bluuebunny/crossref_metadata_2025_split huggingface dataset:
AlphaFold2-aware protein-DNA binding site prediction using graph transformer
Authors: Yuan Qianmu , Chen Sheng , Rao Jiahua , Zheng Shuangjia , Zhao Huiying , Yang Yuedong 
Published: August 2021

AbstractProtein-DNA interactions play crucial roles in the biological systems, and identifying protein-DNA binding sites is the first step for mechanistic understanding of various biological activities (such as transcription and repair) and designing novel drugs. How to accurately identify DNA-binding residues from only protein sequence remains a challenging task. Currently, most existing sequence-based methods only consider contextual features of the sequential neighbors, which are limited to capture spatial information. Based on the recent breakthrough in protein structure prediction by AlphaFold2, we propose an accurate predictor, GraphSite, for identifying DNA-binding residues based on the structural models predicted by AlphaFold2. Here, we convert the binding site prediction problem into a graph node classification task and employ a transformer-based variant model to take the protein structural information into account. By leveraging predicted protein structures and graph transformer, GraphSite substantially improves over the latest sequence-based and structure-based methods. The algorithm is further confirmed on the independent test set of 181 proteins, where GraphSite surpasses the state-of-the-art structure-based method by 16.4% in AUPR and 11.2% in MCC, respectively. We provide the datasets, the predicted structures, and the source codes along with the pre-trained models of GraphSite athttps://github.com/biomed-AI/GraphSite. The GraphSite web server is freely available athttps://biomed.nscc-gz.cn/apps/GraphSite.
Directing an mRNA-LNP vaccine toward lymph nodes improves humoral and cellular immunity against SARS-CoV-2
Authors: Francis David M. , Chen Runqiang , Khorsandzadeh Sahba , Hu Qidong , Lyu Xiaoxuan , Wang Hua , Lim Wan-lin , Sun Haotian , Xie Hui , Shaabani Namir , Ross Russell , Cooley Brian , Ji Henry 
Published: August 2021

AbstractThe exploration and identification of safe and effective vaccines for the SARS-CoV-2 pandemic has captured the world’s attention and remains an ongoing issue in order to protect against emerging variants of concern (VoCs) while generating long lasting immunity. Here, we report the synthesis of a novel messenger ribonucleic acid (mRNA) encoding the spike protein in a lipid nanoparticle formulation (LNP) (STI-7264) that generates robust humoral and cellular immunity following immunization of C57Bl6 mice. In efforts to continually improve immunity, a lymphatic drug delivery device (MuVaxx) was engineered and tested to modulate immune cells at the injection site (epidermis and dermis) and draining lymph node (LN) to elicit adaptive immunity. Using MuVaxx, immune responses were elicited and maintained at a 10-fold dose reduction compared to traditional intramuscular (IM) administration as measured by anti-spike antibodies, cytokine producing CD8 T cells, and neutralizing antibodies against the Washington (Wild Type, WT) and South African (beta) variants. Remarkably, a 4-fold elevated T cell response was observed in MuVaxx administered vaccination as compared to that of IM administered vaccination. Thus, these data support further investigation into STI-7264 and lymphatic mediated delivery using MuVaxx for SARS-CoV-2 and VoCs vaccines.
Circular economy: a conceptual model to measure readiness for manufacturing SMEs
Authors: Thorley John , Garza-Reyes Jose Arturo , Anosike Anthony 
Published: August 2021

