bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contrasting new and available reference genomes to highlight uncertainties in assemblies and areas for future improvement: an example with monodontid species
Authors: Bringloe Trevor T. , Parent Geneviève J. 
Published: November 2023

Abstract
Background
Reference genomes provide a foundational framework for evolutionary investigations, ecological analysis, and conservation science, yet uncertainties in the assembly of reference genomes are difficult to assess, and by extension rarely quantified. Reference genomes for monodontid cetaceans span a wide spectrum of data types and analytical approaches, providing the context to derive broader insights related to discrepancies and regions of uncertainty in reference genome assembly. We generated three beluga (Delphinapterus leucas) and one narwhal (Monodon monoceros) reference genomes and contrasted these with published chromosomal scale assemblies for each species to quantify discrepancies associated with genome assemblies.

Results
The new reference genomes achieved chromosomal scale assembly using a combination of PacBio long reads, Illumina short reads, and Hi-C scaffolding data. For beluga, we identified discrepancies in the order and orientation of contigs in 2.2–3.7% of the total genome depending on the pairwise comparison of references. In addition, unsupported higher order scaffolding was identified in published reference genomes. In contrast, we estimated 8.2% of the compared narwhal genomes featured discrepancies, with inversions being notably abundant (5.3%). Discrepancies were linked to repetitive elements in both species.

Conclusions
We provide several new reference genomes for beluga (Delphinapterus leucas), while highlighting potential avenues for improvements. In particular, additional layers of data providing information on ultra-long genomic distances are needed to resolve persistent errors in reference genome construction. The comparative analyses of monodontid reference genomes suggested that the three new reference genomes for beluga are more accurate compared to the currently published reference genome, but that the new narwhal genome is less accurate than one published. We also present a conceptual summary for improving the accuracy of reference genomes with relevance to end-user needs and how they relate to levels of assembly quality and uncertainty.
Effects of dexmedetomidine dosage on the short-term cognitive function of elderly patients undergoing cardiac surgery
Authors: Fang Jun , Yang Jia , Zhai Mingyu , Zhang Qiong , Zhang Min , Xie Yanhu 
Published: November 2023

Abstract
Background
This study aimed to investigate the effects of perioperative dexmedetomidine (DEX) infusion rates on the postoperative short-term cognitive function.

Methods
A total of 88 patients aged ≥ 60 years who underwent cardiac surgery from January 2022 to November 2022 at the First Affiliated Hospital of The University of Science and Technology of China (USTC) were included. Based on a single-center pilot analysis, patients were divided into two groups according to the rate of intraoperative DEX infusion, which started after tracheal intubation and continued until 1 h before extubation in the cardiac surgery intensive care unit. In Group L (n = 44), the infusion rate was 0.1–0.5 µg/kg/h (low-dose group), whereas in Group H (n = 44), the infusion rate was 0.5–0.9 µg/kg/h (high-dose group). Clinical outcomes were then compared between the groups. The Mini–Mental State Evaluation (abbreviated as MMSE1, MMSE2, MMSE3, and MMSE4) scale was used for the assessment of cognitive function, which was conducted on postoperative Days 2 (T1), 7 (T2), 14 (T3), and 28 (T4), with the score from postoperative Day 2 (MMSE1) considered as the primary observation.

Results
Patients in Group L had higher MMSE1 scores compared to those in Group H (26.0 [24.0, 27.0] vs. 24.5 [22.0, 26.0], p = 0.046), and there was no significant difference in the scores between the groups at all subsequent time points. Group H exhibited a higher incidence of hypotension and bradycardia compared to Group L (p = 0.044 and p = 0.047, respectively).

Conclusions
Compared to a high dose (0.5–0.9 µg/kg/h) of DEX infusion, a low-dose (0.1–0.5 µg/kg/h) infusion started after induction of anesthesia and continued until 1 h before extubation improved postoperative cognitive function scores on postoperative Day 2 in patients aged 60 years and older.

Trial registration
URL: www.chictr.org.cn with registration number ChiCTR2100055093, registered on 31/12/2021.
The effect of disease misclassification on the ability to detect a gene-environment interaction: implications of the specificity of case definitions for research on Gulf War illness
Authors: Haley Robert W. , Dever Jill A. , Kramer Gerald , Teiber John F. 
Published: November 2023

Abstract
Background
Since 1997, research on Gulf War illness (GWI) has predominantly used 3 case definitions—the original Research definition, the CDC definition, and modifications of the Kansas definition—but they have not been compared against an objective standard.

