar MBO. The RBO rate was 13.5% (5/37) and the median TRBO was 212 (interquartile range [IQR], 154‐296) days. No food impaction occurred in this study. Procedure related adverse events occurred in 5.4% (2/37) of cases. Reintervention was attempted in five patients and all succeeded (four patients underwent SEMS replacement, and one underwent plastic stent placement).ConclusionsSEMS placement for unresectable MBO using a short SBE in patients with SAA is effective and safe in similar ways to that in patients with normal anatomy in terms of bilateral stenting, stent patency, and reintervention.
Automation of Quantifying Axonal Loss in Patients with Peripheral Neuropathies through Deep Learning Derived Muscle Fat Fraction
Authors: Chen Yongsheng , Moiseev Daniel , Kong Wan Yee , Bezanovski Alexandar , Li Jun 
Published: January 2021

BackgroundAxonal loss denervates muscle, leading to an increase of fat accumulation in the muscle. Therefore, fat fraction (FF) in whole limb muscle using MRI has emerged as a monitoring biomarker for axonal loss in patients with peripheral neuropathies. In this study, we are testing whether deep learning‐based model can automate quantification of the FF in individual muscles. While individual muscle is smaller with irregular shape, manually segmented muscle MRI images have been accumulated in this lab; and make the deep learning feasible.PurposeTo automate segmentation on muscle MRI images through deep learning for quantifying individual muscle FF in patients with peripheral neuropathies.Study TypeRetrospective.Subjects24 patients and 19 healthy controls.Field Strength/Sequences3T; Interleaved 3D GRE.AssessmentA 3D U‐Net model was implemented in segmenting muscle MRI images. This was enabled by leveraging a large set of manually segmented muscle MRI images. B1+ and B1− maps were used to correct image inhomogeneity. Accuracy of the automation was evaluated using Pixel Accuracy (PA), Dice Coefficient (DC) in binary masks; and Bland‐Altman and Pearson correlation by comparing FF values between manual and automated methods.Statistical TestsPA and DC were reported with their median value and standard deviation. Two methods were compared using the ± 95% confidence intervals (CI) of Bland‐Altman analysis and the Pearson’s coefficient (r2).ResultsDC values were from 0.83 ± 0.17 to 0.98 ± 0.02 in thigh and from 0.63 ± 0.18 to 0.96 ± 0.02 in calf muscles. For FF values, the overall ± 95% CI and r2 were [0.49, –0.56] and 0.989 in thigh and [0.84, –0.71] and 0.971 in the calf.Data ConclusionAutomated results well agreed with the manual results in quantifying FF for individual muscles. This method mitigates the formidable time consumption and intense labor in manual segmentations; and enables the use of individual muscle FF as outcome measures in upcoming longitudinal studies.Level of Evidence3Technical Efficacy Stage1
Differential proteome analysis of the leaves of lead hyperaccumulator, Rhoeo discolor (L. Her.) Hance
Authors: Enot Melania M. , Weiland Florian , Mittal Parul , Hoffmann Peter , Sillero‐Mahinay Myrna , Pukala Tara 
Published: January 2021

AbstractThe present study investigated Rhoeo discolor (L. Her.) Hance for its ability to accumulate Pb, which is of relevance to phytoremediation applications. Based on this analysis, plants were found to accumulate greater than 10 mg/g (0.1%) of dry weight Pb in the shoots, which classifies the plant a Pb hyperaccumulator. Further, changes in the leaf proteome profiles in response to Pb stress were investigated. Wild‐type plants were subjected to a high concentration of Pb(NO3)2, and the levels of Pb that accumulated in different plant tissues were determined using atomic absorption spectrophotometry. Using 2D‐difference gel electrophoresis, 181 protein spots were detected to be differentially abundant in response to Pb stress and selected spots exhibiting the strongest differential abundance suggested an impairment of the photosynthetic apparatus of the plant under Pb stress. Subsequently, a more extensive, proteome wide analysis utilizing label‐free quantitation further identified a predominant decrease in protein levels and a significant effect on the nuclear proteome, as well as photosynthesis, carbon fixation and metabolism, providing insight into the Pb tolerance of this system in a potential phytoremediation context.
Collision energies on QTof and Orbitrap instruments: How to make proteomics measurements comparable?
Authors: Szabó Dániel , Schlosser Gitta , Vékey Károly , Drahos László , Révész Ágnes 
Published: January 2021

