bluuebunny/crossref_metadata_2025 huggingface dataset:
The political economy of vaccine distribution and China's Belt and Road Initiative
Authors: Vadlamannati Krishna Chaitanya , Jung Yoo Sun
Published: February 2023

To what extent do national strategic interests influence countries’ distribution of health assistance during a global health crisis? We examine China's global COVID-19 vaccine allocation, focusing on the relationship between its vaccine prioritization and its geopolitical expansion through the Belt and Road Initiative (BRI). We claim China uses its vaccine diplomacy as a comprehensive tool to promote its grand strategy and expand its global leadership and influence. Employing a newly available dataset on Chinese COVID-19 vaccine deliveries for a cross-section of 108 BRI member countries, our study shows that countries with foreign direct investment flows into BRI projects have received more vaccines from China. Our findings confirm that donor strategic concerns affect bilateral foreign assistance. Our results remain robust to several robustness checks, including endogeneity concerns.
Development and validation of a quantitative food frequency questionnaire to assess free sugar intake among Sri Lankan preschool children
Authors: Mututanthri Shanika , Thoradeniya Tharanga , Harris Rebecca
Published: February 2023

The present study aims to develop a quantitative food frequency questionnaire (FFQ) to assess free sugar intake as a whole and at the food group levels, retrospectively, over the past 3 months among 4 to 5-year-old preschool children in the Colombo district, Sri Lanka. Then, to assess its reliability and relative validity. In the development phase, three 24-hour dietary recalls (24 hDRs) of 518 preschool children were collected from caregivers. Based on that, a 67-item FFQ was developed, including commonly consumed free sugar-containing food items. The validation study was conducted among another 108 preschool children. The relative validity of the FFQ was assessed by comparing it with the 24 hDRs. The test–retest reliability was assessed by repeated application of the FFQ to the same population after 6 weeks. Wilcoxon sign rank test, cross-classification with weighted Kappa statistic, Spearman rank correlation and Bland–Altman plots were used for comparison. Comparing the free sugar intake calculated by the two methods showed no difference (P = 0⋅13), a good correlation (0⋅89), good agreement in cross-classifying participants (78⋅4 % correctly classified) and a good agreement in Bland–Altman plots. Repeated application of the FFQ yielded; no differences in free sugar intake values (P = 0⋅45) a good correlation (0⋅71), acceptable agreement in cross-classifying participants (52⋅3 % correctly classified) and acceptable agreement in the Bland–Altman plot. Results were the same for all food groups. According to the results, the newly developed quantitative FFQ provides a relatively valid and reliable measure for quantifying free sugar intake among preschool children as a whole or by food group.
Random effects in dynamic network actor models
Authors: Uzaheta Alvaro , Amati Viviana , Stadtfeld Christoph
Published: February 2023

Dynamic Network Actor Models (DyNAMs) assume that an observed sequence of relational events is the outcome of an actor-oriented decision process consisting of two decision levels. The first level represents the time until an actor initiates the next relational event, modeled by an exponential distribution with an actor-specific activity rate. The second level describes the choice of the receiver of the event, modeled by a conditional multinomial logit model. The DyNAM assumes that the parameters are constant over the actors and the context. This homogeneity assumption, albeit statistically and computationally convenient, is difficult to justify, e.g., in the presence of unobserved differences between actors or contexts. In this paper, we extend DyNAMs by including random-effects parameters that vary across actors or contexts and allow controlling for unknown sources of heterogeneity. We illustrate the model by analyzing relational events among the users of an online community of aspiring and professional digital and graphic designers.
How technological change affects regional voting patterns
Authors: Schöll Nikolas , Kurer Thomas
Published: February 2023

Does technological change fuel political disruption? Drawing on fine-grained labor market data from Germany, this paper examines how technological change affects regional electorates. We first show that the well-known decline in manufacturing and routine jobs in regions with higher robot adoption or investment in information and communication technology (ICT) was more than compensated by parallel employment growth in the service sector and cognitive non-routine occupations. This change in the regional composition of the workforce has important political implications: Workers trained for these new sectors typically hold progressive political values and support progressive pro-system parties. Overall, this composition effect dominates the politically perilous direct effect of automation-induced substitution. As a result, technology-adopting regions are unlikely to turn into populist-authoritarian strongholds.
Urinary iodine excretion and optimal time point for sampling when estimating 24-h urinary iodine
Authors: Eriksson Janna , Barregard Lars , Sallsten Gerd , Berlinger Balazs , Weinbruch Stephan , Manousou Sofia , Ellingsen Dag G. , Nyström Helena Filipsson
Published: February 2023

