bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome assembly and resequencing analyses provide new insights into the evolution, domestication and ornamental traits of crape myrtle
Authors: Zhou Yang , Zheng Tangchun , Cai Ming , Feng Lu , Chi Xiufeng , Shen Ping , Wang Xin , Wan Zhiting , Yuan Cunquan , Zhang Man , Han Yu , Wang Jia , Pan Huitang , Cheng Tangren , Zhang Qixiang 
Published: July 2023

Abstract
Crape myrtle (Lagerstroemia indica) is a globally used ornamental woody plant and is the representative species of Lagerstroemia. However, studies on the evolution and genomic breeding of L. indica have been hindered by the lack of a reference genome. Here we assembled the first high-quality genome of L. indica using PacBio combined with Hi-C scaffolding to anchor the 329.14-Mb genome assembly into 24 pseudochromosomes. We detected a previously undescribed independent whole-genome triplication event occurring 35.5 million years ago in L. indica following its divergence from Punica granatum. After resequencing 73 accessions of Lagerstroemia, the main parents of modern crape myrtle cultivars were found to be L. indica and L. fauriei. During the process of domestication, genetic diversity tended to decrease in many plants, but this was not observed in L. indica. We constructed a high-density genetic linkage map with an average map distance of 0.33 cM. Furthermore, we integrated the results of quantitative trait locus (QTL) using genetic mapping and bulk segregant analysis (BSA), revealing that the major-effect interval controlling internode length (IL) is located on chr1, which contains CDL15, CRG98, and GID1b1 associated with the phytohormone pathways. Analysis of gene expression of the red, purple, and white flower-colour flavonoid pathways revealed that differential expression of multiple genes determined the flower colour of L. indica, with white flowers having the lowest gene expression. In addition, BSA of purple- and green-leaved individuals of populations of L. indica was performed, and the leaf colour loci were mapped to chr12 and chr17. Within these intervals, we identified MYB35, NCED, and KAS1. Our genome assembly provided a foundation for investigating the evolution, population structure, and differentiation of Myrtaceae species and accelerating the molecular breeding of L. indica.
Peristomal adenocarcinoma 16 years after colorectal adenocarcinoma resection with curative intent
Authors: van Dam Kayleigh A M , Tweed Thaís T T , de Vries Bart , Belgers Henricus J 
Published: July 2023

Abstract
Metachronous colorectal cancer is relatively rare, occurring in 0.7–3.6% of patients diagnosed with colorectal adenocarcinoma. Cutaneous metastases are similarly a rare presentation, occurring in &lt;6% of metastatic colorectal cancer patients. Even more rare are the cutaneous recurrences at the peristomal site. Clinically, it is difficult to distinguish between metachronous cancer and cutaneous metastases. This paper reports a case of an elderly woman presenting with a slowly progressing peristomal cutaneous lesion 16 years after surgical resection for colorectal cancer. Core punch biopsy revealed a cutaneous localization of an intestinal type of adenocarcinoma. A surgical resection of the peristomal area was carried out whereby a new colostomy was created on the contralateral side. Definite histopathological examination showed a superficially located intestinal type adenocarcinoma with extensive pagetoid spread in the epidermal surface. In conclusion, it is important to remain alert and strive for early detection for cutaneous abnormalities following colorectal cancer.
Management of median arcuate ligament syndrome: a case-based review
Authors: Cunha Roberto , Silva Manuel , Henrique Alberto , Maximiano Pedro , Correia Mafalda , Vieira Isabel , Cássio Isabel , Oliveira Nelson , Dias Emanuel 
Published: July 2023

Abstract
Dunbar syndrome or median arcuate ligament syndrome is a rare pathology that has a great impact on the quality of life of patients. This brief report aims to present a case report of a successful treatment of Dunbar syndrome and to review the current management of this entity. We present the case of a 37 year-old patient, who was treated by median arcuate ligament laparoscopic resection. The median arcuate ligament syndrome is associated with significant morbidity. There are no diagnostic criteria established so alternative causes of abdominal pain must be excluded. Celiac artery decompression by laparoscopic approach is currently the preferred treatment. Early diagnosis and treatment of this pathology allow a significant improvement in the quality of life of patients.
Imaging telomerase reverse transcriptase expression in oligodendrogliomas using hyperpolarized δ-[1-13C]-gluconolactone
Authors: Batsios Georgios , Taglang Celine , Gillespie Anne Marie , Viswanath Pavithra 
Published: July 2023