AbstractQuadrupole time‐of‐flight (QTof) collision‐induced dissociation (CID) and Orbitrap higher‐energy collisional dissociation (HCD) are the most commonly used fragmentation techniques in mass spectrometry‐based proteomics workflows. The information content of the MS/MS spectra is first and foremost determined by the applied collision energy. How can we set up the two instrument types to achieve maximum transferability? To answer this question, we compared MS/MS spectra obtained on a Bruker QTof CID and a Thermo Q‐Exactive Focus Orbitrap HCD instrument as a function of collision energy using the similarity index. Results show that with a few eV lower collision energy setting on HCD (Orbitrap‐specific CID) than on QTof CID, nearly identical MS/MS spectra can be obtained for leucine enkephalin pentapeptide standard, for selected +2 and +3 enolase tryptic peptides and for a large number of peptides in a HeLa protein digest. The Bruker QTof was able to produce colder ions, which may be significant to study inherently labile compounds. Further, we examined energy dependence of peptide identification confidence, as characterized by Mascot scores, on the HeLa peptides. In line with earlier QTof results, this dependence shows one or two maxima (unimodal or bimodal behavior) on Orbitrap. The fraction of bimodal peptides is lower on Orbitrap. Optimal energies as a function of m/z show a similar linear trend on both instruments, which suggests that with appropriate collision energy adjustment, matching conditions for proteomics can be achieved. Data have been deposited in the MassIVE repository (MSV000086434).
Benchmark estimate of the effect of anthropogenic emissions on the ocean surface
Authors: Stone Dáithí A. , Pall Pardeep 
Published: January 2021

AbstractInvestigations into the role of anthropogenic emissions in the occurrence of extreme weather often use a method that compares simulations of atmospheric climate models run under a factual scenario of historical boundary conditions observed during the period of the event against simulations run under a counterfactual scenario of what those boundary conditions might naturally have been over that same period in the absence of anthropogenic emissions. A particular requirement for this experiment design is an accurate estimation of ocean surface boundary conditions for use by the counterfactual natural simulations. Here we use output from the CMIP5 multi‐climate‐model archive to develop a robust estimate of sea surface temperatures and sea ice conditions for use in counterfactual natural simulations, intended as a benchmark estimate to facilitate comparison across climate models and across studies. This development includes tests to ensure that the final estimate is stable from year‐to‐year and stable against other perturbations to the methodology, as well as consideration of the strengths and weaknesses in comparison to other available attributable warming estimates. While this estimate is tailored specifically for the International CLIVAR C20C+ Detection and Attribution Project, it can be used by related projects as well.
Refinement of spectra using a deep neural network: Fully automated removal of noise and background
Authors: Gebrekidan Medhanie Tesfay , Knipfer Christian , Braeuer Andreas Siegfried 
Published: January 2021

AbstractWe report the potential of U‐Net deep neural network for the efficient removal of noise and background from raw Raman spectra. The U‐Net method was first trained on simulated spectra and then tested with experimental spectra. The quality of the test results was quantified via different signal‐to‐noise ratios and the structural similarity index metric. The U‐Net recovered Raman spectra feature a high structural similarity index, even for raw spectra that were dominated by background. The U‐Net model does not rely on any human intervention.
A green molecular imprinted solid‐phase extraction protocol for bisphenol A monitoring with HPLC‐UV to guarantee the quality and safety of walnuts under different storage conditions
Authors: Kalogiouri Natasa P. , Pritsa Agathi , Kabir Abuzar , Furton Kenneth G. , Samanidou Victoria F. 
Published: January 2021

