bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolutionary shortcuts via multi-nucleotide substitutions and their impact on natural selection analyses
Authors: Lucaci Alexander G , Zehr Jordan D , Enard David , Thornton Joseph W. , Kosakovsky Pond Sergei L.
Published: December 2022

Inference and interpretation of evolutionary processes, in particular of the types and targets of natural selection affecting coding sequences, are critically influenced by the assumptions built into statistical models and tests. If certain aspects of the substitution process (even when they are not of direct interest) are presumed absent or are modeled with too crude of a simplification, estimates of key model parameters can become biased, often systematically, and lead to poor statistical performance. Previous work established that failing to accommodate multi-nucleotide (or multi-hit, MH) substitutions strongly biases dN/dS-based inference towards false positive inferences of diversifying episodic selection, as does failing to model variation in the rate of synonymous substitution (SRV) among sites. Here we develop an integrated analytical framework and software tools to simultaneously incorporate these sources of evolutionary complexity into selection analyses. We found that both MH and SRV are ubiquitous in empirical alignments, and incorporating them has a strong effect on whether or not positive selection is detected, (1.4-fold reduction) and on the distributions of inferred evolutionary rates. With simulation studies, we show that this effect is not attributable to reduced statistical power caused by using a more complex model. After a detailed examination of 21 benchmark alignments and a new high-resolution analysis showing which parts of the alignment provide support for positive selection, we show that MH substitutions occurring along shorter branches in the tree explain a significant fraction of discrepant results in selection detection. Our results add to the growing body of literature which examines decadesold modeling assumptions (including MH) and finds them to be problematic for comparative genomic data analysis. Because multi-nucleotide substitutions have a significant impact on natural selection detection even at the level of an entire gene, we recommend that selection analyses of this type consider their inclusion as a matter of routine. To facilitate this procedure, we developed, implemented, and benchmarked a simple and well-performing model testing selection detection framework able to screen an alignment for positive selection with two biologically important confounding processes: site-to-site synonymous rate variation, and multi-nucleotide instantaneous substitutions.
Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes acrossDrosophilanatural strains
Authors: Coronado-Zamora Marta , González Josefa
Published: December 2022

Transcriptomes are dynamic, with cells, tissues, and body parts expressing particular sets of transcripts. Transposons are a known source of transcriptome diversity, however studies often focus on a particular type of chimeric transcript, analyze single body parts or cell types, or are based on incomplete transposon annotations from a single reference genome. In this work, we have implemented a method based onde novotranscriptome assembly that minimizes the potential sources of errors while identifying a comprehensive set of gene-TE chimeras. We applied this method to head, gut and ovary dissected from fiveDrosophila melanogasternatural strains, with individual reference genomes available. We found that ∼19% of body part- specific transcripts are gene-TE chimeras. Overall, chimeric transcripts contribute a mean of 43% to the total gene expression, and they provide DNA binding, catalytic activity, and DNA polymerase activity protein domains. Our comprehensive dataset is a rich resource for follow- up analysis. Moreover, because transposable elements are present in virtually all species sequenced to date, their relevant role in spatially restricted transcript expression is likely not exclusive to the species analyzed in this work.
Genetic fine-mapping from summary data using a non-local prior improves detection of multiple causal variants
Authors: Karhunen Ville , Launonen Ilkka , Järvelin Marjo-Riitta , Sebert Sylvain , Sillanpää Mikko J.
Published: December 2022

Genome-wide association studies (GWAS) have been successful in identifying genomic loci associated with complex traits. Genetic fine-mapping aims to detect independent causal variants from the GWAS-identified loci, adjusting for linkage disequilibrium (LD) patterns. The use of GWAS summary statistics and an adequate LD reference enable large sample sizes for fine-mapping, without direct access to individual-level data. We presentFiniMOM(fine-mapping using a product inverse-moment priors), a novel Bayesian fine-mapping method for summarized genetic associations. For causal effects, the method uses a non-local inverse-moment prior, which is a natural prior distribution to model non-null effects in finite samples. A beta-binomial prior is set for the number of causal variants, with a parameterization that can be used to control for potential misspecifications in the LD reference. We test the performance of our method against a current state-of-the-art fine-mapping method SuSiE (sum-of-single-effects) across a range of simulated scenarios aimed to mimic a typical GWAS on circulating protein levels, and an applied example. The results show improved credible set coverage and power of the proposed method, especially in the case of multiple causal variants within a locus. The superior performance and the flexible parameterization to control for misspecified LD reference makeFiniMOMa competitive alternative to other fine-mapping methods for summarized genetic data.
Estimating Biochemical Concentration in Food Using Untargeted Metabolomics
Authors: Sebek Michael , Menichetti Giulia , Barabási Albert-László
Published: December 2022

