bluuebunny/crossref_metadata_2025 huggingface dataset:
An efficient distributed algorithm with application to COVID-19 data from heterogeneous clinical sites
Authors: Tong Jiayi , Luo Chongliang , Islam Md Nazmul , Sheils Natalie , Buresh John , Edmondson Mackenzie , Merkel Peter A. , Lautenbach Ebbing , Duan Rui , Chen Yong
Published: November 2020

Objectives

Integrating electronic health records (EHR) data from several clinical sites offers great opportunities to improve estimation with a more general population compared to analyses based on a single clinical site. However, sharing patient-level data across sites is practically challenging due to concerns about maintaining patient privacy. The objective of this study is to develop a novel distributed algorithm to integrate heterogeneous EHR data from multiple clinical sites without sharing patient-level data.

Materials and Methods

The proposed distributed algorithm for binary regression can effectively account for between-site heterogeneity and is communication-efficient. Our method is built on a pairwise likelihood function in the extended Mantel-Haenszel regression, which is known to be statistically highly efficient. We construct a surrogate pairwise likelihood function through approximating the target pairwise likelihood by its surrogate. We show that the proposed surrogate pairwise likelihood leads to a consistent and asymptotically normal estimator by effective communication without sharing individual patient-level data. We study the empirical performance of the proposed method through a systematic simulation study and an application with data of 14,215 COVID-19 patients from 230 clinical sites at UnitedHealth Group Clinical Research Database.

Results

The proposed method was shown to perform close to the gold standard approach under extensive simulation settings. When the event rate is <5%, the relative bias of the proposed estimator is 30% smaller than that of the meta-analysis estimator. The proposed method retained high accuracy across different sample sizes and event rates compared with meta-analysis. In the data evaluation, the proposed estimate has a relative bias <9% when the event rate is <1%, whereas the meta-analysis estimate has a relative bias at least 10% higher than that of the proposed method.

Conclusions

Our simulation study and data application demonstrate that the proposed distributed algorithm provides an estimator that is robust to heterogeneity in event rates when effectively integrating data from multiple clinical sites. Our algorithm is therefore an effective alternative to both meta-analysis and existing distributed algorithms for modeling heterogeneous multi-site binary outcomes.
Resuming professional football (soccer) during the COVID-19 pandemic in a country with high infection rates: A prospective cohort study
Authors: Schumacher Yorck Olaf , Tabben Montassar , Hassoun Khalid , Al Marwani Asmaa , Al Hussain Ibrahim , Coyle Peter , Abbassi Ahmed Khellil , Ballan Hani Taleb , Al Kuwari Abdulaziz Jaham , Chamari Karim , Bahr Roald
Published: November 2020

Objectives

The risk of viral transmission associated with contact sports such as football (soccer) during the COVID-19 pandemic is unknown. The aim of this study was to describe the infective and immune status of professional football players, team staff and league officials over a truncated football season resumed at the height of the COVID-19 pandemic in a country with high infection rates and to investigate the clinical symptoms related to COVID-19 infection in professional football players.

Methods

Prospective cohort study of 1337 football players, staff and officials during a truncated football season (9 weeks) with a tailored infection control program based on preventive measures and regular SARS-CoV-2 PCR swab testing (every 3-5 days) combined with serology testing for immunity (every 4 weeks). Clinical symptoms in positive participants were recorded using a 26-item, Likert-scale-based scoring system.

Results

During the study period, 85 subjects returned positive (cycle threshold (cT)≤30) or reactive (30<cT<40) PCR tests, of which 36 were players. The infection rate was consistent with that of the general population during the same time period. More than half of infected subjects were asymptomatic, and the remaining had only mild symptoms with no one requiring hospitalization. Symptom severity was associated with lower cT values. Social contacts and family were the most common sources of infection, and no infection could be traced to training or matches. Of the 36 infected players, 15 presented positive serology during the study period.

Conclusion

Football played outdoors involving close contact between athletes represents a limited risk for SARS-CoV-2 infection and severe illness when preventive measures are in place.
Optimizing Vaccine Allocation to Combat the COVID-19 Pandemic
Authors: Bertsimas Dimitris , Ivanhoe Joshua , Jacquillat Alexandre , Li Michael , Previero Alessandro , Lami Omar Skali , Bouardi Hamza Tazi
Published: November 2020

The outbreak of COVID-19 has spurred extensive research worldwide to develop a vaccine. However, when a vaccine becomes available, limited production and distribution capabilities will likely lead to another challenge: who to prioritize for vaccination to mitigate the near-end impact of the pandemic? To tackle that question, this paper first expands a state-of-the-art epidemiological model, called DELPHI, to capture the effects of vaccinations and the variability in mortality rates across subpopulations. It then integrates this predictive model into a prescriptive model to optimize vaccine allocation, formulated as a bilinear, non-convex optimization model. To solve it, this paper proposes a coordinate descent algorithm that iterates between optimizing vaccine allocations and simulating the dynamics of the pandemic. We implement the model and algorithm using real-world data in the United States. All else equal, the optimized vaccine allocation prioritizes states with a large number of projected cases and sub-populations facing higher risks (e.g., older ones). Ultimately, the optimized vaccine allocation can reduce the death toll of the pandemic by an estimated 10–25%, or 10,000–20,000 deaths over a three-month period in the United States alone.

