bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic comparison of bone marrow CD34 + cells and peripheral blood neutrophils from ET patients with JAK2 or CALR mutations
Authors: Guijarro-Hernández Ana , Vizmanos José Luis 
Published: August 2023

AbstractBackgroundEssential thrombocythemia (ET) is one of the most common types ofPh-negative myeloproliferative neoplasms, an infrequent group of blood cancers that arise from a CD34 + hematopoietic stem cell (HSC) in the bone marrow (BM) primarily due to driver mutations inJAK2,CALRorMPL. These aberrations result in an overproduction of mature myeloid cells in peripheral blood (PB). To date, no targeted therapies have been approved for ET patients, so the study of the molecular mechanisms behind the disease and the identification of new therapeutic targets may be of interest. For this reason, in this study, we have compared the transcriptomic profile of undifferentiated CD34 + cells and mature myeloid cells from ET patients (CALRandJAK2-mutated) and healthy donors deposited in publicly available databases. The study of the similarities and differences between these samples might help to better understand the molecular mechanisms behind the disease according to the degree of maturation of the malignant clone and the type of mutation and ultimately help identify new therapeutic targets for these patients.ResultsThe results show that most of the altered hallmarks in neutrophils were also found in CD34 + cells. However, only a few genes showed a similar aberrant expression pattern in both types of cells. We have identified a signature of six genes common to patients withCALRandJAK2mutations (BPI,CRISP3,LTF,MMP8, andPTGS1upregulated, andPBXIP1downregulated), a different signature of seven genes for patients withCALRmutations (BMP6,CEACAM8,ITK,LCN2, andPRG2upregulated, andMAN1A1andMMEdownregulated) and a signature of 13 genes for patients withJAK2mutations (ARG1,CAST,CD177,CLEC5A,DAPP1,EPS15,IL18RAP,OLFM4,OLR1,RIOK3,SELP, andTHBS1upregulated, andIGHMdownregulated).ConclusionsOur results highlight transcriptomic similarities and differences in ET patients according to the degree of maturation of the malignant clone and the type of mutation. The genes and processes altered in both CD34 + cells and mature neutrophils may reveal altered sustained processes that could be studied as future therapeutic targets for ET patients.
High-quality haploid genomes corroborate 29 chromosomes and highly conserved synteny of genes in Hyles hawkmoths (Lepidoptera: Sphingidae)
Authors: Hundsdoerfer Anna K. , Schell Tilman , Patzold Franziska , Wright Charlotte J. , Yoshido Atsuo , Marec František , Daneck Hana , Winkler Sylke , Greve Carola , Podsiadlowski Lars , Hiller Michael , Pippel Martin 
Published: August 2023

Abstract
Background
Morphological and traditional genetic studies of the young Pliocene genus Hyles have led to the understanding that despite its importance for taxonomy, phenotypic similarity of wing patterns does not correlate with phylogenetic relationship. To gain insights into various aspects of speciation in the Spurge Hawkmoth (Hyles euphorbiae), we assembled a chromosome-level genome and investigated some of its characteristics.

Results
The genome of a male H. euphorbiae was sequenced using PacBio and Hi-C data, yielding a 504 Mb assembly (scaffold N50 of 18.2 Mb) with 99.9% of data represented by the 29 largest scaffolds forming the haploid chromosome set. Consistent with this, FISH analysis of the karyotype revealed n = 29 chromosomes and a WZ/ZZ (female/male) sex chromosome system. Estimates of chromosome length based on the karyotype image provided an additional quality metric of assembled chromosome size. Rescaffolding the published male H. vespertilio genome resulted in a high-quality assembly (651 Mb, scaffold N50 of 22 Mb) with 98% of sequence data in the 29 chromosomes. The larger genome size of H. vespertilio (average 1C DNA value of 562 Mb) was accompanied by a proportional increase in repeats from 45% in H. euphorbiae (measured as 472 Mb) to almost 55% in H. vespertilio. Several wing pattern genes were found on the same chromosomes in the two species, with varying amounts and positions of repetitive elements and inversions possibly corrupting their function.