Iodine deficiency may cause thyroid dysfunction. The iodine intake in a population is measured by urinary iodine concentration (UIC) in spot samples or 24-h urinary iodine excretion (24UIE). 24UIE is considered the gold standard and may be estimated using an equation including UIC, urinary creatinine concentration, sex and age (e24UIE). The aims of this study were to evaluate the preferable timing of UIC when using this equation and assess the variability of UIE. Sixty healthy non-smoking women (n 31) and men (n 29) were included in Gothenburg, Sweden. Twelve urine samples were collected at six fixed times on two separate days. Variability was calculated for UIC, 24UIE, e24UIE, iodine excretion per hour (iHr) and UIC adjusted for creatinine and specific gravity. Median 24UIE was 156 µg/24 h and the median UIC (all spot samples) was 104 µg/l. UIC (P < 0·001), 24UIE (P = 0·001) and e24UIE (P < 0·001) were significantly higher in men. e24UIE was relatively similar to 24UIE. However, when e24UIE was calculated from UIC in the first void, it was about 15 % lower than 24UIE (P < 0·001). iHr was lowest in the morning and highest in the afternoon. Median iHr was higher in men (7·4 v. 5·3 µg/h, P < 0·001). The variability of UIE was higher within individuals than between individuals. This study suggests that most time points for estimation of individual 24UIE are appropriate, but they should preferably not be collected in the first void.
The Electoral Politics of Alberta's Sovereignty Act
Authors: Sayers Anthony M. , McMahon Nicole , Koop Royce
Published: February 2023

The Alberta Sovereignty within a United Canada Act is a strategic wedge aimed at raising the salience of western alienation, an issue on which the United Conservative Party and its leader, Danielle Smith, believe they can dominate their opponents and so win the May 2023 provincial election. The act signals the unprecedented circumstances in which the governing party finds itself. It is running neck-and-neck with a formidable opponent and a party leader who previously held the office of premier. Alberta has never experienced such an election.
Data augmentation by separating identity and emotion representations for emotional gait recognition
Authors: Sheng Weijie , Lu Xiaoyan , Li Xinde
Published: February 2023

Human-centered intelligent human–robot interaction can transcend the traditional keyboard and mouse and have the capacity to understand human communicative intentions by actively mining implicit human clues (e.g., identity information and emotional information) to meet individuals’ needs. Gait is a unique biometric feature that can provide reliable information to recognize emotions even when viewed from a distance. However, the insufficient amount and diversity of training data annotated with emotions severely hinder the application of gait emotion recognition. In this paper, we propose an adversarial learning framework for emotional gait dataset augmentation, with which a two-stage model can be trained to generate a number of synthetic emotional samples by separating identity and emotion representations from gait trajectories. To our knowledge, this is the first work to realize the mutual transformation between natural gait and emotional gait. Experimental results reveal that the synthetic gait samples generated by the proposed networks are rich in emotional information. As a result, the emotion classifier trained on the augmented dataset is competitive with state-of-the-art gait emotion recognition works.
The longitudinal interplay between insecure attachment behaviors and psychosocial strengths among children in child welfare services
Authors: Smith Jackson A. , Durham Duane , Price-Cameron Mary , Sloss Imogen , Browne Dillon T.
Published: February 2023

Children who have experienced maltreatment are more likely to have disrupted attachments, fewer psychosocial strengths, and poorer long-term psychosocial outcomes. However, few studies have examined the interplay between attachment security and psychosocial strengths among children involved in therapeutic services in the context of the child welfare system. The present longitudinal study examines the insecure attachment behaviors and psychosocial strengths of 555 children referred to the Therapeutic Family Care program (TFCP) in Cobourg, Ontario between 2000 and 2019. The children were assessed by their caregivers on a regular basis using the Assessment Checklist for Children (ACC) and the complementary strengths-focused ACC+ measure. Average age of children at baseline was 9.57 years (SD = 3.51) and 229 (41.26%) were female. We conducted growth curve and random intercepts cross-lagged panel models to test the longitudinal interplay between insecure attachment behaviors and strengths. Results suggest that females’ attachment security improved, males’ attachment security worsened, and both males and females developed strengths over time. Further, analyses revealed a directional effect, whereby fewer insecure attachment behaviors predicted more psychosocial strengths approximately 6 months later. Implications for attachment-oriented and strengths-based services in the context of child welfare are discussed.
Distribution and habitat requirements of the Bahama Warbler Setophaga flavescens on Grand Bahama in 2018
Authors: Pereira David J. , Gardner Matthew A. , Geary Matthew , Bell Diana J. , Collar Nigel J.
Published: February 2023

The Bahama Warbler Setophaga flavescens is restricted to Grand Bahama and Abaco in the Bahamas Islands, where in recent decades its pine forest habitat has been seriously affected by hurricanes. To assess its conservation status and determine its habitat requirements, we conducted point transects with playback and simultaneously took measurements at 464 locations in pine forest across Grand Bahama from April to June 2018. Warbler presence was predicted by taller Thatch Palms Thrinax radiata and some fire disturbance, and its absence by a higher number of needleless pines. A comparison of these habitat predictors between the combined regions where warblers were detected (Lucayan Estates and East End) vs. where they were not (West End and Freeport) also revealed that Bahama Warblers showed a marked preference for taller Thatch Palms (>140 cm) and habitat plots within the middle fire disturbance category. These findings suggest that the species is adapted to a climax pine forest habitat maintained under a standard fire regime. Our research was intended to provide a first baseline study of the warbler’s distribution and ecology on Grand Bahama, but the distribution may have radically changed following Hurricane Dorian’s devastation of the island in 2019, and the species may now only survive on Abaco. Nevertheless, ecological insights from Grand Bahama seem likely to help conservation management on Abaco, but both islands now need to be surveyed.
How to do human evaluation: A brief introduction to user studies in NLP
Authors: Schuff Hendrik , Vanderlyn Lindsey , Adel Heike , Vu Ngoc Thang
Published: February 2023