PurposeOver the last decade, circular economy (CE) has gathered interest from both industrialists and academics alike. Whilst CE research is widespread in such areas as supply chain and larger organisations, there is limited research into how small to medium enterprises (SMEs) can prepare for adopting CE. There is no comprehensive readiness model for SMEs adopting CE. The purpose of this paper is to explore the literature on change readiness and generate knowledge to fill this gap by developing a conceptual model to measure change readiness for SMEs' adopting CE.Design/methodology/approachThis study is based on a comprehensive literature review of change readiness models and frameworks. The paper reviews publications from Science Direct, Web of Science, Emerald, Scopus and Google Scholar. The readiness for change models and frameworks from the selected publications are evaluated and synthesised to develop a comprehensive conceptual model for change readiness for SMEs adopting a circular economy.FindingsA readiness conceptual model is developed by incorporating several factors as precursors to readiness, i.e. individual/collective difference, structural, contextual factors and related barriers. Eleven factors make up the individual/collective difference. Three factors make up the structural and contextual factors.Practical implicationsThis paper develops a conceptual model that can aid academics and practitioners in better understanding SMEs readiness to adopt CE.Originality/valueThis paper makes a unique contribution by proposing a comprehensive conceptual model of readiness for SMEs adopting CE.
Does risk matter for executive compensation?
Authors: Aldogan Eklund Mehtap 
Published: August 2021

PurposeThe purpose of this study is to examine whether chief executive officer (CEOs) are paid for the systematic and/or unsystematic risks and whether there is any optimum risk premium level in the executive pay.Design/methodology/approachFirm and year fixed effect panel data regression was used to estimate the relationship between total CEO compensation and systematic (market) and unsystematic (firm) risks.FindingsThere is no nexus between CEO pay and unsystematic (diversifiable) risk; however, the association between CEO compensation and systematic (undiversifiable) risk is positively significant in line with agency theory. Moreover, it is revealed that this positive relationship has an optimum point (curvilinear).Research limitations/implicationsThis paper contributes to the controversial argument in the literature by investigating the situation in the Swiss market. Switzerland is an exemplary country because of its direct democracy (consensus) structure for executive pay. This study is limited by the fact that only total CEO compensation is analyzed.Practical implicationsAs a practical implication, it is shown that after the optimal point, the higher compensation does not motivate the CEOs to take higher risks and does not provide the organizations with any additional benefit.Originality/valueThe finding of this study supports agency theory’s risk premium assumption and provides additional evidence to the contradictory results in the literature with a new country setting that has paramount importance in executive compensation phenomena. It is a comparative finding with prior literature also outlines the future research area in the risk and compensation literature.
Mapping “drug places” from below. The lived cities of marginalized drug users
Authors: Germes Mélina , Klaus Luise , Steckhan Svea 
Published: August 2021

PurposeOn top of their legal, economic, social and institutional marginalization, marginalized drug users (MDUs) also experience political marginalization: drug policies shape their lives without their political participation. From a scientific as well as a political perspective, the inclusion of their various viewpoints and situated knowledge is a major challenge, and one to which this paper aims to contribute in light of the experiences and imaginaries of MDUs urban spaces in several German cities.Design/methodology/approachFollowing a socio-geographical approach, this paper interrogates how MDUs appropriate and imagine the city, drawing on Lefebvre’sProduction of Spaceand mixing critical cartographic with grounded theory, in the attempt to both understand and reconstruct the world from the situated perspective of MDUs based on their own words, drawings and emotions.FindingsThe narratives and drawings of participants show another cityscape, radically different from the hegemonic discourses and mappings antagonizing MDUs and making their existence a social problem. Space appears as a means of marginalization: there are barely any places that MDUs can legitimately appropriate-least of all so-called “public space.” By contrast, MDUs’ imaginaries of an ideal city would accommodate their existence and address further social justice issues.Originality/valueThe notion of “public places” appears unable to express MDU’s experiences. Instead of focusing on the problem of public spaces, policymakers should tackle the question of placemaking for MDUs beyond the level of solely drug-related places.
From high school to workplace: investigating the effects of soft skills on career engagement through the role of psychological capital in different age groups
Authors: Aryani Farida , Wirawan Hillman , Saman Abdul , Samad Sulaiman , Jufri Muhammad 
Published: August 2021

