bluuebunny/crossref_metadata_2025 huggingface dataset:
Kinetic and thermodynamic modeling of a voltage-gated sodium channel
Authors: Almog Mara , Degani-Katzav Nurit , Korgnreen Alon
Published: September 2021

Like all biological and chemical reactions, ion channel kinetics are highly sensitive to changes in temperature. Therefore, it is prudent to investigate channel dynamics at physiological temperatures. However, most ion channel investigations are performed at room temperature due to practical considerations, such as recording stability and technical limitations. This problem is especially severe for the fast voltage-gated sodium channel, whose activation kinetics are faster than the time constant of the standard patch-clamp amplifier at physiological temperatures. Thus, biologically detailed simulations of the action potential generation evenly scale the kinetic models of voltage-gated channels acquired at room temperature. To quantitatively study voltage-gated sodium channels’ temperature sensitivity, we recorded sodium currents from nucleated patches extracted from the rat’s layer five neocortical pyramidal neurons at several temperatures from 13.5 to 30oC. We use these recordings to model the kinetics of the voltage-gated sodium channel as a function of temperature. We show that the temperature dependence of activation differs from that of inactivation. Furthermore, we show that the sustained current has a different temperature dependence than the fast current. Our kinetic and thermodynamic analysis of the current provided a numerical model spanning the entire temperature range. This model reproduced vital features of channel activation and inactivation. Furthermore, the model also reproduced action potential dependence on temperature. Thus, we provide an essential building block for the generation of biologically detailed models of cortical neurons.
Anchorage by seed mucilage prevents seed dislodgement in high surface flow: a mechanistic investigation
Authors: Pan Vincent S. , Girvin Cecilia , LoPresti Eric F.
Published: September 2021

Background and Aims:Seed mucilage is a common and highly diverse trait shared among thousands of angiosperm species. While long recognized that mucilage allows seeds to anchor to substrates (antitelechory), resisting abiotic and biotic dislodgement, we still lack a mechanistic understanding of this process.

Methods:We propose a mechanistic model of how mucilage affects substrate anchorage and fluid resistance, ultimately contributing to dislodgement resistance. To test this model, we subjected mucilaginous seeds of 52 species, varying in eight measured seed traits, to seven days of continuous water flow at a range of dislodgement potentials.

Key Results:Supporting our model, mucilage mass increased force necessary to dislodge both dry and wet seeds; our measurement of the dislodgement force of dry mucilage explained time to dislodgement well. The effect size was remarkably large; increasing the standardized mucilage mass by one standard deviation resulted in a 280-fold increase in the time to dislodgement. Fluid resistance was largely dependent on speed of water flow and the seed’s modified drag coefficient, but not seed traits. Neither mucilage expansion speed nor mucilage decay rate explained dislodgement potential well.

Conclusions:Our results suggest that the degree of anchorage to substrate, measured with a simple dislodgement force assay, is highly predictive of mucilaginous seed retention in highly erosive environments. In contrast, we found that other seed and mucilage traits are of lesser importance to anchorage.
Cross-species cell-type assignment of single-cell RNA-seq by a heterogeneous graph neural network
Authors: Liu Xingyan , Shen Qunlun , Zhang Shihua
Published: September 2021

Cross-species comparative analyses of single-cell RNA sequencing (scRNA-seq) data allow us to explore, at single-cell resolution, the origins of cellular diversity and the evolutionary mechanisms that shape cellular form and function. Here, we aimed to utilize a heterogeneous graph neural network to learn aligned and interpretable cell and gene embeddings for cross-species cell type assignment and gene module extraction (CAME) from scRNA-seq data. A systematic evaluation study on 649 pairs of cross-species datasets showed that CAME outperformed six benchmarking methods in terms of cell-type assignment and model robustness to insufficiency and inconsistency of sequencing depths. Comparative analyses of the major types of human and mouse brains by CAME revealed shared cell type-specific functions in homologous gene modules. Alignment of the trajectories of human and macaque spermatogenesis by CAME revealed conservative gene expression dynamics during spermatogenesis between humans and macaques. Owing to the utilization of non-one-to-one homologous gene mappings, CAME made a significant improvement on cell-type characterization cross zebrafish and other species. Overall, CAME can not only make an effective cross-species assignment of cell types on scRNA-seq data but also reveal evolutionary conservative and divergent features between species.
The chromosomal distribution of sex-biased microRNAs in Drosophila is non-adaptive
Authors: Marco Antonio
Published: September 2021