Abstract

Background
Telomere maintenance by telomerase reverse transcriptase (TERT) is essential for immortality in most cancers, including oligodendrogliomas. Agents that disrupt telomere maintenance such as the telomere uncapping agent 6-thio-2’-deoxyguanosine (6-thio-dG) are in clinical trials. We previously showed that TERT expression in oligodendrogliomas is associated with upregulation of glucose-6-phosphate dehydrogenase (G6PD), the rate-limiting enzyme of the pentose phosphate pathway (PPP). We also showed that hyperpolarized δ-[1-13C]-gluconolactone metabolism to 6-phosphogluconate (6-PG) can be used to probe the PPP in glioblastomas. The goal of this study was to determine whether hyperpolarized 13C imaging using δ-[1-13C]-gluconolactone can monitor TERT expression and response to 6-thio-dG in oligodendrogliomas.

Methods
We examined patient-derived oligodendroglioma cells and orthotopic tumors to assess the link between TERT and hyperpolarized δ-[1-13C]-gluconolactone metabolism. We performed in vivo imaging to assess the ability of hyperpolarized δ-[1-13C]-gluconolactone to report on TERT and response to 6-thio-dG in rats bearing orthotopic oligodendrogliomas in vivo.

Results
Doxycycline-inducible TERT silencing abrogated 6-PG production from hyperpolarized δ-[1-13C]-gluconolactone in oligodendroglioma cells, consistent with the loss of G6PD activity. Rescuing TERT expression by doxycycline removal restored G6PD activity and, concomitantly, 6-PG production. 6-PG production from hyperpolarized δ-[1-13C]-gluconolactone demarcated TERT-expressing tumor from surrounding TERT-negative normal brain in vivo. Importantly, 6-thio-dG abrogated 6-PG production at an early timepoint preceding MRI-detectable alterations in rats bearing orthotopic oligodendrogliomas in vivo.

Conclusions
These results indicate that hyperpolarized δ-[1-13C]-gluconolactone reports on TERT expression and early response to therapy in oligodendrogliomas. Our studies identify a novel agent for imaging tumor proliferation and treatment response in oligodendroglioma patients.
A Brief Peer-Led Intervention to Increase COVID-19 Vaccine Uptake Among People Who Inject Drugs in San Diego County: Results From a Pilot Randomized Controlled Trial
Authors: Strathdee Steffanie A , Abramovitz Daniela , Harvey-Vera Alicia Y , Stamos-Buesig Tara , Vera Carlos F , Artamonova Irina , Logan Jenna , Patterson Thomas L , Servin Argentina E , Bazzi Angela R 
Published: July 2023

Abstract

Background
We evaluated the impact of a brief peer-led intervention on COVID-19 vaccination among people who inject drugs (PWID) presenting at syringe services program (SSP) locations in San Diego County, California.

Methods
Between March and July 2022, PWID aged ≥18 years without recent voluntary COVID-19 testing who were not up to date on COVID-19 vaccinations received a single-session motivational interviewing intervention (LinkUP) or an attention-matched didactic control condition from trained peer counselors at SSP sites randomized by week. Following either 30-minute session, counselors offered referrals to local vaccination services. Multivariable log binomial regression via generalized estimating equations assessed LinkUP effects on (1) acceptance of COVID-19 vaccination referrals immediately postintervention and (2) COVID-19 vaccine uptake at 6-month follow-up.

Results
COVID-19 vaccination outcomes were obtained on 135 (90.6%) of 149 participants. In multivariable analysis, participants receiving LinkUP had greater acceptance of COVID-19 vaccination referrals than controls (adjusted relative risk, 3.50; 95% CI, 1.01–12.2) and were marginally more likely to report receiving a new COVID-19 vaccine dose (adjusted relative risk, 1.57; 95% CI, .99–2.48). After 6 months, 20% reported receiving a new vaccine dose; however, if COVID-19 vaccine had been available at SSPs, this proportion could have been as high as 34.3% (45.3% LinkUP vs 24.3% control; P = .01).

Conclusions
A brief peer-led SSP-based intervention significantly improved COVID-19 vaccination among PWID. Further improvements could likely be obtained by supporting SSPs to offer COVID-19 vaccination on-site instead of relying on referrals.

