bluuebunny/crossref_metadata_2025 huggingface dataset:
Gender and the rural–urban divide: family wealth and first marriage among young adults in China
Authors: Zhang Yang
Published: February 2023

In recent decades, owing to rapidly rising marriage expenses, family wealth has gained importance in regard to one’s first marriage. Nevertheless, little is known about how family wealth shapes first marriage in China, where gender and the rural–urban divide affect marriage practices. Drawing on six waves of data from the China Family Panel Studies, I used discrete-time hazard models and a prospective research design to examine the link between family wealth and the subsequent first marriage of young adults aged 16–40 years, and to identify how this link varies by gender and hukou status. The findings indicate a strong positive association between household total asset value and first marriage for rural men and women, and urban men. They also show that ownership of major household assets was positively associated with men’s first marriage, but not with that of women. However, household savings were more predictive for rural women’s first marriage, compared to that of rural men. Family wealth inequality provides a new lens for understanding the marriage patterns of young adults in China. Gendered marriage practices and family wealth arrangements may contribute to women’s disadvantaged positions in wealth possession and accumulation and result in the perpetuation of gender inequality.
Detecting frequency-dependent selection through the effects of genotype similarity on fitness components
Authors: Sato Yasuhiro , Takahashi Yuma , Xu Chongmeng , Shimizu Kentaro K
Published: February 2023

Frequency-dependent selection (FDS) is an evolutionary regime that can maintain or reduce polymorphisms. Despite the increasing availability of polymorphism data, few effective methods are available for estimating the gradient of FDS from the observed fitness components. We modeled the effects of genotype similarity on individual fitness to develop a selection gradient analysis of FDS. This modeling enabled us to estimate FDS by regressing fitness components on the genotype similarity among individuals. We detected known negative FDS on the visible polymorphism in a wild Arabidopsis and damselfly by applying this analysis to single-locus data. Further, we simulated genome-wide polymorphisms and fitness components to modify the single-locus analysis as a genome-wide association study (GWAS). The simulation showed that negative or positive FDS could be distinguished through the estimated effects of genotype similarity on simulated fitness. Moreover, we conducted the GWAS of the reproductive branch number in Arabidopsis thaliana and found that negative FDS was enriched among the top-associated polymorphisms of FDS. These results showed the potential applicability of the proposed method for FDS on both visible polymorphism and genome-wide polymorphisms. Overall, our study provides an effective method for selection gradient analysis to understand the maintenance or loss of polymorphism.
Multi-generation selective landscapes and sub-lethal injuries in stickleback
Authors: Reimchen Thomas E , Bergstrom Carolyn A
Published: February 2023

The interaction between predation landscape and phenotypic variability within prey populations is of substantial significance in evolutionary biology. Extending from several decades of studies at a remote freshwater lake on Haida Gwaii, western Canada, we analyze the incidence of predator-induced sub-lethal injuries in 8,069 wild-captured threespine stickleback (Gasterosteus aculeatus) and using cohort analyses test whether the distribution of injuries informs the selective landscape influencing the bell-shaped frequency distribution of the traits. Our results indicate that (1) the incidence of injuries varies among phenotypes differing in the number and position of lateral plates, (2) these differences occur only among younger fish, (3) the incidence of injuries is inversely related to the estimated population frequencies of plate phenotypes, with the modal phenotype generally having the fewest injuries, (4) direct estimates of selective differentials and relative fitness based on analyses of 1,735 fish from 6 independent yearly cohorts indicates statistically informative elevated differentials in phenotypes with greater number of plates and elevated relative fitness of non-modal phenotypes, and (5) there are significant differences among yearly cohorts in strength and direction of selection, and an increased prevalence of diversifying versus stabilizing selection despite longer-term stasis (4 decades) in trait means. We conclude that the presence of multiple “optimal” phenotypes complements the renewed interests in quantifying short-term temporal or spatial variation in ecological processes in studies of fitness landscapes and intrapopulation variability.
The impact of variation in out-of-hours doctors’ referral practices: a Norwegian registry-based observational study
Authors: Blinkenberg Jesper , Hetlevik Øystein , Sandvik Hogne , Baste Valborg , Hunskaar Steinar
Published: February 2023

Background

In a gatekeeping system, the individual doctor’s referral practice is an important factor for hospital activity and patient safety.

Objective

The aim of the study was to investigate the variation in out-of-hours (OOH) doctors’ referral practice, and to explore these variations’ impact on admissions for selected diagnoses reflecting severity, and 30-day mortality.

Methods

National data from the doctors’ claims database were linked with hospital data in the Norwegian Patient Registry. Based on the doctor’s individual referral rate adjusted for local organizational factors, the doctors were sorted into quartiles of low-, medium-low-, medium-high-, and high-referral practice. The relative risk (RR) for all referrals and for selected discharge diagnoses was calculated using generalized linear models.

Results

The OOH doctors’ mean referral rate was 110 referrals per 1,000 consultations. Patients seeing a doctor in the highest referring practice quartile had higher likelihood of being referred to hospital and diagnosed with the symptom of pain in throat and chest, abdominal pain, and dizziness compared with the medium-low quartile (RR 1.63, 1.49, and 1.95). For the critical conditions of acute myocardial infarction, acute appendicitis, pulmonary embolism, and stroke, we found a similar, but weaker, association (RR 1.38, 1.32, 1.24, and 1.19). The 30-day mortality among patients not referred did not differ between the quartiles.