PurposeThis study aims at investigating the indirect effect of soft skills on career engagement through the role of psychological capital (PsyCap) in different age groups. The social cognitive theory (SCT) and job demands-resource model (JD-R) were employed to explain the effect of perceived skill mastery on PsyCap and career engagement.Design/methodology/approachThe data were collected from 707 high school students, 150 university students and 165 employees using a three-wave data collection technique. This study measured soft skills, PsyCap and career engagement at different age groups (i.e. high school students, university students and employees). The data were analysed using a moderated-mediation technique.FindingsThe results showed that soft skills positively influenced PsyCap and eventually increased career engagement in all age groups. However, the effect was stronger for students (both in high school and university) than employees in the workplaces. Unlike most students, employees related soft skills to performance. Regardless of the effect on performance, students would be more likely than employees to perceive soft skill mastery as a source of efficacy.Research limitations/implicationsFirst, the education system should direct more attention to developing students' non-cognitive skills. Second, people should understand that their career advancement continues in the workplace context. Organizations can foster employees' soft skills by providing more opportunities to develop new skills.Originality/valueThis study sheds light on the importance of soft skills beyond academic and workplace performance. This study is among the few empirical investigations that reveal career engagement factors across different career development stages.
Measurement and evaluation the impact of perceived healthcare service quality on guest loyalty during COVID-19
Authors: Mohammed Husam Jasim , Mohammed Qasim Ali , Rhima Mustafa Hatwan 
Published: August 2021

Purpose
The aim of the study is to investigate the effects of perceived healthcare service quality (human aspects, technical aspects and tangible aspects) on satisfaction and guest loyalty in the hotel industry in the COVID-19 pandemic era.

Design/methodology/approach
A total of 130 guests in the hotel were selected purposively in Iraq. Data from self-administered questionnaires were analyzed through the VB-SEM statistical technique using Smart-PLS software towards testing the hypotheses.

Findings
The findings indicated that perceived service quality influences satisfaction and guest loyalty of guests in the hotel. This study reveals that human aspects, technical aspects and tangible aspects directly positively affect satisfaction and guest loyalty in the hotel industry.

Originality/value
This study highlights that perceived service quality (human aspects, technical aspects and tangible aspects) are vital and practical strategic tools that could be positioned to accelerate guest loyalty in the hotel industry. Furthermore, satisfaction mediates the relationship between human aspects, technical aspects, tangible aspects and guest loyalty.
Stable jump control for the wheel-legged robot based on TMS-DIP model
Authors: Li Xu , Fan Yixiao , Yu Haoyang , Zhou Haitao , Feng Haibo , Fu Yili 
Published: August 2021

Purpose
The purpose of this paper is to propose a novel jump control method based on Two Mass Spring Damp Inverted Pendulum (TMS-DIP) model, which makes the third generation of hydraulic driven wheel-legged robot prototype (WLR-3P) achieve stable jumping.

Design/methodology/approach
First, according to the configuration of the WLR, a TMS-DIP model is proposed to simplify the dynamic model of the robot. Then the jumping process is divided into four stages: thrust, ascent, descent and compression, and each stage is modeled and solved independently based on TMS-DIP model. Through WLR-3P kinematics, the trajectory of the upper and lower centroids of the TMS-DIP model can be mapped to the joint space of the robot. The corresponding control strategies are proposed for jumping height, landing buffer, jumping attitude and robotic balance, so as to realize the stable jump control of the WLR.

Findings
The TMS-DIP model proposed in this paper can simplify the WLR dynamic model and provide a simple and effective tool for the jumping trajectory planning of the robot. The proposed approach is suitable for hydraulic WLR jumping control. The performance of the proposed wheel-legged jump method was verified by experiments on WLR-3P.

Originality/value
This work provides an effective model (TMS-DIP) for the jump control of WLR-3P. The results showed that the number of landing shock (twice) and the pitch angle fluctuation range (0.44 rad) of center of mass of the jump control method based on TMS-DIP model are smaller than those based on spring-loaded inverted pendulum model. Therefore, the TMS-DIP model makes the jumping process of WLR more stable and gentler.
Australian market response to COVID-19 as moderated by social media
Authors: Maia Vinicius Mothé , Tommasetti Roberto , Macedo Marcelo Alvaro da Silva 
Published: August 2021

Purpose
Emerging as a black swan event that stifled the global economy, COVID-19 is the first social media (SM) pandemic. In an unsocial age due to social distancing, SM relevance is intuitively magnified during a pandemic. This study aims to investigate the direct and moderating impact of Twitter on the Australian stock market during the COVID-19 info-pandemic.

