bluuebunny/crossref_metadata_2025_split huggingface dataset:
Demographic uniformitarianism: the theoretical basis of prehistoric demographic research and its cross-disciplinary challenges
Authors: French Jennifer C. , Chamberlain Andrew T. 
Published: November 2020

A principle of demographic uniformitarianism underpins all research into prehistoric demography (palaeodemography). This principle—which argues for continuity in the evolved mechanisms underlying modern human demographic processes and their response to environmental stimuli between past and present—provides the cross-disciplinary basis for palaeodemographic reconstruction and analysis. Prompted by the recent growth and interest in the field of prehistoric demography, this paper reviews the principle of demographic uniformitarianism, evaluates how it relates to two key debates in palaeodemographic research and seeks to delimit its range of applicability to past human and hominin populations.This article is part of the theme issue ‘Cross-disciplinary approaches to prehistoric demography’.
Modifiable reporting unit problems and time series of long-term human activity
Authors: Bevan A. , Crema E. R. 
Published: November 2020

This paper responds to a resurgence of interest in constructing long-term time proxies of human activity, especially but not limited to models of population change over the Pleistocene and/or Holocene. While very much agreeing with the need for this increased attention, we emphasize three important issues that can all be thought of as modifiable reporting unit problems: the impact of (i) archaeological periodization, (ii) uneven event durations and (iii) geographical nucleation-dispersal phenomena. Drawing inspiration from real-world examples from prehistoric Britain, Greece and Japan, we explore their consequences and possible mitigation via a reproducible set of tactical simulations.This article is part of the theme issue ‘Cross-disciplinary approaches to prehistoric demography’.
MNI-FTD Templates: Unbiased Average Templates of Frontotemporal Dementia Variants
Authors: Dadar Mahsa , Manera Ana L. , Fonov Vladimir S. , Ducharme Simon , Collins D. Louis 
Published: November 2020

AbstractStandard anatomical templates are widely used in human neuroimaging processing pipelines to facilitate group level analyses and comparisons across different subjects and populations. The MNI-ICBM152 template is the most commonly used standard template, representing an average of 152 healthy young adult brains. However, in patients with neurodegenerative diseases such as frontotemporal dementia (FTD), the high levels of atrophy lead to significant differences between the brain shape of the individuals and the MNI-ICBM152 template. Such differences might inevitably lead to registration errors or subtle biases in downstream analyses and results. Disease-specific templates are therefore desirable to reflect the anatomical characteristics of the populations of interest and to reduce potential registration errors when processing data from such populations.Here, we present MNI-FTD136, MNI-bvFTD70, MNI-svFTD36, and MNI-pnfaFTD30, four unbiased average templates of 136 FTD patients, 70 behavioural variant (bv), 36 semantic variant (sv), and 30 progressive nonfluent aphasia (pnfa) variant FTD patients as well as a corresponding age matched average template of 133 healthy controls (MNI-CN133), along with probabilistic tissue maps for each template. The public availability of these templates will facilitate analyses of FTD cohorts and enable comparisons between different studies in a common standardized space appropriate to FTD populations.
Prevalence and stability of SARS CoV-2 RNA on Bangladeshi banknotes
Authors: Akter Selina , Roy Pravas Chandra , Ferdaus Amina , Ibnat Habiba , Ul Alam A.S.M. Rubayet , Nigar Shireen , Jahid Iqbal Kabir , Hossain M. Anwar 
Published: November 2020

