bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interobserver reproducibility of the PRECISE scoring system for prostate MRI on active surveillance: results from a two-centre pilot study
Authors: Giganti Francesco , Pecoraro Martina , Stavrinides Vasilis , Stabile Armando , Cipollari Stefano , Sciarra Alessandro , Kirkham Alex , Allen Clare , Punwani Shonit , Emberton Mark , Catalano Carlo , Moore Caroline M. , Panebianco Valeria 
Published: December 2019

Abstract
Objectives
We aimed to determine the interobserver reproducibility of the Prostate Cancer Radiological Estimation of Change in Sequential Evaluation (PRECISE) criteria for magnetic resonance imaging in patients on active surveillance (AS) for prostate cancer (PCa) at two different academic centres.

Methods
The PRECISE criteria score the likelihood of clinically significant change over time. The system is a 1-to-5 scale, where 1 or 2 implies regression of a previously visible lesion, 3 denotes stability and 4 or 5 indicates radiological progression. A retrospective analysis of 80 patients (40 from each centre) on AS with a biopsy-confirmed low- or intermediate-risk PCa (i.e. ≤ Gleason 3 + 4 and prostate-specific antigen ≤ 20 ng/ml) and ≥ 2 prostate MR scans was performed. Two blinded radiologists reported all scans independently and scored the likelihood of radiological change (PRECISE score) from the second scan onwards. Cohen’s κ coefficients and percent agreement were computed.

Results
Agreement was substantial both at a per-patient and a per-scan level (κ = 0.71 and 0.61; percent agreement = 79% and 81%, respectively) for each PRECISE score. The agreement was superior (κ = 0.83 and 0.67; percent agreement = 90% and 91%, respectively) when the PRECISE scores were grouped according to the absence/presence of radiological progression (PRECISE 1–3 vs 4–5). Higher inter-reader agreement was observed for the scans performed at University College London (UCL) (κ = 0.81 vs 0.55 on a per-patient level and κ = 0.70 vs 0.48 on a per-scan level, respectively). The discrepancies between institutions were less evident for percent agreement (80% vs 78% and 86% vs 75%, respectively).

Conclusions
Expert radiologists achieved substantial reproducibility for the PRECISE scoring system, especially when data were pooled together according to the absence/presence of radiological progression (PRECISE 1–3 vs 4–5).

Key Points
• Inter-reader agreement between two experienced prostate radiologists using the PRECISE criteria was substantial.
• The agreement was higher when the PRECISE scores were grouped according to the absence/presence of radiological progression (i.e. PRECISE 1–3 vs PRECISE 4 and 5).
• Higher inter-reader agreement was observed for the scans performed at UCL, but the discrepancies between institutions were less evident for percent agreement.
Quantitative measurement of density fluctuations with a full-field laser interferometric vibrometer
Authors: Greiffenhagen Felix , Woisetschläger Jakob , Gürtler Johannes , Czarske Jürgen 
Published: December 2019

Abstract
Modern, lean and premixed gas turbine combustion concepts for low NOx emissions are prone to combustion instabilities. In a previous work it was shown that laser interferometric vibrometry (LIV) can be used to record global as well as local heat release fluctuations in swirl-stabilized premixed methane flames quantitatively, if other effects influencing density are small. In this work a newly developed camera-based full-field LIV system (CLIV) was applied to a lean, confined, premixed and swirl-stabilized methane flame under atmospheric conditions. Instead of time-consuming pointwise scanning of the flame, CLIV records full-field line-of-sight density fluctuations with high spatio-temporal resolution. With a recording rate of 200 kHz, CLIV enables the visualization of highly unsteady processes in fluid dynamics and combustion research. As an example for an unsteady process, the propagation of the flame front through a lean, premixed gas volume is visualized during an ignition process. A discussion of algorithms and assumptions necessary to calculate heat release oscillations from density oscillations is presented and applied to phase-averaged data recorded with CLIV for this type of flame. As reference, OH* chemiluminescence data were recorded simultaneously. While density gradients travelling with the flow are recorded by LIV and CLIV, chemiluminescence imaging will show nothing in the absence of chemical reaction.

