bluuebunny/crossref_metadata_2025 huggingface dataset:
An image-computable model on how endogenous and exogenous attention differentially alter visual perception
Authors: Jigo Michael , Heeger David J. , Carrasco Marisa
Published: January 2021

Attention alters perception across the visual field. Typically, endogenous (voluntary) and exogenous (involuntary) attention similarly improve performance in many visual tasks, but they have differential effects in some tasks. Extant models of visual attention assume that the effects of these two types of attention are identical and consequently do not explain differences between them. Here, we develop a model of spatial resolution and attention that distinguishes between endogenous and exogenous attention. We focus on texture-based segmentation as a model system because it has revealed a clear dissociation between both attention types. For a texture for which performance peaks at parafoveal locations, endogenous attention improves performance across eccentricity, whereas exogenous attention improves performance where the resolution is low (peripheral locations) but impairs it where the resolution is high (foveal locations) for the scale of the texture. Our model emulates sensory encoding to segment figures from their background and predict behavioral performance. To explain attentional effects, endogenous and exogenous attention require separate operating regimes across visual detail (spatial frequency). Our model reproduces behavioral performance across several experiments and simultaneously resolves three unexplained phenomena: (1) the parafoveal advantage in segmentation, (2) the uniform improvements across eccentricity by endogenous attention and (3) the peripheral improvements and foveal impairments by exogenous attention. Overall, we unveil a computational dissociation between each attention type and provide a generalizable framework for predicting their effects on perception across the visual field.
Predicting the Specificity-Determining Positions of Paralogous Complexes
Authors: Karakulak Tülay , Rifaioglu Ahmet Sureyya , Rodrigues João P.G.L.M. , Karaca Ezgi
Published: January 2021

Due to its clinical relevance, modulation of functionally relevant amino acids in protein-protein complexes has attracted a great deal of attention. To this end, many approaches have been proposed to predict partner-selecting, i.e., specificity-determining positions in evolutionarily close complexes. These approaches can be grouped into sequence-based machine learning and structure-based energy-driven methods. In this work, we assessed these methods’ ability to map the specificity-determining positions of Axl, a receptor tyrosine kinase involved in cancer progression and immune-related diseases. For this, we used three sequence-based predictors – SDPred, Multi-RELIEF, and Sequence Harmony – and a structure-based approach by utilizing HADDOCK and extensive molecular dynamics simulations. As a result, we show that (i) sequence-based methods overpredict the number of specificity-determining positions for Axl complexes and that (ii) combining sequence-based approaches with HADDOCK provides the most coherent set of predictions. Our work lays out a critical study on the comparative performance specificity-determining position predictors. It also presents a combined sequence-structure-based approach, which can guide the development of therapeutic molecules capable of combatting Axl misregulation in different types of diseases.
A hierarchical Bayesian model to investigate trade-offs between growth and reproduction in a long-lived plant
Authors: Journé Valentin , Papaïx Julien , Walker Emily , Courbet François , Lefèvre François , Oddou-Muratorio Sylvie , Davi Hendrik
Published: January 2021

1

A trade-off between growth and fecundity, reflecting the inability of simultaneously investing in both functions when resources are limited, is a fundamental feature of life history theory. This particular trade-off is the result of evolutionary and environmental constrains shaping reproductive and growth traits, but it remains difficult to pinpoint in natural populations of long-lived plants. We developed a hierarchical Bayesian model to estimate the inter-individual correlation among growth and reproduction, using observations at individual level over several years combined with resource simulations from an ecophysiological-based model (CASTANEA). In the Bayesian model, the resource, simulated by CASTANEA and incorporated as a latent variable, is allocated to tree growth, reproductive buds initiation and fruit maturation. Then, we used individual random effects correlated among energetic sinks to investigate potential trade-offs. We applied this original approach to a Mediterranean coniferous tree, Atlas Cedar (Cedrus atlantica), at two contrasted levels of competition, high versus low density population. We found that trees initializing many reproductive buds had a higher growth. Moreover, a negative correlation was detected between growth and fruit survival during maturation. Finally, trees investing more resource to maturate fruits initiated less reproductive buds. The level of competition did not impact the sign of these three correlations, but changed the level of resource allocation: low density population favored growth whereas high density favored reproduction. The level of resource have an impact on individual strategies. This new modeling framework allowed us to detect various individual strategies of resource allocation to growth versus late-stage reproduction on the one hand, and to early-versus late-stage reproduction on the other hand. Moreover, the sign of the correlation between growth and reproductive traits depends on the stage of reproduction considered. Hence, we suggest that the investigation of potential trade-offs between growth and reproduction requires to integrate the dynamics of resource and sink’s phenology, from initiation to maturation of reproductive organs.
Somatic mutations reveal widespread mosaicism and mutagenesis in human placentas
Authors: Coorens Tim H. H. , Oliver Thomas R. W. , Sanghvi Rashesh , Sovio Ulla , Cook Emma , Vento-Tormo Roser , Haniffa Muzlifah , Young Matthew D. , Rahbari Raheleh , Sebire Neil , Campbell Peter J. , Charnock-Jones D. Stephen , Smith Gordon C. S. , Behjati Sam
Published: January 2021

