bluuebunny/crossref_metadata_2025_split huggingface dataset:
Explaining deep neural networks for knowledge discovery in electrocardiogram analysis
Authors: Hicks Steven A. , Isaksen Jonas L. , Thambawita Vajira , Ghouse Jonas , Ahlberg Gustav , Linneberg Allan , Grarup Niels , Strümke Inga , Ellervik Christina , Olesen Morten Salling , Hansen Torben , Graff Claus , Holstein-Rathlou Niels-Henrik , Halvorsen Pål , Maleckar Mary M. , Riegler Michael A. , Kanters Jørgen K. 
Published: May 2021

AbstractDeep learning-based tools may annotate and interpret medical data more quickly, consistently, and accurately than medical doctors. However, as medical doctors are ultimately responsible for clinical decision-making, any deep learning-based prediction should be accompanied by an explanation that a human can understand. We present an approach called electrocardiogram gradient class activation map (ECGradCAM), which is used to generate attention maps and explain the reasoning behind deep learning-based decision-making in ECG analysis. Attention maps may be used in the clinic to aid diagnosis, discover new medical knowledge, and identify novel features and characteristics of medical tests. In this paper, we showcase how ECGradCAM attention maps can unmask how a novel deep learning model measures both amplitudes and intervals in 12-lead electrocardiograms, and we show an example of how attention maps may be used to develop novel ECG features.
Parental morph combination does not influence innate immune function in nestlings of a colour-polymorphic African raptor
Authors: Nebel Carina , Amar Arjun , Hegemann Arne , Isaksson Caroline , Sumasgutner Petra 
Published: May 2021

AbstractConditions experienced during early life can have long-term individual consequences by influencing dispersal, survival, recruitment and productivity. Resource allocation during development can have strong carry-over effects onto these key parameters and is directly determined by the quality of parental care. In the black sparrowhawk (Accipiter melanoleucus), a colour-polymorphic raptor, parental morphs influence nestling somatic growth and survival, with pairs consisting of different colour morphs (‘mixed-morph pairs’) producing offspring with lower body mass indices, but higher local apparent survival rates. Resource allocation theory could explain this relationship, with nestlings of mixed-morph pairs trading off a more effective innate immune system against somatic growth. We quantified several innate immune parameters of nestlings (hemagglutination, hemolysis, bacteria-killing capacity and haptoglobin concentration) and triggered an immune response by injecting lipopolysaccharides. Although we found that nestlings with lower body mass index had higher local survival rates, we found no support for the proposed hypothesis: neither baseline immune function nor the induced immune response of nestlings was associated with parental morph combination. Our results suggest that these immune parameters are unlikely to be involved in providing a selective advantage for the different colour morphs’ offspring, and thus innate immunity does not appear to be traded off against a greater allocation of resources to somatic growth. Alternative hypotheses explaining the mechanism of a low nestling body mass index leading to subsequent higher local survival could be related to the post-fledgling dependency period or differences in dispersal patterns for the offspring from different morph combinations.
Design of non-autonomous pH oscillators and the existence of chemical beat phenomenon in a neutralization reaction
Authors: Lawson Hugh Shearer , Holló Gábor , Német Norbert , Teraji Satoshi , Nakanishi Hideyuki , Horvath Robert , Lagzi István 
Published: May 2021

AbstractThe beat in physical systems is a transparent and well-understood phenomenon. It may occur in forced oscillatory systems and as a result of the interference of two waves of slightly different frequencies. However, in chemical systems, the realization of the latter type of the beat phenomenon has been lacking. Here we show that a periodic titration of acid and alkaline solutions with each other using programmable syringe pumps in a continuous stirred-tank reactor exhibits the beat phenomenon in the temporal pH oscillation pattern if the time periods of sinusoidal inflow rates of the reagents are slightly different. Interestingly, the frequency of the chemical beat pattern follows the well-known relationship from physics, namely the frequency of the beat is equal to the absolute value of the difference of the two wave frequencies. Based on our strategy, we can design and engineer non-autonomous pH oscillatory systems, in which the characteristics of the temporal oscillations (amplitude, time period) can easily and precisely be controlled by the experimental conditions such as the inflow rates and feed concentrations. The demonstrated phenomena can be exploited in practical applications, we use the non-autonomous pH oscillators to drive the reversible assembly and disassembly of pH-sensitive building blocks (oleic acid and gold nanoparticles), both highly relevant in nanotechnology and biomedical applications.
Accelerated annealing of colloidal crystal monolayers by means of cyclically applied electric fields
Authors: Kao Peng-Kai , VanSaders Bryan J. , Glotzer Sharon C. , Solomon Michael J. 
Published: May 2021

