bluuebunny/crossref_metadata_2025 huggingface dataset:
Dental long axes using digital dental models compared to cone‐beam computed tomography
Authors: Cong Amalia , Massaro Camila , Ruellas Antonio Carlos de Oliveira , Barkley Mary , Yatabe Marilia , Bianchi Jonas , Ioshida Marcos , Alvarez María Antonia , Aristizabal Juan Fernando , Rey Diego , Cevidanes Lucia
Published: May 2021

Objective

Standard methods of evaluating tooth long axes are not comparable (digital dental models [DDMs], panoramic and cephalometric radiographs) or expose patients to more radiation (cone‐beam computed tomography [CBCT]). This study aimed to compare angular changes in tooth long axes using DDMs vs using CBCTs.

Settings and sample population

Secondary data analysis of DDMs and CBCTs, taken before and after orthodontic treatment with piezocision of 24 patients.

Methods

Angular changes in tooth long axes were evaluated using landmarks on first molars (centre of the occlusal surface and centre of the furcation), canines and incisors (cusp tip and centre of the root at the cementoenamel junction). Wilcoxon test, intraclass correlation coefficient (ICC) and Bland‐Altman plots were used to test intra‐ and inter‐rater agreement and compare DDM and CBCT measurements.

Results

The mesiodistal angulation and buccolingual inclination DDM measurements were reproducible. Overall mean differences between DDM and CBCT measurements of mesiodistal angulation, 1.9°±1.5°, and buccolingual inclination, 2.2 ± 2.2°, were not significant for all teeth. ICC between DDM and CBCT measurements ranged from good (0.85 molars) to excellent (0.94 canines; 0.96 incisors). The percentages of measurements outside the range of ±5 were 17.4% for molars, 13.8% for canines and 4.5% for incisors.

Conclusions

DDM assessment of changes in tooth long axes has good reproducibility and yields comparable measurements to those obtained from CBCT within a 5° range. These findings lay the groundwork for machine learning approaches that synthesize crown and root canal information towards planning tooth movement without the need for ionizing radiation scans.
A community detection analysis of malocclusion classes from orthodontics and upper airway data
Authors: Di Carlo Gabriele , Gili Tommaso , Caldarelli Guido , Polimeni Antonella , Cattaneo Paolo M.
Published: May 2021

Objective

The interaction between skeletal class and upper airway has been extensively studied. Nevertheless, this relationship has not been clearly elucidated, with the heterogeneity of results suggesting the existence of different patterns for patients' classification, which has been elusive so far, probably due to oversimplified approaches. Hence, a network analysis was applied to test whether different patterns in patients' grouping exist.

Settings and sample population

Ninety young adult patients with no obvious signs of respiratory diseases and no previous adeno‐tonsillectomy procedures, with thirty patients characterized as Class I (0 < ANB < 4); 30 Class II (ANB > 4); and 30 as Class III (ANB < 0).

Materials and methods

A community detection approach was applied on a graph obtained from a previously analysed sample: thirty‐two measurements (nineteen cephalometric and thirteen upper airways data) were considered.

Results

An airway‐orthodontic complex network has been obtained by cross‐correlating patients. Before entering the correlation, data were controlled for age and gender using linear regression and standardized. By including or not the upper airway measurements as independent variables, two different community structures were obtained. Each contained five modules, though with different patients' assignments.

Conclusion

The community detection algorithm found the existence of more than the three classical skeletal classifications. These results support the development of alternative tools to classify subjects according to their craniofacial morphology. This approach could offer a powerful tool for implementing novel strategies for clinical and research in orthodontics.
Epidemiology of tongue squamous cell carcinoma: A retrospective cohort study
Authors: da Silva Souto Ana Carolina , Vieira Heimlich Fernanda , Lima de Oliveira Leticia , Bergmann Anke , Dias Fernando Luiz , Spíndola Antunes Héliton , de Melo Andreia Cristina , Thuler Luiz Claudio Santos , Cohen Goldemberg Daniel
Published: May 2021

Objective

To analyze the epidemiological profile and the specific survival of patients diagnosed with tongue squamous cell carcinoma at the National Cancer Institute (INCA).

Materials and methods

Hospital Cancer Registry System Data and Mortality Information from 2007 to 2009 were retrieved in a retrospective cohort study of patients diagnosed with tongue squamous cell carcinoma. Specific survival was estimated using the Kaplan–Meier method. The association between independent variables and the risk of death was explored in a Cox proportional hazards regression model.

Results

A total of 346 patients were eligible, mostly male (77.5%), smokers (87.6%), with alcohol consumption (80.9%), with low education (65.6%), advanced staging at the time of diagnosis (71.1%), and presenting a high mortality rate (72.5%). In total, 44.5% of patients underwent a surgical approach alone or associated with another treatment modality, of which 85.1% of patients underwent neck dissection and 90.1% had free surgical margins. Specific survival was 40.6% in two years and 31.2% in five years.

Conclusion

The 5‐year specific survival was considered worse in individuals over 60 years, and who did not undergo surgical treatment or had surgery associated with another treatment, compared to patients undergoing isolated surgery.
Pattern and localization of perineural invasion predict poor survival in oral tongue carcinoma
Authors: Caponio Vito Carlo Alberto , Troiano Giuseppe , Togni Lucrezia , Zhurakivska Khrystyna , Santarelli Andrea , Laino Luigi , Rubini Corrado , Lo Muzio Lorenzo , Mascitti Marco
Published: May 2021

Background

Survival rate for oral tongue squamous cell carcinoma (OTSCC) is still poor and, despite Tumor–Node–Metastasis staging system has been recently updated, patients included under the same stage still show difference in prognosis. Perineural invasion (PNI) emerged to be an indicator of tumor aggressive behavior and unfortunate events. In this study, we investigate the clinic and prognostic value of PNI in a cohort of OTSCC patients.

