bluuebunny/crossref_metadata_2025_split huggingface dataset:
Studying and mitigating the effects of data drifts on ML model performance at the example of chemical toxicity data
Authors: Morger Andrea , Garcia de Lomana Marina , Norinder Ulf , Svensson Fredrik , Kirchmair Johannes , Mathea Miriam , Volkamer Andrea 
Published: May 2022

AbstractMachine learning models are widely applied to predict molecular properties or the biological activity of small molecules on a specific protein. Models can be integrated in a conformal prediction (CP) framework which adds a calibration step to estimate the confidence of the predictions. CP models present the advantage of ensuring a predefined error rate under the assumption that test and calibration set are exchangeable. In cases where the test data have drifted away from the descriptor space of the training data, or where assay setups have changed, this assumption might not be fulfilled and the models are not guaranteed to be valid. In this study, the performance of internally valid CP models when applied to either newer time-split data or to external data was evaluated. In detail, temporal data drifts were analysed based on twelve datasets from the ChEMBL database. In addition, discrepancies between models trained on publicly-available data and applied to proprietary data for the liver toxicity and MNT in vivo endpoints were investigated. In most cases, a drastic decrease in the validity of the models was observed when applied to the time-split or external (holdout) test sets. To overcome the decrease in model validity, a strategy for updating the calibration set with data more similar to the holdout set was investigated. Updating the calibration set generally improved the validity, restoring it completely to its expected value in many cases. The restored validity is the first requisite for applying the CP models with confidence. However, the increased validity comes at the cost of a decrease in model efficiency, as more predictions are identified as inconclusive. This study presents a strategy to recalibrate CP models to mitigate the effects of data drifts. Updating the calibration sets without having to retrain the model has proven to be a useful approach to restore the validity of most models.
Fast evaluation technique for the shear viscosity and ionic conductivity of electrolyte solutions
Authors: Baba Takeshi , Kajita Seiji , Shiga Tohru , Ohba Nobuko 
Published: May 2022

AbstractWith the growing need to obtain ideal materials for various applications, there is an increasing interest in computational methods to rapidly and accurately search for materials. Molecular dynamics simulation is one of the successful methods used to investigate liquid electrolytes with high transport properties applied in lithium-ion batteries. However, further reduction in computational cost is required to find a novel material with the desired properties from a large number of combinations. In this study, we demonstrate an effective fast evaluation technique for shear viscosity and ionic conductivity by molecular dynamics simulation for an exhaustive search of electrolyte materials with high transport properties. The proposed model was combined with a short-time correlation function of the stress tensor and empirical relationships to address the issues of inefficient and uncertain evaluation by conventional molecular dynamics methods. Because we focus on liquid electrolytes consisting of organic solvents and lithium salts, our model requires dissociation ratio and effective diffusion size of lithium salts. Our method is applied to search for the compositional combinations of electrolytes with superior transport properties even at low temperatures. These results correlate well with experimental results.
Seasonal dynamics of ammonia-oxidizing bacteria but not archaea influence soil nitrogen cycling in a semi-arid agricultural soil
Authors: Fisk L. M. , Barton L. , Maccarone L. D. , Jenkins S. N. , Murphy D. V. 
Published: May 2022

AbstractNitrification, a key pathway of nitrogen (N) loss from agricultural soils, is performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). We examined the seasonal dynamics (2 years) of ammonia oxidizer gene abundances across a gradient of soil carbon (C) and N in a semi-arid soil after 8 years of tillage and crop residue treatments. AOB was more dominant than AOA in the surface soil, as AOA were undetected in 96% of samples. Seasonal variation in AOB abundance was related to substrate availability; AOB gene copy numbers increased at the end of the growing season (during summer fallow) following higher concentrations in dissolved organic matter soil water. This suggests increased co-location between AOB and substrate resources in pores still filled with water as the soils dried. AOB was however not statistically related to soil ammonium concentrations, soil water content, rainfall or temperature. Organic matter inputs enhanced AOB abundance independent of seasonal variation. AOB abundance was greatest in autumn and immediately preceding the start of the growing season, and coincided with elevated soil nitrate concentrations. The growth of the AOB population is likely to contribute to increased risk of N loss through leaching and/or denitrification at the start of the crop growing season following summer fallow.
Biochemical and molecular characterization of three serologically different Vibrio harveyi strains isolated from farmed Dicentrarchus labrax from the Adriatic Sea
Authors: Pavlinec Željko , Zupičić Ivana Giovanna , Oraić Dražen , Lojkić Ivana , Fouz Belén , Zrnčić Snježana 
Published: May 2022