Design/methodology/approach
As a natural experiment, a time-series regression measures the effect of the COVID-19 virus, proxied by the active cases and the marginal impact of SM user attention and sentiment on the Australian stock market.

Findings
Results show that SM user attention and sentiment to COVID-19 related fear topics are significant in explaining market returns and in predicting their volatility. It demonstrates that SM plays a role between COVID-19 and Australian stock market performance by amplifying the pandemic impact.

Originality
The study goes beyond a purely empirical investigation of the catalyst (i.e. the pandemic), thus contributing to current theoretical debates on the impact of SM on investor behaviour.

Practical implications
Policymakers and market participants could benefit from the empirical findings of this research in the case of analogous epidemics.
Refractory serum immunoglobulin M elevation during anti‐interleukin (IL)‐1‐ or IL‐6‐targeted treatment in four patients with Schnitzler syndrome
Authors: Takimoto‐Ito Riko , Kambe Naotomo , Kogame Toshiaki , Otsuka Atsushi , Nomura Takashi , Izawa Kazushi , Tabuchi Yuya , Yoshifuji Hajime , Takeuchi Yohei , Kabashima Kenji 
Published: August 2021

AbstractSchnitzler syndrome is characterized by chronic urticarial rash, neutrophilic dermal infiltrate, recurrent fever, bone pain, elevated C‐reactive protein, and neutrophilic leukocytosis. The pathophysiology of Schnitzler syndrome is unknown, but it is considered to be an acquired form of an autoinflammatory disease because of the resemblance to clinical phenotypes of cryopyrin‐associated periodic syndrome, in which a gain‐of‐function mutation in NLRP3 causes overexpression of interleukin (IL)‐1β. Schnitzler syndrome is generally accompanied by a monoclonal immunoglobulin (Ig)M gammopathy with a long‐term risk of lymphoproliferation that is possibly associated with an MYD88 mutation. Herein, we present the following four patients with Schnitzler syndrome: a 63‐year‐old woman; a 65‐year‐old man; a 43‐year‐old woman; and a 63‐year‐old woman. Each patient fulfilled the Strasbourg diagnostic criteria, but none of the patients had any mutation in NLRP3 or MYD88 detected in their peripheral blood. Although approved treatment options for Schnitzler syndrome are lacking, our patients were treated with IL‐1‐targeted therapy (anakinra or canakinumab) or anti‐IL‐6 (tocilizumab). The acute inflammatory clinical manifestations improved completely with canakinumab and partially with anakinra and tocilizumab, but the serum IgM levels were gradually increased in all patients, even during treatment. To determine whether treatment with anti‐IL‐1β or IL‐6 prevents conversion to a hematopoietic disorder, further collection of cases and long‐term follow‐up will be needed.
Indecent Disclosures: Anticorruption Reforms and Political Selection
Authors: Szakonyi David 
Published: August 2021

AbstractDoes the passage of anticorruption reforms affect the types of people that want to serve in government? This article evaluates the effects of a common tool to fight corruption—financial disclosures—using data on 25,642 elections in Putin‐era Russia. I argue that financial disclosures function like a personal audit, generating information for journalists and prosecutors to investigate illicit gains earned inside and outside of government. Exploiting staggered elections, I find that requiring financial disclosures leads to roughly 25% fewer incumbents seeking reelection and 10% fewer candidates with suspicious financial histories. Greater media freedom and law enforcement capacity further increase the risk of corruption and tax evasion being uncovered, resulting in even fewer candidacies from those criminally exposed. Increasing transparency changes the incentives for serving in elected office, even in settings where other political motives may be at play.
Simultaneous feature selection and outlier detection with optimality guarantees
Authors: Insolia Luca , Kenney Ana , Chiaromonte Francesca , Felici Giovanni 
Published: August 2021

