bluuebunny/crossref_metadata_2025_split huggingface dataset:
HGC: fast hierarchical clustering for large-scale single-cell data
Authors: Zou Ziheng , Hua Kui , Zhang Xuegong 
Published: February 2021

AbstractClustering is a key step in revealing heterogeneities in single-cell data. Cell heterogeneity can be explored at different resolutions and the resulted varying cell states are inherently nested. However, most existing single-cell clustering methods output a fixed number of clusters without the hierarchical information. Classical hierarchical clustering provides dendrogram of cells, but cannot scale to large datasets due to the high computational complexity. We present HGC, a fastHierarchicalGraph-basedClustering method to address both problems. It combines the advantages of graph-based clustering and hierarchical clustering. On the shared nearest neighbor graph of cells, HGC constructs the hierarchical tree with linear time complexity. Experiments showed that HGC enables multiresolution exploration of the biological hierarchy underlying the data, achieves state-of-the-art accuracy on benchmark data, and can scale to large datasets. HGC is freely available for academic use athttps://www.github.com/XuegongLab/HGC.Contactzhangxg@tsinghua.edu.cn,stevenhuakui@gmail.com
c-MAF dependent perivascular macrophages regulate diet induced metabolic syndrome
Authors: Silva Hernandez Moura , Kitoko Jamil Zola , Queiroz Camila Pereira , Kroehling Lina , Matheis Fanny , Yang Katharine Lu , Ren-Fielding Christine , Littman Dan Rudolph , Bozza Marcelo Torres , Mucida Daniel , Lafaille Juan José 
Published: February 2021

SUMMARYMacrophages are an essential part of tissue development and physiology. Perivascular macrophages have been described in tissues and appear to play a role in development and disease processes, although it remains unclear what are the key features of these cells. Here, we identify a subpopulation of perivascular macrophages in several organs, characterized by their dependence on the transcription factor c-MAF, displaying non-conventional macrophage markers including LYVE1, Folate receptor 2 and CD38. Conditional deletion of c-MAF in macrophage lineages caused ablation of perivascular macrophages in the brain and altered muscularis macrophages program in the intestine. In the white adipose tissue (WAT), c-MAF deficient perivascular macrophages displayed an altered gene expression profile, which was linked to an increased vascular branching into the tissue. Upon feeding on high fat diet (HFD), mice with c-MAF deficient macrophages showed improved metabolic parameters compared to wild-type mice, including less weight gain, greater glucose tolerance and reduced inflammatory cell profile in WAT. These results define c-MAF as a central regulator of perivascular macrophages cell identity and transcriptional programin vivoand reveal a novel role for this tissue resident macrophage population in the regulation of metabolic syndrome.
Heterologous expression of human pro-inflammatory Caspase-1 inSaccharomyces cerevisiaeand comparison to pro-apoptotic Caspase-8
Authors: Valenti Marta , Molina María , Cid Víctor J 
Published: February 2021

AbstractCaspases are a family of cysteine proteases that play an essential role in inflammation, apoptosis, cell death, and development. Here we delve into the effects caused by heterologous expression of human Caspase-1 in the yeastSaccharomyces cerevisiaeand compare them to those of Caspase-8. Overexpression of both caspases in the heterologous model led to their activation, and caused mitochondrial depolarization, ROS production, damage to different organelles, and cell death. All these effects were dependent on their protease activity, and Caspase-8 was more aggressive than Caspase-1. Growth arrest could be at least partially explained by dysfunction of the actin cytoskeleton as a consequence of the processing of the yeast Bni1 formin, which we identify here as a likely direct substrate of both caspases. Through the modulation of theGAL1promoter by using different galactose:glucose ratios in the culture medium, we have established a scenario in which Caspase-1 is sufficiently expressed to become activated while yeast growth is not impaired. Finally, we used the yeast model to explore the role of death-fold domains (DD) of both caspases in their activity. Peculiarly, the DDs of either caspase showed an opposite involvement in its intrinsic activity, as the deletion of the caspase activation and recruitment domain (CARD) of Caspase-1 enhanced its activity, while the deletion of the death effector domain (DED) of Caspase-8 diminished it. We propose the yeast model as a useful and manageable tool to explore Caspase-1 structure-function relationships, the impact of mutations or the activity of putative inhibitors or regulators.
Age-related deficits in rapid visuomotor decision-making
Authors: Gómez-Granados Ana , Barany Deborah A. , Schrayer Margaret , Kurtzer Isaac , Bonnet Cédrick , Singh Tarkeshwar 
Published: February 2021

