bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incorporating selfing to purge deleterious alleles in a cassava genomic selection program
Authors: Somo Mohamed , Jannink Jean-Luc 
Published: April 2020

AbstractCassava has been found to carry high levels of recessive deleterious mutations and it is known to suffer from inbreeding depression. Breeders therefore consider specific approaches to decrease cassava’s genetic load. Using self fertilization to unmask deleterious recessive alleles and therefore accelerate their purging is one possibility. Before implementation of this approach we sought to understand better its consequences through simulation. Founder populations with high directional dominance were simulated using a natural selection forward simulator. The founder population was then subjected to five generations of genomic selection in schemes that did or did not include a generation of phenotypic selection on selfed progeny. We found that genomic selection was less effective under the directional dominance model than under the additive models that have commonly been used in simulations. While selection did increase favorable allele frequencies, increased inbreeding during selection caused decreased gain in genotypic values under the directional dominance. While purging selection on selfed individuals was effective in the first breeding cycle, it was not effective in later cycles, an effect we attributed to the fact that the generation of selfing decreased the relatedness of the genomic prediction training population from selection candidates. That decreased relatedness caused genomic prediction accuracy to be lower in schemes incorporating selfing. We found that selection on individuals partially inbred by one generation of selfing did increase mean genetic value of the partially inbred population, but that this gain was accompanied by a relatively small increase in favorable allele frequencies such that improvement in the outbred population was lower than might have been intuited.
Characterization of exosporium layer variability ofClostridioides difficilespores in the epidemically relevant strain R20291
Authors: Pizarro-Guajardo Marjorie , Calderón Paulina , Romero-Rodriguez Alba , Paredes-Sabja Daniel 
Published: April 2020

AbstractClostridioides difficileis a Gram-positive anaerobic intestinal pathogenic bacterium and the causative agent of antibiotic-associated diarrhea and spores are the transmission vehicle of the disease. InC. difficilespores, the outermost exosporium layer is the first barrier of interaction with the host and should carry spore ligands involved in spore-host interactions.C. difficileforms two types of spores (i.e., thin and thick exosporium layers). In this communication, we contribute to understand several biological aspects of these two exosporium morphotypes. By transmission electron microscopy, we demonstrate that both exosporium morphotypes appear simultaneously during sporulation and that the laminations of the spore-coat are formed under anaerobic conditions. Nycodenz density-gradient allows enrichment of spores with a thick-exosporium layer morphotype and presence of polar appendage. Using translational fluorescent fusions with exosporium proteins BclA3, CdeA, CdeC and CdeM as well as with several spore coat proteins, we observed that expression intensity and distribution of SNAP-translational fusions in R20291 strain is highly heterogeneous. Electron micrographs demonstrate that multicopy expression of CdeC, but not CdeM, SNAP translational fusion, increases the abundance of the thick exosporium morphotype. Collectively, these results raise further questions on how these distinctive exosporium morphotypes are made during spore formation.
Citrus vascular proteomics highlights the role of peroxidases and serine proteases during Huanglongbing disease progression
Authors: Franco Jessica Y. , Thapa Shree P. , Pang Zhiqian , Gurung Fatta B. , Liebrand Thomas W.H. , Stevens Danielle M , Ancona Veronica , Wang Nian , Coaker Gitta 
Published: April 2020