Genes are often differentially expressed between males and females. In Drosophila melanogaster, the analysis of sex-biased microRNAs (short non-coding regulatory molecules) has revealed striking differences with protein-coding genes. Mainly, the X chromosome is enriched in male-biased microRNA genes, although it is depleted of male-biased protein-coding genes. The paucity of male-biased genes in the X chromosome is generally explained by an evolutionary process called demasculinization. I suggest that the excess of male-biased microRNAs in the X chromosome is due to high-rates of de novo emergence of microRNAs (mostly in other neighboring microRNAs), a tendency of novel microRNAs in the X chromosome to be expressed in testis, and to a lack of a demasculinization process. To test this hypothesis I analysed the expression profile of microRNAs in males, females and gonads in D. pseudoobscura, in which an autosome translocated into the X chromosome effectively becoming part of a sex chromosome (neo-X). I found that the pattern of sex-biased expression is generally conserved between D. melanogaster and D. pseudoobscura. Also, orthologous microRNAs in both species conserve their chromosomal location, indicating that there is no evidence of demasculinization or other inter-chromosomal movement of microRNAs. D. pseudoobscuraspecific microRNAs in the neo-X chromosome tend to be male-biased and particularly expressed in testis. In summary, the apparent paradox resulting from male-biased protein-coding genes depleted in the X chromosome and an enrichment in male-biased microRNAs is consistent with different evolutionary dynamics between coding genes and short RNAs.
Single-molecule analysis of specificity and multivalency in binding of short linear substrate motifs to the APC/C
Authors: Hartooni Nairi , Sung Jongmin , Jain Ankur , Morgan David O.
Published: September 2021

Robust regulatory signals in the cell often depend on interactions between short linear motifs (SLiMs) and globular proteins. Many of these interactions are poorly characterized because the binding proteins cannot be produced in the amounts needed for traditional methods. To address this problem, we developed a single-molecule off-rate (SMOR) assay based on microscopy of fluorescent ligand binding to immobilized protein partners. We used it to characterize substrate binding to the Anaphase-Promoting Complex/Cyclosome (APC/C), a ubiquitin ligase that triggers chromosome segregation. We find that SLiMs in APC/C substrates (the D box and KEN box) display distinct affinities and specificities for the substrate-binding subunits of the APC/C, and we show that multiple SLiMs in a substrate generate a high-affinity multivalent interaction. The remarkably adaptable substrate-binding mechanisms of the APC/C have the potential to govern the order of substrate destruction in mitosis.
Large-scale comparative small RNA analyses reveal genomic structural variants in driving expression dynamics and differential selection pressures on distinct small RNA classes during tomato domestication
Authors: Qing You , Zheng Yi , Mlotshwa Sizolwenkosi , Smith Heather N. , Wang Xin , Zhai Xuyang , van der Knaap Esther , Wang Ying , Fei Zhangjun
Published: September 2021

Tomato has undergone extensive selections during domestication. Recent progress has shown that genomic structural variants (SVs) have contributed to gene expression dynamics during tomato domestication, resulting in changes of important traits. Here, through comprehensive analyses of small RNAs (sRNAs) from nine representative tomato accessions, we demonstrate that SVs substantially contribute to the dynamic expression of the three major classes of plant sRNAs: microRNAs (miRNAs), phased secondary short interfering RNAs (phasiRNAs), and 24-nt heterochromatic siRNAs (hc-siRNAs). Changes in the abundance of phasiRNAs and 24-nt hc-siRNAs likely contribute to the alteration of mRNA gene expression during tomato’s recent evolution, particularly for genes associated with biotic and abiotic stress tolerance. We also observe that miRNA expression dynamics are associated with imprecise processing, alternative miRNA-miRNA* selections, and SVs. SVs mainly affect the expression of less-conserved miRNAs that do not have established regulatory functions or low abundant members in highly expressed miRNA families, highlighting different selection pressures on miRNAs compared to phasiRNAs and 24-nt hc-siRNAs. Our findings provide insights into plant sRNA evolution as well as SV-based gene regulation during crop domestication. Furthermore, our dataset provides a rich resource for mining the sRNA regulatory network in tomato.
Cryo-EM structure of a single-chain β1-adrenoceptor – AmpC β-lactamase fusion protein
Authors: Collu Gabriella , Mohammed Inayathulla , Lafita Aleix , Bierig Tobias , Poghosyan Emiliya , Bliven Spencer , Benoit Roger M.
Published: September 2021

