bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting the evolution of SARS-Covid-2 in Portugal using an adapted SIR Model previously used in South Korea for the MERS outbreak
Authors: Teles Pedro 
Published: March 2020

AbstractThe covid-19 has spread very quickly worldwide, leading the World Health Organization (WHO) to declare a state of pandemic. Moreover, the WHO has announced that the European continent is now the main centre of the pandemic.One of the questions many governments are asking is how the spread is going to evolve in time. In this study, an adapted SIR model previously used in South Korea to model the MERS outbreak was applied to estimate the evolution of the curve of active cases in the case of the Portuguese situation. As some of the parameters were unknown, and the data for Portugal is still scarce, given that the outbreak started later (first case on the 2nd of March) I used Italian data (first reported case in Italy on the 31st of January) to predict them. I then construct five different scenarios for the evolution of covid-19 in Portugal, considering both the effectiveness of the mitigation measurements implemented by the government, and the self-protective measures taken by the population, as explained in the South Korean model.In the out of control scenario, the number of active cases could reach as much as 40,000 people by the beginning of April. In the best-case-scenario considered, the active cases could reach circa 7,000 people. The actual figure probably lies between the interval (7,000-13,000) and the peak will be reached between 9th and the 20th of April 2020.Without control and self-protective measures, this model predicts that the figures of active cases of SARS-covid-2 would reach a staggering 40,000 people It shows the importance of control and self-protecting measure to bring down the number of affected people by following the recommendations of the WHO and health authorities. With the appropriate measures, this number can be brought down to 7,000-13,000 people
parSMURF, a High Performance Computing tool for the genome-wide detection of pathogenic variants
Authors: Petrini Alessandro , Mesiti Marco , Schubach Max , Frasca Marco , Danis Daniel , Re Matteo , Grossi Giuliano , Cappelletti Luca , Castrignanò Tiziana , Robinson Peter N. , Valentini Giorgio 
Published: March 2020

AbstractSeveral prediction problems in Computational Biology and Genomic Medicine are characterized by both big data as well as a high imbalance between examples to be learned, whereby positive examples can represent a tiny minority with respect to negative examples. For instance, deleterious or pathogenic variants are overwhelmed by the sea of neutral variants in the non-coding regions of the genome: as a consequence the prediction of deleterious variants is a very challenging highly imbalanced classification problem, and classical prediction tools fail to detect the rare pathogenic examples among the huge amount of neutral variants or undergo severe restrictions in managing big genomic data. To overcome these limitations we propose parSMURF, a method that adopts a hyper-ensemble approach and oversampling and undersampling techniques to deal with imbalanced data, and parallel computational techniques to both manage big genomic data and significantly speed-up the computation. The synergy between Bayesian optimization techniques and the parallel nature of parSMURF enables efficient and user-friendly automatic tuning of the hyper-parameters of the algorithm, and allows specific learning problems in Genomic Medicine to be easily fit. Moreover, by using MPI parallel and machine learning ensemble techniques, parSMURF can manage big data by partitioning them across the nodes of a High Performance Computing cluster.Results with synthetic data and with single nucleotide variants associated with Mendelian diseases and with GWAS hits in the non-coding regions of the human genome, involving millions of examples, show that parSMURF achieves state-of-the-art results and a speed-up of 80× with respect to the sequential version.In conclusion parSMURF is a parallel machine learning tool that can be trained to learn different genomic problems, and its multiple levels of parallelization and its high scalability allow us to efficiently fit problems characterized by big and imbalanced genomic data.Availability and ImplementationThe C++ OpenMP multi-core version tailored to a single workstation and the C++ MPI/OpenMP hybrid multi-core and multi-node parSMURF version tailored to a High Performance Computing cluster are both available from github: https://github.com/AnacletoLAB/parSMURF
Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs
Authors: He Shuai , Wang Lin-He , Liu Yang , Li Yi-Qi , Chen Hai-Tian , Xu Jing-Hong , Peng Wan , Lin Guo-Wang , Wei Pan-Pan , Li Bo , Xia Xiaojun , Wang Dan , Bei Jin-Xin , He Xiaoshun , Guo Zhiyong 
Published: March 2020

