bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exposure Assessment Techniques Applied to the Highly Censored Deepwater Horizon Gulf Oil Spill Personal Measurements
Authors: Stenzel Mark R , Groth Caroline P , Banerjee Sudipto , Ramachandran Gurumurthy , Kwok Richard K , Engel Lawrence S , Sandler Dale P , Stewart Patricia A 
Published: July 2021

Abstract
The GuLF Long-term Follow-up Study (GuLF STUDY) is investigating potential adverse health effects of workers involved in the Deepwater Horizon (DWH) oil spill response and cleanup (OSRC). Over 93% of the 160 000 personal air measurements taken on OSRC workers were below the limit of detection (LOD), as reported by the analytic labs. At this high level of censoring, our ability to develop exposure estimates was limited. The primary objective here was to reduce the number of measurements below the labs’ reported LODs to reflect the analytic methods’ true LODs, thereby facilitating the use of a relatively unbiased and precise Bayesian method to develop exposure estimates for study exposure groups (EGs). The estimates informed a job-exposure matrix to characterize exposure of study participants. A second objective was to develop descriptive statistics for relevant EGs that did not meet the Bayesian criteria of sample size ≥5 and censoring ≤80% to achieve the aforementioned level of bias and precision. One of the analytic labs recalculated the measurements using the analytic method’s LOD; the second lab provided raw analytical data, allowing us to recalculate the data values that fell between the originally reported LOD and the analytical method’s LOD. We developed rules for developing Bayesian estimates for EGs with &gt;80% censoring. The remaining EGs were 100% censored. An order-based statistical method (OBSM) was developed to estimate exposures that considered the number of measurements, geometric standard deviation, and average LOD of the censored samples for N ≥ 20. For N &lt; 20, substitution of ½ of the LOD was assigned. Recalculation of the measurements lowered overall censoring from 93.2 to 60.5% and of the THC measurements, from 83.1 to 11.2%. A total of 71% of the EGs met the ≤15% relative bias and &lt;65% imprecision goal. Another 15% had censoring &gt;80% but enough non-censored measurements to apply Bayesian methods. We used the OBSM for 3% of the estimates and the simple substitution method for 11%. The methods presented here substantially reduced the degree of censoring in the dataset and increased the number of EGs meeting our Bayesian method’s desired performance goal. The OBSM allowed for a systematic and consistent approach impacting only the lowest of the exposure estimates. This approach should be considered when dealing with highly censored datasets.
Tracing the evolution of aneuploid cancers by multiregional sequencing with CRUST
Authors: Chattopadhyay Subhayan , Karlsson Jenny , Valind Anders , Andersson Natalie , Gisselsson David 
Published: July 2021

Abstract
Clonal deconvolution of mutational landscapes is crucial to understand the evolutionary dynamics of cancer. Two limiting factors for clonal deconvolution that have remained unresolved are variation in purity and chromosomal copy number across different samples of the same tumor. We developed a semi-supervised algorithm that tracks variant calls through multi-sample spatiotemporal tumor data. While normalizing allele frequencies based on purity, it also adjusts for copy number changes at clonal deconvolution. Absent à priori copy number data, it renders in silico copy number estimations from bulk sequences. Using published and simulated tumor sequences, we reliably segregated clonal/subclonal variants even at a low sequencing depth (~50×). Given at least one pure tumor sample (&gt;70% purity), we could normalize and deconvolve paired samples down to a purity of 40%. This renders a reliable clonal reconstruction well adapted to multi-regionally sampled solid tumors, which are often aneuploid and contaminated by non-cancer cells.
Distance-guided protein folding based on generalized descent direction
Authors: Wang Liujing , Liu Jun , Xia Yuhao , Xu Jiakang , Zhou Xiaogen , Zhang Guijun 
Published: July 2021

