bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diffuse leptomeningeal glioneuronal tumor with high-grade features masquerading as tubercular meningitis—a case report
Authors: Peer Sameer , Murumkar Vivek , Kulanthaivelu Karthik , Prasad Chandrajit , Rao Shilpa , Santosh Vani 
Published: June 2021

Abstract
Background
Diffuse leptomeningeal glioneuronal tumor (DLGNT) has been recently described in the literature. The complete neuroimaging spectrum and histopathological characteristics of this entity are yet to be elucidated. In an endemic region, diffuse leptomeningeal enhancement on neuroimaging with associated communicating hydrocephalus is usually suggestive of infective meningitis and the patients are started on empirical anti-microbial therapy. However, it is important to consider other differential diagnosis of leptomeningeal enhancement in such cases, particularly if the clinical condition does not improve on anti-microbial therapy. An early diagnosis of a neoplastic etiology may be of particular importance as the treatment regimens vary considerably depending on the underlying disease condition.

Case presentation
In this case report, we describe a case of DLGNT with high-grade histopathological features which was initially managed as tubercular meningitis based on the initial neuroimaging findings. Due to worsening of the clinical course and subsequent imaging findings at follow-up, a diagnosis of DLGNT was considered and subsequently proven to be DLGNT with features of anaplasia on histopathological examination of leptomeningeal biopsy specimen.

Conclusion
This case highlights the importance of recognizing certain subtle finding on MRI which may help in an early diagnosis of DLGNT which is crucial for appropriate treatment.
Detecting COVID-19 in chest images based on deep transfer learning and machine learning algorithms
Authors: Rezaeijo Seyed Masoud , Ghorvei Mohammadreza , Abedi-Firouzjah Razzagh , Mojtahedi Hesam , Entezari Zarch Hossein 
Published: June 2021

Abstract
Background
This study aimed to propose an automatic prediction of COVID-19 disease using chest CT images based on deep transfer learning models and machine learning (ML) algorithms.

Results
The dataset consisted of 5480 samples in two classes, including 2740 CT chest images of patients with confirmed COVID-19 and 2740 images of suspected cases was assessed. The DenseNet201 model has obtained the highest training with an accuracy of 100%. In combining pre-trained models with ML algorithms, the DenseNet201 model and KNN algorithm have received the best performance with an accuracy of 100%. Created map by t-SNE in the DenseNet201 model showed not any points clustered with the wrong class.

Conclusions
The mentioned models can be used in remote places, in low- and middle-income countries, and laboratory equipment with limited resources to overcome a shortage of radiologists.
Frequency and Prognostic Impact of ALK Amplifications and Mutations in the European Neuroblastoma Study Group (SIOPEN) High-Risk Neuroblastoma Trial (HR-NBL1)
Authors: Bellini Angela , Pötschger Ulrike , Bernard Virginie , Lapouble Eve , Baulande Sylvain , Ambros Peter F. , Auger Nathalie , Beiske Klaus , Bernkopf Marie , Betts David R. , Bhalshankar Jaydutt , Bown Nick , de Preter Katleen , Clément Nathalie , Combaret Valérie , Font de Mora Jaime , George Sally L. , Jiménez Irene , Jeison Marta , Marques Barbara , Martinsson Tommy , Mazzocco Katia , Morini Martina , Mühlethaler-Mottet Annick , Noguera Rosa , Pierron Gaelle , Rossing Maria , Taschner-Mandl Sabine , Van Roy Nadine , Vicha Ales , Chesler Louis , Balwierz Walentyna , Castel Victoria , Elliott Martin , Kogner Per , Laureys Geneviève , Luksch Roberto , Malis Josef , Popovic-Beck Maja , Ash Shifra , Delattre Olivier , Valteau-Couanet Dominique , Tweddle Deborah A. , Ladenstein Ruth , Schleiermacher Gudrun 
Published: June 2021