Methods
All 3 case definitions were measured in the U.S. Military Health Survey by a computer-assisted telephone interview in a random sample (n = 6,497) of the 1991 deployed U.S. military force. The interview asked whether participants had heard nerve agent alarms during the conflict. A random subsample (n = 1,698) provided DNA for genotyping the PON1 Q192R polymorphism.

Results
The CDC and the Modified Kansas definition without exclusions were satisfied by 41.7% and 39.0% of the deployed force, respectively, and were highly overlapping. The Research definition, a subset of the others, was satisfied by 13.6%. The majority of veterans meeting CDC and Modified Kansas endorsed fewer and milder symptoms; whereas, those meeting Research endorsed more symptoms of greater severity. The group meeting Research was more highly enriched with the PON1 192R risk allele than those meeting CDC and Modified Kansas, and Research had twice the power to detect the previously described gene-environment interaction between hearing alarms and RR homozygosity (adjusted relative excess risk due to interaction [aRERI] = 7.69; 95% CI 2.71–19.13) than CDC (aRERI = 2.92; 95% CI 0.96–6.38) or Modified Kansas without exclusions (aRERI = 3.84; 95% CI 1.30–8.52) or with exclusions (aRERI = 3.42; 95% CI 1.20–7.56). The lower power of CDC and Modified Kansas relative to Research was due to greater false-positive disease misclassification from lower diagnostic specificity.

Conclusions
The original Research case definition had greater statistical power to detect a genetic predisposition to GWI. Its greater specificity favors its use in hypothesis-driven research; whereas, the greater sensitivity of the others favor their use in clinical screening for application of future diagnostic biomarkers and clinical care.
Development of a tool for assessing the performance of long-term care systems in relation to care transition: Transitional Care Assessment Tool in Long-Term Care (TCAT-LTC)
Authors: Wieczorek Estera , Kocot Ewa , Evers Silvia , Sowada Christoph , Pavlova Milena 
Published: November 2023

Abstract
Background
Improving the quality and safety of care transitions is a priority in many countries. Carrying out performance measurements play a significant role in improving quality of decisions undertaken by different actors involved in reforms. Therefore, the main objective of this paper is to present the development of an evaluation tool for assessing the performance of long-term care systems in relation to care transition, namely the Transitional Care Assessment Tool in Long-Term Care (TCAT-LTC). This study is performed as part of a larger European TRANS-SENIOR project.

Methods
The development of the TCAT-LTC involved three steps. First, we developed a conceptual model based on Donabedian’s quality framework and literature review. Second, we carried out a thorough process of item pool generation using deductive (systematic literature review) and deductive-inductive methods (in-depth interviews) with experts in the field of long-term care. Third, we conducted preliminary validation of the tool by asking experts in research and practice to provide an opinion on a tool and to assess content validity. Future fourth step will involve a tool’s pilot with country experts from Germany, the Netherlands and Poland.

Results
By applying methodological triangulation, we developed the TCAT-LTC, which consists of 2 themes, 12 categories and 63 items. Themes include organizational and financial aspects. Organizational aspects include categories such as communication, transfer of information, availability and coordination of resources, training and education of staff, education/support of the patient/informal caregiver, involvement of the patient/informal caregiver, telemedicine and e-Health, and social care. Financial aspects include categories such as primary care, hospital, and long-term care. We also present the instructions on the application of the TCAT-LTC.

Conclusions
In this paper, we presented the development of the TCAT-LTC evaluation tool for assessing the performance of long-term care systems in relation to care transition. The TCAT-LTC is the first tool to assess the performance of long-term care systems in relation to care transition. Assessments can be carried out at the national and international level and enable to monitor, evaluate, and compare performance of the long-term care systems in relation to care transition within and across countries.
CT features of calcified micro-gastric gastrointestinal stromal tumors: a case series
Authors: Chen Li-Jun , Han Yue-Dong , Zhang Ming 
Published: November 2023

Abstract
Background
Due to the lack of corresponding clinical symptoms, small calcified gastric gastrointestinal stromal tumors (GISTs) are often overlooked in clinical practice. Therefore, there is an unmet need to define the imaging features of calcified micro-gastric GISTs to facilitate diagnosis. This study retrospectively analyzed the computed tomography (CT) features of pathologically confirmed calcified micro-gastric GISTs.