The insertion of fusion proteins has enabled the crystallization of a wide range of G-protein-coupled receptors (GPCRs). Here, we explored the possibility of using a larger fusion protein, inserted into the third intracellular loop (ICL3) of β1-adrenoceptor (β1AR) via rigid chimeric helix fusions. The aim was to engineer a single-chain fusion protein that comprises sufficient mass and rigidity to allow single-particle cryo-EM data collection, without depending on binding proteins, such as G-proteins or nanobodies. Through parsing of the protein data bank (PDB), we identified the protein AmpC β-lactamase as a suitable candidate. Both termini of this protein are α-helical and the helices are antiparallel to each other. The distance between their centroids measures ∼11 Å. Such a geometry is ideal to design extended chimeric helices with transmembrane (TM) helices 5 and 6 of β1AR, and the insertion of the protein adds ∼39 kDa of mass to the receptor. We expressed the β1AR - AmpC β-lactamase fusion protein in mammalian cells. The binding of the antagonists propranolol and cyanopindolol to the purified fusion protein was confirmed by CPM-based thermofluor assays. The cryo-EM structure was solved to a nominal overall resolution of 3.6 Å and the seven helix architecture and helix eight were clearly resolved. Superimposition of the structure with known X-ray crystal structures of β1AR suggests that the protein is in its inactive conformation. The fusion protein described here provides a basis for high-throughput structure elucidation of class A GPCRs by cryo-EM for drug discovery research as well as for the elucidation of inactive state or wild-type GPCR structures. The fusion protein geometry theoretically fits a wide range of class A GPCRs and therefore can be applied to a multitude of receptors.
Metabolite profiling reveals organ-specific flavone accumulation in Scutellaria and identifies a scutellarin isomer isoscutellarein 8-O-β-glucuronopyranoside
Authors: Askey Bryce C. , Liu Dake , Rubin Garret M. , Kunik Andrew R. , Song Yeong Hun , Ding Yousong , Kim Jeongim
Published: September 2021

Scutellaria is a genus of plants containing multiple species with well-documented medicinal effects. S. baicalensis and S. barbata are among the best-studied Scutellaria species, and previous works have established flavones to be the primary source of their bioactivity. Recent genomic and biochemical studies with S. baicalensis and S. barbata have advanced our understanding of flavone biosynthesis in Scutellaria. However, as over several hundreds of Scutellaria species occur throughout the world, flavone biosynthesis in most species remains poorly understood. In this study, we analyzed organ-specific flavone profiles of seven Scutellaria species, including S. baicalensis, S. barbata and two species native to the Americas (S. wrightii to Texas and S. racemosa to Central and South America). We found that the roots of almost all these species produce only 4’-deoxyflavones, while 4’-hydroxyflavones are accumulated exclusively in their aerial parts. On the other hand, S. racemosa and S. wrightii also accumulated high levels of 4’-deoxyflavones in their aerial parts, different with the flavone profiles of S. baicalensis and S. barbata. Furthermore, our metabolomics and NMR study identified the accumulation of isoscutellarein 8-O-β-glucuronopyranoside, a rare 4’-hydroxyflavone, in the stems and leaves of several Scutellaria species including S. baicalensis and S. barbata, but not in S. racemosa and S. wrightii. Distinctive organ-specific metabolite profiles among Scutellaria species indicate the selectivity and diverse physiological roles of flavones.
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

The 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

Natural 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 summary

Natural 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

The 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

Purpose

The 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/approach

Using 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.