Methods

About 200 patients with OTSCC were retrospectively evaluated the presence of PNI. PNI was furtherly descripted as uni‐/multifocal and as intra‐/peritumoral. Disease‐Specific and Relapse‐Free Survival (DSS; RFS) were estimated; moreover, we included PNI in the current AJCC 8th Staging System, improving the prognostication model.

Results

Perineural invasion was found in 40.5% of patients. Intratumoral PNI predicted patients at high risk of being diagnosed with lymph–node metastasis. Tumors with positive PNI reported a worse DSS (Hazard Ratio=1.878, p‐value = 0.008). Moreover, patients exhibiting both multifocal intra‐ and peritumoral PNI reported poorest DSS (Hazard Ratio = 2.409, p‐value = 0.010). Patients were reclassified in a new staging system in case of multifocal PNI, providing better stratification capacity.

Conclusions

Perineural invasion might serve as an additional prognostic factor in OTSCC, and by integrating PNI in the staging system, further improvements in prognostication might be reached.
Nurses’ experiences of caring for persons with dementia experiencing responsive behaviours in an acute hospital: A qualitative descriptive study
Authors: Dookhy Joshi , Daly Louise
Published: May 2021

Objective

To explore nurses’ experiences of caring for persons with dementia experiencing responsive behaviours in an acute hospital.

Background

Caring for persons with dementia who have an acute medical illness and are experiencing responsive behaviours in acute hospitals can be challenging for nurses. While existing research has explored the experiences of nurses in providing dementia care in this setting, there is limited knowledge about the specific care experiences of nurses when working to meet the needs of persons with dementia who experience responsive behaviours alongside an admitting diagnosis.

Method

A qualitative descriptive design was implemented. Semi‐structured interviews were carried out with nine nurses working in medical and surgical wards. A thematic analysis approach was used to analyse the data. Ethical approval to conduct the study was received from the writers’ university.

Results

Three themes were found: (a) challenges encountered, (b) a person‐centred response and (c) dementia preparedness. Key findings about challenges encountered by nurses included: the acute hospital environment; increased need for enhanced knowledge; and emotional challenges. Person‐centred responses such as working in partnership with others and reminiscence were identified as strategies to address the challenges. Finally, nurses identified particular interventions that were supportive to them in enhancing their preparedness to meet the needs of persons with dementia who experience responsive behaviours.

Conclusions

Persons with dementia who are acutely unwell and are experiencing responsive behaviours, within acute hospitals, have specific and individualised care needs. Nurses working in these settings must therefore be supported in developing competence in managing these frequently complex clinical cases, while also providing person‐centred care.

Implication for practice

Nurses’ narratives demonstrate that they continue to experience challenges in the presence of responsive behaviours. There is a consequent need for dementia‐specific education on person‐centred ways to address responsive behaviours within acute hospital settings.
Clinical, immunological, and genetic features in 780 patients with autoimmune lymphoproliferative syndrome (ALPS) and ALPS‐like diseases: A systematic review
Authors: Hafezi Nasim , Zaki‐Dizaji Majid , Nirouei Matineh , Asadi Gelayol , Sharifinejad Niusha , Jamee Mahnaz , Erfan Rasouli Seyed , Hamedifar Haleh , Sabzevari Araz , Chavoshzadeh Zahra , Yazdani Reza , Abolhassani Hassan , Aghamohammadi Asghar , Azizi Gholamreza
Published: May 2021

Background

Autoimmune lymphoproliferative syndrome (ALPS) is a group of genetic disorders characterized by early‐onset lymphoproliferation, autoimmune cytopenias, and susceptibility to lymphoma. The majority of ALPS patients carry heterozygous germline mutations in the TNFRSF6 gene. In this study, we conducted a systematic review of patients with ALPS and ALPS‐like syndrome.

Methods

The literature search was performed in Web of Science, Scopus, and PubMed databases to find eligible studies. Additionally, the reference list of all included papers was hand‐searched for additional studies. Demographic, clinical, immunological, and molecular data were extracted and compared between the ALPS and ALPS‐like syndrome.

Results

Totally, 720 patients with ALPS (532 genetically determined and 189 genetically undetermined ALPS) and 59 cases with ALPS‐like phenotype due to mutations in genes other than ALPS genes were assessed. In both ALPS and ALPS‐like patients, splenomegaly was the most common clinical presentation followed by autoimmune cytopenias and lymphadenopathy. Among other clinical manifestations, respiratory tract infections were significantly higher in ALPS‐like patients than ALPS. The immunological analysis showed a lower serum level of IgA, IgG, and lymphocyte count in ALPS‐like patients compared to ALPS. Most (85%) of the ALPS and ALPS‐like cases with determined genetic defects carry mutations in the FAS gene. About one‐third of patients received immunosuppressive therapy with conventional or targeted immunotherapy agents. A small fraction of patients (3.3%) received hematopoietic stem cell transplantation with successful engraftment, and all except two patients survived after transplantation.