AbstractHuanglongbing (HLB) is the most devastating and widespread citrus disease. All commercial citrus varieties are susceptible to the HLB-associated bacterium,CandidatusLiberibacter asiaticus (CLas), which resides in the phloem. The phloem is part of the plant vascular system and is involved in sugar transport. To investigate the plant response toCLas, we enriched for proteins surrounding the phloem in an HLB susceptible sweet orange variety, Washington navel (Citrus sinensis(L) Osbeck). Quantitative proteomics revealed global changes in the citrus proteome afterCLas inoculation. Plant metabolism and translation were suppressed, while defense-related proteins such as peroxidases, proteases and protease inhibitors were induced in the vasculature. Transcript accumulation and enzymatic activity of plant peroxidases in CLas infected sweet orange varieties under greenhouse and field conditions were assessed. While peroxidase transcript accumulation was induced inCLas infected sweet orange varieties, peroxidase enzymatic activity varied. Specific serine proteases were upregulated in Washington navel in the presence ofCLas based on quantitative proteomics. Subsequent activity-based protein profiling revealed increased activity of two serine proteases, and reduced activity of one protease in twoC. sinensissweet orange varieties under greenhouse and field conditions. The observations in the current study highlight global reprogramming of the citrus vascular proteome and differential regulation of enzyme classes in response toCLas infection. These results open an avenue for further investigation of diverse responses to HLB across different environmental conditions and citrus genotypes.
Learning to see the Ebbinghaus illusion in the periphery reveals a top-down stabilization of size perception across the visual field
Authors: Eymond Cécile , Malkinson Tal Seidel , Naccache Lionel 
Published: April 2020

AbstractOur conscious visual perception relies on predictive signals, notably in the periphery where sensory uncertainty is high. We investigated how such signals could support perceptual stability of objects’ size across the visual field. When attended carefully, the same object appears slightly smaller in the periphery compared to the fovea. Could this perceptual difference be encoded as a strong prior to predict the peripheral perceived size relative to the fovea? Recent studies emphasized the role of foveal information in defining peripheral size percepts. However, they could not disentangle bottom-up from top-down mechanisms. Here, we revealed a pure top-down contribution to the perceptual size difference between periphery and fovea. First, we discovered a novel Ebbinghaus illusion effect, inducing a typical reduction of foveal perceived size, but a reversed increase effect in the periphery. The size percept was similar at both retinal locations and deviated from the classic perceptual difference. Then through an updating process of successive peripheral-foveal viewing, the unusual peripheral perceived size decreased. The classic perceptual eccentricity difference was restored and the peripheral illusion effect changed into a fovea-like reduction. Therefore, we report the existence of a prior that actively shapes peripheral size perception and stabilizes it relative to the fovea.
Urine proteome changes in an α-synuclein transgenic mouse model of Parkinson’s disease
Authors: Li Lujun , Pan Xuanzhen , Wang Ting , Hua Yuanrui , Gao Youhe 
Published: April 2020

AbstractUrine accommodates more changes than other fluids, and it is a good source in the search for early sensitive biomarkers. The present study collected urine samples from 2-, 4-, 6-, 8- and 10-month-old α-synuclein transgenic mice. Based on data-independent acquisition (DIA) technology, liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used for quantitative analysis. Seventeen human homologous differential proteins were screened and compared with those in the urine of 2-month-old mice, and 9 proteins were related to Parkinson’s disease (PD). Formin-2, Splicing factor 3A subunit 1, and Isopentenyl-diphosphate Delta-isomerase 1 changed continuously in months 6, 8 and 10. These experiments and analyses demonstrated that the urine proteome reflected the development of α-synuclein transgenic mice and provided clues for the early clinical diagnosis of PD.
“Amantadine disrupts lysosomal gene expression; potential therapy for COVID19”
Authors: Smieszek Sandra P. , Przychodzen Bart P , Polymeropoulos Mihael H 
Published: April 2020