Highlights

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This paper formulates an optimization model for vaccine allocation in response to the COVID-19 pandemic. This model, referred to as DELPHI–V–OPT, integrates a predictive epidemiological model into a prescriptive model to support the allocation of vaccines across geographic regions (e.g., US states) and across risk classes (e.g., age groups).

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This paper develops a scalable coordinate descent algorithm to solve the DELPHI–V–OPT model. The proposed algorithm converges effectively and in short computational times. Therefore, the proposed approach can be implemented efficiently, and allows extensive sensitivity analyses for scenario planning and policy analysis.

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Computational results demonstrate that optimized vaccine allocation strategies can curb the death toll of the COVID-19 pandemic by an estimated at 10–25%, or 10,000–20,000 deaths over a three-month period in the United States alone. These results highlight the critical role of vaccine allocation to combat the COVID-19 pandemic, in addition to vaccine design and vaccine production.
The expression ofPDCD1andCD274in T cells and macrophages correlated positively with COVID-19 severity
Authors: Gao Qianqian , Liu Shang , Ding Renpeng , Chen Huanyi , Dong Xuan , Xie Jiarui , Li Yijian , Chen Lei , Liu Huan , Mu Feng
Published: November 2020

The immune responses underlying the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remain unclear. To help understand the pathology of coronavirus disease 2019 (COVID-19) pandemics, public data were analyzed and the expression ofPDCD1(encoding PD-1) andCD274(encoding PD-L1) in T cells and macrophages were identified to correlate positively with COVID-19 severity.
Metagenomic profiling of host-associated bacteria from 8 datasets of the red algaPorphyra purpurea, with MetaPhlAn 3.0
Authors: Nousias Orestis , Montesanto Federica
Published: November 2020

Microbial communities play a fundamental role in the association with marine algae, in fact they are recognized to be actively involved in growth and morphogenesis.

Porphyra purpureais a red algae commonly found in the intertidal zone with an high economical value, indeed several species belonging to the genusPorphyraare intensely cultivated in the Eastern Asian countries. Moreover,P. purpureais widely used as model species in different fields, mainly due to its peculiar life cycle. Despite of that, little is known about the microbial community associated to this species. Here we report the microbial-associated diversity ofP. purpureain four different localities (Ireland, Italy United Kingdom and USA) through the analysis of eight metagenomic datasets obtained from the publicly available metagenomic nucleotide database (https://www.ebi.ac.uk/ena/). The metagenomic datasets were quality controlled with FastQC version 0.11.8, pre-processed with Trimmomatic version 0.39 and analysed with Methaplan 3.0, with a reference database containing clade specific marker genes from ~ 99.500 bacterial genomes, following the pan-genome approach, in order to identify the putative bacterial taxonomies and their relative abundances. Furthermore, we compared the results to the 16S rRNA metagenomic analysis pipeline of MGnify database to evaluate the effectiveness of the two methods. Out of the 43 bacterial species identified with MetaPhlAn 3.0 only 5 were common with the MGnify results and from the 21 genera, only 9 were common. This approach highlighted the different taxonomical resolution of a 16S rRNA OTU-based method in contrast to the pan-genome approach deployed by MetaPhlAn 3.0.
Enforced dimerization between XBP1s and ATF6f enhances the protective effects of the unfolded protein response (UPR) in models of neurodegeneration
Authors: Vidal René L. , Sepulveda Denisse , Troncoso-Escudero Paulina , Garcia-Huerta Paula , Gonzalez Constanza , Plate Lars , Jerez Carolina , Canovas José , Rivera Claudia A. , Castillo Valentina , Cisternas Marisol , Leal Sirley , Martinez Alexis , Grandjean Julia , Lashuel Hilal A. , Martin Alberto J.M. , Latapiat Veronica , Matus Soledad , Sardi S. Pablo , Wiseman R. Luke , Hetz Claudio
Published: November 2020

Alteration to endoplasmic reticulum (ER) proteostasis is observed on a variety of neurodegenerative diseases associated with abnormal protein aggregation. Activation of the unfolded protein response (UPR) enables an adaptive reaction to recover ER proteostasis and cell function. The UPR is initiated by specialized stress sensors that engage gene expression programs through the concerted action of the transcription factors ATF4, ATF6f, and XBP1s. Although UPR signaling is generally studied as unique linear signaling branches, correlative evidence suggests that ATF6f and XBP1s may physically interact to regulate a subset of UPR-target genes. Here, we designed an ATF6f-XBP1s fusion protein termed UPRplus that behaves as a heterodimer in terms of its selective transcriptional activity. Cell-based studies demonstrated that UPRplus has stronger an effect in reducing the abnormal aggregation of mutant huntingtin and alpha-synuclein when compared to XBP1s or ATF6 alone. We developed a gene transfer approach to deliver UPRplus into the brain using adeno-associated viruses (AAVs) and demonstrated potent neuroprotectionin vivoin preclinical models of Parkinson’s and Huntington’s disease. These results support the concept where directing UPR-mediated gene expression toward specific adaptive programs may serve as a possible strategy to optimize the beneficial effects of the pathway in different disease conditions.
In-vitro virucidal activity of hypothiocyanite and hypothiocyanite/lactoferrin mix against SARS-CoV-2
Authors: Cegolon Luca , Mirandola Mattia , Salaris Claudio , Salvati Maria Vittoria , Salata Cristiano , Mastrangelo Giuseppe
Published: November 2020

