bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expansion microsopy reveals Plasmodium falciparum blood-stage parasites undergo anaphase with a chromatin bridge in the absence of mini-chromosome maintenance complex binding protein
Authors: Liffner Benjamin , Absalon Sabrina 
Published: September 2021

ABSTRACTThe malaria parasite Plasmodium falciparum undergoes closed mitosis, which occurs within an intact nuclear envelope, and differs significantly from its human host. Mitosis is underpinned by the dynamics of microtubules and the nuclear envelope. To date, our ability to study P. falciparum mitosis by microscopy has been hindered by the small size of P. falciparum nuclei. Ultrastructure expansion microscopy (U-ExM) has recently been developed for P. falciparum, allowing visualization of mitosis at the individual nucleus level. Using U-ExM, three intranuclear microtubule structures are observed: hemispindles, mitotic spindles and interpolar spindles. A previous study demonstrated that the mini-chromosome maintenance complex binding-protein (MCMBP) depletion caused abnormal nuclear morphology and microtubule defects. To investigate the role of microtubules following MCMBP depletion and study the nuclear envelope in these parasites, we developed the first nuclear stain enabled by U-ExM in P. falciparum. MCMBP deficient parasites show aberrant hemispindles and mitotic spindles. Moreover, anaphase chromatin bridges, and individual nuclei containing multiple microtubule structures were observed following MCMBP knockdown. Collectively, this study refines our understanding of MCMBP-deficient parasites and highlights the utility of U-ExM coupled with a nuclear envelope stain for studying mitosis in P. falciparum.
In silicoexperiments uncover a novel mechanism underlying mutation rate evolution in sexually reproducing populations
Authors: Rozhok Andrii , Eldredge Niles , DeGregori James 
Published: September 2021

AbstractNatural selection is believed to universally work to lower mutation rates (MR) due to the negative impact of mutations on individual fitness. Mutator alleles can be co-selected by genetic linkage with adaptive alleles in asexual organisms. However, sexual reproduction disrupts genetic linkage, allowing selection to efficiently eradicate mutator alleles, lowering MR to the extent limited by the overall selection efficiency.In the present paper, we apply Monte Carloin silicoexperimentation to study MR evolution in sexually reproducing populations.We demonstrate that both higher and lower MR can evolve depending on the mode of selection acting on adaptive phenotypic traits. We reveal a previously unreported co-selective process that determines the direction of MR evolution. We show that MR evolution is substantially influenced by multigenic inheritance of both MR and adaptive traits. Our study corroborates that MR evolution is significantly impacted by genetic drift; however, its primary source appears to be the amount of standing genetic variation, with a lesser role for population size.Based on our study, we propose an expanded population genetics theory of MR evolution in sexually reproducing populations, with potential implications for understanding rapid adaptive speciation and related macroevolutionary patterns, as well as for human health.Lay summaryNatural selection is believed to always work to lower mutation rates in sexual organisms. Here we apply a Monte Carlo model of a sexually reproducing population and demonstrate that both lower and higher mutation rates can evolve, contingent on selection acting on adaptive traits in a sexually reproducing population.
A neural network-based method for exhaustive cell label assignment using single cell RNA-seq data
Authors: Li Ziyi , Feng Hao 
Published: September 2021