Clinical investigations of human fetuses have revealed that placentas occasionally harbour chromosomal aberrations that are absent from the fetus1. The basis of this genetic segregation of the placenta, termed confined placental mosaicism, remains unknown. Here, we investigated the phylogeny of human placentas reconstructed from somatic mutations, using whole genome sequencing of 86 placental biopsies and of 106 microdissections. We found that every placental biopsy represented a clonal expansion that is genetically distinct. Biopsies exhibited a genomic landscape akin to childhood cancer, in terms of mutation burden and mutational imprints. Furthermore, unlike any other human normal tissue studied to date, placental genomes commonly harboured copy number changes. Reconstructing phylogenetic relationships between tissues from the same pregnancy, revealed that developmental bottlenecks confined placental tissues, by separating trophectodermal from inner cell mass-derived lineages. Of particular note were cases in which inner cell mass-derived and placental lineages fully segregated within a few cell divisions of the zygote. Such early embryonic bottlenecks may enable the normalisation of zygotic aneuploidy. We observed direct evidence for this in a case of mosaic trisomic rescue. Our findings reveal cancer-like mutagenesis in placental tissues and portray confined mosaicism as the normal outcome of placental development.
Modeling by artificial neural networks of silver carp (Hypophthalmichthys molitrixi) with sous vide processing on the effects of storage and processing temperatures on the microbiological status
Authors: Hosseini Seyed Vali , Pero Milad , Tahergorabi Reza , Kazemzadeh Shirin , Alemán Ricardo Santos , Fuentes Jhunior Abrahan Marcia , Fernández Ismael Montero , Sosa Lilian , Sanchez Xesus Feas
Published: January 2021

To evaluate and anticipate the microbial changes of silver carp (Hypophthalmichthys molitrixi) during cold storage (0, 5, 10, 15 & 21 day) at different sous vide processing temperatures (60, 65, 70, and 75 °C), changes in microbial load of Enterobacteriaceae, Lactic Acid bacteria (LAB), Pseudomonas, Psychrotrophs, and total viable count (TVC) were considered. A radial basis function neural network (RBFNN) model was established to predict the changes in the microbial content of silver carp. The critical temperature for inactivation of Enterobacteriaceae and lactic acid bacteria was 65 °C and for Pseudomonas and Psychrotrophs was 70 °C and the highest value (75 °C) was observed for the total viable count. In samples processed at 75 °C, the presence of Enterobacteriaceae, Pseudomonas and Psychrotrophs were not detectable up to 15 days of storage and lactic acid bacteria were not detectable even at the end of the storage period. The optimal ANN topology for modeling Enterobacteriaceae, Pseudomonas, and Psychrotroph contained 9 neurons in the hidden layer, but for TVC and LAB, it was 14 neurons.
Comprehensive analysis of male-free reproduction inMonomorium triviale(Formicidae: Myrmicinae)
Authors: Idogawa Naoto , Sasaki Tomonori , Tsuji Kazuki , Dobata Shigeto
Published: January 2021

We report comprehensive evidence for obligatory thelytokous parthenogenesis in an antMonomorium triviale. This species is characterized by distinct queen–worker dimorphism with strict reproductive division of labor: queens produce both workers and new queens without mating, whereas workers are completely sterile. We collected 333 nests of this species from 14 localities and three laboratory-reared populations in Japan. All wild queens dissected had no sperm in their spermathecae. Laboratory observation confirmed that virgin queens produced workers without mating. Furthermore, microsatellite genotyping showed identical heterozygous genotypes between mothers and their respective daughters, suggesting an extremely low probability of sexual reproduction. Microbial analysis detected no bacterial genera that are known to induce thelytokous parthenogenesis in Hymenoptera. Finally, the lack of variation in partial sequences of mitochondrial DNA among individuals sampled from across Japan suggests recent rapid spread or selective sweep.M. trivialewould be a promising model system of superorganism-like adaptation through comparative analysis with well-studied sexual congeners, including the pharaoh antM. pharaonis.
Comparison of mouse models reveals a molecular distinction between psychotic illness in PWS and schizophrenia
Authors: Zahova Simona K. , Humby Trevor , Davies Jennifer R. , Morgan Joanne E. , Isles Anthony R.
Published: January 2021

Prader-Willi Syndrome (PWS) is a neurodevelopmental disorder caused by mutations affecting paternal chromosome 15q11-q13, and characterized by hypotonia, hyperphagia, impaired cognition and behavioural problems. Psychotic illness is a challenging problem for individuals with PWS and has different rates of prevalence in distinct PWS genotypes. Previously, we demonstrated behavioural and cognitive endophenotypes of relevance to psychiatric illness in a mouse model for one of the associated PWS genotypes, namely PWS-IC, in which deletion of the imprinting centre leads to loss of paternal imprinted gene expression and over-expression ofUbe3a. Here we examine the broader gene expression changes that are specific to the psychiatric endophenotypes seen in this model. To do this we compared the brain transcriptomic profile of the PWS-IC mouse to the PWS-cr model that carries a deletion of the PWS minimal critical interval spanning the snoRNASnord116andIpw. Firstly, we examined the same behavioural and cognitive endophenotypes of relevance to psychiatric illness in the PWS-cr mice. Unlike the PWS-IC mice, PWS-cr exhibit no differences in locomotor activity, sensory-motor gating, and attention. RNA-seq analysis of neonatal whole brain tissue revealed a greater number of transcriptional changes between PWS-IC and wild-type littermates, than between PWS-cr and wild-type littermates. Moreover, the differentially expressed genes in the PWS-IC brain were enriched for GWAS variants of episodes of psychotic illness but, interestingly, not schizophrenia. These data illustrate the molecular pathways that may underpin psychotic illness in PWS and have implication for potential therapeutic interventions.
Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects
Authors: Van den Berge Koen , Chou Hsin-Jung , Roux de Bézieux Hector , Street Kelly , Risso Davide , Ngai John , Dudoit Sandrine
Published: January 2021