Clinical Trials Registration
ClinicalTrials.gov NCT05181657.
Online sleep diaries: considerations for system development and recommendations for data management
Authors: Shaffer Kelly M , Daniel Katharine E , Frederick Christina , Buysse Daniel J , Morin Charles M , Ritterband Lee M 
Published: July 2023

Abstract

Study Objectives
To present development considerations for online sleep diary systems that result in robust, interpretable, and reliable data; furthermore, to describe data management procedures to address common data entry errors that occur despite those considerations.

Methods
The online sleep diary capture component of the Sleep Healthy Using the Internet (SHUTi) intervention has been designed to promote data integrity. Features include diary entry restrictions to limit retrospective bias, reminder prompts and data visualizations to support user engagement, and data validation checks to reduce data entry errors. Despite these features, data entry errors still occur. Data management procedures relying largely on programming syntax to minimize researcher effort and maximize reliability and replicability. Presumed data entry errors are identified where users are believed to have incorrectly selected a date or AM versus PM on the 12-hour clock. Following these corrections, diaries are identified that have unresolvable errors, like negative total sleep time.

Results
Using the example of one of our fully-powered, U.S. national SHUTi randomized controlled trials, we demonstrate the application of these procedures: of 45,598 total submitted diaries, 487 diaries (0.01%) required modification due to date and/or AM/PM errors and 27 diaries (&lt;0.001%) were eliminated due to unresolvable errors.

Conclusion
To secure the most complete and valid data from online sleep diary systems, it is critical to consider the design of the data collection system and to develop replicable processes to manage data.

Clinical Trial Registration
Sleep Healthy Using The Internet for Older Adult Sufferers of Insomnia and Sleeplessness (SHUTiOASIS); https://clinicaltrials.gov/ct2/show/NCT03213132; ClinicalTrials.gov ID: NCT03213132
Development of a nomogram for predicting survival in clinical T1N0M1 lung adenocarcinoma: a population-based study
Authors: Lin Xuejing , Tian Weicheng , Sun Ni , Xia Ziyang , Ma Pei 
Published: July 2023

Objective
This study aimed to establish a prognostic model for clinical T1N0M1 (cT1N0M1) lung adenocarcinoma patients to evaluate the prognosis of patients in terms of overall survival (OS) rate and cancer-specific survival (CSS) rate.

Methods
Data of patients with metastatic lung adenocarcinoma from 2010 to 2016 were collected from the Surveillance, Epidemiology and End Results database. Multivariate Cox regression analysis was conducted to identify relevant prognostic factors and used to develop nomograms. The receiver operating characteristic (ROC) curve and calibration curve are used to evaluate the predictive ability of the nomograms.

Results
A total of 45610 patients were finally included in this study. The OS and CSS nomograms were constructed by same clinical indicators such as age (<60 years or ≥60 years), sex (female or male), race (white, black, or others), surgery, radiation, chemotherapy, and the number of metastatic sites, based on the results of statistical Cox analysis. From the perspective of OS and CSS, surgery contributed the most to the prognosis. The ROC curve analysis showed that the survival nomograms could accurately predict OS and CSS. According to the points obtained from the nomograms, survival was estimated by the Kaplan–Meier method, then cT1N0M1 patients were divided into three groups: low-risk group, intermediate-risk group, and high-risk group, and the OS (P < 0.001) and CSS (P < 0.001) were significantly different among the three groups.

Conclusion
The nomograms and risk stratification model provide a convenient and reliable tool for individualized evaluation and clinical decision-making of patients with cT1N0M1 lung adenocarcinoma.
Tacrolimus population pharmacokinetics in adult heart transplant patients
Authors: Paschier Adrien , Destere Alexandre , Monchaud Caroline , Labriffe Marc , Marquet Pierre , Woillard Jean‐Baptiste 
Published: July 2023