ABSTRACTThe fast-advancing single cell RNA sequencing (scRNA-seq) technology enables researchers to study the transcriptome of heterogeneous tissues at a single cell level. The initial important step of analyzing scRNA-seq data is usually to accurately annotate cells. The traditional approach of annotating cell types based on unsupervised clustering and marker genes is time-consuming and laborious. Taking advantage of the numerous existing scRNA-seq databases, many supervised label assignment methods have been developed. One feature that many label assignment methods shares is to label cells with low confidence as “unassigned.” These unassigned cells can be the result of assignment difficulties due to highly similar cell types or caused by the presence of unknown cell types. However, when unknown cell types are not expected, existing methods still label a considerable number of cells as unassigned, which is not desirable. In this work, we develop a neural network-based cell annotation method called NeuCA (Neural network-based Cell Annotation) for scRNA-seq data obtained from well-studied tissues. NeuCA can utilize the hierarchical structure information of the cell types to improve the annotation accuracy, which is especially helpful when data contain closely correlated cell types. We show that NeuCA can achieve more accurate cell annotation results compared with existing methods. Additionally, the applications on eight real datasets show that NeuCA has stable performance for intra- and inter-study annotation, as well as cross-condition annotation. NeuCA is freely available as an R/Bioconductor package at https://bioconductor.org/packages/NeuCA.
The effect of high-speed train meet on wheel wear at different speeds
Authors: Zhu AiHua , Zhu AiHua , Ma Chaochao , Yang Jianwei , Hou Xin , Li Hongxiao , Sun Peiwen 
Published: September 2021

Purpose
Considering that a meet between high-speed trains can generate aerodynamic loads, this study aims to investigate the effect of high-speed train meet on wheel wear at different speeds to provide a more accurate wheel wear model and a new idea for reducing wheel wear.

Design/methodology/approach
The train speed was set at 250, 300, 350 and 400 km/h separately, and a vehicle system dynamics model was constructed using the parameters of an actual high-speed train on a line. The aerodynamic forces arising from constant-speed train meet were then applied as additional excitation. Semi-Hertzian theory and Kalker’s simplified theory were used to solve the wheel/rail contact problems. The wheel wear was calculated using Archard wear model. The effect of train meet on wheel wear was analyzed for the whole train, different cars and different axles.

Findings
According to the results, all wheels show a wear increase in the case of one train meet, compared to the case of no train meet. At 250, 300, 350 and 400 km/h, the total wheel wear increases by 4.45%, 4.91%, 7.57% and 5.71%, respectively, over the entire operational period. The change in speed has a greater impact on wheel wear increase in the head and tail cars than in the middle car. Moreover, the average wear increase in front-axle wheels is 1.04–2.09 times that in rear-axle wheels on the same bogie.

Practical implications
The results will help to analyze wheel wear more accurately and provide theoretical guidance for wheel repair and maintenance from the perspective of high-speed train meet.

Originality/value
At present, there is a lot of focus on the impact of high-speed train meet on the dynamic performance of vehicles. However, little research is available on the influence of train meet on wheel wear. In this study, a vehicle dynamics model was constructed and the aerodynamic forces generated during high-speed train meet were applied as additional excitation. The effect of train meet on wheel wear was analyzed for the whole train, different cars and different axles. The proposed method can provide a more accurate basis for wear prediction and wheel repair.
Competitive advantage in SMEs: effect of supply chain management practices, logistics capabilities and logistics integration in a developing country
Authors: Tukamuhabwa Benjamin , Mutebi Henry , Kyomuhendo Rhona 
Published: September 2021

PurposeThe purpose of this paper is to explore the relationship between supply chain management practices, logistics capabilities, logistics integration and competitive advantage of Small and Medium Enterprises (SMEs) in a developing country.Design/methodology/approachUsing a structured questionnaire survey, cross-sectional data collected from 204 SMEs in Kampala – Uganda were analysed using exploratory and confirmatory factor analysis, and Structural Equation Modelling (SEM) using AMOS version 26 to validate the theorised relationships.FindingsThe study findings revealed that both supply chain management practices and logistics integration are positively and significantly associated with competitive advantage. Also, both supply chain management practices and logistics capabilities are positively and significantly associated with logistics integration. Additionally, the authors found that logistics integration partially mediates in the relationships between supply chain management practices and competitive advantage, and logistics capabilities and competitive advantage. Conclusively, the three independent variables collectively account for 11% variance in competitive advantage of SMEs.Originality/valueGiven the general observation that SMEs are fundamental to socio-economic development, yet resource constrained, this study uses Resource-based and dynamic capabilities theoretical perspectives to provide an empirical understanding of the supply chain and logistics resources and capabilities necessary for building competitive advantage of SMEs in the context of a developing economy.
Online or onsite? Comparison of the relative merit of delivery format of Aboriginal cultural-awareness-training to undergraduate chiropractic students
Authors: Amorin-Woods Lyndon , Gonzales Hugo , Amorin-Woods Deisy , Losco Barrett , Skeffington Petra 
Published: September 2021

