bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep learning in systems medicine
Authors: Wang Haiying , Pujos-Guillot Estelle , Comte Blandine , de Miranda Joao Luis , Spiwok Vojtech , Chorbev Ivan , Castiglione Filippo , Tieri Paolo , Watterson Steven , McAllister Roisin , de Melo Malaquias Tiago , Zanin Massimiliano , Rai Taranjit Singh , Zheng Huiru 
Published: November 2020

AbstractSystems medicine (SM) has emerged as a powerful tool for studying the human body at the systems level with the aim of improving our understanding, prevention and treatment of complex diseases. Being able to automatically extract relevant features needed for a given task from high-dimensional, heterogeneous data, deep learning (DL) holds great promise in this endeavour. This review paper addresses the main developments of DL algorithms and a set of general topics where DL is decisive, namely, within the SM landscape. It discusses how DL can be applied to SM with an emphasis on the applications to predictive, preventive and precision medicine. Several key challenges have been highlighted including delivering clinical impact and improving interpretability. We used some prototypical examples to highlight the relevance and significance of the adoption of DL in SM, one of them is involving the creation of a model for personalized Parkinson’s disease. The review offers valuable insights and informs the research in DL and SM.
Data-Driven Classification of Spectral Profiles Reveals Brain Region-Specific Plasticity in Blindness
Authors: Lubinus Christina , Orpella Joan , Keitel Anne , Gudi-Mindermann Helene , Engel Andreas K , Roeder Brigitte , Rimmele Johanna M 
Published: November 2020

Abstract
Congenital blindness has been shown to result in behavioral adaptation and neuronal reorganization, but the underlying neuronal mechanisms are largely unknown. Brain rhythms are characteristic for anatomically defined brain regions and provide a putative mechanistic link to cognitive processes. In a novel approach, using magnetoencephalography resting state data of congenitally blind and sighted humans, deprivation-related changes in spectral profiles were mapped to the cortex using clustering and classification procedures. Altered spectral profiles in visual areas suggest changes in visual alpha-gamma band inhibitory-excitatory circuits. Remarkably, spectral profiles were also altered in auditory and right frontal areas showing increased power in theta-to-beta frequency bands in blind compared with sighted individuals, possibly related to adaptive auditory and higher cognitive processing. Moreover, occipital alpha correlated with microstructural white matter properties extending bilaterally across posterior parts of the brain. We provide evidence that visual deprivation selectively modulates spectral profiles, possibly reflecting structural and functional adaptation.
Foraging and Spatial Ecology of a Polydomous Carpenter Ant,Camponotus leydigi(Hymenoptera: Formicidae), in Tropical Cerrado Savanna: A Natural History Account
Authors: Soares Hélio , Oliveira Paulo S 
Published: November 2020

AbstractCarpenter ants (genus Camponotus) are considered to be predominantly omnivorous, mixing several feeding habits that include predation, scavenging of animal matter, and plant-derived resources. Nitrogen acquisition is crucial for the nutritional ecology of ant colonies because growing larvae require sustainable protein provisioning. Here, we investigate the foraging ecology and the spatial nesting structure of the carpenter ant, Camponotus leydigi Forel, in Brazilian cerrado savanna. By marking workers from different nests with distinct colors, we revealed that C. leydigi occupies physically separated but socially connected nests (up to 30 m apart), a phenomenon known as polydomy. Observational data on aboveground internest movements in C. leydigi corroborate cooperative exchanges between nest units and confirm several types of social connections, including internest transfer of liquid and solid food, transport of colony members (brood, workers), movement of solitary workers, and internest recruitment. Polydomous C. leydigi allocate foragers throughout 1,700 m2, feeding mostly on termites and plant-derived exudates. Influx of exudates is threefold higher compared with solid food. Uric acid pellets excreted by lizards comprise 20% of the solid diet in C. leydigi, a rare quantitative assessment of this peculiar type of nitrogen complementation in ants. Based on video recordings, we hypothesize that nest decentralization in C. leydigi may reduce foraging constraints caused by overt interference by the aggressive ant, Ectatomma brunneum Smith, F. (Hymenoptera: Formicidae), which regularly blocks nest entrances. Our field study enhances the importance of natural history data to clarify selective pressures underlying the evolution of particular behavioral patterns (nutritional and nesting habits) in ants.
The changing nature of gender selection into employment over the great recession
Authors: Dolado Juan J , García-Peñalosa Cecilia , Tarasonis Linas 
Published: November 2020