ABSTRACTBackgroundAs core units of organ tissues, cells of various types play their harmonious rhythms to maintain the homeostasis of the human body. It is essential to identify the characteristics of cells in human organs and their regulatory networks for understanding the biological mechanisms related to health and disease. However, a systematic and comprehensive single-cell transcriptional profile across multiple organs of a normal human adult is missing.ResultsWe perform single-cell transcriptomes of 84,363 cells derived from 15 tissue organs of one adult donor and generate an adult human cell atlas. The adult human cell atlas depicts 252 subtypes of cells, including major cell types such as T, B, myeloid, epithelial, and stromal cells, as well as novelCOCH+fibroblasts and FibSmo cells, each of which is distinguished by multiple marker genes and transcriptional profiles. These collectively contribute to the heterogeneity of major human organs. Moreover, T cell and B cell receptor repertoire comparisons and trajectory analyses reveal direct clonal sharing of T and B cells with various developmental states among different tissues. Furthermore, novel cell markers, transcription factors and ligand-receptor pairs are identified with potential functional regulations in maintaining the homeostasis of human cells among tissues.ConclusionsThe adult human cell atlas reveals the inter- and intra-organ heterogeneity of cell characteristics and provides a useful resource in uncovering key events during the development of human diseases in the context of the heterogeneity of cells and organs.
CoMut: Visualizing integrated molecular information with comutation plots
Authors: Crowdis Jett , He Meng Xiao , Reardon Brendan , Van Allen Eliezer M. 
Published: March 2020

AbstractMotivationLarge-scale sequencing studies have created a need to succinctly visualize genomic characteristics of patient cohorts linked to widely variable phenotypic information. This is often done by visualizing the co-occurrence of variants with comutation plots. Current tools lack the ability to create highly customizable and publication quality comutation plots from arbitrary user data.ResultsWe developed CoMut, a stand-alone, object-oriented Python package that creates comutation plots from arbitrary input data, including categorical data, continuous data, bar graphs, side bar graphs, and data that describes relationships between samples.Availability and ImplementationThe CoMut package is open source and is available athttps://github.com/vanallenlab/comutunder the MIT License, along with documentation and examples. A no installation, easy-to-use implementation is available on Google Colab (see GitHub).Contacteliezerm_vanallen@dfci.harvard.edu
A prospect on the use of antiviral drugs to control local outbreaks of COVID-19
Authors: Torneri Andrea , Libin Pieter , Vanderlocht Joris , Vandamme Anne-Mieke , Neyts Johan , Hens Niel 
Published: March 2020

AbstractBackgroundCurrent outbreaks of COVID-19 are threatening the health care systems of several countries around the world. Control measures, based on isolation and quarantine, have been shown to decrease and delay the burden of the ongoing epidemic. With respect to the ongoing COVID-19 epidemic, recent modelling work shows that this intervention technique may be inadequate to control local outbreaks, even when perfect isolation is assumed. Furthermore, the effect of infectiousness prior to symptom onset combined with a significant proportion of asymptomatic infectees further complicates the use of contact tracing. Antivirals, which decrease the viral load and reduce the infectiousness, could be integrated in the control measures in order to augment the feasibility of controlling the epidemic.MethodsUsing a simulation-based model of viral transmission we tested the efficacy of different intervention measures for the control of COVID-19. For individuals that were identified through contact tracing, we evaluate two procedures: monitoring individuals for symptoms onset and testing of individuals. Moreover, we investigate the effect of a potent antiviral compound on the contact tracing process.FindingsThe use of an antiviral drug, in combination with contact tracing, quarantine and isolation, results in a significant decrease of the final size, the peak incidence, and increases the probability that the outbreak will fade out.InterpretationFor an infectious disease in which presymptomatic infections are plausible, an intervention measure based on contact tracing performs better when realized together with testing instead of monitoring, provided that the test is able to detect infections during the incubation period. In addition, in all tested scenarios, the model highlights the benefits of the administration of an antiviral drug in addition to quarantine, isolation and contact tracing. The resulting control measure, could be an effective strategy to control local and re-emerging out-breaks of COVID-19.
Htr6 and Sstr3 ciliary targeting relies on both IC3 loops and C-terminal tails
Authors: Barbeito Pablo , Tachibana Yuki , Martin-Morales Raquel , Moreno Paula , Mykytyn Kirk , Kobayashi Tetsuo , Garcia-Gonzalo Francesc R. 
Published: March 2020