Graphic abstract
a Time-averaged density gradient within the combustor in lateral direction. b Density fluctuations along line-of-sight 7 ms after ignition. c Phase-averaged and local heat release fluctuations at 225 Hz perturbation frequency
Isoluminant stimuli in a familiar discrete keying sequence task can be ignored
Authors: Verwey Willem B. 
Published: December 2019

AbstractMotor sequencing models suggest that when with extensive practice sequence representations have developed, stimuli indicating the individual sequence elements may no longer be used for sequence execution. However, it is not clear whether participants can at all refrain from processing these stimuli. Two experiments were performed in which participants practiced two 7-keypress sequences by responding to isoluminant key-specific stimuli. In the mixed condition of the ensuing test phase, the stimuli were displayed only occasionally, and the question was whether this would make participants stop processing these stimuli. In Experiment 1, the benefit of displaying stimuli was assessed after substantial practice, while Experiment 2 examined development of this benefit across practice. The results of Experiment 1 showed that participants rely a little less on these stimuli when they are displayed only occasionally, but Experiment 2 revealed that participants quickly developed high awareness, and that they ignored these stimuli already after limited practice. These findings confirm that participants can choose to ignore these isoluminant stimuli but tend to use them when they are displayed. These and other findings show in some detail how various cognitive systems interact to produce familiar keying sequences.
In the eyes of the beholder: investigating the effect of visual probing on accuracy and gaze fixations when attending to facial expressions among primary and secondary callous-unemotional variants
Authors: Kyranides Melina Nicole , Fanti Kostas A. , Petridou Maria , Kimonis Eva R. 
Published: December 2019

AbstractIndividuals with callous-unemotional (CU) traits show deficits in facial emotion recognition. According to preliminary research, this impairment may be due to attentional neglect to peoples’ eyes when evaluating emotionally expressive faces. However, it is unknown whether this atypical processing pattern is unique to established variants of CU traits or modifiable with intervention. This study examined facial affect recognition and gaze patterns among individuals (N = 80; M age = 19.95, SD = 1.01 years; 50% female) with primary vs secondary CU variants. These groups were identified based on repeated measurements of conduct problems, CU traits, and anxiety assessed in adolescence and adulthood. Accuracy and number of fixations on areas of interest (forehead, eyes, and mouth) while viewing six dynamic emotions were assessed. A visual probe was used to direct attention to various parts of the face. Individuals with primary and secondary CU traits were less accurate than controls in recognizing facial expressions across all emotions. Those identified in the low-anxious primary-CU group showed reduced overall fixations to fearful and painful facial expressions compared to those in the high-anxious secondary-CU group. This difference was not specific to a region of the face (i.e. eyes or mouth). Findings point to the importance of investigating both accuracy and eye gaze fixations, since individuals in the primary and secondary groups were only differentiated in the way they attended to specific facial expression. These findings have implications for differentiated interventions focused on improving facial emotion recognition with regard to attending and correctly identifying emotions.
A Multi-million Mammography Image Dataset and Population-Based Screening Cohort for the Training and Evaluation of Deep Neural Networks—the Cohort of Screen-Aged Women (CSAW)
Authors: Dembrower Karin , Lindholm Peter , Strand Fredrik 
Published: December 2019

