bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating transcriptome complexities across eukaryotes
Authors: Titus-McQuillan James E. , Nanni Adalena V. , McIntyre Lauren M. , Rogers Rebekah L. 
Published: May 2023

Abstract
Background
Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth of knowledge ripe for exploration. With the “remarkable lack of correspondence” between genome size and complexity, there needs to be a way to quantify complexity across organisms. In this study, we use a set of complexity metrics that allow for evaluating changes in complexity using TranD.

Results
We ascertain if complexity is increasing or decreasing across transcriptomes and at what structural level, as complexity varies. In this study, we define three metrics – TpG, EpT, and EpG- to quantify the transcriptome's complexity that encapsulates the dynamics of alternative splicing. Here we compare complexity metrics across 1) whole genome annotations, 2) a filtered subset of orthologs, and 3) novel genes to elucidate the impacts of orthologs and novel genes in transcript model analysis. Effective Exon Number (EEN) issued to compare the distribution of exon sizes within transcripts against random expectations of uniform exon placement. EEN accounts for differences in exon size, which is important because novel gene differences in complexity for orthologs and whole-transcriptome analyses are biased towards low-complexity genes with few exons and few alternative transcripts.

Conclusions
With our metric analyses, we are able to quantify changes in complexity across diverse lineages with greater precision and accuracy than previous cross-species comparisons under ortholog conditioning. These analyses represent a step toward whole-transcriptome analysis in the emerging field of non-model evolutionary genomics, with key insights for evolutionary inference of complexity changes on deep timescales across the tree of life. We suggest a means to quantify biases generated in ortholog calling and correct complexity analysis for lineage-specific effects. With these metrics, we directly assay the quantitative properties of newly formed lineage-specific genes as they lower complexity.
A comprehensive analysis of copy number variations in diverse apple populations
Authors: Xu Jinsheng , Zhang Weihan , Zhang Ping , Sun Weicheng , Han Yuepeng , Li Li 
Published: May 2023

Abstract
Background
As an important source of genetic variation, copy number variation (CNV) can alter the dosage of DNA segments, which in turn may affect gene expression level and phenotype. However, our knowledge of CNV in apple is still limited. Here, we obtained high-confidence CNVs and investigated their functional impact based on genome resequencing data of two apple populations, cultivars and wild relatives.

Results
In this study, we identified 914,610 CNVs comprising 14,839 CNV regions (CNVRs) from 346 apple accessions, including 289 cultivars and 57 wild relatives. CNVRs summed to 71.19 Mb, accounting for 10.03% of the apple genome. Under the low linkage disequilibrium (LD) with nearby SNPs, they could also accurately reflect the population structure of apple independent of SNPs. Furthermore, A total of 3,621 genes were covered by CNVRs and functionally involved in biological processes such as defense response, reproduction and metabolic processes. In addition, the population differentiation index ($${V}_{st}$$

V

st

) analysis between cultivars and wild relatives revealed 127 CN-differentiated genes, which may contribute to trait differences in these two populations.

Conclusions
This study was based on identification of CNVs from 346 diverse apple accessions, which to our knowledge was the largest dataset for CNV analysis in apple. Our work presented the first comprehensive CNV map and provided valuable resources for understanding genomic variations in apple.
Comparative short-term and survival outcomes of three specimen extraction techniques in laparoscopic low rectal cancer surgery: does it affect ileostomy closure?
Authors: Chen Haipeng , Huang Fei , Yang Ming , Zhao Zhixun , Guan Xu , Liu Zheng , Jiang Zheng , Liu Qian , Zheng Zhaoxu , Wang Xishan 
Published: May 2023

Abstract
Introduction
This study aimed to compare the short-term and survival outcomes in laparoscopic low rectal cancer surgery with three different specimen extraction techniques, and whether it affects loop ileostomy closure.

Materials and methods
A consecutive series of patients with low rectal cancer who underwent laparoscopic low anterior resection plus protective loop ileostomy (LAR-PLI) were enrolled. Three main techniques, namely specimen extraction through auxiliary incision (EXAI), specimen extraction through stoma incision (EXSI), and specimen eversion and extra-abdominal resection (EVER), were employed. The postoperative short-term and survival outcomes of the three techniques and the impact on loop ileostomy closure were compared.