AbstractMany goal-directed actions that require rapid visuomotor planning and perceptual decision-making are affected in older adults, causing difficulties in execution of many functional activities of daily living. Visuomotor planning and perceptual decision-making are mediated by the dorsal and ventral visual streams, respectively, but it is unclear how age-induced changes in sensory processing in these streams contribute to declines in goal-directed actions. Previously, we have shown that in healthy adults task demands affect the integration of sensory information between the two streams and more motorically demanding tasks induce earlier decisions and more decision errors. Here, we asked the question if older adults would exhibit larger declines in interactions between the two streams during demanding motor tasks. Older adults (n=15) and young controls (n=26) performed a simple reaching task and a more demanding interception task towards virtual objects. In some blocks of trials, participants also had to select an appropriate movement based on the shape of the object. Our results showed that older adults made a similar number of initial decision errors during both the reaching and interception tasks but corrected fewer of those errors during movement. During the more demanding interception decision task, older adults made more decision- and execution-related errors than young adults, which were related to early initiation of their movements. Together, these results suggest that older adults have a reduced ability to integrate new perceptual information to guide online action, which may reflect impaired ventral-dorsal stream interactions.HighlightsOlder adults showed reduced performance in a visuomotor decision-making taskInitial decision errors were similar between young and older adultsOlder adults were less likely to correct initial decision errorsMore demanding movements were associated with earlier and less accurate decisions
Enhanced MATE transporter DTX6/PQT15 confers paraquat resistance
Authors: Xia Jin-Qiu , Nazish Tahmina , Javaid Ayesha , Ali Mohsin , Liu Qian-Qian , Wang Liang , Zhang Zheng-Yi , Zhang Zi-Sheng , Huang Yi-Jie , Wu Jie , Yang Zhi-Sen , Sun Lin-Feng , Chen Yu-Xing , Xiang Cheng-Bin 
Published: February 2021

ABSTRACTParaquat is one of the most widely used non-selective herbicides and has elicited the emergence of paraquat resistant weeds. However, the molecular mechanisms of paraquat resistance are not completely understood. Here we report an Arabidopsis gain-of-function mutantpqt15-Dwith significantly enhanced resistance to paraquat and the correspondingPQT15encoding the MATE transporter DTX6. A point mutation at +932 bp inDTX6causing the G311E amino acid residue change brings about the enhanced paraquat resistance ofpqt15-D. Overexpression ofDTX6/PQT15in the wild type also confers strong paraquat resistance, whereas theDTX6/PQT15knockout mutants exhibits hypersensitive phenotype to paraquat. Moreover, heterologous expression ofDTX6andDTX6-DinE. colisignificantly enhances bacterial resistance to paraquat. DTX6/PQT15 mainly localizes in the plasma membrane as shown by DTX6-GFP and functions as a paraquat efflux transporter as demonstrated by paraquat efflux assays with isolated protoplasts and bacterial cells. Taken together, our results demonstrate that DTX6/PQT15 is an efflux transporter and confers paraquat resistance by exporting paraquat out of cytosol, therefore unraveling a molecular mechanism of paraquat resistance in higher plants and providing a promising candidate of generating paraquat resistance crops.
A DNA-origami NanoTrap for studying the diffusion barriers formed by Phe-Gly-rich nucleoporins
Authors: Shen Qi , Tian Taoran , Xiong Qiancheng , Ellis Fisher Patrick D. , Xiong Yong , Melia Thomas J. , Lusk C. Patrick , Lin Chenxiang 
Published: February 2021