Conclusions
Our two-fold comparative genomics approach revealed high gene synteny of the Hyles genomes to other Sphingidae and high correspondence to intact Merian elements, the ancestral linkage groups of Lepidoptera, with the exception of three simple fusion events. We propose a standardized approach for genome taxonomy using nucleotide homology via scaffold chaining as the primary tool combined with Oxford plots based on Merian elements to infer and visualize directionality of chromosomal rearrangements. The identification of wing pattern genes promises future understanding of the evolution of forewing patterns in the genus Hyles, although further sequencing data from more individuals are needed. The genomic data obtained provide additional reliable references for further comparative studies in hawkmoths (Sphingidae).
Prognostic and biological function value of OSBPL3 in colorectal cancer analyzed by multi-omic data analysis
Authors: Wang Chengxing , He Yaoming , He Yu , Liang Weijun , Zhou Chaorong , Wu Meimei , Meng Zijie , Li Wanglin , Cao Jie 
Published: August 2023

Abstract
Background
Colorectal cancer (CRC) is one of the most common malignancies in the world. This study proposes to reveal prognostic biomarkers for the prognosis and treatment of CRC patients.

Methods
Differential analysis of OSBPL3 was performed in pan-cancer, and the correlation between clinical stage and OSBPL3 was analyzed. Multiple omics analysis was used to compare the relationship between survival of patients and copy number variation, single nucleotide variant, and methylation status. Survival differences between high and low OSBPL3 expression groups were analyzed. Differentially expressed genes (DEGs) between high and low OSBPL3 expression groups were obtained, and functional enrichment analysis was implemented. Correlations between immune cells and OSBPL3 was analyzed. Drug sensitivity between the two OSBPL3 expression groups was compared. Moreover, the expression of OSBPL3 was verified by immunohistochemistry and real-time quantitative PCR.

Results
OSBPL3 was differentially expressed in 13 tumors and had some correlations with T and N stages. OSBPL3 expression was regulated by methylation and higher OSBPL3 expression was associated with poorer prognosis in CRC. 128 DEGs were obtained and they were mainly involved in signaling receptor activator activity, aspartate and glutamate metabolism. T cell gamma delta and T cell follicular helper were significantly different in the high and low OSBPL3 expression groups. Moreover, OSBPL3 showed negative correlations with multiple drugs. OSBPL3 was significantly upregulated in CRC samples compared to normal samples.

Conclusions
A comprehensive analysis demonstrated that OSBPL3 had potential prognostic value, and guiding significance for CRC chemotherapeutic.
Development of a clinical risk score system for peritoneal dialysis-associated peritonitis treatment failure
Authors: Mao Yuhe , Xiao Dan , Deng Shengjing , Xue Shaoqing 
Published: August 2023

Abstract
Objective
This study aimed to construct a clinical risk score system for peritoneal dialysis-associated peritonitis (PDAP) treatment failure to provide a theoretical basis for clinical workers.

Methods
A total of 161 PDAP individuals admitted to our hospital were included, among whom 70 cases were in the treatment-improved group and 87 cases were in the treatment failure group. We compared the general condition, clinical manifestations, and laboratory examination indicators of the two groups of individuals, used multivariate logistic regression analysis to identify the factors influencing PDAP treatment failure, and developed a clinical risk score system. The diagnostic performance of the risk score system was evaluated utilizing the receiver operating characteristic (ROC) curve.

Results
Significant differences (P < 0.05) were observed between the two groups in terms of contamination, peritoneal fluid culture results, blood urea nitrogen (BUN) level, C-reactive protein (CRP) level, B-type natriuretic peptide (BNP) level, average residual urine (RU) volume, and urea clearance rate (UCR). Multivariate logistic regression analysis showed that BUN level, CRP level, BNP level, average RU volume, and UCR were independent risk factors affecting PDAP patient treatment outcomes (P < 0.05). The ROC curve analysis of the risk score system for predicting treatment failure in PDAP individuals showed an area under the curve of 0.895 [95% confidence interval (0.847–0.943)]. The optimal cut-off point was 2.5 points, with corresponding sensitivity and specificity of 88.5% and 74.3%, separately.