SARS-CoV-2 replicates efficiently in the upper airway during prodromal stage with resulting viral shedding into the environment from patients with active disease as well as from asymptomatic individuals. So far, virus spread has been exclusively contained by non-pharmacological interventions (social distancing, face masks, hand washing and several measures limiting business activities or movement of individuals)1,2. There is a need to find pharmacological interventions to mitigate the viral spread, supporting yet limiting the existing health protection measures while an effective and safe vaccine will hopefully become available. Hypothiocyanite and lactoferrin as part of the innate human immune system were shown to have a large spectrum of cidal activity against bacteria, fungi and viruses2,3. To test their virucidal activity against SARS-CoV-2 we conducted an in-vitro study. Here we show a dose-dependent virucidal activity of hypothiocyanite at micromolar concentrations, slightly improved by the presence of lactoferrin. The two substances are devoid of any cytotoxicity and may be administered combined by aerosol to exploit their antiviral activity at the port of entry (mouth, nasal cavity, conjunctiva) or exit (mouth, through emission of respiratory droplets) of SARS-CoV-2 in the human body. Furthermore, aerosol with hypothiocyanite and lactoferrin combined could also have a therapeutic effect in the lower respiratory tract, at the level of gas exchange units of the lung, preventing the devastating infection of alveolar type II cells where ACE2 is highly expressed. An in-vivo validation of in-vitro results is urgently required.
Design to Data for mutants of β-glucosidase B fromPaenibacillus polymyxa:L171M, H178M, M221L, E406W, N160E, F415M
Authors: Huang Xiaoqing , Kim Daniel , Huang Peishan , Vater Ashley , Siegel Justin B.
Published: November 2020

Computational protein design is growing in popularity as a means to engineer enzymes. Currently, protein design algorithms can predict the stability and function of the enzymes to only a limited degree. Thus, further experimental data is required for training software to more accurately characterize the structure-function relationship of enzymes. To date, the Design2Data (D2D) database holds 129 single point mutations of β-glucosidase B (BglB) characterized by kinetic and thermal stability biophysical parameters. In this study, we introduced six mutants into the BglB database and examined their catalytic activity and thermal stability: L171M, H178M, M221L, E406W, N160E, and F415M.
Sequential ER stress and inflammatory responses are induced by SARS-CoV-2 ORF3 through ERphagy
Authors: Zhang Xiaolin , Yang Ziwei , Long Xubing , Sun Qinqin , Wang Fan , Wang Pei-hui , Li Xiaojuan , Kuang Ersheng
Published: November 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have resulted in a number of severe cases of COVID-19 and deaths worldwide. However, knowledge of SARS-CoV-2 infection, diseases and therapy remains limited, underlining the urgency of fundamental studies and drug development. Studies have shown that induction of autophagy and hijacking of autophagic machinery are essential for infection and replication of SARS-CoV-2; however, the mechanism of this manipulation and function of autophagy during SARS-CoV-2 infection remain unclear. In the present study, we identified ORF3 as an inducer of autophagy and revealed that ORF3 localizes to the ER and induces FAM134B-related ERphagy through the HMGB1-Beclin1 pathway. As a consequence, ORF3 induces ER stress and inflammatory responses through ERphagy and sensitizes cells to ER stress-induced cell death, suggesting that SARS-CoV-2 ORF3 hijacks ERphagy and then harms ER homeostasis to induce inflammatory responses through excessive ER stress. These findings reveal a sequential induction of ERphagy, ER stress and acute inflammatory responses during SARS-CoV-2 infection and provide therapeutic potential for ERphagy and ER stress-related drugs for COVID-19 treatment and prevention.

Importance

SARS-CoV-2 infection and replication require autophagosome-like double-membrane vacuoles. Inhibition of autophagy suppresses viral replication, indicating the essential role of autophagy in SARS-CoV-2 infection. However, how SARS-CoV-2 hijacks autophagy and the function of autophagy in the disease progression remain unknown. Here, we reveal that SARS-CoV-2 ORF3 induces ERphagy and consequently induces ER stress to trigger acute inflammatory responses and enhance sensitivity to ER stress-induced apoptosis. Our studies uncover ERphagy-induced inflammatory responses during SARS-CoV-2 infection and provide a promising therapeutic approach for treating SARS-CoV-2 infection and inflammatory responses in COVID-19 by manipulating autophagy and ER stress.
A unique adhesive motif of protein disulfide isomerase P5 supports its function via dimerization
Authors: Okumura Masaki , Kanemura Shingo , Matsusaki Motonori , Kinoshita Misaki , Saio Tomohide , Ito Dai , Hirayama Chihiro , Kumeta Hiroyuki , Watabe Mai , Amagai Yuta , Lee Young-Ho , Akiyama Shuji , Inaba Kenji
Published: November 2020