Conclusions

Doctors with high-referral practice referred more patients who were later discharged with all types of diagnoses, including serious and critical conditions. With low-referral practice, severe conditions might have been overlooked, although the 30-day mortality was not affected.
Evidence of structural rearrangements in ESBL-positive pESI(like) megaplasmids ofS.Infantis
Authors: Alba Patricia , Carfora Virginia , Feltrin Fabiola , Diaconu Elena Lavinia , Sorbara Luigi , Dell'Aira Elena , Cerci Tamara , Ianzano Angela , Donati Valentina , Franco Alessia , Battisti Antonio
Published: February 2023

The increasing prevalence of pESI(like)-positive, multidrug-resistant (MDR) S. Infantis in Europe is a cause of major concern. As previously demonstrated, the pESI(like) megaplasmid is not only a carrier of antimicrobial resistant (AMR) genes (at least tet, dfr, and sul genes), but also harbours several virulence and fitness genes, and toxin/antitoxin systems that enhance its persistence in the S. Infantis host. In this study, five prototype pESI(like) plasmids, of either CTX-M-1 or CTX-M-65 ESBL-producing strains, were long-read sequenced using Oxford Nanopore Technology (ONT), and their complete sequences were resolved. Comparison of the structure and gene content of the five sequenced plasmids, and further comparison with previously published pESI(like) sequences, indicated that although the sequence of such pESI(like) ‘mosaic’ plasmids remains almost identical, their structures appear different and composed of regions inserted or transposed after different events. The results obtained in this study are essential to better understand the plasticity and the evolution of the pESI(like) megaplasmid, and therefore to better address risk management options and policy decisions to fight against AMR and MDR in Salmonella and other food-borne pathogens.

Graphical representation of the pESI-like plasmid complete sequence (ID 12037823/11). Block colours indicate the function of the genes: red: repB gene; pink: class I integrons (IntI); yellow; mobile elements; blue: resistance genes; green: toxin/anti-toxin systems; grey: mer operon; light green: genes involve in conjugation.
A Chromosome-length Assembly of the Black Petaltail (Tanypteryx hageni) Dragonfly
Authors: Tolman Ethan R , Beatty Christopher D , Bush Jonas , Kohli Manpreet , Moreno Carlos M , Ware Jessica L , Weber K Scott , Khan Ruqayya , Maheshwari Chirag , Weisz David , Dudchenko Olga , Aiden Erez Lieberman , Frandsen Paul B
Published: February 2023

We present a chromosome-length genome assembly and annotation of the Black Petaltail dragonfly (Tanypteryx hageni). This habitat specialist diverged from its sister species over 70 million years ago, and separated from the most closely related Odonata with a reference genome 150 million years ago. Using PacBio HiFi reads and Hi-C data for scaffolding we produce one of the most high-quality Odonata genomes to date. A scaffold N50 of 206.6 Mb and a single copy BUSCO score of 96.2% indicate high contiguity and completeness.
Horizontal Gene Transfer and Fusion Spread Carotenogenesis Among Diverse Heterotrophic Protists
Authors: Rius Mariana , Rest Joshua S , Filloramo Gina V , Novák Vanclová Anna M G , Archibald John M , Collier Jackie L
Published: February 2023

Thraustochytrids (phylum: Labyrinthulomycota) are nonphotosynthetic marine protists. Some thraustochytrids have crtIBY, a trifunctional fusion gene encoding a protein capable of β-carotene biosynthesis from geranylgeranyl pyrophosphate. Here we show that crtIBY is essential in, and encodes the sole pathway for, carotenoid biosynthesis in the thraustochytrid Aurantiochytrium limacinum ATCC MYA-1381. We explore the evolutionary origins of CrtIBY and discover that the closest related protein domains are present in a small but diverse group of other heterotrophic protists, including the apusomonad Thecamonas trahens and the dinoflagellates Oxyrrhis marina and Noctiluca scintillans. Each organism within this cluster also contains one or more β-carotene 15-15′ oxygenase genes (blh and rpe65), suggesting that the acquisition of β-carotene biosynthesis genes may have been related to the production of retinal. Our findings support a novel origin of eukaryotic (apo)carotenoid biosynthesis by horizontal gene transfer from Actinobacteria, Bacteroidetes, and/or Archaea. This reveals a remarkable case of parallel evolution of eukaryotic (apo)carotenogenesis in divergent protistan lineages by repeated gene transfers.
Evolutionary History of thePoecilia pictaSex Chromosomes
Authors: Fong Lydia J M , Darolti Iulia , Metzger David C H , Morris Jake , Lin Yuying , Sandkam Benjamin A , Mank Judith E
Published: February 2023

The degree of divergence between the sex chromosomes is not always proportional to their age. In poeciliids, four closely related species all exhibit a male heterogametic sex chromosome system on the same linkage group, yet show a remarkable diversity in X and Y divergence. In Poecilia reticulata and P. wingei, the sex chromosomes remain homomorphic, yet P. picta and P. parae have a highly degraded Y chromosome. To test alternative theories about the origin of their sex chromosomes, we used a combination of pedigrees and RNA-seq data from P. picta families in conjunction with DNA-seq data collected from P. reticulata, P. wingei, P. parae, and P. picta. Phylogenetic clustering analysis of X and Y orthologs, identified through segregation patterns, and their orthologous sequences in closely related species demonstrates a similar time of origin for both the P. picta and P. reticulata sex chromosomes. We next used k-mer analysis to identify shared ancestral Y sequence across all four species, suggesting a single origin to the sex chromosome system in this group. Together, our results provide key insights into the origin and evolution of the poeciliid Y chromosome and illustrate that the rate of sex chromosome divergence is often highly heterogenous, even over relatively short evolutionary time frames.
Least-squares collocation: a spherical harmonic representer theorem
Authors: Chang Guobin , Bian Shaofeng
Published: February 2023