AbstractSARS-coronavirus 2 is the causal agent of the COVID-19 outbreak. SARS-Cov-2 entry into a cell is dependent upon binding of the viral spike (S) protein to cellular receptor and on cleavage of the spike protein by the host cell proteases such as Cathepsin L and Cathepsin B. CTSL/B are crucial elements of lysosomal pathway and both enzymes are almost exclusively located in the lysosomes.CTSL disruption offers potential for CoVID-19 therapies. The mechanisms of disruption include: decreasing expression of CTSL, direct inhibition of CTSL activity and affecting the conditions of CTSL environment (increase pH in lysosomes).We have conducted a high throughput drug screen gene expression analysis to identify compounds that would downregulate the expression of CTSL/CTSB. One of the top significant results shown to downregulate the expression of the CTSL gene is Amantadine. Amantadine was approved by the US Food and Drug Administration in 1968 as a prophylactic agent for influenza and later for Parkinson’s disease. It is available as a generic drug..Amantadine in addition to downregulating CTSL appears to further disrupt lysosomal pathway, hence interfering with the capacity of the virus to replicate. It acts as a lysosomotropic agent altering the CTSL functional environment. We hypothesize that Amantadine could decrease the viral load in SARS-CoV-2 positive patients and as such it may serve as a potent therapeutic decreasing the replication and infectivity of the virus likely leading to better clinical outcomes. Clinical studies will be needed to examine the therapeutic utility of amantadine in COVID-19 infection.
Zα2 domain of ZBP1 is a molecular switch regulating Influenza-induced PANoptosis and perinatal lethality during development
Authors: Kesavardhana Sannula , Subbarao Malireddi R. K. , Burton Amanda R. , Porter Shaina N. , Vogel Peter , Pruett-Miller Shondra M. , Kanneganti Thirumala-Devi 
Published: April 2020

ABSTRACTZ-DNA-binding protein 1 (ZBP1) is an innate nucleic acid sensor which regulates host defense responses and development. ZBP1 activation triggers inflammation and pyroptosis, necroptosis, and apoptosis (PANoptosis) by activating RIPK3, caspase-8, and the NLRP3 inflammasome. ZBP1 is unique among innate sensors because of its N-terminal Zα1 and Zα2 domains, which bind to nucleic acids in the Z-conformation. However, the specific role of these Zα domains in orchestrating ZBP1 activation and subsequent inflammation and cell death is not clear. Here we have generatedZbp1ΔZα2/ΔZα2mice that lack the Zα2 domain of ZBP1 and demonstrate that this domain is critical for influenza A virus (IAV)-induced PANoptosis and perinatal lethality in RIPK1-RHIM mutated (Ripk1RHIM/RHIM) mice. Deletion of the Zα2 domain in ZBP1 abolished IAV-induced PANoptosis and NLRP3 inflammasome activation. Furthermore, deletion of the Zα2 domain of ZBP1 was sufficient to rescueRipk1RHIM/RHIMmice from the perinatal lethality which is caused by ZBP1-driven cell death and inflammation. Our findings identify the essential role of the Zα2 domain of ZBP1 in physiological functions and establish a link between sensing of Z-RNAs via the Zα2 domain and the promotion of influenza-induced PANoptosis and perinatal lethality.
Pavlov’s pea plants? Not so fast. An attempted replication of Gaglianoet al. (December 2016)
Authors: Markel Kasey 
Published: April 2020

AbstractGaglianoet al. (Learning by association in plants, 2016) reported associative learning in pea plants. Associative learning has long been considered a behavior performed only by animals, making this claim particularly newsworthy and interesting. In the experiment, plants were trained in Y-shaped mazes for three days with fans and lights attached at the top of the maze. Training consisted of wind consistently preceding light from either the same or the opposite arm of the maze. When plant growth forced a decision between the two arms of the maze, fans alone were able to influence growth direction, whereas the growth direction of untrained plants was not affected by fans. Importantly, some plants were trained to grow towards the fan and others to grow away, demonstrating the flexibility of associative learning. However, a replication of their protocol failed to demonstrate the same result, calling for further verification and study before mainstream acceptance of this paradigm-shifting phenomenon. This replication attempt used a larger sample size and fully blinded analysis.
Exploring ligand binding pathways on proteins using hypersound–accelerated molecular dynamics
Authors: Araki Mitsugu , Matsumoto Shigeyuki , Bekker Gert-Jan , Isaka Yuta , Sagae Yukari , Kamiya Narutoshi , Okuno Yasushi 
Published: April 2020

