bluuebunny/crossref_metadata_2025_split huggingface dataset:
O26 Intertumoural heterogeneity in the structure of the neurovascular unit in glioma: a retrospective observational cohort study
Authors: Keni S , Smith C , Thompson G , Brennan P M 
Published: July 2021

Abstract

Introduction
The neurovascular unit (NVU) is implicated in glioma tumourigenesis and treatment resistance but intertumoural heterogeneity is not well characterised. We evaluated the structure of the glioma NVU across tumour grades, in primary and recurrent disease. We determined association to overall survival.

Method
Ethics approval was obtained (15/ES/0094). A tissue microarray was constructed using biopsies from 137 patients and was immunostained for endothelial cells (CD31), extracellular matrix (collagen-IV), pericytes (PDGFR-β and α-SMA) and tight junctions (claudin-V). The immunostaining was assessed using QuPath software and compared by one-way analysis of variance with Tukey post-hoc testing. Association to overall survival was by univariate Cox regression with hazard ratios (HR).

Result
Primary grade IV tumours had greater CD31+ than grade II tumours (P = 0.046) or recurrent tumours (P = 0.013). After normalising to CD31+, collagen-IV+ was greater in recurrent tumours than in primary grade IV tumours (P = 0.013). PDGFR-β+ was greater in primary grade II tumours than in primary grade III tumours (P = 0.002), primary grade IV tumours (P &lt; 0.001) or recurrent tumours (P &lt; 0.001). Normalised α-SMA+ was greater in recurrent tumours than in primary grade IV tumours (P = 0.021). CD31 + (HR: 1.028, P = 0.004) and collagen-IV + (HR: 1.014, P = 0.008) were negative prognostic factors. After normalisation, PDGFR-β + (HR: 0.975, P = 0.004), α-SMA + (HR: 0.971, P = 0.020) and claudin-V + (HR: 0.994, P = 0.021) were positive prognostic factors.

Conclusion
Neurovascular remodeling is a feature of malignancy and recurrent tumours have altered neurovascular phenotypes. Markers for pericytes, extracellular matrix and tight junctions supplement classical grading features and predict tumour behavior.

Take-home Message
Neurovascular remodeling is a feature of malignancy and recurrent tumours have altered neurovascular phenotypes. Markers for pericytes, extracellular matrix and tight junctions supplement classical grading features and predict tumour behavior.
O28 Can styloid process and internal carotid artery anatomy be used to predict carotid artery dissection?
Authors: Cruddas L , Joffe M , Baker D 
Published: July 2021

Abstract

Introduction
Carotid artery dissection is a common cause of stroke in the young. It has been related to the association of the carotid artery with fixed neighbouring anatomical structures. This study assesses the association between styloid process length, internal carotid artery position and cervical carotid artery dissection (CCAD). This information would provide potential predicative radiological measurements, which could prevent delays in CCAD diagnosis.

Method
Retrospective data was collected from two central London hospitals over five years. CCAD cases were identified from individuals who underwent computer topography angiography (CTA) of the neck for suspected CCAD. The following data was collected: evidence of CCAD; bilateral styloid process length and presence of styloid-hyoid ligament calcification; bilateral styloid process-internal carotid distance; calcification of carotid arteries and whether their position was aberrant. Cases were dissection-side, age and gender matched with two non-dissection controls.

Result
Three hundred and fifty-five individuals were identified. Fifty individuals had CCAD, of which 4 had bilateral dissection. In individuals with CCAD, average styloid process length was 27.5 mm and styloid process-internal carotid distance was 5.14 mm. There was no significant association between styloid process length or styloid process-internal carotid distance, and CCAD when compared with matched controls. Internal carotid artery aberrancy was significant for non-dissection.

Conclusion
In this study, there was no association between styloid process length and styloid process-internal carotid distance with CCAD. These measurements can not be used to predict the possibility of a CCAD following trauma.