Untargeted metabolomics can detect hundreds of biochemicals in food, yet without standards, it cannot quantify them. Here we show that we can take advantage of the universal scaling of nutrient concentrations to estimate the concentration of all biochemicals detected by untargeted metabolomics. We validate our method on 20 raw foods, finding an excellent agreement between the predicted and the experimentally observed concentrations.
Field testing of an enzymatic quorum quencher coating additive to reduce biocorrosion of steel
Authors: Huang Siqian , Bergonzi Celine , Smith Sherry , Hicks Randall E. , Elias Mikael H.
Published: December 2022

Microbial colonization can be detrimental to the integrity of metal surfaces and lead to microbiologically influenced corrosion (MIC). Biocorrosion is a serious problem for aquatic and marine industries in the world and severely affects the maritime transportation industry by destroying port infrastructure and increasing fuel usage and the time and cost required for maintenance of transport vessels. Here, we evaluate the potential of a stable quorum quenching lactonase enzyme to reduce biocorrosion in the field. Over the course of 21 months, steel samples coated with lactonase-containing acrylic paint were submerged at two different sites and depths in the Duluth Superior Harbor (DSH; Lake Superior, MN, USA) and benchmarked against controls, including the biological biocide surfactin. In this experiment, the lactonase treatment outperformed the surfactin biocide treatment and significantly reduced the number of corrosion tubercles (37% (p<0.01)) and the corroded surface area (39% (p<0.01)) as compared to the acrylic-coated control coupons. In an attempt to evaluate the effects of signal disruption of surface microbial communities and the reasons for lower corrosion levels, 16S rRNA sequencing was performed and community populations were analyzed. Interestingly, surface communities were similar between all treatments, and only minor changes could be observed. Among these changes, several groups including sulfate-reducing bacteria (SRBs) appeared to correlate with corrosion levels, and more specifically, SRBs abundance levels were lower on lactonase treated steel coupons. We surmise that these minute community changes may have large impacts on corrosion rates. Overall, these results highlight the potential use of stable quorum quenching lactonases as an eco-friendly antifouling coating additive.
Robust dimethyl-based multiplex-DIA workflow doubles single-cell proteome depth via a reference channel
Authors: Thielert Marvin , Itang Corazon Ericka Mae , Ammar Constantin , Schober Florian A , Bludau Isabell , Skowronek Patricia , Wahle Maria , Zeng Wen-Feng , Zhou Xie-Xuan , Brunner Andreas-David , Richter Sabrina , Theis Fabian J , Steger Martin , Mann Matthias
Published: December 2022

Single-cell proteomics aims to characterize biological function and heterogeneity at the level of proteins in an unbiased manner. It is currently limited in proteomic depth, throughput and robustness, a challenge that we address here by a streamlined multiplexed workflow using data-independent acquisition (mDIA). We demonstrate automated and complete dimethyl labeling of bulk or single-cell samples, without losing proteomic depth. In single runs of mammalian cells, a three-plex analysis of tryptic peptides quantified 7,700 proteins per channel. The Lys-N enzyme enables five-plex quantification at MS1 and MS2 level. Because the multiplex channels are quantitatively isolated from each other, mDIA accommodates a reference channel that does not interfere with the target channels. Our algorithm RefQuant takes advantage of this feature and confidently quantifies close to 4,000 proteins in single cells with excellent reproducibility, while our workflow currently allows routine analysis of 80 single cells per day. The concept of a stable proteome still holds at this deeper proteome coverage.
To build the soul of the socialist political economy with Chinese characteristics
Authors: Hong Yinxing
Published: December 2022

Purpose

The socialist political economy with Chinese characteristics is the scientific fruit of Xi Jinping thought on socialist economy with Chinese characteristics for a new era. People-centred philosophy is the core values of the Communist Party of China (CPC) Central Committee's governance of China with Xi Jinping as the core and has become the core values of the socialist political economy with Chinese characteristics. According to Xi Jinping thought on socialist economy with Chinese characteristics, it represents the interests of all people and determines the disciplinary attribute of the socialist political economy with Chinese characteristics, that is, people-centred economics. Xi Jinping has defined the essence of the socialism as eliminating poverty, improving people's livelihood and gradually realising common prosperity. That determines the main line of socialist political economy with Chinese characteristics is to liberate, develop and protect the productive forces and achieve common prosperity. This study aims to discuss the aforementioned statements.

Design/methodology/approach

Xi Jinping's scientific judgement on the new stage of development and the principal contradiction facing Chinese society has put forward the requirement of problem orientation for the study of socialist political economy with Chinese characteristics, involving the main contradiction facing Chinese society, high-quality development and modernisation. China's socialist basic economic system consists of a socialist market economy in which public ownership plays the leading role alongside other forms of ownership and distribution according to work is the mainstay, while other forms of distribution coexist alongside it. And this socialist basic economic system, marked out from three dimensions—production, distribution and exchange analysis, is the key of analysis of systems in the socialist political economy with Chinese characteristics. The economic operation analysis in political economy mainly involves resource allocation and the government's macroeconomic regulation and control.

Findings

The new thought and new practices about the role of the market and the government in the new era have opened up a new realm for the economic operation analysis in the socialist political economy with Chinese characteristics. The new development philosophy and new development paradigm define the content of the economic development theory in the socialist political economy with Chinese characteristics. The new development paradigm reflects the dual circulation theory of social reproduction.