Conclusion

Our results showed that the FAS gene with 85% frequency is the main etiological cause of genetically diagnosed patients with ALPS phenotype; therefore, the genetic defect of the majority of suspected ALPS patients could be confirmed by mutation analysis of FAS gene.
Chorus2: design of genome‐scale oligonucleotide‐based probes for fluorescence in situ hybridization
Authors: Zhang Tao , Liu Guanqing , Zhao Hainan , Braz Guilherme T. , Jiang Jiming
Published: May 2021

Oligonucleotide (oligo)‐fluorescence in situ hybridization (FISH) has rapidly becoming the new generation of FISH technique in plant molecular cytogenetics research. Genome‐scale identification of single‐copy oligos is the foundation of successful oligo‐FISH experiments. Here, we introduce Chorus2, a software that is developed specifically for oligo selection. We demonstrate that Chorus2 is highly effective to remove all repetitive elements in selection of single‐copy oligos, which is critical for the development of successful FISH probes. Chorus2 is more effective than Chorus, the original version of the pipeline, and OligoMiner for repeat removal. Chorus2 allows to select oligos that are conserved among related species, which extends the usage of oligo‐FISH probes among phylogenetically related plant species. We also implemented a new function in Chorus2 that allows development of FISH probes from plant species without an assembled genome. We anticipate that Chorus2 can be used in plants as well as in mammalian and other non‐plant species. Chorus2 will broadly facilitate the design of FISH probes for various types of application in molecular cytogenetics research.
Self, partner, and observers' humor perceptions: Relative validity of ratings across sources
Authors: Chong Jia Y. , Theisen Jaclyn C. , Fraley Robert Chris , Ogolsky Brian G.
Published: May 2021

Prior studies examining humor in romantic relationships often assume that behavioral ratings obtained from different sources (i.e., self, partner, and observer) are interchangeable. However, it is unclear if humor ratings across sources reflect a common construct. The current study (N = 160 couples, Mage = 20 years, Mrelationshiplength = 15 months) investigated whether partner and observer ratings of humor offer unique information beyond actor ratings. Additionally, the relative predictive validity of humor ratings was evaluated. In general, the results showed that ratings tend to converge across sources. In addition, partner and observer ratings generally did not explain unique variance beyond self‐ratings. These results suggest that rating sources for assessing humor are largely interchangeable, with a few exceptions. This study offers recommendations for the methodological consideration of rating sources regarding humor reports in close relationships.
Water Effect on Peroxyoxalate Kinetics and Mechanism for Oxalic Esters with Distinct Reactivities
Authors: Cabello Maidileyvis C. , Baader Wilhelm J.
Published: May 2021

The peroxyoxalate reaction is being widely used for various analytical and bioanalytical applications, and however, few mechanistic studies are performed in aqueous media, important mainly for bioanalytical applications, where low chemiluminescence emission quantum yields are obtained. In this sense, we report here kinetic studies on the peroxyoxalate reaction, using two commercially available and widely utilized esters, bis(2,4‐dinitrophenyl) oxalate (DNPO) and bis(2,4,6‐trichlorophenyl) oxalate (TCPO), in 1,2‐dimethoxyethane:water mixtures. The reaction of the much more reactive DNPO, in anhydrous and aqueous media, occurs by a direct nucleophilic attack of H2O2 to the oxalic ester, not involving nucleophilic catalysis by imidazole. Contrary, in the reaction of the less reactive TCPO with H2O2, imidazole acts mainly as nucleophilic catalyst. For both esters, experimental conditions are established where precise kinetic data and emission quantum yields can be obtained. Interestingly, the quantum yields in 1,2‐dimethoxyethane water mixtures increase up to a water concentration of 0.7 mol L–1 and decrease significantly with higher concentrations.
The role of photoprotection in defence of two wheat genotypes against Zymoseptoria tritici
Authors: Ajigboye Olubukola O. , Jayaweera Dasuni P. , Angelopoulou Dimitra , Ruban Alexander V. , Murchie Erik H. , Pastor Victoria , Summers Richard , Ray Rumiana V.
Published: May 2021

This study provides new insights into the role of photoprotection in preformed and induced defence of two wheat genotypes with contrasting phenotypes to infection by Zymoseptoria tritici. We investigated the mechanisms of the photoprotective response during early infection, including nonphotochemical quenching (NPQ), β‐carotene‐derived xanthophylls, reactive oxygen species, and the phytohormones abscisic acid (ABA), jasmonic acid (JA), and salicylic acid (SA). Furthermore, we quantified the effects of pathogenesis on photosynthesis, stomatal control, and expression of plant defence molecular markers. The photoprotective mechanism of successful defence involved the qI component of NPQ leading to rapid down‐regulation of photosystem II quantum yield and chlorophyll a:b, increased biosynthesis of the xanthophyll neoxanthin and ABA, and the expression of chloroplast‐specific enzymes to engage in scavenging of O2●−. Elevated ABA in the resistant genotype correlated with preformed leaf defence traits including low stomatal density, increased expression of wax biosynthesis, and lignification. Z. tritici exhibited reduced germination and branching on the resistant host genotype and hijacked stomatal control in both genotypes by enhancing stomatal sensitivity to light. Increased biosynthesis of JA and anthocyanins, in contrast to SA, were quantified in the incompatible interaction. Our results indicate that ABA and JA in antagonistic action to SA were associated with defence in the resistant genotype, Cougar, against Z. tritici.
Biocontrol of potato early blight and suppression of Alternaria grandis sporulation by Clonostachys spp.
Authors: da Silva Hiago Antonio O. , Teixeira William D. , Borges Álefe V. , Silva Junior Amarildo L. , Alves Kaique S. , Rodrigues Junior Orlando M. , de Abreu Lucas M.
Published: May 2021