Many research topics in natural language processing (NLP), such as explanation generation, dialog modeling, or machine translation, require evaluation that goes beyond standard metrics like accuracy or F1score toward a more human-centered approach. Therefore, understanding how to design user studies becomes increasingly important. However, few comprehensive resources exist on planning, conducting, and evaluating user studies for NLP, making it hard to get started for researchers without prior experience in the field of human evaluation. In this paper, we summarize the most important aspects of user studies and their design and evaluation, providing direct links to NLP tasks and NLP-specific challenges where appropriate. We (i) outline general study design, ethical considerations, and factors to consider for crowdsourcing, (ii) discuss the particularities of user studies in NLP, and provide starting points to select questionnaires, experimental designs, and evaluation methods that are tailored to the specific NLP tasks. Additionally, we offer examples with accompanying statistical evaluation code, to bridge the gap between theoretical guidelines and practical applications.
Ethnicity as a predictor of outcomes of psychological therapies for anxiety and depression: a retrospective cohort analysis
Authors: Amati Federica , Green John , Kitchin Lauren , Watt Hilary , Jones Sophie , AlRubaye Noor , McCann Lucy , Greenfield Geva
Published: February 2023

Background:

Studies on predictors of outcomes of treatment for common mental health disorders (CMDs) in community mental health settings are scarce, and sample sizes are often small. Research on the impact of identifying as a member of an ethnic minority group on treatment outcomes is limited.

Aims:

To ascertain whether ethnicity is an independent predictor of outcome and the extent to which any association is mediated by other sociodemographic factors.

Method:

Retrospective observational study of anonymised treatment data collected for routine clinical purposes. Data were analysed from nine Improving Access to Psychological Therapy (IAPT) services from 2009 to 2016. Social functioning, ethnic group, age, gender, occupation and baseline severity of the mental health disorder were analysed as predictors of outcome.

Results:

Outcomes varied with ethnic group. Levels of occupation, social deprivation, initial morbidity and social functioning varied between ethnic groups at baseline. After adjustment for these factors the impact of ethnicity was attenuated and only some ethnic groups remained as significant independent predictors of treatment outcome.

Conclusions:

Ethnic minority status is a marker for multiple disadvantages. Some of the differences in outcome seen between ethnic groups may be the result of more general factors present in all ethnic groups but at greater intensity in some ethnic minority groups.
Three ways to change your mind: an epistemic framework for cognitive interventions
Authors: Moorey Stirling
Published: February 2023

Belief change is an important element of much CBT, yet very little consideration has been given to the theories of knowledge, the epistemology, which underlie this process. This article argues that understanding the epistemic basis of the techniques therapists use can help guide their choice of interventions. The empirical evidence for cognitive restructuring is considered, the importance of distancing and decentring noted, and three epistemic styles are identified: the rational-empiricist, pragmatist and ‘constructivist’ approaches. Different schools of CBT emphasise one or more of these. The article describes how these epistemes can be used to make decisions about which cognitive interventions to use, particularly when clients may be sceptical about reality testing because of entrenched beliefs or real-life adversity.
Can foreign aid improve the donor country's image among a third-party country's public? The case of a world heritage site restoration project
Authors: Kim Eunji , Lim Sijeong
Published: February 2023

This study explores whether and under what conditions foreign aid can help improve the donor country's image in countries that did not receive aid. We identified a world heritage site restoration project, which is visible, localized, has no political strings attached, and deals with global public good, as a most-likely type of foreign aid that can generate this positive effect. In light of the literature suggesting that tensions with the target country undermine public diplomacy effectiveness, we expect the positive effect will be more pronounced in non-recipient countries with which the donor country has a more amicable relationship. To empirically investigate our argument, we field a survey experiment in a developed non-aid-recipient country, Australia. We provide information to the Australian public about an aid project to restore the Angkor Monument in Cambodia conducted either by China or South Korea. We find that information on Korea's aid to Cambodia improves the image of Korea and the willingness to cooperate with the Korean government among Australians. No such effect, however, is observed in the case of similar aid by China whose relations with Australia have been strained in multiple domains. Our findings have policy implications for donor countries seeking to utilize the soft power element of foreign aid as a public diplomacy tool.
Adaptation Strategy Can Ensure Seed and Food Production With Improving Water and Nitrogen Use Efficiency Under Climate Change
Authors: Chen Shichao , Liu Wenfeng , Yan Zongzheng , Morel Julien , Parsons David , Du Taisheng
Published: February 2023

Adaptation strategies can reduce the negative impacts of climate change on food security. As an important part of food security, more attention should be paid to seed security, as it determines the crop planting area and ultimately affects food production, especially in major seed production locations, such as the Hexi Corridor in China. This region is an important production base of grain (including field maize and wheat) and maize seed, but the shortage of water resources and low use efficiency of water and nitrogen (N) seriously constrain the sustainable development of agriculture. Formulating an adaptation strategy to balance the seed and food production and resource use efficiency is an important way to maintain regional as well as national food production. We established an optimization‐simulation framework, which consists of a novel crop production function and a grid‐based crop model, APSIM. This framework was used to optimize agricultural management and evaluate its performance considering the spatio‐temporal variability of climate and soil properties, actual crop water consumption and N uptake during each growth stage, and interactive sensitivity coefficients of water and N at different growth stages under climate change. We show that the proposed adaptation strategy could save 0.31 km³ of irrigation water and 22 thousand tonnes of N fertilizer, and increase seed and food production by 33 thousand tonnes, compared with traditional practices. Significant increases in irrigation water productivity and N use efficiency can be expected by using the adaptation supporting the sustainable development of agriculture.
Increased dendritic cell density and altered morphology in allergic conjunctivitis
Authors: Tajbakhsh Zahra , Golebiowski Blanka , Stapleton Fiona , Alghamdi Ali , Gray Paul E. , Altavilla Betina , Briggs Nancy , Jalbert Isabelle
Published: February 2023