Modern assays have enabled high-throughput studies of epigenetic regulation of gene expression using DNA sequencing. In particular, the assay for transposase-accessible chromatin using sequencing (ATAC-seq) allows the study of chromatin configuration for an entire genome. Despite the gain in popularity of the assay, there have been limited studies investigating the analytical challenges related to ATAC-seq data, and most studies leverage tools developed for bulk transcriptome sequencing (RNA-seq). Here, we show that GC-content effects are omnipresent in ATAC-seq datasets. Since the GC-content effects are sample-specific, they can bias downstream analyses such as clustering and differential accessibility analysis. We introduce a normalization method based on smooth-quantile normalization within GC-content bins, and evaluate it together with eleven different normalization procedures on eight public ATAC-seq datasets. Our work clearly shows that accounting for GC-content effects in the normalization is crucial for common downstream ATAC-seq data analyses, leading to improved accuracy and interpretability of the results. Using two case studies, we show that exploratory data analysis is essential to guide the choice of an appropriate normalization method for a given dataset.
Towards Similarity-based Differential Diagnostics For Common Diseases
Authors: Slater Luke T , Karwath Andreas , Williams John A , Russell Sophie , Makepeace Silver , Carberry Alexander , Hoehndorf Robert , Gkoutos Georgios V
Published: January 2021

Ontology-based phenotype profiles have been utilised for the purpose of differential diagnosis of rare genetic diseases, and for decision support in specific disease domains. Particularly, semantic similarity facilitates diagnostic hypothesis generation through comparison with disease phenotype profiles. However, the approach has not been applied for differential diagnosis of common diseases, or generalised clinical diagnostics from uncurated text-derived phenotypes. In this work, we describe the development of an approach for deriving patient phenotype profiles from clinical narrative text, and apply this to text associated with MIMIC-III patient visits. We then explore the use of semantic similarity with those text-derived phenotypes to classify primary patient diagnosis, comparing the use of patient-patient similarity and patient-disease similarity using phenotype-disease profiles previously mined from literature. We also consider a combined approach, in which literature-derived phenotypes are extended with the content of text-derived phenotypes we mined from 500 patients. The results reveal a powerful approach, showing that in one setting, uncurated text phenotypes can be used for differential diagnosis of common diseases, making use of information both inside and outside the setting. While the methods themselves should be explored for further optimisation, they could be be applied to a variety of clinical tasks, such as differential diagnosis, cohort discovery, document and text classification, and outcome prediction.
Modelling the deathbed of ASF-infected wild boars in South Korea using 2019-2020 national surveillance data
Authors: Lim Jun-Sik , Vergne Timothée , Pak Son-Il , Kim Eutteum
Published: January 2021

In September 2019, African swine fever (ASF) was reported in South Korea for the first time. Since then, more than 651 ASF cases in wild boars and 14 farm outbreaks have been notified in the country. The purpose of this study was to characterize the spatial distribution of ASF-positive wild boar carcasses to identify the risk factors associated with the presence of ASF and number of ASF-positive wild boar carcasses in the affected areas. To achieve this objective, we divided the study into two periods (October 2, 2019, to January 19, 2020, and January 19 to April 28, 2020) and aggregated the number of reported ASF-positive carcasses into a regular grid of hexagons. To account for imperfect detection, we adjusted spatial zero-inflated Poisson regression models to the number of ASF-positive wild boar carcasses per hexagons. During the first study period, only proximity to North Korea was identified as a risk factor for the presence of African swine fever virus (ASFV). In addition, there were more reports in the affected hexagons with a high habitat suitability for wild boar, low heat load index (HLI), and high human density. During the second study period, proximity to an ASF-positive carcass reported during the first period was the only significant risk factor for the presence of ASF-positive carcasses. Additionally, high HLI and low elevation were associated with an increased number of ASF-positive carcasses reported in the affected hexagons. Although the proportion of ASF-affected hexagons increased from 0.06 (95% credible interval [CrI]: 0.05-0.07) to 0.09 (95% CrI: 0.08-0.10), the probability of reporting ASF-affected hexagons increased substantially from 0.49 (95% CrI: 0.41-0.57) to 0.73 (95% CrI: 0.66-0.81) between the two study periods. These results can be used to further advance risk-based surveillance.
Self-organization in natural swarms ofPhotinus carolinussynchronous fireflies
Authors: Sarfati Raphaël , Hayes Julie C. , Peleg Orit
Published: January 2021

