bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization and filtering of profile and areal surface topography by combining the discrete Legendre and cosine transforms
Authors: Haitjema Han
Published: March 2023

In the standardized processing of surface topography data, the form removal and filtering operations are clearly separated. This is reflected in the current ISO standards concerning profile surface texture and areal surface texture, the ISO 21920 and the ISO 25178 series respectively. When the scale-limited surface texture is significant compared to the form to be removed, for example with additive manufactured surfaces, the dependence of the surface Fourier spectrum on the removed form and orientation may become significant. This may lead to interaction between the form removal and filtering operations. To counter this interaction, in this paper, the lower-order discrete Legendre polynomials that describe the form are combined with cosine functions that describe the surface texture. This set of base functions is orthonormalized using a Gram-Schmidt procedure. This results in a set of orthonormal functions that allow an independent parameterization of both form and texture. The concept and the related theory are given and illustrated using examples of filtering profiles and areal topographies, description of cylinders and treatment of missing data. The examples show that the concept as presented in this paper is useful for filtering surfaces with a dominant form and can be used in the parametrization of surfaces and cylindrical geometries. Also, the methods presented here can be used for filtering and parametrization in the case of missing points in the data, actual holes in the profile or non-rectangular surfaces.
Photothermal ultra-high molecular weight polyethylene/MXene aerogel for crude oil adsorption and water evaporation
Authors: Zhang Mingtao , Su Meng , Qin Yijing , Liu Chuntai , Shen Changyu , Ma Jun , Liu Xianhu
Published: March 2023

The frequent oil spill accidents during oil exploration and transportation have caused large economic loss and catastrophic environmental disasters. Due to low cost and simplicity, adsorption and filtration materials are often chosen to deal with oil spills, but the outcomes are not satisfactory mainly because of the awfully high viscosity of crude oil. Herein a photothermal ultra-high molecular weight polyethylene/MXene composite aerogel with a high light absorption (99.97%) and water repellency (water contact angle >148°) is developed by thermally induced phase separation method. The composite aerogel endows durable hydrophobicity with which the water contact angle is more than 142° in acidic/alkaline environments, and the maximum absorption capacity of 81 g g−1. In addition, it exhibits an excellent photothermal performance, rising surface temperature to 70 °C within 60 s under 1 sun irradiation, that can drastically reduce the crude oil absorption time from 60 min to 60 s, saving 98% of absorption time and reaching a crude oil absorption capacity of 21 g g−1. More interestingly, the designed solar evaporation device with the obtained composite aerogel can achieve an evaporation rate of 1.15 kg m−2h−1 and evaporation efficiency of 74%. The designed composite aerogel opens a possible pathway for solar-powered crude oil adsorption applications.
Investigation of the J-TEXT plasma events by k-means clustering algorithm
Authors: LI Jianchao , ZHANG Xiaoqing , ZHANG Yu , BALA Abba Alhaji , LIU Huiping , ZHOU Guohong , WANG Nengchao , LI Da , CHEN Zhongyong , YANG Zhoujun , CHEN Zhipeng , DONG Jiaolong , DING Yonghua
Published: March 2023

Various types of plasma events emerge in specific parameter ranges and exhibit similar characteristics in diagnostic signals, which can be applied to identify these events. A semi-supervised machine learning algorithm, the k-means clustering algorithm, is utilized to investigate and identify plasma events in the J-TEXT plasma. This method can cluster diverse plasma events with homogeneous features, and then these events can be identified if given few manually labeled examples based on physical understanding. A survey of clustered events reveals that the k-means algorithm can make plasma events (rotating tearing mode, sawtooth oscillations, and locked mode) gathering in Euclidean space composed of multi-dimensional diagnostic data, like soft x-ray emission intensity, edge toroidal rotation velocity, the Mirnov signal amplitude and so on. Based on the cluster analysis results, an approximate analytical model is proposed to rapidly identify plasma events in the J-TEXT plasma. The cluster analysis method is conducive to data markers of massive diagnostic data.
Global modeling of SDG indicators related to small-scale farmers: testing in a changing climate
Authors: Nozaki Noriko , Hosokawa Nanae , Doi Yasuhiro , Kim Wonsik , Iizumi Toshichika
Published: March 2023

Some indicators used to track the progress of the Sustainable Development Goals (SDGs) suffer from a lack of reported data, and therefore need estimates to fill the data gaps. Using crop model outputs and global cropping system datasets, we present a modeling of small-scale farmer productivity and agricultural output (conceptually similar to the formal SDG 2.3.1 and 2.3.2 indicator, respectively). We analyze the responses of the indicators for 106 low- and middle-income countries for the periods 2051–2060 and 2091–2100, relative to 2001–2010, to various scenarios of climate, socioeconomic development, cost-free adaptation, and irrigation expansion. The results show the potentials of modeling in gap-filling of reported national data, and that the agricultural output indicator indicates the positive effect of climate mitigation to small-scale farmers. The contributions of adaptation are evident when agricultural output indicator is used but are no longer visible, or even wrongly interpreted, when productivity indicator is used, underling the importance of selecting robust indicators to track SDG goals in a changing climate. Also discussed are the caveats identified in the SDG 2.3 indicators that enable the design of indicators more aligned with the other development goals, such as poverty eradication.
On the role of local and large-scale atmospheric variability in snow cover duration: a case study of Montevergine Observatory (Southern Italy)
Authors: Annella Clizia , Budillon Giorgio , Capozzi Vincenzo
Published: March 2023

