bluuebunny/crossref_metadata_2025 huggingface dataset:
Histone Acetyltransferase 1 is Required for DNA Replication Fork Function and Stability
Authors: Agudelo Garcia Paula A. , Lovejoy Callie , Nagarajan Prabakaran , Park Dongju , Popova Liudmila , Freitas Michael A. , Parthun Mark R.
Published: March 2020

The replisome functions in a dynamic environment that is at the intersection of parental and nascent chromatin. Parental nucleosomes are disrupted in front of the replication fork. The daughter duplexes are packaged with an equal amount of parental and newly synthesized histones in the wake of the replication fork through the action of the replication-coupled chromatin assembly pathway. Histone acetyltransferase 1 (Hat1) is responsible for the cytosolic diacetylation of newly synthesized histone H4 on lysines 5 and 12 that accompanies replication-coupled chromatin assembly. Analysis of the role of Hat1 in replication-coupled chromatin assembly demonstrates that Hat1 also physically associates with chromatin near sites of DNA replication. The association of Hat1 with newly replicated DNA is transient but can be stabilized by replication fork stalling. The association of Hat1 with nascent chromatin may be functionally relevant as loss of Hat1 results in a decrease in replication fork progression and an increase in replication fork stalling. In addition, in the absence of Hat1, stalled replication forks are unstable and newly synthesized DNA becomes susceptible to Mre11-dependent degradation. These results suggest that Hat1 links replication fork function to the proper processing and assembly of newly synthesized histones.
Preliminary evidence that higher temperatures are associated with lower incidence of COVID-19, for cases reported globally up to 29th February 2020
Authors: Bannister-Tyrrell Melanie , Meyer Anne , Faverjon Céline , Cameron Angus
Published: March 2020

Seasonal variation in COVID-19 incidence could impact the trajectory of the pandemic. Using global line-list data on COVID-19 cases reported until 29th February 2020 and global gridded temperature data, and after adjusting for surveillance capacity and time since first imported case, higher average temperature was strongly associated with lower COVID-19 incidence for temperatures of 1°C and higher. However, temperature explained a relatively modest amount of the total variation in COVID-19 incidence. These preliminary findings support stringent containment efforts in Europe and elsewhere.
Antibody responses to SARS-CoV-2 in COVID-19 patients: the perspective application of serological tests in clinical practice
Authors: Long Quan-xin , Deng Hai-jun , Chen Juan , Hu Jie-li , Liu Bei-zhong , Liao Pu , Lin Yong , Yu Li-hua , Mo Zhan , Xu Yin-yin , Gong Fang , Wu Gui-cheng , Zhang Xian-xiang , Chen Yao-kai , Li Zhi-jie , Wang Kun , Zhang Xiao-li , Tian Wen-guang , Niu Chang-chun , Yang Qing-jun , Xiang Jiang-lin , Du Hong-xin , Liu Hua-wen , Lang Chun-hui , Luo Xiao-He , Wu Shao-bo , Cui Xiao-ping , Zhou Zheng , Wang Jing , Xue Cheng-jun , Li Xiao-feng , Wang Li , Tang Xiao-jun , Zhang Yong , Qiu Jing-fu , Liu Xia-mao , Li Jin-jing , Zhang De-chun , Zhang Fan , Cai Xue-fei , Wang De-qiang , Hu Yuan , Ren Ji-hua , Tang Ni , Liu Ping , Li Qin , Huang Ai-long
Published: March 2020

Background

We aim to investigate the profile of acute antibody response in COVID-19 patients, and provide proposals for the usage of antibody test in clinical practice.

Methods

A multi-center cross-section study (285 patients) and a single-center follow-up study (63 patients) were performed to investigate the feature of acute antibody response to SARS-CoV-2. A cohort of 52 COVID-19 suspects and 64 close contacts were enrolled to evaluate the potentiality of the antibody test.

Results

The positive rate for IgG reached 100% around 20 days after symptoms onset. The median day of seroconversion for both lgG and IgM was 13 days after symptoms onset. Seroconversion of IgM occurred at the same time, or earlier, or later than that of IgG. IgG levels in 100% patients (19/19) entered a platform within 6 days after seroconversion. The criteria of ‘IgG seroconversion’ and ‘> 4-fold increase in the IgG titers in sequential samples’ together diagnosed 82.9% (34/41) of the patients. Antibody test aided to confirm 4 patients with COVID-19 from 52 suspects who failed to be confirmed by RT-PCR and 7 patients from 148 close contacts with negative RT-PCR.