SUMMARYDNA nanotechnology provides a versatile and powerful tool to dissect the structure-function relationship of biomolecular machines like the nuclear pore complex (NPC), an enormous protein assembly that controls molecular traffic between the nucleus and cytoplasm. To understand how the intrinsically disordered, Phe-Gly-rich nucleoporins (FG-nups) within the NPC’s central transport channel impede the diffusion of macromolecules, we built a DNA-origami NanoTrap. The NanoTrap comprises precisely arranged FG-nups in an NPC-like channel, which sits on a baseplate that captures macromolecules that pass through the FG network. Using this biomimetic construct, we determined that the FG-motif type, grafting density and spatial arrangement are critical determinants of an effective diffusion barrier. Further, we observe that diffusion barriers formed with cohesive FG-interactions dominate in mixed-FG-nup scenarios. Our DNA-origami platform thus sheds light on how NPCs sieve inert macromolecules and will provide a valuable tool for studying nuclear transport.
Biophysical and proteomic analyses suggest functions ofPseudomonas syringaepvtomatoDC3000 extracellular vesicles in bacterial growth during plant infection
Authors: Janda Martin , Ludwig Christina , Rybak Katarzyna , Meng Chen , Stigliano Egidio , Botzenhardt Leon , Szulc Beata , Sklenar Jan , Menke Frank L.H. , Malone Jacob G. , Brachmann Andreas , Klingl Andreas , Robatzek Silke 
Published: February 2021

SummaryVesiculation is a process employed by Gram-negative bacteria to release extracellular vesicles (EVs) into the environment. Bacterial EVs contain molecular cargo from the donor bacterium and play important roles in bacterial survival and growth. Here, we describe EV production in plant-pathogenicPseudomonas syringaepv.tomatoDC3000 (PtoDC3000), the causal agent of bacterial speck disease. CulturedPtoDC3000 exhibited EV structures both on the cell surface and in the vicinity of bacterial cells, observed as outer membrane vesicle (OMV) release. We used in-solution trypsin digestion coupled to mass spectrometry to identify 369 proteins enriched in EVs recovered from culturedPtoDC3000. The predicted localization profile of EV proteins supports the production of EVs also in the form of outer-inner-membrane vesicles (OIMVs). EV production varied slightly between bacterial lifestyles and also occurredin planta. The potential contribution of EVs toPtoDC3000 plant infection was assessed using plant treatments and bioinformatic analysis of the EV-enriched proteins. While these results identify immunogenic activities of the EVs, they also point at roles for EVs in bacterial defences and nutrient acquisition byPtoDC3000.
Environmental impact of pollutants from commercial aircrafts at Hasan Polatkan airport
Authors: Atasoy Vehbi Emrah , Suzer Ahmet Esat , Ekici Selcuk 
Published: February 2021

Purpose
This paper aims to investigate the environmental impact of various pollutant emissions including carbon monoxide (CO), carbon dioxide (CO2), nitrogen oxide (NOx) and hydrocarbon (HC) from aircraft exhaust gases during the landing and take-off (LTO) cycles at Eskisehir Hasan Polatkan Airport, Turkey, between 2017 and 2018.

Design/methodology/approach
The methodology approach used to calculate the emissions from aircrafts is based on the ICAO databank and the actual data records taken from Presidency of The Republic of Turkey Directorate of Communications (DoC).

Findings
The maximum amount of total fuel burnt during the two years is 80.898 and 70.168 tons in 2017 and 2018, respectively, while the average fuel burnt per year from 2017 to 2018 is approximately 369.773 tons. The highest CO, CO2, NOx and HC emissions are found to be 248.3 kg in 2017, 261.380 tons, 1.708 tons and 22.15 kg, during the 2018 year, respectively. Average CO, HC, NOx and CO2 emissions amount per year are observed to be 1.392 tons, 135 kg, 6.909 tons and 1,143 tons, respectively. Considering the average of total emission amount as an environmental factor, as expected, CO2 emissions contributed the most to the total emissions while HC emissions contributed the least to the total emissions from the airport.