Take-home Message
Anatomy of the styloid process and calcification of the styloid-hyoid ligament are highly variable and many independent factors may contribute to the risk of cervical carotid artery dissection. Radiological measurements of the styloid process alone cannot be used to predict risk and likelihood of cervical carotid artery dissection.
Atypical twin atrioventricular nodal re-entrant tachycardia in a congenitally corrected transposition of the great arteries patient with a surgical repair of a ventricular septal defect: a case report
Authors: Gardey Kévin , Thevenard Rémi , Joly Hervé , Bessière Francis 
Published: August 2021

Abstract

Background
Twin atrioventricular (AV) nodal tachycardia is a rare mechanism of supraventricular arrhythmia, only seen in some specific congenital heart defects (CHD). It consists of a re-entrant circuit between two distinct AV nodes (anterior and inferior). Since both nodes have antegrade and retrograde conduction, there is usually two QRS morphologies in sinus rhythm.

Case summary
This case is about an atypical twin AV nodal tachycardia in a 15 years old patient with congenitally corrected transposition of the great arteries and previous history of a ventricular septal defect repair. The surgical closure was probably responsible of a poor antegrade conduction over the inferior AV node, which was responsible for a unique QRS morphology. He finally received a catheter ablation of the inferior AV node. He remained asymptomatic without anti-arrhythmic drugs at 8-months post-ablation.

Discussion
Twin AV nodal re-entrant tachycardia is a rare phenomenon. The presentation and electrophysiological study can be both atypical due to previous surgical repair. The operator should be aware of specific CHD where twin AV nodal re-entrant tachycardias are expected.
Neither cowardly nor greedy? Buying and selling escape from conscription in revolutionary and post-revolutionary France
Authors: Heuer Jennifer Ngaire 
Published: August 2021

Abstract
In late revolutionary and Napoleonic France, arranging for a paid substitute to fight in one’s place could be a straightforward contract. But it was also a vexed relationship; those who avoided fighting could appear cowardly and selfish and those who accepted money to risk their lives foolhardy or greedy. This article examines replacement from its uneasy institution with conscription in the late Revolution, through its apparent banalization under Napoleon, to its end with peace and a new government—and its quiet return as part of a new law on recruitment in 1818. This approach uncovers the centrality of ideas of family, free choice and sacrifice for both proponents and critics of the practice. It also shows how much the consequences of revolution and war reverberated long after peace was declared, as contemporaries wrestled with the ideological and practical legacies of obligatory military service and the contracts that had promised ways of escaping such service.
Quantifying the origin of membrane polarization
Authors: Li Qiuzi , Feng Lang , Cameron Stephen D , Deckman Harry W , Ertaş Deniz 
Published: August 2021

SUMMARY
There has been substantial interest in applying induced polarization phenomena, which broadly include electrode and membrane polarization, to characterize organic contamination and biogeochemical environments. Several phenomenological models, semi-quantitative models and models for particular pore shapes have been proposed for understanding membrane polarization. Here, we present a theoretical framework that directly relates membrane polarization to intrinsic statistical properties of porous materials through a two-point correlation function of fixed charges in the pore space. Our framework provides a new way of modelling complex pore structures with a few statistical parameters and quantifies how two distinct physical processes drive complex conductivity response in the absence of conducting grains. One process is a coupling of the static inhomogeneous conductivity to the induced oscillatory electric field, whereas the second process is a coupling of the static electric field to the induced conductivity modulation. Including both effects, we quantitatively predict the frequency-dependent membrane polarization and show excellent agreement between our predictions and experiments in model porous materials.
Evaluation of three approaches for simulating 3-D time-domain electromagnetic data
Authors: Rochlitz Raphael , Seidel Marc , Börner Ralph-Uwe 
Published: August 2021