Fireflies flashing in unison is a mesmerizing manifestation of animal collective behavior and an archetype of biological synchrony. To elucidate synchronization mechanisms and inform theoretical models, we recorded the collective display of thousands ofPhotinus carolinusfireflies in natural swarms, and provide the first spatiotemporal description of the onset of synchronization. At low firefly density, flashes appear uncorrelated. At high density, the swarm produces synchronous flashes within periodic bursts. Using three-dimensional reconstruction, we demonstrate that flash bursts nucleate and propagate across the swarm in a relay-like process. Our results suggest that fireflies interact locally through a dynamic network of visual connections defined by visual occlusion from terrain and vegetation. This model illuminates the importance of the environment in shaping self-organization and collective behavior.
Taurine suppresses liquid-liquid phase separation of lysozyme protein
Authors: Tsubotani Kanae , Maeyama Sayuri , Murakami Shigeru , Schaffer Stephen W , Ito Takashi
Published: January 2021

Taurine is a compatible osmolyte that infers stability to proteins. Recent studies have revealed that liquid-liquid phase separation (LLPS) of proteins underlie the formation of membraneless organelles in cells. In the present study, we evaluated the role of taurine on LLPS of hen egg lysozyme. We demonstrated that taurine decreases the turbidity of the polyethylene glycol-induced crowding solution of lysozyme. We also demonstrated that taurine attenuates LLPS-dependent cloudiness of lysozyme solution with 0.5 or 1M NaCl at a critical temperature. Moreover, we observed that taurine inhibits LLPS formation of a heteroprotein mix solution of lysozyme and ovalbumin. These data indicate that taurine can modulate the formation of LLPS of proteins.
The Shape of Trees – Limits of Current Diversification Models
Authors: Schwery Orlando , O’Meara Brian C.
Published: January 2021

To investigate how biodiversity arose, the field of macroevolution largely relies on model-based approaches to estimate rates of diversification and what factors influence them. The number of available models is rising steadily, facilitating the modeling of an increasing number of possible diversification dynamics, and multiple hypotheses relating to what fueled or stifled lineage accumulation within groups of organisms. However, growing concerns about unchecked biases and limitations in the employed models suggest the need for rigorous validation of methods used to infer. Here, we address two points: the practical use of model adequacy testing, and what model adequacy can tell us about the overall state of diversification models. Using a large set of empirical phylogenies, and a new approach to test models using aspects of tree shape, we test how a set of staple models performs with regards to adequacy. Patterns of adequacy are described across trees and models and causes for inadequacy – particularly if all models are inadequate – are explored. The findings make clear that overall, only few empirical phylogenies cannot be described by at least one model. However, finding that the best fitting of a set of models might not necessarily be adequate makes clear that adequacy testing should become a step in the standard procedures for diversification studies.
Sequence signatures of two IGHV3-53/3-66 public clonotypes to SARS-CoV-2 receptor binding domain
Authors: Tan Timothy J.C. , Yuan Meng , Kuzelka Kaylee , Padron Gilberto C. , Beal Jacob R. , Chen Xin , Wang Yiquan , Rivera-Cardona Joel , Zhu Xueyong , Stadtmueller Beth M. , Brooke Christopher B. , Wilson Ian A. , Wu Nicholas C.
Published: January 2021

Since the COVID-19 pandemic onset, the antibody response to SARS-CoV-2 has been extensively characterized. Antibodies to the receptor binding domain (RBD) on the spike protein are frequently encoded by IGHV3-53/3-66 with a short CDR H3. Germline-encoded sequence motifs in CDRs H1 and H2 play a major role, but whether any common motifs are present in CDR H3, which is often critical for binding specificity, have not been elucidated. Here, we identify two public clonotypes of IGHV3-53/3-66 RBD antibodies with a 9-residue CDR H3 that pair with different light chains. Distinct sequence motifs on CDR H3 are present in the two public clonotypes that appear to be related to differential light chain pairing. Additionally, we show that Y58F is a common somatic hypermutation that results in increased binding affinity of IGHV3-53/3-66 RBD antibodies with a short CDR H3. Overall, our results advance fundamental understanding of the antibody response to SARS-CoV-2.
E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil
Authors: Ferrareze Patrícia Aline Gröhs , Franceschi Vinícius Bonetti , de Menezes Mayer Amanda , Caldana Gabriel Dickin , Zimerman Ricardo Ariel , Thompson Claudia Elizabeth
Published: January 2021

The COVID-19 pandemic caused by SARS-CoV-2 has affected millions of people since its beginning in 2019. The propagation of new lineages and the discovery of key mechanisms adopted by the virus to overlap the immune system are central topics for the entire public health policies, research and disease management. Since the second semester of 2020, the mutation E484K has been progressively found in the Brazilian territory, composing different lineages over time. It brought multiple concerns related to the risk of reinfection and the effectiveness of new preventive and treatment strategies due to the possibility of escaping from neutralizing antibodies. To better characterize the current scenario we performed genomic and phylogenetic analyses of the E484K mutated genomes sequenced from Brazilian samples in 2020. From October, 2020, more than 40% of the sequenced genomes present the E484K mutation, which was identified in three different lineages (P1, P2 and B.1.1.33) in four Brazilian regions. We also evaluated the presence of E484K associated mutations and identified selective pressures acting on the spike protein, leading us to some insights about adaptive and purifying selection driving the virus evolution.
Low-Dose Ad26.COV2.S Protection Against SARS-CoV-2 Challenge in Rhesus Macaques
Authors: He Xuan , Chandrashekar Abishek , Zahn Roland , Wegmann Frank , Yu Jingyou , Mercado Noe B. , McMahan Katherine , Martinot Amanda J. , Piedra-Mora Cesar , Beecy Sidney , Ducat Sarah , Chamanza Ronnie , Huber Sietske Rosendahl , van der Fits Leslie , Borducchi Erica N. , Lifton Michelle , Liu Jinyan , Nampanya Felix , Patel Shivani , Peter Lauren , Tostanoski Lisa H. , Pessaint Laurent , Van Ry Alex , Finneyfrock Brad , Velasco Jason , Teow Elyse , Brown Renita , Cook Anthony , Andersen Hanne , Lewis Mark G. , Schuitemaker Hanneke , Barouch Dan H.
Published: January 2021