Practical implications
The study presents the approach in determining the amounts of emissions released into the interannual atmosphere and it explicitly provides researchers and policymakers how to follow emissions from commercial aircraft activities at different airports.

Originality/value
The value of the study lies in the transparent computation of the amounts of pollutants by providing the data directly from the first hand-DoC.
Data literacy and management of research data – a prerequisite for the sharing of research data
Authors: Palsdottir Agusta 
Published: February 2021

PurposeThe purpose of this paper is to investigate the knowledge and attitude about research data management, the use of data management methods and the perceived need for support, in relation to participants’ field of research.Design/methodology/approachThis is a quantitative study. Data were collected by an email survey and sent to 792 academic researchers and doctoral students. Total response rate was 18% (N = 139). The measurement instrument consisted of six sets of questions: about data management plans, the assignment of additional information to research data, about metadata, standard file naming systems, training at data management methods and the storing of research data.FindingsThe main finding is that knowledge about the procedures of data management is limited, and data management is not a normal practice in the researcher's work. They were, however, in general, of the opinion that the university should take the lead by recommending and offering access to the necessary tools of data management. Taken together, the results indicate that there is an urgent need to increase the researcher's understanding of the importance of data management that is based on professional knowledge and to provide them with resources and training that enables them to make effective and productive use of data management methods.Research limitations/implicationsThe survey was sent to all members of the population but not a sample of it. Because of the response rate, the results cannot be generalized to all researchers at the university. Nevertheless, the findings may provide an important understanding about their research data procedures, in particular what characterizes their knowledge about data management and attitude towards it.Practical implicationsAwareness of these issues is essential for information specialists at academic libraries, together with other units within the universities, to be able to design infrastructures and develop services that suit the needs of the research community. The findings can be used, to develop data policies and services, based on professional knowledge of best practices and recognized standards that assist the research community at data management.Originality/valueThe study contributes to the existing literature about research data management by examining the results by participants’ field of research. Recognition of the issues is critical in order for information specialists in collaboration with universities to design relevant infrastructures and services for academics and doctoral students that can promote their research data management.
The impact of online reviews on product returns
Authors: Li Xiaofei , Ma Baolong , Chu Hongrui 
Published: February 2021

PurposeThe value of online reviews has been well documented by academics and practitioners. However, to maximise the benefits of consumer reviews, online sellers must avoid the negative consequences associated with customer feedback, such as reputation loss, or product returns after purchase. In developing a better understanding of the relationships between online reviews and their potential for negative impacts, this research aims to explore product returns. Through a quantitative model, this research demonstrates why online reviews can result in product return behaviours.Design/methodology/approachThe hypotheses were tested via two studies. In Study 1, the authors examine the direct effects of review valence and review volume on product returns by analysing secondary data on 4,995 stores on China's Taobao.com. Study 2 further extends and validates the findings of Study 1 with a survey sample of 795 participants across several online shopping platforms. This analysis examines the mechanics and conditions that influence the relationships between online reviews and product returns through partial least squares-structural equation modelling (PLS-SEM).FindingsThe results show that both review valence (i.e. average star ratings) and the number of reviews can increase the probability of product returns due to the high expectations that result from positive online reviews. Further, the effect of review valence on product returns is stronger for first-time purchasers at a store. In terms of mitigation, the analysis shows that bilateral communications between sellers and buyers can temper the unrealistic expectations set by positive reviews, leading to fewer product returns.Originality/valueThis research adds to the literature on online reviews by exploring the negative consequences of online reviews and the role they play in online purchasing decisions. The findings also provide direct evidence as to why online reviews can result in more product returns, adding clarity to extant research which contains conflicting conclusions as to how online reviews affect product return behaviours.
Reason versus feeling: relational norms influence gift choices
Authors: Yu Lingzhi , Zhao Tingting , Fan Xiucheng 
Published: February 2021