SUMMARY
We implemented and compared the implicit Euler time-stepping approach, the inverse Fourier transform-based approach and the Rational Arnoldi method for simulating 3-D transient electromagnetic data. We utilize the finite-element method with unstructured tetrahedral meshes for the spatial discretization supporting irregular survey geometries and anisotropic material parameters. Both, switch-on and switch-off current waveforms, can be used in combination with direct current solutions of Poisson problems as initial conditions. Moreover, we address important topics such as the incorporation of source currents and opportunities to simulate impulse as well as step response magnetic field data with all approaches for supporting a great variety of applications. Three examples ranging from simple to complex real-world geometries and validations against external codes provide insight into the numerical accuracy, computational performance and unique characteristics of the three applied methods. We further present an application of logarithmic Fourier transforms to convert transient data into the frequency domain. We made all approaches available in the open-source Python toolbox custEM, which previously supported only frequency-domain electromagnetic data. The object-oriented software implementation is suited for further elaboration on distinct modelling topics and the presented examples can serve for benchmarking other codes.
Catholics at Ground Zero: Negotiating (Post) Memory
Authors: McClelland Gwyn 
Published: July 2021

Abstract
As atomic eyewitness memory passes on, and the hibakusha (atomic-bomb survivor) population dwindles, their trauma is increasingly communicated and negotiated by new generations. After the hibakusha, various protagonists are picking up the baton to continue telling the story of Nagasaki, some children of hibakusha and others not. More than seventy-five years after the bomb ‘postmemory’ describes the future of memory after the eyewitnesses are no longer present. Marianne Hirsch introduced this term with the aftermath of the Jewish Holocaust in mind to suggest both continuity and rupture. It has subsequently been used in many other contexts. Here postmemory is applied to the communal memorializing of the atomic bomb event in Nagasaki. Processes of imaginative ‘memory work’ co-create postmemory (in Japanese parlance ni-sei/san-sei or second and third-generation discourse), influencing public history via the Catholic and surrounding community. By observing traces of a multifarious history, including Chinese, Korean, and European influences, and through the lens of emerging postmemory, in this article I reconsider the place of Nagasaki in atomic history.
Fictional Creations
Authors: Steenhagen Maarten 
Published: August 2021

Abstract
Many people assume that fictional entities are encapsulated in the world of fiction. I show that this cannot be right. Some works of fiction tell us about pieces of poetry, music, or theatre written by fictional characters. Such creations are fictional creations, as I call them. Their authors do not exist. But that does not take away that we can perform, recite, or otherwise generate actual instances of such works. This means we can bring such individuals actually into existence, as the works they are. I conclude that the assumption about encapsulation is untenable, unless an exception is made for types.
False detection of rifampicin resistance using Xpert® MTB/RIF Ultra assay due to an A451V mutation in Mycobacterium tuberculosis
Authors: Fitzgibbon Margaret M , Roycroft Emma , Sheehan Gerard , Mc Laughlin Anne-Marie , Quintyne Keith Ian , Brabazon Elaine , O’Meara Mary , Flanagan Peter R , Seagar A -Louise , Laurenson Ian F , Keane Joseph , Rogers Thomas R 
Published: July 2021

Abstract

Background
In a 12 month period, three Irish-born adult cases with pulmonary TB were initially diagnosed by Xpert® MTB/RIF Ultra assay, which detected a rifampicin resistance-conferring mutation prompting treatment as potential MDR cases.

Methods
Further laboratory investigations on the cultured isolates included GenoType MTBDRplus assay, phenotypic drug susceptibility tests using the BD BACTEC MGIT culture system and MIC broth microdilution tests. Sequencing of the rpoB gene was performed using Sanger sequencing and WGS.

Results
Phenotypic drug susceptibility tests determined the isolates to be rifampicin susceptible. Molecular investigations identified an A451V (codon 532) mutation in the Mycobacterium tuberculosis rpoB gene that has not previously been found to cause rifampicin resistance. Genome sequencing revealed that the three isolates’ genomes differed by ≤5 SNPs, indicating a high likelihood of recent transmission events. Furthermore, a cluster of six related M. tuberculosis isolates from our in-house typing database showed four were highly related; all were rifampicin susceptible and lacked this mutation.