Abstract
Advances in the prediction of the inter-residue distance for a protein sequence have increased the accuracy to predict the correct folds of proteins with distance information. Here, we propose a distance-guided protein folding algorithm based on generalized descent direction, named GDDfold, which achieves effective structural perturbation and potential minimization in two stages. In the global stage, random-based direction is designed using evolutionary knowledge, which guides conformation population to cross potential barriers and explore conformational space rapidly in a large range. In the local stage, locally rugged potential landscape can be explored with the aid of conjugate-based direction integrated into a specific search strategy, which can improve the exploitation ability. GDDfold is tested on 347 proteins of a benchmark set, 24 template-free modeling (FM) approaches targets of CASP13 and 20 FM targets of CASP14. Results show that GDDfold correctly folds [template modeling (TM) score ≥ = 0.5] 316 out of 347 proteins, where 65 proteins have TM scores that are greater than 0.8, and significantly outperforms Rosetta-dist (distance-assisted fragment assembly method) and L-BFGSfold (distance geometry optimization method). On CASP FM targets, GDDfold is comparable with five state-of-the-art full-version methods, namely, Quark, RaptorX, Rosetta, MULTICOM and trRosetta in the CASP 13 and 14 server groups.
A critical appraisal of the circulating levels of differentially expressed microRNA in endometriosis
Authors: Leonova Anna , Turpin Victoria E , Agarwal Sanjay K , Leonardi Mathew , Foster Warren G 
Published: July 2021

Abstract
Endometriosis is a common gynecological condition characterized by estrogen dependence, chronic pelvic pain, infertility, and diagnostic delay of between 5.4 and 12 years. Despite extensive study, no biomarker, either alone or in combination with other markers, has proven superior to laparoscopy for the diagnosis of endometriosis. Recent studies report that circulating levels of differentially expressed microRNA (miRNA) in women with endometriosis compared with controls are potential diagnostic tools. However, the lack of replication and absence of validated differential expression in novel study populations have led some to question the diagnostic value of miRNA. To elucidate potential reasons for the lack of replication of study results and explore future directions to enhance replicability of circulating miRNA results, we carried out an electronic search of the miRNA literature published between 2000 and 2020. Eighteen studies were identified in which 63 different miRNAs were differentially expressed in the circulation of women with endometriosis compared with controls. However, the differential expressions of only 14 miRNAs were duplicated in one or more studies. While individual miRNAs lacked diagnostic value, miRNA panels yielded sensitivity and specificity equal to or better than laparoscopy in five studies. Important differences in study design, sample processing, and analytical methods were identified rendering direct comparisons across studies problematic and could account for the lack of reproducibility of study results. We conclude that while the results of miRNA studies to date are encouraging, refinements to study design and analytical methods should enhance the reliability of circulating miRNA for the diagnosis of endometriosis.
Identifying online risk markers of hard-to-observe crimes through semi-inductive triangulation: The case of human trafficking in the United States
Authors: de Vries Ieke , Radford Jason 
Published: July 2021

Abstract
Many types of crime are difficult to study because they are hard to operationalize, hidden from the public, or both. With communication increasingly moving to online domains, recent work has begun to examine whether the online domain contains traces of such hard-to-observe crimes. This study explores the online linguistic contours of hard-to-observe crimes through a rigorous mixed-methods approach that combines interviews and computational text analysis. Using human trafficking in illicit massage businesses as a proof-of-concept, we show how this approach, which we call semi-inductive triangulation, meets the empirical contextuality and relationality of crime traces in the online domain. The findings contribute to an emerging field of computational criminology and call for an integration of linguistic approaches in criminology.
Prediction Rules for Ruling Out Endocarditis in Patients With Staphylococcus aureus Bacteremia
Authors: van der Vaart Thomas W , Prins Jan M , Soetekouw Robin , van Twillert Gitte , Veenstra Jan , Herpers Bjorn L , Rozemeijer Wouter , Jansen Rogier R , Bonten Marc J M , van der Meer Jan T M 
Published: July 2021

Abstract

Background
Staphylococcus aureus bacteremia (SAB) is in 10% to 20% of cases complicated by infective endocarditis. Clinical prediction scores may select patients with SAB at highest risk for endocarditis, improving the diagnostic process of endocarditis. We compared the accuracy of the Prediction Of Staphylococcus aureus Infective endocarditiseTime to positivity, Iv drug use, Vascular phenomena, preExisting heart condition (POSITIVE), Predicting Risk of Endocarditis Using a Clinical Tool (PREDICT), and VIRSTA scores for classifying the likelihood of endocarditis in patients with SAB.

Methods
Between August 2017 and September 2019, we enrolled consecutive adult patients with SAB in a prospective cohort study in 7 hospitals in the Netherlands. Using the modified Duke Criteria for definite endocarditis as reference standard, sensitivity, specificity, negative predictive (NPV), and positive predictive values were determined for the POSITIVE, PREDICT, and VIRSTA scores. An NPV of at least 98% was considered safe for excluding endocarditis.