AbstractExternal fields are commonly applied to accelerate colloidal crystallization; however, accelerated self-assembly kinetics can negatively impact the quality of crystal structures. We show that cyclically applied electric fields can produce high quality colloidal crystals by annealing local disorder. We find that the optimal off-duration for maximum annealing is approximately one-half of the characteristic melting half lifetime of the crystalline phase. Local six-fold bond orientational order grows more rapidly than global scattering peaks, indicating that local restructuring leads global annealing. Molecular dynamics simulations of cyclically activated systems show that the ratio of optimal off-duration for maximum annealing and crystal melting time is insensitive to particle interaction details. This research provides a quantitative relationship describing how the cyclic application of fields produces high quality colloidal crystals by cycling at the fundamental time scale for local defect rearrangements; such understanding of dynamics and kinetics can be applied for reconfigurable colloidal assembly.
Evolution of disease transmission during the COVID-19 pandemic: patterns and determinants
Authors: Zhu Jie , Gallego Blanca 
Published: May 2021

AbstractEpidemic models are being used by governments to inform public health strategies to reduce the spread of SARS-CoV-2. They simulate potential scenarios by manipulating model parameters that control processes of disease transmission and recovery. However, the validity of these parameters is challenged by the uncertainty of the impact of public health interventions on disease transmission, and the forecasting accuracy of these models is rarely investigated during an outbreak. We fitted a stochastic transmission model on reported cases, recoveries and deaths associated with SARS-CoV-2 infection across 101 countries. The dynamics of disease transmission was represented in terms of the daily effective reproduction number ($$R_t$$

R
t

). The relationship between public health interventions and $$R_t$$

R
t

was explored, firstly using a hierarchical clustering algorithm on initial $$R_t$$

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t

patterns, and secondly computing the time-lagged cross correlation among the daily number of policies implemented, $$R_t$$

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t

, and daily incidence counts in subsequent months. The impact of updating $$R_t$$

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t

every time a prediction is made on the forecasting accuracy of the model was investigated. We identified 5 groups of countries with distinct transmission patterns during the first 6 months of the pandemic. Early adoption of social distancing measures and a shorter gap between interventions were associated with a reduction on the duration of outbreaks. The lagged correlation analysis revealed that increased policy volume was associated with lower future $$R_t$$

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t

(75 days lag), while a lower $$R_t$$

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t

was associated with lower future policy volume (102 days lag). Lastly, the outbreak prediction accuracy of the model using dynamically updated $$R_t$$

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t

produced an average AUROC of 0.72 (0.708, 0.723) compared to 0.56 (0.555, 0.568) when $$R_t$$

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t

was kept constant. Monitoring the evolution of $$R_t$$

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t

during an epidemic is an important complementary piece of information to reported daily counts, recoveries and deaths, since it provides an early signal of the efficacy of containment measures. Using updated $$R_t$$

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t

values produces significantly better predictions of future outbreaks. Our results found variation in the effect of early public health interventions on the evolution of $$R_t$$

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t

over time and across countries, which could not be explained solely by the timing and number of the adopted interventions.
Occurrence of comorbidities in newly diagnosed type 2 diabetes patients and their impact after 11 years’ follow-up
Authors: Eilat-Tsanani Sophia , Margalit Avital , Golan Liran Nevet 
Published: May 2021