Snow cover plays an important role in Earth’s climate, hydrological and biological systems as well as in socio-economical dynamics, especially in mountain regions. The objective of this work is to provide the first evidence about snow cover variability in the Italian Southern Apennines and investigate the forcing mechanisms controlling it. To this purpose, we present a new historical long-term (from 1931 to 2008) series of snow cover duration data observed at Montevergine Observatory, a mountainous site located at 1280 m above sea level. From the analysis of this series, it emerged a strong interannual variability, an overall reduction over time of snow cover days until mid-1990s and a recovery in the last 10-years. We model snow cover duration employing a multiple linear regression, considering both local and large-scale climate factors as explanatory variables. Our findings show that snow cover duration appears to be primarily dependent on temperature, which exhibits a positive trend in the considered time interval. However, the interannual and decadal fluctuations of the examined parameter are also strongly modulated by two large-scale patterns, the Arctic Oscillation and the Eastern Mediterranean Pattern. In the last segment of the considered time interval, the increase in temperature is not consistent with the dominant patterns of large-scale indices, which proved to be more effective in capturing the recent rebound in snow cover duration. The results demonstrate that snow cover duration is linked to the global warming by a non-trivial relationship and that its behaviour, in specific periods, can be largely independent from rising temperature tendency, according to the prevailing phase of large-scale atmospheric patterns.
Using concentration gradients to examine the effects of Al, Ga and Sn additions on the low-activation VCrMnFe system
Authors: Carruthers A W , Shahmir H , Rigby M , Gandy A S , Pickering E J
Published: March 2023

A critical design criterion for future fusion reactor components is low activation. The equiatomic multi-principal element alloy VCrMnFe is comprised solely of low activation elements and forms a single-phase solid solution at temperatures over 1000 °C. However, at lower temperatures it forms detrimental sigma phase. In this work, compositional gradients of Ga, Sn or Al were induced in VCrMnFe using only a furnace to investigate their effect on intermetallic formation. By examining how the microstructure changed across a region with varying composition, phase stability limits could be assessed. For example, all three elements were found to prevent sigma phase from forming within the alloy when they were present at relatively low concentrations (2–5 at%). Al was found to be the most promising addition (in terms of not causing embrittlement), and the approach used enabled the characterisation of the VCrMnFe–Al pseudo binary phase diagram up to 50 at% Al after heat treatment of 800 °C/240 h followed by ageing at 600 °C/240 h, with numerous ordered phases found using electron diffraction. The level of Al addition required to suppress the sigma phase has been identified more precisely, which will be useful for future alloy development work.
An investigation on machinability of AISI D2 steel during hard milling with multi-resolution analysis of vibration
Authors: Chattopadhyay Arghya , Mandal Nirmal Kumar , Maity Arpan
Published: March 2023

Vibration is a major concern in hard milling process as it adversely affects productivity, surface finish, tool wear, energy consumption, etc. The aim of this paper is to investigate the effects of cutting parameters on acceleration of vibration, acoustic pressure, surface finish, and tool flank wear in face milling of AISI D2 steel. Each cutting parameter was varied in four levels while keeping the maximum value of the other two parameters as constant. Wavelet transform was used to decompose the signals of vibration. Acceleration of vibration has been found to rise with increasing cutting speed in the range of 100 to 180 m min−1. In general, acoustic pressure was found to increase with increasing depth of cut and cutting speed. The results showed that increasing cutting speed leads to reduction in surface roughness while feed rate and cutting depth have opposite effects. It was revealed that while flank wear increases with increasing depth of cut and feed rate, it reduces when cutting speed is raised in the range of 100 to 180 m min−1.
Prediction of the settlement associated with construction on soft clay improved using rigid inclusions considering the installation effect
Authors: Samy Marco , Abdelfattah Ali , Fayed Ayman , Sorour Tamer , Elshawaf Mahmoud
Published: March 2023