Early blight, caused by Alternaria solani and A. grandis, severely affects potato crops around the world, and few management options apart from intensive fungicide use are available. In this work, we tested whether biocontrol treatments with different species of the mycoparasitic fungus Clonostachys could reduce early blight severity on the foliage of pot‐grown potatoes of cultivar Ágata, and affect the survival and sporulation of the causal pathogen A. grandis. Twenty isolates from five Clonostachys species were screened in a preliminary biocontrol trial, and nine of them were selected and tested further in two confirmation trials. Treatments with three isolates from three species (C. chloroleuca, C. pseudochroleuca, C. rhizophaga) resulted in a significant reduction in disease severity in both confirmation trials, with control efficacy ranging from 88.7% to 92.9% in the first trial, and from 83.1% to 84.7% in the second trial. All Clonostachys isolates used in the confirmation trials survived on potato leaf tissues for at least 15 days, and resumed growth when subjected to high humidity, resulting in mycoparasitic overgrowth and significant reduction of the pathogen sporulation. Our results provide evidence that different species of Clonostachys, not only the ubiquitous C. rosea, are sources of useful candidates for the biocontrol of potato early blight and possibly other plant diseases caused by fungal pathogens.
A Political Economy Approach to the Grammar of Institutions: Theory and Methods
Authors: Vannoni Matia
Published: May 2021

This article proposes a political economy approach to the grammar of institutions, by building on the study of contracts in economics. First, I argue that more attention needs to be paid to the costs and benefits of institutions, thus allowing researchers to derive empirically testable hypotheses on the evolution of institutions. In this vein, the role of conditions in studying the grammar of institutions becomes central. Second, I propose, validate, and test an innovative method to study the grammar, based on computational linguistics. This method allows extracting the elements of the grammar in an automated and unsupervised manner, paving the way to large‐N analyses. In so doing, this article seeks to bridge the gap between public policy and political economy.
Do lonely and socially isolated individuals think they die earlier? The link between loneliness, social isolation and expectations of longevity based on a nationally representative sample
Authors: Hajek André , König Hans‐Helmut
Published: May 2021

Background

Loneliness and social isolation both have been linked to morbidity and mortality. However, there is a lack of studies investigating whether these factors are associated with expectations of longevity. Therefore, we aimed to clarify this association.

Methods

Cross‐sectional data were taken from a nationally representative sample of middle‐aged and older individuals (analytical sample, n = 4857). Well‐established scales were used to measure loneliness and social isolation. Equally to other large cohort studies, expectations of longevity were assessed using the question ‘What age do you think you will live to?’ It was adjusted for various socioeconomic and health‐related factors.

Results

After adjusting for various socioeconomic and health‐related covariates, multiple linear regressions showed that both loneliness (total sample: β = −0.97, P < 0.001; men: β = −1.04, P < 0.001; women: β = −0.97, P < 0.01) and social isolation (total sample: β = −0.93, P < 0.001; men: β = −0.86, P < 0.001; women: β = −0.91, P < 0.01) were associated with lower expectations of longevity in the total sample and stratified by gender. Furthermore, lower expectations of longevity were consistently associated with younger age (β = 0.32, P < 0.001), being retired (β = −2.39, P < 0.001), not being employed (β = −1.97, P < 0.001), worse self‐rated health (β = −1.31, P < 0.001), and a higher number of chronic illnesses (β = −0.38, P < 0.001) in the total sample, and in both genders.

Conclusions

Even after adjusting for various covariates, findings still indicate an association between both loneliness and social isolation and markedly lower expectations of longevity. Future studies based on longitudinal data are required to gain further insights.
The influence of progesterone and prostaglandin F2αon decorin and the adhesion of caruncular epithelial cells of bovine placenta at early‐mid pregnancy—Part II
Authors: Jamioł Monika , Wawrzykowski Jacek , Kankofer Marta
Published: May 2021

One of the most important processes determining the proper course of gestation and its physiological termination in cows is the adhesion of epithelial cells allowing for direct contact of maternal and foetal parts of the placenta. Throughout pregnancy, placental cells are under strict hormonal control, which among others regulates the concentration and activity of specific proteins participating in the extracellular matrix remodelling of foetal membranes. The aim of the study was to evaluate the influence of progesterone and prostaglandin F2αon the adhesion of epithelial cells at early‐mid pregnancy in cows. Additionally, the impact of selected hormones on anti‐adhesive properties of decorin was evaluated. Caruncular epithelial cells were isolated from healthy cows during pregnancy, immediately after slaughter. Primary cell cultures derived from the 2nd and 4th month of gestation were used in the experiments. The viability of cells was assessed by MTT assay. The adhesion of cells to fibronectin was measured spectrophotometrically. The activity of metalloproteinases was confirmed by the metalloproteinase assay. Progesterone (10–5and 10–7 mol/L) and prostaglandin F2α(10–4,10–5and 10–7 mol/L) increased the viability of bovine caruncular epithelial cells in the 2nd month of pregnancy. The treatment with prostaglandin F2αsignificantly reduced the number of adherent cells from the 2nd month of gestation at the doses of 10–4and 10–5 mol/L. Both progesterone and prostaglandin F2αwere shown to have an effect of decorin resulting in both a decrease in metalloproteinase activity and an increase in adhesion of cells to fibronectin.
Effectiveness of EmergentAd HocCoordination Groups in Public Health Emergencies
Authors: Kim Yushim , Lee Kangbae , Oh Seong Soo , Park Heejin
Published: May 2021