Methods
The medical records (gastroscopy, pre-treatment gastric CT imaging [pre- and post-contrast scans], pathology) of patients with calcified gastric GISTs < 1 cm in diameter confirmed pathologically after endoscopic submucosal dissection, endoscopic submucosal excavation, or endoscopic full-thickness resection were retrospectively reviewed.

Results
Seven patients had 8 calcified gastric GISTs < 1 cm in diameter. Six patients hadsingle lesions, and 1patients had multiple lesions. Six patients had lesions in the gastric fundus, 1 patient had a lesion in the body of the stomach. Lesions had a mean diameter of 5.2 mm (range, 1.3 mm ~ 7 mm). Unenhanced CT scans showed spots and high-density nodular calcifications in 3 submucosal lesions, 2 lesions in the muscularis propria, and 3 subserosal lesions that protruded outside the stomach. Among the 8 lesions, only two had solid soft tissue components surrounding the calcification, with one of these two showing post contrast enhancement of the solid soft tissue component.

Conclusions
Novel CT features of gastric GISTs included: commonly found in the gastric antrum, small size (< 1 cm in diameter), calcification, few solid soft tissue components, and no abnormal enhancement in most cases.
Enhancing the clinical diagnosis of the acute and subacute phases of autoimmune encephalitis and predicting the risk factors: the potential advantages of 18F-FDG PET/CT
Authors: Liu Lili , Lyu Zhehao , Li Huimin , Bai Lin , Wan Yong , Li Ping 
Published: November 2023

Abstract
Background
2-deoxy-2-[18F]fluoro-D-glucose positron emission tomography (18F-FDG PET) could help evaluate metabolic abnormalities by semi-quantitative measurement to identify autoimmune encephalitis (AE). Few studies have been conducted to analyze the prognostic factors of AE. The study aimed to explore the values of diagnosis and treatment evaluation by 18F-FDG PET and preliminarily discussed the potential value in predicting the prognosis of AE patients.

Methods
AE patients underwent 18F-FDG PET/CT and magnetic resonance imaging (MRI). There were two steps to analyse 18F-FDG PET imaging data. The first step was visual assessment. The second step was to analyse 18F-FDG PET parameters using Scenium software (Siemens Molecular Imaging Ltd). The mean standardized uptake value (SUVmean) and maximum standardized uptake value (SUVmax) of brain relative regional metabolism (BRRM) were quantified in the case and control groups according to the anatomical automatic labeling (AAL) partition. The main statistical method was the Kruskal–Wallis test. Finally, the simple linear regression method was used to analyse the relationships between 18F-FDG PET parameters and the modified Rankin Scale (mRS) scores before and after treatment.

Results
The results on 18F-FDG PET showed that visual assessment abnormalities were in the mesial temporal lobe (MTL) (70.8%), (mainly infringing on the hippocampus and amygdala), basal ganglia (62.5%), frontal lobes (37.5%), occipital lobes (29.2%), and parietal lobes (12.5%). The positive rate of abnormalities on 18F-FDG PET was more sensitive than that on MRI (95.5% vs 32.2%, p = 0.001). The number of lesions on PET was positively correlated with the mRS scores before and after treatment, and the correlation before treatment was more significant. Before treatment, the SUVmean of the left occipital lobe was the most remarkable (SUVmean, R2 = 0.082, p > 0.05) factor associated with the mRS score, and the correlation was negative. With regard to prognosis, the SUVmax of the MTL was the most notable (R2 = 0.1471, p > 0.05) factor associated with the mRS score after treatment, and the correlation was positive.

Conclusions
18F-FDG PET could be more sensitive and informative than MRI in the early phases of AE. The common pattern of AE was high MTL metabolism on 18F-FDG PET, which was associated with hypometabolism of the occipital lobe, and the number of lesions on PET before treatment may be significant factors in assessing disease severity. The SUVmax of MTL hypermetabolism may serve as a prognostic biomarker in AE.
LMP2 and TAP2 impair tumor growth and metastasis by inhibiting Wnt/β-catenin signaling pathway and EMT in cervical cancer
Authors: Cheng Zhengyan , Wang Hongbo , Yang Zewei , Li Jiaxu , Chen Xing 
Published: November 2023

Abstract
Background
The roles of low molecular mass polypeptide 2 (LMP2) and transporter-associated with antigen processing (TAP2) in tumorigenesis are controversial. Here we aimed to explore the effect of LMP2 and TAP2 on the oncogenesis and metastasis of cervical cancer cells.