The functional analysis of the least-squares collocation (LSC) for gravity potential modelling using m measurements is revisited starting from an explicit spherical harmonic expansion. A spherical harmonic representer theorem (SHRT) is given: the model of the potential is a linear combination of m kernels or covariances. This theorem is independent of the specific forms of the data-fitting loss and the regularizer, showing that it is a stronger result than the LSC theory. The corresponding reproducing kernel Hilbert space is explicitly specified. When the least-squares data-fitting loss and the quadratic regularizer are employed, the SHRT gives exactly the LSC method for variable prediction. The nominal prediction precision assessment of the SHRT and that of the LSC are also explicitly compared; this contributes to the unification of the deterministic and stochastic analyses of the LSC theory.
Source characteristics of icequakes caused by surface crevasses on Urumqi Glacier No. 1, Tianshan, China
Authors: Ma Haichao , Chu Risheng , Sheng Minhan , Wei Zigen , Zeng Xiangfang , Wang Wei
Published: February 2023

Icequakes associated with crevassing provide key information on stress fields and water flow pathways inside glaciers, conditions which are sensitive to temperature and precipitation. In this study, we analyse seismic data from 321 days recorded by five broad-band seismometers on Urumqi Glacier No. 1, Tianshan, China, to investigate the source characteristics of icequakes. We first apply a multidimensional autoregressive maximum-likelihood algorithm to detect 12 template events from 62 days of continuous waveform data. The centroid locations of the 12 template events are located using a grid-search approach. We then obtain a catalogue of 41 895 icequakes by compiling all seismic data through a template-matching method. The local magnitudes of all icequakes range between −3.3 and 0.5, with a completeness magnitude of −2.95 and Gutenberg–Richter b-value of 1.08. The particle motion and frequency contents of the 12 template events show that the dominant phases on the vertical component are Rayleigh waves at 5–40 Hz, suggesting that these icequakes were generated by near-surface crevasses. The average daily icequake number for each month and diurnal icequake variations show clear seasonal features. The icequakes may be related to growth of the surface crevasses due to additional melting water and precipitation in summer and to the thermal contraction of the ice body in winter.
Partitioning a rock mass based on electrical resistivity data: the choice of clustering method
Authors: Lharti Habiba , Sirieix Colette , Riss Joëlle , Verdet Cécile , Salmon Fabien , Lacanette Delphine
Published: February 2023

The goal of data classification is to organize them into relevant groups using algorithms. In this study, two clustering algorithms are applied to classify a set of geophysical measurements performed around the Lascaux Cave (Dordogne, France). Based on a non-destructive geophysical method, electrical resistivity tomography (ERT), the data (resistivity values) are supposed to characterize the rock mass around the cave.

The rock mass must be divided into an optimal number of homogeneous domains with specific thermal properties to integrate them in the future thermo-aeraulic simulations of the cave. Since the data are georeferenced, a given resistivity cluster corresponds to a specific spatial domain of the rock mass.

This study aims to compare two different clustering methods, the Hierarchical Agglomerative Clustering (HAC) and the K-means methods, on the resistivity data set. Thus, the objective of this study is to determine which of the two methods leads to a partition of the massif with an optimal number of classes, allowing us to find the geological structures partially known thanks to previous studies. The results of these methods are analyzed in light of two different indices, the Silhouette Index (SI) and the Coefficient of Variation (CV). Based on these indices alone, K-means might seem to be the best algorithm, but a fine analysis of each cluster shows that the HAC method gives better results. Indeed, only the HAC method highlights areas already known to be either waterlogged or clayey. Our partial geological knowledge, which is of paramount importance in such a study, also supports the choice of the HAC method.
Unfair Commercial Practices and Individual Consumer Claims for Damages – The Transposition of Art. 11a UCP Directive in Germany and Austria
Authors: Alexander Christian
Published: February 2023

Article 11a(1) UCP Directive obliges the Member States to provide individual rights for consumers harmed by unfair commercial practices. This new provision is intended to ensure that consumers have access to proportionate and effective remedies, including compensation for damage suffered and, where relevant, a price reduction or the termination of the contract. Although the laws against unfair competition in Germany and Austria have similar basic structures, the transposition of Art. 11a(1) UCP Directive shows some significant differences in the way national law provides individual protection for consumers. The legal systems in Germany and Austria are confronted with challenges both in the correct transposition of Art. 11a(1) UCP Directive and the incorporation of individual consumer claims for damages into the structures of domestic law. This article intends both to give a first overview and also to attempt to answer some of the open questions.
Factors contributing to school food program acceptance: a Review of Canadian literature
Authors: Everitt Tracy , Ward Stephanie , Martin Wanda , Engler-Stringer Rachel
Published: February 2023