AbstractVibrio harveyi is recognized as one of the major causes of vibriosis, a disease that threatens the long-term sustainability of aquaculture. Current research shows that the Mediterranean strains of V. harveyi are serologically heterogeneous, though research comparing the traits of different strains is scarce. This study aims to describe the biochemical, physiological and genetic characteristics of three serologically different strains of V. harveyi isolated from farmed European Sea bass (Dicentrarchus labrax) from the Adriatic Sea. A total of 32 morphological and biochemical markers were examined and, the susceptibility to 13 antimicrobials tested, and then compared the results of high-throughput sequencing and in silico analyses. This study also presents the first whole genome sequences of V. harveyi isolated from European sea bass. A large number of nonsynonymous variations were detected among sequences of the three strains. The prediction analysis of resistance genes did not correspond with the in vitro antimicrobial susceptibility tests. Six virulence genes previously unrelated to virulence of vibrios were detected in all three studied strains. The results show that differences were detected at every level of comparison among the three studied strains isolated from the same fish species originating from a small geographic area.
Mosaic attenuation in non-fibrotic areas as a predictor of non-usual interstitial pneumonia pathologic diagnosis
Authors: Gayá García-Manso Ignacio , Arenas-Jiménez Juan , García-Sevila Raquel , Ruiz-Alcaraz Sandra , Sirera-Matilla Marina , García-Garrigós Elena , Martínez-García María Ángeles , Hernández-Blasco Luis 
Published: May 2022

AbstractThe new radiological diagnostic criteria for diagnosing idiopathic pulmonary fibrosis (IPF) seek to optimize the indications for surgical lung biopsy (SLB). We applied the new criteria to a retrospective series of patients with interstitial lung disease (ILD) who underwent SLB in order to analyse the correlation between the radiological findings suggestive of another diagnosis (especially mosaic attenuation and its location with respect to fibrotic areas) and the usual interstitial pneumonia (UIP) pathologic diagnosis. Two thoracic radiologists reviewed the HRCT images of 83 patients with ILD and SLB, describing the radiological findings and patterns based on the new criteria. The association of each radiological finding with radiological patterns and histology was analysed. Mosaic attenuation is highly prevalent in both the UIP and non-UIP pathologic diagnosis and with similar frequency (80.0% vs. 78.6%). However, the presence of significant mosaic attenuation (≥ 3 lobes) only in non-fibrotic areas was observed in 60.7% of non-UIP pathologic diagnosis compared to 20.0% in UIP. This finding was associated with other diagnoses different from IPF, mostly connective tissue disease-associated interstitial lung disease (CTD-ILD) and hypersensitivity pneumonitis (HP). In our series of pathologically confirmed ILD, mosaic attenuation in non-fibrotic areas was a predictor of non-UIP pathologic diagnosis, and was associated with other diagnoses different from UIP, mostly CTD-ILD and HP. If confirmed in larger series, this finding could constitute a valuable tool for improving the interpretation of radiological patterns.
Giant nonlinear self-phase modulation of large-amplitude spin waves in microscopic YIG waveguides
Authors: Merbouche H. , Divinskiy B. , Nikolaev K. O. , Kaspar C. , Pernice W. H. P. , Gouéré D. , Lebrun R. , Cros V. , Ben Youssef J. , Bortolotti P. , Anane A. , Demokritov S. O. , Demidov V. E. 
Published: May 2022

AbstractNonlinear self-phase modulation is a universal phenomenon responsible, for example, for the formation of propagating dynamic solitons. It has been reported for waves of different physical nature. However its direct experimental observation for spin waves has been challenging. Here we show that exceptionally strong phase modulation can be achieved for spin waves in microscopic waveguides fabricated from nanometer-thick films of magnetic insulator, which support propagation of spin waves with large amplitudes corresponding to angles of magnetization precession exceeding 10°. At these amplitudes, the nonstationary nonlinear dynamic response of the spin system causes an extreme broadening of the spectrum of spin-wave pulses resulting in a strong spatial variation of the spin-wave wavelength and a temporal variation of the spin-wave phase across the pulse. Our findings demonstrate great complexity of nonlinear wave processes in microscopic magnetic structures and importance of their understanding for technical applications of spin waves in integrated devices.
Taxonomic and functional trait-based approaches suggest that aerobic and anaerobic soil microorganisms allow the natural attenuation of oil from natural seeps
Authors: Cébron Aurélie , Borreca Adrien , Beguiristain Thierry , Biache Coralie , Faure Pierre 
Published: May 2022