AbstractFor AI researchers, access to a large and well-curated dataset is crucial. Working in the field of breast radiology, our aim was to develop a high-quality platform that can be used for evaluation of networks aiming to predict breast cancer risk, estimate mammographic sensitivity, and detect tumors. Our dataset, Cohort of Screen-Aged Women (CSAW), is a population-based cohort of all women 40 to 74 years of age invited to screening in the Stockholm region, Sweden, between 2008 and 2015. All women were invited to mammography screening every 18 to 24 months free of charge. Images were collected from the PACS of the three breast centers that completely cover the region. DICOM metadata were collected together with the images. Screening decisions and clinical outcome data were collected by linkage to the regional cancer center registers. Incident cancer cases, from one center, were pixel-level annotated by a radiologist. A separate subset for efficient evaluation of external networks was defined for the uptake area of one center. The collection and use of the dataset for the purpose of AI research has been approved by the Ethical Review Board. CSAW included 499,807 women invited to screening between 2008 and 2015 with a total of 1,182,733 completed screening examinations. Around 2 million mammography images have currently been collected, including all images for women who developed breast cancer. There were 10,582 women diagnosed with breast cancer; for 8463, it was their first breast cancer. Clinical data include biopsy-verified breast cancer diagnoses, histological origin, tumor size, lymph node status, Elston grade, and receptor status. One thousand eight hundred ninety-one images of 898 women had tumors pixel level annotated including any tumor signs in the prior negative screening mammogram. Our dataset has already been used for evaluation by several research groups. We have defined a high-volume platform for training and evaluation of deep neural networks in the domain of mammographic imaging.
Characterization of microbial communities in ethanol biorefineries
Authors: Firmino Fernanda C , Porcellato Davide , Cox Madison , Suen Garret , Broadbent Jeffery R , Steele James L 
Published: December 2019

Abstract
Bacterial contamination of corn-based ethanol biorefineries can reduce their efficiency and hence increase their carbon footprint. To enhance our understanding of these bacterial contaminants, we temporally sampled four biorefineries in the Midwestern USA that suffered from chronic contamination and characterized their microbiomes using both 16S rRNA sequencing and shotgun metagenomics. These microbiotas were determined to be relatively simple, with 13 operational taxonomic units (OTUs) accounting for 90% of the bacterial population. They were dominated by Firmicutes (89%), with Lactobacillus comprising 80% of the OTUs from this phylum. Shotgun metagenomics confirmed our 16S rRNA data and allowed us to characterize bacterial succession at the species level, with the results of this analysis being that Lb. helveticus was the dominant contaminant in this fermentation. Taken together, these results provide insights into the microbiome of ethanol biorefineries and identifies a species likely to be commonly responsible for chronic contamination of these facilities.
Risk factors for cancer-associated thrombosis in patients undergoing treatment with immune checkpoint inhibitors
Authors: Ando Yosuke , Hayashi Takahiro , Sugimoto Reiko , Nishibe Seira , Ito Kaori , Kawada Kenji , Ikeda Yoshiaki , Yamada Shigeki , Imaizumi Kazuyoshi 
Published: December 2019

SummaryPurpose Anticancer agents are known to increase cancer-associated thrombosis (CAT) onset. CAT onset rate is reported to be 1.92% in cisplatin-based therapy, 6.1% in paclitaxel plus ramucirumab combination therapy, and 11.9% in bevacizumab monotherapy. Because immune checkpoint inhibitors (ICIs) cause a sudden increase in T cell number, an association between administration of these drugs and increase in CAT incidence is likely. However, the extent to which ICI administration affects CAT incidence remains unclear. Further, risk factors for CAT incidence have not yet been identified. The present study investigated CAT incidence and associated risk factors in patients receiving ICI. Methods Patients administered nivolumab or pembrolizumab at Fujita Health University Hospital from April 2017 to March 2018 were enrolled. We collected retrospective data regarding age, sex, cancer type, BMI, medical history, laboratory data at treatment initiation, medications, and computed tomography (CT) interpretations from electronic medical records. Results We identified 122 eligible participants from 135 patients receiving nivolumab or pembrolizumab. Ten patients (8.2%) developed CAT. A history of venous thromboembolism (VTE) or arterial thromboembolism (ATE) was a risk factor for CAT incidence (odds ratio: 6.36, P = 0.039). A history of heart disease may be a risk factor for CAT incidence (odds ratio 6.56, P = 0.052). Significantly higher usage of antiplatelet and anticoagulant therapy was noted in patients who developed CAT (60%) than in those who did not (13.4%, p < 0.01). Conclusion High (8.2%) CAT incidence during ICI administration suggested that ICI is not associated with a lower blood clot risk than other anticancer agents investigated in previous studies. For patients with VTE, ATE, or heart disease history, it is crucial to consider the possibility of CAT even with antiplatelet therapy.
Structural, Electronic, and Magnetic Properties of Mn4N Perovskite: Density Functional Theory Calculations and Monte Carlo Study
Authors: Azouaoui A. , Haoua M. El , Salmi S. , Grini A. El , Benzakour N. , Hourmatallah A. , Bouslykhane K. 
Published: December 2019