SUMMARY
The Great Recession has strongly influenced employment patterns across skill and gender groups in EU countries. We analyse how these changes in workforce composition might distort comparisons of conventional measures of gender wage gaps via non-random selection of workers into EU labour markets. We document that male selection (traditionally disregarded) has become positive during the recession, particularly in Southern Europe. As for female selection (traditionally positive), our findings are twofold. Following an increase in the labour-force participation of less-skilled women, due to an added-worker effect, these biases declined in some countries where new female entrants were able to find jobs, whereas they went up in other countries which suffered large female employment losses. Finally, we document that most of these changes in selection patterns were reversed during the subsequent recovery phase, confirming their cyclical nature.
Anomalous Phylogenetic Behavior of Ribosomal Proteins in Metagenome-Assembled Asgard Archaea
Authors: Garg Sriram G , Kapust Nils , Lin Weili , Knopp Michael , Tria Fernando D K , Nelson-Sathi Shijulal , Gould Sven B , Fan Lu , Zhu Ruixin , Zhang Chuanlun , Martin William F 
Published: November 2020

Abstract
Metagenomic studies permit the exploration of microbial diversity in a defined habitat, and binning procedures enable phylogenomic analyses, taxon description, and even phenotypic characterizations in the absence of morphological evidence. Such lineages include asgard archaea, which were initially reported to represent archaea with eukaryotic cell complexity, although the first images of such an archaeon show simple cells with prokaryotic characteristics. However, these metagenome-assembled genomes (MAGs) might suffer from data quality problems not encountered in sequences from cultured organisms due to two common analytical procedures of bioinformatics: assembly of metagenomic sequences and binning of assembled sequences on the basis of innate sequence properties and abundance across samples. Consequently, genomic sequences of distantly related taxa, or domains, can in principle be assigned to the same MAG and result in chimeric sequences. The impacts of low-quality or chimeric MAGs on phylogenomic and metabolic prediction remain unknown. Debates that asgard archaeal data are contaminated with eukaryotic sequences are overshadowed by the lack of evidence indicating that individual asgard MAGs stem from the same chromosome. Here, we show that universal proteins including ribosomal proteins of asgard archaeal MAGs fail to meet the basic phylogenetic criterion fulfilled by genome sequences of cultured archaea investigated to date: These proteins do not share common evolutionary histories to the same extent as pure culture genomes do, pointing to a chimeric nature of asgard archaeal MAGs. Our analysis suggests that some asgard archaeal MAGs represent unnatural constructs, genome-like patchworks of genes resulting from assembly and/or the binning process.
The Origin and Evolution of Antistasin-like Proteins in Leeches (Hirudinida, Clitellata)
Authors: Iwama Rafael Eiji , Tessler Michael , Siddall Mark E , Kvist Sebastian 
Published: November 2020

AbstractBloodfeeding is employed by many parasitic animals and requires specific innovations for efficient feeding. Some of these innovations are molecular features that are related to the inhibition of hemostasis. For example, bloodfeeding insects, bats, and leeches release proteins with anticoagulatory activity through their salivary secretions. The antistasin-like protein family, composed of serine protease inhibitors with one or more antistasin-like domains, is tightly linked to inhibition of hemostasis in leeches. However, this protein family has been recorded also in non-bloodfeeding invertebrates, such as cnidarians, mollusks, polychaetes, and oligochaetes. The present study aims to 1) root the antistasin-like gene tree and delimit the major orthologous groups, 2) identify potential independent origins of salivary proteins secreted by leeches, and 3) identify major changes in domain and/or motif structure within each orthologous group. Five clades containing leech antistasin-like proteins are distinguishable through rigorous phylogenetic analyses based on nine new transcriptomes and a diverse set of comparative data: the trypsin + leukocyte elastase inhibitors clade, the antistasin clade, the therostasin clade, and two additional, unnamed clades. The antistasin-like gene tree supports multiple origins of leech antistasin-like proteins due to the presence of both leech and non-leech sequences in one of the unnamed clades, but a single origin of factor Xa and trypsin + leukocyte elastase inhibitors. This is further supported by three sequence motifs that are exclusive to antistasins, the trypsin + leukocyte elastase inhibitor clade, and the therostasin clade, respectively. We discuss the implications of our findings for the evolution of this diverse family of leech anticoagulants.
Application of machine learning techniques to predict rupture propagation and arrest in 2-D dynamic earthquake simulations
Authors: Ahamed Sabber , Daub Eric G 
Published: November 2020