AbstractNatural attenuation, involving microbial adaptation, helps mitigating the effect of oil contamination of surface soils. We hypothesized that in soils under fluctuating conditions and receiving oil from seeps, aerobic and anaerobic bacteria as well as fungi could coexist to efficiently degrade hydrocarbons and prevent the spread of pollution. Microbial community diversity was studied in soil longitudinal and depth gradients contaminated with petroleum seeps for at least a century. Hydrocarbon contamination was high just next to the petroleum seeps but this level drastically lowered from 2 m distance and beyond. Fungal abundance and alpha-diversity indices were constant along the gradients. Bacterial abundance was constant but alpha-diversity indices were lower next to the oil seeps. Hydrocarbon contamination was the main driver of microbial community assemblage. 281 bacterial OTUs were identified as indicator taxa, tolerant to hydrocarbon, potentially involved in hydrocarbon-degradation or benefiting from the degradation by-products. These taxa belonging to lineages of aerobic and anaerobic bacteria, have specific functional traits indicating the development of a complex community adapted to the biodegradation of petroleum hydrocarbons and to fluctuating conditions. Fungi are less impacted by oil contamination but few taxa should contribute to the metabolic complementary within the microbial consortia forming an efficient barrier against petroleum dissemination.
Course of disease and risk factors for hospitalization in outpatients with a SARS-CoV-2 infection
Authors: Schäfer Eik , Scheer Christian , Saljé Karen , Fritz Anja , Kohlmann Thomas , Hübner Nils-Olaf , Napp Matthias , Fiedler-Lacombe Lizon , Stahl Dana , Rauch Bernhard , Nauck Matthias , Völker Uwe , Felix Stephan , Lucchese Guglielmo , Flöel Agnes , Engeli Stefan , Hoffmann Wolfgang , Hahnenkamp Klaus , Tzvetkov Mladen V. 
Published: May 2022

AbstractWe analyzed symptoms and comorbidities as predictors of hospitalization in 710 outpatients in North-East Germany with PCR-confirmed SARS-CoV-2 infection. During the first 3 days of infection, commonly reported symptoms were fatigue (71.8%), arthralgia/myalgia (56.8%), headache (55.1%), and dry cough (51.8%). Loss of smell (anosmia), loss of taste (ageusia), dyspnea, and productive cough were reported with an onset of 4 days. Anosmia or ageusia were reported by only 18% of the participants at day one, but up to 49% between days 7 and 9. Not all participants who reported ageusia also reported anosmia. Individuals suffering from ageusia without anosmia were at highest risk of hospitalization (OR 6.8, 95% CI 2.5–18.1). They also experienced more commonly dyspnea and nausea (OR of 3.0, 2.9, respectively) suggesting pathophysiological connections between these symptoms. Other symptoms significantly associated with increased risk of hospitalization were dyspnea, vomiting, and fever. Among basic parameters and comorbidities, age > 60 years, COPD, prior stroke, diabetes, kidney and cardiac diseases were also associated with increased risk of hospitalization. In conclusion, due to the delayed onset, ageusia and anosmia may be of limited use in differential diagnosis of SARS-CoV-2. However, differentiation between ageusia and anosmia may be useful for evaluating risk for hospitalization.
Sleep enhances reconsolidation-based strengthening of visuospatial memories
Authors: Jones Bethany J. , Chen Margaret E. , Simoncini Lindsey , Spencer Rebecca M. C. 
Published: May 2022