AbstractThe burden of type 2 diabetes is growing, not only through increased incidence, but also through its comorbidities. Concordant comorbidities for type 2 diabetes, such as cardiovascular diseases, are considered expected outcomes of the disease or disease complications, while discordant comorbidities are not considered to be directly related to type 2 diabetes and are less extensively addressed under diabetes management. Here we show that the combination of concordant and discordant comorbidities appears frequently in persons with diabetes (75%). Persons with combined comorbidities visited family physicians more than persons with discordant, concordant or no comorbidity (17.3 ± 10.2, 11.6 ± 6.5, 8.7 ± 6.8, 6.3 ± 6.6 visits/person/year respectively, p < 0.0001). The risk of death during the study period was highest in persons with combined comorbidities and discordant only comorbidities (HR = 33.4; 95% CI 12.5–89.2 and HR = 33.5; 95% CI 11.7–95.8), emphasizing the contribution of discordant comorbidities to the outcome. Our study is unique as a long-term follow-up of an 11-year cohort of 9725 persons with new-onset type 2 diabetes. The findings highlight the contribution of discordant comorbidity to the burden of the disease. The high prevalence of the combination of both concordant and discordant comorbidities, and their appearance before the onset of type 2 diabetes, indicates a continuum of morbidity.
Simplification of culture conditions and feeder-free expansion of bovine embryonic stem cells
Authors: Soto Delia Alba , Navarro Micaela , Zheng Canbin , Halstead Michelle Margaret , Zhou Chuan , Guiltinan Carly , Wu Jun , Ross Pablo Juan 
Published: May 2021

AbstractBovine embryonic stem cells (bESCs) extend the lifespan of the transient pluripotent bovine inner cell mass in vitro. After years of research, derivation of stable bESCs was only recently reported. Although successful, bESC culture relies on complex culture conditions that require a custom-made base medium and mouse embryonic fibroblasts (MEF) feeders, limiting the widespread use of bESCs. We report here simplified bESC culture conditions based on replacing custom base medium with a commercially available alternative and eliminating the need for MEF feeders by using a chemically-defined substrate. bESC lines were cultured and derived using a base medium consisting of N2B27 supplements and 1% BSA (NBFR-bESCs). Newly derived bESC lines were easy to establish, simple to propagate and stable after long-term culture. These cells expressed pluripotency markers and actively proliferated for more than 35 passages while maintaining normal karyotype and the ability to differentiate into derivatives of all three germ lineages in embryoid bodies and teratomas. In addition, NBFR-bESCs grew for multiple passages in a feeder-free culture system based on vitronectin and Activin A medium supplementation while maintaining pluripotency. Simplified conditions will facilitate the use of bESCs for gene editing applications and pluripotency and lineage commitment studies.
High mercury accumulation in deep-ocean hadal sediments
Authors: Sanei Hamed , Outridge Peter M. , Oguri Kazumasa , Stern Gary A. , Thamdrup Bo , Wenzhöfer Frank , Wang Feiyue , Glud Ronnie N. 
Published: May 2021

AbstractOcean sediments are the largest sink for mercury (Hg) sequestration and hence an important part of the global Hg cycle1. Yet accepted global average Hg flux data for deep-ocean sediments (> 200 m depth) are not based on measurements on sediments but are inferred from sinking particulates2. Mercury fluxes have never been reported from the deepest zone, the hadal (> 6 km depth). Here we report the first measurements of Hg fluxes from two hadal trenches (Atacama and Kermadec) and adjacent abyssal areas (2–6 km). Mercury concentrations of up to 400 ng g−1 were the highest recorded in marine sediments remote from anthropogenic or hydrothermal sources. The two trench systems differed significantly in Hg concentrations and fluxes, but hadal and abyssal areas within each system did not. The relatively low recent mean flux at Kermadec was 6–15 times higher than the inferred deep-ocean average1,3, while the median flux across all cores was 22–56 times higher. Thus, some hadal and abyssal sediments are Hg accumulation hot-spots. The hadal zone comprises only ~ 1% of the deep-ocean area, yet a preliminary estimate based on sediment Hg and particulate organic carbon (POC) fluxes suggests total hadal Hg accumulation may be 12–30% of the estimate for the entire deep-ocean. The few abyssal data show equally high Hg fluxes near trench systems. These results highlight a need for further research into deep-ocean Hg fluxes to better constrain global Hg models.
Analysis of the intracellular traffic of IgG in the context of Down syndrome (trisomy 21)
Authors: Cejas R. B. , Tamaño-Blanco M. , Blanco J. G. 
Published: May 2021