Conclusion
BUN level, CRP level, BNP level, average RU volume, and UCR are independent risk factors for PDAP treatment failure. The clinical risk score system based on these five independent risk factors can accurately predict the risk of treatment failure in PDAP individuals.
Development of the national Dutch PEWS: the challenge against heterogeneity and implementation difficulties of PEWS in the Netherlands
Authors: Fuijkschot Joris , Stevens Jikke , Teheux Lara , de Loos Erica , Rippen Hester , Meurs Maaike , de Groot Janke 
Published: August 2023

Abstract
Background
For the early recognition of deteriorating patients several Pediatric Early Warning Score (PEWS) systems have been developed with the assumption that early detection can prevent further deterioration. Although PEWS are widely being used in hospitals in the Netherlands, there is no national consensus on which score to use and how to embed the score into a PEWS system. This resulted in a substantial heterogeneity of PEWS systems, of which many are unvalidated or self-designed. The primary objective of this study was to develop a pragmatic consensus-based PEWS system that can be utilized in all Dutch hospitals (University Medical Centers, teaching hospitals, and general hospitals).

Methods
This study is an iterative mixed-methods study. The methods from the Core Outcome Measures in Effectiveness Trials (COMET) initiative were used and consisted of two Delphi rounds, two inventories set out to all Dutch hospitals and a focus group session with parents. The study was guided by five expert meetings with different stakeholders and a final consensus meeting that resulted in a core PEWS set.

Results
The first Delphi round was completed by 292 healthcare professionals, consisting of pediatric nurses and physicians. In the second Delphi round 217 healthcare professionals participated. Eventually, the core PEWS set was been developed comprising of the parameters work of breathing, respiratory rate, oxygen therapy, heart rate and capillary refill time, and AVPU (Alert, Verbal, Pain, and Unresponsive). In addition, risk stratification was added to the core set with standardized risk factors consisting of [1] worried signs from healthcare professionals and parents and [2] high-risk treatment, with the option to add applicable local defined risk factors. Lastly, the three categories of risk stratification were defined (standard, medium, and high risk) in combination with standardized actions of the professionals for each category.

Conclusion
This study demonstrates a way to end a country’s struggle with PEWS heterogeneity by co-designing a national Dutch PEWS system. Currently, the power of the system is being investigated in a large multi-center study in the Netherlands.
A scoping review of trauma informed approaches in acute, crisis, emergency, and residential mental health care
Authors: Saunders Katherine R. K. , McGuinness Elizabeth , Barnett Phoebe , Foye Una , Sears Jessica , Carlisle Sophie , Allman Felicity , Tzouvara Vasiliki , Schlief Merle , Vera San Juan Norha , Stuart Ruth , Griffiths Jessica , Appleton Rebecca , McCrone Paul , Rowan Olive Rachel , Nyikavaranda Patrick , Jeynes Tamar , K T. , Mitchell Lizzie , Simpson Alan , Johnson Sonia , Trevillion Kylee 
Published: August 2023

AbstractExperiences of trauma in childhood and adulthood are highly prevalent among service users accessing acute, crisis, emergency, and residential mental health services. These settings, and restraint and seclusion practices used, can be extremely traumatic, leading to a growing awareness for the need for trauma informed care (TIC). The aim of TIC is to acknowledge the prevalence and impact of trauma and create a safe environment to prevent re-traumatisation. This scoping review maps the TIC approaches delivered in these settings and reports related service user and staff experiences and attitudes, staff wellbeing, and service use outcomes.We searched seven databases (EMBASE; PsycINFO; MEDLINE; Web of Science; Social Policy and Practice; Maternity and Infant Care Database; Cochrane Library Trials Register) between 24/02/2022-10/03/2022, used backwards and forwards citation tracking, and consulted academic and lived experience experts, identifying 4244 potentially relevant studies. Thirty-one studies were included.Most studies (n = 23) were conducted in the USA and were based in acute mental health services (n = 16). We identified few trials, limiting inferences that can be drawn from the findings. The Six Core Strategies (n = 7) and the Sanctuary Model (n = 6) were the most commonly reported approaches. Rates of restraint and seclusion reportedly decreased. Some service users reported feeling trusted and cared for, while staff reported feeling empathy for service users and having a greater understanding of trauma. Staff reported needing training to deliver TIC effectively.TIC principles should be at the core of all mental health service delivery. Implementing TIC approaches may integrate best practice into mental health care, although significant time and financial resources are required to implement organisational change at scale. Most evidence is preliminary in nature, and confined to acute and residential services, with little evidence on community crisis or emergency services. Clinical and research developments should prioritise lived experience expertise in addressing these gaps.
Objective cognitive functioning in patients with stress-related disorders: a cross-sectional study using remote digital cognitive testing
Authors: Franke Föyen Ludwig , Sennerstam Victoria , Kontio Evelina , Lekander Mats , Hedman-Lagerlöf Erik , Lindsäter Elin 
Published: August 2023