Background

Corneal and conjunctival epithelial dendritic cells (DC) have an established role in vernal keratoconjunctivitis, however, their role in more prevalent forms of allergic eye disease remains unclear. This study evaluated corneal and conjunctival epithelial DC density, morphology, and distribution observed using in vivo confocal microscopy (IVCM) in allergic conjunctivitis.

Methods

In this prospective, observational study, 66 participants (mean age 36.6 ± 12.0 years, 56% female): 33 with allergic conjunctivitis and 33 controls were recruited. IVCM was performed at the corneal centre, inferior whorl, corneal periphery, corneal limbus, and temporal bulbar conjunctiva. DC were counted and their morphology was assessed as follows: largest cell body size, presence of dendrites, and presence of long and thick dendrites. Mixed model analysis (DC density) and non-parametric tests (DC morphology) were used.

Results

DC density was higher in allergic participants at all locations (p ≤ 0.01), (corneal centre median (IQR) 21.9 (8.7–50.9) cells/mm2 vs 13.1 (2.8–22.8) cells/mm2; periphery 37.5 (15.6-67.2) cells/mm2 vs 20 (9.4–32.5) cells/mm2; limbus 75 (60-120) cells/mm2 vs 58.1 (44.4–66.2) cells/mm2; conjunctiva 10 (0–54.4) cells/mm2 vs 0.6 (0–5.6) cells/mm2, but not at the inferior whorl 21.9 (6.2–34.4) cells/mm2 vs 12.5 (1.9–37.5) cells/mm2, p = 0.20. At the corneal centre, allergic participants had larger DC bodies (p = 0.02), a higher proportion of DC with dendrites (p = 0.02) and long dendrites (p = 0.003) compared to controls.

Conclusions

Corneal and conjunctival DC density was increased, and morphology altered in allergic conjunctivitis. These findings imply that the ocular surface immune response was upregulated and support an increased antigen-capture capacity of DC in allergic conjunctivitis.
Newly identified sex chromosomes in the Sphagnum (peat moss) genome alter carbon sequestration and ecosystem dynamics
Authors: Healey Adam L. , Piatkowski Bryan , Lovell John T. , Sreedasyam Avinash , Carey Sarah B. , Mamidi Sujan , Shu Shengqiang , Plott Chris , Jenkins Jerry , Lawrence Travis , Aguero Blanka , Carrell Alyssa A. , Nieto-Lugilde Marta , Talag Jayson , Duffy Aaron , Jawdy Sara , Carter Kelsey R. , Boston Lori-Beth , Jones Teresa , Jaramillo-Chico Juan , Harkess Alex , Barry Kerrie , Keymanesh Keykhosrow , Bauer Diane , Grimwood Jane , Gunter Lee , Schmutz Jeremy , Weston David J. , Shaw A. Jonathan
Published: February 2023

Peatlands are crucial sinks for atmospheric carbon but are critically threatened due to warming climates. Sphagnum (peat moss) species are keystone members of peatland communities where they actively engineer hyperacidic conditions, which improves their competitive advantage and accelerates ecosystem-level carbon sequestration. To dissect the molecular and physiological sources of this unique biology, we generated chromosome-scale genomes of two Sphagnum species: S. divinum and S. angustifolium. Sphagnum genomes show no gene colinearity with any other reference genome to date, demonstrating that Sphagnum represents an unsampled lineage of land plant evolution. The genomes also revealed an average recombination rate an order of magnitude higher than vascular land plants and short putative U/V sex chromosomes. These newly described sex chromosomes interact with autosomal loci that significantly impact growth across diverse pH conditions. This discovery demonstrates that the ability of Sphagnum to sequester carbon in acidic peat bogs is mediated by interactions between sex, autosomes and environment.
Interpretable machine learning for maximum corrosion depth and influence factor analysis
Authors: Song Yuhui , Wang Qinying , Zhang Xingshou , Dong Lijin , Bai Shulin , Zeng Dezhi , Zhang Zhi , Zhang Huali , Xi Yuchen
Published: February 2023

We have employed interpretable methods to uncover the black-box model of the machine learning (ML) for predicting the maximum pitting depth (dmax) of oil and gas pipelines. Ensemble learning (EL) is found to have higher accuracy compared with several classical ML models, and the determination coefficient of the adaptive boosting (AdaBoost) model reaches 0.96 after optimizing the features and hyperparameters. In this work, the running framework of the model was clearly displayed by visualization tool, and Shapley Additive exPlanations (SHAP) values were used to visually interpret the model locally and globally to help understand the predictive logic and the contribution of features. Furthermore, the accumulated local effect (ALE) successfully explains how the features affect the corrosion depth and interact with one another.
Polarized branched Actin modulates cortical mechanics to produce unequal-size daughters during asymmetric division
Authors: Daeden Alicia , Mietke Alexander , Derivery Emmanuel , Seum Carole , Jülicher Frank , Gonzalez-Gaitan Marcos
Published: February 2023