Conclusion

IgM and IgG should be detected simultaneously at the early phase of infection. The serological diagnosis criterion of seroconversion or the ‘>; 4-fold increase in the IgG titer’ is suitable for a majority of COVID-19 patients. Serologic test is helpful for the diagnosis of SARS-CoV-2 infection in suspects and close contacts.
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

The 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

Several 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 Implementation

The 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

Background

As 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.

Results

We 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.

Conclusions

The 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

Motivation

Large-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.

Results

We 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 Implementation

The 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).

Contact

eliezerm_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

Background

Current 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.

Methods

Using 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.

Findings

The 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.

Interpretation

For 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

G 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.
CD56 regulates human NK cell cytotoxicity through Pyk2
Authors: Gunesch Justin T. , Dixon Amera L. , Ebrahim Tasneem , Berrien-Elliott Melissa , Tatineni Swetha , Kumar Tejas , Solloa Everardo Hegewisch , Fehniger Todd A. , Mace Emily M.
Published: March 2020

Natural killer (NK) cells are innate immune cells that control viral infection and tumorigenic cell growth through targeted cell lysis and cytokine secretion. Human NK cells are classically defined as CD56+CD3−in peripheral blood. CD56 is neural cell adhesion molecule (NCAM1), and despite its ubiquitous expression on human NK cells, the role of CD56 in human NK cell cytotoxic function has not been fully explored. In non-immune cells, NCAM can induce signaling, mediate adhesion, and promote exocytosis, in part through interactions with focal adhesion kinase (FAK). Here we describe the generation and use of CD56-deficient human NK cell lines to define a novel requirement for CD56 in target cell lysis. Namely, we demonstrate that deletion of CD56 on the NK92 cell line led to impaired cytotoxic function against multiple susceptible target cell lines. Deletion of CD56 in a second NK cell line, YTS cells, led to a less severe cytotoxicity defect but impairment in cytokine secretion. Confocal microscopy of wild-type and CD56-KO NK92 cells conjugated to susceptible targets revealed that CD56-KO cells failed to polarize during immunological synapse (IS) formation and had severely impaired exocytosis of lytic granules at the IS. Phosphorylation of the FAK family member Pyk2 at tyrosine 402 was decreased in NK92 CD56-KO cells, demonstrating a functional link between CD56 and IS formation and signaling in human NK cells. Cytotoxicity, lytic granule exocytosis, and the phosphorylation of Pyk2 were rescued by the reintroduction of NCAM140 (CD56), into NK92 CD56-KO cells. These data highlight a novel functional role for CD56 in stimulating exocytosis and promoting cytotoxicity in human NK cells.
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

A 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

Background

Experimental 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.

Results

Bacterial 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.

Conclusions

Our 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.
Spatiotemporal reconstruction of emergent flash synchronization in firefly swarms via stereoscopic 360-degree cameras
Authors: Sarfati Raphaël , Hayes Julie , Sarfati Élie , Peleg Orit
Published: March 2020

During mating season, males of synchronous firefly species flash in unison within swarms of thousands of individuals. These strongly-correlated collective displays have inspired numerous mathematical models to explain how global synchronous patterns emerge from local interactions. Yet, experimental data to validate these models remains sparse. To address this gap, we develop a method for three-dimensional tracking of firefly flashes, using a stereoscopic setup of 360-degree cameras. We apply this method to record flashing displays of the North American synchronous speciesPhotinus carolinusin its natural habitat as well as within controlled environments, and obtain the 3D reconstruction of flash occurrences in the swarm. Our results show that even a small number of interacting males synchronize their flashes; however, periodic flash bursts only occur in groups larger than 15 males. Moreover, flash occurrences are correlated over several meters, indicating long-range interactions. While this suggests emergent collective behaviour and cooperation, we identify distinct individual trajectories that hint at additional competitive mechanisms. These reveal possible behavioural differentiation with early flashers being more mobile and flashing longer than late followers. Our experimental technique is inexpensive and easily implemented. It is extensible to tracking light communication in various firefly species and flight trajectories in other insect swarms.
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

Background

Immune 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.

Methods

A 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.

Results

PD-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.