We previously reported that a single immunization with an adenovirus serotype 26 (Ad26) vector-based vaccine expressing an optimized SARS-CoV-2 spike (Ad26.COV2.S) protected rhesus macaques against SARS-CoV-2 challenge. In this study, we evaluated the immunogenicity and protective efficacy of reduced doses of Ad26.COV2.S. 30 rhesus macaques were immunized once with 1×1011, 5×1010, 1.125×1010, or 2×109vp Ad26.COV2.S or sham and were challenged with SARS-CoV-2 by the intranasal and intratracheal routes. Vaccine doses as low as 2×109vp provided robust protection in bronchoalveolar lavage, whereas doses of 1.125×1010vp were required for protection in nasal swabs. Activated memory B cells as well as binding and neutralizing antibody titers following vaccination correlated with protective efficacy. At suboptimal vaccine doses, viral breakthrough was observed but did not show evidence of virologic, immunologic, histopathologic, or clinical enhancement of disease compared with sham controls. These data demonstrate that a single immunization with a relatively low dose of Ad26.COV2.S effectively protected against SARS-CoV-2 challenge in rhesus macaques. Moreover, our findings show that a higher vaccine dose may be required for protection in the upper respiratory tract compared with the lower respiratory tract.
Diversity, activity and abundance of benthic microbes in the southeastern Mediterranean Sea: A baseline for monitoring
Authors: Rubin-Blum Maxim , Sisma-Ventura Guy , Yudkovski Yana , Belkin Natalia , Kanari Mor , Herut Barak , Rahav Eyal
Published: January 2021

Microbes are key players in marine sediments, yet they are not accessed routinely by monitoring programs. Here, we investigate the spatial and vertical trends in the abundance, activity and diversity of benthic archaea, bacteria and fungi of the southeastern Mediterranean Sea (SEMS), based on ∼150 samples collected by the National Monitoring Program in 2018-2020 in coastal, as well as deep-sea transects across the Israeli exclusive economic zone, using vertical profiles of short sediment cores (0-1, 1-2, 4-5, 9-10 and 19-20 cm below surface). Microbial abundance was usually low (0.01 ×108to 0.21×108cells gr-1sediment), while heterotrophic productivity was the highest in the nearshore stations (12±4 ng C gr-1sediment h-1), as opposed to 0.5±0.9 ng C gr-1sediment h-1at the offshore sites. Using amplicon sequencing of marker genes, we identified the changes in the diversity of microbes along environmental gradients, in the four dimensions (geographic location, seabed depth, distance from the sediment surface and time). We show high taxonomic diversity of bacteria and archaea (Shannon’sH’5.0-6.9) and lesser diversity of fungi (Shannon’sH’0.2-4.8). We use DESeq2 analyses to highlight the role of ammonia-oxidizing Nitrososphaeria in the aerated sediments of the continental slope and deep bathyal plain stations and organotrophic lineages in coastal, shelf, slope, and abyssal plain sediments. Based on taxonomic diversity, we infer the metabolic potential of these communities. Analyses of fungi diversity and guilds suggest the prevalence of the saprotrophic and pathotrophic microfungi Ascomycota (70±23%) and Basidiomycota (16±18%) in the SEMS sediments. We provide a comprehensive baseline of benthic microbial populations in the SEMS and pledge for the use of microbial indices in biomonitoring of the marine environment.
On the determination of residual stresses in additively manufactured lattice structures
Authors: Fritsch Tobias , Sprengel Maximilian , Evans Alexander , Farahbod-Sternahl Lena , Saliwan-Neumann Romeo , Hofmann Michael , Bruno Giovanni
Published: January 2021

The determination of residual stresses becomes more complicated with increasing complexity of the structures investigated. Additive manufacturing techniques generally allow the production of `lattice structures' without any additional manufacturing step. These lattice structures consist of thin struts and are thus susceptible to internal stress-induced distortion and even cracks. In most cases, internal stresses remain locked in the structures as residual stress. The determination of the residual stress in lattice structures through nondestructive neutron diffraction is described in this work. It is shown how two difficulties can be overcome: (a) the correct alignment of the lattice structures within the neutron beam and (b) the correct determination of the residual stress field in a representative part of the structure. The magnitude and the direction of residual stress are discussed. The residual stress in the strut was found to be uniaxial and to follow the orientation of the strut, while the residual stress in the knots was more hydrostatic. Additionally, it is shown that strain measurements in at least seven independent directions are necessary for the estimation of the principal stress directions. The measurement directions should be chosen according to the sample geometry and an informed choice on the possible strain field. If the most prominent direction is not measured, the error in the calculated stress magnitude increases considerably.
Expanding the family of mineral-like anhydrous alkali copper sulfate framework structures: new phases, topological analysis and evaluation of ion migration potentialities
Authors: Borisov Artem S. , Siidra Oleg I. , Kovrugin Vadim M. , Golov Andrey A. , Depmeier Wulf , Nazarchuk Evgeny V. , Holzheid Astrid
Published: January 2021