AbstractOriginating at December 2019 in China, SARS-CoV-2 has emerged as the deadliest pandemic in the history of mankind. Along with direct contact and droplet contaminations, possibility of infections through contaminated surfaces and fomites are being investigated. In this study, we aim to assess the prevalence of SARS-CoV-2 viral RNA by real time one-step reverse transcriptase PCR on banknotes being circulating in Bangladesh. We also assessed the persistence of the virus on banknotes spiked with SARS-CoV-2 positive diluted human nasopharyngeal samples. Among the 425 banknote samples collected from different entities, 7.29% (n= 31) were tested positive for targeted genes. Twenty four representative positive samples were assessed for N gene fragments by conventional PCR and sequenced. All the samples carry viral RNA belonged to GR clade, the predominant circulating clade in Bangladesh. In the test of stability, the N gene was detected for up to 72 h on banknotes spiked with nasopharyngeal samples and CT values increases significantly with time (p<0.05). ORF1b gene was observed to be less stable specially on old banknotes and usually went beyond detectable limit within 8 to 10 h. The stability of virus RNA was well fitted by Weibull model and concave curve for new banknotes and convex curve for old banknotes have been revealed. Handling of banknotes is unavoidable; hence these findings implicated that in order to limit SARS-CoV-2 transmission through banknotes proper hygiene practice are needed.
Genetic associations and architecture of asthma-chronic obstructive pulmonary disease overlap
Authors: John C. , Guyatt A.L. , Shrine N. , Packer R. , Olafsdottir T.A. , Liu J. , Hayden L.P. , Chu S.H. , Koskela J.T. , Luan J. , Li X. , Terzikhan N. , Xu H. , Bartz T.M. , Petersen H. , Leng S. , Belinsky S.A. , Cepelis A. , Hernández Cordero A.I. , Obeidat M. , Thorleifsson G. , Meyers D.A. , Bleecker E.R. , Sakoda L.C. , Iribarren C. , Tesfaigzi Y. , Gharib S.A. , Dupuis J. , Brusselle G. , Lahousse L. , Ortega V.E. , Jonsdottir I. , Sin D. D. , Bossé Y. , van den Berge M. , Nickle D. , Quint J.K. , Sayers I. , Hall I.P. , Langenberg C. , Ripatti S. , Laitinen T. , Wu A.C. , Lasky-Su J. , Bakke P. , Gulsvik A. , Hersh C.P. , Hayward C. , Langhammer A. , Brumpton B. , Stefansson K. , Cho M.H. , Wain L.V. , Tobin M.D. 
Published: November 2020

AbstractSome individuals have characteristics of both asthma and COPD (asthma-COPD overlap, ACO), and evidence suggests they experience worse outcomes than those with either condition alone. Improved knowledge of the genetic architecture would contribute to understanding whether determinants of risk in this group differ from those in COPD or asthma.We conducted a genome-wide association study in 8,068 cases and 40,360 controls of European ancestry from UK Biobank (stage 1). After excluding variants only associated with asthma or COPD we selected 31 variants for further investigation in 12 additional cohorts (stage 2), and discovered eight novel signals for ACO in a meta-analysis of stage 1 and 2 studies.Our signals include an intergenic signal on chromosome 5 not previously associated with asthma, COPD or lung function, and suggest a spectrum of shared and distinct genetic influences in asthma, COPD and ACO. A number of signals may represent loci that predispose to serious long-term consequences in people with asthma.
Atrophy-centered subtyping of mild cognitive impairment
Authors: Kwak Kichang , Giovanello Kelly S. , Styner Martin , Dayan Eran ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: November 2020