PURPOSE In neuroblastoma (NB), the ALK receptor tyrosine kinase can be constitutively activated through activating point mutations or genomic amplification. We studied ALK genetic alterations in high-risk (HR) patients on the HR-NBL1/SIOPEN trial to determine their frequency, correlation with clinical parameters, and prognostic impact. MATERIALS AND METHODS Diagnostic tumor samples were available from 1,092 HR-NBL1/SIOPEN patients to determine ALK amplification status (n = 330), ALK mutational profile (n = 191), or both (n = 571). RESULTS Genomic ALK amplification ( ALKa) was detected in 4.5% of cases (41 out of 901), all except one with MYCN amplification (MNA). ALKa was associated with a significantly poorer overall survival (OS) (5-year OS: ALKa [n = 41] 28% [95% CI, 15 to 42]; no- ALKa [n = 860] 51% [95% CI, 47 to 54], [ P < .001]), particularly in cases with metastatic disease. ALK mutations ( ALKm) were detected at a clonal level (> 20% mutated allele fraction) in 10% of cases (76 out of 762) and at a subclonal level (mutated allele fraction 0.1%-20%) in 3.9% of patients (30 out of 762), with a strong correlation between the presence of ALKm and MNA ( P < .001). Among 571 cases with known ALKa and ALKm status, a statistically significant difference in OS was observed between cases with ALKa or clonal ALKm versus subclonal ALKm or no ALK alterations (5-year OS: ALKa [n = 19], 26% [95% CI, 10 to 47], clonal ALKm [n = 65] 33% [95% CI, 21 to 44], subclonal ALKm (n = 22) 48% [95% CI, 26 to 67], and no alteration [n = 465], 51% [95% CI, 46 to 55], respectively; P = .001). Importantly, in a multivariate model, involvement of more than one metastatic compartment (hazard ratio [HR], 2.87; P < .001), ALKa (HR, 2.38; P = .004), and clonal ALKm (HR, 1.77; P = .001) were independent predictors of poor outcome. CONCLUSION Genetic alterations of ALK (clonal mutations and amplifications) in HR-NB are independent predictors of poorer survival. These data provide a rationale for integration of ALK inhibitors in upfront treatment of HR-NB with ALK alterations.
Identification of Transgender People With Cancer in Electronic Health Records: Recommendations Based on CancerLinQ Observations
Authors: Alpert Ash B. , Komatsoulis George A. , Meersman Stephen C. , Garrett-Mayer Elizabeth , Bruinooge Suanna S. , Miller Robert S. , Potter Danielle , Koronkowski Becky , Stepanski Edward , Dizon Don S. 
Published: June 2021

PURPOSE: Cancer prevalence and outcomes data, necessary to understand disparities in transgender populations, are significantly hampered because gender identity data are not routinely collected. A database of clinical data on people with cancer, CancerLinQ, is operated by the ASCO and collected from practices across the United States and multiple electronic health records. METHODS: To attempt to identify transgender people with cancer within CancerLinQ, we used three criteria: (1) International Classification of Diseases 9/10 diagnosis (Dx) code suggestive of transgender identity; (2) male gender and Dx of cervical, endometrial, ovarian, fallopian tube, or other related cancer; and (3) female gender and Dx of prostate, testicular, penile, or other related cancer. Charts were abstracted to confirm transgender identity. RESULTS: Five hundred fifty-seven cases matched inclusion criteria and two hundred and forty-two were abstracted. Seventy-six percent of patients with Dx codes suggestive of transgender identity were transgender. Only 2% and 3% of the people identified by criteria 2 and 3 had evidence of transgender identity, respectively. Extrapolating to nonabstracted data, we would expect to identify an additional four individuals in category 2 and an additional three individuals in category 3, or a total of 44. The total population in CancerLinQ is approximately 1,300,000. Thus, our methods could identify 0.003% of the total population as transgender. CONCLUSION: Given the need for data regarding transgender people with cancer and the deficiencies of current data resources, a national concerted effort is needed to prospectively collect gender identity data. These efforts will require systemic efforts to create safe healthcare environments for transgender people.
BOIN12: Bayesian Optimal Interval Phase I/II Trial Design for Utility-Based Dose Finding in Immunotherapy and Targeted Therapies
Authors: Lin Ruitao , Zhou Yanhong , Yan Fangrong , Li Daniel , Yuan Ying 
Published: June 2021