Results
Of 477 SAB patients enrolled, 33% had community-acquired SAB, 8% had a prosthetic valve, and 11% a cardiac implantable electronic device. Echocardiography was performed in 87% of patients, and 42% received transesophageal echocardiography (TEE). Eighty-seven (18.2%) had definite endocarditis. Sensitivity was 77.6% (65.8%–86.9%), 85.1% (75.8%–91.8%), and 98.9% (95.7%–100%) for the POSITIVE (n = 362), PREDICT, and VIRSTA scores, respectively. NPVs were 92.5% (87.9%–95.8%), 94.5% (90.7%–97.0%), and 99.3% (94.9%–100%). For the POSITIVE, PREDICT, and VIRSTA scores, 44.5%, 50.7%, and 70.9% of patients with SAB, respectively, were classified as at high risk for endocarditis.

Conclusions
Only the VIRSTA score had an NPV of at least 98%, but at the expense of a high number of patients classified as high risk and thus requiring TEE.

Clinical Trials Registration
Netherlands Trial Register code 6669.
Impact of nest sanitation behavior on hosts’ egg rejection: an empirical study and meta-analyses
Authors: Li Qihong , Bi Jianli , Wu Jiangwen , Yang Canchao 
Published: July 2021

Abstract
Egg rejection in birds is a specific adaptation toward avian brood parasitism, whereas nest sanitation is a general behavior for cleaning the nest and avoiding predation. However, both behaviors refer to the action of ejecting objects out of the nest, and nest sanitation has been proposed as a pre-adaptation for egg rejection. Here, we tested the eliciting effect of nest sanitation on egg rejection in the red-whiskered bulbul Pycnonotus jocosus, a potential host species that are sympatric with parasitic cuckoos. We conducted meta-analyses of previous studies on both nest sanitation and egg rejection, in order to evaluate the consistency of our conclusions. Our results showed that nest sanitation did not elicit egg rejection in P. jocosus. The conclusions concerning such an eliciting effect from previous studies were mixed, whereas the methodologies were inconsistent, making the studies unsuitable for comparisons. However, the ejection frequency of nest sanitation was consistently higher than the frequency of egg rejection across different host species or populations. These results suggest that nest sanitation, which is an ancient behavior, is more fundamental than egg rejection, but the effect of the former on the latter is complex and needs further study. Standardized methodologies and the integration of behavior, physiology, and modeling may provide better opportunities to explore the relationship between nest sanitation and egg rejection.
Safety, feasibility and prognostic value of stress perfusion CMR in patients with pacemaker
Authors: Pezel T , Lacotte J , Toupin S , Garot P , Hovasse T , Unterseeh T , Sanguineti F , Ait Said M , Salerno F , Fiorina L , Manenti V , Horvilleur J , Garot J 
Published: July 2021

Abstract

Funding Acknowledgements
Type of funding sources: None.

BACKGROUND
Several studies have shown the excellent prognostic value of stress cardiovascular magnetic resonance (CMR). However, its prognostic value in patients with pacemaker (PM) remains unknown because most studies excluded PM patients.

PURPOSE
This study aimed to assess the prognostic value of vasodilator stress perfusion CMR in patients with PM.

METHODS
Consecutive patients with MR-conditional pacemakers referred for stress perfusion CMR at 1.5 T were followed for the occurrence of major adverse cardiovascular events (MACE), defined by cardiovascular death or nonfatal myocardial infarction. Cox regressions analyses were performed to determine the prognostic value of CMR-parameters. The quality of CMR was rated by two observers blinded to clinical details. Data on pacemaker and leads were collected pre- and post-CMR.

RESULTS
Of 224 patients who completed the stress CMR protocol, 2 patients had inconclusive stress CMR due to artefact and 203 patients (72.9% male, mean age 71.4 ± 8.7 years) completed the follow-up (median [interquartile range], 7.0 [5.2-7.3] years). Among those, 23 experienced a MACE (11.3%). Stress CMR was well tolerated with no major adverse events. All scans were completed successfully with no significant change in lead thresholds or pacing parameters. Overall, the image quality was rated good or excellent in 84.1% of segments. Using Kaplan-Meier analysis, inducible ischemia and late gadolinium enhancement (LGE) were significantly associated with the occurrence of MACE (hazard ratio, HR: 11.80 [95% CI, 4.63-30.30]; and HR: 6.74 [95% CI, 2.47-18.40], both p &lt; 0.001; respectively). In multivariable Cox regression, inducible ischemia and LGE were independent predictors of a higher incidence of MACE (HR: 5.24 [95% CI, 2.61-14.40]; and HR: 2.98 [95% CI, 2.25-4.02]; both p &lt; 0.001; respectively). In patients with ischemia, CMR-related coronary revascularization showed no benefit in reducing MACE (p = 0.25).