Results
In all, 254 patients were enrolled in this study: 104 (40.9%) in the EXAI group, 104 (40.9%) in the EXSI group, and 46 (18.1%) in the EVER group. For primary surgery, EXAI group had significantly longer operative time (P < 0.001), more intraoperative bleeding (P < 0.001), longer length of abdominal incision (P<0.001), longer time to first flatus (P < 0.001), longer time to first defecation (P < 0.001), longer time to first eat (P < 0.001), and longer postoperative hospital stays (P = 0.005) than the EXSI and EVER groups. The primary postoperative complication rate in the EXAI and EVER group was significantly higher than in the EXSI group (P = 0.005). In loop ileostomy closure, EXAI group had significantly longer operative time (P = 0.001), more bleeding volume, and longer postoperative hospital stays (P < 0.001) than the EXSI and EVER groups. For survival outcomes, the 3-year local recurrence-free survival (LRFS) is 92.6% for all patients. The 3-year LRFS for patients in EXAI, EXSI, and EVER were 90.1%, 95.4%, and 92.7%, with P = 0.476.

Conclusions
Our single-center results found that in LAR-PLI surgery for low rectal cancer, the short-term outcomes of specimen extraction through the stoma incision or anus were better than that through the auxiliary incision, but the 3-year LRFS was no statistically different.
Changes to physical activity behavior during the COVID-19 pandemic and their associated factors: a cross sectional survey of Mexican women
Authors: Stratton Catherine , Fourtassi Maryam , Ramia Ioana , Pandiyan Uma , Cooper Rory , Hajjioui Abderrazak , Krassioukov Andrei , Peterson Mark D. , Balikuddembe Joseph K , Palomba Angela , Hong Bo-Young , Tripathi Deo Rishi , Tuakli-Wosornu Yetsa A , Muñoz Velasco Laura Paulina 
Published: May 2023

Abstract
Background
On March 24, 2020, the Mexican Government established social distancing measures to address the outbreak of the COVID-19 pandemic. The resulting home confinement affected daily lifestyle habits such as eating, sleeping, and physical activity (PA). The objectives of this study were to determine changes in PA behaviors among Mexican women due to the COVID-19 pandemic and to assess potential factors associated with these changes.

Methods
This was a cross-sectional study based on an anonymous online questionnaire developed by the Task Force on Physical Activity for Persons with Disabilities (PAPD) within the International Society of Physical and Rehabilitation Medicine (ISPRM). Descriptive, quantitative statistics were used for data analysis. A Chi-squared (χ²) test was used to explore associations between dependent and independent variables.

Results
A total of 1882 surveys were completed. Among the respondents, 53.3% declared that their PA was reduced during the pandemic, 26.6% reported similar PA behavior, and 20.1% declared that their PA had increased during the pandemic. Lower PA behavior during the pandemic was associated with lower education levels, stricter pandemic constraints, obesity, and lower self-perceived functioning levels. A statistically significant association between poorer self-perceived mental health and decreased PA behaviors was also found. Respondents who were younger, self-perceived as unimpaired, not overweight, and whose income was not impacted by COVID-19 were associated with higher levels of reported physical and mental health.

Conclusions
The study results identify disparities experienced in PA behavior during the COVID-19 pandemic among Mexican women and highlights the need for social support for PA participation.
An eConsultant versus a hospital-based outpatient consultation for general (internal) medicine: a costing analysis
Authors: Job Jenny , Nicholson Caroline , Donald Maria , Jackson Claire , Byrnes Joshua 
Published: May 2023