The control of cell shape during cytokinesis requires a precise regulation of mechanical properties of the cell cortex. Only few studies have addressed the mechanisms underlying the robust production of unequal-sized daughters during asymmetric cell division. Here we report that unequal daughter-cell sizes resulting from asymmetric sensory organ precursor divisions in Drosophila are controlled by the relative amount of cortical branched Actin between the two cell poles. We demonstrate this by mistargeting the machinery for branched Actin dynamics using nanobodies and optogenetics. We can thereby engineer the cell shape with temporal precision and thus the daughter-cell size at different stages of cytokinesis. Most strikingly, inverting cortical Actin asymmetry causes an inversion of daughter-cell sizes. Our findings uncover the physical mechanism by which the sensory organ precursor mother cell controls relative daughter-cell size: polarized cortical Actin modulates the cortical bending rigidity to set the cell surface curvature, stabilize the division and ultimately lead to unequal daughter-cell size.
Universal logic with encoded spin qubits in silicon
Authors: Weinstein Aaron J. , Reed Matthew D. , Jones Aaron M. , Andrews Reed W. , Barnes David , Blumoff Jacob Z. , Euliss Larken E. , Eng Kevin , Fong Bryan H. , Ha Sieu D. , Hulbert Daniel R. , Jackson Clayton A. C. , Jura Michael , Keating Tyler E. , Kerckhoff Joseph , Kiselev Andrey A. , Matten Justine , Sabbir Golam , Smith Aaron , Wright Jeffrey , Rakher Matthew T. , Ladd Thaddeus D. , Borselli Matthew G.
Published: February 2023

Quantum computation features known examples of hardware acceleration for certain problems, but is challenging to realize because of its susceptibility to small errors from noise or imperfect control. The principles of fault tolerance may enable computational acceleration with imperfect hardware, but they place strict requirements on the character and correlation of errors1. For many qubit technologies2–21, some challenges to achieving fault tolerance can be traced to correlated errors arising from the need to control qubits by injecting microwave energy matching qubit resonances. Here we demonstrate an alternative approach to quantum computation that uses energy-degenerate encoded qubit states controlled by nearest-neighbour contact interactions that partially swap the spin states of electrons with those of their neighbours. Calibrated sequences of such partial swaps, implemented using only voltage pulses, allow universal quantum control while bypassing microwave-associated correlated error sources1,22–28. We use an array of six 28Si/SiGe quantum dots, built using a platform that is capable of extending in two dimensions following processes used in conventional microelectronics29. We quantify the operational fidelity of universal control of two encoded qubits using interleaved randomized benchmarking30, finding a fidelity of 96.3% ± 0.7% for encoded controlled NOT operations and 99.3% ± 0.5% for encoded SWAP. The quantum coherence offered by enriched silicon5–9,16,18,20,22,27,29,31–37, the all-electrical and low-crosstalk-control of partial swap operations1,22–28 and the configurable insensitivity of our encoding to certain error sources28,33,34,38 all combine to offer a strong pathway towards scalable fault tolerance and computational advantage.
Simultaneous sequencing of genetic and epigenetic bases in DNA
Authors: Füllgrabe Jens , Gosal Walraj S. , Creed Páidí , Liu Sidong , Lumby Casper K. , Morley David J. , Ost Tobias W. B. , Vilella Albert J. , Yu Shirong , Bignell Helen , Burns Philippa , Charlesworth Tom , Fu Beiyuan , Fordham Howerd , Harding Nicolas J. , Gandelman Olga , Golder Paula , Hodson Christopher , Li Mengjie , Lila Marjana , Liu Yang , Mason Joanne , Mellad Jason , Monahan Jack M. , Nentwich Oliver , Palmer Alexandra , Steward Michael , Taipale Minna , Vandomme Audrey , San-Bento Rita Santo , Singhal Ankita , Vivian Julia , Wójtowicz Natalia , Williams Nathan , Walker Nicolas J. , Wong Nicola C. H. , Yalloway Gary N. , Holbrook Joanna D. , Balasubramanian Shankar
Published: February 2023

DNA comprises molecular information stored in genetic and epigenetic bases, both of which are vital to our understanding of biology. Most DNA sequencing approaches address either genetics or epigenetics and thus capture incomplete information. Methods widely used to detect epigenetic DNA bases fail to capture common C-to-T mutations or distinguish 5-methylcytosine from 5-hydroxymethylcytosine. We present a single base-resolution sequencing methodology that sequences complete genetics and the two most common cytosine modifications in a single workflow. DNA is copied and bases are enzymatically converted. Coupled decoding of bases across the original and copy strand provides a phased digital readout. Methods are demonstrated on human genomic DNA and cell-free DNA from a blood sample of a patient with cancer. The approach is accurate, requires low DNA input and has a simple workflow and analysis pipeline. Simultaneous, phased reading of genetic and epigenetic bases provides a more complete picture of the information stored in genomes and has applications throughout biomedicine.
SpliceVault predicts the precise nature of variant-associated mis-splicing
Authors: Dawes Ruebena , Bournazos Adam M. , Bryen Samantha J. , Bommireddipalli Shobhana , Marchant Rhett G. , Joshi Himanshu , Cooper Sandra T.
Published: February 2023