SUMMARYSimulating dynamic earthquake rupture propagation is challenging due to uncertainties in the underlying physics of fault slip, stress conditions and the fault frictional properties. A trial and error approach is often used to determine the unknown parameters describing rupture, though running many simulations usually requires human review to determine how to adjust parameter values and is thus inefficient. We leverage machine learning approaches to reduce computational cost and improve the ability to determine reasonable stress and friction parameters. Two models have been developed using neural networks and the random forest to predict if a rupture can break 2-D geometrically complex fault. We train the models using a database of 1600 dynamic rupture simulations computed numerically. Fault geometry, stress conditions and friction parameters vary in each simulation. Both models distinguish the underlying complex data patterns that reflect the physics of the rupture. For example, our models identify in a quantitative fashion, how higher normal and shear stress components and low static and dynamic friction can be tied to the probability of rupture propagation. Both models are efficient in predicting rupture propagation such that 400 unseen examples are predicted in a fraction of a second, leading to potential applications of dynamic rupture that have previously not been possible due to the computational demands of physics-based rupture simulations.
A viscoelastic model for seismic attenuation using fractal mechanical networks
Authors: Xing Guangchi , Zhu Tieyuan 
Published: November 2020

SUMMARY
Seismic attenuation (quantified by the quality factor Q) has a significant impact on the seismic waveforms, especially in the fluid-saturated rocks. This dissipative process can be phenomenologically represented by viscoelastic models. Previous seismological studies show that the Q value of Earth media exhibits a nearly frequency-independent behaviour (often referred to as constant-Q in literature) in the seismic frequency range. Such attenuation can be described by the mathematical Kjartansson constant-Q model, which lacks of a physical representation in the viscoelastic sense. Inspired by the fractal nature of the pore fluid distribution in patchy-saturated rocks, here we propose two fractal mechanical network (FMN) models, that is, a fractal tree model and a quasi-fractal ladder model, to phenomenologically represent the frequency-independent Q behaviour. As with the classic viscoelastic models, the FMN models are composed of mechanical elements (spring and dashpots) arranged in different hierarchical patterns. A particular parametrization of each model can produce the same complex modulus as in the Kjartansson model, which leads to the constant-Q. Applying the theory to several typical rock samples, we find that the seismic attenuation signature of these rocks can be accurately represented by either one of the FMN models. Besides, we demonstrate that the ladder model in particular exhibits the realistic multiscale fractal structure of the saturated rocks. Therefore, the FMN models as a proxy could provide a new way to estimate the microscopic rock structure property from macroscopic seismic attenuation observation.
Heat-mortality risk and the population concentration of metropolitan areas in Japan: a nationwide time-series study
Authors: Lee Whanhee , Ebi Kristie L , Kim Yoonhee , Hashizume Masahiro , Honda Yasushi , Hideki Hashimoto , Choi Hayon Michelle , Choi Moonjung , Kim Ho 
Published: November 2020

Abstract

Background
The complex role of urbanisation in heat-mortality risk has not been fully studied. Japan has experienced a rapid population increase and densification in metropolitan areas since the 2000s; we investigated the effects of population concentration in metropolitan areas on heat-mortality risk using nationwide data.

Methods
We collected time-series data for mortality and weather variables for all 47 prefectures in Japan (1980–2015). The prefectures were classified into three sub-areas based on population size: lowest (&lt;1 500 000), intermediate (1 500 000 to 3 000 000), and highest (&gt;3 000 000; i.e. metropolitan areas). Regional indicators associated with the population concentration of metropolitan areas were obtained.

Results
Since the 2000s, the population concentration intensified in the metropolitan areas, with the highest heat-mortality risk in prefectures with the highest population. Higher population density and apartment % as well as lower forest area and medical services were associated with higher heat-mortality risk; these associations have generally become stronger since the 2000s.