AbstractMild cognitive impairment (MCI) is considered as the transitional phase between normal cognitive aging and Alzheimer’s disease (AD). Nevertheless, trajectories of cognitive decline vary considerably among individuals with MCI. To address this heterogeneity, subtyping approaches have been developed, with the objective of identifying more homogenous subgroups and ultimately improving prognostic outcomes. To date, subtyping of MCI has been based primarily on cognitive performance measures, often resulting in indistinct boundaries between the proposed subgroups and limited validity. The degree to which markers of neurodegeneration such as brain atrophy can be used to subtype MCI into biologically and clinically meaningful subgroups remains unclear. Here we introduce and validate a data-driven subtyping method for MCI based solely upon measures of atrophy derived from structural magnetic resonance imaging (MRI). We trained a dense convolutional neural network to differentiate between patients with AD and age-matched cognitively normal (CN) subjects based on whole brain MRI features. We then deployed the trained model to classify individuals with MCI, as MCI-CN or MCI-AD, based on the degree to which their whole brain gray matter volume resembles CN-like or AD-like patterns. We subsequently validated the model-based subgroups using cognitive, clinical, fluid biomarker, and molecular neuroimaging data. Namely, we observed marked differences between the MCI-CN and MCI-AD groups in baseline and longitudinal cognitive and clinical rating scales, disease-free survival, cerebrospinal fluid (CSF) levels of amyloid beta and tau, fluorodeoxyglucose (FDG) and amyloid PET. Overall, the results suggest that patterns of atrophy in MCI are sufficiently distinct and heterogeneous, and can thus be used to subtype individuals into biologically and clinically meaningful subgroups.
Epidemiological and Economic Impact of COVID-19 in the US
Authors: Chen Jiangzhuo , Vullikanti Anil , Santos Joost , Venkatramanan Srinivasan , Hoops Stefan , Mortveit Henning , Lewis Bryan , You Wen , Eubank Stephen , Marathe Madhav , Barrett Chris , Marathe Achla 
Published: November 2020

AbstractThis research measures the epidemiological and economic impact of COVID-19 spread in the US under different mitigation scenarios, comprising of non-pharmaceutical interventions. A detailed disease model of COVID-19 is combined with a model of the US economy to estimate the direct impact of labor supply shock to each sector arising from morbidity, mortality, and lockdown, as well as the indirect impact caused by the interdependencies between sectors. During a lockdown, estimates of jobs that are workable from home in each sector are used to modify the shock to labor supply. Results show trade-offs between economic losses, and lives saved and infections averted are non-linear in compliance to social distancing and the duration of lockdown. Sectors that are worst hit are not the labor-intensive sectors such as Agriculture and Construction, but the ones with high valued jobs such as Professional Services, even after the teleworkability of jobs is accounted for. Additionally, the findings show that a low compliance to interventions can be overcome by a longer shutdown period and vice versa to arrive at similar epidemiological impact but their net effect on economic loss depends on the interplay between the marginal gains from averting infections and deaths, versus the marginal loss from having healthy workers stay at home during the shutdown.
Characterizing the transmission patterns of seasonal influenza in Italy: lessons from the last decade
Authors: Trentini Filippo , Pariani Elena , Bella Antonino , Diurno Giulio , Crottogini Lucia , Rizzo Caterina , Merler Stefano , Ajelli Marco 
Published: November 2020

AbstractBackgroundDespite thousands of influenza cases annually recorded by surveillance systems around the globe, estimating the transmission patterns of seasonal influenza is challenging.MethodsWe develop an age-structured mathematical model to influenza transmission to analyze ten consecutive seasons (from 2010-2011 to 2019-2020) of influenza epidemiological and virological data reported to the Italian surveillance system.ResultsWe estimate that 18.4%-29.3% of influenza infections are detected by the surveillance system. Influenza infection attack rate varied between 18.0% and 35.6% and is generally larger for seasons characterized by the circulation of A/H3N2 and/or B types/subtypes. Individuals aged 14 years or less are the most affected age-segment of the population, with A viruses especially affecting children aged 0-4 years. For all influenza types/subtypes, the mean effective reproduction number is estimated to be generally in the range 1.1-1.4 (8 out of 10 seasons) and never exceeding 1.55. The age-specific susceptibility to infection appears to be a type/subtype-specific feature.ConclusionsThe results presented in this study provide insights on type/subtype-specific transmission patterns of seasonal influenza that could be instrumental to fine-tune immunization strategies and non-pharmaceutical interventions aimed at limiting seasonal influenza spread and burden.
Bioelectrical Interfaces with Cortical Spheroids in Three-Dimensions
Authors: Kalmykov Anna , Reddy Jay W. , Bedoyan Esther , Wang Yingqiao , Garg Raghav , Rastogi Sahil K. , Cohen-Karni Devora , Chamanzar Maysamreza , Cohen-Karni Tzahi 
Published: November 2020