ABSTRACTG protein-coupled receptors (GPCRs) are the most common pharmacological target in clinical practice. To perform their signaling functions, many GPCRs must accumulate at primary cilia, microtubule-based plasma membrane protrusions that work as cellular antennae. Despite their great importance, the molecular mechanisms underlying GPCR ciliary targeting remain poorly understood. Serotonin receptor 6 (Htr6) and somatostatin receptor 3 (Sstr3) are two brain-enriched ciliary GPCRs controlling cognition and involved in multiple pathologies such as Alzheimer’s disease and cancer. We previously showed that the third intracellular loops (IC3s) of Htr6 and Sstr3 contain ciliary targeting sequences (CTSs) that are sufficient to confer ciliary localization to non-ciliary GPCRs. However, these CTSs are dispensable for the ciliary targeting of Htr6 and Sstr3 themselves, suggesting these GPCRs have additional CTSs. Herein, we show that the C-terminal tails of Htr6 and Sstr3 also contain CTSs, which act redundantly with those in the IC3s. Accordingly, simultaneous disruption of CTS1 (IC3) and CTS2 (C-terminal tail) abolishes ciliary targeting of both receptors. Mapping the individual residues required for Htr6 ciliary targeting reveals RKQ and LPG motifs critical for CTS1 and CTS2 function, respectively. In Sstr3, CTS1 function relies on the tandem AP[AS]CQ motifs and a subsequent arginine-rich stretch, whereas CTS2 operation requires the juxtamembrane residues. Furthermore, we shed light on the mechanisms of action of Htr6 CTSs by showing how they regulate binding to Tulp3 and Rabl2, two adapters needed for ciliary GPCR targeting.
Functional analysis of the chromosomal passenger complex in Arabidopsis
Authors: Komaki Shinichiro , Takeuchi Hidenori , Hamamura Yuki , Heese Maren , Hashimoto Takashi , Schnittger Arp 
Published: March 2020

SUMMARYA key regulator of cell division in all eukaryotes is the kinase Aurora B, which is encoded by the Aurora 3 (AUR3) gene in Arabidopsis. Aurora B has at least two central functions during cell division. On the one hand, it is essential for the correct, i.e. balanced, segregation of chromosomes in mitosis and meiosis by controlling kinetochore function. On the other hand, Aurora B acts at the division plane, where it is necessary to complete cytokinesis. To accomplish these two spatially distinct functions, Aurora B in animals is guided to its sites of action by Borealin, INCENP, and Survivin that build together with Aurora B the chromosome passenger complex (CPC). However, besides Aurora homologs, only a candidate gene with restricted homology to INCENP has so far been described in Arabidopsis raising the question whether there exists a full complement of the CPC in plants and how Aurora homologs are targeted subcellularly. Here, we have identified and functionally characterized a Borealin homolog, BOREALIN RELATED (BORR), in Arabidopsis. This, together with detailed localization studies including the putative Arabidopsis INCENP homolog, supports the existence of a CPC in plants.
Meta-analysis suggests the microbiome responds to Evolve and Resequence experiments inDrosophila melanogaster
Authors: Henry Lucas P. , Ayroles Julien F. 
Published: March 2020