Conclusions

High 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.
Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes
Authors: Poramba-Liyanage Deepani W. , Korthout Tessy , Cucinotta Christine E. , van Kruijsbergen Ila , van Welsem Tibor , El Atmioui Dris , Ovaa Huib , Tsukiyama Toshio , van Leeuwen Fred
Published: March 2020

Transcription of a chromatin template involves the concerted interaction of many different proteins and protein complexes. Analyses of specific factors showed that these interactions change during stress and upon developmental switches. However, how the binding of multiple factors at any given locus is coordinated has been technically challenging to investigate. Here we used Epi-Decoder in yeast to systematically decode, at one transcribed locus, the chromatin binding changes of hundreds of proteins in parallel upon perturbation of transcription. By taking advantage of improved Epi-Decoder libraries, we observed broad rewiring of local chromatin proteomes following chemical inhibition of RNA polymerase. Rapid reduction of RNA polymerase II binding was accompanied by reduced binding of many other core transcription proteins and gain of chromatin remodelers. In quiescent cells, where strong transcriptional repression is induced by physiological signals, eviction of the core transcriptional machinery was accompanied by the appearance of quiescent cell–specific repressors and rewiring of the interactions of protein-folding factors and metabolic enzymes. These results show that Epi-Decoder provides a powerful strategy for capturing the temporal binding dynamics of multiple chromatin proteins under varying conditions and cell states. The systematic and comprehensive delineation of dynamic local chromatin proteomes will greatly aid in uncovering protein–protein relationships and protein functions at the chromatin template.
Accurate and complete genomes from metagenomes
Authors: Chen Lin-Xing , Anantharaman Karthik , Shaiber Alon , Eren A. Murat , Banfield Jillian F.
Published: March 2020

Genomes are an integral component of the biological information about an organism; thus, the more complete the genome, the more informative it is. Historically, bacterial and archaeal genomes were reconstructed from pure (monoclonal) cultures, and the first reported sequences were manually curated to completion. However, the bottleneck imposed by the requirement for isolates precluded genomic insights for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as community genomics and subsequently as genome-resolved metagenomics, can circumvent this limitation by obtaining metagenome-assembled genomes (MAGs); but gaps, local assembly errors, chimeras, and contamination by fragments from other genomes limit the value of these genomes. Here, we discuss genome curation to improve and, in some cases, achieve complete (circularized, no gaps) MAGs (CMAGs). To date, few CMAGs have been generated, although notably some are from very complex systems such as soil and sediment. Through analysis of about 7000 published complete bacterial isolate genomes, we verify the value of cumulative GC skew in combination with other metrics to establish bacterial genome sequence accuracy. The analysis of cumulative GC skew identified potential misassemblies in some reference genomes of isolated bacteria and the repeat sequences that likely gave rise to them. We discuss methods that could be implemented in bioinformatic approaches for curation to ensure that metabolic and evolutionary analyses can be based on very high-quality genomes.
The impact of violence on tourism to Rio de Janeiro
Authors: Montes Gabriel Caldas , Bernabé Solimar de Pinho
Published: March 2020

Purpose

Rio 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/approach

The 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.

Findings

The 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/value

The 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 review

The 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

Purpose

This article aims to highlight the stigmatization attached to the unemployment of educated youth in rural regions of Khyber Pakhtunkhwa province of Pakistan.

Design/methodology/approach

The 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.

Findings

The 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/value

This 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

Purpose

The 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/approach

This 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.

Findings

The 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/value

This 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.
Staff perceptions of PRN medication in a residential care setting
Authors: Stubbings Daniel Robert , Hughes Kyle , Limbert Caroline
Published: March 2020

Purpose

The purpose of this paper is to explore the perceptions of staff towards psychotropic Pro Re Nata (PRN) medication in a residential care setting.

Design/methodology/approach

Three male and seven female participants were interviewed using a semi-structured interview. Transcripts were analysed using thematic analysis.

Findings

Four themes pertaining to PRN medication emerged from the data: behaviour change, calming effect, importance of timing and perceived uniqueness.

Research limitations/implications

The participant group was not homogenous and findings may have been different in a more qualified cohort. This care setting may not be representative of other environments where PRN medication is administered. The findings do, however, highlight some of the challenges facing the administration of PRN medication in mental health and care settings.

Practical implications

The awareness of these themes is significant for improving staff knowledge, training practices and policies towards the use and administration of psychotropic PRN medication.

Originality/value

This is the first study to engage in a thematic analysis of staff views towards the administration of PRN medication.
How and when group cohesion influences employee voice
Authors: Kong Fang , Liu Peng , Weng Jie
Published: March 2020

Purpose

This study examines how and when group cohesion influences employee voice.