Originality/value

The socialist political economy with Chinese characteristics is to study laws of economics in various aspects from economic system, economic operation, economic development to foreign economy and provide the basic principles of socialist political economy with Chinese characteristics. Its mainstream economic position will be consolidated continuously.
Identifying surface points based on machine learning algorithms: a comprehensive analysis
Authors: Bulut Vahide
Published: December 2022

Purpose

Surface curvature is needed to analyze the range data of real objects and is widely applied in object recognition and segmentation, robotics, and computer vision. Therefore, it is not easy to estimate the curvature of the scanned data. In recent years, machine learning classification methods have gained importance in various fields such as finance, health, engineering, etc. The purpose of this study is to classify surface points based on principal curvatures to find the best method for determining surface point types.

Design/methodology/approach

A feature selection method is presented to find the best feature vector that achieves the highest accuracy. For this reason, ten different feature selections are used and six sample datasets of different sizes are classified using these feature vectors.

Findings

The author examined the surface examples based on the feature vector using the machine learning classification methods. Also, the author compared the results for each experiment.

Originality/value

To the best of the author's knowledge, this is the first study to examine surface points according to principal curvatures using machine learning classification methods.
From offline to online: understanding users' switching intentions from traditional wealth management services to mobile wealth management applications
Authors: Lee Jung-Chieh , Wang Jing
Published: December 2022

Purpose

Financial technology (Fintech) brings about innovative financial services, such as the possibility of introducing mobile wealth management applications (apps) into consumers' lives. Despite the rapid development of such apps, few studies have focused on users' switching intentions from traditional wealth management services to mobile settings (apps).

Design/methodology/approach

Through a survey research method, a total of 378 responses were collected to examine the model. The partial least squares (PLS) technique was employed for data analysis.

Findings

To fill this research gap, this paper adopts a push-pull-mooring (PPM) theoretical framework to develop a model for exploring users' switching intentions. According to the empirical results, several push (i.e. perceived inconvenience), pull (i.e. transaction efficiency, perceived personalization and mobile wealth management scenarios) or mooring (i.e. product market expertise and affective commitment) factors are identified that significantly affect switching intention. This study provides theoretical contributions and practical implications for the existing wealth management literature and also offers future research directions.

Originality/value

This study innovatively extends the PPM framework to the traditional and mobile wealth management domains to understand users' switching intentions from offline wealth management services to mobile wealth management apps. The authors uncover several push, pull and mooring factors that are critical for determining users’ switching decisions.
Physical properties of wood-based materials for liquid deposition modeling
Authors: Rosenthal Michael , Rüggeberg Markus , Gerber Christian , Beyrich Lukas , Faludi Jeremy
Published: December 2022

Purpose

The purpose of this study is to quantify the vertical shrinkage rates and the mechanical strength of three-dimensional (3D) printed parts for a variety of wood-based materials for liquid deposition modeling.

Design/methodology/approach

The overall hypothesis was that a well-chosen combination of binders, fibers and fillers could reduce shrinkage in the Z dimension and increase compressive and flexural strength (DIN 52185, 52186). To test this assumption, eight sub-hypotheses were formulated. Mixtures of the ingredients were chosen in different ratios to measure the performance of prints. For time efficiency, an iterative heuristic approach was used – not testing all variations of all variables in even increments, but cutting off lines of testing when mixtures were clearly performing poorly.

Findings

The results showed that some mixtures had high dimensional accuracy and strength, while others had neither, and others had one but not the other. Shrinkage of 3D printed objects was mainly caused by water release during drying. An increase of the wood as well as the cement, sand, salt and gypsum content led to reduced vertical shrinkage, which varied between 0 and 23%. Compressive and flexural strength showed mixed trends. An increase in wood and salt content worsened both strength properties. The addition of fibers improved flexural, and the addition of cement improved compression strength. The highest strength values of 14 MPa for compressive and 8 MPa for flexural strength were obtained in the test series with gypsum.

Originality/value

This paper is an important milestone in the development of environmentally friendly materials for additive manufacturing. The potential of many ingredients to improve physical properties could be demonstrated.
No risk—no fun: Penalty and recovery from spring frost damage in deciduous temperate trees
Authors: Baumgarten Frederik , Gessler Arthur , Vitasse Yann
Published: December 2022

Phenological shifts in response to changing climatic conditions is a key acclimation process for the persistence of perennial plants in temperate and boreal climates. The optimal time to leaf‐out is the result of an evolutionary process determined by the trade‐off between minimizing the risk of freezing damages and herbivory pressure while maximizing resource uptake to increase competitiveness against the other plants.

We quantified the penalty exerted by frost damage at the time of leaf emergence on plant development (reduction in leaf area, canopy duration and growth) over the potential gains without frost (increased biomass and non‐structural carbohydrate reserves), depending on when leaf‐out occurs. To this purpose, we exposed 960 saplings of four temperate deciduous tree species with contrasting cold hardiness to two frost intensities shortly after leaf emergence, which was artificially induced at four occasions to reflect the whole range of natural leaf‐out dates.