AbstractCapturing the dynamic processes of biomolecular systems in atomistic detail remains difficult despite recent experimental advances. Although molecular dynamics (MD) techniques enable atomic-level observations, simulations of “slow” biomolecular processes (with timescales longer than submilliseconds) are challenging, due to current computer speed limitations. Therefore, we developed a new method to accelerate MD simulations by high-frequency ultrasound perturbation. The binding events between the protein CDK2 and its small-molecule inhibitors were nearly undetectable in 100-ns conventional MD, but the new method successfully accelerated their slow binding rates by up to 10–20 times. The accelerated MD simulations revealed a variety of microscopic kinetic features of the inhibitors on the protein surface, such as the existence of different binding pathways to the active site. Moreover, the simulations allowed estimating the corresponding kinetic parameters and exploring other druggable pockets. This method can thus provide deeper insight into the microscopic interactions controlling biomolecular processes.
Unbundling subjective career success: a sequential mediation analysis
Authors: Rossenkhan Zubeida , Au Wee Chan , Ahmed Pervaiz Khalid 
Published: April 2020

PurposeThis study aims to contribute to subjective career success (SCS) literature using sequential mediation modeling to interrogate the inter-relationships between dimensions of SCS, including interpersonal success, financial success, job success and hierarchical success. In doing so, the research provides a nuanced understanding of career behavior among young adults using the perspective of a non-western developing context.Design/methodology/approachThe study is operationalized using 342 survey questionnaires from Malaysian young working adults (18-34 years). Partial least square structural equation modeling is used as the main analytic tool.FindingsThe results of the study revealed that dimensions of SCS were related in a sequential mediating manner. Specifically, an individual’s interpersonal success is the foundation for one to accomplish job tasks (job success), which then leads to increased prospects for promotion (hierarchical success) and subsequently financial success.Practical implicationsThese findings highlight the importance of interpersonal success as a foundation of career success and provide evidence for the study recommendation to support young working adults in building interpersonal relationships, which will help realize other forms of career success. However, the establishment of a sequential mediation pathway suggests that developing relationships alone are not sufficient. Study roles and tasks must also be designed to align with individuals’ personal goals for advancement and success.Originality/valueThe research contributes to knowledge on understanding career behavior specifically relating to the dynamics and complexities of SCS. The study sheds light on the potential limitation of operationalizing SCS as a multi-dimensional aggregate construct and provides empirical support for the proposed sequential mediation model of SCS.
An elderly assistive device substitutes for traditional online library catalogs
Authors: Chiang Cheng-Wei , Liu Yi-Hui , Wang Chien-Po 
Published: April 2020

Purpose
This paper aims to present an augmented reality (AR) application to aid the elderly in library reference search. The application supports the elderly in searching books and videos in a large library when librarians have insufficient time to meet their needs. The elderly searching in a large library could be difficult for them due to the vast area, complicated online library catalogs and their physical deterioration, such as failing eyesight, tendinitis and memory problems. Our system, SearchAR, fully supports the 3D images of object content based on books and videos in Ling Tung University (LTU) library catalogs. Using the latest AR technology, users can use mobile phone to scan the quick response (QR) code in front of the LTU library, and then the elderly can experience LTU library map labeled by different colors in real-time and understand the locations of the video areas and book shelves areas. Later, they can use SearchAR to scan the QR codes on bookshelves, books or videos to view the 3D graphics without reading complicated catalogs and content. The results show that among the images, the elderly recognition of the “3 D images” was the highest, and the experimental group using AR technology as a searching aid shows a higher searching effectiveness than the control group; 60 per cent of the elderly felt they saved more time for searching books and videos with the help of SearchAR, and it was easy to arouse their association; the elderly indicated that combined image of the library map and the labels with different colors are clear and simple; the content of books and videos are easy associated with the 3D images; the elderly mentioned that using SearchAR is a great experience without any reading complicated online catalogs. Finally, this study concludes that AR technology does enhance the elderly searching ability in LTU large library.

Design/methodology/approach
The SearchAR application was an integrating library catalog, which provides AR and 3D graphics. The elderly can also use SearchAR to see a library map and every library element via 3D graphics before they start searching in a wide area.