Conclusions
Population concentration in metropolitan areas intensified interregional disparities in demography, living environments, and medical services in Japan; these disparities were associated with higher heat-mortality risk. Our results can contribute to policies to reduce vulnerability to high temperatures.
Buprenorphine Prevalence in DUID Cases in Southwestern Virginia: Case Studies and Observations
Authors: Kuhlman James J , Harris Chad , Wright Trista 
Published: November 2020

Abstract
Buprenorphine, a semisynthetic mixed agonist/antagonist opioid used primarily for the treatment of opioid use disorder, was reported in 194 driving under the influence of drugs (DUID) cases in Southwestern Virginia during the period from 2017 through 2019. Identifying and confirming buprenorphine in DUID cases is common in this region. Interpretation is complex due to the large range of concentrations of buprenorphine found in blood and frequent combinations with other therapeutic and abused drugs. Buprenorphine was identified by immunoassay and quantified by liquid chromatography–tandem mass spectrometry. A sensitive method was necessary as one-third of concentrations of buprenorphine and/or norbuprenorphine were &lt;1.0 µg/L. Concentrations of buprenorphine ranged from &lt;0.5 to 11 µg/L (mean 2.5 µg/L, median 1.8 µg/L) and concentrations of norbuprenorphine ranged from &lt;0.5 to &gt;20 µg/L (mean 3.3 µg/L, median 2.2 µg/L). Buprenorphine polysubstance use was common. Only 10% of the cases examined did not contain other drugs confirmed in routine DUID screening tests. The most common drug groups confirmed were benzodiazepines, amphetamines and cannabinoids. The DUID case histories presented represent examples of buprenorphine abuse, buprenorphine with no other drug groups, buprenorphine combined with other drug groups, cases consistent with impairment and cases with minimal impairment. Central nervous system depressant and narcotic analgesic symptoms were commonly observed; however, some cases contained stimulant symptoms. Buprenorphine-to-norbuprenorphine (B/NB) ratios had a mean and median ratio of 1.1 and 0.8, respectively. B/NB ratios &gt;3.0 were found in 4.7% of the cases. The finding of a higher B/NB ratio may indicate a more recent buprenorphine administration and a greater potential for impairment. No relationship between the concentration of buprenorphine and/or norbuprenorphine in blood and the performance on drug recognition expert evaluation or standardized field sobriety tests could be determined.
Iron deficiency-inducible peptide-coding genes OsIMA1 and OsIMA2 positively regulate a major pathway of iron uptake and translocation in rice
Authors: Kobayashi Takanori , Nagano Atsushi J , Nishizawa Naoko K 
Published: November 2020

Abstract
Under low iron (Fe) availability, plants transcriptionally induce various genes responsible for Fe uptake and translocation to obtain adequate amounts of Fe. Although transcription factors and ubiquitin ligases involved in these Fe deficiency responses have been identified, the mechanisms coordinating these pathways have not been clarified in rice. Recently identified Fe-deficiency-inducible IRON MAN (IMA)/FE UPTAKE-INDUCING PEPTIDE (FEP) positively regulates many Fe-deficiency-inducible genes for Fe uptake in Arabidopsis. Here, we report that the expression of two IMA/FEP genes in rice, OsIMA1 and OsIMA2, is strongly induced under Fe deficiency, positively regulated by the transcription factors IDEF1, OsbHLH058, and OsbHLH059, as well as OsIMA1 and OsIMA2 themselves, and negatively regulated by HRZ ubiquitin ligases. Overexpression of OsIMA1 or OsIMA2 in rice conferred tolerance to Fe deficiency and accumulation of Fe in leaves and seeds. These OsIMA-overexpressing rice exhibited enhanced expression of all of the known Fe-deficiency-inducible genes involved in Fe uptake and translocation, except for OsYSL2, a Fe–nicotianamine transporter gene, in roots but not in leaves. Knockdown of OsIMA1 or OsIMA2 caused minor effects, including repression of some Fe uptake- and translocation-related genes in OsIMA1 knockdown roots. These results indicate that OsIMA1 and OsIMA2 play key roles in enhancing the major pathway of the Fe deficiency response in rice.
Absolute Lymphocytes, Ferritin, C-Reactive Protein, and Lactate Dehydrogenase Predict Early Invasive Ventilation in Patients With COVID-19
Authors: Payán-Pernía Salvador , Gómez Pérez Lucía , Remacha Sevilla Ángel F , Sierra Gil Jordi , Novelli Canales Silvana 
Published: November 2020

Abstract

Objective
Early detection of patients with COVID-19 who will need mechanical invasive ventilation (MIV) may aid in delivering proper care and optimizing the use of limited resources.