P5, also known as PDIA6, is a PDI-family member that plays an important role in the ER quality control. Herein, we revealed that P5 dimerizes via a unique adhesive motif contained in the N-terminal thioredoxin-like domain. This motif is apparently similar to, but radically different from conventional leucine-zipper motifs, in that the former includes a periodic repeat of leucine or valine residues at the third or fourth position spanning five helical turns on 15-residue anti-parallel α-helices, unlike the latter of which the leucine residues appear every two helical turns on ∼30-residue parallel α-helices at dimer interfaces. A monomeric P5 mutant with the impaired adhesive motif showed structural instability and local unfolding, and behaved as an aberrant protein that induces the ER stress response. Disassembly of P5 to monomers compromised its ability to inactivate IRE1α via reduction of intermolecular disulfide bonds and its Ca2+-dependent regulation of chaperone functionin vitro. Thus, the leucine-valine adhesive motif supports structure and physiological function of P5.
The impact of early public health interventions on SARS-CoV-2 transmission and evolution
Authors: Duchene Sebastian , Featherstone Leo , de Blasio Birgitte Freiesleben , Holmes Edward C. , Bohlin Jon , Pettersson John H.-O.
Published: November 2020

Background

Many countries have attempted to mitigate and control COVID-19 through the implementation of non-pharmaceutical interventions, particularly with the aim of reducing population movement and contact. However, it remains unclear how the different control strategies impacted the local phylodynamics of the causative SARS-CoV-2 virus.

Aim

To assess the duration of chains of virus transmission within individual countries and the extent to which countries export viruses to their geographic neighbours.

Methods

To address core questions in genomic epidemiology and public health we analysed complete SARS-CoV-2 genomes to infer the relative frequencies of virus importation and exportation, as well as virus transmission dynamics, within countries of northern Europe. To this end, we examined virus evolution and phylodynamics in Denmark, Finland, Iceland, Norway and Sweden during the first year of the pandemic.

Results

The Nordic countries differed markedly in the invasiveness of control strategies implemented. In particular, Sweden did not initially employ any strict population movement limitations and experienced markedly different transmission chain dynamics, which were more numerous and tended to have more cases, a set of features that increased with time during the first eight months of 2020.

Conclusion

Together with Denmark, Sweden was also characterised as a net exporter of SARS-CoV-2. Hence, Sweden effectively constituted an epidemiological and evolutionary ‘refugia’ that enabled the virus to maintain active transmission and spread to other geographic localities. In sum, our analysis reveals the utility of genomic surveillance where active transmission chain monitoring is a key metric.
COVIDStrategyCalculator: A software to assess testing- and quarantine strategies for incoming travelers, contact person management and de-isolation
Authors: van der Toorn Wiep , Oh Djin-Ye , von Kleist Max
Published: November 2020

While large-scale vaccination campaigns against SARS-CoV-2 are rolled out at the time of writing, non-pharmaceutical interventions (NPIs), including the isolation of infected individuals, and quarantine of exposed individuals remain central measures to contain the spread of SARS-CoV-2. Strategies that combine NPIs with innovative SARS-CoV-2 testing strategies may increase containment efficacy and help to shorten quarantine durations.

We developed a user-friendly software-tool that implements a recently published stochastic within-host viral dynamics model that captures temporal attributes of the viral infection, such as test sensitivity, infectiousness and the occurrence of symptoms. Based on this model, the software allows to evaluate the efficacy of user-defined, arbitrary NPI and testing strategies in reducing the transmission potential in different contexts. The software thus enables decision makers to explore NPI strategies and perform hypothesis testing, e.g. with regards to the utilization of novel diagnostics or with regards to containing novel virus variants.
Sub-centrosomal mapping identifies augmin-γTuRC as part of a centriole-stabilizing scaffold
Authors: Schweizer Nina , Haren Laurence , Viais Ricardo , Lacasa Cristina , Dutto Ilaria , Merdes Andreas , Lüders Jens
Published: November 2020

Centriole biogenesis and maintenance are crucial for cells to generate cilia and assemble centrosomes that function as microtubule organizing centers (MTOCs). Centriole biogenesis and MTOC function both require the microtubule nucleator γ-tubulin ring complex (γTuRC). The widely accepted view is that γTuRC localizes to the pericentriolar material (PCM), where it nucleates microtubules. γTuRC has also been observed at centriolar regions that lack PCM, but the significance of these findings is unclear. Here we have used expansion microscopy to map spatially and functionally distinct sub-populations of centrosomal γTuRC including in the centriole lumen. Luminal localization is mediated by augmin and both complexes are linked to the centriole inner scaffold through POC5. Disruption of luminal localization impairs centriole stability and cilia assembly, defects that are also observed in γTuRC mutant fibroblasts derived from a patient suffering from microcephaly with chorioretinopathy. These results identify a novel, non-canonical role of augmin-γTuRC in the centriole lumen that is linked to human disease.
Dysglycemia is associated withMycobacterium tuberculosislineages in tuberculosis patients of North Lima - Peru
Authors: Lopez Kattya , Arriaga María B. , Aliaga Juan G. , Barreda Nadia N. , Sanabria Oswaldo M. , Huang Chuan-Chin , Zhang Zibiao , García-de-la-Guarda Ruth , Lecca Leonid , Calçada Carvalho Anna Cristina , Kritski Afrânio L. , Calderon Roger I.
Published: November 2020