Findings

The 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/value

Given 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

Extended 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

In 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

In 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

This 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

Over 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

This 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 Application

TP, 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

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.
Ecotype‐specific effects of fungal endophytes on germination responses of seeds of the South American wild forage grass Bromus auleticus
Authors: Stefanoni‐Rubio Pablo J. , Gundel Pedro E. , Novas María V. , Iannone Leopoldo J.
Published: September 2021

Bromus auleticus is a winter wild species with promissory characteristics for domestication as forage that inhabits temperate‐warm grasslands from a wide region from South America. Populations from regions with different environmental conditions are considered as ecotypes and are associated with different seedborne Epichloë fungal endophytes. Association with Epichloë provides B. auleticus with increased growth capacity and resistance against pathogens. The seeds mature at the end of spring and germinate in autumn, remaining dormant during wet and warm summer. As the persistence of Epichloë endophytes in the seed is highly sensitive to temperature and humidity, we studied how the endophytes modulate seed germination in response to these factors in two B. auleticus ecotypes named La Pampa (LP) and El Palmar (EP). We also studied how environmental factors during germination affect endophyte survival. In the LP ecotype, adapted to coldest temperatures in autumn, Epichloë improved final germination under alternating temperatures, but had no effects on germination inhibition imposed by low water availability. In the EP ecotype, adapted to warm humid summer and autumn, the endophyte promoted germination at constant 25°C and alternating 15/25°C temperatures, and prevented germination at low water potentials. At 30°C, seed germination was inhibited and whereas seeds remained viable, endophyte survival was significantly lowered. The effect of Epichloë on B. auleticus seed germination was ecotype‐specific: promoting germination at alternating temperatures in La Pampa ecotype or at high temperatures in El Palmar ecotype, while inhibiting it at low water availabilities, could be an endophyte‐mediated ecotypic strategy minimising endophyte mortality and increasing seedling establishment.
A nationwide nested case‐control study of new‐onset obsessive‐compulsive disorder following antipsychotics use in schizophrenia
Authors: Park Chun Il , Han Minkyung , Jung Inkyung , Kim Eun Hwa , Kang Jee In , Kim Se Joo
Published: September 2021

Objective

A substantial proportion of patients with schizophrenia suffer from comorbid obsessive‐compulsive disorder (OCD) possibly associated with antipsychotics. However, little is known about the comparative risks of the antipsychotics. The present study aimed to investigate the risk of new‐onset OCD following the initiation of different antipsychotic medications for schizophrenia relative to haloperidol.

Methods

Using the Korean national claims data, patients aged 15–60 years newly diagnosed with schizophrenia between 2010 and 2018 were identified. Of the 47,808 patients with schizophrenia treated with nine commonly prescribed antipsychotics, 775 new‐onset OCD patients were matched to 3,100 patients without OCD using nested case‐control design with 1:4 case‐control matching based on the sex, age of index date, date of schizophrenia diagnosis, observation period, locations of medical institutions, and level of medical facilities. Using multivariable conditional logistic regression analysis, odd ratios (ORs) for new‐onset OCD comparing each antipsychotic agent relative to haloperidol were computed.

Results

The risk for new‐onset OCD during treatment with clozapine was significantly higher than that with haloperidol (adjusted OR 2.86; 95% confidence interval [1.63–5.03]). The risks for new‐onset OCD with other antipsychotics were not significantly different from that with haloperidol. In subgroup analysis, the early and intermediate, but not late‐onset schizophrenia group showed significant risk for OCD associated with clozapine use.

Conclusion

The present findings, based on real‐world national representative data, provide reliable evidence for the risk of new‐onset OCD in patients with schizophrenia receiving clozapine at a population level.
Institutional Environment, State Ownership and Family Business Succession: Evidence from China*
Authors: Yang Baili , Song Zengji , Feng Yedong
Published: September 2021

We examine the impact of the lack of institutional environment on the succession of family businesses and explore the moderating role of state ownership in the relationship. The empirical results show that in areas with poor institutional environment, it is more difficult for family business to inherit from generation to generation. State ownership in a family business can be used as an informal system to mitigate the negative impact of an imperfect institutional environment on succession. We also find that when state ownership comes from the local government or participates in corporate governance, its moderating effect is more significant.
City‐State Ideological Incongruence and Municipal Preemption
Authors: Barber Michael , Dynes Adam M.
Published: September 2021