AbstractBackgroundThe eConsultant model of care is an outpatient substitution approach which has been evaluated and implemented extensively internationally. It provides an asynchronous, digital, clinician-to-clinician advice service, giving primary care physicians remote access to specialist support for patient care within 3 business days. Results from initial trials of the eConsultant model in Australia support international evidence of reduced wait times and improved access to specialist input, avoidance of face-to-face hospital outpatient visits, and better integrated care. This study compared the cost of delivery of an eConsultant episode of care with that of a hospital-based outpatient appointment.MethodsA cost-minimisation analysis, using a decision analytic model, was used to compare the two approaches. eConsultant costs were calculated from specialist reported data (minutes spent preparing the response; the number of patients referred subsequently for a hospital-based outpatient appointment) and administration staff data (time spent recording the occasion-of-service). Outpatient costs were calculated using finance data and information from outpatient clinic managers at the hospital-based outpatient clinic. The primary outcome was incremental cost saving per patient from a hospital system perspective. Uncertainty was explored using one-way sensitivity analyses and characterised with probabilistic sensitivity analysis using 10,000 Monte Carlo simulations.ResultsThe traditional referral pathway cost estimate was $587.20/consult compared to $226.13/consult for an eConsultant episode: an efficiency saving of $361.07 per patient. The incremental difference between eConsultant and traditional care was most sensitive to the cost estimate of an outpatient attendance, the time for a specialist to complete an eConsult, and the probability of a patient requiring a face-to-face hospital-based attendance following an eConsult. However, at the upper bounds of each of these estimates, an eConsult remained the most cost-efficient model. In 96.5% of the Monte Carlo simulations eConsult was found to be more cost efficient than the traditional approach.ConclusionsThe eConsultant model of care was associated with a 61.5% efficiency gain, allowing diversion of support to hospital-based outpatient appointments.
Microbial tolerance engineering for boosting lactic acid production from lignocellulose
Authors: Shan Wenwen , Yan Yongli , Li Yongda , Hu Wei , Chen Jihong 
Published: May 2023

AbstractLignocellulosic biomass is an attractive non-food feedstock for lactic acid production via microbial conversion due to its abundance and low-price, which can alleviate the conflict with food supplies. However, a variety of inhibitors derived from the biomass pretreatment processes repress microbial growth, decrease feedstock conversion efficiency and increase lactic acid production costs. Microbial tolerance engineering strategies accelerate the conversion of carbohydrates by improving microbial tolerance to toxic inhibitors using pretreated lignocellulose hydrolysate as a feedstock. This review presents the recent significant progress in microbial tolerance engineering to develop robust microbial cell factories with inhibitor tolerance and their application for cellulosic lactic acid production. Moreover, microbial tolerance engineering crosslinking other efficient breeding tools and novel approaches are also deeply discussed, aiming to providing a practical guide for economically viable production of cellulosic lactic acid.
Robustness of radiomics features of virtual unenhanced and virtual monoenergetic images in dual-energy CT among different imaging platforms and potential role of CT number variability
Authors: Zhong Jingyu , Pan Zilai , Chen Yong , Wang Lingyun , Xia Yihan , Wang Lan , Li Jianying , Lu Wei , Shi Xiaomeng , Feng Jianxing , Yan Fuhua , Zhang Huan , Yao Weiwu 
Published: May 2023

Abstract
Objectives
To evaluate robustness of dual-energy CT (DECT) radiomics features of virtual unenhanced (VUE) image and virtual monoenergetic image (VMI) among different imaging platforms.

Methods
A phantom with sixteen clinical-relevant densities was scanned on ten DECT platforms with comparable scan parameters. Ninety-four radiomic features were extracted via Pyradiomics from VUE images and VMIs at energy level of 70 keV (VMI70keV). Test–retest repeatability was assessed by Bland–Altman analysis. Inter-platform reproducibility of VUE images and VMI70keV was evaluated by coefficient of variation (CV) and quartile coefficient of dispersion (QCD) among platforms, and by intraclass correlation coefficient (ICC) and concordance correlation coefficient (CCC) between platform pairs. The correlation between variability of CT number radiomics reproducibility was estimated.

Results
92.02% and 92.87% of features were repeatable between scan–rescans for VUE images and VMI70keV, respectively. Among platforms, 11.30% and 28.39% features of VUE images, and 15.16% and 28.99% features of VMI70keV were with CV < 10% and QCD < 10%. The average percentages of radiomics features with ICC > 0.90 and CCC > 0.90 between platform pairs were 10.00% and 9.86% in VUE images and 11.23% and 11.23% in VMI70keV. The CT number inter-platform reproducibility using CV and QCD showed negative correlations with percentage of the first-order radiomics features with CV < 10% and QCD < 10%, in both VUE images and VMI70keV (r2 0.3870–0.6178, all p < 0.001).