AbstractThree-dimensional (3D) neuronal spheroid culture serves as a powerful model system for the investigation of neurological disorders and drug discovery. The success of such a model system requires techniques that enable high-resolution functional readout across the entire spheroid. Conventional microelectrode arrays and implantable neural probes cannot monitor the electrophysiology activity across the entire native 3D geometry of the cellular construct. Here, we demonstrate a 3D self-rolled biosensor array (3D-SR-BA) integrated with a 3D cortical spheroid culture for simultaneousin-vitroelectrophysiology recording, functional Ca2+imaging, and drug effect monitoring. We have also developed a signal processing pipeline to detect neural firings with high spatiotemporal resolution from the electrophysiology recordings based on established spike sorting methods. The 3D-SR-BAs cortical spheroid interface provides a stable, high sensitivity recording of neural action potentials (< 50 μV peak-to-peak amplitude). The 3D-SR-BA is demonstrated as a potential drug screening platform through the investigation of the neural response to the excitatory neurotransmitter glutamate. Upon addition of glutamate, the neuronal firing rates increased notably corresponding well with the functional Ca2+imaging. Our entire system, including the 3D-SR-BA integrated with neural spheroid culture, enables simultaneous electrophysiology recording and functional Ca2+imaging with high spatiotemporal resolution in conjunction with chemical stimulation. We demonstrate a powerful toolset for future studies of tissue development, disease progression, and drug testing and screening, especially when combined with native spheroid cultures directly extracted from humans.
Seeing the forest through the trees: Identifying functional interactions from Hi-C
Authors: Liu Ning , Low Wai Yee , Alinejad-Rokny Hamid , Pederson Stephen , Sadlon Timothy , Barry Simon , Breen James 
Published: November 2020

AbstractEukaryotic genomes are highly organised within the nucleus of a cell, allowing widely dispersed regulatory elements such as enhancers to interact with gene promoters through physical contacts in three-dimensional space. Recent chromosome conformation capture methodologies such as Hi-C have enabled the analysis of interacting regions of the genome providing a valuable insight into the three-dimensional organisation of the chromatin in the nucleus, including chromosome compartmentalisation and gene expression. Complicating the analysis of Hi-C data however is the massive amount of identified interactions, many of which do not directly drive gene function, thus hindering the identification of potentially biologically functional 3D interactions. In this review, we collate and examine the downstream analysis of Hi-C data with particular focus on methods that identify significant functional interactions. We classify three groups of approaches; structurally-associated domain discovery methods e.g. topologically-associated domains and compartments, detection of statistically significant interactions via background models, and the use of epigenomic data integration to identify functional interactions. Careful use of these three approaches is crucial to successfully identifying functional interactions within the genome.
Action Observation Network activity related to object-directed and socially-directed actions in Adolescents
Authors: Lesourd Mathieu , Afyouni Alia , Geringswald Franziska , Cignetti Fabien , Raoul Lisa , Sein Julien , Nazarian Bruno , Anton Jean-Luc , Grosbras Marie-Hélène 
Published: November 2020