AbstractIntroductionTacrolimus is an immunosuppressant largely used in heart transplantation. However, the calculation of its exposure based on the area under the curve (AUC) requires the use of a population pharmacokinetic (PK) model. The aims of this work were (i) to develop a population PK model for tacrolimus in heart transplant patients, (ii) to derive a maximum a posteriori Bayesian estimator (MAP‐BE) based on a limited sampling strategy (LSS) and (iii) to estimate probabilities of target attainment (PTAs) for AUC and trough concentration (C0).Material and MethodsForty‐seven PK profiles (546 concentrations) of 18 heart transplant patients of the Pharmacocinétique des Immunosuppresseurs chez les patients GREffés Cardiaques study receiving tacrolimus (Prograf®) were included. The database was split into a development (80%) and a validation (20%) set. PK parameters were estimated in MONOLIX® and based on this model a Bayesian estimator using an LSS was built. Simulations were performed to calculate the PTA for AUC and C0.ResultsThe best model to describe the tacrolimus PK was a two‐compartment model with a transit absorption and a linear elimination. Only the CYP3A5 covariate was kept in the final model. The derived MAP‐BE based on the LSS (0‐1‐2 h postdose) yielded an AUC bias ± SD = 2.7 ± 10.2% and an imprecision of 9.9% in comparison to the reference AUC calculated using the trapezoidal rule. PTAs based on AUC or C0 allowed new recommendations to be proposed for starting doses (0.11 mg·kg−1·12 h−1 for the CYP3A5 nonexpressor and 0.22 mg·kg1·12 h−1 for the CYP3A5 expressor).ConclusionThe MAP‐BE developed should facilitate estimation of tacrolimus AUC in heart transplant patients.
Substituting a randomised placebo control group with a historical placebo control in an endometriosis pain trial: a case study re-evaluating trial data using historical control data from another trial
Authors: Sieverding Marius , Gerlinger Christoph , Seitz Christian 
Published: July 2023

ObjectiveThe substitution of an in-study control population with a historical control (HC) population is considered a viable option for reducing the necessary recruitment of control patients. However, it is necessary to evaluate whether this method is applicable to studies on indications targeting endometriosis-associated pelvic pain (EAPP). This study aims to evaluate the potential bias in the results of an EAPP study with an HC arm.MethodsFor this case study, we re-evaluated data from a randomised, placebo-controlled trial using dienogest daily to treat EAPP with an HC arm based on data from a second randomised, placebo-controlled trial in the same indication. Propensity Score (PS) matching was used to match between the treatment and HC arm on all baseline variables. To evaluate the effect of matching on the introduced bias, we evaluated efficacy parameters with the full treatment and control group, as well as the matched group.ResultsThe difference between means (placebo minus treatment) in change in pain, as measured on the Visual Analogue Scale from baseline to end of treatment, deviates in the comparison treatment/pool of HC (7.15 (0.22 to 14.08)) from the overall in-study group (reference: 11.89 (6.06 to 17.73)). After PS matching on the baseline variables, the difference between means (11.79 (4.09 to 19.5)) is close to the reference.ConclusionsUsing HC with PS matching has proven to be useful in the setting of treating EAPP, while emphasis must be given to the selection mechanism and the underlying assumptions. This case study has shown that even for studies which are very similar in design, heterogeneity and between-study variations are present. With the use of an HC arm, it was possible to reproduce similar results than in the original study, while the PS matching improved the comparability considerably. For the main endpoint, PS matching could reproduce the original study results.Trial registration numberNCT00225199,NCT00185341
Short-course antibiotic therapy of 5 days in community-acquired pneumonia (CAP5): study protocol for a randomised controlled trial
Authors: Israelsen Simone Bastrup , Tingsgård Sandra , Thorlacius-Ussing Louise , Knudsen Andreas , Lindegaard Birgitte , Johansen Isik S , Mygind Lone Hagens , Ravn Pernille , Benfield Thomas 
Published: July 2023

IntroductionThe optimal duration of antibiotic therapy for community-acquired pneumonia (CAP) is unsettled. Short-course therapy has proved successful in clinical trials but is not yet implemented in everyday clinical practice. Validation of results from randomised controlled trials is crucial to evaluate existing evidence and provide clinicians with assurance of using new treatment strategies. In a pragmatic framework, we aim to assess the use of short-course antibiotic therapy guided by the onset of clinical stability in patients hospitalised with CAP.Methods and analysisThis study is a randomised controlled trial with a non-inferiority design that will examine the efficacy of short-course antibiotic therapy in patients hospitalised with CAP. From six hospitals across Denmark, we plan to enrol 564 patients between 2019 and 2024. Within 3–5 days after initiating antibiotic therapy, participants will be randomised 1:1 to parallel treatment arms: (1) short-course antibiotic therapy of 5 days or (2) antibiotic therapy of at least 7 days. The primary outcome will be 90-day readmission-free survival and will be estimated as an absolute risk difference with a predefined non-inferiority margin of −6%. Secondary outcomes will comprise other safety measures including new antibiotics, adverse events, length of hospital stay and postdischarge outpatient visits. Both intention-to-treat and per-protocol analyses will be performed.Ethics and disseminationThis study has been approved by the Health Research Ethics Committee of the Capital Region of Denmark (identifier number: H-19014479). Trial data will be made available in anonymous form when the trial has ended.Trial registration numberNCT04089787, ClinicalTrials.Gov.
Efficacy of quadruple therapy with clarithromycin based on faecal molecular antimicrobial susceptibility tests as first-line treatment forHelicobacter pyloriinfection: a protocol of a single-centre, single-blind, randomised clinical trial in China
Authors: Wu Yaoyi , Wang Yujing , Liu Xiaochen , Liao Oulan , Lou Guochun , Li Yan , Wu Hao , Du Qin , Ye Jun 
Published: July 2023

