bluuebunny/crossref_metadata_2025_split huggingface dataset:
Haplogenome assembly reveals structural variation in Eucalyptus interspecific hybrids
Authors: Lötter Anneri , Duong Tuan A , Candotti Julia , Mizrachi Eshchar , Wegrzyn Jill L , Myburg Alexander A 
Published: August 2023

Abstract

Background
De novo phased (haplo)genome assembly using long-read DNA sequencing data has improved the detection and characterization of structural variants (SVs) in plant and animal genomes. Able to span across haplotypes, long reads allow phased, haplogenome assembly in highly outbred organisms such as forest trees. Eucalyptus tree species and interspecific hybrids are the most widely planted hardwood trees with F1 hybrids of Eucalyptus grandis and E. urophylla forming the bulk of fast-growing pulpwood plantations in subtropical regions. The extent of structural variation and its effect on interspecific hybridization is unknown in these trees. As a first step towards elucidating the extent of structural variation between the genomes of E. grandis and E. urophylla, we sequenced and assembled the haplogenomes contained in an F1 hybrid of the two species.

Findings
Using Nanopore sequencing and a trio-binning approach, we assembled the separate haplogenomes (566.7 Mb and 544.5 Mb) to 98.0% BUSCO completion. High-density SNP genetic linkage maps of both parents allowed scaffolding of 88.0% of the haplogenome contigs into 11 pseudo-chromosomes (scaffold N50 of 43.8 Mb and 42.5 Mb for the E. grandis and E. urophylla haplogenomes, respectively). We identify 48,729 SVs between the two haplogenomes providing the first detailed insight into genome structural rearrangement in these species. The two haplogenomes have similar gene content, 35,572 and 33,915 functionally annotated genes, of which 34.7% are contained in genome rearrangements.

Conclusions
Knowledge of SV and haplotype diversity in the two species will form the basis for understanding the genetic basis of hybrid superiority in these trees.
Dispersion of Scholte wave under horizontally layered viscoelastic seabed
Authors: Zhang Yi , Wang Yun , Wang Xiangchun , Yuan Hemin , Liu Xiaobo , Zhang Huimin 
Published: August 2023

SUMMARY
Dispersion inversion of Scholte wave is an effective method for constructing the shear wave velocity models of seabed sediments, but it is usually conducted based on the elastic layered medium theory, which ignores the viscoelasticity of sediments. In this work, we use the transitive matrix method to establish the dispersion equation for Scholte wave under horizontally layered viscoelastic seabed. This equation integrates the kinematic property of seismic wave in a viscoelastic media and the fluid–solid coupling mechanism. The phase velocity and attenuation coefficient dispersion curves of Scholte wave are presented by the real and imaginary parts of the complex-valued roots of the dispersion equation at different frequencies solved by Muller iteration algorithm, respectively. We perform numerical comparisons and analyses on the dispersion curves of Scholte waves for three typical seabed models under both elastic and viscoelastic conditions. Results demonstrate that the seabed viscoelasticity could greatly affect the propagation and dispersion characteristics of Scholte wave. Moreover, the dispersion curves of Scholte wave are sensitive to the variations in S-wave velocity and quality factor of seabed sediments.
Characteristics of short-term acute care hospitals that experienced a ransomware attack from 2016 to 2021
Authors: McGlave Claire C , Nikpay Sayeh S , Henning-Smith Carrie , Rydberg Katie , Neprash Hannah T 
Published: August 2023

Abstract
As cybercrime increasingly targets the health care sector, hospitals face the growing threat of ransomware attacks. Ransomware is a type of malicious software that prevents users from accessing their electronic systems—demanding payment to restore access. In response, momentum is gathering to enact policy that will help hospitals strengthen their cybersecurity defenses. However, to design effective policy, it is crucial to understand the characteristics of hospitals associated with the risk of ransomware attack. In this paper, we compare the characteristics of ransomware-attacked and non-attacked short-term acute care hospitals in the United States. Using data from the American Hospital Association's Annual Survey and the Healthcare Cost Report Information System, we found that ransomware-attacked hospitals were larger, had higher net operating revenue, were more likely to be financially profitable, and more likely to provide trauma, emergency, and obstetric care than non-attacked hospitals. Measures of information technology sophistication did not vary between ransomware-attacked and non-attacked hospitals. These results can be used to tailor policy interventions in order to most effectively respond to and prevent cybercrime in health care.
Do private health providers help achieve Universal Health Coverage? A scoping review of the evidence from low-income countries
Authors: Coveney Laura , Musoke David , Russo Giuliano 
Published: August 2023