AbstractConsolidated memories can be returned to a labile state upon reactivation. The re-stabilization of reactivated memories, or reconsolidation, can allow for change in previously established memories. Given the role of sleep in the initial consolidation of memories, sleep may be important for reconsolidation as well. However, effects of sleep on reconsolidation and specific aspects of sleep that may contribute are unclear. Here, participants learned 30 picture-location pairs. After overnight sleep, initial consolidation was tested. Following either one day (Experiment 1) or one week (Experiment 2), participants were tested again to reactivate their memory and then learned 30 novel picture-location pairs. Control groups (Experiment 1) received no reactivation prior to new learning. Twelve hours later, after daytime wakefulness or overnight sleep, participants completed a final memory test. Sleep participants underwent polysomnography between reactivation and final tests. In Experiment 1, reactivation led to preservation of memory compared to no reactivation. Sleep was associated with less post-reactivation memory decline than waking, with memory preservation positively related to time spent in non-rapid-eye movement sleep. In Experiment 2, sleep was associated with greater post-reactivation memory improvement than waking, with improvement positively related to sigma activity. These results suggest sleep enhances reconsolidation-based strengthening of episodic memories.
Liver secretin receptor predicts portoenterostomy outcomes and liver injury in biliary atresia
Authors: Godbole Nimish , Nyholm Iiris , Hukkinen Maria , Davidson Joseph R. , Tyraskis Athanasios , Lohi Jouko , Heikkilä Päivi , Eloranta Katja , Pihlajoki Marjut , Davenport Mark , Heikinheimo Markku , Kyrönlahti Antti , Pakarinen Mikko P. 
Published: May 2022

AbstractBiliary atresia (BA) is a chronic neonatal cholangiopathy characterized by fibroinflammatory bile duct damage. Reliable biomarkers for predicting native liver survival (NLS) following portoenterostomy (PE) surgery are lacking. Herein we explore the utility of 22 preidentified profibrotic molecules closely connected to ductular reaction (DR) and prevailing after successful PE (SPE), in predicting PE outcomes and liver injury. We used qPCR and immunohistochemistry in a BA cohort including liver samples obtained at PE (n = 53) and during postoperative follow-up after SPE (n = 25). Of the 13 genes over-expressed in relation to cholestatic age-matched controls at PE, only secretin receptor (SCTR) expression predicted cumulative 5-year NLS and clearance of jaundice. Patients in the highest SCTR expression tertile showed 34–55% lower NLS than other groups at 1–5 years after PE (P = 0.006–0.04 for each year). SCTR expression was also significantly lower [42 (24–63) vs 75 (39–107) fold, P = 0.015] among those who normalized their serum bilirubin after PE. Liver SCTR expression localized in cholangiocytes and correlated positively with liver fibrosis, DR, and transcriptional markers of fibrosis (ACTA2) and cholangiocytes (KRT7, KRT19) both at PE and after SPE. SCTR is a promising prognostic marker for PE outcomes and associates with liver injury in BA.
In-vitro NET-osis induced by COVID-19 sera is associated to severe clinical course in not vaccinated patients and immune-dysregulation in breakthrough infection
Authors: Romano Alessandra , Parrinello Nunziatina Laura , Barchitta Martina , Manuele Rosy , Puglisi Fabrizio , Maugeri Andrea , Barbato Alessandro , Triolo Anna Maria , Giallongo Cesarina , Tibullo Daniele , La Ferla Lucia , Botta Ciro , Siragusa Sergio , Iacobello Carmelo , Montineri Arturo , Volti Giovanni Li , Agodi Antonella , Palumbo Giuseppe Alberto , Di Raimondo Francesco 
Published: May 2022