Conclusions
False detection of rifampicin resistance, albeit rare, should be considered possible with Xpert® MTB/RIF Ultra assay, particularly in low TB incidence settings. Confirmatory sequencing methods should be performed to prevent the unnecessary use of second-line anti-tuberculous drugs.
DOPE: D-Optimal Pooling Experimental design with application for SARS-CoV-2 screening
Authors: Daon Yair , Huppert Amit , Obolski Uri 
Published: July 2021

Abstract

Objective
Testing individuals for the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen causing the coronavirus disease 2019 (COVID-19), is crucial for curtailing transmission chains. Moreover, rapidly testing many potentially infected individuals is often a limiting factor in controlling COVID-19 outbreaks. Hence, pooling strategies, wherein individuals are grouped and tested simultaneously, are employed. Here, we present a novel pooling strategy that builds on the Bayesian D-optimal experimental design criterion.

Materials and Methods
Our strategy, called DOPE (D-Optimal Pooling Experimental design), is built on a novel Bayesian formulation of pooling. DOPE defines optimal pooled tests as those maximizing the mutual information between data and infection states. We estimate said mutual information via Monte-Carlo sampling and employ a discrete optimization heuristic to maximize it.

Results
We compare DOPE to other, commonly used pooling strategies, as well as to individual testing. DOPE dominates the other strategies as it yields lower error rates while utilizing fewer tests. We show that DOPE maintains this dominance for a variety of infection prevalence values.

Discussion
DOPE has several additional advantages over common pooling strategies: it provides posterior distributions of the probability of infection rather than only binary classification outcomes; it naturally incorporates prior information of infection probabilities and test error rates; and finally, it can be easily extended to include other, newly discovered information regarding COVID-19.

Conclusion
DOPE can substantially improve accuracy and throughput over current pooling strategies. Hence, DOPE can facilitate rapid testing and aid the efforts of combating COVID-19 and other future pandemics.
Electronic health record note review in an outpatient specialty clinic: who is looking?
Authors: Chen Jimmy S , Hribar Michelle R , Goldstein Isaac H , Rule Adam , Lin Wei-Chun , Dusek Haley , Chiang Michael F 
Published: July 2021

Abstract
Note entry and review in electronic health records (EHRs) are time-consuming. While some clinics have adopted team-based models of note entry, how these models have impacted note review is unknown in outpatient specialty clinics such as ophthalmology. We hypothesized that ophthalmologists and ancillary staff review very few notes. Using audit log data from 9775 follow-up office visits in an academic ophthalmology clinic, we found ophthalmologists reviewed a median of 1 note per visit (2.6 ± 5.3% of available notes), while ancillary staff reviewed a median of 2 notes per visit (4.1 ± 6.2% of available notes). While prior ophthalmic office visit notes were the most frequently reviewed note type, ophthalmologists and staff reviewed no such notes in 51% and 31% of visits, respectively. These results highlight the collaborative nature of note review and raise concerns about how cumbersome EHR designs affect efficient note review and the utility of prior notes in ophthalmic clinical care.
FIBER: enabling flexible retrieval of electronic health records data for clinical predictive modeling
Authors: Datta Suparno , Sachs Jan Philipp , FreitasDa Cruz Harry , Martensen Tom , Bode Philipp , Morassi Sasso Ariane , Glicksberg Benjamin S , Böttinger Erwin 
Published: August 2021

Abstract

Objectives
The development of clinical predictive models hinges upon the availability of comprehensive clinical data. Tapping into such resources requires considerable effort from clinicians, data scientists, and engineers. Specifically, these efforts are focused on data extraction and preprocessing steps required prior to modeling, including complex database queries. A handful of software libraries exist that can reduce this complexity by building upon data standards. However, a gap remains concerning electronic health records (EHRs) stored in star schema clinical data warehouses, an approach often adopted in practice. In this article, we introduce the FlexIBle EHR Retrieval (FIBER) tool: a Python library built on top of a star schema (i2b2) clinical data warehouse that enables flexible generation of modeling-ready cohorts as data frames.

Materials and Methods
FIBER was developed on top of a large-scale star schema EHR database which contains data from 8 million patients and over 120 million encounters. To illustrate FIBER’s capabilities, we present its application by building a heart surgery patient cohort with subsequent prediction of acute kidney injury (AKI) with various machine learning models.