Whether emergent groups positively or negatively influence a disaster response remains inconclusive in the literature. We analyzed the effect of an emergent group on two interorganizational networks for information communication and resource coordination during a public health emergency response. Using the 2015 Middle East Respiratory Syndrome (MERS) Coronavirus in Korea as a study case, we identified anad hocentity that appeared in both networks. This emergent group, which consists of government officials and public health specialists, directed and coordinated organizations at the center of the response networks. We found that the emergent group positively contributed to efficient information communication but had no effect on the resource network's efficiency. Our interpretation is that thead hocentity was filling relational gaps in the information network, but was redundant in the resource network.
A Computationally Efficient Bayesian Seemingly Unrelated Regressions Model for High-Dimensional Quantitative Trait Loci Discovery
Authors: Bottolo Leonardo , Banterle Marco , Richardson Sylvia , Ala-Korpela Mika , Järvelin Marjo-Riitta , Lewin Alex
Published: May 2021

Our work is motivated by the search for metabolite quantitative trait loci (QTL) in a cohort of more than 5000 people. There are 158 metabolites measured by NMR spectroscopy in the 31-year follow-up of the Northern Finland Birth Cohort 1966 (NFBC66). These metabolites, as with many multivariate phenotypes produced by high-throughput biomarker technology, exhibit strong correlation structures. Existing approaches for combining such data with genetic variants for multivariate QTL analysis generally ignore phenotypic correlations or make restrictive assumptions about the associations between phenotypes and genetic loci. We present a computationally efficient Bayesian seemingly unrelated regressions model for high-dimensional data, with cell-sparse variable selection and sparse graphical structure for covariance selection. Cell sparsity allows different phenotype responses to be associated with different genetic predictors and the graphical structure is used to represent the conditional dependencies between phenotype variables. To achieve feasible computation of the large model space, we exploit a factorisation of the covariance matrix. Applying the model to the NFBC66 data with 9000 directly genotyped single nucleotide polymorphisms, we are able to simultaneously estimate genotype–phenotype associations and the residual dependence structure among the metabolites. The R package BayesSUR with full documentation is available at https://cran.r-project.org/web/packages/BayesSUR/
Associations of temperament types and gender of early adolescents and teachers with adolescents’ school well‐being
Authors: Puonti Ville , Hirvonen Riikka , Kiuru Noona
Published: May 2021

This study examined the role of temperament type and gender of adolescents and teachers in adolescents’ well‐being in school. The sample consisted of 677 Finnish students and 56 classroom teachers. Parents rated adolescent temperament and teachers rated their own temperament in autumn of Grade 6. Self‐reports of school well‐being among adolescents were obtained in autumn and the fall of Grade 6. The results showed that being a girl and having resilient temperament type predicted higher school well‐being. In turn, boys with undercontrolled temperament, who were otherwise at risk for decreased school well‐being, particularly benefited from having a female teacher with resilient temperament. Overall, the results suggest that both adolescent temperament type and gender play important roles in adolescents’ well‐being in school.
On the conditional noncentral beta distribution
Authors: Orsi Carlo
Published: May 2021

The beta family owes its privileged status within unit interval distributions to several relevant features such as, for example, easiness of interpretation and versatility in modeling different types of data. However, the flexibility of its density at the endpoints of the support is poor enough to prevent from properly modeling the data portions having values next to zero and one. Such a drawback can be overcome by resorting to the class of the noncentral beta distributions. Indeed, the latter allows the density to take on arbitrary positive and finite limits which have a really simple form. Nevertheless, the analytical and mathematical complexity of this distribution poses strong limitations on its use as a model for data on the real interval (0, 1). That said, an in‐depth study of a newly found analogue of the noncentral beta distribution is carried out in this article. The latter preserves the applicative potential of the standard noncentral beta class but with the advantage of showing a more straightforward and easily handleable density.
A chromosome‐levelAmaranthus cruentusgenome assembly highlights gene family evolution and biosynthetic gene clusters that may underpin the nutritional value of this traditional crop
Authors: Ma Xiao , Vaistij Fabián E. , Li Yi , Jansen van Rensburg Willem S. , Harvey Sarah , Bairu Michael W. , Venter Sonja L. , Mavengahama Sydney , Ning Zemin , Graham Ian A. , Van Deynze Allen , Van de Peer Yves , Denby Katherine J.
Published: May 2021