AbstractIn this paper, we have studied the structural, electronic, and magnetic properties of the cubic perovskite system Mn4N using the first principles calculations based on density functional theory (DFT) with the generalized gradient approximation (GGA). The obtained data from DFT calculations are used as input data in Monte Carlo simulation with a mixed spin-5/2 and 1 Ising model to calculate the magnetic properties of this compound, such as the total, partial thermal magnetization, and the critical temperatures (TC). The obtained results show that Mn4N has a ferrimagnetic structure with two different sites of Mn in the lattice and presents a metallic behavior. The obtained TC is in good agreement with experimental results.
The Risk of QTc-Interval Prolongation in Breast Cancer Patients Treated with Tamoxifen in Combination with Serotonin Reuptake Inhibitors
Authors: Hussaarts Koen G. A. M. , Berger Florine A. , Binkhorst Lisette , Oomen - de Hoop Esther , van Leeuwen Roelof W. F. , van Alphen Robbert J. , Mathijssen - van Stein Daniëlle , de Groot Natasja M. S. , Mathijssen Ron H. J. , van Gelder Teun 
Published: December 2019

Abstract
Purpose
Antidepressants like the serotonin reuptake inhibitors (SRIs) are often used concomitantly with tamoxifen (e.g. for treatment of depression). This may lead to an additional prolongation of the QTc-interval, with an increased risk of cardiac side effects. Therefore we investigated whether there is a drug-drug interaction between tamoxifen and SRIs resulting in a prolonged QTc-interval.

Methods
Electrocardiograms (ECGs) of 100 patients were collected at steady state tamoxifen treatment, with or without concomitant SRI co-medication. QTc-interval was manually measured and calculated using the Fridericia formula. Primary outcome was difference in QTc-interval between tamoxifen monotherapy and tamoxifen concomitantly with an SRI.

Results
The mean QTc-interval was 12.4 ms longer when tamoxifen was given concomitantly with an SRI (95% CI:1.8–23.1 ms; P = 0.023). Prolongation of the QTc-interval was particularly pronounced for paroxetine (17.2 ms; 95%CI:1.4–33.0 ms; P = 0.04), escitalopram (12.5 ms; 95%CI:4.4–20.6 ms; P < 0.01) and citalopram (20.7 ms; 95%CI:0.7–40.7 ms; P = 0.047), where other agents like venlafaxine did not seem to prolong the QTc-interval. None of the patients had a QTc-interval of >500 ms.

Conclusions
Concomitant use of tamoxifen and SRIs resulted in a significantly higher mean QTc-interval, which was especially the case for paroxetine, escitalopram and citalopram. When concomitant administration with an SRI is warranted venlafaxine is preferred.
A phylogenetically conserved APETALA2/ETHYLENE RESPONSE FACTOR, ERF12, regulates Arabidopsis floral development
Authors: Chandler J. W. , Werr W. 
Published: December 2019

Abstract
Key message
Arabidopsis ETHYLENE RESPONSE FACTOR12 (ERF12), the rice MULTIFLORET SPIKELET1 orthologue pleiotropically affects meristem identity, floral phyllotaxy and organ initiation and is conserved among angiosperms.