Results
Using FIBER, we were able to build the heart surgery cohort (n = 12 061), identify the patients that developed AKI (n = 1005), and automatically extract relevant features (n = 774). Finally, we trained machine learning models that achieved area under the curve values of up to 0.77 for this exemplary use case.

Conclusion
FIBER is an open-source Python library developed for extracting information from star schema clinical data warehouses and reduces time-to-modeling, helping to streamline the clinical modeling process.
An exploratory data quality analysis of time series physiologic signals using a large-scale intensive care unit database
Authors: Afshar Ali S , Li Yijun , Chen Zixu , Chen Yuxuan , Lee Jae Hun , Irani Darius , Crank Aidan , Singh Digvijay , Kanter Michael , Faraday Nauder , Kharrazi Hadi 
Published: August 2021

Abstract
Physiological data, such as heart rate and blood pressure, are critical to clinical decision-making in the intensive care unit (ICU). Vital signs data, which are available from electronic health records, can be used to diagnose and predict important clinical outcomes; While there have been some reports on the data quality of nurse-verified vital sign data, little has been reported on the data quality of higher frequency time-series vital signs acquired in ICUs, that would enable such predictive modeling. In this study, we assessed the data quality issues, defined as the completeness, accuracy, and timeliness, of minute-by-minute time series vital signs data within the MIMIC-III data set, captured from 16009 patient-ICU stays and corresponding to 9410 unique adult patients. We measured data quality of four time-series vital signs data streams in the MIMIC-III data set: heart rate (HR), respiratory rate (RR), blood oxygen saturation (SpO2), and arterial blood pressure (ABP). Approximately, 30% of patient-ICU stays did not have at least 1 min of data during the time-frame of the ICU stay for HR, RR, and SpO2. The percentage of patient-ICU stays that did not have at least 1 min of ABP data was ∼56%. We observed ∼80% coverage of the total duration of the ICU stay for HR, RR, and SpO2. Finally, only 12.5%%, 9.9%, 7.5%, and 4.4% of ICU lengths of stay had ≥ 99% data available for HR, RR, SpO2, and ABP, respectively, that would meet the three data quality requirements we looked into in this study. Our findings on data completeness, accuracy, and timeliness have important implications for data scientists and informatics researchers who use time series vital signs data to develop predictive models of ICU outcomes.
Comparison of early warning scores for sepsis early identification and prediction in the general ward setting
Authors: Yu Sean C , Shivakumar Nirmala , Betthauser Kevin , Gupta Aditi , Lai Albert M , Kollef Marin H , Payne Philip R O , Michelson Andrew P 
Published: August 2021

Abstract
The objective of this study was to directly compare the ability of commonly used early warning scores (EWS) for early identification and prediction of sepsis in the general ward setting. For general ward patients at a large, academic medical center between early-2012 and mid-2018, common EWS and patient acuity scoring systems were calculated from electronic health records (EHR) data for patients that both met and did not meet Sepsis-3 criteria. For identification of sepsis at index time, National Early Warning Score 2 (NEWS 2) had the highest performance (area under the receiver operating characteristic curve: 0.803 [95% confidence interval [CI]: 0.795–0.811], area under the precision recall curves: 0.130 [95% CI: 0.121–0.140]) followed NEWS, Modified Early Warning Score, and quick Sequential Organ Failure Assessment (qSOFA). Using validated thresholds, NEWS 2 also had the highest recall (0.758 [95% CI: 0.736–0.778]) but qSOFA had the highest specificity (0.950 [95% CI: 0.948–0.952]), positive predictive value (0.184 [95% CI: 0.169–0.198]), and F1 score (0.236 [95% CI: 0.220–0.253]). While NEWS 2 outperformed all other compared EWS and patient acuity scores, due to the low prevalence of sepsis, all scoring systems were prone to false positives (low positive predictive value without drastic sacrifices in sensitivity), thus leaving room for more computationally advanced approaches.