Methods
The expressions of LMP2 and TAP2 in cervical cancer and normal tissues were determined by qPCR. Plate colony formation, cell counting kit-8 analysis and in vivo tumor xenograft assays were used to detect the tumor growth. Wound healing and transwell assays were used to detect the metastasis of cervical cancer. Gelatin zymography and western blotting assays were used to detect the effect of LMP2 and TAP2 on the EMT and Wnt/β-catenin pathway in cervical cancer cells.

Results
In the present study, we reported that LMP2 and TAP2 levels were overexpressed in cervical cancer. Overexpression of LMP2 and TAP2 impaired the proliferation of Hela cells. In vivo studies substantiated that LMP2 and TAP2 antagonized tumor growth. Likewise, LMP2 and TAP2 overexpression decreased the migration and invasion ability of Hela cells by regulating the process of epithelial-mesenchymal transition (EMT). Mechanically, LMP2 and TAP2 subverted the protein abundance of Wnt1 and β-catenin, thereby downregulating their downstream targets Cyclin D1 and c-Myc. In addition, Wnt1 overexpression partially rescued the observed consequences of ectopic expression of LMP2 and TAP2 in cervical cancer cells. Taken together, our study revealed that LMP2 and TAP2 suppress the oncogenesis and metastasis of cervical cancer cells by Wnt/β-catenin pathway and altering EMT.

Conclusion
LMP2 and TAP2 may inhibit the oncogenesis and metastasis of cervical cancer cells by inhibiting the process of EMT and the Wnt/β-catenin signaling pathway, which may provide important insight into prospective targets for the treatment of cervical cancer.
Evaluation of a person-centred, nurse-led model of care delivering hepatitis C testing and treatment in priority settings: a mixed-methods evaluation of the Tasmanian Eliminate Hepatitis C Australia Outreach Project, 2020–2022
Authors: Dawe Joshua , Hughes Megan , Christensen Shannon , Walsh Louisa , Richmond Jacqueline A. , Pedrana Alisa , Wilkinson Anna L. , Owen Louise , Doyle Joseph S. ,   on behalf of the EC Australia Partnership, Hellard Margaret , Stoove Mark , Scott Nick , Howell Jess , Selvey Linda , Michaels Jessica , Crawford Sione , Fowlie Carrie , Singhal Shweta , Davies Jane , Manu Geoff , Ward James , Drenkhahn Geoff , Bastian Lisa , Dore Greg , Bryant Mellissa , Marshall Catherine , Llyod Andrew , McMahon Maria , Sattell Garry , Casey Dawn , Shaw David , Rees Tom , Thompson Alex 
Published: November 2023

Abstract
Introduction
Australia has experienced sustained reductions in hepatitis C testing and treatment and may miss its 2030 elimination targets. Addressing gaps in community-based hepatitis C prescribing in priority settings that did not have, or did not prioritise, hepatitis C testing and treatment care pathways is critical.

Methods
The Tasmanian Eliminate Hepatitis C Australia Outreach Project delivered a nurse-led outreach model of care servicing hepatitis C priority populations in the community through the Tasmanian Statewide Sexual Health Service, supported by the Eliminating Hepatitis C Australia partnership. Settings included alcohol and other drug services, needle and syringe programs and mental health services. The project provided clients with clinical care across the hepatitis C cascade of care, including testing, treatment, and post-treatment support and hepatitis C education for staff.

Results
Between July 2020 and July 2022, a total of 43 sites were visited by one Clinical Nurse Consultant. There was a total of 695 interactions with clients across 219 days of service delivery by the Clinical Nurse Consultant. A total of 383 clients were tested for hepatitis C (antibody, RNA, or both). A total of 75 clients were diagnosed with hepatitis C RNA, of which 95% (71/75) commenced treatment, 83% (62/75) completed treatment and 52% (39/75) received a negative hepatitis C RNA test at least 12 weeks after treatment completion.