Traditional crops have historically provided accessible and affordable nutrition to millions of rural dwellers but have been neglected, with most modern agricultural systems over‐reliant on a small number of internationally traded crops. Traditional crops are typically well‐adapted to local agro‐ecological conditions and many are nutrient‐dense. They can play a vital role in local food systems through enhanced nutrition (particularly where diets are dominated by starch crops), food security and livelihoods for smallholder farmers, and a climate‐resilient and biodiverse agriculture. Using short‐read, long‐read and phased sequencing technologies, we generated a high‐quality chromosome‐level genome assembly forAmaranthuscruentus, an under‐researched crop with micronutrient‐ and protein‐rich leaves and gluten‐free seed, but lacking improved varieties, with respect to productivity and quality traits. The 370.9 Mb genome demonstrates a shared whole genome duplication with a related species,Amaranthushypochondriacus. Comparative genome analysis indicates chromosomal loss and fusion events following genome duplication that are common to both species, as well as fission of chromosome 2 inA. cruentusalone, giving rise to a haploid chromosome number of 17 (versus 16 inA. hypochondriacus). Genomic features potentially underlying the nutritional value of this crop include twoA. cruentus‐specific genes with a likely role in phytic acid synthesis (an anti‐nutrient), expansion of ion transporter gene families, and identification of biosynthetic gene clusters conserved within the amaranth lineage. TheA. cruentusgenome assembly will underpin much‐needed research and global breeding efforts to develop improved varieties for economically viable cultivation and realization of the benefits to global nutrition security and agrobiodiversity.
Boron deficiency‐induced root growth inhibition is mediated by brassinosteroid signalling regulation in Arabidopsis
Authors: Zhang Cheng , He Mingliang , Wang Sheliang , Chu Liuyang , Wang Chuang , Yang Ningmei , Ding Guangda , Cai Hongmei , Shi Lei , Xu Fangsen
Published: May 2021

Brassinosteroids (BRs) are pivotal phytohormones involved in the control of root development. Boron (B) is an essential micronutrient for plants, and root growth is rapidly inhibited under B deficiency conditions. However, the mechanisms underlying this inhibition are still unclear. Here, we identified BR‐related processes underlying B deficiency at the physiological, genetic, molecular/cell biological and transcriptomic levels and found strong evidence that B deficiency can affect BR biosynthesis and signalling, thereby altering root growth. RNA sequencing analysis revealed strong co‐regulation between BR‐regulated genes and B deficiency‐responsive genes. We found that the BR receptor mutants bri1‐119 and bri1‐301 were more insensitive to decreased B supply, and the gain‐of‐function mutants bes1‐D and pBZR1‐bzr1‐D exhibited insensitivity to low‐B stress. Under B deficiency conditions, exogenous 24‐epibrassinolide rescued the inhibition of root growth, and application of the BR biosynthesis inhibitor brassinazole exacerbated this inhibitory effect. The nuclear‐localised signal of BES1 was reduced under low‐B conditions compared with B sufficiency conditions. We further found that B deficiency hindered the accumulation of brassinolide to downregulate BR signalling and modulate root elongation, which may occur through a reduction in BR6ox1 and BR6ox2 mRNA levels. Taken together, our results reveal a role of BR signalling in root elongation under B deficiency.
Two loss‐of‐function alleles of the glutathione S‐transferase (GST) gene cause anthocyanin deficiency in flower and fruit skin of peach (Prunus persica)
Authors: Lu Zhenhua , Cao Huihui , Pan Lei , Niu Liang , Wei Bin , Cui GuoChao , Wang Luwei , Yao Jia‐Long , Zeng Wenfang , Wang Zhiqiang
Published: May 2021

Flower and fruit colors are important agronomic traits. To date, there is no forward genetic evidence that the glutathione S‐transferase (GST) gene is responsible for the white flower color in peach (Prunus persica). In this study, genetic analysis indicated that the white‐flower trait is monogenetic, is recessive to the non‐white allele, and shows pleiotropic effects with non‐white‐flowered types. The genetic locus underpinning this trait was mapped onto chromosome 3 between 0.421951 and 3.227115 Mb by using bulked segregant analysis in conjunction with whole‐genome sequencing, and was further mapped between 0 and 1.178149 Mb by using the backcross 1 (BC1) population. Finally, the locus was fine‐mapped within 535.974‐ and 552.027‐kb intervals by using 151 F2 individuals and 75 individuals from a BC1 self‐pollinated (BC1S1) population, respectively. Pp3G013600, encoding a GST that is known to transport anthocyanin, was identified within the mapping interval. The analysis of genome sequence data showed Pp3G013600 in white flowers has a 2‐bp insertion or a 5‐bp deletion in the third exon. These variants likely render the GST non‐functional because of early stop codons that reduce the protein length from 215 amino acids to 167 and 175 amino acids, respectively. Genetic markers based on these variants validated a complete correlation between the GST loss‐of‐function alleles and white flower in 128 peach accessions. This correlation was further confirmed by silencing of Pp3G013600 using virus‐induced gene silencing technology, which reduced anthocyanin accumulation in peach fruit. The new knowledge from this study is useful for designing peach breeding programs to generate cultivars with white flower and fruit skin.
Improved genome assembly and pan‐genome provide key insights into eggplant domestication and breeding
Authors: Barchi Lorenzo , Rabanus‐Wallace Mark Timothy , Prohens Jaime , Toppino Laura , Padmarasu Sudharsan , Portis Ezio , Rotino Giuseppe Leonardo , Stein Nils , Lanteri Sergio , Giuliano Giovanni
Published: May 2021