Abstract
Universal Health Coverage (UHC) is the dominant paradigm in health systems research, positing that everyone should have access to a range of affordable health services. Although private providers are an integral part of world health systems, their contribution to achieving UHC is unclear, particularly in low-income countries (LICs). We scoped the literature to map out the evidence on private providers’ contribution to UHC progress in LICs. Literature searches of PubMed, Scopus and Web of Science were conducted in 2022. A total of 1049 documents published between 2002 and 2022 were screened for eligibility using predefined inclusion criteria, focusing on formal as well as informal private health sectors in 27 LICs. Primary qualitative, quantitative and mixed-methods evidence was included, as well as original analysis of secondary data. The Joanna Briggs Institute’s critical appraisal tool was used to assess the quality of the studies. Relevant evidence was extracted and analysed using an adapted UHC framework. We identified 34 papers documenting how most basic health care services are already provided through the private sector in countries such as Uganda, Afghanistan and Somalia. A substantial proportion of primary care, mother, child and malaria services are available through non-public providers across all 27 LICs. Evidence exists that while formal private providers mostly operate in well-served urban settings, informal and not-for-profit ones cater for underserved rural and urban areas. Nonetheless, there is evidence that the quality of the services by informal providers is suboptimal. A few studies suggested that the private sector fails to advance financial protection against ill-health, as costs are higher than in public facilities and services are paid out of pocket. We conclude that despite their shortcomings, working with informal private providers to increase quality and financing of their services may be key to realizing UHC in LICs.
Discourses of Efficacy in the Ritual Use of Daoist Talismans
Authors: Capitanio Joshua 
Published: August 2023

AbstractProducing and manipulating talismans is a part of many Daoist rituals, from discrete procedures to long and complex liturgical programs. Therefore, the success of a rite depends in part on the efficacious application of the talismans used within it. Ritual manuals describing the production of talismans contain detailed instructions for rendering those talismans efficacious, and the discourses used within those instructions thus serve to define the parameters of ritual efficacy for the Daoists who carry them out. These discourses can be broadly divided into discourses of objective efficacy, which posit that ritual efficacy derives from conditions external to the ritualist, and discourses of subjective efficacy, which focus instead on the practitioner’s internal dispositions. Here, I examine the different forms that these discourses can take and the ways in which they are employed within Daoist ritual texts, arguing that discourses of subjective efficacy emerged as a form of ritual criticism.
Changes in gut microbiota and short-chain fatty acids are involved in the process of canine obesity after neutering
Authors: Yang Kang , Lin Xinye , Jian Shiyan , Wen Jiawei , Jian Xiaoying , He Shansong , Wen Chaoyu , Liu Tingting , Qi Xin , Yin Yulong , Deng Baichuan 
Published: August 2023