Conclusions
Providing outreach hepatitis C services in community-based services was effective in engaging people living with and at-risk of hepatitis C, in education, testing, and care. Nurse-led, person-centred care was critical to the success of the project. Our evaluation underscores the importance of employing a partnership approach when delivering hepatitis C models of care in community settings, and incorporating workforce education and capacity-building activities when working with non-specialist healthcare professionals.
Will tobacco price increases lead more people who smoke to vape? The results from a discrete choice experiment amongst U.S. adults
Authors: Zarate-Gonzalez Gilda , Brown Paul , Cameron Linda D. , Song Anna V. 
Published: November 2023

Abstract

Objective

To understand the extent to which people who smoke, people who vape and nonsmokers would switch between smoking cigarettes and vaping in response to policies (price increases, restrictions on nicotine, places, and information on addictiveness and/or health risks) aimed at decreasing tobacco use by people who smoke and vaping by nonsmokers.

Design
A total of 525 adults aged 18 to 88 years completed a discrete choice survey of 16 choices between two smoking/vaping alternatives. Analysis was conducted using conditional logistic regression for the entire sample and stratified by nonsmokers, people who smoke, and people who vape.

Results
The results suggest that most people who vape also smoke. Nonsmokers were more favorable to vaping and were concerned about long-term health risks and cost associated with vaping. Marginal analysis suggests that price increases will have only modest success in moving people who smoke to start vaping or encouraging people who vape to vape rather than use cigarettes. Nonsmokers are not very sensitive to price changes but are sensitive to information about health impacts.

Conclusions
Findings indicate that increasing the price of cigarettes would lead to a limited increase in the probability of people who smoke switch to vaping. The study advances our understanding of the views of current nonsmokers toward cigarettes and vaping, suggesting that price increases and increased knowledge of addiction would likely deter nonsmokers from vaping. Changing the amount of nicotine associated with smoking would increase the probability of vaping slightly and have little impact on nonsmokers or vaping preferences, but the most significant change would come from increasing the perceptions of the risk of smoking.
Integration of point-of-care screening for type 2 diabetes mellitus and hypertension into the COVID-19 vaccine programme in Johannesburg, South Africa
Authors: Brennan Alana T , Vetter Beatrice , Masuku Sithabiso D , Mtshazo Bukelwa , Mashabane Nkuli , Sokhela Simiso , Venter Willem DF , Kao Kekeletso , Meyer-Rath Gesine 
Published: November 2023

Abstract
Background
South Africa grapples with a substantial burden of non-communicable diseases (NCDs), particularly type 2 diabetes (diabetes) and hypertension. However, these conditions are often underdiagnosed and poorly managed, further exacerbated by the strained primary healthcare (PHC) system and the disruptive impact of the COVID-19 pandemic. Integrating NCD screening with large-scale healthcare initiatives, such as COVID-19 vaccination campaigns, offers a potential solution, especially in low- and middle-income countries (LMICs). We investigated the feasibility and effectiveness of this integration.

Methods
A prospective cohort study was conducted at four government health facilities in Johannesburg, South Africa. NCD screening was incorporated into the COVID-19 vaccination campaign. Participants underwent COVID-19 rapid tests, blood glucose checks, blood pressure assessments, and anthropometric measurements. Those with elevated blood glucose or blood pressure values received referrals for diagnostic confirmation at local PHC centers.

Results
Among 1,376 participants screened, the overall diabetes prevalence was 4.1%, combining previously diagnosed cases and newly identified elevated blood glucose levels. Similarly, the hypertension prevalence was 19.4%, comprising pre-existing diagnoses and newly detected elevated blood pressure cases. Notably, 46.1% of participants displayed waist circumferences indicative of metabolic syndrome, more prevalent among females. Impressively, 7.8% of all participants screened were potentially newly diagnosed with diabetes or hypertension. Approximately 50% of individuals with elevated blood glucose or blood pressure successfully linked to follow-up care within four weeks.

Conclusion
Our study underscores the value of utilizing even brief healthcare interactions as opportunities for screening additional health conditions, thereby aiding the identification of previously undiagnosed cases. Integrating NCD screenings into routine healthcare visits holds promise, especially in resource-constrained settings. Nonetheless, concerted efforts to strengthen care linkage are crucial for holistic NCD management and control. These findings provide actionable insights for addressing the NCD challenge and improving healthcare delivery in LMICs.