Eggplant (Solanum melongena L.) is an important horticultural crop and one of the most widely grown vegetables from the Solanaceae family. It was domesticated from a wild, prickly progenitor carrying small, round, non‐anthocyanic fruits. We obtained a novel, highly contiguous genome assembly of the eggplant ‘67/3’ reference line, by Hi‐C retrofitting of a previously released short read‐ and optical mapping‐based assembly. The sizes of the 12 chromosomes and the fraction of anchored genes in the improved assembly were comparable to those of a chromosome‐level assembly. We resequenced 23 accessions of S. melongena representative of the worldwide phenotypic, geographic, and genetic diversity of the species, and one each from the closely related species Solanum insanum and Solanum incanum. The eggplant pan‐genome contained approximately 51.5 additional megabases and 816 additional genes compared with the reference genome, while the pan‐plastome showed little genetic variation. We identified 53 selective sweeps related to fruit color, prickliness, and fruit shape in the nuclear genome, highlighting selection leading to the emergence of present‐day S. melongena cultivars from its wild ancestors. Candidate genes underlying the selective sweeps included a MYBL1 repressor and CHALCONE ISOMERASE (for fruit color), homologs of Arabidopsis GLABRA1 and GLABROUS INFLORESCENCE STEMS2 (for prickliness), and orthologs of tomato FW2.2, OVATE, LOCULE NUMBER/WUSCHEL, SUPPRESSOR OF OVATE, and CELL SIZE REGULATOR (for fruit size/shape), further suggesting that selection for the latter trait relied on a common set of orthologous genes in tomato and eggplant.
Factors affecting the global distribution ofHydrilla verticillata(L. fil.) Royle: A review
Authors: Patrick Anton E. S. , Florentine Singarayer
Published: May 2021

Hydrilla verticillata(Hydrocharitaceae) is a submerged freshwater flowering plant within the monotypic genus. Over the geological periods, fossils of this family and genus have shown distinct diversifications between warm and cool fluctuations with more adaptations occurring in warmer periods and suppressions during severely cold paleoclimate changes. Recently,H. verticillatahas shown a wide range of adaptive plasticity, allowing successful proliferation into non‐native regions, whilst also undergoing unexplained disappearance from its native localities, and this phenomenon has stimulated this inquiry. Against this somewhat complex background, particular interest for this investigation has been focussed on an understanding of which aspects of climate change have contributed towards global adaptations and distribution patterns ofH.verticillata. Whilst it is recognised that some of these changes are natural, other aggravating impacts are due to anthropogenic influences. Identifying the appropriate combinations of these climatic factors (temperature, rainfall, photoperiod), in concert with environmental (water level, CO2, salinity, eutrophication), geographical (altitude, latitude) and other factors (UV‐B) are necessary precursors for instituting appropriate management strategies. In this respect, control measures are needed in non‐native regions and restoration of this plant in native habitats are essential for its ecologically balanced global distribution.
Insights into the skin microbiome of sickle cell disease leg ulcers
Authors: Byeon Julia , Blizinsky Katherine D. , Persaud Anitra , Findley Keisha , Lee Jung‐Jin , Buscetta Ashley J. , You Shuo , Bittinger Kyle , Minniti Caterina P. , Bonham Vence L. , Grice Elizabeth A.
Published: May 2021

Leg ulcers are estimated to occur in 1%–10% of North American patients with sickle cell disease (SCD). Their pathophysiology remains poorly defined, but as with other chronic wounds, it is hypothesised that the microbial milieu, or microbiome, contributes to their healing and clinical outcomes. This study utilises 16S ribosomal RNA (rRNA) gene sequencing to describe, for the first time, the microbiome of the SCD leg ulcer and its association with clinical factors. In a cross‐sectional analysis of 42 ulcers, we recovered microbial profiles similar to other chronic wounds in the predominance of anaerobic bacteria and opportunistic pathogens including Staphylococcus, Corynebacterium, and Finegoldia. Ulcers separated into two clusters: one defined by predominance of Staphylococcus and smaller surface area, and the other displaying a greater diversity of taxa and larger surface area. We also find that the relative abundance of Porphyromonas is negatively associated with haemoglobin levels, a key clinical severity indicator for SCD, and that Finegoldia relative abundance is negatively associated with CD19+ B cell count. Finally, ratios of Corynebacterium:Lactobacillus and Staphylococcus:Lactobacillus are elevated in the intact skin of individuals with a history of SCD leg ulcers, while the ratio of Lactobacillus:Bacillus is elevated in that of individuals without a history of ulcers. Investigations of the skin microbiome in relation to SCD ulcer pathophysiology can inform clinical guidelines for this poorly understood chronic wound, as well as enhance broader understanding about the role of the skin microbiome in delayed wound healing.
Biomimetic analyses of interactions between macrophages and palmar fascia myofibroblasts derived from Dupuytren's disease reveal distinct inflammatory cytokine responses
Authors: Gonga‐Cavé Brianna C. , Pena Diaz Ana Maria , O'Gorman David B.
Published: May 2021

Dupuytren's disease (DD) is a common and heritable fibrosis of the hand. It is characterized by the shortening and thickening of the palmar fascia into myofibroblastic nodules that can progress to palmar‐digital contractures and permanent loss of dexterity. Molecular analyses of DD tissues and the presence of inflammatory cell infiltrates suggest a pathogenesis initiated by a proinflammatory fascial milieu that promotes myofibroblast activation and palmar fascia contractures. However, the relative contributions of vascular and/or tissue derived immune system cells and cytokine‐sensitive stromal myofibroblasts to the development of this proinflammatory microenvironment are poorly understood. To gain insights into this process, we have developed and tested a collagen‐based 3D tissue biomimetic co‐culture system to assess paracrine interactions between THP‐1‐derived pro‐inflammatory macrophages and primary human palmar fascia myofibroblasts (PFMs). We observed significant and reproducible impacts of collagen‐adherent macrophage and PFM co‐cultures on the cytokine gene expression profiles of these cells compared to their respective monocultures, and significant changes to the resulting cytokine milieu in their shared culture media, notably TNF and IL‐6. Our findings are consistent with central roles for PFMs in cytokine production and immunoregulation of the pro‐inflammatory milieu hypothesized to promote DD development.
Antimicrobial resistance in bacterial isolates from companion animals in Buenos Aires, Argentina: 2011–2017 retrospective study
Authors: Rumi María Valeria , Nuske Ezequiel , Mas Javier , Argüello Andrea , Gutkind Gabriel , Di Conza José
Published: May 2021