One year above‐ground biomass (AGB) increments following the frost revealed a clear ranking among the species depending on their strategy to cope with damaging frosts. Prunus avium (−41% of AGB‐increment compared to control saplings) resprouted from the stem base, Quercus robur (−62%) rapidly produced new leaves from dormant reserve buds, Fagus sylvatica (−98%) showed highest chlorophyll content in autumn and delayed senescence together with Carpinus betulus (−105%), which overcompensated NSC reserves after the growing season but showed highest mortality (up to 32%). In all species, NSC reserves recovered rapidly to control levels at the expense of growth.

The timing of leaf‐out (advanced and delayed artificially) significantly affected the performance and recovery (regreening and growth) of both frozen and non‐frozen saplings, with the lowest performance found at the most delayed leaf‐out date. We propose that the potential to recover from frost damages is an important component of a tree's performance, particularly at the juvenile stage. The ability to recover may become even more decisive in the future with the predicted increase of false springs in many extratropical regions.

Read the free Plain Language Summary for this article on the Journal blog.
Seismic data interpolation using deeply supervised U‐Net++ with natural seismic training sets
Authors: Wu Geng , Liu Yang , Liu Cai , Zheng Zhisheng , Cui Yang
Published: December 2022

Interpolation techniques provide an effective method for recovery of missing traces. In recent years, many researchers have applied deep learning methods to seismic data interpolation. Generally, one can choose synthetic data as a training set; however, the features of synthetic data are always inconsistent with those of field data, which may lead to inaccurate interpolation. Meanwhile, U‐Net is a common network structure used in seismic data interpolation; however, the four downsampling and upsampling structures of U‐Net have limited adaptability for different data. In this study, the deep learning method based on U‐Net++ was proposed for seismic data interpolation, which contains U‐Net with different depths. The different depths were connected by skip pathways, and the best depth of the network was chosen for different seismic data by deep supervision. Furthermore, a new strategy for training sets was designed: frequency‐wavenumber (f‐k) bandpass filters were used to convert natural images into a natural seismic training set, which has a stronger generalization capability than synthetic data as the training set. The characteristics of the new training set can effectively improve the accuracy of missing data reconstruction. Compared with the conventional U‐Net and traditional interpolation techniques, for example, the Fourier Bregman method, the proposed method produces more accurate and reasonable interpolation results. Further, it can reconstruct both irregular and regular missing seismic data, even in the presence of strong random noise and aliasing. Synthetic and field data tests showed the effectiveness, robustness and generalization of the proposed method.
Temperature‐controlled gelation of casein concentrates enabled by the utilisation of acid whey permeate as a diafiltration medium in microfiltration
Authors: Reitmaier Michael , Kulozik Ulrich
Published: December 2022

In this study, ultrafiltration permeate obtained from acid whey (AWP) was applied as a diafiltration (DF) medium during skim milk microfiltration. The thereby induced acidification of differently concentrated retentates was assessed regarding suitability to generate gels from micellar casein concentrates further downstream. While aggregation was avoided during cold DF, subsequent heating induced controlled spontaneous formation of gels with concentration‐ and pH‐dependent firmness ranging from 26 to 1420 Pa. By employing its typical compounds, AWP as a rather problematic dairy side stream could thus be utilised for the production of calcium‐rich acidic casein gels providing sensory characteristics of cultured dairy products.
Clinical features and risk factors of catheter removal among 1062 episodes of peritoneal dialysis‐associated peritonitis: A multicenter 7‐year study
Authors: Liu Shichen , Yang Liming , Zhu Xueyan , Zhang Xiaoxuan , Meng Lingfei , Li Xinyang , Zhao Jing , Zhuang Xiaohua , Cui Wenpeng
Published: December 2022

Introduction

Studies focusing on catheter removal and the pathogenic spectrum of peritoneal dialysis‐associated peritonitis (PDAP) need to be updated.

Methods

Data were collected from four peritoneal dialysis (PD) centers. Peritonitis rates were compared using Poisson regression and Logistic regression was used to examine the risk factors for catheter removal.

Results

The PD duration (odds ratio [OR], 1.021; 95% confidence interval [CI], 1.010–1.032), number of previous PDAP episodes (OR, 1.267; 95% CI, 1.039–1.545), dialysate white cell count >100 × 106/L on Day 5 of PDAP (OR, 6.088; 95% CI, 3.277–11.312), Pseudomonas aeruginosa (OR, 4.122; 95% CI, 1.071–15.874) and polymicrobial infections (OR, 3.257; 95% CI, 1.519–6.982) were independent predictors of catheter removal (p < 0.05). The prevalence of polymicrobial peritonitis and fungal peritonitis has increased (p < 0.05).