Diet quality and food security are a concern in school-aged children in Canada. In 2019, the Canadian federal government announced the intention to work towards a national school food program. Understanding the factors that impact school food program acceptability can inform planning to ensure that students are willing to participate. A scoping review of school food programs in Canada completed in 2019 identified 17 peer-reviewed and 18 grey literature publications. Of these, five peer-reviewed and nine grey literature publications included a discussion of factors that impact the acceptance of school food programs. These factors were thematically analyzed into categories: stigmatization, communication, food choice and cultural considerations, administration, location and timing, and social considerations. Considering these factors while planning can help to maximize program acceptability.
Physical activity as an investment or consumption good—a mixed methods approach
Authors: Kuvaja-Köllner Virpi , Laulainen Sanna , Kautonen Juuso , Valtonen Hannu
Published: February 2023

Studying individuals’ motivation to engage in physical activity raises the question of whether physical activity is a consumption good (enjoyment) or an investment good (a health investment). The aims of the study were: (i) What kind of motivational background is it possible to identify for different forms of physical activity among adults, and (ii) Is there an association between different motivational factors and the form and amount of physical activity among adults. A mixed methods approach was applied using interviews (n = 20) and a questionnaire (n = 156). The qualitative data was analysed using content analysis. The quantitative data were analysed using factor and regression analysis. Among the interviewees, different types of motivation were found: ‘enjoyment’, ‘health reasons’ and ‘mixed motivations’, and from the quantitative data: (i) mixed motivation, a combination of enjoyment and investment, (ii) dislike of physical activity, (iii) social, (iv) goal focused, (v) appearance focused and (vi) exercising only within the comfort zone. Mixed-motivational background, with both enjoyment and investment in health, increased weekly physical activity hours significantly (β = 1.733; p = 0.001). Personal appearance-based motivation increased weekly muscle training (β = 0.540; p = 0.000) and brisk physical activity hours (β = 0651; p = 0.014). Conducting such physical activity which provides enjoyment during the performance of the activity, increased weekly balance-focused exercise hours (β = 0.224; p = 0.034). People have different kind of motivational backgrounds for engaging in physical activity. Mixed motivational background, including enjoyment and investment in health, yielded more physical activity in hours than if the person had only one of these motivations.
Association between Loneliness, Mental Health Symptoms, and Treatment Use among Emerging Adults
Authors: Bessaha Melissa , Mushonga Dawnsha , Fedina Lisa , DeVylder Jordan
Published: February 2023

Loneliness research has focused primarily on older adult populations. There is limited research on how loneliness and social support impact young people’s mental health and mental health services use. This article reports an assessment of whether loneliness and social support are associated with mental health services use and mental health symptoms (psychological distress and suicidal ideation) among emerging adults. A subsample of emerging adults ages 18 to 29 (N = 307) was drawn from the 2017 Survey of Police-Public Encounters, a cross-sectional, general population survey administered to residents of New York City and Baltimore. Ordinary least squares and binary logistic regression analyses were performed to model associations between loneliness and mental health symptoms and services use outcomes. Emerging adults with higher levels of loneliness reported higher levels of distress and suicidal ideation. Having more social support, experiencing higher levels of distress, and suicidal ideation were associated with increased odds for using services. First-generation American emerging adults and Black emerging adults were less likely to use services than their U.S.-born and non-Black counterparts. The significant impact of loneliness on mental health symptoms and the effect of social support on service use highlight the importance of developing interventions to prevent and reduce loneliness over the life course.
What Do Newsjunkies Consume and What Do They Know? Two Studies on Intrinsic Need For Orientation, News Diets, and Political Knowledge
Authors: Martin Justin D , Sharma Krishna
Published: February 2023

Recent research on the newsjunkie trait—intrinsic need for orientation (INFO)—has not yet examined specific kinds of information newsjunkies consume or whether the newsjunkie characteristic predicts outcomes like political knowledge. Study 1 surveyed U.S. adults’ (N = 2,059) INFO, hard news consumption, soft news consumption, use of partisan outlets FOX News, and MSNBC, and use of less-partisan outlets like BBC and NBC. The newsjunkie trait was one of the strongest predictors of hard news consumption (like news about foreign affairs and the economy), after controlling for numerous factors, and it did not predict soft news consumption (news about entertainment, sports, etc.). The newsjunkie trait was positively associated with the use of both partisan and less-partisan outlets. Study 2 examined U.S. adults’ (N = 1,054) INFO and political knowledge while holding constant most of the variables controlled for in Study 1. Despite some evidence from Study 1 that newsjunkies are sophisticated news consumers, INFO did not positively predict political knowledge; the strongest positive predictor of political knowledge was consuming political news, and the only other significant news use correlate was the use of FOX News, which was negatively associated with political knowledge. Implications for research on the intrinsic need for orientation, news use, and political outcomes are discussed.
Vaccination Ameliorates Cellular Inflammatory Responses in SARS-CoV-2 Breakthrough Infections
Authors: Huapaya Julio A , Higgins Jeanette , Kanth Shreya , Demirkale Cumhur Y , Gairhe Salina , Aboye Etsubdink A , Regenold David , Sahagun Seynt Jiro , Pastor Gloria , Swaim Doris , Dewar Robin , Rehman Tauseef , Highbarger Helene C , Lallemand Perrine , Laverdure Sylvain , Adelsberger Joseph , Rupert Adam , Li Willy , Krack Janell , Teferi Gebeyehu , Kuruppu Janaki , Strich Jeffrey R , Davey Richard , Childs Richard , Chertow Daniel , Kovacs Joseph A , Barnett Christopher , Torabi-Parizi Parizad , Suffredini Anthony F ,   the COVID-ARC Study Group, Purdy Julia , Chairez Cheryl , McClaughlin Mary , Dee Nicola , Curl Kara A , Caldararo Rocco , Rehm Catherine , Santamaria Ulisses , Giles Natalie , Fallouh Nabil , DeVille Michelle , Moriarity Theresa , Pouomogne Diane Boyom , Gonzales Melissa , Shenoy Aarthi
Published: February 2023