This study was performed to investigate the role of dysglycemia on the genetic diversity ofMycobacterium tuberculosis(MTB) among pulmonary tuberculosis (TB) patients to build scientific evidence about the possible mechanisms of TB transmission. MTB isolates obtained of patients affected by pulmonary tuberculosis from health care facilities of North Lima - Peru, were analyzed using whole genome sequencing and 24-locus mycobacterial interspersed repetitive-unit-variable-number tandem repeats (MIRU-VNTR). Subsequently, clinical and epidemiological characteristics were associated with clustering, lineages and comorbid conditions. The analysis carried out 112 pulmonary TB patients from various health centers in North Lima, 17 (15%) had diabetes mellitus (DM) and 33 (29%) had pre-diabetes (PDM). Latin American-Mediterranean, Haarlem and Beijing were the most frequent MTB lineages found in those patients. Previous TB (adjusted odds ratio [aOR]=3.65; 95%CI: 1.32-17.81), age (aOR=1.12; 95%CI: 1.03-1.45) and Beijing lineage (aOR=3.53; 95%CI: 1.08-13.2) were associated with TB-DM comorbidity. Alcoholism (aOR=2.92; 95%CI: 1.10-8.28), age (aOR=1.05; 95%CI: 1.03-1.12) and Haarlem lineage (aOR=2.54; 95%CI: 1.04-6.51) were associated with TB-PDM comorbidity. Beijing and Haarlem lineages were independently associated with TB-DM and TB-PDM comorbidities, respectively. Although these findings may be surprising, we must be cautious to suggest that dysglycemia could be associated with a highly clustering and predisposition of MTB lineages related to a serious impact on the severity of TB disease, which requires further research.
Single-cell Transcriptome of Bronchoalveolar Lavage Fluid Reveals Dynamic Change of Macrophages During SARS-CoV-2 Infection in Ferrets
Authors: Lee Jeong Seok , Koh June-Young , Yi Kijong , Kim Young-Il , Park Su-Jin , Kim Eun-Ha , Kim Se-Mi , Park Sung Ho , Ju Young Seok , Choi Young Ki , Park Su-Hyung
Published: November 2020

Although the profile of immune cells changes during the natural course of SARS-CoV-2 inflection in human patients, few studies have used a longitudinal approach to reveal their dynamic features. Here, we performed single-cell RNA sequencing of bronchoalveolar lavage fluid cells longitudinally obtained from SARS-CoV-2-infected ferrets. Landscape analysis of the lung immune microenvironment showed dynamic changes in cell proportions and characteristics in uninfected control, at 2 days post-infection (dpi) (early stage of SARS-CoV-2 infection with peak viral titer), and 5 dpi (resolution phase). NK cells and CD8+T cells exhibited activated subclusters with interferon-stimulated features, which were peaked at 2 dpi. Intriguingly, macrophages were classified into 10 distinct subpopulations, and their relative proportions changed over the time. We observed prominent transcriptome changes among monocyte-derived infiltrating macrophages and differentiated M1/M2 macrophages, especially at 2 dpi. Moreover, trajectory analysis revealed gene expression changes from monocyte-derived infiltrating macrophages toward M1 or M2 macrophages and identified the distinct macrophage subpopulation that had rapidly undergone SARS-CoV-2-mediated activation of inflammatory responses. Finally, we found that different spectrums of M1 or M2 macrophages showed distinct patterns of gene modules downregulated by immune-modulatory drugs. Overall, these results elucidate fundamental aspects of the immune response dynamics provoked by SARS-CoV-2 infection.
HLA class I genotypes customize vaccination strategies in immune simulation to combat COVID-19
Authors: Huang Shouxiong , Tan Ming
Published: November 2020

Memory CD8+T cells are associated with a better outcome in Coronavirus Disease 2019 (COVID-19) and recognized as promising vaccine targets against viral infections. This study determined the efficacy of population-dominant and infection-relevant human leukocyte antigens (HLA) class I proteins to present severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) peptides through calculating binding affinities and simulating CD8+T cell responses. As a result, HLA class I proteins distinguished or shared various viral peptides derived from viruses. HLA class I supertypes clustered viral peptides through recognizing anchor and preferred residues. SARS-CoV-2 peptides overlapped significantly with SARS but minimally with common human coronaviruses. Immune simulation of CD8+T cell activation using predicted SARS-CoV-2 peptide antigens depended on high-affinity peptide binding, anchor residue interaction, and synergistic presentation of HLA class I proteins in individuals. Results demonstrated that multi-epitope vaccination, employing a strong binding affinity, viral adjuvants, and heterozygous HLA class I genes, induced potent immune responses. Therefore, optimal CD8+T cell responses can be achieved and customized contingent on HLA class I genotypes in human populations, supporting a precise vaccination strategy to combat COVID-19.
Structural basis of ligand selectivity by a bacterial adhesin lectin involved in multi- species biofilm formation
Authors: Guo Shuaiqi , Vance Tyler D.R. , Zahiri Hossein , Eves Robert , Stevens Corey , Hehemann Jan-Hendrik , Vidal-Melgosa Silvia , Davies Peter L.
Published: November 2020