Conclusion

Attention should be paid to patients with long PD duration or a history of previous episodes of PDAP characteristics.
Utility of head computed tomography for older adults with suspected delirium in the emergency department: A retrospective observational study
Authors: Butcher Josh D. , Smith Mckinley C. , Roberts Lauren , Ellis Brittany
Published: December 2022

Background

Delirium in older people is associated with significant morbidity and mortality and has life‐threatening etiologies making prompt recognition essential. Computed tomography of the head (CT‐head) may have a role in determining the cause of delirium; however, inpatient studies suggest it is overused. There is a paucity of emergency department (ED)‐based research surrounding the use of CT‐head in delirium. This study aims to describe the utility of CT‐head in older patients presenting to the ED with symptoms of delirium.

Methods

We conducted a retrospective chart review of patients 65 years and older with symptoms of delirium who visited local EDs over a 3.5‐year period (2016–2020). We compared patients who did and did not receive CT‐head. Our primary objective was to determine the proportion of acute findings in patients who received CT‐head. Our secondary objectives were to describe the proportions of patients who did and did not receive CT‐head in terms of their demographics, presenting symptoms, disposition, and indications for and results of CT‐head scans. Chi‐square tests were utilized for comparisons.

Results

A total of 630 encounters were identified through database searching; 526 met inclusion criteria. Thirty‐four were excluded for presenting directly to consultants, leaving 492 included encounters. Of those who received a CT‐head (n = 279), 13 (4.7%) had acute findings. Of the encounters with acute findings, four (30.77%) had focal neurological deficits (FND), and two (15.38%) had Glasgow Coma Scale (GCS) score < 14. Patients without CT‐head (n = 213) were more likely to be discharged (p < 0.01) and less likely to have a FND (p < 0.01).

Conclusions

CT‐head is ordered for over half of older ED patients with symptoms of delirium despite infrequent acute findings. Acute findings typically occur in the context of symptoms suggestive of intracranial abnormalities such as FND or GCS < 14. This suggests physicians should be more selective when ordering CT‐heads in patients with symptoms of delirium.
Dental enamel defects and dental caries of primary teeth among Indigenous children in Western Australia
Authors: Arrow P , Piggott S , Jamieson L , Brennan D , Tonmukayakul U , Kularatna S , Atkinson D , Nanda S
Published: December 2022

Background

Teeth affected with enamel defects (EDs) are at an increased risk of dental caries. In spite of improving oral health status overall in Australia, Indigenous Australians still experience higher rates of dental caries than non‐Indigenous Australians. This study reports on the prevalence of EDs and dental caries experience among Indigenous children in the Kimberley region of Western Australia.

Methods

Health status of all the primary teeth (ICDAS II criteria) and the presence of EDs on index teeth (modified Dental Defects of Enamel index; DDE) of young Indigenous children who participated in a 2‐arm intervention trial was recorded. Generalized estimating equations were used to estimate the association between EDs and dental caries and effect estimates were presented as odds ratios and associated 95% confidence intervals.

Results

Person‐level prevalence, from 237 children (mean age 3.6 years, standard deviation 1.7) assessed for EDs, was 58% and tooth‐level prevalence was 24%. Teeth affected with demarcated or diffuse defects were associated with a twofold higher odds of having caries experience, odds ratio (OR) 2.5, 95% confidence interval (CI) 1.7–3.7 and OR 2.7, 95% CI 1.7–4.0 respectively.

Conclusions

The presence of EDs among young Indigenous children was associated with a higher odds of caries experience among affected teeth.
Oral health research funding in relation to disease burden in Australia
Authors: Ghanbarzadegan A , Ivanovski S , Sloan AJ , Spallek H
Published: December 2022

Background

This study aims to investigate and compare the major Australian government research funding schemes for oral health science with other disciplines from the burden of disease perspective.

Methods

Major government research funding scheme outcomes were identified. An innovative index of Fair Research Funding (FRF) was developed to examine the extent to which National Health and Medical Research Council funding is aligned with the disease burden. In addition to comparing different diseases, overall governmental research funding for different areas of oral health sciences was explored.

Results

Oral disorders with $15 million NHMRC grant funds (2017–2021) and FRF of 10.7 has the lowest and most inequitable amount of Australian government support in relation to disease burden. The share of oral health science in the Australian Research Council and Medical Research Future Fund was very minimal, with $3.43 and $1.88 million respectively.

Conclusion

Governmental research funding for oral health sciences is inequitable according to the disease burden. More dedicated oral health sciences research funding schemes are essential. Funding for prevention‐focused public oral health programmes is a vital requirement towards reducing the inequalities in population oral health.
Fenestration and dehiscence defects in maxillary anterior teeth using two classification systems
Authors: Nalbantoğlu AM , Yanık D
Published: December 2022

Background

The primary objective of the study was to assess the buccal bone thickness (BT), evaluate and compare the prevalence of bone fenestration and dehiscence in anterior maxillary teeth using cone‐beam computed tomography (CBCT).