The widespread use of antimicrobial therapy in companion animals could lead to increased levels of resistance. Monitoring these levels is critical to understand not only the zoonotic threat of resistant bacteria but also the interspecies transmission of resistance mechanisms. However, data on resistance levels in companion animals of urban areas in Latin America are lacking. In this retrospective study, we analysed 23,922 isolates recovered from clinical samples of dogs and cats between 2011 and 2017. Growing trends of resistance to fluoroquinolones were observed in most bacterial species of veterinary importance with zoonotic potential (Enterobacterales, Pseudomonas and Staphylococcus). Furthermore, an increase of resistance levels to third‐generation cephalosporins was also detected in Enterobacterales. Currently, Pseudomonas aeruginosa, Enterococcus spp. and Streptococcus spp. did not seem to represent a clinical challenge. A high proportion of multidrug‐resistant (MDR) Enterobacterales isolated from urine was reported. It is interesting to outline that resistance to amikacin was exceptional. This study might be considered as a baseline for prospective antimicrobial resistance surveillance in companion animals in our region.
INTRODUCTION TO THE SYMPOSIUM ON EVOLUTION, ORIGINAL SIN, AND THE FALL
Authors: De Cruz Helen , De Smedt Johan
Published: May 2021

This is an introduction to the Symposium on “Evolution, Original Sin, and the Fall,” which has been designed as a thematic section for Zygon: Journal of Religion and Science. The Symposium investigates the enduring question of whether hamartiology (the theological study of sin) is compatible with evolutionary theory. We trace the origins of this question to the debate between Modernists and Traditionalists at the turn of the previous century. Our contributors make headway in these discussions by delving into details, namely, by asking whether the hamartiological views of particular theologians, such as Augustine or Aquinas, can be reconciled with specific aspects of evolutionary theory. They also extend hamartiology in novel directions through the application of critical race theory and literary science to shed new light on the origin and transmission of original sin.
Striated muscle activator of Rho signalling (STARS) overexpression in the mdx mouse enhances muscle functional capacity and regulates the actin cytoskeleton and oxidative phosphorylation pathways
Authors: Sadler Kate J. , Gatta Paul A. Della , Naim Timur , Wallace Marita A. , Lee Albert , Zaw Thiri , Lindsay Angus , Chung Roger S. , Bello Luca , Pegoraro Elena , Lamon Séverine , Lynch Gordon S. , Russell Aaron P.
Published: May 2021

New Findings

What is the central question of this study?

Striated muscle activator of rho signalling (STARS) is an actin‐binding protein that regulates transcriptional pathways controlling muscle function, growth and myogenesis, processes that are impaired in dystrophic muscle: what is the regulation of the STARS pathway in Duchenne muscular dystrophy (DMD)?

What is the main finding and its importance?

Members of the STARS signalling pathway are reduced in the quadriceps of patients with DMD and in mouse models of muscular dystrophy. Overexpression of STARS in the dystrophic deficient mdx mouse model increased maximal isometric specific force and upregulated members of the actin cytoskeleton and oxidative phosphorylation pathways. Regulating STARS may be a therapeutic approach to enhance muscle health.

Duchenne muscular dystrophy (DMD) is characterised by impaired cytoskeleton organisation, cytosolic calcium handling, oxidative stress and mitochondrial dysfunction. This results in progressive muscle damage, wasting and weakness and premature death. The striated muscle activator of rho signalling (STARS) is an actin‐binding protein that activates the myocardin‐related transcription factor‐A (MRTFA)/serum response factor (SRF) transcriptional pathway, a pathway regulating cytoskeletal structure and muscle function, growth and repair. We investigated the regulation of the STARS pathway in the quadriceps muscle from patients with DMD and in the tibialis anterior (TA) muscle from the dystrophin‐deficient mdx and dko (utrophin and dystrophin null) mice. Protein levels of STARS, SRF and RHOA were reduced in patients with DMD. STARS, SRF and MRTFA mRNA levels were also decreased in DMD muscle, while Stars mRNA levels were decreased in the mdx mice and Srf and Mrtfa mRNAs decreased in the dko mice. Overexpressing human STARS (hSTARS) in the TA muscles of mdx mice increased maximal isometric specific force by 13% (P < 0.05). This was not associated with changes in muscle mass, fibre cross‐sectional area, fibre type, centralised nuclei or collagen deposition. Proteomics screening followed by pathway enrichment analysis identified that hSTARS overexpression resulted in 31 upregulated and 22 downregulated proteins belonging to the actin cytoskeleton and oxidative phosphorylation pathways. These pathways are impaired in dystrophic muscle and regulate processes that are vital for muscle function. Increasing the STARS protein in dystrophic muscle improves muscle force production, potentially via synergistic regulation of cytoskeletal structure and energy production.