Purpose
The purpose of this paper is to work with Aboriginal and Torres Strait Islander people (ATSI), it is expected that non-ATSI health-care professionals become culturally aware; however, participants’ perceptions of the relative merit of cultural awareness training (CAT) formats is uncertain.

Design/methodology/approach
The authors compared undergraduate students’ perceptions of an asynchronous online format with onsite delivery formats of CAT using a mixed-method design. Students from five successive cohorts (n = 64) in an undergraduate programme were invited to complete a post-training survey which gathered quantitative and qualitative data.

Findings
Whilst feedback was positive regarding both formats, the onsite format was preferred qualitatively with several valuable learning outcome themes emerging from the results. These themes included; “perceived benefits of self-evaluation of students’ own culture whilst learning about Aboriginal culture”; “encouraging to be provided with scenarios, examples and exercises to enhance cultural awareness” and “engagement with the interactive facilitator approach”. There were differing views about the benefits of learning the history of oppression which warrant further research.

Research limitations/implications
Results may be applicable to undergraduate allied health students who participate in clinical immersion placements (CIPs) who participate in Aboriginal CAT.

Practical implications
Given the changing dynamic in education forced by the COVID-19 pandemic, more resources may need to be directed to improving online training and possibly combining formats in course delivery.

Social implications
The strength of the study is that the authors achieved a response rate of 100%, thus the results are highly significant for the sample. This sample represents 41.3% of chiropractic students who attended CAT and CIPs at this university over the course of 9 years, thus the results could be generalized to chiropractic students who participated in these types of placements.

Originality/value
To the best of the authors’ knowledge, this is the first study to compare student perceptions of different formats of Aboriginal CAT for final year chiropractic undergraduate students in Australia.
Analysis of the upstream genetic structures of the ISEcp1‐blaCTX‐M transposition units in Escherichia coli isolates carrying blaCTX‐M obtained from the Indonesian and Vietnamese communities
Authors: Widyatama Fikri S. , Yagi Nobuyoshi , Sarassari Rosantia , Shirakawa Toshiro , Le Danh Tuyen , Bui Mai Huong Thi , Kuntaman Kuntaman , Hirai Itaru 
Published: September 2021

AbstractExtended spectrum β‐lactamase (ESBL)‐producing Escherichia coli have been found in healthy individuals in Indonesia and Vietnam. The ISEcp1‐blaCTX‐M transposition unit of ESBL‐producing bacterial isolates has been considered responsible for the production of CTX‐M type ESBL and it is important for the dissemination of blaCTX‐M. This study aimed to characterize the upstream genetic structure (UGS) of E. coli isolates possessing blaCTX‐M‐1 group and/or blaCTX‐M‐9 group genes obtained from healthy individuals in Indonesia and Vietnam. A total of 501 CTX‐M type ESBL‐producing E. coli isolates possessing blaCTX‐M‐1 group and/or blaCTX‐M‐9 group genes were obtained from healthy individuals of the two countries in 2018. The UGSs of the ISEcp1‐blaCTX‐M transposition unit of the 501 ESBL‐producing E. coli isolates were amplified by barcode‐adaptor‐ligation‐mediated PCR and analyzed using the Nanopore sequencer. The obtained sequence information was used to classify the UGSs of the ISEcp1‐blaCTX‐M transposition unit. From the 501 ESBL‐producing E. coli isolates, 502 UGSs were obtained, which were classified into 85 UGS types based on the sequence. ISEcp1 of 359 (71.5%) of the 502 UGSs was disrupted by gene insertion, and ISEcp1‐blaCTX‐M transposition unit of most (87.1%) of the determined UGSs was confirmed as plasmidic. Only 6 (7.1%) of the 85 UGS types were common to both countries. Our results indicated that many different UGSs of ISEcp1‐blaCTX‐M transposition units were detected in Indonesia and Vietnam; hence, we suggest that structurally different kinds of plasmids harboring blaCTX‐M were separately distributed in the two countries.
Lived time and the affordances of clinical research participation
Authors: Brenman Natassia , Milne Richard 
Published: September 2021