Findings
This makes it easier for elderly to navigate a library without using complicated online catalogs, and it reduces time spent on reading and searching.

Originality/value
AR has been used for a variety of guiding and educational purposes. However, AR has been rarely applied to supplement traditional library services for elderly.
Identifying the factors of China's seasonal retail sales of consumer goods using a data grouping approach–based GRA method
Authors: Wang Zheng-Xin , Wu Ji-Min , Zhou Chao-Jun , Li Qin 
Published: April 2020

PurposeSeasonal fluctuation interference often affects the relational analysis of economic time series. The main purpose of this paper is to propose a new grey relational model for relational analysis of seasonal time series and apply it to identify and eliminate the influence of seasonal fluctuation of retail sales of consumer goods in China.Design/methodology/approachFirst, the whole quarterly time series is divided into four groups by data grouping method. Each group only contains the time series data in the same quarter. Then, the new series of four-quarters are used to establish the grey correlation model and calculate its correlation coefficient. Finally, the correlation degree of factors in each group of data was calculated and sorted to determine its importance.FindingsThe data grouping method can effectively reflect the correlation between time series in different quarters and eliminate the influence of seasonal fluctuation.Practical implicationsIn this paper, the main factors influencing the quarterly fluctuations of retail sales of consumer goods in China are explored by using the grouped grey correlation model. The results show that the main factors are different from quarter to quarter: in the first quarter, the main factors are money supply, tax and per capita disposable income of rural residents. In the second quarter are money supply, fiscal expenditure and tax. In the third quarter are money supply, fiscal expenditure and per capita disposable income of rural residents. In the fourth quarter are money supply, fiscal expenditure and tax.Originality/valueThis paper successfully realizes the application of grey relational model in quarterly time series and extends the applicable scope of grey relational model.
Technology as a driver to achieve the performance of family businesses supply chain
Authors: Hendayani Ratih , Febrianta Mochamad Yudha 
Published: April 2020

PurposeThe purpose of this study is to investigate the relationship between technology and efficiency and effectiveness in the performance of family business halal supply chains.Design/methodology/approachMethodology used in this research is a quantitative method. The research's type is explanatory research with multivariate data analysis methods using partial least square (PLS). Samples used in this research are 100 family halal food businesses in Indonesia.FindingsThe result shows that there is a positive and significant relationship between each technology and effectiveness. Technology can be used to ensure that all supply chain processes follow Sharia procedures effectively in the family halal food business, but on other hand the technology does not show a positive effect on family halal food business efficiency.Research limitations/implicationsFurther research can be done by applying the model provided in this study for other industries. And investigating the model in a big company to prove the technology may also show a positive relationship to the efficiency.Practical implicationsThe contribution of this research is that the family halal food business can guarantee that technology they use can improve the effectiveness of their supply chain.Social implicationsThe improvement of halal supply chain effectiveness through the technology can improve the product's quality and fulfill the customers' requirements. Also, the family business can assure the society about their halal product.Originality/valueThis research proves that the family business can improve their halal supply chain effectiveness through technology, although lowering their efficiency, which is empirically proven.
Learning in The World Café: an empirical evaluation
Authors: Ropes Donald , van Kleef Han , Douven Giovanni 
Published: April 2020

Purpose
This study aims to evaluate The World Café (TWC) method as a social collaborative learning environment. TWC is a widely used large-scale intervention for such things as organizational change and development or community development programs.

Design/methodology/approach
Three World Cafés were organized as part of a university research project on promoting sustainability-oriented innovation in the logistics sector. A total of 18 participants representing public and commercial organizations were interviewed on their experiences.

Findings
Learning processes are linked to social and cognitive aspects that TWC intervention effectively structures.

Practical implications
If a World Café is implemented according to the basic principles, it can be an effective environment for organizing non-formal learning in organizations.

Originality/value
Although the gray literature on World Cafés is full of anecdotal evidence about its effectiveness, there is a dearth of empirical research underpinning the claims.