Carbohydrate recognition by lectins governs critical host-microbe interactions.MpPA14lectin is a domain of a 1.5-MDa adhesin responsible for a symbiotic bacterium-diatom interaction in Antarctica. Here we showMpPA14 binds various monosaccharides, with L-fucose and N-acetyl glucosamine being the strongest ligands (Kd~ 150 μM). High-resolution structures ofMpPA14 with 15 different sugars bound elucidated the molecular basis for the lectin’s apparent binding promiscuity but underlying selectivity.MpPA14 mediates strong Ca2+-dependent interactions with the 3, 4 diols of L-fucopyranose and glucopyranoses, and binds other sugars via their specific minor isomers. Thus,MpPA14 only binds polysaccharides like branched glucans and fucoidans with these free end-groups. Consistent with our findings, adhesion ofMpPA14 to diatom cells was selectively blocked by L-fucose, but not by N-acetyl galactosamine. WithMpPA14 lectin homologs present in adhesins of several pathogens, our work gives insight into an anti-adhesion strategy to block infection via ligand-based antagonists.
Representations of local spatial information in the human medial temporal lobe during memory-guided navigation
Authors: Wang Shao-Fang , Carr Valerie A. , Favila Serra E. , Bailenson Jeremy N. , Brown Thackery I. , Jiang Jiefeng , Wagner Anthony D.
Published: November 2020

The hippocampus (HC) and surrounding medial temporal lobe (MTL) cortical regions play a critical role in spatial navigation and episodic memory. However, it remains unclear how the interaction between the HC’s conjunctive coding and mnemonic differentiation contributes to neural representations of spatial environments. Multivariate functional magnetic resonance imaging (fMRI) analyses enable examination of how human HC and MTL cortical regions encode multidimensional spatial information to support memory-guided navigation. We combined high-resolution fMRI with a virtual navigation paradigm in which participants relied on memory of the environment to navigate to goal locations in two different virtual rooms. Within each room, participants were cued to navigate to four learned locations, each associated with one of two reward values. Pattern similarity analysis revealed that when participants successfully arrived at goal locations, activity patterns in HC and parahippocampal cortex (PHC) represented room-goal location conjunctions and activity patterns in HC subfields represented room-reward-location conjunctions. These results add to an emerging literature revealing hippocampal conjunctive representations during goal-directed behavior.
Effects of service authenticity, customer participation and customer-perceived service climate on customers' service evaluation
Authors: Bae Byung Ryul
Published: November 2020

Purpose

The purpose of this study is to examine the effect of service authenticity, customer participation (CP) and customer-perceived service climate on customers' service evaluation within the context of smartphone repair services in South Korea. A conceptual model, including customer-perceived service climate, service authenticity, CP, service value and service satisfaction, was proposed and tested.

Design/methodology/approach

The authors test the research model using a structural equation modeling approach (Amos) based on a mobile survey of 430 South Korean consumers. The authors design the research based on causal relationships and collect the data using the convenience sampling method.

Findings

The authors found that the independent variables (customer-perceived service climate, service authenticity and CP) have a positive effect on service value as well as service satisfaction. Further, service value has a mediating effect on the relationships between the independent variables and service satisfaction.

Originality/value

This is the first study to examine the effects of smartphone repair service on customers' evaluation. As the number of smartphone users increases, the results obtained from this study will provide important managerial implications for service managers.
The determinants of energy intensity in Indonesia
Authors: Rudenko Dmitry , Tanasov Georgii
Published: November 2020

Purpose

Indonesia is the fourth most populous country in the world, which has a strong effect on primary energy use and depletion of natural resources. This paper considers energy intensity (EI) defined as a measure of the amount of energy it takes to produce a dollar's worth of economic output. The purpose of the paper is to explore how different factors contributed to the decline in Indonesia's EI.

Design/methodology/approach

The cointegration regression methodology is applied to explore the long-term nexus between EI and its factors in Indonesia during 1990–2016.

Findings

Results show that domestic credit to the private sector, as well as the share of alternative energy, has a significant impact on the decline of EI in Indonesia.

Research limitations/implications

We do not try to rule out other possible determinants of EI. We consider the determinants of EI using time series data, while an ideal analysis would be based on panel-level data. Another limitation is that the study covers only the small-time period from 1990 to 2016.

Practical implications

Our findings serve to aid the government and policymakers in prioritizing improvements in the sphere of energy policy. An important policy implication, regarding Indonesia, that arises from our study is that, for the country to be able to decrease its EI, it must be able to develop its financial market and zero-carbon energy sources, mainly geothermal energy with its huge potential.

Originality/value

We show that energy prices, financial development and the share of alternative energy sources contribute to EI decrease. Policy recommendations include geothermal and solar energy development as one of the most prospective sources of alternative energy in Indonesia.
ERIP: service quality model of management consulting projects
Authors: Veres Zoltan , Varga-Toldi Katalin
Published: November 2020

Purpose

There is still no generally accepted quality model of consulting services. This is particularly the case for management consulting projects, where scope is often indefinite. The purpose of this paper is to identify the clients’ underlying utility preferences and their perceived quality dimensions.

Design/methodology/approach

The research is a qualitative data collection from 22 expert interviews performed in the financial service sector. Interviewees from the client-side were decision-makers from different hierarchical levels with considerable experience in working with consultants, while the consultant sample was obtained by selecting professionals with relevant project experience. The model development was based on the grounded theory.

Findings

Based on a content analysis of a 600-page transcript of interviews, it was found that customers construct their judgments on consulting service quality through five main attributes: consultants, client adaption, consulting process, deliverables and communication. Because of the strong overlaps of the attributes, four better separable quality dimensions – as a conceptual model – were identified: expertise, relations, involvement and performance.