AbstractMonitoring the residual toxicant concentrations in foods is the key step for minimizing potential hazards. The huge interest about food contamination and exposure to endocrine disruptors such as bisphenol A has emerged the development of sensitive analytical methodologies to guarantee the safety and quality of foods. In this work, a green molecularly imprinted solid‐phase extraction protocol coupled with high‐performance liquid chromatography with UV detection was optimized following the principles of green analytical chemistry. An imprinted sol–gel silica‐based hybrid inorganic–organic polymeric sorbent was used to monitor the leaching of bisphenol A from different packaging materials (glass vessels, cans, and polypropylene containers) in walnuts stored within a period of 6 months at 25 and 4°C. Extraction parameters including loading time (5–20 min), solvent type (acetonitrile, ethanol, methanol, acetone, acetonitrile:methanol, 50:50, v/v), and elution flow rate (0.2–1 mL/min) were optimized with one‐factor‐at‐a‐time method. The selected extraction optimum parameters incorporated elution with acetonitrile at 0.2 mL/min flow rate, for 10 min sample holding time. The imprinting factor was equal to 4.55 ± 0.26 (n = 3). The optimized method presented high recovery (94.3 ± 4.2%, n = 3), good linearity (>0.999), intra‐assay repeatability (90.2–95.6%, n = 3), and interassay precision (86.7–93.1%, n = 3).
Level of Foxp3, DNMTs, methylation of Foxp3 promoter region, and CD4 + CD25 + CD127low regulatory T cells in vulvar lichen sclerosus
Authors: Wang Lin , Yi Jin‐Ling , Chen Hai‐Yan , Wang Pei‐Liang , Shen Yan‐Li 
Published: January 2021

AbstractThis study is to investigate the pathogenesis of vulvar lichen sclerosus (VLS) by analyzing the level of Foxp3, DNMTs, methylation of Foxp3 promoter region, and CD4 + CD25 + CD127low Regulatory T cells (Tregs). This study enrolled 15 VLS patients and 25 controls. Lesional and extralesional vulvar skin tissues, normal vulvar skin tissues and peripheral blood were collected. Compared with the control group, Foxp3 protein in the lesional and extralesional skin of VLS group was significantly reduced. The levels of DNMT1 and DNMT3b proteins in lesional skin of VLS group were significantly increased. There was no difference in the total methylation rates of the promoter region of the Foxp3 gene. The methylation rates of CpG1, CpG4, CpG9, and CpG10 were significantly higher in lesional skin of VLS group than in control group. There was no correlation between the total methylation rates of 10 CpG sites and the level of Foxp3 and DNMT1 proteins; there was a positive correlation between Foxp3 and DNMT1 protein in lesional skin of VLS group (r = 0.675, p < 0.05), and a negative correlation (r = −0.665, p < 0.05) in extralesional skin of VLS group. However, there was no correlation of Foxp3 with DNMT3b. The number of CD4 + CD25 + CD127low Tregs VLS decreased significantly. The expression of Foxp3 protein and the quantity of CD4 + CD25 + CD127low Tregs in patients with VLS decreased, which may cause local or systemic abnormal immunosuppression of Tregs, leading to the occurrence of VLS. This may be related with methylation or DNMT1, which needs further verification.
One Hundred Cases of Localized Laryngeal Amyloidosis ‐ Evidence for Future Management
Authors: Harris Georgina , Lachmann Helen , Hawkins Philip , Sandhu Guri 
Published: January 2021