AbstractThe Action Observation Network (AON) encompasses brain areas consistently engaged when we observe other’s actions. Although the core nodes of the AON are present from childhood, it is not known to what extent they are sensitive to different action features during development. As social cognitive abilities continue to mature during adolescence, the AON response to socially-oriented actions, but not to object-related actions, may differ in adolescents and adults. To test this hypothesis, we scanned with functional magnetic resonance imaging (fMRI) 28 typically-developing teenagers and 25 adults while they passively watched videos of hand actions varying along two dimensions: sociality (i.e. directed towards another person or not) and transitivity (i.e. involving an object or not). We found that observing actions recruited the same fronto-parietal and occipito-temporal regions in adults and adolescents. The modulation of voxelwise activity by the social or transitive nature of the action was similar in both groups of participants. Multivariate pattern analysis, however, revealed that the accuracy in decoding the social dimension from the brain activity patterns, increased with age in lateral occipital and parietal regions, known to be involved in semantic representations of actions, as well as in posterior superior temporal sulcus, a region commonly associated with perception of high level features necessary for social perception. Change in decoding the transitive dimension was observed only in the latter region. These findings indicate that the representation of others’ actions, and in particular their social dimensions, in the adolescent AON is still not as robust as in adults.Significance statementThe activity of the action observation network in the human brain is modulated according to the purpose of the observed action, in particular the extent to which it involves interaction with an object or another person. How this conceptual representation of actions is implemented during development is largely unknown. Here, using multivoxel pattern analysis of fMRI data, we discovered that, while the action observation network is in place in adolescence, the fine-grain organization of its posterior regions is less robust than in adults to decode the social or transitive dimensions of an action. This finding highlights the late maturation of social processing in the human brain.
Immunofocusing humoral immunity potentiates the functional efficacy of the AnAPN1 malaria transmission-blocking vaccine antigen
Authors: Bender Nicole G. , Khare Prachi , Martinez Juan , Tweedell Rebecca E. , Nyasembe Vincent O. , López-Gutiérrez Borja , Tripathi Abhai , Miller Dustin , Hamerly Timothy , Vela Eric M. , Howard Randall F. , Nsango Sandrine , Cobb Ronald R. , Harbers Matthias , Dinglasan Rhoel R. 
Published: November 2020

AbstractMalaria transmission-blocking vaccines (TBVs) are a critical tool for disease elimination. TBVs prevent completion of the developmental lifecycle of malarial parasites within the mosquito vector, effectively blocking subsequent infections. The mosquito midgut protein Anopheline alanyl aminopeptidase N (AnAPN1) is the leading, mosquito-based TBV antigen and structure-function studies have identified two Class II epitopes that induce potent transmission-blocking (T-B) antibodies. Here, we functionally screened new immunogens and down-selected to the UF6b construct that has two glycine-linked copies of the T-B epitopes. We established a process for manufacturing UF6b and evaluated in outbred female CD1 mice the immunogenicity of the preclinical product with the human-safe adjuvant Glucopyranosyl Lipid Adjuvant in a liposomal formulation with saponin QS21 (GLA-LSQ). UF6b:GLA-LSQ was immunogenic and immunofocused the humoral response to one of the key T-B epitopes resulting in potent T-B activity and establishing UF6b as a prime TBV candidate to aid in malaria elimination and eradication efforts.
Holistic green BIM: a scientometrics and mixed review
Authors: Shukra Zahra Abdulhadi , Zhou Ying 
Published: November 2020

PurposeDespite the construction industry's significant impact on high energy use and a growing carbon footprint, technologies like Green BIM help to optimize natural resources, reduce pollution, use sustainable space and work on human comfort and health. But the trend in a holistic approach is minimal. Thus, the paper aimed to systematically investigate Green BIM research and implementation trends using a mixed-method and also show the prospects of holistic Green BIM implementation.Design/methodology/approachFirst, we conducted a Scientometrics analysis on the topic using the Scopus database for the time interval of (2013–present). Secondly, the Qualitative Content Review method asserted the Scientometrics analysis result. Lastly, exploratory research was done on secondary data to compare the AEC industry trend for a comprehensive view.FindingsThe merged findings confirmed the partial implementation of Green BIM and of which 43% of research focused only on energy analysis. Despite the potential of BIM and the interrelationship among green building parameters, the result showed other aspects of green building and sustainable design parameters as green material selection, sustainable site, waste management and water-use efficiency not comprised.Originality/valueThe authors propose a new conceptual framework for integrating green building parameters, BIM tools and green building assessment tools in a life cycle of a project that adds into the sustainability of the Architectural, Engineering and Construction sector. The study would help to provoke researchers, software developers and practitioners for further innovative effort in holistic Green BIM implementation.