Practical implications

Among managerial implications for consulting firms, support of buying organization in setting clear project objectives, flexibility in partnership and readiness for overperformance can be underlined.

Originality/value

There is little empirical research that focuses on the conceptualization of management consulting service quality from a client perspective. The value of the paper is the exploration of perceived service quality dimensions of management consulting projects and a consulting context-specific list of quality attributes.
Antecedents and consequences of supply chain resilience and reconfiguration: an empirical study in an emerging economy
Authors: Al Naimi Maryam , Faisal Mohd Nishat , Sobh Rana , Uddin S.M. Fatah
Published: November 2020

Purpose

The purpose of this paper is twofold: to investigate the antecedents of resilience and to highlight the importance of resilience in achieving reconfiguration in supply chains.

Design/methodology/approach

This paper draws on literature on supply chain resilience and collects data from 253 companies in Qatar to understand the influence of the antecedents of supply chain resilience and the impact of resilience on reconfiguration using partial least squares structural equation modeling.

Findings

The findings show that antecedents like risk management culture, agility and collaboration positively affect the supply chain resilience. Further, the study establishes that companies can leverage their supply chain resilience to reconfigure supply chain in case of disruptions.

Practical implications

This study is important for supply chain managers in Qatar, as the country faced major disruption of supply chains in wake of the blockade imposed by its neighbors with which it had the only land route and maximum trade. The findings from this study should aid mangers in developing resilient supply chains.

Originality/value

This paper highlights the role of supply chain resilience in achieving reconfiguration. Further, novelty of the work reported in this paper lies in its context where supply chains recently faced actual disruptions.
Enhancing the role of facilities management in the fight against the COVID-19 (SARS-CoV-2) pandemic in developing countries’ public hospitals
Authors: Amos Daniel , Au-Yong Cheong Peng , Musa Zairul Nisham
Published: November 2020

Purpose

This paper aims to present a review of the current COVID-19 pandemic with particular emphasis on developing countries in Africa. It aims to demonstrate how facilities management (FM) services delivery in public hospitals can be improved for the fight against the COVID-19 pandemic.

Design/methodology/approach

This paper embraces a review of current literature on COVID-19 and FM together with credible media updates. The paper critically synthesizes knowledge on the pandemic to position a technical view on how FM can be improved in the fight against the COVID-19 pandemic.

Findings

The COVID-19 pandemic presents unprecedented challenges and realities to the health-care system of most African countries. Despite the significant efforts being made by various governments, there appears to be a lack of a coherent and strategic FM plan to fight the pandemic. To create the necessary antivirus built environment, actionable and timely FM interventions are needed.

Research limitations/implications

The report herein is case guarded, based on the prevailing data and information as at the time of writing the paper. Nevertheless, the recommendations from the paper are useful for a worse future trajectory of the pandemic.

Practical implications

Knowledge of the proposed interventions will inform and assist health-care facilities managers in the fight against the COVID-19 pandemic.

Originality/value

The paper presents the first step towards encapsulating knowledge on FM and the COVID-19 pandemic. It sets forth recommendations that are useful for most developing countries’ public hospitals’ FM practices in the fight against this global pandemic. The authors intend to follow-up with future empirical studies for more objective assessments of FM and the COVID-19 pandemic.
The influence of consumer personality traits on mobile shopping intention
Authors: Camoiras-Rodriguez Zaira , Varela Concepción
Published: November 2020

Purpose

This study aims to increase the understanding of the drivers of mobile shopping, by analyzing when and how two personality traits – value consciousness and shopping enjoyment – impact mobile shopping intention through usefulness and ease-of-use perceptions.

Design/methodology/approach

To test the conditioned indirect effects, path analysis is used.

Findings

The results indicate that both consumers’ value consciousness and shopping enjoyment have a positive indirect effect on mobile shopping intention. However, shopping enjoyment is related only through usefulness, whereas value consciousness is related via both usefulness and ease of use. The results also suggest the need to consider boundary conditions when examining the impact of personality traits.

Practical implications

Mobile retailers need to conduct market segmentation based on users’ personalities when trying to increase their customer base.

Originality/value

Despite the relevance of personality traits on individual behavior, studies on the effects that different aspects of personality have on the participation of individuals in mobile commerce are very scarce and show inconsistent results regarding their impact. Thus, this study tries to contribute to the mobile commerce research by analyzing the interplay between two customer characteristics and two mediating variables: ease-of-use and usefulness perceptions.
Evaluation of cyromazine transferred from feed to chicken products and subsequent assessment of dietary risks to Chinese consumers
Authors: Ji Xiaofeng , Yang Hua , Lyu Wentao , Wang Jianmei , Wang Xinquan , Wang Xiaoli , Qian Mingrong
Published: November 2020