Methods
In this single-center retrospective observational study, we aimed to identify simple laboratory parameters that in combination with ferritin (a surrogate marker of severe inflammation) may help predict early (first 48 hours) MIV. A total of 160 patients with COVID-19 in whom serum ferritin, absolute lymphocyte count (ALC), platelet count, C-reactive protein (CRP), and lactate dehydrogenase (LDH) had been analyzed at admission were included.

Results
We found that ferritin, LDH, ALC, and CRP predicted with 88% accuracy the probability of early MIV. Results indicated that LDH showed the greater area under the curve (AUC), with a value of 89.1%. Using the AUC, we established cutoff values for clinical application. Finally, we developed a classification tree based on LDH for its clinical use.

Conclusion
Ferritin, LDH, ALC, and CRP predict with 88% accuracy the probability of early MIV.
Cherokee Historical Fiction and Indigenous Science Fiction inRiding the Trail of Tears
Authors: Jackson Joshua , Vallowe Megan 
Published: November 2020

AbstractTurning to Indigenous genre theory, this article interprets Blake M. Hausman's Riding the Trail of Tears (2011) as a work of both Indigenous science fiction and Cherokee historical fiction. By defying the temporal constraints of science fiction and historical fiction, as conventionally defined, the novel imagines Cherokee people effectively resisting Removal via digital, Cherokee-made technology and reclaiming Cherokee historical lands. To understand how historical and tribal specificity combine in the novel's imagination of these possibilities, the authors apply Cherokee literary history and definitions of Cherokee Beloved Path and Chickamauga consciousness to explain how the novel's science fictional framework and historical narrative enable characters to resist settler-colonial technologies of dominance and survive the novel's seemingly infinite loop of Removal. To describe how the novel uses Native-made technologies to connect elements of Cherokee historical fiction to elements of Indigenous science fiction, we combine Allison Adelle Hedge Coke's use of the term throughways with Grace L. Dillon's definition of the genre Native slipstream. The article concludes that discussions of genre, and specifically historical fiction, should pay careful attention to the way that multiple cultural contexts inform definitions of history, time, and space.
Polarized radiation transfer in neutron star surface layers
Authors: Barchas Joseph A , Hu Kun , Baring Matthew G 
Published: November 2020

ABSTRACT
The study of polarized radiation transfer in the highly magnetized surface locales of neutron stars is of great interest to the understanding of accreting X-ray pulsars, rotation-powered pulsars, and magnetars. This paper explores scattering transport in the classical magnetic Thomson domain that is of broad applicability to these neutron star classes. The development of a Monte Carlo simulation for the polarized radiative transfer is detailed: it employs an electric field vector formalism to enable a breadth of utility in relating linear, circular, and elliptical polarizations. The simulation can be applied to any neutron star surface locale, and is adaptable to accretion column and magnetospheric problems. Validation of the code for both intensity and Stokes parameter determination is illustrated in a variety of ways. Representative results for emergent polarization signals from surface layers are presented for both polar and equatorial magnetic locales, exhibiting contrasting signatures between the two regions. There is also a strong dependence of these characteristics on the ratio of the frequency $\, \omega \,$ of a photon to the cyclotron frequency $\, \omega _{\mathrm{B}}=eB/mc\,$. Polarization signatures for high-opacity domains are presented, highlighting compact analytical approximations for the Stokes parameters and anisotropy relative to the local field direction for an extended range of frequencies. These are very useful in defining injection conditions deep in the simulation slab geometries, expediting the generation of emission signals from highly opaque stellar atmospheres. The results are interpreted throughout using the polarization characteristics of the magnetic Thomson differential cross-section.