Background

Data on cellular immune responses in persons with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection following vaccination are limited. The evaluation of these patients with SARS-CoV-2 breakthrough infections may provide insight into how vaccinations limit the escalation of deleterious host inflammatory responses.

Methods

We conducted a prospective study of peripheral blood cellular immune responses to SARS-CoV-2 infection in 21 vaccinated patients, all with mild disease, and 97 unvaccinated patients stratified based on disease severity.

Results

We enrolled 118 persons (aged 50 years [SD 14.5 years], 52 women) with SARS-CoV-2 infection. Compared to unvaccinated patients, vaccinated patients with breakthrough infections had a higher percentage of antigen-presenting monocytes (HLA-DR+), mature monocytes (CD83+), functionally competent T cells (CD127+), and mature neutrophils (CD10+); and lower percentages of activated T cells (CD38+), activated neutrophils (CD64+), and immature B cells (CD127+CD19+). These differences widened with increased disease severity in unvaccinated patients. Longitudinal analysis showed that cellular activation decreased over time but persisted in unvaccinated patients with mild disease at 8-month follow-up.

Conclusions

Patients with SARS-CoV-2 breakthrough infections exhibit cellular immune responses that limit the progression of inflammatory responses and suggest mechanisms by which vaccination limits disease severity. These data may have implications for developing more effective vaccines and therapies.

Clinical Trials Registration. NCT04401449.
Analysis of Plasmablasts From Children With Kawasaki Disease Reveals Evidence of a Convergent Antibody Response to a Specific Protein Epitope
Authors: Rowley Anne H , Arrollo David , Shulman Stanford T , Torres Abigail , O’Brien Amornrat , Wylie Kristine , Kim Kwang-Youn A , Baker Susan C
Published: February 2023

Background

Kawasaki disease (KD) is a febrile illness of young childhood that can result in coronary artery aneurysms and death. Coronavirus disease 2019 (COVID-19) mitigation strategies resulted in a marked decrease in KD cases worldwide, supporting a transmissible respiratory agent as the cause. We previously reported a peptide epitope recognized by monoclonal antibodies (MAbs) derived from clonally expanded peripheral blood plasmablasts from 3 of 11 KD children, suggesting a common disease trigger in a subset of patients with KD.

Methods

We performed amino acid substitution scans to develop modified peptides with improved recognition by KD MAbs. We prepared additional MAbs from KD peripheral blood plasmablasts and assessed MAb characteristics that were associated with binding to the modified peptides.

Results

We report a modified peptide epitope that is recognized by 20 MAbs from 11 of 12 KD patients. These MAbs predominantly use heavy chain VH3-74; two-thirds of VH3-74 plasmablasts from these patients recognize the epitope. The MAbs were nonidentical between patients but share a common complementarity-determining region 3 (CDR3) motif.

Conclusions

These results demonstrate a convergent VH3-74 plasmablast response to a specific protein antigen in children with KD, supporting one predominant causative agent in the etiopathogenesis of the illness.
Multi-trait ensemble genomic prediction and simulations of recurrent selection highlight importance of complex trait genetic architecture for long-term genetic gains in wheat
Authors: Fradgley Nick , Gardner Keith A , Bentley Alison R , Howell Phil , Mackay Ian J , Scott Michael F , Mott Richard , Cockram James
Published: February 2023

Cereal crop breeders have achieved considerable genetic gain in genetically complex traits, such as grain yield, while maintaining genetic diversity. However, focus on selection for yield has negatively impacted other important traits. To better understand multi-trait selection within a breeding context, and how it might be optimized, we analysed genotypic and phenotypic data from a genetically diverse, 16-founder wheat multi-parent advanced generation inter-cross population. Compared to single-trait models, multi-trait ensemble genomic prediction models increased prediction accuracy for almost 90 % of traits, improving grain yield prediction accuracy by 3–52 %. For complex traits, non-parametric models (Random Forest) also outperformed simplified, additive models (LASSO), increasing grain yield prediction accuracy by 10–36 %. Simulations of recurrent genomic selection then showed that sustained greater forward prediction accuracy optimized long-term genetic gains. Simulations of selection on grain yield found indirect responses in related traits, involving optimized antagonistic trait relationships. We found multi-trait selection indices could effectively optimize undesirable relationships, such as the trade-off between grain yield and protein content, or combine traits of interest, such as yield and weed competitive ability. Simulations of phenotypic selection found that including Random Forest rather than LASSO genetic models, and multi-trait rather than single-trait models as the true genetic model accelerated and extended long-term genetic gain whilst maintaining genetic diversity. These results (i) suggest important roles of pleiotropy and epistasis in the wider context of wheat breeding programmes, and (ii) provide insights into mechanisms for continued genetic gain in a limited genepool and optimization of multiple traits for crop improvement.
File Search: A Contrast Between Beliefs and Behavior
Authors: Bergman Ofer , Sher Esther
Published: February 2023