Two novel compounds, K2Cu3(SO4)4 and KNaCu(SO4)2, were synthesized. The crystal structure of K2Cu3(SO4)4 is based on a [Cu3(SO4)4]2− framework with relatively simple bond topology, but with four different CuO
n
polyhedron geometries. The K+ cations reside in the pores of the framework. The [Cu(SO4)2]2− framework in KNaCu(SO4)2 encloses large elliptical channels running along [001]. Larger channels are occupied by K+, whereas smaller ones are filled by Na+. The bond-valence energy landscape (BVEL) approach has been demonstrated to be a useful method for the prediction of the mobility of alkali metal ions in various structures. By means of this approach, the threshold energies at which isosurfaces begin to percolate as well as the directions of possible ion migration in the structures were determined. The modelling of ion migration maps by the analysis of the procrystal electron-density distribution was used to rapidly identify ion migration pathways and limiting barriers between particular crystallographic sites in the structures under consideration. Its consistency and complementarity with the BVEL method have been demonstrated. Both approaches revealed a relatively low ion threshold percolation and migration barriers in the cryptochalcite-type structures [cryptochalcite: K2Cu5O(SO4)5]. Hence, one may assume that its 3D framework type is suited for ion transport applications. The review of all known members of the groups of anhydrous copper sulfates did not reveal a correlation between the porosity of the framework structures and a manifestation of ion conduction properties.
Evolution of dislocation microstructure in irradiated Zr alloys determined by X-ray peak profile analysis
Authors: Groma István , Szenthe Ildikó , Ódor Éva , Jóni Bertalan , Zilahi Gyula , Dankházi Zoltán , Ribárik Gábor , Hózer Zoltán
Published: January 2021

During neutron irradiation of metals, owing to the enhanced number of vacancies and interstitial atoms, the climb motion of dislocations becomes significant at room temperature, leading to a recrystallization of the material. Moreover, the vacancies and interstitial atoms tend to form prismatic dislocation loops that play a crucial role in the plastic properties of the materials. X-ray peak profile analysis is an efficient nondestructive method to determine the properties of dislocation microstructure. In the first half of this article, the foundation of the asymptotic peak broadening theory and the related restricted-moments peak-evaluation method is summarized. After this, the microstructural parameters obtained by X-ray peak profile analysis are reported for irradiated E110 and E110G Zr alloys used as cladding material in the nuclear industry.
Modelling the Reserve Bank of Australia's Policy Decisions and the Case for a Negative Cash Rate
Authors: Anderson Timothy , Hawkins John
Published: January 2021

Taylor's eponymous ‘rule’ models how central banks set policy rates in response to inflation and output. We estimate a Taylor rule for the Reserve Bank of Australia (RBA), modifying it to make it more realistic, while retaining its simplicity. The model implies that if the Bank responds to recent forecasts as it has on average since 1995, the cash rate could have briefly gone negative in 2020. But the RBA is wary of negative cash rates. There are grounds for caution; the economic outlook is particularly uncertain and the economy's response to negative rates is uncharted territory.
Modelling the Spread of the Coronavirus: A View from Economics
Authors: Lloyd Peter , Dixon Robert
Published: January 2021

This article reviews the modelling of the spread in Australia of COVID‐19 from the point of view of the discipline of Economics. After a brief overview of the epidemiological approach, we show that other modelling is needed for policy purposes and especially to provide a full understanding of the economic and social costs of disease control. We look at microeconomic aspects of infection, focusing on individual behaviour, the choices facing the individual and implications for policy. The use of a cost–benefit approach and macroeconomic aspects of the pandemic are examined together with the economic consequences of policy response.
Dulce de leche: Product types, production processes, quality aspects and innovations minor EDITS
Authors: Vargas Maryella Osório , Prestes Amanda Alves , Miotto Marília , Prudêncio Elane Schwinden
Published: January 2021

This article provides information regarding dulce de leche, a dairy product obtained by heating milk and sugar under controlled conditions. Some denominations of this product, and the physicochemical and microbiological parameters defined by legislation are also presented. Dulce de leche has three main forms of production with fewer common varieties; their differences are reported and highlighted. Adjuvants used in the process are detailed as well, due to their importance in the process and their influence on the final product’s characteristics. Furthermore, innovations in dulce de leche production are also discussed.
SambaR: An R package for fast, easy and reproducible population‐genetic analyses of biallelic SNP data sets
Authors: de Jong Menno J. , de Jong Joost F. , Hoelzel A. Rus , Janke Axel
Published: January 2021