Methods

Images of 300 maxillary anterior teeth were investigated. The BT was measured at the bone crest, 3, 6 and 9 mm from the bone crest, and apical. Fenestration and dehiscence were recorded according to Yang and Pan's classification. Student's t‐test and one‐way ANOVA were performed for statistical analysis.

Results

Fenestration and dehiscence rates were 35.66% and 20%, respectively. Type III fenestration was higher in group 3 (>65 years) (P = 0.028). Type I and IV fenestration and CII DII dehiscence were more common in canines (P > 0.05). Fenestration involving two‐thirds (46.76%) and one‐third (44.84%) of the root length was more common. Fenestrations involving the entire root were 8.4%. Most of the dehiscence (63.3%) involved one‐third of the root length. Dehiscence involving two‐thirds of the root length and the entire root was 5% and 9.95%, respectively. The coexistence of fenestration and dehiscence was 8.3%. Dehiscence on the palatal aspect was detected in 1.65% of the anterior maxilla.

Conclusions

The rate of BT ≤1 mm was 80.08%, and ≥2 mm was 3.66%. Fenestration was most common in canines. Fenestration was mostly located in the apical third, while dehiscence was mostly located in the coronal third. © 2022 Australian Dental Association.
Influence of environmental conditions and initial sapling size in Nothofagus survival and growth: Implications for restoration of burnt sub‐Antarctic forests
Authors: Mestre Luciana M. , Argañaraz Carina I. , Preiß‐Daimler Inga , Fernandez Loreto , Turi Luis , Soler Rosina
Published: December 2022

The sub‐Antarctic forests in Tierra del Fuego mountains are considered one of the few remaining wilderness areas on the planet; however, human disturbances like wildfires, exotic species, and so forth exacerbate their degradation. In 2012, a human‐caused wildfire started in a remote forest‐mountain area, and 2 years after that, a reforestation project began to restore the natural canopy layer. Saplings of the native Nothofagus trees were obtained through the bare root method from undisturbed areas. In this study, we evaluated the influence of (1) macro‐ (considering natural topography and vegetation physiognomy) and micro‐environments (topography, canopy cover, substrate, and understory cover) affected by fire; and (2) the extraction size of the saplings (initial size), on survival and growth of planted saplings, over 5 years. Total sapling survival was 41.4% with a mean growth rate of 8.46 cm year−1. Survival and growth were influenced by the studied variables. At a macro‐environment level, tree saplings showed higher success in well‐drained zones, meanwhile at the micro‐environment level saplings performed better in those that contribute to retain soil moisture and avoiding evapotranspiration. We conclude that environmental features influence differentially depending on the scale of analysis. To restore burnt temperate forests applying the bare root method, we recommended using Nothofagus saplings <40 cm tall for better results. In this sense, we demonstrated the effectiveness of the method since comparable results were obtained in other restoration experiences. This method can also be applied in areas without nursery material, when the biology of tagged plants was appropriated, for example shallow growth of root systems, formation of natural tree seedling banks. This work represents one of the few medium‐term restoration experiences reported for the southernmost forests of the planet: our findings could be applied in other reforestation experiences, making noticeable improvements in the recovery process.
A regulatory role of Piezo1 in apoptosis of periodontal tissue and periodontal ligament fibroblasts during orthodontic tooth movement
Authors: Shen Xuanjiang , Wu Weilli , Ying Yukang , Zhou Liyuan , Zhu Haiqian
Published: December 2022

Investigation on the effect of Piezo1 on periodontal tissue and periodontal ligament fibroblasts (PDLFs) under mechanical stress and the underlying mechanism. The orthodontic tooth movement rat model was established via an orthodontic spiral tension spring. PDLFs were cultured and subjected to 2.0 g/cm2 static compressive loading. Blocked the Piezo1 via Piezo1 inhibitor, GsMTx4. TUNEL staining and flow cytometry determined the apoptosis rate of periodontal tissue and PDLFs in rats. Expression of Piezo1, p‐p38 and ERK1/2 was analysed by immunofluorescence assay and western blotting. Piezo1 inhibitor GsMTx4 relieved the increased expression of Piezo1, ERK1/2 and p‐p38, and alleviated apoptosis in periodontal tissue and PDLFs under compressive loading. Piezo1 inhibition can alleviate force‐induced apoptosis and damage in rats' periodontal tissue and PDLFs, and regulate the p38/ERK1/2 signalling pathway.
Evaluation of six machine learning classification algorithms in pig breed identification usingSNPsarray data
Authors: Liu Ruiqi , Xu Zhiting , Teng Jinyan , Pan Xiangchun , Lin Qing , Cai Xiaodian , Diao Shuqi , Feng Xueyan , Yuan Xiaolong , Li Jiaqi , Zhang Zhe
Published: December 2022