CONCLUSION
Stress CMR is safe, feasible and has a good discriminative prognostic value in consecutive patients with PM.
Myocardial perfusion after COVID-19 infection: No persisting impaired myocardial blood flow in surviving patients
Authors: Thornton G , Shetye A , Knott K , Razvi Y , Vimalesvaran K , Kurdi H , Artico J , Yousef S , Antonakaki D , Kellman P , Knight D , Cole GD , Moon JC , Fontana M , Treibel TA 
Published: July 2021

Abstract

Funding Acknowledgements
Type of funding sources: None.

Background
Acute myocardial damage is common in hospitalized patients with severe COVID-19, with evidence of myocardial infarction and myocarditis demonstrated on cardiovascular magnetic resonance (CMR). Post-mortem studies have also implicated microvascular thrombosis, which may cause persistent microvascular disease.

Purpose
To determine the long-term coronary sequelae in recovered COVID-19 using multiparametric CMR including state-of-the-art inline quantitative stress myocardial blood flow (sMBF) mapping to assess global and regional sMBF.

Methods
Prospective, multicentre observational study of recovered COVID-19 patients scanned at three London CMR units. Results were compared to a propensity-matched, pre-COVID chest pain cohort (104 patients referred for perfusion CMR, with subsequently demonstrated unobstructed coronary arteries) and 27 healthy volunteers (HV). Perfusion image analysis was performed using a novel artificial intelligence approach deriving global and regional stress and rest MBF with a cut-off of &gt;2.25mL/g/min signifying normal sMBF and &lt;1.82mL/g/min abnormal sMBF (Kotecha JCVI 2019).

Results
104 recovered, post-COVID patients (median age 62 years, 76% male; 89[87%] hospitalised, 41/89[46%] requiring ICU) underwent adenosine-stress perfusion CMR at a median 131(IQR 43-179) days from COVID-19 diagnosis. Median LVEF was 67% (IQR 60-71%; 12 (11.5%) with impaired LVEF), 51 patients (49%) had late gadolinium enhancement (LGE); 18% infarct-pattern and 33% non-ischaemic LGE. Global stress MBF in post-COVID patients was no different to age-, sex- and co-morbidities-matched controls (2.57 ± 0.77 vs. 2.40 ± 0.75 ml/g/min, p = 0.11, Figure 1), though lower than HV (3.00 ± 0.76 ml/g/min, p = 0.001). Post-COVID, multivariate predictors of low sMBF were male sex (OR 0.57, 95%CI 0.41-0.80, p = 0.001) and hypertension (OR 0.67, 95%CI 0.51-0.88, p = 0.004), but not COVID-19 disease severity (ICU admission) or presence of scar (ischemic/non-ischemic). 21/42 with reduced sMBF (&lt;2.25mL/g/min) had regional perfusion defects consistent with epicardial coronary disease.

Conclusions
COVID-19 survivors do not demonstrate evidence of reduced global MBF by CMR compared to risk factor matched controls. Stress perfusion CMR identifies etiology of acute myocardial damage (infarction/myocarditis) and presence of occult coronary ischemia.
Liver magnetic resonance relaxometry can provide useful markers for the assessment of right heart failure in dilated cardiomyopathy
Authors: Rafouli-Stergiou P , Symons R , Droogne W , Dresselaers T , Masci PG , Bogaert J 
Published: July 2021

Abstract

Funding Acknowledgements
Type of funding sources: None.

Introduction
In dilated cardiomyopathy (DCM) patients at risk of developing right heart failure (RHF), early depiction of congestive heart failure (CHF) is pivotal to inform about the hemodynamic status and tailor medical therapy.

Purpose
We hypothesized that increased liver relaxation times measured at routine cardiovascular magnetic resonance (CMR), reflecting passive hepatic congestion, may be a valuable imaging biomarker to depict CHF.

Methods
The study cohort included DCM patients with (n = 48) and without (n = 46) right ventricular dysfunction (RVD), defined as a right ventricular ejection fraction &lt;35%, and &gt;45%, respectively, and a control group (n = 40). Native T1, T2, and extracellular volume (ECV) liver values were measured on routinely acquired cardiac maps.