Abstract
Background
Patients with stress-related mental disorders often report cognitive impairment, but studies investigating objective cognitive impairment in patients with stress-related disorders have produced inconsistent findings.

Aim
The primary aim of this study was to investigate objective cognitive functioning in patients diagnosed with the stress-related disorders adjustment disorder or exhaustion disorder, compared to a healthy normative group. Secondary aims were to conduct subgroup analyses of cognitive functioning between the diagnostic groups and explore associations between self-reported symptoms and cognitive functioning.

Methods
Cognitive test results on a digitally self-administered cognitive test battery from 266 patients (adjustment disorder, n = 131; exhaustion disorder, n = 135) were cross-sectionally compared with results from a healthy normative group (N = 184 to 692) using one-tailed t-tests. ANOVAs were conducted for subgroup analyses, and regression analyses for associations between self-reported symptoms and cognitive functioning. Effect sizes were calculated.

Results
Patients performed significantly worse than the normative group on all measures with small to moderate effect sizes ranging from d = -.13 to -.57. Those diagnosed with exhaustion disorder performed worse than norms on more measures than did patients with adjustment disorder, but no significant differences between diagnostic groups were found on any measure. Self-reported memory impairment was weakly associated with one of two memory measures. No clear associations between self-reported burnout symptoms and objective cognitive functioning were found.

Conclusions
This study adds to the literature indicative of small to moderate objective cognitive impairments in patients diagnosed with stress-related mental disorders. Further exploration into mechanisms of cognitive functioning in different populations is needed for development of theoretical models that may explain the weak correlation between self-reported symptoms and objective measures.

Trial registration
ClinicalTrial.gov: NCT04797273. Trial registration date 15 March 2021. This study was also pre-registered on Open Science Framework (osf.io) with https://doi.org/10.17605/OSF.IO/TQXZV.
Lessons learned through the 20-year development of a national fatal drowning database in Australia
Authors: Peden Amy E , Willcox-Pidgeon Stacey , Scarr Justin-Paul , Franklin Richard C 
Published: August 2023

Abstract
Background
Co-ordinated, evidence-based policy and programmatic efforts are needed to respond to complex drowning prevention problems. Comprehensive, current, and robust data are vital for agenda setting, burden and risk factor identification, intervention design and evaluation, as well as setting policy. We aim to record methods used in, and identify impacts of, the development of a national fatal drowning database (NFDD) in Australia, including lessons learned across research, policy, and practice.

Methods
We employ a case study method using process mapping and document review to explore the evolution, drivers and impacts of the NFDD. We analyse methodological approaches including those relating to data definitions, drowning case collection, and management, as well as tracking the various outputs of the NFDD. We describe a development timeline that presents impact of drowning prevention policy, and research agendas on database development, and research investments more specifically.

Results
Our study identified that the collected variables grew 20-fold from 2002 to 2022, reaching 259 variables, and 5,692 unique cases of fatal drowning. The NFDD employs data triangulation methodology, combining keyword and targeted searches of coronial files, media report monitoring, and organisational data provision. Database development is influenced by the Australia Water Safety Strategy, policymaker and practitioner-initiated research agendas, and identification of knowledge gaps. We identified numerous outputs spanning publications, media, intervention development, and legislative submissions.