IntroductionHelicobacter pyloriis the most well-known risk factor for gastric cancer. Antibiotic resistance is the main reason for the failure ofH. pylorieradication, and understanding the antibiotic resistance before treatment may be the main determinant of successful eradication ofH. pylori. This study aims to evaluate the efficacy and safety of quadruple therapy based on faecal molecular antimicrobial susceptibility tests for the first-line eradication ofH. pyloriinfection.Methods and analysisThis is a single-centre, single-blind, randomised controlled trial, enrolling 855 patients withH. pyloriinfection. Patients are randomised to three groups for a 14-day treatment: group A: amoxicillin- and clarithromycin-based bismuth-containing quadruple therapy (BQT) (rabeprazole 10 mg, amoxicillin 1 g, clarithromycin 500 mg and colloidal bismuth 200 mg two times per day); group B: clarithromycin medication history-based BQT (rabeprazole 10 mg, amoxicillin 1 g, furazolidone 100 mg (with clarithromycin medication history)/clarithromycin 500 mg (without clarithromycin medication history) and colloidal bismuth 200 mg two times per day); group C: antimicrobial susceptibility test-based BQT (rabeprazole 10 mg, amoxicillin 1 g, clarithromycin 500 mg (clarithromycin-sensitive)/furazolidone 100 mg (clarithromycin resistant) and colloidal bismuth 200 mg two times per day). The primary end point is the eradication rate. The secondary end points are the incidence of adverse events and compliance.Ethics and disseminationThis study was approved by the Ethics Committee of Second Affiliated Hospital, School of Medicine, Zhejiang University (Number 20230103). The results will be published in the appropriate peer-reviewed journal.Trial registration numberNCT05718609.
Application of the whole-course care model (IWF/C Care) for postintensive care syndrome based on an early warning system in critically ill patients: a randomised controlled trial study protocol
Authors: Liu Xiaohui , Long Jianmei , Chang Yonghu , Gao Huiming , Zhang Xia , Chen Junxi , Hu Rujun 
Published: July 2023

IntroductionCritically ill patients are at risk of developing postintensive care syndrome (PICS), which is manifested by physical, psychological and cognitive impairment. Currently, there are no programmes that combine early warning systems with interventions for PICS. We hypothesise that a comprehensive care model for PICS based on an early warning system would reduce medical costs and the incidence of PICS.Methods and analysisThe Intensive Care Unit (ICU) -Ward-Family/Community whole-course care (IWF/C Care) trial will be a unicentric, randomised, controlled trial. A total of 138 ICU patients from two ICUs at a university hospital in Guizhou province, China, will be enrolled in February 2023. The inclusion criteria are an age of 18 years or older, an ICU stay of more than 48 hours, provide informed consent and the ability to communicate normally. Patients will be followed for 12 months and randomised in a 1:1:1 ratio to three groups.InterventionsPatients in intervention group 1 will be assessed by the PICS early warning system within 24 hours of ICU discharge, and precise interventions will be carried out according to the results; that is, high-risk patients will receive care based on the IWF/C Care model and low-risk patients will receive routine care. All patients in intervention group 2 will receive care based on the IWF/C Care model. The control group will receive routine care. The primary endpoints are the incidence of PICS and quality of life. The secondary endpoints include the incidence of adverse events: the unplanned readmission rate, cost-effectiveness, and the experiences and feelings of patients receiving care based on the IWF/C Care model. The incidence of PICS will be measured at ICU discharge, general ward discharge, the home/community stage and 1 month and 3, 6, 9, and 12 months after discharge.Ethics and disseminationEthics approval was obtained from Biomedical Research Ethics Committee of the Affiliated Hospital of Zunyi Medical University (approval number: KLL-2022-780). The results of this study will be distributed through peer-reviewed journals.Trial registration numberChiCTR2300068135.