AbstractPersons with Down syndrome (DS, trisomy 21) have widespread cellular protein trafficking defects. There is a paucity of data describing the intracellular transport of IgG in the context of endosomal-lysosomal alterations linked to trisomy 21. In this study, we analyzed the intracellular traffic of IgG mediated by the human neonatal Fc receptor (FcRn) in fibroblast cell lines with trisomy 21. Intracellular IgG trafficking studies in live cells showed that fibroblasts with trisomy 21 exhibit higher proportion of IgG in lysosomes (~ 10% increase), decreased IgG content in intracellular vesicles (~ 9% decrease), and a trend towards decreased IgG recycling (~ 55% decrease) in comparison to diploid cells. Amyloid-beta precursor protein (APP) overexpression in diploid fibroblasts replicated the increase in IgG sorting to the degradative pathway observed in cells with trisomy 21. The impact of APP on the expression of FCGRT (alpha chain component of FcRn) was investigated by APP knock down and overexpression of the APP protein. APP knock down increased the expression of FCGRT mRNA by ~ 60% in both diploid and trisomic cells. Overexpression of APP in diploid fibroblasts and HepG2 cells resulted in a decrease in FCGRT and FcRn expression. Our results indicate that the intracellular traffic of IgG is altered in cells with trisomy 21. This study lays the foundation for future investigations into the role of FcRn in the context of DS.
Brain networks involved in the influence of religion on empathy in male Vietnam War veterans
Authors: Cristofori Irene , Zhong Wanting , Cohen-Zimerman Shira , Bulbulia Joseph , Gordon Barry , Krueger Frank , Grafman Jordan 
Published: May 2021

AbstractHumans all over the world believe in spirits and deities, yet how the brain supports religious cognition remains unclear. Drawing on a unique sample of patients with penetrating traumatic brain injuries (pTBI) and matched healthy controls (HCs) we investigate dependencies of religious cognition on neural networks that represent (1) others agents’ intentions (Theory of Mind, ToM) and (2) other agents’ feelings (Empathy). Extending previous observations that ToM networks are recruited during prayer, we find that people with vmPFC damage report higher scores on the personal relationship with God inventory even when they are not praying. This result offers evidence that it is the modulation of ToM networks that support beliefs in supernatural agents. With respect to empathetic processing, we observed that vmPFC and pSTS/TPJ lesions mediated by the strength of the personal relationship with God affect empathetic responses. We suggest that the neurological networks underpinning God representations amplify human empathetic responses. The cultural evolutionary study of religion has argued that supernatural beliefs evoke pro-social responses because people fear the wrath of Gods. Our findings imply greater attention should be paid to the mechanisms by which religious cognition may regulate empathetic responses to others.
Ocular findings among patients surviving COVID-19
Authors: Costa Ílen Ferreira , Bonifácio Livia Pimenta , Bellissimo-Rodrigues Fernando , Rocha Eduardo Melani , Jorge Rodrigo , Bollela Valdes Roberto , Antunes-Foschini Rosalia 
Published: May 2021

AbstractTo describe the medium-term ophthalmological findings in patients recovering from COVID-19. Patients recovered from the acute phase of COVID-19 underwent a complete ophthalmological evaluation, including presenting and best-corrected visual acuity (BCVA), refractometry, biomicroscopy, tonometry, break-up time and Schirmer tests, indirect ophthalmoscopy, color fundus picture, and retinal architecture evaluation using optical coherence tomography. Socio-demographic data and personal medical history were also collected. According to the severity of systemic manifestations, patients were classified into mild-to-moderate, severe, and critical. Sixty-four patients (128 eyes) were evaluated 82 ± 36.4 days after the onset of COVID’s symptoms. The mean ± SD duration of hospitalization was 15.0 ± 10.7 days. Seven patients (10.9%) had mild-to-moderate, 33 (51.5%) severe, and 24 (37.5%) critical disease. Median [interquartile ranges (IQR)] presenting visual acuity was 0.1 (0–0.2) and BCVA 0 (0–0.1). Anterior segment biomicroscopy was unremarkable, except for dry eye disease, verified in 10.9% of them. The mean ± SD intraocular pressure (IOP) in critical group (14.16 ± 1.88 mmHg) was significantly higher than in severe group (12.51 ± 2.40 mmHg), both in the right (p 0.02) and left eyes (p 0.038). Among all, 15.6% had diabetic retinopathy, and two patients presented with discrete white-yellowish dots in the posterior pole, leading to hyporreflective changes at retinal pigment epithelium level, outer segment, and ellipsoid layers. The present study identified higher IOP among critical cases, when compared to severe cases, and discrete outer retina changes 80 days after COVID-19 infection. No sign of uveitis was found.
Spatiotemporal contact density explains the disparity of COVID-19 spread in urban neighborhoods
Authors: Verma Rajat , Yabe Takahiro , Ukkusuri Satish V. 
Published: May 2021