This study sheds light on the disparities between file search beliefs and as opposed to file search behavior. Using a questionnaire (N = 110), we measured participants’ intuitive beliefs regarding query-based search usage and compared it to well-validated scientific findings. Our participants believed that search is the dominant retrieval strategy; search engine technology strongly increases search usage and will eventually eliminate folder navigation; and that young people search more than older ones. Contrary to these beliefs, research has shown that users prefer folder-based navigation, with search being used only as a last resort for a small minority of retrievals; search engine technology has little effect on search usage or folder organization; folder navigation has deep neuro-cognitive roots and there is a positive correlation between age and search percentage. We then discuss possible reasons for these contrasts and conclude that evidence-based personal information management education should be used to correct these baseless beliefs.
Intergenic region polymorphism analysis: a novel genotyping method forKlebsiella pneumoniae
Authors: Kong Nianqing , Shu Shenghuang , Zhang Cangyun , Li Chuyi , Luo Yongwen , Fang Shuying , Bi Shuilian
Published: February 2023

Aims

The ability to distinguish between Klebsiella pneumoniae strains is critical for outbreak investigations. A new typing method, intergenic region polymorphism analysis (IRPA), was developed, validated, and the discriminatory power was determined by comparison with multiple-locus variable-number tandem repeat analysis (MLVA) in this study.

Methods and results

This method is based on the idea that every IRPA locus (polymorphic fragment of intergenic regions present in one strain but not in other strains or different fragment sizes in other strains) could divide strains into different genotypes. A 9-loci IRPA scheme was designed to type 64 K. pneumoniae isolates. Five IRPA loci were identified that conferred the same level of discrimination as the 9-loci initially examined. Among these K. pneumoniae isolates, 7.81% (5/64), 6.25% (4/64), 4.96% (3/64), 9.38% (6/64), and 1.56% (1/64) were capsular serotypes K1, K2, K5, K20, and K54, respectively. The discriminatory power of the IRPA method was better than that of MLVA expressed in Simpson's index of diversity (SI) at 0.997 and 0.988, respectively. The congruent analysis of the IRPA method and MLVA showed moderate congruence between the two methods (AR = 0.378). The AW indicated that if IRPA data are availabl, one can accurately predict the MLVA cluster.

Conclusion

The IRPA method was found to have higher discriminatory power than MLVA and allowed for simpler band profile interpretation. The IRPA method is a rapid, simple, and high-resolution technique for molecular typing of K. pneumoniae.
Genomic insights intoCronobacterspp. recovered from food and human clinical cases in Zhejiang province, China (2008–2021)
Authors: Li Yi , Lin Guankai , Zhang Leyi , Hu Yuqin , Hong Chengji , Xie Airong , Fang Lei
Published: February 2023

Aims

Cronobacter spp. are emerging food-borne pathogens capable of causing life-threatening illness via several distinct routes. Although endeavors to reduce the incidence of Cronobacter infections are implemented, potential risk of these microorganisms on food safety remains poorly understood. Here, we evaluated the genomic features of clinical Cronobacter and the possible food reservoirs of these infections.

Methods and results

Whole-genome sequencing (WGS) data of all human clinical cases (n = 15) during 2008–2021 in Zhejiang were used and compared to sequenced Cronobacter genomes (n = 76) representing various food products. Cronobacter strains exhibited a high degree of genetic diversity by WGS-based subtyping. A variety of serotypes (n = 12) and sequence types (n = 36) were identified, including six novel STs (ST762-ST765, ST798, and ST803) first-time described in this study. Nine clinical clusters representing 12/15 (80%) patients match a potential food source. Genomic insights into virulence genes revealed species/hosts specificity signatures associated with autochthonous populations. Resistance to streptomycin, azithromycin, sulfanilamide isoxazole, cefoxitin, amoxicillin, ampicillin, and chloramphenicol, as well as multidrug resistance, was noted. WGS data can be used to predict resistance phenotypes in amoxicillin, ampicillin, and chloramphenicol, which were extensively used in clinical treatment.

Conclusions

The wide dissemination of pathogenic potential and antibiotic-resistant strains in multiple food sources emphasized the importance of rigorous food safety policies to reduce Cronobacter contamination in China.
Freshwater environment as a reservoir of extended-spectrum β-lactamase-producing Enterobacteriaceae
Authors: Cho Sohyun , Jackson Charlene R , Frye Jonathan G
Published: February 2023

Surface water receives large quantities of wastes from human and animal sources, thus providing an ideal setting for the accumulation, development, and dissemination of antibiotic resistant bacteria, including extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae. The rapid spread of ESBL-producing Enterobacteriaceae, particularly Escherichia coli and Klebsiella pneumoniae, is a growing threat to public health, and there have been increasing reports on the prevalence and abundance of ESBL-producing Enterobacteriaceae in aquatic environments all over the globe. The objective of this review is to understand the extent of ESBL-producing Enterobacteriaceae contamination in aquatic environments and to enhance our knowledge on the role of the freshwater environment as a reservoir and transmission routes for these bacteria. In this review, we present the prevalence and distribution of ESBL-producing Enterobacteriaceae and their ESBL genes in the freshwater environment, potential sources of these bacteria in the aquatic environment, as well as their potential drivers in the environment, including anthropogenic and environmental factors.
Effects of feeding levels on ileal amino acid digestibility of extruded full fat soybeans in nongestating sows
Authors: Wang Ya , Ma Xiangyuan , Li Guowei , Sun Mengmeng , Xu Shengyu , Lin Yan , Hua Lun , Li Jian , Feng Bin , Fang Zhengfeng , Jiang Xuemei , Zhuo Yong , Che Lianqiang , Wu De
Published: February 2023