PURPOSE For immunotherapy, such as checkpoint inhibitors and chimeric antigen receptor T-cell therapy, where the efficacy does not necessarily increase with the dose, the maximum tolerated dose may not be the optimal dose for treating patients. For these novel therapies, the objective of dose-finding trials is to identify the optimal biologic dose (OBD) that optimizes patients’ risk-benefit trade-off. METHODS We propose a simple and flexible Bayesian optimal interval phase I/II (BOIN12) trial design to find the OBD that optimizes the risk-benefit trade-off. The BOIN12 design makes the decision of dose escalation and de-escalation by simultaneously taking account of efficacy and toxicity and adaptively allocates patients to the dose that optimizes the toxicity-efficacy trade-off. We performed simulation studies to evaluate the performance of the BOIN12 design. RESULTS Compared with existing phase I/II dose-finding designs, the BOIN12 design is simpler to implement, has higher accuracy to identify the OBD, and allocates more patients to the OBD. One of the most appealing features of the BOIN12 design is that its adaptation rule can be pretabulated and included in the protocol. During the trial conduct, clinicians can simply look up the decision table to allocate patients to a dose without complicated computation. CONCLUSION The BOIN12 design is simple to implement and yields desirable operating characteristics. It overcomes the computational and implementation complexity that plagues existing Bayesian phase I/II dose-finding designs and provides a useful design to optimize the dose of immunotherapy and targeted therapy. User-friendly software is freely available to facilitate the application of the BOIN12 design.
Broken Automatons and Barbed Ecologies in Ligia Lewis's Choreographic Imaginary
Authors: D'Oleo Dixa Ramírez 
Published: June 2021

AbstractThis article considers choreographer Ligia Lewis's hour-long ensemble performance Water Will (in Melody) to theorize on the relationship between ecological fugitivity and black fugitive movement. It explores how Lewis's choreography disrupts the colonial space-times of colonialism and slavery by offering portals into other space-times. In Water Will (in Melody), racialized assemblages break down from overuse and from glaring surveillance in the form of illumination. The last few minutes of the piece evoke an ambivalent postapocalyptic space-time where darkness becomes textured with what seems to be moonlight peeking into a wet cave. This ending evokes the ecological of histories of fugitivity and the earthiness of Édouard Glissant's concept of opacity, both frequently overlooked in discussions of black fugitivity. The final section traces Lewis's fugitive choreography into what the article calls the barbed ecologies of the hills of the Dominican Republic and Haiti, sites of black and indigenous marronage and symbiosis.
Introduction
Authors: Andersen Tore Rye , Kjerkegaard Stefan , Stougaard Pedersen Birgitte 
Published: June 2021

AbstractThe digitization of the publishing business has provided publishers with new media and new means of distribution, which in turn have created new modes of reading. The impact of the digital revolution on the production and distribution of literature has already been widely discussed, but much less has been written about how current media developments have affected reading and readers. A central thesis of this special issue is that the phenomenon of reading should be studied from various disciplinary perspectives. Reading as a phenomenon evolves in the intersections among media developments, literary trends, and social practices. By bringing together scholars from literary theory, media studies, aesthetics, anthropology, psychology, and linguistics, the special issue explores different perspectives on how the technological, sensorial, cognitive, participatory, and aesthetic aspects of reading have evolved in recent decades. Reading practices are changing rapidly in close conjunction with the evolving formats in which literature is distributed to its readers. The purpose of the special issue is to provide a forum in which to rethink existing categories and challenge prevalent notions of reading.
Reading, Fast and Slow
Authors: Kukkonen Karin 
Published: June 2021

AbstractReading literature is often contrasted to the use of digital media in terms of speed. While readers engage slowly with a book, they rush through digital environments at an ever faster pace. This article argues against a simple binary between slow/literary and fast/digital. This binary is in fact not native to the public debate about literature in the digital age but can be traced back from the digital revolution to modernist attitudes on literature, as they emerge in Viktor Shklovsky and Walter Benjamin. Drawing on results about reading speed in reading science and on current narrative theory, this article devises an alternative argument for literary reading as a process that unfolds over multiple time scales linked to different layers of meaning making. Reading literature, from this perspective, is not exclusively slow but, rather, works through a combination of both fast and slow processes. The article develops its argument through the example of Alexander Pushkin's classic novella “The Queen of Spades” and then applies this new theoretical account of multispeed literary reading to two novels engaging explicitly with the digital revolution.
“Wave Fronts of Calculation”
Authors: Robles-Anderson Erica 
Published: June 2021