One of the most common methods in soil improvement of soft soils is using rigid inclusions (RI) that enhance the stiffness of the soil surrounding and beneath the inclusions. This paper aims to develop simple and user-friendly charts to estimate the settlement improvement factor (N) that correlates the settlement values without soil improvement to the settlement values after improvement, considering the installation effect of the rigid inclusions in soft clay formations. The cavity expansion method is used to model the installation process of the rigid inclusions. A parametric study is carried out using numerical modelling to predict the variation in the improvement factor with the variation of the treated soil stiffness and geometry of the RI system. The analyses are performed using a verified numerical model for a case study of a zone loading test performed at New Mansoura city in Egypt, employing the finite element software (PLAXIS 3D). The cavity expansion approach is first utilized for an axisymmetric model by imposing a prescribed displacement equivalent to the inclusion radius to simulate the construction effect of the rigid inclusion. From the axisymmetric model, the enhancement in the deformation modulus and the over consolidation ratio of the soft clay, resulting from the construction of the rigid inclusions, are determined. In the second stage of the analysis, the improved soil parameters are then implemented in the 3D finite element model, in which the external stresses due to superstructure are applied over the improved soil. The settlement associated with loading both the improved and unimproved soils is then compared for each studied condition in the parametric study to determine the improvement factor (N). The performed analyses clearly showed the high effect of the rigid inclusions in reducing the settlement associated with the construction on the improved soft clay. The achieved improvement factor varies between 2.88 to 58.10, with an average value of about 12.00. Based on the conducted parametric study, design charts are developed to provide a simple tool for predicting the settlement values associated with construction on improved soft clay formations with rigid inclusions under different conditions.
The tubulin structure, a quarter of a century later
Authors: Nogales Eva
Published: March 2023

This retrospective on the 25th anniversary of the publication of the first structure of tubulin is shaped by my own personal experiences rather than being a strict and complete historical account of the event. It is a reflection on how working in science felt many years ago, on the struggles and the joys of reaching for the high-hanging fruit, and, ultimately, on how relevant or not our personal scientific contributions are to the broader scientific community. Writing it brought back memories of my unique and sadly lost postdoctoral advisor Ken Downing, who dreamt of this structure and brought it to fruition against all odds.
Fine-grained selective similarity integration for drug–target interaction prediction
Authors: Liu Bin , Wang Jin , Sun Kaiwei , Tsoumakas Grigorios
Published: March 2023

The discovery of drug–target interactions (DTIs) is a pivotal process in pharmaceutical development. Computational approaches are a promising and efficient alternative to tedious and costly wet-lab experiments for predicting novel DTIs from numerous candidates. Recently, with the availability of abundant heterogeneous biological information from diverse data sources, computational methods have been able to leverage multiple drug and target similarities to boost the performance of DTI prediction. Similarity integration is an effective and flexible strategy to extract crucial information across complementary similarity views, providing a compressed input for any similarity-based DTI prediction model. However, existing similarity integration methods filter and fuse similarities from a global perspective, neglecting the utility of similarity views for each drug and target. In this study, we propose a Fine-Grained Selective similarity integration approach, called FGS, which employs a local interaction consistency-based weight matrix to capture and exploit the importance of similarities at a finer granularity in both similarity selection and combination steps. We evaluate FGS on five DTI prediction datasets under various prediction settings. Experimental results show that our method not only outperforms similarity integration competitors with comparable computational costs, but also achieves better prediction performance than state-of-the-art DTI prediction approaches by collaborating with conventional base models. Furthermore, case studies on the analysis of similarity weights and on the verification of novel predictions confirm the practical ability of FGS.
TEINet: a deep learning framework for prediction of TCR–epitope binding specificity
Authors: Jiang Yuepeng , Huo Miaozhe , Cheng Li Shuai
Published: March 2023

The adaptive immune response to foreign antigens is initiated by T-cell receptor (TCR) recognition on the antigens. Recent experimental advances have enabled the generation of a large amount of TCR data and their cognate antigenic targets, allowing machine learning models to predict the binding specificity of TCRs. In this work, we present TEINet, a deep learning framework that utilizes transfer learning to address this prediction problem. TEINet employs two separately pretrained encoders to transform TCR and epitope sequences into numerical vectors, which are subsequently fed into a fully connected neural network to predict their binding specificities. A major challenge for binding specificity prediction is the lack of a unified approach to sampling negative data. Here, we first assess the current negative sampling approaches comprehensively and suggest that the Unified Epitope is the most suitable one. Subsequently, we compare TEINet with three baseline methods and observe that TEINet achieves an average AUROC of 0.760, which outperforms baseline methods by 6.4–26%. Furthermore, we investigate the impacts of the pretraining step and notice that excessive pretraining may lower its transferability to the final prediction task. Our results and analysis show that TEINet can make an accurate prediction using only the TCR sequence (CDR3$\beta $) and the epitope sequence, providing novel insights to understand the interactions between TCRs and epitopes.
scAnnotate: an automated cell-type annotation tool for single-cell RNA-sequencing data
Authors: Ji Xiangling , Tsao Danielle , Bai Kailun , Tsao Min , Xing Li , Zhang Xuekui
Published: March 2023

Motivation

Single-cell RNA-sequencing (scRNA-seq) technology enables researchers to investigate a genome at the cellular level with unprecedented resolution. An organism consists of a heterogeneous collection of cell types, each of which plays a distinct role in various biological processes. Hence, the first step of scRNA-seq data analysis is often to distinguish cell types so they can be investigated separately. Researchers have recently developed several automated cell-type annotation tools, requiring neither biological knowledge nor subjective human decisions. Dropout is a crucial characteristic of scRNA-seq data widely used in differential expression analysis. However, no current cell annotation method explicitly utilizes dropout information. Fully utilizing dropout information motivated this work.