Design/methodology/approach

The sample comprises 215 employees from 41 workgroups in China. Multilevel path analyses were used to test the hypotheses.

Findings

The results show that group cohesion is positively related to employee voice. Group psychological safety mediates the positive relationship between group cohesion and employee voice. Further, high cohesion strength enhances the association of group cohesion with employee voice as well as the mediating effect of group cohesion on voice behavior through group psychological safety.

Research limitations/implications

This study employs a cross-sectional design and does not establish causal relationships among the variables examined. This study offers research implications because it adds to our knowledge on the situational antecedents of voice behavior.

Practical implications

The findings suggest that group cohesion plays an important role in influencing employee voice. To encourage employees to speak up, managers should pay attention to group cohesion in terms of both cohesion level and strength.

Originality/value

This study is the first to examine the mechanism and condition of the effect of group cohesion on employee voice, thus extending knowledge on the situational factors influencing voice behavior.
Perception and preferences of hiring managers
Authors: Chen Reuben Yong Soon , Hussain Kashif , Low Chris Kam Loong
Published: March 2020

Purpose

This study aims to explore the perception and preferences of hiring managers toward employing airline cabin crew for management positions in food and beverage outlets.

Design/methodology/approach

A phenomenological approach is adopted for this study purposefully selecting food and beverage hiring managers and airline cabin crews.

Findings

The study concludes that with customized and effective re-training, food and beverage hiring managers are willing to employ airline cabin crews to assume managerial positions.

Originality/value

This study outlines the practicalities of re-training individuals to improve personal and organizational performance.
Macrofauna bivalve diversity from the deep northern Gulf of Mexico
Authors: Wei Chih‐Lin , Chen Min , Wicksten Mary K. , Rowe Gilbert T.
Published: March 2020

Abundance, α diversity, and faunal zonation of infaunal bivalve mollusks were measured along multiple depth transects in the deep northern Gulf of Mexico (GoM) covering depths of 213 to 3,732 m. Density decreased exponentially from the shallow continental slope (0.2–1.0 km) down to the abyssal plain depths (3.0–3.7 km). Diversity increased down the slope to a maximum at intermediate depths (1.2 to 1.8 km), followed by a decrease down to the Sigsbee Deep. The maximum diversities coincided with an organic carbon input of 10 to 16.3 mg C m−2 d−1, whereas the minimum was encountered at the high (ca. 52–78 mg C m−2 d−1) and low extremes (ca. 3–5 mg C m−2 d−1) of the detrital food input. Seven faunal zones could be identified on the basis of species composition with faunal changes being more abrupt on the upper slope compared to the lower slope and abyssal plain, possibly due to steeper gradients in physical variables.
Porter model of economic development at the back of an envelope
Authors: Pol Eduardo
Published: March 2020

The Porter model of economic development links the phases of development with national competitiveness. His model lies at the heart of the Global Competitiveness Index. It appears, curiously enough, that there is nowhere in the economics literature a concise explanation of the Porter model of economic development. This paper not only fills this gap but also draws the line of separation between formal economic models and narrative economic models; provides a rigorous presentation of Porter model of economic development; distinguishes between the Porter development path and Porter's law of economic development; strips Porter model to its bare essentials in a single picture; and finally, shows that the Porter model satisfies the condition known as the way the world works (www) constraint.
Decisions in Designing an Australian Macroeconomic Model
Authors: Murphy Chris
Published: March 2020

This paper discusses the decisions made in designing a new Australian macroeconometric model to be used for both policy analysis and forecasting. Serving these dual functions requires a reasonable level of consistency with both macroeconomic theory (emphasised in New Keynesian dynamic stochastic general equilibrium models) and macroeconomic data (emphasised in vector autoregression models). The key decisions made in modelling household, business, government and foreign behaviour are explained. The design decisions taken are reflected in the new model, which is the latest in a series developed by the author. The use of the latest model is illustrated in optimal control simulations.
A Minimax Regret Approach to Decision Making Under Uncertainty
Authors: Mishra Ashok K. , Tsionas Mike G.
Published: March 2020

We propose a minimax regret approach to optimal factor demand under uncertainty. Regret is the deviation of any given decision from the optimal decision based on a specified set of possible scenarios for the uncertain variables. This approach does not require the specification of instrumental variables to control for unobserved states of nature, and also does not require specification of the number of possible states in advance. Importantly, ex post production shocks can be estimated using our approach, and full statistical inferences can be obtained. Econometric techniques are based on Bayesian analysis using Markov Chain Monte Carlo techniques. A substantive empirical application is provided to illustrate the new approach.
Modern Nightingales
Authors: Langkjær-Bain Robert
Published: March 2020