AbstractThe rapid early spread of COVID-19 in the US was experienced very differently by different socioeconomic groups and business industries. In this study, we study aggregate mobility patterns of New York City and Chicago to identify the relationship between the amount of interpersonal contact between people in urban neighborhoods and the disparity in the growth of positive cases among these groups. We introduce an aggregate spatiotemporal contact density index (CDI) to measure the strength of this interpersonal contact using mobility data collected from mobile phones, and combine it with social distancing metrics to show its effect on positive case growth. With the help of structural equations modeling, we find that the effect of CDI on case growth was consistently positive and that it remained consistently higher in lower-income neighborhoods, suggesting a causal path of income on case growth via CDI. Using the CDI, schools and restaurants are identified as high contact density industries, and the estimation suggests that implementing specific mobility restrictions on these point-of-interest categories is most effective. This analysis can be useful in providing insights for government officials targeting specific population groups and businesses to reduce infection spread as reopening efforts continue to expand across the nation.
The carbon source-dependent pattern of antimicrobial activity and gene expression in Pseudomonas donghuensis P482
Authors: Matuszewska Marta , Maciąg Tomasz , Rajewska Magdalena , Wierzbicka Aldona , Jafra Sylwia 
Published: May 2021

AbstractPseudomonas donghuensis P482 is a tomato rhizosphere isolate with the ability to inhibit growth of bacterial and fungal plant pathogens. Herein, we analysed the impact of the carbon source on the antibacterial activity of P482 and expression of the selected genes of three genomic regions in the P482 genome. These regions are involved in the synthesis of pyoverdine, 7-hydroxytropolone (7-HT) and an unknown compound (“cluster 17”) and are responsible for the antimicrobial activity of P482. We showed that the P482 mutants, defective in these regions, show variations and contrasting patterns of growth inhibition of the target pathogen under given nutritional conditions (with glucose or glycerol as a carbon source). We also selected and validated the reference genes for gene expression studies in P. donghuensis P482. Amongst ten candidate genes, we found gyrB, rpoD and mrdA the most stably expressed. Using selected reference genes in RT-qPCR, we assessed the expression of the genes of interest under minimal medium conditions with glucose or glycerol as carbon sources. Glycerol was shown to negatively affect the expression of genes necessary for 7-HT synthesis. The significance of this finding in the light of the role of nutrient (carbon) availability in biological plant protection is discussed.
Influence of intrinsic and extrinsic attributes on neonate survival in an invasive large mammal
Authors: Chinn Sarah M. , Kilgo John C. , Vukovich Mark A. , Beasley James C. 
Published: May 2021

AbstractUnderstanding factors influencing survival of neonates for wild species is important for successful management, particularly for determining drivers of population dynamics. Wild pigs (Sus scrofa) are invasive and populations are rapidly increasing in part due to high reproductive capacity. Survival of adults is generally high, however, survival of piglets, and particularly neonates, is largely unknown. We located neonates at the natal nest and quantified survival in relation to individual and maternal biological attributes, and environmental variables. During 2017–2020, we captured 50 neonates from 13 litters and documented 28 mortalities (56%) over six weeks. Survival was positively influenced by pelage coloration, likely as a form of camouflage from predators. Male neonates had higher survival. They were born larger than females, which could be beneficial for thermoregulation and competition for milk. Neonates born to larger sows had lower survival. Sow size was positively correlated with litter size, and this finding may reflect the increased nutritional demands of sustaining large litters, or difficulties in defending more neonates against predators. Neonates born in warmer months had higher survival than those born in cooler months. Neonates are inefficient thermoregulators, thus being born in warmer months could be beneficial for maintaining homeostasis as well as access to more food resources. These are the largest and most complete data for neonate wild pig survival and will inform population models for the development of management strategies to reduce negative impacts of this destructive invasive species on native ecosystems.