Abstract
Neutering is a significant risk factor for obesity in dogs. Changes in gut microbiota and its metabolites have been identified as a key player during obesity progression. However, the mechanisms that promote neuter-associated weight gain are not well understood. Therefore, in this study, sixteen clinically healthy Beagle dogs (6 male and 10 female, mean age = 8.22 ± 0.25 mo old) were neutered. Body weight (BW) and body condition score (BCS) were recorded at 1 d before neutering, 3, 6, 10, 16, and 21 mo after neutering. Dogs were grouped based on their BCS as ideal weight group (IW, n = 4, mean BW = 13.22 ± 1.30 kg, mean BCS = 5.00 ± 0.41) and obese group (OB, n = 12, mean BW = 18.57 ± 1.08 kg, mean BCS = 7.92 ± 0.82) at 21 mo after neutering. Serum lipid profile, glucose, and hormones and fecal microbiota and short-chain fatty acids (SCFAs) were measured. Our results showed that OB dogs had greater (P &lt; 0.0001) BW (18.57 vs. 13.22 kg), BCS (7.92 vs. 5.00), and average daily gain (12.27 vs. 5.69 g/d) than IW dogs at 21 mo after neutering, and the obesity rate was up to 60%. In addition, significant increases (P &lt; 0.05) in serum triglyceride (TG, 1.10 vs. 0.56 mmol/L) and high-density lipoprotein cholesterol (HDL-C, 6.96 vs. 5.40 mmol/L) levels and a significant decrease (P &lt; 0.05) in serum adiponectin (APN, 54.06 vs. 58.39 μg/L) level were observed in OB dogs; serum total cholesterol (4.83 vs. 3.75 mmol/L) (P = 0.075) and leptin (LEP, 2.82 vs. 2.53 μg/L) (P = 0.065) levels tended to be greater in OB dogs; there was a trend towards a lower (P = 0.092) APN/LEP (19.32 vs. 21.81) in OB dogs. Results of fecal microbial alpha-diversity showed that Observed_species and Chao1 indices tended to be lower (P = 0.069) in OB dogs. The STAMP and LEfSe analyses revealed that OB dogs had a greater (P &lt; 0.05 and LDA &gt; 2) reduction in relative abundances of Bacteroides, Prevotella_9, and Megamonas than IW dogs. In addition, OB dogs also had greater (P &lt; 0.05) reduction in fecal acetate, propionate, and butyrate concentrations than IW dogs. Moreover, clear negative correlations (|r| &gt; 0.5 and P &lt; 0.05) were found between SCFAs-producing bacteria and BW, TG, and HDL-C. The functional predictions of microbial communities based on PICRUSt2 analysis revealed that lipid metabolism and endocrine system were significantly disturbed in obese dogs after neutering. Thus, intervention with SCFAs-producing bacteria might represent a new target for the prevention or treatment of canine obesity after neutering. Moreover, weight control before neutering may also contribute to the prevention of canine obesity after neutering.
Assessment of urinary 6-hydroxy-2,4-cyclohexadienyl mercapturic acid as a novel biomarker of benzene exposure
Authors: Bowman Brett A , Lewis Erica V , Goldy Devon W , Kim Jenny Y , Elio Deanna M , Blount Benjamin C , Bhandari Deepak 
Published: August 2023

Abstract
Assessing benzene exposure is a public health priority due to its deleterious health effects and ubiquitous industrial and environmental sources of exposure. Phenyl mercapturic acid (PhMA) is a commonly used urinary biomarker to assess benzene exposure. However, recent work has identified significant interlaboratory variation in urinary PhMA concentrations related to methodological differences. In this study, we present urinary 6-hydroxy-2,4-cyclohexadienyl mercapturic acid (pre-PhMA), a metabolite that undergoes acid-catalyzed dehydration to form PhMA, as a novel and specific urinary biomarker for assessing benzene exposure. We developed and validated the first quantitative liquid chromatography–tandem mass spectrometry assay for measuring urinary concentrations of pre-PhMA. The pH effect on the method of ruggedness testing determined that pre-PhMA is stable across the normal human urine pH range and that neutral conditions must be maintained throughout quantification for robust and accurate measurement of urinary pre-PhMA concentrations. The method exhibited below 2 ng/mL sensitivity for pre-PhMA, linearity over three orders of magnitude, and precision and accuracy within 10%. Urinary pre-PhMA concentrations were assessed in 369 human urine samples. Smoking individuals exhibited elevated levels of pre-PhMA compared to non-smoking individuals. Furthermore, the relationship between benzene exposure and urinary pre-PhMA levels was explored by examining the correlation of pre-PhMA with 2-cyanoethyl mercapturic acid, a smoke exposure biomarker. The urinary biomarkers exhibited a positive correlation (r = 0.720), indicating that pre-PhMA levels increased with benzene exposure. The results of this study demonstrate that urinary pre-PhMA is a rugged and effective novel biomarker of benzene exposure that can be widely implemented for future biomonitoring studies.
Segmental analysis and long-term monitoring of vadadustat in equine hair for the purpose of doping control
Authors: Ishii Hideaki , Shibuya Mariko , Kusano Kanichi , Sone Yu , Kamiya Takahiro , Wakuno Ai , Ito Hideki , Miyata Kenji , Yamada Masayuki , Leung Gary Ngai-Wa 
Published: August 2023