Five statisticians keeping the spirit of Florence Nightingale alive. Interviews by Robert Langkjær-Bain
Evaluating the effectiveness of chemotherapy for thymic epithelial tumors using the CD‐DST method
Authors: Yu Lei , Zhang Bao‐xun , Du Xin , Yu Zhen , Yang Xing‐guo , Jiang Yu‐xuan
Published: March 2020

Background

Thymic epithelial tumors (TET) are frequently eligible for curative‐intent surgical resection. For locally advanced TETs, chemotherapy has been used to both reduce the tumor burden and achieve prolonged disease control. However, effective therapy for this disease largely remains to be determined. Here, we report the chemosensitivity of 100 patients with TETs determined by the collagen gel droplet embedded culture‐drug sensitivity test (CD‐DST).

Methods

A total of 100 patients with TETs underwent surgical resection. The efficacy of antitumor agents on TET cells was tested by CD‐DST.

Results

Thymic epithelial tumors were pathologically confirmed after surgery: two cases were type A thymoma, 17 were type AB, 12 were type B1, 44 were type B2, 12 were type B3, and there were 13 cases with thymic carcinoma. A total of 36% patients with TETs were sensitive to different types of chemotherapeutic agents. There was no significant differences in age, histological type, clinical staging, or association with autoimmune diseases between sensitive and nonsensitive cases. Type B1 and B2 thymoma were relatively more sensitive to chemotherapeutic agents (6/12 and 18/44, respectively), while sensitivity of type B3 cases to chemotherapeutic agents was much lower (only 2/12). Cases with type A thymoma were not sensitive to any antitumor drugs. Among 11 chemotherapeutic agents tested in our study, the sensitivity of TETs to EPI was the highest (16%). No patients with thymoma were sensitive to Alimta (Pemetrexed).

Conclusions

Our work illuminates the effectiveness of chemotherapy for TETs and provides important clues for choosing antitumor drugs with relatively high drug sensitivity to TETs in advance.
Performance of lung cancer screening with low‐dose CT in Gejiu, Yunnan: A population‐based, screening cohort study
Authors: Wei Meng‐Na , Su Zheng , Wang Jian‐Ning , Gonzalez Mendez Maria J. , Yu Xiao‐Yun , Liang Hao , Zhou Qing‐Hua , Fan Ya‐Guang , Qiao You‐Lin
Published: March 2020

Background

The performance of lung cancer screening with low‐dose computed tomography (CT) (LDCT) in China is uncertain. This study aimed to evaluate the performance of LDCT lung cancer screening in the Chinese setting.

Methods

In 2014, a screening cohort of lung cancer with LDCT was established in Gejiu, Yunnan Province, a screening center of the Lung Cancer Screening Program in Rural China (LungSPRC). Participants received a baseline screening and four rounds of annual screening with LDCT in two local hospitals until June 2019. We analyzed the rates of participation, detection, early detection, and the clinical characteristics of lung cancer.

Results

A total of 2006 participants had complete baseline screening results with a compliance rate of 98.4%. Of these, 1411 were high‐risk and 558 were nonhigh‐risk participants. During this period, 40 lung cancer cases were confirmed, of these, 35 were screen‐detected, four were post‐screening and one was an interval case. The positive rate of baseline and annual screening was 9.7% and 9.0%, while the lung cancer detection rate was 0.4% and 0.6%, respectively. The proportion of early lung cancer increased from 37.5% in T0 to 75.0% in T4. Adenocarcinoma was the most common histological subtype. Lung cancer incidence according to the criteria of LungSPRC and National Lung Cancer Screening Trial (NLST) was 513.31 and 877.41 per 100 000 person‐years, respectively.

Conclusions

The program of lung cancer screening with LDCT showed a successful performance in Gejiu, Yunnan. However, further studies are warranted to refine a high‐risk population who will benefit most from LDCT screening and reduce the high false positive results.

Key points

This study reports the results of lung cancer screening with LDCT in Gejiu, Yunnan, a high‐risk area of lung cancer, and it demonstrates that lung cancer screening with LDCT is effective in detecting early‐stage lung cancer. Our program provides an opportunity to explore the performance of LDCT lung cancer screening in the Chinese context.