Results
DCM with RVD patients had higher C-reactive protein, troponin I and NT-pro BNP values, and worse LV functional parameters than DCM without RVD patients (all p &lt; 0.001). T1, T2 and ECV liver values were significantly higher in DCM with, compared to DCM without, RVD patients and also compared to controls [T1: 675 ± 88ms vs. 538 ± 39ms and 540 ± 34ms; T2: 54 ± 8ms vs. 45 ± 5ms and 46 ± 4ms; ECV: 36 ± 7% vs. 29 ± 4% and 30 ± 3%, respectively (all p &lt; 0.001)]. Gamma glutamyltranspeptidase (γGT) correlated moderately but significantly with liver native T1 (r2 =0.34), T2 (r2 =0.27), and ECV (r2 =0.23) (all p &lt; 0.001). Using right atrial pressure (RAP &gt; 5 mmHg), as a surrogate measure of RHF, liver native T1 yielded at ROC analysis the highest AUC (0.906), significantly higher than liver ECV (0.813), γGT (0.806), liver T2 (0.797), total bilirubin (0.737) and alkaline phosphatase (0.561) [Figure 1]. A liver native T1 value of 617 ms showed a sensitivity of 79.5% and a specificity of 91.0% in identifying RHF. Density plots to discriminate between presence and absence of RHF are demonstrated at Figure 2. Excellent intra-/inter-observer agreement was found for assessment of native T1/T2/ECV liver values.

Conclusion
In DCM patients, assessment of liver relaxation times acquired on a CMR exam, may provide valuable information with regard to the presence of RHF.
Outcomes of cardiovascular magnetic resonance imaging in people living with HIV
Authors: Arendt C , De Leuw P , Haberl A , Kann G , Wolf T , Stephan C , Schuettfort G , Arcari L , Vasquez M , Albrecht M , Escher F , Vogl T , Zeiher A , Nagel E , Puntmann V 
Published: July 2021

Abstract

Funding Acknowledgements
Type of funding sources: None.
Background/Introduction
People living with human immunodeficiency virus (HIV, PLWH) are at increased risk of cardiovascular disease (CVD). HIV infection and accelerated traditional risk factors due to highly-active antiretroviral therapy (HAART) are proposed mechanisms for increased rate of heart failure (HF). The pathophysiological drivers of myocardial dysfunction and worse cardiovascular outcome in HIV remain poorly understood.
Purpose
To examine prognostic relationships of cardiac imaging measures with cardiovascular outcome in PLWH on HAART.

Methods
This is a prospective observational longitudinal study using cardiac magnetic resonance (CMR) imaging in consecutive PLHWH on long-term HAART who were screened for underlying CVD and followed up clinically for adjudicated adverse cardiovascular events (cardiovascular mortality, non-fatal acute coronary syndrome, an appropriate device discharge, or a documented HF hospitalization). Imaging protocol included routine assessment of cardiac volumes and function, scar by late gadolinium enhancement, myocardial perfusion and native T1 /T2 mapping. Time-to-event analysis was performed from the index CMR exam to the first single event per patient Systematic risk scores for CVD (Framingham risk score (FRS), Data Collection on Adverse effects of anti-HIV Drugs score, D:A:D and MAGGIC integer score) were calculated using original online calculators.

Results
156 participants (males 62%, 50 [42-57] years of age) were included. 24 events were observed (4 HF deaths, 1 sudden cardiac death, 2 non-fatal acute myocardial infarction, 1 appropriate device discharge and 16 HF hospitalizations) during a median follow-up of 13 [9-19] months. Patients with events had higher native T1 (ms, 1149 [1115-1163] ms vs. 1110 [1075-1138] ms), native T2 (ms, 40 [38-41] vs. 37 [36-39]), LV mass index (g/m², 65 [49-77] vs. 57 [49-64]) p &lt; 0.05 for all). In multivariable analyses, native T1 was independently predictive of adverse events (ChiSq 15.9, p &lt; 0.001, native T1 (10 ms) hazard ratio (95% confidence interval) 1.20 (1.08-1.33), p = 0.001), followed by a model that also included LV mass (ChiSq 17.1, p &lt; 0.001). Traditional cardiovascular risk scores were not predictive of the adverse events.

Conclusions
Native myocardial T1 and LV mass by CMR, as opposed to traditional cardiovascular risk scores, predict cardiovascular outcome in PLWH, together reflecting the pathological myocardial remodeling of myocardial fibrosis and inflammation that potentially explain higher rates of HF in PLWH as compared to the non-infected population. These findings may inform personalized approaches to screening and early intervention to reduce the burden of HF.