SNP data sets can be used to infer a wealth of information about natural populations, including information about their structure, genetic diversity, and the presence of loci under selection. However, SNP data analysis can be a time‐consuming and challenging process, not in the least because at present many different software packages are needed to execute and depict the wide variety of mainstream population‐genetic analyses. Here, we present SambaR, an integrative and user‐friendly R package which automates and simplifies quality control and population‐genetic analyses of biallelic SNP data sets. SambaR allows users to perform mainstream population‐genetic analyses and to generate a wide variety of ready to publish graphs with a minimum number of commands (less than 10). These wrapper commands call functions of existing packages (including adegenet, ape, LEA, poppr, pcadapt and StAMPP) as well as new tools uniquely implemented in SambaR. We tested SambaR on online available SNP data sets and found that SambaR can process data sets of over 100,000 SNPs and hundreds of individuals within hours, given sufficient computing power. Newly developed tools implemented in SambaR facilitate optimization of filter settings, objective interpretation of ordination analyses, enhance comparability of diversity estimates from reduced representation library SNP data sets, and generate reduced SNP panels and structure‐like plots with Bayesian population assignment probabilities. SambaR facilitates rapid population genetic analyses on biallelic SNP data sets by removing three major time sinks: file handling, software learning, and data plotting. In addition, SambaR provides a convenient platform for SNP data storage and management, as well as several new utilities, including guidance in setting appropriate data filters. The SambaR source script, manual and example data set are distributed through GitHub: https://github.com/mennodejong1986/SambaR.
A rare case of primary solitary endobronchial plasmacytoma
Authors: Park Jong Il , Lee Yin Young , Lee Seok Soo , Ahn June Hong
Published: January 2021

Extramedullary plasmacytoma (EMP) is a rare plasma cell tumor involving the organs but without bone marrow involvement or the characteristics of multiple myeloma. Primary solitary endobronchial plasmacytoma is extremely rare. Here we present the case of an 86‐year‐old male ex‐smoker who visited our outpatient clinic for an endobronchial mass in the left upper lobe of the lung. Fiberoptic bronchoscopy revealed a protruding mass in the left upper lobar bronchus; based on the bronchoscopic biopsy findings, a primary solitary endobronchial plasmacytoma was diagnosed. After radiation therapy the patient was well and 6 months after treatment showed no evidence of disease recurrence. Extramedullary plasmacytoma should be considered in the differential diagnosis of an endobronchial mass.
Precise resection of multiple pulmonary nodules using a three‐dimensional reconstruction model: A case report
Authors: Chu Xiang‐Peng , Chen Zi‐Hao , Lin Shao‐Min , Tang Wen‐Fang , Zhang Jia‐Tao , Lai Yao‐Ming , Fu Rui , Qiu Zhen‐Bin , Lin Jun‐Tao , Nie Qiang , Yang Xue‐Ning , Wu Yi‐Long , Zhong Wen‐Zhao
Published: January 2021

A 48‐year‐old woman presented to our department and chest computed tomography (CT) revealed five pulmonary nodules, two of which were in the left upper lobe of the lung and three in the superior segment of the left lower lobe., All the lesions were resected for comprehensive histological assessment in order to distinguish synchronous multiple primary lung cancers (SMPLCs) from intrapulmonary metastases. The nodules were all successfully removed by minimally invasive surgery under the guidance of three dimensional (3D) reconstruction, in order to preserve as much lung function for the patient as possible. Postoperative histopathological examination demonstrated the presence of SMPLC. The patient was discharged from hospital on postoperative day 4 without any complications.
Characteristics, management and survival of ICU patients with coronavirus disease‐19 in Norway, March‐June 2020. A prospective observational study
Authors: Laake Jon H. , Buanes Eirik A. , Småstuen Milada C. , Kvåle Reidar , Olsen Brita F. , Rustøen Tone , Strand Kristian , Sørensen Vibecke , Hofsø Kristin
Published: January 2021

Background

Norwegian hospitals have operated within capacity during the COVID‐19 pandemic. We present patient and management characteristics, and outcomes for the entire cohort of adult (>18 years) COVID‐19 patients admitted to Norwegian intensive care units (ICU) from 10 March to 19 June 2020.

Methods

Data were collected from The Norwegian intensive care and pandemic registry (NIPaR). Demographics, co‐morbidities, management characteristics and outcomes are described. ICU length of stay (LOS) was analysed with linear regression, and associations between risk factors and mortality were quantified using Cox regression.

Results

In total, 217 patients were included. The male to female ratio was 3:1 and the median age was 63 years. A majority (70%) had one or more co‐morbidities, most frequently cardiovascular disease (39%), chronic lung disease (22%), diabetes mellitus (20%), and obesity (17%). Most patients were admitted for acute hypoxaemic respiratory failure (AHRF) (91%) and invasive mechanical ventilation (MV) was used in 86%, prone ventilation in 38% and 25% of patients received a tracheostomy. Vasoactive drugs were used in 79% and renal replacement therapy in 15%. Median ICU LOS and time of MV was 14.0 and 12.0 days. At end of follow‐up 45 patients (21%) were dead. Age, co‐morbidities and severity of illness at admission were predictive of death. Severity of AHRF and male gender were associated with LOS.

Conclusions

In this national cohort of COVID‐19 patients, mortality was low and attributable to known risk factors. Importantly, prolonged length‐of‐stay must be taken into account when planning for resource allocation for any next surge.
Triaging abnormal cervical cancer screening tests using p16INK4a detection by ELISA on fresh cervical samples
Authors: Leung Shuk On Annie , Feldman Sarah , Kalyanaraman Rajeshwari , Shanmugam Vignesh , Worley Michael J. , Berkowitz Ross S. , Horowitz Neil S. , Feltmate Colleen M. , Muto Michael G. , Lee Larissa J. , King Martin T. , Einarsson Jon I. , Ajao Mobolaji O. , Elias Kevin M.
Published: January 2021

Problem

Cervical cancer screening strategies in the United States include cotesting (human papillomavirus (HPV) with cytology), primary HPV with genotyping and reflex cytology, and cytology alone. An ongoing challenge is the appropriate triage of patients to colposcopy to those at highest risk. We investigated whether incorporation of p16INK4a immunodetection by enzyme‐linked immunosorbent assay (ELISA) on fresh cervical samples obtained at the time of screening could improve appropriate referral to colposcopy.