Results

We present scAnnotate, a cell annotation tool that fully utilizes dropout information. We model every gene’s marginal distribution using a mixture model, which describes both the dropout proportion and the distribution of the non-dropout expression levels. Then, using an ensemble machine learning approach, we combine the mixture models of all genes into a single model for cell-type annotation. This combining approach can avoid estimating numerous parameters in the high-dimensional joint distribution of all genes. Using 14 real scRNA-seq datasets, we demonstrate that scAnnotate is competitive against nine existing annotation methods. Furthermore, because of its distinct modelling strategy, scAnnotate’s misclassified cells differ greatly from competitor methods. This suggests using scAnnotate together with other methods could further improve annotation accuracy.

Availability and implementation

We implemented scAnnotate as an R package and made it publicly available from CRAN: https://cran.r-project.org/package=scAnnotate.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
Decreasing incidence of dialysis in older patients in The Netherlands as compared with other European countries: an international perspective
Authors: van Oevelen Mathijs , Abrahams Alferso C , Hoekstra Tiny , ten Dam Marc A G J , Kramer Anneke , Jager Kitty J , Ocak Gurbey , van Buren Marjolijn , Bos Willem Jan W
Published: March 2023

Introduction

After decades of increasing dialysis incidence, we observed a decreasing trend in the Netherlands in the last decade. We compared this trend with trends in other European countries.

Materials and Methods

Aggregated data for calendar years 2001–2019 from the Dutch registries of kidney replacement therapy patients and the European Renal Association Registry were used. Dialysis incidence in the Netherlands was compared with that in 11 other European countries/regions using three age groups: 20–64, 65–74, and ≥75 years, taking into account pre-emptive kidney transplantation (PKT) incidence. Time trends were assessed as annual percentage change (APC) with 95% confidence intervals (CI) using joinpoint regression analysis.

Results

Between 2001 and 2019 the Dutch dialysis incidence decreased slightly among patients aged 20–64 years (APC −0.9, 95% CI −1.4; −0.5). For patients 65–74 and ≥75 years old, a peak was seen in 2004 and 2009, respectively. Afterwards, the decrease was most marked in patients aged ≥75 years: APC −3.2 (−4.1; −2.3) versus APC −1.8 (−2.2; −1.3) for patients 65–74 years old. PKT incidence increased significantly during the study period but remained limited compared to the observed decrease in dialysis incidence, especially among older patients. Large differences in dialysis incidence were observed among European countries/regions. A decreasing dialysis incidence among older patients was also seen in Austria, Denmark, England/Wales, Finland, Scotland, and Sweden.

Conclusions

The Dutch dialysis incidence decreased most profoundly among older patients. This was also observed in several other European countries/regions. Although PKT incidence increased, it can only explain a minor part of the decrease in dialysis incidence.
A New Fuzzy Smoothing Term Model For Stereo Matching
Authors: Hongjin Zhang , Hui Wei , Bo Wang
Published: March 2023

In this study, we construct a smoothing term structure, which is an essential part of the energy function in binocular matching. However, the existing energy models are mainly deterministic, which cannot adapt to processing low-quality images, especially when there exists a large proportion of vague areas. In order to perform better in processing these low-quality images, in this paper, we construct the smoothing term based on a fuzzy model, which includes fuzzy segmentation, the fuzzy network between the superpixels and the fuzzy relationship between the pixels. These can be compatible with the uncertainty in the image. In addition, to explain the rationality of the calculation of the degree of correlation between superpixels and further elaborate on the property of these degrees between each superpixel, we propose five corresponding theorems with proofs. After we solve the energy model combined with our proposed smoothing term, we compare our disparity results with the corresponding deterministic model and several state-of-the-art algorithms in the experiment. The results verify the effectiveness of the proposed algorithm.
Effectiveness and Safety of Vedolizumab in Inflammatory Bowel Disease: A Comprehensive Meta-analysis of Observational Studies
Authors: Macaluso Fabio Salvatore , Ventimiglia Marco , Orlando Ambrogio
Published: March 2023

Background and Aims

Many observational studies on the use of vedolizumab [VDZ] in patients with Crohn’s disease [CD] and ulcerative colitis [UC] have been published in the past few years. We aimed to comprehensively summarise its effectiveness and safety by pooling data only from observational studies.

Methods

PubMed/Medline and Embase were systematically searched for observational studies on patients with CD and UC treated with VDZ through December 2021. The rates of clinical remission and overall adverse events were the primary outcomes. The rates of steroid-free clinical remission, clinical response, mucosal healing, C-reactive protein normalisation, loss of response, VDZ dose escalation, colectomy, serious adverse events, infections, and malignancies were considered as secondary outcomes.

Results

In all, 88 studies comprising 25 678 patients [13 663 with CD and 12 015 with UC] met the inclusion criteria. In patients with CD, the pooled estimate rates of clinical remission were 36% at induction and 39% at maintenance. In patients with UC, the pooled estimate rates of clinical remission were 40% at induction and 45% at maintenance. The pooled estimate of incidence rate of adverse events was 34.6 per 100 person-years. At multivariable meta-regression analysis, studies with increased male proportion were independently associated with higher rates of clinical remission and steroid-free clinical remission at both induction and maintenance, and clinical response at maintenance in patients with CD. Studies with increased disease duration were independently associated with higher mucosal healing rates at maintenance in patients with UC.