Objective/HypothesisTo update the current understanding of localized laryngeal amyloidosis by analyzing the NHS National Amyloidosis Database and to further clarify the important ongoing management issues.Study DesignRetrospective review, case series.MethodsPatients with laryngeal amyloid were identified from the database of the NHS National Amyloidosis Center, UCL, Royal Free Hospital, London between 2000 and 2017. Patient demographics and disease profile were collated, including the exact location of amyloid deposit, treatments if any, and progression of disease.ResultsOne hundred and three patients with localized laryngeal amyloid where identified from the database, with a mean age of 54 at diagnosis and female to male ratio of 54:49. Three patients were excluded from further analysis due to limited database information. The majority of amyloid was found in either the supraglottis (44) or glottis (53) but all the laryngeal subsites were involved. One‐third of the patients (34) had amyloid in more than one laryngeal subsite. No patients were found to progress to systemic amyloid, but many progressed locally to other subsites or further down the LTB tree (29%). Three patients were successfully treated with radiotherapy after other modalities had failed.ConclusionsThis is the largest case series reported to date of localized laryngeal amyloidosis. It highlights the high incidence of multifocal disease and the significant proportion of patients who progressed, not to systemic amyloidosis but to more extensive localized amyloid. We recommend that in all cases of laryngeal amyloid, patients should undergo a thorough assessment of the upper and lower airways and have ongoing surveillance for at least 15 years.Level of Evidence4 Laryngoscope, 131:E1912–E1917, 2021
PET/CT Poorly Predicts AJCC 8th Edition Pathologic Staging in HPV‐Related Oropharyngeal Cancer
Authors: Snyder Vusala , Goyal Lindsey K. , Bowers Eve M. R. , Kubik Mark , Kim Seungwon , Ferris Robert L. , Johnson Jonas T. , Duvvuri Umamaheswar , Gooding William E. , Branstetter Barton F. , Rath Tanya J. , Sridharan Shaum S. 
Published: January 2021

ObjectiveThe American Joint Committee on Cancer (AJCC) 8th edition introduced distinct clinical and pathological staging paradigms for human papilloma virus positive (HPV+) oropharyngeal squamous cell carcinoma (OPSCC). Treatment planning for OPSCC often utilizes positron emission tomography/computed tomography (PET/CT) to assess clinical stage. We hypothesize that PET/CT will accurately predict final pathologic AJCC 8th edition staging in patients with HPV+ OPSCC.MethodsAll patients with primary HPV+ OPSCC with preoperative PET/CT who underwent transoral robotic surgery and neck dissection between 2011 and 2017 were identified. Data were collected via chart review. Two neuroradiologists performed blinded re‐evaluation of all scans. Primary tumor size and cervical nodal disease characteristics were recorded and TNM staging was extrapolated. Cohen's kappa statistic was used to assess interrater reliability. Test for symmetry was performed to analyze discordance between radiologic and pathologic staging.ResultsForty‐nine patients met inclusion criteria. Interrater reliability was substantial between radiologists for nodal (N) and overall staging (OS) (κ = 0.715 and 0.715). Radiologist A review resulted in identical OS for 67% of patients, overstaging for 31%, and understaging for 2%. Radiologist B review resulted in 61% identical OS, 39% overstaging, and 0% understaging. In misclassified cases, the test of symmetry shows strong bias toward overstaging N stage and OS (P < .001). Radiologic interpretation of extracapsular extension showed poor interrater reliability (κ = 0.403) and poor accuracy.ConclusionPET/CT predicts a higher nodal and overall stage than pathologic staging. PET/CT should not be relied upon for initial tumor staging, as increased FDG uptake is not specific for nodal metastases. PET/CT is shown to be a poor predictor of ECE.Level of Evidence4 Laryngoscope, 131:1535–1541, 2021
Bullying and Children who are Deaf or Hard‐of‐hearing: A Scoping Review
Authors: Bouldin Emerson , Patel Shubham R. , Tey Ching Siong , White Mia , Alfonso Kristan P. , Govil Nandini 
Published: January 2021

Objective/HypothesisThe goal of this scoping review is to evaluate and synthesize the published research regarding bullying and children who are deaf or hard‐of‐hearing (DHH).Study DesignThe Preferred Reporting Items for Systematic Reviews and Meta‐Analyses extension for scoping review (PRISMA‐ScR) statement was used as the guideline for conducting this review.MethodsThis review included studies assessing pediatric (0–21 years) DHH children. Seventy records underwent the initial title‐abstract screening, 33 underwent full‐text review, and 23 studies met inclusion criteria. During the data extraction process, an additional six were excluded, resulting in a total of 17 evaluated studies.ResultsOf the 17 studies assessed, nine compared peer victimization of DHH children and their hearing peers. Of those, seven studies reported that hearing loss (HL) is significantly associated with increased victimization. Two studies found that HL is significantly associated with decreased bullying perpetration. Notably, bullying in DHH children was not associated with a visible sign of disability, such as a hearing assistive device. Rather, variables such as educational setting, parental, and peer support are more likely to mediate bullying in this population.ConclusionsDHH children have a higher risk of peer victimization and may bully others less often than their hearing peers. Studies described the health consequences of bullying in children who are DHH, including sleep issues and anxiety. These consequences may have implications for the patients' overall HL management. Additional research regarding bullying interventions and prevention in this population should be conducted.Level of EvidenceNA Laryngoscope, 131:1884–1892, 2021
Improving Head and Neck Microvascular Reconstructive Care with a Novel Perioperative Checklist
Authors: Kain Joshua J. , Johns James D. , Alexander David , Carroll William R. , Grayson Jessica W. , Buczek Erin J. 
Published: January 2021