Breed identification utilizing multiple information sources and methods is widely applicated in the field of animal genetics and breeding. Simultaneously, with the development of artificial intelligence, the integration of high‐throughput genomic data and machine learning techniques is increasingly used for breed identification. In this context, we used 654 individuals from 15 pig breeds, evaluating the performance of machine learning and stacking ensemble learning classifiers, as well as the function of feature selection and anomaly detection in different scenarios. Our results showed that, when using a training set of 16 individuals per breed and 32 features (SNPs), the accuracy of breed identification with feature selection (eXtreme Gradient Boosting, XGBoost) could exceed 95.00% (nine breeds), and was improved by 7.04% over the results with random selection. For stacking ensemble learning, feature selection methods (including random selection method) were used before different base learners. When these base learners’ training set had 16 individuals per breed and 32 features, the accuracy of stacking ensemble learning improved by 9.24% over the best base learner (nine breeds), but did not significantly increase the advantage over the models with XGBoost feature selection. When using a training set of 16 individuals and 512 features per breed, breed identification with anomaly detection (local outlier factor, LOF) and random selection could achieve an accuracy of 89.06% (15 breeds). These results show that machine learning could be an effective tool for breed identification and this study will also provide useful information for the application of machine learning in animal genetics and breeding.
Sex disparities in left ventricular assist device implantation outcomes: A systematic review and meta‐analysis of over 50 000 patients
Authors: Arjomandi Rad Arian , Kapadia Sharan , Zubarevich Alina , Nanchahal Sukanya , Van den Eynde Jef , Vardanyan Robert , Bareka Metaxia , Krasopoulos George , Quarto Cesare , Ruhparwar Arjang , Athanasiou Thanos , Weymann Alexander
Published: December 2022

Background

Left ventricular assist devices (LVAD) represent an important therapeutic option for patients progressing to end‐stage heart failure. Women have been historically underrepresented in LVAD studies, and have been reported to have worse outcomes despite technological optimisation. We aimed to systematically explore the evidence on sex disparities in the use and outcomes of LVAD implantation.

Methods

A systematic database search with meta‐analysis was conducted of comparative original articles of men versus women undergoing LVAD implantation, in EMBASE, MEDLINE, Cochrane database and Google Scholar, from inception to July 2022. Primary outcomes were stroke (haemorrhagic and ischaemic) and early/overall mortality. Secondary outcomes were LVAD thrombosis, right VAD implantation, major bleeding, kidney dysfunction, and device/driveline infection.

Results

Our search yielded 137 relevant studies, including 22 meeting the inclusion criteria with a total of 53 227 patients (24.2% women). Overall mortality was higher in women (odds ratio [OR] 1.35, 95% confidence interval [CI] 1.05–1.62, p = 0.02), as was overall stroke (OR 1.32, 95%CI 1.06–1.66, p = 0.01), including ischemic (OR 1.80, 95%CI 1.22–2.64, p = 0.003) and haemorrhagic (OR 1.72, 95%CI 1.09–2.70, p = 0.02). Women had more frequent right VAD implantation (OR 2.11, 95%CI 1.24–3.57, p = 0.006) and major bleeding (OR 1.40, 95%CI 1.06–1.85, p = 0.02). Kidney dysfunction, LVAD thrombosis, and device/driveline infections were comparable between sexes.

Conclusions

Our analysis suggests that women face a greater risk of adverse events and mortality post‐LVAD implantation. Although the mechanisms remain unclear, the difference in outcomes is thought to be multifactorial. Further research, that includes comprehensive pre‐operative characteristics and post‐operative outcomes, is encouraged.
Effects of slashing on native and invasive species, and community structure of a remnant natural grassland of South Australia
Authors: Facelli José M. , Facelli Evelina
Published: December 2022

Questions

We investigated the feasibility of slashing as a management tool to reduce the abundance of the exotic invasive species Avena barbata and favour native species and diversity in remnants of semi‐arid native grasslands. We asked how slashing affects: (1) the seed production and seed bank of A. barbata, (2) the mortality of perennial native tussock grasses, and (3) plant community composition.

Location

Near Burra, Mid North region of South Australia.

Methods

We established two parallel experiments in an invaded grassland: one in a stand dominated by exotic and invasive species (“poor” condition), and the other in a less‐degraded stand with an abundance of native perennial grasses (“good” condition). The experiments had a randomized block design (six blocks) with three treatments each: no slashing, slashing once a year or slashing every other year, applied over 3 years. We assessed the effects of the treatments on the number of seeds per m2 and soil seed bank of A. barbata, number of death native tussock grasses, and floristic composition and diversity.

Results

Slashing reduced seed production and the soil seed bank of A. barbata in both stands. Slashing increased the mortality of native grasses in the stand in good condition, and slightly changed floristic composition only in the stand in poor condition. Here, slashing decreased the abundance of the invasive species A. barbata and Bromus rigens but favoured other exotic species. No changes in species richness or diversity were detected.