In this work, levels of cyromazine and its metabolite melamine in chicken products and its transfer factors (TFs) and dietary risks assessment for Chinese consumers are presented. Cyromazine was added to chicken feed at doses of 5, 25, and 50 mg/kg for 42 days. Cyromazine residues were found in frequently consumed chicken products (meat, heart, liver, gizzard, and eggs), with liver and eggs displaying the highest concentrations (0.935 and 1.281 mg/kg, respectively). Low levels of melamine residues (<0.029 mg/kg) were detected in chicken products from chickens treated with 25 and 50 mg/kg cyromazine, but not in eggs from chickens treated with 5 mg/kg cyromazine. The TFs for the investigated chicken products varied from 0.0074 to 0.0229 across the dosage levels. The chronic exposure assessment showed that 0.001 to 0.190% of the acceptable daily intake (0.06 mg/kg body weight [b.w.]/day) of cyromazine was consumed through chicken products among the various age and gender groups of Chinese consumers. The acute exposure assessments of different age and gender groups were 0.0004% to 0.178% of the acute reference dose (0.1 mg/kg b.w.). Although the results suggest that the risk associated with cyromazine residues in chicken products was low in China, the possible risk associated with cyromazine residues in chicken products should not be ignored while cyromazine remains a legal feed additive.

Practical Application

The present analytical method could be used for cyromazine and melamine detection in different chicken products, and dietary risk assessments of cyromazine provided a support for the work of regulatory bodies to conduct surveillance programs regarding food safety evaluation of cyromazine.
Is 99mTc bone scintigraphy necessary in the preoperative workup for patients with cT1N0 subsolid lung cancer? A prospective multicenter cohort study
Authors: Li Hang , Ye Ting , Li Nan , Xia Guozhan , Li Bin , Zhang Yang , Hu Hong , Sun Yihua , Zhang Yawei , Xiang Jiaqing , Ma Dongchun , Weng Yuan , Liu Shilei , Jia Chunyi , Qian Bin , Gu Yajia , Li Yuan , Song Shaoli , Chen Haiquan
Published: November 2020

Background

99mTc bone scintigraphy (BS) is still the most common approach for the evaluation of bone metastasis in China. The purpose of this study was to investigate the necessity of BS as part of a routine preoperative workup for patients with cT1N0 subsolid lung cancer.

Methods

This was a prospective multicenter clinical trial (NCT03689439). Patients with cT1N0 subsolid nodules who were candidates for surgical resection were consecutively enrolled into the study. BS was performed preoperatively. The surgical plan could be changed if a positive result was detected. The primary endpoint was the incidence rate of the surgical plan being changed because of positive BS results. The secondary endpoint was the rate of positive BS findings and the rate of related complications.

Results

From November 2018 to July 2019, 691 patients were enrolled into the study. None of the patients had positive BS results and no surgical plans were changed by BS findings. There were 222 male and 469 female patients. The average age was 54.8 ± 3.7 years old. The average tumor diameter was 14.9 ± 4.2 mm. There were 282 patients with pure GGO nodules and 409 with part‐solid nodules. A total of 470 patients had a single nodule, while 221 patients had multifocal lesions. The number of patients whose pathological diagnosis was invasive adenocarcinoma, minimally invasive adenocarcinoma, adenocarcinoma in situ and mucinous adenocarcinoma was 357, 293, 32 and nine, respectively. The number of patients who underwent lobectomy, segmentectomy and wedge resection was 234, 199 and 258, respectively.

Conclusions

99mTc bone scintigraphy is unnecessary in the preoperative workup for patients with cT1N0 subsolid lung cancer.

Key points

Significant findings of the study

In this prospective study of 691 patients with cT1N0 subsolid lung cancer, no surgical plans were affected by positive bone scan findings.

What this study adds

We suggest physicians consider canceling BS from preoperative workup for cT1 subsolid lung cancer patients.

Clinical trial registry number: NCT03689439.
Key structural features in cis‐carane, (+)‐3‐carene, cis‐pinane, (+)‐α‐pinene, and (−)‐β‐pinene influencing red turpentine beetle primary attraction when released with ethanol
Authors: Kelsey Rick G. , Westlind Douglas J.
Published: November 2020

In US Pacific Northwest ponderosa pine forests the primary attraction order shown previously for red turpentine beetle, Dendroctonus valens (Coleoptera: Curculionidae: Scolytinae), is (−)‐β‐pinene+ethanol > (+)‐3‐carene+ethanol > (+)‐α‐pinene+ethanol. The monoterpenes are bicyclic C10H16 isomers containing one 6‐carbon ring with one double bond. Both pinenes have a 4‐carbon second ring and differ only by their endocyclic or exocyclic double bond. The (+)‐3‐carene second ring has 3‐carbons; its double bond is endocyclic like (+)‐α‐pinene.

Ring system and double bond influences on primary attraction were evaluated by hydrogenating (+)‐3‐carene and (+)‐α‐pinene to cis‐carane and cis‐pinane, respectively. Field test primary attraction strengths were (−)‐β‐pinene+ethanol > cis‐carane+ethanol > cis‐pinane+ethanol > ethanol.

In combination with ethanol (i) a double bond is not required in either ring system to attract D. valens, (ii) the cis‐carane bicyclic 3, 6‐carbon ring system provides stronger beetle attraction than the cis‐pinane 4, 6‐carbon bicyclic ring system, and likely structural basis for stronger (+)‐3‐carene attraction over (+)‐α‐pinene, (iii) adding an exocyclic double bond to the 4, 6‐carbon ring system elevates attraction above the 3, 6‐carbon ring system with no double bond, and (iv) the 4, 6‐carbon ring system is a much stronger attractant with an exocyclic rather than endocyclic double bond.