ABSTRACTBackgroundExperimental evolution has a long history of uncovering fundamental insights into evolutionary processes, but has largely neglected one underappreciated component--the microbiome. As eukaryotic hosts evolve, the microbiome may also evolve. However, the microbial contribution to host evolution remains poorly understood. Here, we re-analyzed genomic data to characterize the metagenomes from ten Evolve and Resequence (E&R) experiment inDrosophila melanogasterto determine how the microbiome changed in response to host selection.ResultsBacterial diversity was significantly different in 5/10 studies, primarily in traits associated with metabolism or immunity. Duration of selection did not significantly influence bacterial diversity, highlighting the importance of associations with specific host traits. Additionally, we find that excluding reads from a facultative symbiont,Wolbachia, in the analysis of bacterial diversity changes the inference, raising important questions for future E&R experiments in theD. melanogastermicrobiome.ConclusionsOur genomic re-analysis suggests the microbiome often responds to host selection; thus, the microbiome may contribute to the response ofDrosophilain E&R experiments. We outline important considerations for incorporating the microbiome into E&R experiments. The E&R approach may provide critical insights into host-microbiome interactions and fundamental insight into the genomic basis of adaptation.
Characterization of clinical significance of PD-1/PD-Ls expression and methylation in patients with low grade glioma
Authors: Mei Jie , Cai Yun , Xu Rui , Yang Xuejing , Zhou Weijian , Wang Huiyu , Liu Chaoying 
Published: March 2020

AbstractBackgroundImmune checkpoints play crucial roles in immune escape of cancer cells. However, the exact prognostic values of expression and methylation of programmed death 1 (PD-1), programmed death-ligand 1 (PD-L1) and PD-L2 in low-grade glioma (LGG) have not been defined yet.MethodsA total of 514 LGG samples from TCGA dataset containing both PD-1, PD-L1 and PD-L2 expression, DNA methylation, and survival data were enrolled into our study. The clinical significance of PD-1/PD-Ls expression and methylation in LGG were explored. Besides, the correlation between PD-1/PD-Ls expression and methylation with the infiltration levels of tumor-infiltrating immune cells (TIICs) was assessed. Moreover, GO enticement analysis of PD-1/PD-Ls co-expressed genes was performed as well. R 3.6.2 and GraphPad Prism 8 were applied as main tools for the statistical analysis and graphical exhibition.ResultsPD-1/PD-Ls had distinct co-expression patterns in LGG tissues. The expression and methylation status of PD-1/PD-Ls seemed to be various in different LGG subtypes. Besides, upregulated PD-1/PD-Ls expression and hypo-methylation of PD-1/PD-Ls were associated with worse survival in LGG patients. In addition, PD-1/PD-Ls expression was revealed to be positively associated with TIICs infiltration, while their methylation was negatively associated with TIICs infiltration. Moreover, the PD-1/PDLs correlated gene profiles screening and Gene Ontology (GO) enrichment analysis uncovered that PD-1/PDLs and their positively correlated gene mainly participated in immune response related biological processes.ConclusionsHigh expression and hypo-methylation of PD-1/PD-Ls significantly correlated with unfavorable survival in LGG patients, suggesting LGG patients may benefit from PD1/PD-Ls checkpoint inhibitors treatment.
The impact of violence on tourism to Rio de Janeiro
Authors: Montes Gabriel Caldas , Bernabé Solimar de Pinho 
Published: March 2020

PurposeRio de Janeiro has a high tourism potential, and it is the only Brazilian city among the 100 most visited in the world. However, the National Confederation of Commerce of Goods, Services and Tourism estimates that from the total loss of revenue from tourism activities of the State of Rio de Janeiro in 2017, approximately 29 percent of this loss can be attributed to increased violence in the State. Thus, this study aims to estimate the impact of violence on tourist arrivals to Rio de Janeiro.Design/methodology/approachThe analysis is based on a sample of tourist arrivals to Rio de Janeiro from 51 countries, for the period between 2003 and 2016. Violence is represented by violent deaths in the State of Rio de Janeiro as well as in the capital. The estimates are based on panel data methodology. This study reports fixed-effect estimates as well as dynamic panel data estimates obtained through S-GMM. The study runs regressions for the full sample and also for two other samples: one with tourists coming from developed countries and another with tourists from developing countries.FindingsThe results reveal that violence negatively impacts tourism to Rio, and it shows that tourists from developed countries are more affected by violence than tourists from developing countries. The findings indicate that for each violent death in the capital of Rio de Janeiro, almost four tourists from developed countries and approximately three tourists from developing countries quit going to Rio de Janeiro.Originality/valueThe paper is one of the few to investigate the impacts of urban violence on tourism. The paper provides two contributions. First, it addresses the effect of violent deaths on tourism, bringing evidence to a destination with a high tourism potential, but which suffers from urban violence. Second, the study is the first to investigate whether this relation is different for tourists from countries with distinct levels of development (and thus with different levels of violence).Peer reviewThe peer review history for this article is available at:https://publons.com/publon/10.1108/IJSE-09-2019-0590
Unemployment and social stigma
Authors: Shah Rahat , Jafeer Qurat-Ul-Ain , Saeed Sadia , Aslam Saba , Ali Ijaz 
Published: March 2020