Abstract
This article is a response to Achille Mbembe's “Futures of Life and Futures of Reason,” which is featured in the same issue of Public Culture. The article builds on Mbembe's concept of “wave fronts of calculation” as a means of amplifying a language for political possibilities in a moment when calculability and incalculability determine the boundaries between the biological, social, and technical.
Embryonic stem cells are devoid of macropinocytosis, a trafficking pathway for activin A in differentiated cells
Authors: Kostopoulou Nikoleta , Bellou Sofia , Bagli Eleni , Markou Maria , Kostaras Eleftherios , Hyvönen Marko , Kalaidzidis Yiannis , Papadopoulos Angelos , Chalmantzi Varvara , Kyrkou Athena , Panopoulou Ekaterini , Fotsis Theodore , Murphy Carol 
Published: June 2021

ABSTRACT
Ligand–receptor complexes formed at the plasma membrane are internalised via various endocytic pathways that influence the ultimate signalling output by regulating the selection of interaction partners by the complex along the trafficking route. We report that, in differentiated cells, activin A–receptor complexes are internalised via clathrin-mediated endocytosis (CME) and macropinocytosis (MP), whereas in human embryonic stem cells (hESCs) internalisation occurs via CME. We further show that hESCs are devoid of MP, which becomes functional upon differentiation towards endothelial cells through mesoderm mediators. Our results reveal, for the first time, that MP is an internalisation route for activin A in differentiated cells, and that MP is not active in hESCs and is induced as cells differentiate.
Intracellular flow cytometric lipid analysis – a multiparametric system to assess distinct lipid classes in live cells
Authors: Boumelhem Badwi B. , Pilgrim Chelsea , Zwicker Vincent E. , Kolanowski Jacek L. , Yeo Jia Hao , Jolliffe Katrina A. , New Elizabeth J. , Day Margot L. , Assinder Stephen J. , Fraser Stuart T. 
Published: June 2021

ABSTRACT
The lipid content of mammalian cells varies greatly between cell type. Current methods for analysing lipid components of cells are technically challenging and destructive. Here, we report a facile, inexpensive method to identify lipid content – intracellular flow cytometric lipid analysis (IFCLA). Distinct lipid classes can be distinguished by Nile Blue fluorescence, Nile Red fluorescence or violet autofluorescence. Nile Blue is fluorescent in the presence of unsaturated fatty acids with a carbon chain length greater than 16. Cis-configured fatty acids induce greater Nile Blue fluorescence than their trans-configured counterparts. In contrast, Nile Red exhibits greatest fluorescence in the presence of cholesterol, cholesteryl esters, some triglycerides and phospholipids. Multiparametric spanning-tree progression analysis for density-normalized events (SPADE) analysis of hepatic cellular lipid distribution, including vitamin A autofluorescence, is presented. This flow cytometric system allows for the rapid, inexpensive and non-destructive identification of lipid content, and highlights the differences in lipid biology between cell types by imaging and flow cytometry.
This article has an associated First Person interview with the first author of the paper.
Neural and behavioural responses of the pollen-specialist beeAndrena vagatoSalixodours
Authors: Burger Hannah , Marquardt Melanie , Babucke Katharina , Heuel Kim C. , Ayasse Manfred , Dötterl Stefan , Galizia C. Giovanni 
Published: June 2021

ABSTRACTAn effective means of finding food is crucial for organisms. Whereas specialized animals select a small number of potentially available food sources, generalists use a broader range. Specialist (oligolectic) bees forage on a small range of flowering plants for pollen and use primarily olfactory and visual cues to locate their host flowers. So far, however, little is known about the specific cues oligoleges use to discriminate between hosts and non-hosts and how floral scent compounds of hosts and non-hosts are processed in the bees' olfactory system. In this study, we recorded physiological responses of the antennae (electroantennographic detection coupled to gas chromatography; GC-EAD) and in the brain (optical imaging; GC imaging), and studied host-finding behaviour of oligolectic Andrena vaga bees, a specialist on Salix plants. In total, we detected 37 physiologically active compounds in host and non-host scents. 4-Oxoisophorone, a common constituent in the scent of many Salix species, evoked strong responses in the antennal lobe glomeruli of A. vaga, but not the generalist honeybee Apis mellifera. The specific glomerular responses to 4-oxoisophorone in natural Salix scents reveals a high degree of specialization in A. vaga for this typical Salix odorant component. In behavioural experiments, we found olfactory cues to be the key attractants for A. vaga to Salix hosts, which are also used to discriminate between hosts and non-hosts, and A. vaga demonstrated a behavioural activity for 4-oxoisophorone. A high sensitivity to floral scents enables the specialized bees to effectively find flowers and it appears that A. vaga bees are highly tuned to 4-oxoisophorone at a very low concentration.
Machine learning-based CT radiomics features for the prediction of pulmonary metastasis in osteosarcoma
Authors: Pereira Helcio Mendonça , Leite Duarte Maria Eugenia , Ribeiro Damasceno Igor , de Oliveira Moura Santos Luiz Afonso , Nogueira-Barbosa Marcello Henrique 
Published: June 2021