PurposeRelational norms, referring to shared values about behavioral rules, distinguish communal and exchange relationships based on different reciprocal expectations between actors. This research explains how reciprocal expectations behind the two relationships trigger gift givers' disparate behavioral goals and further determine their gift choices.Design/methodology/approachThe current work uses three lab experiments (N = 482) and one consumer survey (N = 422) to collect Chinese gifting data. Multiple data-analysis methods – crosstab analysis, ANOVA, linear regression and bootstrapping procedures – confirm the hypotheses.FindingsGift givers distinguish communal and exchange recipients. When selecting gifts for communal (exchange) recipients, people depended more strongly on rational analyses (intuition), preferring products superior on cognitive (affective) attributions. Further, givers primed to be rational decision-makers by anticipating that recipients would evaluate the gifts immediately in their presence, regardless of the communal or exchange context, preferred cognitively superior products.Practical implicationsFrom a managerial perspective, marketers can make targeted recommendations by highlighting the appropriate attribute dimension (cognitive or affective) after learning givers' reciprocal expectations.Originality/valueThis work contributes to the gift-giving literature by revealing the direct link between gifting goals and gift choices, extending the understanding of consumers' gift-selection strategies.
Salespersons' self-monitoring, psychological capital and sales performance
Authors: Wang Xiaoyan , Li Ping , Zheng Yi , Jiang Ling (Alice) , Yang Zhilin 
Published: February 2021

PurposeDrawing on conservation of resources (COR) theory and the motivation-opportunity-ability (MOA) framework, this study examines how salespersons' self-monitoring and psychological capital influence sales performance.Design/methodology/approachThis study uses survey data from 293 salespersons employed in China and their archival sales performance to test the hypotheses posited.FindingsThe results show that both salespersons' self-monitoring and psychological capital enhance sales performance via adaptive selling. However, these elements are primarily substitutes in influencing adaptive selling. In addition, by dividing social capital into two types (i.e. family-based social capital and customer-based social capital), the results reveal that salespersons' self-monitoring enhances family-based social capital, but not customer-based social capital. Finally, customer-based social capital, but not family-based capital, improves sales performance.Research limitations/implicationsThis paper extends the literature on sales force management, which examines various psychological traits and their influences on sales performance. While self-monitoring and psychological capital have been investigated separately, this research simultaneously examines these two factors by drawing on resource conservation theory. Furthermore, it explores how these psychological traits impact salespersons' ability development (i.e. adaptive selling) and capital accumulation (i.e., family-based social capital and customer-based social capital), which, in turn, affect sales performance.Practical implicationsThe results offer managerial insights into sales force selection and management. In particular, managers should encourage salespersons to obtain greater customer-based social capital, which is more valuable than family-based social capital in boosting sales performance.Social implicationsThe present research is also beneficial for employee psychological health management, as it seeks to illuminate the role of psychological traits, ability development and capital accumulation. It offers insights into sociological research on social capital by categorizing it into family-based and customer-based capital.Originality/valueThis paper extends the literature on salespersons' psychological traits, selling abilities and social capital by examining the impacts of self-monitoring and psychological capital on adaptive selling and social capital. Specifically, this study examines the interplay between self-monitoring and psychological capital from the perspective of resources conservation theory.
Understanding Chinese consumers' pre-purchase value expectations: the role of country of origin effect
Authors: Qu Mengnan , Quach Sara , Thaichon Park , Frazer Lorelle , Lawley Meredith , Arli Denni , Weaven Scott , Roberts Robin E. 
Published: February 2021

PurposeThis study aims to examine the effect of country of origin (COO) on customers' value expectation and willingness to pay by employing signalling theory and cue utilisation.Design/methodology/approachThe data were collected from 386 customers via an online survey in the context of Australian food retail franchise stores in China.FindingsThe findings indicate that COO origin is an important determinant of customer expectations including service quality, social value, emotional value, monetary price, behavioural price and reputation. Furthermore, the only social value was a significant predictor of willingness to pay. Although the direct effect of COO on willingness to purchase was not significant, the COO had a significant indirect effect on willingness to pay via social value. Finally, the COO has a stronger effect on monetary price expectation among customers who were aware of the country brands than those who were unaware.Originality/valueThe study extends the body of knowledge related to the effect of COO during the pre-purchase process and provides important implications for retailers who are looking to enter an overseas market such as China.