PurposeThis article aims to highlight the stigmatization attached to the unemployment of educated youth in rural regions of Khyber Pakhtunkhwa province of Pakistan.Design/methodology/approachThe study explicates the subjective experiences of the youth as being unemployed and societal attitudes toward them through an in-depth qualitative approach. A total of 30 unemployed male individuals were interviewed through an interview guide.FindingsThe study reveals that unemployed individuals are stigmatized and discriminately treated. They experience the difference in social support from their family and friends during unemployment, which is a discouraging aspect. This finding is in contrast to the existing literature on the subject in which family and friends are described as a major source of social support. As the study is conducted in the rural context, it is observed that local factors coupled with the joint family system have intensified negative attitudes toward the unemployed youth. Subsequently, the negative societal treatment serves as a factor for psychological challenges in their lives.Originality/valueThis article serves the need of exploring the experiences of unemployed individuals precisely in the Pakistani context.
Historic urban landscape
Authors: Rey-Pérez Julia , Pereira Roders Ana 
Published: March 2020

PurposeThe main aim of this paper is to determine how well the UNESCO 2011 Recommendation on Historic Urban Landscape (hereafter, the HUL approach) is understood by the academic community today. It will review relevant research, highlight shortcomings regarding the HUL concept and approach and explore how well the six proposed steps are being considered when implementing the HUL approach.Design/methodology/approachThis paper presents and discusses the results of a systematic review of 140 peer-reviewed publications, published in international academic journals between 2008 and 2019 and available in databases such as WoS and Scopus, such as journal articles, book chapters and books. More specifically, this research takes the six-step process as its theoretical framework in order to understand if the six steps are being followed in the case studies where the HUL approach has been implemented. Following this, it assesses gaps in the HUL concept and approach. The paper explores the HUL implementation management process, investigating what is being done, how it is being done and who is involved.FindingsThe concept ‘Historic Urban Landscape’ has been used in research since 2008. However, the first case studies implementing the HUL approach were not published until 2013. While there is an abundance of theoretical research in relation to the HUL concept and approach from different perspectives and to varying degrees of depth, the case studies which practically demonstrate the HUL approach and its six steps are scarce. This paper will also show how feasible the steps are and which are used the most.Originality/valueThis research demonstrates if the HUL approach is being understood in the academic field and if the implementation of the six steps is being reflected in the literature. This approach will reveal how these steps are being implemented and if this is having an effect on the heritage planning process.
Project scheduling by incorporating potential quality loss cost in time-cost tradeoff problems
Authors: Mahmoudi Amin , Javed Saad Ahmed 
Published: March 2020

Purpose
The study aims to introduce two new models of project scheduling by incorporating potential quality loss cost (PQLC) in time–cost tradeoff problems by overcoming the drawbacks of the existing Kim, Khang and Hwang (KKH) model. The proposed methods are named the Revised KKH-I (RKKH-I) and Revised KKH-II (RKKH-II) models for project scheduling.

Design/methodology/approach
The performance of the existing KKH model has been tested using a numerical example followed by the identification of the main shortcomings of the KKH method. Later, a concrete effort has been made to address its shortcomings while improving its performance significantly. The comparative analysis of the Revised KKH models with the original model has also been presented along with sensitivity analyses.

Findings
The study recognizes that the construct on which the original KKH method was built is important; however, certain drawbacks make it unable to consider PQLC in projects, thus making its practical use questionable. The comparative analysis of the proposed methodology with the original method demonstrated that the new models (RKHH-I and II) are more comprehensive and intelligent than the existing KKH model.

Originality/value
The comparative analysis of the original KKH model and its improved version reveals that the revised model is far more suitable for project scheduling. The study is important for project managers who recognize project scheduling being one of the key parameters associated with project management process, crucial to control every day during the management of projects.