Conclusions

The slight response of the plant community to slashing suggests that these grasslands are resistant to changes in management. However, the reduction in seed production and soil seed bank of A. barbata suggest that longer term application of slashing could reduce its abundance and allow native species to recruit. The mortality of native tussocks can, however, negate the benefit of reducing abundance of invasive species.
Soft regulation of women on boards: Evidence from Canada
Authors: Oldford Erin
Published: December 2022

In this study, I examine the effectiveness of a national board gender diversity disclosure requirement, which is, arguably, on the “soft” end of the continuum of boardroom interventions. Using a panel dataset of 1847 hand‐collected corporate disclosures from 2015 to 2018, I perform a post‐event, historical trend analysis of the efficacy of Canada's 2014 intervention. I find evidence of real progress in the 4 years following intervention against several benchmarks. Specifically, improvements in critical mass are documented, with the proportion of boards with three of more women reaching 18.8% in 2018. Tokenism remains an issue with very little change in the number of Canadian boards with only one woman. Further analyses using a sorting methodology and panel regression analysis reveal that progress toward board gender diversity is achieved by those with board gender targets, board seat renewal policies, and written board diversity policies. In addition, I find that larger companies achieve greater progress and that progress is clustered by industry.
Generative adversarial networks for modelling clinical biomarker profiles with race/ethnicity
Authors: Nair Rahul , Mohan Deen Dayal , Frank Sandra , Setlur Srirangaraj , Govindaraju Venugopal , Ramanathan Murali
Published: December 2022

Aims

Modelling biomarker profiles for under‐represented race/ethnicity groups are challenging because the underlying studies frequently do not have sufficient participants from these groups. The aim was to investigate generative adversarial networks (GANs), an artificial intelligence technology that enables realistic simulations of complex patterns, for modelling clinical biomarker profiles of under‐represented groups.

Methods

GANs consist of generator and discriminator neural networks that operate in tandem. GAN architectures were developed for modelling univariate and joint distributions of a panel of 16 diabetes‐relevant biomarkers from the National Health and Nutrition Examination Survey, which contains laboratory and clinical biomarker data from a population‐based sample of individuals of all ages, racial groups and ethnicities. Conditional GANs were used to model biomarker profiles for race/ethnicity categories. GAN performance was assessed by comparing GAN outputs to test data.

Results

The biomarkers exhibited non‐normal distributions and varied in their bivariate correlation patterns. Univariate distributions were modelled with generator and discriminator neural networks consisting of 2 dense layers with rectified linear unit‐activation. The distributions of GAN‐generated biomarkers were similar to the test data distributions. The joint distributions of the biomarker panel in the GAN‐generated data were dispersed and overlapped with the joint distribution of the test data as assessed by 3 multidimensional projection methods. Conditional GANs satisfactorily modelled the joint distribution of the biomarker panel in the Black, Hispanic, White and Other race/ethnicity categories.

Conclusion

GAN is a promising artificial intelligence approach for generating virtual patient data with realistic biomarker distributions for under‐represented race/ethnicity groups.
The human LAT1–4F2hc (SLC7A5–SLC3A2) transporter complex: Physiological and pathophysiological implications
Authors: Kahlhofer Jennifer , Teis David
Published: December 2022

LAT1 and 4F2hc form a heterodimeric membrane protein complex, which functions as one of the best characterized amino acid transporters. Since LAT1–4F2hc is required for the efficient uptake of essential amino acids and hormones, it promotes cellular growth, in part, by stimulating mTORC1 (mechanistic target of rapamycin complex 1) signalling and by repressing the integrated stress response (ISR). Gain or loss of LAT1–4F2hc function is associated with cancer, diabetes, and immunological and neurological diseases. Hence, LAT1–4F2hc represents an attractive drug target for disease treatment. Specific targeting of LAT1–4F2hc will be facilitated by the increasingly detailed understanding of its molecular architecture, which provides important concepts for its function and regulation. Here, we summarize (i) structural insights that help to explain how LAT1 and 4F2hc assemble to transport amino acids across membranes, (ii) the role of LAT1–4F2hc in key metabolic signalling pathways, and (iii) how derailing these processes could contribute to diseases.
Adult children of parents with mental illness: Family stigma and coping on sense of self
Authors: Campbell Chynna , Patrick Pamela
Published: December 2022

Family stigma is associated with persistent negative outcomes among adult children of parents with mental illness (ACOPMI). Loss of sense of self has been reported by ACOPMI; however, the role of family stigma on sense of self remains unclear. Additionally, research suggests coping behaviour (i.e. adaptive or maladaptive) influences the effect of stigmatization on sense of self. This study investigated the impact of family stigma and coping on sense of self among ACOPMI (N = 134, 63.4% female). As hypothesized, high family stigma was associated with weak sense of self (p  < 0.001), and ACOPMI who endorsed adaptive coping demonstrated higher sense of self than those who coped maladaptively (p  < 0.001). Further, coping moderated the relationship between family stigma and sense of self (p  < 0.001). Unexpectedly, this relationship was only significant for ACOPMI with adaptive coping skills (p  < 0.001). At higher levels of stigmatization, post hoc analysis revealed coping styles did not exert an influence on sense of self. Results suggest family stigma contributes to loss of sense of self among ACOPMI, with adaptive coping being protective only at lower levels of family stigma. Findings highlight the need for a systemic approach to eradicate family stigma.