The objectives of this study were to investigate the effect of feeding levels on amino acid (AA) digestibility of extruded full fat soybeans (EFSB) fed to nongestating sows and to provide a reference for setting feed intake level when evaluating the quality of nutrients in the feed ingested by sows. Twelve nongestating sows (parity 3 to 5) were fitted with a T-cannula at the distal ileum. After recovery, sows were assigned to a replicated 6 × 3 incomplete Latin square design using two diets (nitrogen-free and EFSB) and three levels of feed intake (1.3, 2.0, and 3.4 times the maintenance requirement for metabolizable energy (ME)). The design included six dietary treatments and three periods, and each period contained two replicates for a total of six replicate sows per treatment. All diets contained 0.3% chromic oxide as an indigestible marker. In each period, ileal digesta samples were collected continuously for 12 h on days 6 and 7 after 5 d of acclimation to the experimental diet. Results of the experiment indicated that different feeding levels (1.3, 2.0, and 3.4 times the maintenance requirement for ME) had no effects on apparent ileal digestibility (AID) of AA and standardized ileal digestibility (SID) of AA, but feeding level did affect the endogenous AA loss estimated using the nitrogen-free diet method. Endogenous phenylalanine excretion was greater with 1.3 times than with 3.4 times the maintenance requirement for ME (P = 0.03), and endogenous tyrosine excretion was greater with 1.3 and 2.0 times than with 3.4 times the maintenance requirement for ME (P = 0.01). Increasing feed consumption resulted in greater loss of total endogenous AAs and crude protein (CP). In conclusion, feeding levels of 1.3 to 3.4 times the maintenance requirement for ME did not affect the AID and SID of AA of EFSB fed to nongestating sows.
Quantitative Analysis of Lysergic Acid Diethylamide and Metabolite in Urine by Automated Extraction and Liquid Chromatography–Tandem Mass Spectrometry
Authors: Patton Amy L , Brown Jordan , Heine Kimberley , Sartori David A , Karschner Erin L , Walterscheid Jeffrey P
Published: February 2023

Recently, lysergic acid diethylamide (LSD) has become a resurgent drug of abuse. The detection of LSD is problematic because of the low dosage taken by users, light and heat sensitivity of the analyte and the lack of efficient analytical methods. Presented here is the validation of an automated sample preparation method for the analysis of LSD and its primary urinary metabolite, 2-oxo-3-hydroxy-LSD (OHLSD), in urine samples by liquid chromatography–tandem mass spectrometry. Analytes were extracted from urine using an automated Dispersive Pipette XTRaction method on Hamilton STAR and STARlet liquid handling systems. The limit of detection for both analytes was administratively defined at the lowest calibrator used in the experiments, and the limit of quantitation was 0.05 ng/mL for both analytes. All validation criteria were acceptable per Department of Defense Instruction 1010.16 requirements. This method offers an efficient, sensitive analytical solution to routinely evaluate large numbers of urine specimens for LSD in workplace drug deterrence programs.
Demographic and Socioeconomic Risk Factors for Granulomatous Mastitis in the United States: A Case-Control Study
Authors: Capiro Nina , Naik Priyanka , Lo Amanda , Sayre James , Shaheen Magda , Thomas Mariam , Roth Antoinette
Published: February 2023

Objective

Granulomatous mastitis (GM) is a benign breast disease that can have an extended clinical course impacting quality of life and causing breast disfigurement. Granulomatous mastitis has been studied throughout the world; however, less is known about GM patients in the United States. We aim to identify demographic and socioeconomic factors associated with GM in the United States.

Methods

An IRB-approved retrospective case-control study was performed of 92 patients with biopsy-proven GM at two institutions in Los Angeles, California: a safety-net hospital and an academic institution. Age-matched controls were selected from patients presenting for diagnostic breast imaging. Demographic and socioeconomic characteristics were collected. Data were analyzed using univariable test for odds ratios (ORs) with 95% confidence intervals (CIs) and multivariable conditional logistic regression.

Results

Patients with GM were more likely to prefer Spanish language (OR 6.20, 95% CI: 2.71%–14.18%), identify as Hispanic/Latina (OR 5.18, 95% CI: 2.38%–11.30%), and be born in Mexico (OR 3.85, 95% CI: 1.23%–12.02%). Cases were more likely to have no primary care provider (OR 3.76, 95% CI: 1.97%–7.14%) and use California Medicaid for undocumented adults (OR 3.65, 95% CI: 1.89%–7.08%). In the multivariable analysis, participants who preferred Spanish language had four times higher odds of GM versus those who preferred English language (OR 4.32, 95% CI: 1.38%–13.54%).