Method of Study

A derivation group comprised of cervical swabs collected from subjects with high‐grade dysplasia or cancer (positive control) and from subjects with negative screening history (negative control). Samples collected from colposcopy were used to evaluate the existing screening strategies individually and with incorporation of p16INK4a ELISA. Histology was used as the gold standard.

Results

Among 163 subjects recruited, 138 were included. In the derivation group, mean p16INK4a level was 2.86 ng/mL (n = 31) and 0.58 ng/mL (n = 20) among positive and negative controls respectively (p = 0.002) with an area under the receiver operator characteristic curve of 0.79 (p < 0.001). Among colposcopy subjects, sensitivity/specificity for cotesting, primary HPV, and cytology were 94%/42%, 88%/45%, and 88%/49%, respectively. Incorporation of p16INK4a resulted in similar sensitivity and improved specificity (cotesting+p16 88%/58%, primary HPV+p16 88%/57%, cytology+p16 81%/62%; p = 0.23/p = 0.008) with decrease in colposcopy referrals by 15% to 22% (p = 0.01).

Conclusions

These results demonstrate the feasibility of quantifying p16INK4a by ELISA in fresh cervical samples, and its potential as an adjunct to existing screening strategies in the identification of high grade‐dysplasia while reducing the number of colposcopic referrals.
Hypertrophic osteopathy in South Australian koalas (Phascolarctos cinereus) with concurrent pulmonary actinomycosis
Authors: Griffith JE , Stephenson T , McLelland DJ , Woolford L
Published: January 2021

Pulmonary actinomycosis is described in 17 South Australian koalas necropsied between 2016 and 2019. From these cases, four koalas had secondary hypertrophic osteopathy. Plain radiographical and computed tomography images demonstrated periosteal reaction on multiple appendicular skeletal bones in all cases, including scapula, humerus, ulna, radius, ilium, femur, tibia, fibula, metacarpus, metatarsus and phalanx. Grossly, periosteal surfaces of the metaphyses and diaphyses of long bones were thickened and roughened; microscopically, this was characterised by bi‐layered proliferation of well‐differentiated trabecular bony spicules oriented perpendicular to the cortex (pseudocortices) and separated by vascular connective tissue, typical for hypertrophic osteopathy. Well characterised in domestic species and rarely reported in marsupials, this is the first radiographical and pathological characterisation of hypertrophic osteopathy in koalas, associated with pulmonary actinomycosis in all cases.
Catastrophic impact of Covid‐19 on the global stock markets and economic activities
Authors: Chowdhury Emon Kalyan , Khan Iffat Ishrat , Dhar Bablu Kumar
Published: January 2021

This paper intends to know the influence of COVID‐19 on the stock markets and economic activities across the world. To achieve the purpose, daily panel data of 12 selective countries covering four continents from January to April 2020 have been collected. The impact on stock markets has been measured by applying the event study method, while the panel vector autoregressive model has been applied to measure the impact on economic activities. The stock index of each country, purchasing managers’ index, COVID‐19 variables, namely the number of lockdown days, restriction in internal movement, restriction in international travel, fiscal measure, and confirmed cases have been used. The study observes the serious negative impact of the pandemic on stock market returns. European stock markets are the worst sufferer compared to others. All pandemic variables have a negative impact on stock markets; moreover, lockdown days and restriction on movement have a negative impact on economic activities. This study considers such countries which significantly represent the world economy and are a serious victim of COVID‐19 pandemic. The outcome‐based recommendations will help governments, regulatory authority, and policymakers to combat the crisis in different dimensions.
Gaussian graphical model‐based heterogeneity analysis via penalized fusion
Authors: Ren Mingyang , Zhang Sanguo , Zhang Qingzhao , Ma Shuangge
Published: January 2021

Heterogeneity is a hallmark of cancer, diabetes, cardiovascular diseases, and many other complex diseases. This study has been partly motivated by the unsupervised heterogeneity analysis for complex diseases based on molecular and imaging data, for which, network‐based analysis, by accommodating the interconnections among variables, can be more informative than that limited to mean, variance, and other simple distributional properties. In the literature, there has been very limited research on network‐based heterogeneity analysis, and a common limitation shared by the existing techniques is that the number of subgroups needs to be specified a priori or in an ad hoc manner. In this article, we develop a penalized fusion approach for heterogeneity analysis based on the Gaussian graphical model. It applies penalization to the mean and precision matrix parameters to generate regularized and interpretable estimates. More importantly, a fusion penalty is imposed to “automatedly” determine the number of subgroups and generate more concise, reliable, and interpretable estimation. Consistency properties are rigorously established, and an effective computational algorithm is developed. The heterogeneity analysis of non‐small‐cell lung cancer based on single‐cell gene expression data of the Wnt pathway and that of lung adenocarcinoma based on histopathological imaging data not only demonstrate the practical applicability of the proposed approach but also lead to interesting new findings.