Objective: This study aims to build machine learning-based CT radiomic features to predict patients developing metastasis after osteosarcoma diagnosis. Methods and materials: This retrospective study has included 81 patients with a histopathological diagnosis of osteosarcoma. The entire dataset was divided randomly into training (60%) and test sets (40%). A data augmentation technique for the minority class was performed in the training set, along with feature’s selection and model’s training. The radiomic features were extracted from CT’s image of the local osteosarcoma. Three frequently used machine learning models tried to predict patients with lung metastases (MT) and those without lung metastases (non-MT). According to the higher area under the curve (AUC), the best classifier was chosen and applied in the testing set with unseen data to provide an unbiased evaluation of the final model. Results: The best classifier for predicting MT and non-MT groups used a Random Forest algorithm. The AUC and accuracy results of the test set were bulky (accuracy of 73% [ 95% coefficient interval (CI): 54%; 87%] and AUC of 0.79 [95% CI: 0.62; 0.96]). Features that fitted the model (radiomics signature) derived from Laplacian of Gaussian and wavelet filters. Conclusions: Machine learning-based CT radiomics approach can provide a non-invasive method with a fair predictive accuracy of the risk of developing pulmonary metastasis in osteosarcoma patients. Advances in knowledge: Models based on CT radiomic analysis help assess the risk of developing pulmonary metastases in patients with osteosarcoma, allowing further studies for those with a worse prognosis.
Saturation recovery-prepared magnetic resonance angiography for assessment of left atrial and esophageal anatomy
Authors: Siebermair Johannes , Kholmovski Eugene G , Sheffer Douglas , Schroeder Joyce , Jensen Leif , Kheirkhahan Mobin , Baher Alex A , Ibrahim Majd M , Reiter Theresa , Rassaf Tienush , Wakili Reza , Marrouche Nassir F , McGann Christopher J , Wilson Brent D 
Published: June 2021

Objectives:
Magnetic resonance angiography (MRA) has been established as an important imaging method in cardiac ablation procedures. In pulmonary vein (PV) isolation procedures, MRA has the potential to minimize the risk of severe complications, such as atrio-esophageal fistula, by providing detailed information on esophageal position relatively to cardiac structures. However, traditional non-gated, first-pass (FP) MRA approaches have several limitations, such as long breath-holds, non-uniform signal intensity throughout the left atrium (LA), and poor esophageal visualization. The aim of this observational study was to validate a respiratory-navigated, ECG-gated (EC), saturation recovery-prepared MRA technique for simultaneous imaging of LA, LA appendage, PVs, esophagus, and adjacent anatomical structures.

Methods:
Before PVI, 106 consecutive patients with a history of AF underwent either conventional FP-MRA (n = 53 patients) or our new EC-MRA (n = 53 patients). Five quality scores (QS) of LA and esophagus visibility were assessed by two experienced readers. The non-parametric Mann–Whitney U-test was used to compare QS between FP-MRA and EC-MRA groups, and linear regression was applied to assess clinical contributors to image quality.

Results:
EC-MRA demonstrated significantly better image quality than FP-MRA in every quality category. Esophageal visibility using the new MRA technique was markedly better than with the conventional FP-MRA technique (median 3.5 [IQR 1] vs median 1.0, p &lt; 0.001). In contrast to FP-MRA, overall image quality of EC-MRA was not influenced by heart rate.

Conclusion:
Our ECG-gated, respiratory-navigated, saturation recovery-prepared MRA technique provides significantly better image quality and esophageal visibility than the established non-gated, breath-holding FP-MRA. Image quality of EC-MRA technique has the additional advantage of being unaffected by heart rate.

Advances in knowledge:
Detailed information of cardiac anatomy has the potential to minimize the risk of severe complications and improve success rates in invasive electrophysiological studies. Our novel ECG-gated, respiratory-navigated, saturation recovery-prepared MRA technique provides significantly better image quality of LA and esophageal structures than the traditional first-pass algorithm. This new MRA technique is robust to arrhythmia (tachycardic, irregular heart rates) frequently observed in AF patients.