Objective/HypothesisTo appraise the utility of a novel EMR‐based checklist for complex head and neck microvascular free‐tissue reconstruction.Study DesignA prospectively collected retrospective matched cohort study from a single tertiary care academic institution.MethodsA retrospective matched cohort study from an academic tertiary care center with 76 total patients analyzed for disease‐specific and quality outcomes before and after implementation of an EMR‐based checklist tailored to complex head and neck care. The intervention group consisted of 38 consecutive patients undergoing microvascular free tissue reconstruction after implementation of the EMR‐based checklist strategy. A historic cohort of 38 patients was derived by matching patients meticulously for disease‐specific and surgical characteristics. Primary outcomes included post‐operative medical and surgical complications, intensive care requirements, 30‐day reoperation rates, hospital length of stay, and completion of preoperative metastatic evaluations. Secondary outcomes included patterns of antibiotic administration, ultimate discharge dispositions, flap survival, and recognition of preoperative hypothyroidism in previously radiated patients.ResultsImplementation of the perioperative checklist yielded an overall reduction in major medical complications (10.5% vs. 29.0%, P < .05*), post‐operative antibiotic administration (17.4% vs. 44.7%, P < .05*), hospital length of stay (median (IQR) days 6 (1) versus 7 (3.25), P < .05*), and improved metastatic evaluation completion (92.1% vs. 63.2%, P < .05*). There was an improved discharge disposition (92.1% vs. 73.7%, P < .05*). No difference was observed in major wound complications (50.0% vs. 57.9%, P = .49), 30‐day re‐operation rates (31.5% vs. 34.2%, P = .81), 30‐day readmission rates (21.1% vs. 21.1%, P > .99), escalations to intensive‐care (13.2% vs. 21.1%, P = .36), or flap survival (97.4% vs. 89.5%, P = .17).ConclusionsUse of our EMR‐based perioperative checklist reduced major medical complications, post‐operative antibiotic administration, hospital length of stay, and improved discharge outcomes for patients undergoing microvascular free‐tissue reconstruction.Level of Evidence3 Laryngoscope, 131:E2251–E2256, 2021
Characteristics of Imperial College London's COVID‐19 research outputs
Authors: Price Robyn , Ozkan Yusuf 
Published: January 2021

AbstractWe identified 651 research outputs on the topic of COVID‐19 in the form of preprint, report, journal article, dataset, and software/code published by Imperial College London authors between January to September 2020. We sought to understand the distribution of outputs over time by output type, peer review status, publisher, and open access status. Search of Scopus, the institutional repositories, Github, and other databases identified relevant research outputs, which were then combined with Unpaywall open access data and manually‐verified associations between preprints and journal articles. Reports were the earliest output to emerge [median: 103 days, interquartile range (IQR): 57.5–129], but journal articles were the most commonly occurring output type over the entire period (60.8%, 396/651). Thirty preprints were identified as connected to a journal article within the set (15.8%, 30/189). A total of 52 publishers were identified, of which 4 publishers account for 59.6% of outputs (388/651). The majority of outputs were available open access through gold, hybrid, or green route (66.1%, 430/651). The presence of exclusively non‐peer reviewed material from January to March suggests that demand could not be met by journals in this period, and the sector supported this with enhanced preprint services for authors. Connections between preprints and published articles suggests that some authors chose to use both dissemination methods and that, as some publishers also serve across both models, traditional distinctions of output types might be changing. The bronze open access cohort brings widespread ‘free’ access but does not ensure true open access.