Conclusions

Observational studies demonstrated extensively the effectiveness of VDZ, with a reassuring safety profile.
Commentary: Gender differences in payments to cardiothoracic surgeons are unacceptable
Authors: Jacobs Jeffrey P , Nelson Jennifer S , Fuller Stephanie M , Antonoff Mara B , Karamlou Tara , Molena Daniela , Preventza Ourania , Blackmon Shanda , Romano Jennifer
Published: March 2023

Every effort must be made by the leaders in our field, as well as by every individual cardiothoracic surgeon, to assure equal opportunity for all cardiothoracic surgeons, regardless of race, gender or any other sociodemographic source of bias. Every effort must be made by every surgeon, not just those in particular leadership roles. Opportunities for advancement must be equal in multiple domains, including clinical practice, patient referral, clinical leadership, academic leadership, institutional leadership and leadership in professional medical and surgical societies. Such actions to minimize bias and promote inclusivity will also ensure that cardiothoracic surgical care is provided by a workforce that represents the diversity of patients whom we serve. In the final analysis, it is an absolute fact that gender differences in payments to cardiothoracic surgeons are absolutely unacceptable and cannot be tolerated.
Isolation and molecular identification of nematode surface mutants with resistance to bacterial pathogens
Authors: O’Rourke Delia , Gravato-Nobre Maria J , Stroud Dave , Pritchett Emily , Barker Emily , Price Rebecca L , Robinson Sarah A , Spiro Simon , Kuwabara Patricia , Hodgkin Jonathan
Published: March 2023

Numerous mutants of the nematode Caenorhabditis elegans with surface abnormalities have been isolated by utilizing their resistance to a variety of bacterial pathogens (Microbacterium nematophilum, Yersinia pseudotuberculosis, and 2 Leucobacter strains), all of which are able to cause disease or death when worms are grown on bacterial lawns containing these pathogens. Previous work led to the identification of 9 srf or bus genes; here, we report molecular identification and characterization of a further 10 surface-affecting genes. Three of these were found to encode factors implicated in glycosylation (srf-2, bus-5, and bus-22), like several of those previously reported; srf-2 belongs to the GT92 family of putative galactosyltransferases, and bus-5 is homologous to human dTDP-D-glucose 4,6-dehydratase, which is implicated in Catel–Manzke syndrome. Other genes encoded proteins with sequence similarity to phosphatidylinositol phosphatases (bus-6), Patched-related receptors (ptr-15/bus-13), steroid dehydrogenases (dhs-5/bus-21), or glypiation factors (bus-24). Three genes appeared to be nematode-specific (srf-5, bus-10, and bus-28). Many mutants exhibited cuticle fragility as revealed by bleach and detergent sensitivity; this fragility was correlated with increased drug sensitivity, as well as with abnormal skiddy locomotion. Most of the genes examined were found to be expressed in epidermal seam cells, which appear to be important for synthesizing nematode surface coat. The results reveal the genetic and biochemical complexity of this critical surface layer, and provide new tools for its analysis.
Seascape Genomics and Phylogeography of the Sailfish (Istiophorus platypterus)
Authors: Ferrette Bruno Lopes da Silva , Coimbra Raphael T F , Winter Sven , De Jong Menno J , Williams Samuel Mackey , Coelho Rui , Rosa Daniela , Rotundo Matheus Marcos , Arocha Freddy , Mourato Bruno Leite , Mendonça Fernando Fernandes , Janke Axel
Published: March 2023

Permeable phylogeographic barriers characterize the vast open ocean, boosting gene flow and counteracting population differentiation and speciation of widely distributed and migratory species. However, many widely distributed species consists of distinct populations throughout their distribution, evidencing that our understanding of how the marine environment triggers population and species divergence are insufficient. The sailfish is a circumtropical and highly migratory billfish that inhabits warm and productive areas. Despite its ecological and socioeconomic importance as a predator and fishery resource, the species is threatened by overfishing, requiring innovative approaches to improve their management and conservation status. Thus, we presented a novel high-quality reference genome for the species and applied a seascape genomics approach to understand how marine environmental features may promote local adaptation and how it affects gene flow between populations. We delimit two populations between the Atlantic and Indo-Western Pacific oceans and detect outlier loci correlated with sea surface temperature, salinity, oxygen, and chlorophyll concentrations. However, the most significant explanatory factor that explains the differences between populations was isolation by distance. Despite recent population drops, the sailfish populations are not inbred. For billfishes in general, genome-wide heterozygosity was found to be relatively low compared to other marine fishes, evidencing the need to counteract overfishing effects. In addition, in a climate change scenario, management agencies must implement state-of-the-art sequencing methods, consider our findings in their management plans, and monitor genome-wide heterozygosity over time to improve sustainable fisheries and the long-term viability of its populations.
The Effect of Developmental Pleiotropy on the Evolution of Insect Immune Genes
Authors: Williams Alissa M , Ngo Thi Minh , Figueroa Veronica E , Tate Ann T
Published: March 2023