Conclusions
The majority of DECT radiomics features were non-reproducible. The differences in CT number were considered as an indicator of inter-platform DECT radiomics variation.
Critical relevance statement: The majority of radiomics features extracted from the VUE images and the VMI70keV were non-reproducible among platforms, while synchronizing energy levels of VMI to reduce the CT number value variability may be a potential way to mitigate radiomics instability.

Graphical Abstract
Ultrasound imaging of the axilla
Authors: Cocco Giulio , Ricci Vincenzo , Ricci Costantino , Naňka Ondřej , Catalano Orlando , Corvino Antonio , Boccatonda Andrea , Serafini Francesco Lorenzo , Izzi Jacopo , Vallone Gianfranco , Cantisani Vito , Iannetti Giovanni , Caulo Massimo , Ucciferri Claudio , Vecchiet Jacopo , Pizzi Andrea Delli 
Published: May 2023

Abstract
Axilla is a pyramidal-in-shape “virtual cavity” housing multiple anatomical structures and connecting the upper limb with the trunk. To the best of our knowledge, in the pertinent literature, a detailed sonographic protocol to comprehensively assess the axillary region in daily practice is lacking. In this sense, the authors have briefly described the anatomical architecture of the axilla—also using cadaveric specimens—to propose a layer-by-layer sonographic approach to this challenging district. The most common sonographic pathological findings—for each and every anatomical compartment of the axilla—have been accurately reported and compared with the corresponding histopathological features. This ultrasound approach could be considered a ready-to-use educational guidance for the assessment of the axillary region.

Critical relevance statement
Axilla is a pyramidal-in-shape “virtual cavity” housing multiple anatomical structures and connecting
the upper limb with the trunk. The aim of this review article was to describe the anatomical
architecture of the axilla, also using cadaveric specimens, in order to propose a layer-by-layer
sonographic approach to this challenging district.

Graphical abstract
Microbial community structure and diversity in fish-flower (mint) symbiosis
Authors: Wang Jianglong , Xie Yufen , Zhang Guangdi , Pan Lin 
Published: May 2023

AbstractThe fish-flower symbiosis model is an eco-friendly sustainable farming technology combining plants, fish and microorganisms in a recirculating aquaculture system. However, there are few studies on the structure and diversity of microbial communities in fish intestines, culture water and plant roots during fish-flower symbiosis. Here, we cultured carp (Cyprinus carpio), crucian carp (Carassius auratus) and grass carp (Ctenopharyngodon idella) with mint (Mentha spicala L.) and extracted total genomic DNA from intestinal microorganisms, culture-water microorganisms and root microorganisms for each fish species for high-throughput sequencing of 16S rRNA genes. Analysis of microbial community structure and diversity revealed changes in abundance of microbial genera in the intestines and culture water of each fish species, including changes in the dominant taxa. Pirellula, Truepera, Aquincola, Cetobacterium and Luteolibacter were widespread in the fish intestine, culture water and mint root system. This study revealed the effects of mint feeding on the structure and diversity of microbial communities of fish, water bodies and the mint root system during fish-flower symbiosis, providing a theoretical reference for the promotion and application of fish-flower (mint) symbiosis technology and healthy fish culture technology.
One health insights into pastoralists’ perceptions on zoonotic diseases in Ethiopia: perspectives from South Omo Zone of SNNP Region
Authors: Alemu Samuel Tefera , Ero Debebe , Mor Siobhan M. 
Published: May 2023