Conclusion

Patients with GM may have barriers to health care access, such as preferring Spanish language, being an undocumented immigrant, and not having a primary care provider. Given these health care disparities, further research is needed to identify risk factors, etiologies, and treatments for this subset of GM patients.
Estimating phylogenies from genomes: A beginners review of commonly used genomic data in vertebrate phylogenomics
Authors: Carter Javan K , Kimball Rebecca T , Funk Erik R , Kane Nolan C , Schield Drew R , Spellman Garth M , Safran Rebecca J
Published: February 2023

Despite the increasing feasibility of sequencing whole genomes from diverse taxa, a persistent problem in phylogenomics is the selection of appropriate genetic markers or loci for a given taxonomic group or research question. In this review, we aim to streamline the decision-making process when selecting specific markers to use in phylogenomic studies by introducing commonly used types of genomic markers, their evolutionary characteristics, and their associated uses in phylogenomics. Specifically, we review the utilities of ultraconserved elements (including flanking regions), anchored hybrid enrichment loci, conserved nonexonic elements, untranslated regions, introns, exons, mitochondrial DNA, single nucleotide polymorphisms, and anonymous regions (nonspecific regions that are evenly or randomly distributed across the genome). These various genomic elements and regions differ in their substitution rates, likelihood of neutrality or of being strongly linked to loci under selection, and mode of inheritance, each of which are important considerations in phylogenomic reconstruction. These features may give each type of marker important advantages and disadvantages depending on the biological question, number of taxa sampled, evolutionary timescale, cost effectiveness, and analytical methods used. We provide a concise outline as a resource to efficiently consider key aspects of each type of genetic marker. There are many factors to consider when designing phylogenomic studies, and this review may serve as a primer when weighing options between multiple potential phylogenomic markers.
Tea domain transcription factor TEAD4 mitigates TGF-β signaling and hepatocellular carcinoma progression independently of YAP
Authors: Luo Weicheng , Li Yi , Zeng Yi , Li Yining , Cheng Minzhang , Zhang Cheng , Li Fei , Wu Yiqing , Huang Chunhong , Yang Xiaolong , Kremerskothen Joachim , Zhang Jianmin , Zhang Chunbo , Tu Shuo , Li Zhihua , Luo Zhijun , Lin Zhenghong , Yan Xiaohua
Published: February 2023

Tea domain transcription factor 4 (TEAD4) plays a pivotal role in tissue development and homeostasis by interacting with Yes-associated protein (YAP) in response to Hippo signaling inactivation. TEAD4 and YAP can also cooperate with transforming growth factor-β (TGF-β)-activated Smad proteins to regulate gene transcription. Yet, it remains unclear whether TEAD4 plays a YAP-independent role in TGF-β signaling. Here, we unveil a novel tumor suppressive function of TEAD4 in liver cancer via mitigating TGF-β signaling. Ectopic TEAD4 inhibited TGF-β-induced signal transduction, Smad transcriptional activity, and target gene transcription, consequently suppressing hepatocellular carcinoma cell proliferation and migration in vitro and xenograft tumor growth in mice. Consistently, depletion of endogenous TEAD4 by siRNAs enhanced TGF-β signaling in cancer cells. Mechanistically, TEAD4 associates with receptor-regulated Smads (Smad2/3) and Smad4 in the nucleus, thereby impairing the binding of Smad2/3 to the histone acetyltransferase p300. Intriguingly, these negative effects of TEAD4 on TGF-β/Smad signaling are independent of YAP, as impairing the TEAD4–YAP interaction through point mutagenesis or depletion of YAP and/or its paralog TAZ has little effect. Together, these results unravel a novel function of TEAD4 in fine tuning TGF-β signaling and liver cancer progression in a YAP-independent manner.
Hysterectomy, bilateral oophorectomy, and breast cancer risk in a racially diverse prospective cohort study
Authors: Lovett Sharonda M , Sandler Dale P , O’Brien Katie M
Published: February 2023

Background

Gynecologic surgery is hypothesized to reduce risk of breast cancer; however, associations may be modified by subsequent hormone use. Our objective was to examine the association between gynecologic surgery and breast cancer incidence considering the use of hormone therapy.

Methods

The Sister Study is a prospective cohort of initially breast cancer–free women aged 35-74 years with a sister who had breast cancer. We used Cox proportional hazards models to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for the association between gynecologic surgery (no surgery, hysterectomy only, bilateral oophorectomy with or without hysterectomy) and incident breast cancer among 50 701 women.

Results

History of gynecologic surgery was common, with 13.8% reporting hysterectomy only and 18.1% reporting bilateral oophorectomy with or without hysterectomy. During follow-up (median = 11.4 years), 3948 cases were diagnosed. Compared with no surgery, bilateral oophorectomy was inversely associated with breast cancer (HR = 0.91, 95% CI = 0.83 to 1.00), and hysterectomy alone was positively associated (HR = 1.12, 95% CI = 1.02 to 1.23). Compared with no surgery and no hormone therapy, bilateral oophorectomy combined with estrogen only therapy (HR = 0.83, 95% CI = 0.74 to 0.94) was inversely associated with breast cancer, while hysterectomy combined with estrogen plus progestin therapy was positively associated with breast cancer (HR = 1.25, 95% CI = 1.01 to 1.55).

Conclusions

We observed an inverse association between bilateral oophorectomy and breast cancer risk. The positive association between hysterectomy and breast cancer may be due to concomitant estrogen plus progestin therapy.