The pressure to survive ever-changing pathogen exposure explains the frequent observation that immune genes are among the fastest evolving in the genomes of many taxa, but an intriguing proportion of immune genes also appear to be under purifying selection. Though variance in evolutionary signatures of immune genes is often attributed to differences in gene-specific interactions with microbes, this explanation neglects the possibility that immune genes participate in other biological processes that could pleiotropically constrain adaptive selection. In this study, we analyzed available transcriptomic and genomic data from Drosophila melanogaster and related species to test the hypothesis that there is substantial pleiotropic overlap in the developmental and immunological functions of genes involved in immune signaling and that pleiotropy would be associated with stronger signatures of evolutionary constraint. Our results suggest that pleiotropic immune genes do evolve more slowly than those having no known developmental functions and that signatures of constraint are particularly strong for pleiotropic immune genes that are broadly expressed across life stages. These results support the general yet untested hypothesis that pleiotropy can constrain immune system evolution, raising new fundamental questions about the benefits of maintaining pleiotropy in systems that need to rapidly adapt to changing pathogen pressures.
Distinct Wolbachia localization patterns in oocytes of diverse host species reveal multiple strategies of maternal transmission
Authors: Radousky Yonah A , Hague Michael T J , Fowler Sommer , Paneru Eliza , Codina Adan , Rugamas Cecilia , Hartzog Grant , Cooper Brandon S , Sullivan William
Published: March 2023

A broad array of endosymbionts radiate through host populations via vertical transmission, yet much remains unknown concerning the cellular basis, diversity, and routes underlying this transmission strategy. Here, we address these issues, by examining the cellular distributions of Wolbachia strains that diverged up to 50 million years ago in the oocytes of 18 divergent Drosophila species. This analysis revealed 3 Wolbachia distribution patterns: (1) a tight clustering at the posterior pole plasm (the site of germline formation); (2) a concentration at the posterior pole plasm, but with a significant bacteria population distributed throughout the oocyte; and (3) a distribution throughout the oocyte, with none or very few located at the posterior pole plasm. Examination of this latter class indicates Wolbachia accesses the posterior pole plasm during the interval between late oogenesis and the blastoderm formation. We also find that 1 Wolbachia strain in this class concentrates in the posterior somatic follicle cells that encompass the pole plasm of the developing oocyte. In contrast, strains in which Wolbachia concentrate at the posterior pole plasm generally exhibit no or few Wolbachia in the follicle cells associated with the pole plasm. Taken together, these studies suggest that for some Drosophila species, Wolbachia invade the germline from neighboring somatic follicle cells. Phylogenomic analysis indicates that closely related Wolbachia strains tend to exhibit similar patterns of posterior localization, suggesting that specific localization strategies are a function of Wolbachia-associated factors. Previous studies revealed that endosymbionts rely on 1 of 2 distinct routes of vertical transmission: continuous maintenance in the germline (germline-to-germline) or a more circuitous route via the soma (germline-to-soma-to-germline). Here, we provide compelling evidence that Wolbachia strains infecting Drosophila species maintain the diverse arrays of cellular mechanisms necessary for both of these distinct transmission routes. This characteristic may account for its ability to infect and spread globally through a vast range of host insect species.
The proposed role of MSL-lncRNAs in causing sex lability of female poplars
Authors: Mao Jinyan , Wei Suyun , Chen Yingnan , Yang Yonghua , Yin Tongming
Published: March 2023

Labile sex expression is frequently observed in dioecious plants, but the underlying genetic mechanism remains largely unknown. Sex plasticity is also observed in many Populus species. Here we carried out a systematic study on a maleness-promoting gene, MSL, detected in the Populus deltoides genome. Our results showed that both strands of MSL contained multiple cis-activating elements, which generated long non-coding RNAs (lncRNAs) promoting maleness. Although female P. deltoides did not have the male-specific MSL gene, a large number of partial sequences with high sequence similarity to this gene were detected in the female poplar genome. Based on sequence alignment, the MSL sequence could be divided into three partial sequences, and heterologous expression of these partial sequences in Arabidopsis confirmed that they could promote maleness. Since activation of the MSL sequences can only result in female sex lability, we propose that MSL-lncRNAs might play a role in causing sex lability of female poplars.
AGO2a but not AGO2b mediates antiviral defense against infection of wild-type cucumber mosaic virus in tomato
Authors: Zhao Liling , Chen Yingfang , Xiao Xingming , Gao Haiying , Cao Jiamin , Zhang Zhongkai , Guo Zhongxin
Published: March 2023