Abstract
Reproductive development necessitates the coordinated regulation of meristem identity and maturation and lateral organ initiation via positive and negative regulators and network integrators. We have identified ETHYLENE RESPONSE FACTOR12 (ERF12) as the Arabidopsis orthologue of MULTIFLORET SPIKELET1 (MFS1) in rice. Loss of ERF12 function pleiotropically affects reproductive development, including defective floral phyllotaxy and increased floral organ merosity, especially supernumerary sepals, at incomplete penetrance in the first-formed flowers. Wildtype floral organ number in early formed flowers is labile, demonstrating that floral meristem maturation involves the stabilisation of positional information for organogenesis, as well as appropriate identity. A subset of erf12 phenotypes partly defines a narrow developmental time window, suggesting that ERF12 functions heterochronically to fine-tune stochastic variation in wild type floral number and similar to MFS1, promotes meristem identity. ERF12 expression encircles incipient floral primordia in the inflorescence meristem periphery and is strong throughout the floral meristem and intersepal regions. ERF12 is a putative transcriptional repressor and genetically opposes the function of its relatives DORNRÖSCHEN, DORNRÖSCHEN-LIKE and PUCHI and converges with the APETALA2 pathway. Phylogenetic analysis suggests that ERF12 is conserved among all eudicots and appeared in angiosperm evolution concomitant with the generation of floral diversity.
Mass balance and long-term soil accumulation of trace elements in arable crop systems amended with urban composts or cattle manure during 17 years
Authors: Michaud Aurélia Marcelline , Cambier Philippe , Sappin-Didier Valérie , Deltreil Valentin , Mercier Vincent , Rampon Jean-Noël , Houot Sabine 
Published: December 2019

AbstractOrganic waste products (OWP) application to crop lands makes possible nutrients recycling. However, it can result in long-term accumulation of trace elements (TE) in soils. The present study aimed at (i) assessing the impact of regular applications of urban composts and manure on the TE contents of topsoils and crops in a long-term field experiment, (ii) comparing the TE mass balances with the stock variations of TE in soils, and (iii) proposing a prospective evaluation of this practice, based on estimated soil safe threshold values and simulations of soil TE accumulation for 100 years. In the long-term field experiment, physico-chemical properties and TE contents (Cd, Cr, Cu, Hg, Ni, Pb and Zn) have been measured in OWP, soils, plants and leaching waters for the period 1998–2015, and used for mass balance calculations and long-term simulations of TE accumulations. The composts of green wastes and sludge (GWS) and of municipal solid waste (MSW) were the OWP with the largest TE contents, while the farmyard manure tended to have the lowest. Repeated application of OWP led to significant accumulation of Zn and Cu in the topsoil layer (not for Cr, Cd, Hg, Ni, Pb), especially with GWS, without overpassing calculated protective threshold values. No effect of repeated application of OWP has been observed on TE contents in grains (wheat, maize, barley). The positive mass balance has been dominated by the input flux of TE through OWP and resulted in the observed increases of soil stocks for Cu and Zn. Prospective simulation of soil content evolution until 2100 showed that soil content reached 0.4 mg Cd kg−1 soil (GWS, MSW), 38 mg Cu kg−1 soil (GWS) and 109 mg Zn kg−1 soil (GWS), which remained lower than protective threshold values.
Before Entering Adulthood: Developing an Index of Capabilities for Young Adults in Bogota
Authors: Bucheli Fernando 
Published: December 2019

AbstractQoL studies conceptualise urban well-being as a multidimensional process that is influenced by personal and environmental factors. A much less explored field in QoL has to do with the notion of capabilities and functionings as measurements to evaluate the level of quality of life that people experience in cities. By investigating the young adults category, this article develops a measurement of QoL based on the normative framework of the Capability Approach (CA) to capture urban domains that affect quality of life in Bogota. This study introduces a quantitative methodology to use secondary aggregated data to build a QoL measurement based on capabilities. A nonlinear categorical principal component analysis was used to explore the underlying factor structure of a calibration sample (n=6,998). Confirmatory Factor Analysis was conducted to validate identified factors, revealing a good fit (SRMR=0.033, CFI=0.910). The result is a Young Adult Capability Index (YACI) that empirically explores the use of capability achievements as a space for evaluating urban QoL in young adults. A multiple linear regression was calculated to predict YACI based on additional variables which are sensitive to inequality for young adults. Results show that capability scores are lower once young adults enter adulthood. Women arrive with better capabilities from childhood and adolescence than men, but rapidly undergo a marked process of decapitalisation of capabilities during their transition to adulthood, suggesting the need for more attention in the elaboration of public policies for this type of population.