AbstractIn this article, we address the problem of participation and the dominant focus on motivations in clinical research. We explore participation as a relational mode of ‘being in time’ in Alzheimer's dementia prevention—a field profoundly shaped by changing bodies through time, as well as promissory trends towards future‐oriented preventative medicine. Analysis of interviews with older adults in a clinical trial platform demonstrates that what research ‘does’ or might (not) ‘do’ for participants emerges as temporalities of participants’ everyday lives become entangled with the possibilities, constraints and demands of biomedical ‘research time’. As well as consistent desires to help (future) others, we identify incidental possibilities for care that emerged from continued research participation. We argue that longitudinal research participation can productively be understood as a set of evolving affordances: whereby differing limits and possibilities for care and agency emerge in a world where dementia cannot be cured. Future trial participation is considered in terms of ‘therapeutic affordances’, which are likely to fluctuate as certain lived or imagined futures unfold. As such, we open up a conceptual space to think about why, how, and critically, when participation happens, as it emerges in relation to lived times of ageing and everyday life.
Enacting evidence‐based medicine in fertility care: Tensions between commercialisation and knowledge standardisation
Authors: Perrotta Manuela , Geampana Alina 
Published: September 2021

AbstractIn this article we explore the recent enactment of evidence‐based medicine (EBM) in the field of fertility care. We aim to contribute to the medical sociology literature through an analysis of how evidence is produced, interpreted and institutionalised in a relatively new medical field such as in vitro fertilisation (IVF), characterised by high uncertainty due to limited knowledge and high levels of commercialisation. Drawing on extensive ethnographic research conducted in England, this article explores the challenges IVF professionals encounter in producing credible data on the effectiveness of additional treatments, offering novel insights on the tensions between commercialisation and standardisation in the enactment of EBM. Extant medical sociology and Science and Technology Studies literature has shown the hidden professional work required to enact randomised control trials in practice. Our analysis shows that this hidden work is not enough when there is a broader lack of standardisation in both clinical and research practices, as producing ‘good quality’ evidence requires high levels of standardisation of knowledge production.
Reassessing the regressivity of the VAT
Authors: Thomas Alastair 
Published: September 2021

AbstractThis paper reassesses the often‐made conclusion that the value‐added tax (VAT) is regressive, drawing on tax microsimulation models constructed for an unprecedented 27 OECD countries. The paper first considers the competing methodological approaches used in previous distributional studies, highlighting the impact of savings patterns on cross‐sectional analysis when VAT burdens are measured relative to income. It is argued that measuring VAT burdens relative to expenditure – thereby removing the influence of savings – can be expected to provide a more reliable picture of the distributional impact of the VAT. On this basis, the VAT is found to be either roughly proportional or slightly progressive in most of the 27 OECD countries examined. Nevertheless, the results for a small number of countries highlight that broad‐based VAT systems that have few reduced VAT rates or exemptions can produce a small degree of regressivity. Results also show that even a roughly proportional VAT can still have significant equity implications for the poor – potentially pushing some households into poverty. This emphasises the importance of ensuring the progressivity of the tax‐benefit system as a whole in order to compensate poor households for the loss in purchasing power from paying VAT.
Freezing of meat and aquatic food: Underlying mechanisms and implications on protein oxidation
Authors: Bao Yulong , Ertbjerg Per , Estévez Mario , Yuan Li , Gao Ruichang 
Published: September 2021