Even for essential splice-site variants that are almost guaranteed to alter mRNA splicing, no current method can reliably predict whether exon-skipping, cryptic activation or multiple events will result, greatly complicating clinical interpretation of pathogenicity. Strikingly, ranking the four most common unannotated splicing events across 335,663 reference RNA-sequencing (RNA-seq) samples (300K-RNA Top-4) predicts the nature of variant-associated mis-splicing with 92% sensitivity. The 300K-RNA Top-4 events correctly identify 96% of exon-skipping events and 86% of cryptic splice sites for 140 clinical cases subject to RNA testing, showing higher sensitivity and positive predictive value than SpliceAI. Notably, RNA re-analyses showed we had missed 300K-RNA Top-4 events for several clinical cases tested before the development of this empirical predictive method. Simply, mis-splicing events that happen around a splice site in RNA-seq data are those most likely to be activated by a splice-site variant. The SpliceVault web portal allows users easy access to 300K-RNA for informed splice-site variant interpretation and classification.
Potential roles of acyl homoserine lactones (AHLs) in nitrifying bacteria survival under certain adverse circumstances
Authors: Zeng Xiangguo , Hu Huizhi
Published: February 2023

Potential roles of quorum sensing (QS) in nitrifying bacteria activity and ecology, particularly under adverse circumstances have been rarely reported. Herein, eight lab-scale nitrification sequencing batch reactors, with or without adding acyl homoserine lactones (AHLs) were operated under adverse circumstances respectively. The results indicated that the introduction of AHLs significantly enhanced the nitrogen removal efficiency in the presence of nitrification inhibitors (dicyandiamide, DCD), accelerated the low temperature (10 °C) group into stable stage, and improved the utilization efficiency of AHLs in these two groups. Community analysis and qPCR further confirmed that AHLs significantly increased the abundance of nitrifying bacteria in low temperature group and DCD group, especially AOB. For normal condition (28 °C, pH = 8) or low pH level (5.5), however, the AHLs had no significant effect. Canonical correspondence analysis showed that nitrifying bacteria positively responded to AHLs, indicating that adding AHLs was an effective strategy to regulate nitrification process. However, under acid conditions, the effect of this regulatory mechanism was not significant, indicating that the influence of pH on the system was greater than that of AHLs. This study demonstrated that exogenous AHLs could enhance the competitiveness of nitrifying bacteria to utilize more resource and occupy space under some adverse environmental conditions.
Quantifying human performance in chess
Authors: Chowdhary Sandeep , Iacopini Iacopo , Battiston Federico
Published: February 2023

From sports to science, the recent availability of large-scale data has allowed to gain insights on the drivers of human innovation and success in a variety of domains. Here we quantify human performance in the popular game of chess by leveraging a very large dataset comprising of over 120 million games between almost 1 million players. We find that individuals encounter hot streaks of repeated success, longer for beginners than for expert players, and even longer cold streaks of unsatisfying performance. Skilled players can be distinguished from the others based on their gaming behaviour. Differences appear from the very first moves of the game, with experts tending to specialize and repeat the same openings while beginners explore and diversify more. However, experts experience a broader response repertoire, and display a deeper understanding of different variations within the same line. Over time, the opening diversity of a player tends to decrease, hinting at the development of individual playing styles. Nevertheless, we find that players are often not able to recognize their most successful openings. Overall, our work contributes to quantifying human performance in competitive settings, providing a first large-scale quantitative analysis of individual careers in chess, helping unveil the determinants separating elite from beginner performance.
Reduced cardiovascular reserve capacity in long-term allogeneic stem cell transplant survivors
Authors: Dillon Hayley T. , Foulkes Stephen , Horne-Okano Yuki A. , Kliman David , Dunstan David W. , Daly Robin M. , Fraser Steve F. , Avery Sharon , Kingwell Bronwyn A. , La Gerche Andre , Howden Erin J.
Published: February 2023

Premature cardiovascular mortality is increased in long-term allogeneic stem cell transplant (allo-SCT) survivors, but little information exists regarding subclinical cardiovascular dysfunction in this population. We compared peak oxygen uptake ($${{\dot{\mathrm V}}}$$

V
˙

O2peak), a prognostic cardiovascular marker, and its determinants between long-term allo-SCT survivors and non-cancer controls. Fourteen allo-SCT survivors (mean ± SD, 44 ± 15 years, 50% male, median time since allo-SCT: 6.5 years [range 2–20]) and 14 age- and sex-matched controls (46 ± 13 years, 50% male) underwent cardiopulmonary exercise testing to quantify $${{\dot{\mathrm V}}}$$

V
˙

O2peak. Resting echocardiography (left-ventricular ejection fraction and strain), exercise cardiac MRI (peak cardiac and stroke volume index [CIpeak, SVIpeak]), biochemistry (hemoglobin, troponin-I, B-natriuretic peptide), dual-energy x-ray absorptiometry (lean [LM] and fat [FM] mass, percent body fat [%BF]) and Fick-principal calculation (arteriovenous oxygen difference) were also performed. Survivors exhibited impaired $${{\dot{\mathrm V}}}$$