AbstractZoonotic diseases negatively impact pastoral communities in Ethiopia. In addition to impacts on human health, the interaction between people, livestock and environment which is so fundamental to the pastoralist way of life, means zoonoses pose additional challenges to social bonds and protection networks. These challenges are compounded by adverse impacts from climate change, poor health care services, market problems and cultural practices that increase pastoralists’ vulnerability to zoonotic diseases. This research adopted a grounded theory approach and attempted to capture the perception of Hamer and Dassenetch pastoralists on zoonotic diseases and rangeland health through focus group discussions and key informant interviews. Involved in the research were human and animal health experts, and woreda (Woreda is a third level of administrative unit in Ethiopia following region and zone) level government officials. Thematic framework analysis was used to analyse the data. Zoonotic diseases are a significant public health concern and have a substantial economic burden on local livelihoods. Poor access to human and livestock health services contributed towards the widespread transmission of zoonotic pathogens. In most cases, pastoralists were aware of the possibility of zoonotic disease transmission from livestock to humans and were cognizant of infections contracted from animals. However, the level of risk perception from zoonotic diseases and the subsequent measures of protection was poor. In almost all cases, despite pastoralists’ awareness of zoonotic diseases, they did not consider zoonoses as harmful to human health as they are to animals. It was evident that the burden of zoonotic diseases was high in livestock camps away from settlements in Hamer while for Dassenetch the resettlement clusters created a conducive environment for transmission. This research underscored the importance of engaging with local communities on the risk implications of zoonotic diseases including those related to their food habits and practices.
Dual roles of R-loops in the formation and processing of programmed DNA double-strand breaks during meiosis
Authors: Liu Chao , Xu Wei , Wang Liying , Yang Zhuo , Li Kuan , Hu Jun , Chen Yinghong , Zhang Ruidan , Xiao Sai , Liu Wenwen , Wei Huafang , Chen Jia-Yu , Sun Qianwen , Li Wei 
Published: May 2023

Abstract
Background
Meiotic recombination is initiated by Spo11-dependent programmed DNA double-strand breaks (DSBs) that are preferentially concentrated within genomic regions called hotspots; however, the factor(s) that specify the positions of meiotic DSB hotspots remain unclear.

Results
Here, we examined the frequency and distribution of R-loops, a type of functional chromatin structure comprising single-stranded DNA and a DNA:RNA hybrid, during budding yeast meiosis and found that the R-loops were changed dramatically throughout meiosis. We detected the formation of multiple de novo R-loops in the pachytene stage and found that these R-loops were associated with meiotic recombination during yeast meiosis. We show that transcription-replication head-on collisions could promote R-loop formation during meiotic DNA replication, and these R-loops are associated with Spo11. Furthermore, meiotic recombination hotspots can be eliminated by reversing the direction of transcription or replication, and reversing both of these directions can reconstitute the hotspots.

Conclusions
Our study reveals that R-loops may play dual roles in meiotic recombination. In addition to participation in meiotic DSB processing, some meiotic DSB hotspots may be originated from the transcription-replication head-on collisions during meiotic DNA replication.
Addressing health inequalities in Europe: key messages from the Joint Action Health Equity Europe (JAHEE)
Authors: Bucciardini Raffaella , Zetterquist Pi , Rotko Tuulia , Putatti Vania , Mattioli Benedetta , De Castro Paola , Napolitani Federica , Giammarioli Anna Maria , Kumar Bernadette N. , Nordström Charlott , Plantz Christina , Zarneh Yvette Shajanian , Olsson Gabriella , Ahrne Malin , Kilpeläinen Katri , Lopez-Acuña Daniel , Vantarakis Apostolos , Marra Michele , Nessi Cecilia , Costa Giuseppe 
Published: May 2023

AbstractHealth inequalities within and between Member States of the European Union are widely recognized as a public health problem as they determine a significant share of potentially avoidable mortality and morbidity. After years of growing awareness and increasing action taken, a large gap still exists across Europe in terms of policy responses and governance. With the aim to contribute to achieve greater equity in health outcomes, in 2018 a new Joint Action, JAHEE, (Joint Action Health Equity Europe) was funded by the third EU Health Programme, with the main goal of strengthening cooperation between participating countries and of implementing concrete actions to reduce health inequalities. The partnership led by Italy counted 24 countries, conducting actions in five policy domains: monitoring, governance, healthy living environments, health systems and migration, following a three-step implementation approach. Firstly, specific Policy Frameworks for Action (PFA) collecting the available evidence on what practice should be done in each domain were developed. Second, different Country Assessments (CAs) were completed to check the country’s adherence to the recommended practice in each domain. The gap between the expected policy response (PFA) and the present policy response (CA) guided the choice of concrete actions to be implemented in JAHEE, many of which are continuing even after the end of JA. Final recommendations based on the best results achieved during JAHEE were elaborated and agreed jointly with the representatives of the involved Ministries of Health. The JAHEE initiative represented an important opportunity for the participating countries to work jointly, and the results show that almost all have increased their level of action and strengthened their capacities to address health inequalities.