AbstractOver the recent decades,protein oxidation in muscle foods has gained increasing research interests as it is known that protein oxidation can affect eating quality and nutritional value of meat and aquatic products. Protein oxidation occurs during freezing/thawing and frozen storage of muscle foods, leading to irreversible physicochemical changes and impaired quality traits. Controlling oxidative damage to muscle foods during such technological processes requires a deeper understanding of the mechanisms of freezing‐induced protein oxidation. This review focus on key physicochemical factors in freezing/thawing and frozen storage of muscle foods, such as formation of ice crystals, freeze concentrating and macromolecular crowding effect, instability of proteins at the ice–water interface, freezer burn, lipid oxidation, and so on. Possible relationships between these physicochemical factors and protein oxidation are thoroughly discussed. In addition, the occurrence of protein oxidation, the impact on eating quality and nutrition, and controlling methods are also briefly reviewed. This review will shed light on the complicated mechanism of protein oxidation in frozen muscle foods.
Effects of stewing with tea polyphenol on the gel properties, microstructure, and secondary structure of boiled egg white
Authors: Xue Hui , Xu Meng , Zhang Guowen , Feng Feng , Wang Yuting , Cao Danhui , Tu Yonggang , Zhao Yan 
Published: September 2021

AbstractThis study aimed to investigatethe mechanism of stewing with tea polyphenols (TP) on the properties of boiled egg white gel (BEWG). The results indicated that, during the stewing process, soluble protein and hardness showed an overall increasing trend, while surface hydrophobicity showed a decreasing trend with blue‐shift. The free sulfhydryl group showed that TP could promote the formation of disulfide bonds, and the position of immobilized water at T2 showed a decreasing trend. Environmental scanning electron microscopy and SDS‐PAGE showed that the protein gel aggregation degree increased. Moreover, Fourier transform infrared spectrometry showed that protein polarity increased and that α‐helices, β‐turn, intramolecular β‐sheets, as well as intermolecular antiparallel β‐sheets showed an increasing trend. Generally, TP strengthened protein aggregation by promoting the formation of disulfide and hydrogen bonds, thus enhancing the gel strength of BEWG. Moreover, the secondary structure of proteins became more stable under the action of TP, and the higher the concentration of TP, the greater the effect on BEWG.Practical ApplicationTP, an ideal, cheap, and safe natural food additive, can be applied to the processing of egg products because the addition of TP can significantly improve the gel strength of egg white.
Convergence assessment for Bayesian phylogenetic analysis using MCMC simulation
Authors: Fabreti Luiza Guimarães , Höhna Sebastian 
Published: September 2021

Abstract

Posterior distributions are commonly approximated by samples produced from a Markov chain Monte Carlo (MCMC) simulation. Every MCMC simulation has to be checked for convergence, that is, that sufficiently many samples have been obtained and that these samples indeed represent the true posterior distribution.

Here we develop and test different approaches for convergence assessment in phylogenetics. We analytically derive a threshold for a minimum effective sample size (ESS) of 625. We observe that only the initial sequence estimator provides robust ESS estimates for common types of MCMC simulations (autocorrelated samples, adaptive MCMC, Metropolis‐coupled MCMC). We show that standard ESS computation can be applied to phylogenetic trees if the tree samples are converted into traces of absence/presence of splits.

Convergence in distribution between replicated MCMC runs can be assessed with the Kolmogorov–Smirnov test. The commonly used potential scale reduction factor (PSRF) is biased when applied to skewed posterior distribution. Additionally, we provide how the distribution of differences in split frequencies can be computed exactly akin to standard exact tests and show that it depends on the true frequency of a split. Hence, the average standard deviation of split frequencies is too simplistic and the expected difference based on the 95% quantile should be used instead to check for convergence in split frequencies.

We implemented the methods described here in the open‐source R package Convenience (https://github.com/lfabreti/convenience), which allows users to easily test for convergence using output from standard phylogenetic inference software.