Conclusion
A comprehensive and robust NFDD informed by policymaker and practitioner input can enhance surveillance, policy, and intervention development for drowning prevention. Employing mixed data collection and validation methods can supplement weaknesses in official data sources. There is a need for the NFDD to continue to evolve in its application while maintaining rigorous case identification and data quality assurance processes. Despite significant investment, the outputs and influence on drowning prevention practice in Australia has been extremely valuable and contributed to sizeable reductions in Australia’s fatal drowning rate.
The associations between social support change and physical activity trajectory from late adolescence to young adulthood
Authors: Cao Juan , Wang Kun , Shi YuHui , Pan YuQing , Lyu MoHan , Ji Ying 
Published: August 2023

Abstract
Background
Previous research examined the associations between social support and physical activity. However, little is known about the associations between social support change and trajectories of physical activity during the transition from late adolescence to young adulthood.

Methods
The current study sought to examine these issues among 434 Chinese college students (Mage = 19.15, SDage = 0.61; 46.1% male), who completed questionnaires regarding demographics, physical activity, family support change, and peer support change across three waves (the data from one of the waves was retrospective).

Results
After controlling for covariates, the findings revealed that: (a) there was an increase in overall physical activity and duration, but a decrease in frequency during the transition from late adolescence (the second year of high school) to young adulthood (the third year of college); (b) family support change did not contribute to trajectories of physical activity, while peer support change significantly predicted the trajectory of overall physical activity, duration, and frequency.

Conclusions
The findings extend the literature on physical activity from a developmental perspective by revealing different trends among physical activity duration and frequency, and unpacking different effects of family and peer support change on trajectories of physical activity.
PECSS: Pulmonary Embolism Comprehensive Screening Score to safely rule out pulmonary embolism among suspected patients presenting to emergency department
Authors: Tang Luojia , Hu Yundi , Pan Dong , Yang Chun , Tang Cheng , Huang Yunchuan , Gu Jianyong , Min Min , Lin Xiaolei , Tong Chaoyang 
Published: August 2023

Abstract
Background
Pulmonary embolism is a severe cardiovascular disease and can be life-threatening if left untreated. However, the detection rate of pulmonary embolism using existing pretest probability scores remained relatively low and clinical rule out often relied on excessive use of computed tomographic pulmonary angiography.

Methods
We retrospectively collected data from pulmonary embolism suspected patients in Zhongshan Hospital from July 2018 to October 2022. Pulmonary embolism diagnosis and severity grades were confirmed by computed tomographic pulmonary angiography. Patients were randomly divided into derivation and validation set. To construct the Pulmonary Embolism Comprehensive Screening Score (PECSS), we first screened for candidate clinical predictors using univariate logistic regression models. These predictors were then included in a searching algorithm with indicators of Wells score, where a series of points were assigned to each predictor. Optimal D-Dimer cutoff values were investigated and incorporated with PECSS to rule out pulmonary embolism.

Results
In addition to Wells score, PECSS identified seven clinical predictors (anhelation, abnormal blood pressure, in critical condition when admitted, age > 65 years and high levels of pro-BNP, CRP and UA,) strongly associated with pulmonary embolism. Patients can be safely ruled out of pulmonary embolism if PECSS ≤ 4, or if 4 < PECSS ≤ 6 and D-Dimer ≤ 2.5 mg/L. Comparing with Wells approach, PECSS achieved lower failure rates across all pulmonary embolism severity grades. These findings were validated in the held-out validation set.

Conclusions
Compared to Wells score, PECSS approaches achieved lower failure rates and better compromise between sensitivity and specificity. Calculation of PECSS is easy and all predictors are readily available upon emergency department admission, making it widely applicable in clinical settings.

Trail registration
The study was retrospectively registered (No. CJ0647) and approved by Human Genetic Resources in China in April 2022. Ethical approval was received from the Medical Ethics Committee of Zhongshan Hospital (NO.B2021-839R).