AbstractSince neutrophil extracellular traps formation (NET-osis) can be assessed indirectly by treating healthy neutrophils with blood-derived fluids from patients and then measuring the NETs response, we designed a pilot study to convey high-dimensional cytometry of peripheral blood immune cells and cytokines, combined with clinical features, to understand if NET-osis assessment could be included in the immune risk profiling to early prediction of clinical patterns, disease severity, and viral clearance at 28 days in COVID-19 patients. Immune cells composition of peripheral blood, cytokines concentration and in-vitro NETosis were detected in peripheral blood of 41 consecutive COVID-19 inpatients, including 21 mild breakthrough infections compared to 20 healthy donors, matched for sex and age. Major immune dysregulation in peripheral blood in not-vaccinated COVID-19 patients compared to healthy subjects included: a significant reduction of percentage of unswitched memory B-cells and transitional B-cells; loss of naïve CD3+CD4+CD45RA+ and CD3+CD8+CD45RA+ cells, increase of IL-1β, IL-17A and IFN-γ. Myeloid compartment was affected as well, due to the increase of classical (CD14++CD16−) and intermediate (CD14++CD16+) monocytes, overexpressing the activation marker CD64, negatively associated to the absolute counts of CD8+ CD45R0+ cells, IFN-γ and IL-6, and expansion of monocytic-like myeloid derived suppressor cells. In not-vaccinated patients who achieved viral clearance by 28 days we found at hospital admission lower absolute counts of effector cells, namely CD8+T cells, CD4+ T-cells and CD4+CD45RO+ T cells. Percentage of in-vitro NET-osis induced by patients’ sera and NET-osis density were progressively higher in moderate and severe COVID-19 patients than in mild disease and controls. The percentage of in-vitro induced NET-osis was positively associated to circulating cytokines IL-1β, IFN-γ and IL-6. In breakthrough COVID-19 infections, characterized by mild clinical course, we observed increased percentage of in-vitro NET-osis, higher CD4+ CD45RO+ and CD8+ CD45RO+ T cells healthy or mild-COVID-19 not-vaccinated patients, reduced by 24 h of treatment with ACE inhibitor ramipril. Taken together our data highlight the role of NETs in orchestrating the complex immune response to SARS-COV-2, that should be considered in a multi-target approach for COVID-19 treatment.
Artificial neural network-boosted Cardiac Arrest Survival Post-Resuscitation In-hospital (CASPRI) score accurately predicts outcome in cardiac arrest patients treated with targeted temperature management
Authors: Chou Szu-Yi , Bamodu Oluwaseun Adebayo , Chiu Wei-Ting , Hong Chien-Tai , Chan Lung , Chung Chen-Chih 
Published: May 2022

AbstractExisting prognostic models to predict the neurological recovery in patients with cardiac arrest receiving targeted temperature management (TTM) either exhibit moderate accuracy or are too complicated for clinical application. This necessitates the development of a simple and generalizable prediction model to inform clinical decision-making for patients receiving TTM. The present study explores the predictive validity of the Cardiac Arrest Survival Post-resuscitation In-hospital (CASPRI) score in cardiac arrest patients receiving TTM, regardless of cardiac event location, and uses artificial neural network (ANN) algorithms to boost the prediction performance. This retrospective observational study evaluated the prognostic relevance of the CASPRI score and applied ANN to develop outcome prediction models in a cohort of 570 patients with cardiac arrest and treated with TTM between 2014 and 2019 in a nationwide multicenter registry in Taiwan. In univariate logistic regression analysis, the CASPRI score was significantly associated with neurological outcome, with the area under the receiver operating characteristics curve (AUC) of 0.811. The generated ANN model, based on 10 items of the CASPRI score, achieved a training AUC of 0.976 and validation AUC of 0.921, with the accuracy, precision, sensitivity, and specificity of 89.2%, 91.6%, 87.6%, and 91.2%, respectively, for the validation set. CASPRI score has prognostic relevance in patients who received TTM after cardiac arrest. The generated ANN-boosted, CASPRI-based model exhibited good performance for predicting TTM neurological outcome, thus, we propose its clinical application to improve outcome prediction, facilitate decision-making, and formulate individualized therapeutic plans for patients receiving TTM.
Maximizing coverage, reducing time: a usability evaluation method for web-based library systems
Authors: Iqbal Shumaila , Ikram Naveed , Imtiaz Salma , Imtiaz Saima 
Published: May 2022

AbstractThe usability of a Web Based Library System (WBLS) is an important quality attribute that must be met in order for the intended users to be satisfied. These usability quality attributes are available in two forms: general to web systems and domain-specific. It must be evaluated through some evaluation method such as checklist. Many evaluation checklists have been proposed, although they mostly facilitate the evaluation of WBLS’s general usability aspects, but they lack in covering domain-specific usability aspects of WBLS. There is a need to define domain specific usability aspects to maximize the usability for such systems. The purpose of this research is to develop and validates a usability evaluation checklist that supports the evaluation of general as well as specific usability aspects of WBLS. To accomplish this, a control experiment was conducted in the first phase with undergraduate students to develop a usability evaluation checklist that includes both general and specific usability aspects. Another controlled experiment will be used in the second phase to evaluate the effectiveness and efficiency of the proposed checklist with the existing checklist as "Academic Library Website Evaluation Checklist". The manual and statistical result shows that, the proposed usability evaluation checklist is effective with maximum coverage of general and specific usability aspects. Furthermore, the proposed checklist is equally efficient while identifying the usability errors in WBLS. The proposed checklist is beneficial for the academia as well as industry to evaluate the usability of WBLS to an optimal level.