V
˙

O2peak as compared with controls (25.9 ± 5.1 vs. 33.7 ± 6.5 ml kg−1 min−1, p = 0.002), which coincided with reduced CIpeak (6.6 ± 0.8 vs. 8.6 ± 1.9 L min−1 m−2; p = 0.001) secondary to reduced SVIpeak (48 ± 4 vs. 61 ± 8 ml m−2; p < 0.001) rather than chronotropic impairment, and higher %BF (difference, 7.9%, p = 0.007) due to greater FM (5.8 kg; p = 0.069) and lower LM (4.3 kg, p = 0.25). All other measures were similar between groups. Despite comparable resting cardiac function and biomarker profiles, survivors exhibited reduced $${{\dot{\mathrm V}}}$$

V
˙

O2peak and exercise cardiac function and increased %BF relative to controls. These results highlight potential therapeutic avenues and the utility of exercise-based cardiovascular assessment in unmasking cardiovascular dysfunction in allo-SCT survivors.
In silico analysis of TUBA4A mutations in Amyotrophic Lateral Sclerosis to define mechanisms of microtubule disintegration
Authors: Ganne Akshatha , Balasubramaniam Meenakshisundaram , Ayyadevara Haarika , Kiaei Lily , Shmookler Reis Robert J. , Varughese Kottayil I. , Kiaei Mahmoud
Published: February 2023

Amyotrophic lateral sclerosis (ALS) is an inexorably progressive and degenerative disorder of motor neurons with no currently-known cure. Studies to determine the mechanism of neurotoxicity and the impact of ALS-linked mutations (SOD1, FUS, TARDP, C9ORF72, PFN1, TUBA4A and others) have greatly expanded our knowledge of ALS disease mechanisms and have helped to identify potential targets for ALS therapy. Cellular pathologies (e.g., aggregation of mutant forms of SOD1, TDP43, FUS, Ubiqulin2, PFN1, and C9ORF72), mitochondrial dysfunction, neuroinflammation, and oxidative damage are major pathways implicated in ALS. Nevertheless, the selective vulnerability of motor neurons remains unexplained. The importance of tubulins for long-axon infrastructure, and the special morphology and function of motor neurons, underscore the central role of the cytoskeleton. The recent linkage of mutations to the tubulin α chain, TUBA4A, to familial and sporadic cases of ALS provides a new investigative opportunity to shed light on both mechanisms of ALS and the vulnerability of motor neurons. In the current study we investigate TUBA4A, a structural microtubule protein with mutations causal to familial ALS, using molecular-dynamic (MD) modeling of protein structure to predict the effects of each mutation and its overall impact on GTP binding, chain stability, tubulin assembly, and aggregation propensity. These studies predict that each of the reported mutations will cause notable structural changes to the TUBA4A (α chain) tertiary protein structure, adversely affecting its physical properties and functions. Molecular docking and MD simulations indicate certain α chain mutations (e.g. K430N, R215C, and W407X) may cause structural deviations that impair GTP binding, and plausibly prevent or destabilize tubulin polymerization. Furthermore, several mutations (including R320C and K430N) confer a significant increase in predicted aggregation propensity of TUBA4A mutants relative to wild-type. Taken together, these in silico modeling studies predict structural perturbations and disruption of GTP binding, culminating in failure to form a stable tubulin heterocomplex, which may furnish an important pathogenic mechanism to trigger motor neuron degeneration in ALS.
Joint use of location and acceleration data reveals influences on transitions among habitats in wintering birds
Authors: VonBank Jay A. , Schafer Toryn L. J. , Cunningham Stephanie A. , Weegman Mitch D. , Link Paul T. , Kraai Kevin J. , Wikle Christopher K. , Collins Daniel P. , Cao Lei , Ballard Bart M.
Published: February 2023

Quantifying relationships between animal behavior and habitat use is essential to understanding animal decision-making. High-resolution location and acceleration data allows unprecedented insights into animal movement and behavior. These data types allow researchers to study the complex linkages between behavioral plasticity and habitat distribution. We used a novel Markov model in a Bayesian framework to quantify the influence of behavioral state frequencies and environmental variables on transitions among landcover types through joint use of location and tri-axial accelerometer data. Data were collected from 56 greater white-fronted geese (Anser albifrons frontalis) across seven ecologically distinct winter regions over two years in midcontinent North America. We showed that goose decision-making varied across landcover types, ecoregions, and abiotic conditions, and was influenced by behavior. We found that time spent in specific behaviors explained variation in the probability of transitioning among habitats, revealing unique behavioral responses from geese among different habitats. Combining GPS and acceleration data allowed unique study of potential influences of an ongoing large-scale range shift in the wintering distribution of a migratory bird across midcontinent North America. We anticipate that behavioral adaptations among variable landscapes is a likely mechanism explaining goose use of highly variable ecosystems during winter in ways which optimize their persistence.
Introduction of a cascaded segmentation pipeline for parametric T1 mapping in cardiovascular magnetic resonance to improve segmentation performance
Authors: Viezzer Darian , Hadler Thomas , Ammann Clemens , Blaszczyk Edyta , Fenski Maximilian , Grandy Thomas Hiroshi , Wetzl Jens , Lange Steffen , Schulz-Menger Jeanette
Published: February 2023