Evolutionarily conserved antiviral RNA interference (RNAi) mediates a primary antiviral innate immunity preventing infection of broad-spectrum viruses in plants. However, the detailed mechanism in plants is still largely unknown, especially in important agricultural crops, including tomato. Varieties of pathogenic viruses evolve to possess viral suppressors of RNA silencing (VSRs) to suppress antiviral RNAi in the host. Due to the prevalence of VSRs, it is still unknown whether antiviral RNAi truly functions to prevent invasion by natural wild-type viruses in plants and animals. In this research, for the first time we applied CRISPR-Cas9 to generate ago2a, ago2b, or ago2ab mutants for two differentiated Solanum lycopersicum AGO2s, key effectors in antiviral RNAi. We found that AGO2a but not AGO2b was significantly induced to inhibit the propagation of not only VSR-deficient Cucumber mosaic virus (CMV) but also wild-type CMV-Fny in tomato; however, neither AGO2a nor AGO2b regulated disease induction after infection with either virus. Our findings firstly reveal a prominent role of AGO2a in antiviral RNAi innate immunity in tomato and demonstrate that antiviral RNAi evolves to defend against infection of natural wild-type CMV-Fny in tomato. However, AGO2a-mediated antiviral RNAi does not play major roles in promoting tolerance of tomato plants to CMV infection for maintaining health.
Post-traumatic stress disorder among COVID-19-affected high-risk cardiac patients
Authors: Wesemann Ulrich , Sahebi Ali , Vogel Julia , Köhler Kai , Kupusovic Jana , Rassaf Tienush , Siebermair Johannes
Published: March 2023

Background

During the first coronavirus disease 2019 (COVID-19) wave there was a high prevalence of mental health impairments and post-traumatic stress disorder (PTSD), particularly in patients with comorbid cardiac diseases.

Methods

During waves 2–5, all hospitalized patients with cardiac problems and suspected COVID-19 were eligible to participate in this study.

Results

The prevalence of PTSD was 31.4% (n=48) in 153 participants. No age- and gender-related differences for PTSD were found.

Conclusions

The prevalence is lower than during the first wave but higher than in patients reported in other studies who were isolated at home. Routine mental health assessments are strongly recommended for patients at risk.
Adverse birth outcomes of adolescent and young adult women diagnosed with cancer during pregnancy
Authors: Betts Andrea C , Shay L Aubree , Lupo Philip J , Pruitt Sandi L , Roth Michael E , Allicock Marlyn A , Cohn Barbara A , Murphy Caitlin C
Published: March 2023

Background

We examined adverse birth outcomes among adolescent and young adult women diagnosed with cancer (AYA women, ages 15-39 years) during pregnancy.

Methods

We linked data from the Texas Cancer Registry, vital records, and Texas Birth Defects Registry to identify all singleton births to AYA women diagnosed during pregnancy from January 1999 to December 2016. We compared prevalence of adverse live birth outcomes between AYA women and women without cancer (matched 1:4 on age, race and ethnicity, and year). Among AYA women, we used log-binomial regression to identify factors associated with these outcomes. Statistical tests were 2-sided.

Results

AYA women had 1271 singleton live births and 20 stillbirths. AYA women (n = 1291) were 33.3% Hispanic and 9.8% non-Hispanic Black and most commonly had breast (22.5%), thyroid (19.8%), and gynecologic (13.3%) cancers. Among live births, AYA women had a higher prevalence of low birth weight offspring (30.1% vs 9.0%), very preterm (5.7% vs 1.2%), and preterm birth (25.1% vs 7.2%); cesarean delivery (44.3% vs 35.2%); and low Apgar score (2.7% vs 1.5%), compared with women without cancer (n = 5084) (all P < .05). Prevalence of any birth defect by age 12 months did not statistically differ (5.2% vs 4.7%; P = .48), but live births to AYA women more often had heart and circulatory system defects (2.2% vs 1.3%; P = .01). In adjusted models, cancer type and chemotherapy were associated with adverse live birth outcomes.

Conclusions

AYA women diagnosed during pregnancy have higher prevalence of adverse birth outcomes and face difficult decisions in balancing treatment risks and benefits.
Phosphoglucomutase comes into the spotlight
Authors: Doello Sofía , Forchhammer Karl
Published: March 2023

This article comments on:

Ortega-Martínez P, Roldán M, Díaz-Troya S, Florencio FJ. 2023. Stress response requires an efficient glycogen and central carbon metabolism connection by phosphoglucomutases in cyanobacteria. Journal of Experimental Botany 74, 1532–1550
CRISPR/Cas9 and Agrobacterium tumefaciens virulence proteins synergistically increase efficiency of precise genome editing via homology directed repair in plants
Authors: Tang Ye , Zhang Zhennan , Yang Zhiyuan , Wu Jiahe
Published: March 2023