A growing concern among municipal officials across the United States is that their policymaking capacity is under attack by state legislatures who are increasingly likely to preempt those municipalities. However, determining the extent to which municipalities are preempted is challenging. We overcome this by surveying a large sample of municipal officials from across the United States. We find that officials from municipalities that are more ideologically distant from their state overall are more likely to report being preempted by their state government. Moreover, this pattern is driven by more liberal municipalities in both Republican and Democratic states reporting higher rates of preemption. Additionally, municipalities under unified state governments are more likely to report preemption, especially those under unified Republican control. These findings have important implications for the quality of representation in our federalist system and indicate that preemption is not just an issue between Republican states and liberal urban cities.
Perceptions of adolescents and young adults with allergy and/or asthma and their parents on EAACI guideline recommendations about transitional care: A European survey
Authors: Khaleva Ekaterina , Knibb Rebecca , DunnGalvin Audrey , Vazquez‐Ortiz Marta , Comberiati Pasquale , Alviani Cherry , Garriga‐Baraut Teresa , Gowland Mary Hazel , Gore Claudia , Angier Elizabeth , Blumchen Katharina , Duca Bettina , Hox Valérie , Jensen Britt , Mortz Charlotte G. , Pite Helena , Pfaar Oliver , Santos Alexandra F. , Sanchez‐Garcia Silvia , Timmermans Frans , Roberts Graham
Published: September 2021

Background

The European Academy of Allergy and Clinical Immunology has developed a guideline to provide evidence‐based recommendations for healthcare professionals to support the transitional care of adolescents and young adults (AYA) with allergy and/or asthma. The goal of this work was to ensure that the draft recommendations are also important for patients.

Methods

We surveyed patients aged 11–25 years with allergy and/or asthma and their parents across Europe between 17 February and 16 March 2020. The multilingual survey was distributed through national allergy and asthma patient organizations in Europe as well as through social media.

Results

A total of 1210 responses from 24 European countries were collected. There were 415 (34.3%) AYA and 795 (65.7%) parents. The majority of AYA (72.3%) and parents (81.9%) were female. Patients had a history of asthma (61.1%), allergic rhinoconjunctivitis (54.1%), food allergy (53.8%), atopic eczema (42.6%) and anaphylaxis (28.8%). All recommendations achieved the median score of either ‘important’ or ‘very important’. The least supported recommendations were the use of joint clinics with both paediatric and adult physicians attending and the use of web‐based or mobile technologies for communication with the AYA. The most supported recommendation was checking that the AYA is knowledgeable and compliant with their prescribed medication. Qualitative analysis revealed conditional approval for some recommendations.

Conclusions

There was agreement from patients and parents on the importance of the draft recommendations on transitional care for AYA with allergy and/or asthma and their parents. The recommendations now need to be implemented into clinical practice across Europe.
Dear April: The Aesthetics of Black Miscellanea
Authors: McKittrick Katherine
Published: September 2021

Exploring textual accumulation as a methodological practice, this paper (first presented as the 2021 Antipode American Association of Geographers Lecture on 8 April) works through how the aesthetics of black miscellanea, and the engagement with overlapping and conflicting texts that are affixed, uncovers moments of clarity that complicate typical conceptualisations of opacity. The moments of clarity unravel as lessons, with the aesthetics of black miscellanea signalling an experiment in, and the potential politics of, dynamic collaboration, diasporic literacy, and counsel. Krista Franklin’s Under the Knife anchors the discussion.
The significance of isolated aspartate aminotransferase elevation in healthy paediatric patients
Authors: Magen‐Rimon Ramit , Tal Galit , Kaplan Marielle , Shaoul Ron
Published: September 2021

Aim

Aspartate aminotransferase (AST) is an enzyme expressed in several organs; therefore, AST elevation may reflect outside of liver pathology. AST elevation may also be associated with macro‐AST (m‐AST). The aim of this study was to evaluate the long‐term course of children with prolonged isolated AST elevation and the prevalence of m‐AST in our cohort.

Methods

We retrospectively reviewed the medical charts of children diagnosed with prolonged isolated AST elevation and were evaluated for m‐AST.

Results

Thirty‐two patients were included. AST elevation persisted for a median of 66.6 months and ranged from 1.23 to 12‐fold upper limit of normal (ULN). Twenty‐two percent were m‐AST positive and 44% had borderline levels of m‐AST. A statistically significant difference was found for age at presentation between the borderline and the positive m‐AST groups (31 vs. 69 months, respectively. p = 0.045). None of the patients with elevated AST developed significant liver disease.

Conclusion

We confirm the benign course of prolonged isolated AST elevation in general and m‐AST in particular. A fifth of the patients with isolated AST elevation were m‐AST positive. No differences have been found in AST levels between negative, borderline or positive m‐AST.