Abstract
Vadadustat is a newly launched hypoxia-inducible factor stabilizer with anti-anemia and erythropoietic effects; however, its use in horses is expressly forbidden in both racing and equestrian competitions. Following our previous report on the pharmacokinetic study of vadadustat in horse plasma and urine, a long-term longitudinal analysis of vadadustat in horse hair after nasoesophageal administration (3 g/day for 3 days) to three thoroughbred mares is described in this study. Our main objective is to further extend the detection period of vadadustat for the purpose of doping control. Three bunches of mane hair from each horse were collected at 0 (pre), 1, 2, 3 and 6 month(s) post-administration. These hair samples were each cut into 2-cm segments and pulverized after decontamination of hair samples. The analyte in the powdered hair samples was extracted with liquid–liquid extraction followed by further purification by solid-phase extraction with strong anion exchange columns. The amount of vadadustat incorporated into the hair was quantified with a newly developed and validated method using liquid chromatography–high-resolution mass spectrometry. Our results show that vadadustat was confirmed in all post-administration hair samples, but its metabolites were not present. Thus, the detection window for vadadustat could be successfully extended up to 6 months post-administration. Interestingly, the 2-cm segmental analysis revealed that the tip of the drug band in the hair shifted along with the hair shafts in correspondence with the average hair growth rate (∼2.5 cm/month) but gradually diffused more widely from 2 cm at 1 month post-administration to up to 14 cm at 6 months post-administration. However, the loss in the total amount of vadadustat in hair over time was observed to most likely be due to the degradation of vadadustat. These findings will be useful for the control of abuse and/or misuse of vadadustat and the interpretation of positive doping cases.
Biology and management of Ceutorhynchus obstrictus (Coleoptera: Curculionidae) in spring-planted canola on the Northern Great Plains
Authors: Hussain Altaf , Mittapelly Priyanka , Blake Adam J , Dupuis Julian R , Bouchard Patrice , Skolrud Tristan D , Keddie B Andrew , Vankosky Meghan A , Cárcamo Héctor A , Mori Boyd A 
Published: August 2023

Abstract
The cabbage seedpod weevil, Ceutorhynchus obstrictus (Marsham) (Coleoptera: Curculionidae), is an invasive pest infesting canola (Brassica napus L. and B. rapa L. (Brassicales: Brassicaceae)) crops in North America. Larval feeding causes significant damage leading to yield losses of 5–30%. Native to the Palearctic region, the species was accidentally introduced to North America over 90 yr ago, and now occupies most temperate regions of Canada and the United States. Currently, the species has been projected to continue its range expansion to potentially infest most canola producing regions in North America. Here, we review the taxonomic nomenclature, distribution, biology, pest status, and management of the cabbage seedpod weevil in North America with an emphasis on spring-planted canola crops in the Great Plains and highlight areas for future research to develop a comprehensive integrated pest management program against this debilitating pest.
Advances in treatment of alveolar soft part sarcoma: an updated review
Authors: Fujiwara Tomohiro , Kunisada Toshiyuki , Nakata Eiji , Nishida Kenji , Yanai Hiroyuki , Nakamura Tomoki , Tanaka Kazuhiro , Ozaki Toshifumi 
Published: August 2023

Abstract
Alveolar soft part sarcoma is a rare neoplasm of uncertain histogenesis that belongs to a newly defined category of ultra-rare sarcomas. The neoplasm is characterized by a specific chromosomal translocation, der (17) t(X; 17)(p11.2;q25), that results in ASPSCR1–TFE3 gene fusion. The natural history of alveolar soft part sarcoma describes indolent behaviour with slow progression in deep soft tissues of the extremities, trunk and head/neck in adolescents and young adults. A high rate of detection of distant metastasis at presentation has been reported, and the most common metastatic sites in decreasing order of frequency are the lung, bone and brain. Complete surgical resection remains the standard treatment strategy, whereas radiotherapy is indicated for patients with inadequate surgical margins or unresectable tumours. Although alveolar soft part sarcoma is refractory to conventional doxorubicin-based chemotherapy, monotherapy or combination therapy using tyrosine kinase inhibitors and immune checkpoint inhibitors have provided antitumor activity and emerged as new treatment strategies. This article provides an overview of the current understanding of this ultra-rare sarcoma and recent advancements in treatments according to the clinical stage of alveolar soft part sarcoma.
Impact of retention index on the neoadjuvant chemotherapy effect and the prognosis in oesophageal cancer
Authors: Kouzu Keita , Tsujimoto Hironori , Tamura Katsumi , Einama Takahiro , Kishi Yoji , Ishida Jiro , Ueno Hideki 
Published: August 2023

Abstract

Objective
The relationship between retention index calculated from dual-time point 18F-fluorodeoxyglucose positron emission tomography–computed tomography and oesophageal cancer prognosis remains unknown. This study aimed to determine usefulness of retention index as a predictor of long-term prognosis of oesophageal cancer and neoadjuvant chemotherapy efficacy.