AbstractBiomedical research is increasingly data rich, with studies comprising ever growing numbers of features. The larger a study, the higher the likelihood that a substantial portion of the features may be redundant and/or contain contamination (outlying values). This poses serious challenges, which are exacerbated in cases where the sample sizes are relatively small. Effective and efficient approaches to perform sparse estimation in the presence of outliers are critical for these studies, and have received considerable attention in the last decade. We contribute to this area considering high‐dimensional regressions contaminated by multiplemean‐shift outliersaffecting both the response and the design matrix. We develop a general framework and usemixed‐integer programmingto simultaneously perform feature selection and outlier detection with provably optimal guarantees. We prove theoretical properties for our approach, that is, a necessary and sufficient condition for therobustly strong oracle property, where the number of features can increase exponentially with the sample size; the optimal estimation of parameters; and the breakdown point of the resulting estimates. Moreover, we provide computationally efficient procedures to tune integer constraints and warm‐start the algorithm. We show the superior performance of our proposal compared to existing heuristic methods through simulations and use it to study the relationships between childhood obesity and the human microbiome.
Street vendors in Lima in the time of COVID‐19: Guilty or oppressed?
Authors: Coletto Diego , Jaber Lema , Vanhellemont Linus 
Published: August 2021

Key MessagesFor many informal workers—including street vendors—staying at home and stopping working during the pandemic cannot be considered feasible options for many reasons.Analyzing informal street vending activities as a homogeneous phenomenon risks provoking misleading interpretations of street vendors solely as victims or as irresponsible people.Recognizing there is heterogeneity in street vending helps to illuminate the different social representations, identities, and strategies used by street vendors.
A cultural lens on Yucatec Maya families’ COVID‐19 experiences
Authors: Alcalá Lucía , Gaskins Suzanne , Richland Lindsey E. 
Published: August 2021

AbstractHealth guidance during the COVID‐19 pandemic led families around the world to spend more time isolated together, disrupting leisure activities, schooling, social interactions, and family work (UNICEF, 2021). Using the lens of Yucatec Maya families’ cultural values and practices, semi‐structured interviews were conducted with 18 Yucatec Maya rural women in Mexico (Mage = 32; and for comparison, 13 middle‐class European‐American women (Mage = 41)), with children 6–7 years old, to analyze families’ experiences during the pandemic. Faced with the same isolation as in the United States, our exploratory analysis revealed Maya families experienced external stresses but at the same time were generally comfortable with their children's everyday activities and their social‐emotional well‐being, illuminating consequences of the communities’ cultural theories about development.
Temporal dynamics of free‐living nitrogen fixation in the switchgrass rhizosphere
Authors: Smercina Darian N. , Evans Sarah E. , Friesen Maren L. , Tiemann Lisa K. 
Published: August 2021

AbstractFree‐living nitrogen fixation (FLNF) represents an important terrestrial N source and is gaining interest for its potential to contribute plant available N to bioenergy cropping systems. Switchgrass, a cellulosic bioenergy crop, may be particularly reliant on FLNF when grown on low N systems, like marginal lands. However, the potential contributions of FLNF to switchgrass as well as the controls on this process are not well understood. In this study, we evaluated drivers of FLNF rates and N‐fixing microbial (diazotrophic) community composition in field‐grown switchgrass systems over two growing seasons with high temporal sampling. We found that climate variables are strong drivers of FLNF rates in switchgrass systems, compared to other environmental and biological factors including soil nutrients and diazotrophic community composition. Increased soil moisture availability generally promoted FLNF rates, but extreme rainfall events were detrimental. These climate‐related responses suggest a potential for loss of FLNF‐derived N contributions under projected climate shifts. We found a significant, but weak correlation between diazotrophic community composition and FLNF rates. We also observed a significant shift in the diazotrophic community composition between 2017 and 2018 and similarly measured a significant difference in FLNF rates between growing seasons. Lastly, we found that seasonal FLNF N contributions, based on measurement with high temporal resolution, has the potential to meet up to 80% of switchgrass N demands suggesting that FLNF measurements extrapolated from fewer time points or locations may underestimate these potential N contributions.