The manual and often time-consuming segmentation of the myocardium in cardiovascular magnetic resonance is increasingly automated using convolutional neural networks (CNNs). This study proposes a cascaded segmentation (CASEG) approach to improve automatic image segmentation quality. First, an object detection algorithm predicts a bounding box (BB) for the left ventricular myocardium whose 1.5 times enlargement defines the region of interest (ROI). Then, the ROI image section is fed into a U-Net based segmentation. Two CASEG variants were evaluated: one using the ROI cropped image solely (cropU) and the other using a 2-channel-image additionally containing the original BB image section (crinU). Both were compared to a classical U-Net segmentation (refU). All networks share the same hyperparameters and were tested on basal and midventricular slices of native and contrast enhanced (CE) MOLLI T1 maps. Dice Similarity Coefficient improved significantly (p < 0.05) in cropU and crinU compared to refU (81.06%, 81.22%, 72.79% for native and 80.70%, 79.18%, 71.41% for CE data), while no significant improvement (p < 0.05) was achieved in the mean absolute error of the T1 time (11.94 ms, 12.45 ms, 14.22 ms for native and 5.32 ms, 6.07 ms, 5.89 ms for CE data). In conclusion, CASEG provides an improved geometric concordance but needs further improvement in the quantitative outcome.
Plant miRNA osa-miR172d-5p suppressed lung fibrosis by targeting Tab1
Authors: Kumazoe Motofumi , Ogawa Fumiyo , Hikida Ai , Shimada Yu , Yoshitomi Ren , Watanabe Ryoya , Onda Hiroaki , Fujimura Yoshinori , Tachibana Hirofumi
Published: February 2023

Lung fibrosis, including idiopathic pulmonary fibrosis, is an intractable disease accompanied by an irreversible dysfunction in the respiratory system. Its pathogenesis involves the transforming growth factorβ (TGFβ)-induced overproduction of the extracellular matrix from fibroblasts; however, limited countermeasures have been established. In this study, we identified osa-miR172d-5p, a plant-derived microRNA (miR), as a potent anti-fibrotic miR. In silico analysis followed by an in vitro assay based on human lung fibroblasts demonstrated that osa-miR172d-5p suppressed the gene expression of TGF-β activated kinase 1 (MAP3K7) binding protein 1 (Tab1). It also suppressed the TGFβ-induced fibrotic gene expression in human lung fibroblasts. To assess the anti-fibrotic effect of osa-miR172d-5p, we established bleomycin-induced lung fibrosis models to demonstrate that osa-miR172d-5p ameliorated lung fibrosis. Moreover, it suppressed Tab1 expression in the lung tissues of bleomycin-treated mice. In conclusion, osa-miR172d-5p could be a potent candidate for the treatment of lung fibrosis, including idiopathic pulmonary fibrosis.
Association of polysialic acid serum levels with schizophrenia spectrum and bipolar disorder-related structural brain changes and hospitalization
Authors: Müller-Miny Louisa , Thiel Katharina , Meinert Susanne , Hahn Tim , Kircher Tilo , Nenadić Igor , Krug Axel , Hufschmidt Felix , Liao Huan , Neumann Harald , Dannlowski Udo , Lünemann Jan D.
Published: February 2023

Expression of polysialic acid (polySia) in the adult brain is enriched in areas of continuous neurogenesis and plasticity such as the hippocampus. Genome-wide association studies identified variants of glycosylation enzyme-encoding genes, required for the generation of polySia, to be associated with the development of schizophrenia and bipolar disorder. Here, we report that serum levels of polySia are increased in patients with schizophrenia spectrum disorder compared to patients with major depressive disorders or demographically matched healthy controls. Furthermore, elevated polySia serum levels are associated with structural hippocampal gray matter decline in schizophrenia spectrum and bipolar disorder. In patients with schizophrenia spectrum disorder, polySia serum levels correlate with the number, duration of disease-related hospitalizations, early retirement and medical leave as estimators of detrimental long-term disease trajectories. Our data show that polySia serum levels are linked to structural hippocampal brain changes in schizophrenia spectrum and bipolar disorders, and suggest a contribution of polySia to the pathophysiology of these diseases.
A numerical study towards shape memory alloys application in orthotic management of pediatric knee lateral deviations
Authors: Alonso M. G. , Yawny A. , Bertolino G.
Published: February 2023

Exerting a constant load would likely improve orthosis effectiveness in treating knee lateral deviations during childhood and early adolescence. Shape memory alloys are potential candidates for such applications due to their so called pseudoelastic effect. The present study aims to quantitatively define the applicable mechanical loads, in order to reduce treatment duration while avoiding tissular damage and patient discomfort. This is essential for performing a more efficient design of correction devices. We use a patient-specific finite elements model of a pediatric knee to determine safe loading levels. The achievable correction rates are estimated using a stochastic three-dimensional growth model. Results are compared against those obtained for a mechanical stimulus decreasing in proportion to the achieved correction, emulating the behavior of conventional orthoses. A constant flexor moment of 1.1 Nm is estimated to change femorotibial angle at a rate of (7.4 ± 4.6) deg/year (mean ± std). This rate is similar to the achieved by more invasive growth modulation methods, and represents an improvement in the order of 25% in the necessary time for reducing deformities of (10 ± 5) deg by half, as compared with conventional orthoses.