Methods
A total of 151 patients with oesophageal cancer who underwent esophagectomy were evaluated retrospectively in this study. We acquired positron emission tomography scans 60 and 120 min (SUVmax1 and SUVmax2, respectively) after the intravenous administration of 3.7 Mbq/kg 18F-fluorodeoxyglucose. The patients were divided into two groups: high-retention index (retention index ≥29%, 107 patients) and low-retention index (retention index &lt;29%, 44 patients). Retention index was calculated as follows: retention index (%) = [(SUVmax2 − SUVmax1)/SUVmax1] × 100.

Results
The overall survival and relapse-free survival rates in the high-retention index group were significantly lower than those in the low-retention index group (P &lt; 0.001). Our multivariate analysis identified that the high-retention index group contained independent risk factors for overall survival (hazard ratio: 2.44, P = 0.009) and relapse-free survival (hazard ratio: 2.61, P = 0.002). The high-retention index group exhibited a lower partial response rate to neoadjuvant chemotherapy evaluated by computed tomography (P &lt; 0.001) and a lower pathological therapeutic effect in the resected specimen (P = 0.019) than the low-retention index group.

Conclusions
The retention index was associated with neoadjuvant chemotherapy responses and long-term prognosis for oesophageal cancer.
Is adjuvant chemotherapy for completely resected p-stage IA (&gt;2 cm) and stage IB non-small-cell lung cancer beneficial for elderly patients? A large, retrospective cohort study based on real-world data from Japan
Authors: Adachi Hiroyuki , Saito Aya , Shintani Yasushi , Okami Jiro , Ito Hiroyuki , Ohtsuka Takashi , Mori Takeshi , Watanabe Shun-ichi , Chida Masayuki , Endo Shunsuke , Nakanishi Ryoichi , Kadokura Mitsutaka , Suzuki Hidemi , Miyaoka Etsuo , Yoshino Ichiro , Date Hiroshi , Japanese Joint Committee of Lung Cancer Registry  
Published: August 2023

Abstract

Objective
The efficacy of tegafur-uracil as adjuvant chemotherapy for patients with completely resected stage I non-small-cell lung cancer is proven; however, its efficacy for elderly patients remains unclear. Herein, we evaluated the effectiveness of adjuvant chemotherapy for elderly patients with completely resected stage I non-small-cell lung cancer based on real-world Japanese data using propensity score matching.

Methods
This retrospective study extracted data from a nationwide registry study, performed in 2016, on patients ≥75 years who underwent lobectomy with mediastinal nodal dissection for non-small-cell lung cancer in 2010 and were diagnosed with p-stage IA (&gt;2 cm) or stage IB non-small-cell lung cancer. We classified the 1294 patients into two groups—Group A, postoperative adjuvant chemotherapy (n = 295, 22.8%) and Group N, no adjuvant chemotherapy (n = 999, 77.2%)—and analyzed differences in postoperative overall survival between groups.

Results
Group A showed no advantage in overall survival over Group N as a whole (hazard ratio: 0.824 [95% confidence interval: 0.631–1.076]), in p-stage IA (hazard ratio: 0.617 [95% confidence interval: 0.330–1.156]) and in p-stage IB (hazard ratio: 0.806 [95% confidence interval: 0.597–1.088]) subsets. Even after propensity score matching, Group A showed no significant advantage in overall survival over Group N as a whole (hazard ratio: 0.975 [95% confidence interval: 0.688–1.381]), in p-stage IA (hazard ratio: 1.390 [95% confidence interval: 0.539–3.586]) and in p-stage IB (hazard ratio: 0.922 [95% confidence interval: 0.633–1.343]).

Conclusions
adjuvant chemotherapy for completely resected p-stage IA (&gt;2 cm) and stage IB non-small-cell lung cancer showed no benefit for recommendation for elderly patients; considering the risk of adverse events, we do not recommend adjuvant chemotherapy for elderly patients.