CRISPR/Cas9 genome editing and Agrobacterium tumefaciens-mediated genetic transformation are widely-used plant biotechnology tools derived from bacterial immunity-related systems, each involving DNA modification. The Cas9 endonuclease introduces DNA double-strand breaks (DSBs), and the A. tumefaciens T-DNA is released by the VirD2 endonuclease assisted by VirDl and attached by VirE2, transferred to the plant nucleus and integrated into the genome. Here, we explored the potential for synergy between the two systems and found that Cas9 and three virulence (Vir) proteins achieve precise genome editing via the homology directed repair (HDR) pathway in tobacco and rice plants. Compared with Cas9T (Cas9, VirD1, VirE2) and CvD (Cas9-VirD2) systems, the HDR frequencies of a foreign GFPm gene in the CvDT system (Cas9-VirD2, VirD1, VirE2) increased 52-fold and 22-fold, respectively. Further optimization of the CvDT process with a donor linker (CvDTL) achieved a remarkable increase in the efficiency of HDR-mediated genome editing. Additionally, the HDR efficiency of the three rice endogenous genes ACETOLACTATE SYNTHASE (ALS), PHYTOENE DESATURASE (PDS), and NITROGEN TRANSPORTER 1.1 B (NRT1.1B) increased 24-, 32- and 16-fold, respectively, in the CvDTL system, compared with corresponding Cas9TL (Cas9T process with a donor linker). Our results suggest that collaboration between CRISPR/Cas9 and Agrobacterium-mediated genetic transformation can make great progress towards highly efficient and precise genome editing via the HDR pathway.
Intellectual property protection for traditional medical knowledge in China’s context: a round peg in a square hole?
Authors: Xia Nan
Published: March 2023

This article is an examination of the extent to which traditional medical knowledge in China can be protected by intellectual property laws. The analysis begins by providing a global picture with regard to the historic origin of intellectual property, exploring the reasons why China does not have indigenous counterparts to the western system of intellectual property rights protecting its traditional knowledge (including traditional medical knowledge) and stating the problems of transplanting western intellectual property standards in China. A discussion follows on how China, under foreign pressure, has made efforts to comply with the changing standards mandated by various international, regional, and bilateral arrangements related to intellectual property, with examples of the development of China’s patent law. China’s approach towards the protection of traditional medical knowledge in various international fora related to intellectual property is explored. Finally, there is a specific examination of the compatibilities between the western system of intellectual property rights and traditional medical knowledge in China, at the national and community levels. This article argues that the system of intellectual property rights does not easily fit with China’s traditional medical knowledge because of China’s unique cultural traits, distinctive historical context and wide ethnic, religious, and local community diversity.
Study of the radial dependence of Forbush decreases at 0.28–1 au using data from the Helios 1 and 2 spacecraft
Authors: Belov Anatoly , Shlyk Nataly , Abunina Maria , Abunin Artem , Papaioannou Athanasios , Richardson Ian G , Lario David
Published: March 2023

We identify and investigate cosmic ray Forbush decreases (FDs) observed in the E > 50 MeV data from the Helios 1 and 2 spacecraft, spanning from 1974–1985 and covering heliocentric distances in the range 0.28–1 au. A Helios FD catalogue is compiled, including the characteristics of the cosmic ray variations, as well as those of the solar wind (SW) and the interplanetary magnetic field (IMF) of the associated interplanetary disturbances. An extended statistical study considers the radial dependence of the FD magnitude, the SW velocity, and the IMF intensity in these disturbances. It is found that the Helios FD sizes at different distances from the Sun are determined by the parameters of the interplanetary disturbances. In particular, the FD magnitudes observed at Helios, as well as near Earth, correlate well with VB, which is the product of the maximum SW velocity and the IMF intensity when normalized by the average values of these parameters at the radial distance of the observations. However, we found that, on average, the Helios FD sizes are statistically independent of the radial distance in the range of 0.28–1 au.
Testosterone Coordinates Gene Expression Across Different Tissues to Produce Carotenoid-Based Red Ornamentation
Authors: Khalil Sarah , Enbody Erik D , Frankl-Vilches Carolina , Welklin Joseph F , Koch Rebecca E , Toomey Matthew B , Sin Simon Yung Wa , Edwards Scott V , Gahr Manfred , Schwabl Hubert , Webster Michael S , Karubian Jordan
Published: March 2023

Carotenoid pigments underlie most of the red, orange, and yellow visual signals used in mate choice in vertebrates. However, many of the underlying processes surrounding the production of carotenoid-based traits remain unclear due to the complex nature of carotenoid uptake, metabolism, and deposition across tissues. Here, we leverage the ability to experimentally induce the production of a carotenoid-based red plumage patch in the red-backed fairywren (Malurus melanocephalus), a songbird in which red plumage is an important male sexual signal. We experimentally elevated testosterone in unornamented males lacking red plumage to induce the production of ornamentation and compared gene expression in both the liver and feather follicles between unornamented control males, testosterone-implanted males, and naturally ornamented males. We show that testosterone upregulates the expression of CYP2J19, a gene known to be involved in ketocarotenoid metabolism, and a putative carotenoid processing gene (ELOVL6) in the liver, and also regulates the expression of putative carotenoid transporter genes in red feather follicles on the back, including ABCG1. In black feathers, carotenoid-related genes are downregulated and melanin genes upregulated, but we find that carotenoids are still present in the feathers. This may be due to the activity of the carotenoid-cleaving enzyme BCO2 in black feathers. Our study provides a first working model of a pathway for carotenoid-based trait production in free-living birds, implicates testosterone as a key regulator of carotenoid-associated gene expression, and suggests hormones may coordinate the many processes that underlie the production of these traits across multiple tissues.