bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo transcriptome assembly of the cotyledon of Camellia oleifera for discovery of genes regulating seed germination
Authors: Long Wei , Yao Xiaohua , Wang Kailiang , Sheng Yu , Lv Leyan 
Published: May 2022

Abstract
Background
Camellia oleifera (C.oleifera) is one of the most important wood oil species in the world. C.oleifera was propagated by nurse seedling grafting. Since the morphology of rootstocks has a significant impact on grafting efficiency and seedling quality, it is necessary to understand the molecular mechanism of morphogenesis for cultivating high-quality and controllable rootstocks. However, the genomic resource for this species is relatively limited, which hinders us from fully understanding the molecular mechanisms of seed germination in C.oleifera.

Results
In this paper, using transcriptome sequencing, we measured the gene expression in the C.oleifera cotyledon in different stages of development and the global gene expression profiles. Approximately 45.4 gigabases (GB) of paired-end clean reads were assembled into 113,582 unigenes with an average length of 396 bp. Six public protein databases annotate 61.5% (68,217) of unigenes. We identified 11,391 differentially expressed genes (DEGs) throughout different stages of germination. Enrichment analysis revealed that DEGs were mainly involved in hormone signal transduction and starch sucrose metabolism pathways. The gravitropism regulator UNE10, the meristem regulators STM, KNAT1, PLT2, and root-specific transcription factor WOX11 all have higher gene expression levels in the CAM2 stage (seed soaking), which indicates that the cotyledon-regulated program for germination had initiated when the seeds were imbibition. Our data showed differentially reprogrammed to multiple hormone-related genes in cotyledons during C.oleifera seed germination.

Conclusion
Cotyledons play vital roles, both as the main nutrient provider and as one primary instructor for seed germination and seedling growth. Together, our study will significantly enrich the genomic resources of Camellia and help us understand the molecular mechanisms of the development in the seed germination and seedling growth of C.oleifera. It is helpful to culture standard and superior quality rootstock for C.oleifera breeding.
The relationships between IBS and perceptions of physical and mental health—a Norwegian twin study
Authors: Kutschke Julia , Harris Jennifer R. , Bengtson May-Bente 
Published: May 2022

AbstractBackground and aimsPoor quality of life is a main complaint among individuals with irritable bowel syndrome (IBS). Self-rated health (SRH) is a powerful predictor of clinical outcomes, and also reflects psychological and social aspects of life and an overall sense of well-being. This population-based twin study evaluates how IBS affects ratings of physical and mental health, and influences perceptions of hindrance of daily activity by physical or mental health. Further, we examine how IBS is related to these SRH measures.MethodsThe sample included 5288 Norwegian twins aged 40–80, of whom 575 (10.9%) suffer from IBS. Hierarchical regressions were used to estimate the impact of IBS on perceptions of health, before and after accounting for other chronic physical and mental health conditions. Two dimensions of SRH, physical and mental, and two aspects of functional limitations, the extent to which physical or mental health interferes with daily activities, were included as outcomes in separate models. Co-twin control analyses were used to explore whether the relationships between IBS and the four measures of SRH are causal, or due to shared genetic or shared environment effects.ResultsIBS was an independent predictor of poor self-rated physical health (OR = 1.82 [1.41; 2.33]), the size of this effect was comparable to that predicted by chronic somatic conditions. However, in contrast to somatic diseases, IBS was associated with the perception that poorer ratings of mental health (OR = 1.45 [1.02; 2.06]), but not physical health (OR = 1.23 [0.96; 1.58]), interfered with daily activity. The co‐twin control analyses suggest that causal mechanisms best explain the relationships between IBS with self-rated physical health and with hindrance of daily activities. In contrast, the relationship between IBS and self-rated mental health was consistent with shared genetic effects.ConclusionIBS is predictive of poor self-rated physical health. The relationship between IBS and self-rated mental health is best explained by shared genetic effects which might partially explain why mental health interferes with daily activity to a larger degree among those with IBS.
Prevalence of oral anticoagulant use among people with and without Alzheimer’s disease
Authors: Ali Babar Barkat , Vu Mai , Koponen Marjaana , Taipale Heidi , Tanskanen Antti , Kettunen Raimo , Tiihonen Miia , Hartikainen Sirpa , Tolppanen Anna-Maija 
Published: May 2022

Abstract
Background
Although cardio- and cerebrovascular diseases are common among people with Alzheimer’s disease (AD), it is unknown how the prevalence of oral anticoagulant (OAC) use changes in relation to AD diagnosis. We investigated the prevalence of OAC use in relation to AD diagnosis in comparison to a matched cohort without AD.

Methods
Register-based Medication use and Alzheimer’s disease (MEDALZ) cohort includes 70 718 Finnish people with AD diagnosed between 2005–2011. Point prevalence of OAC use (prescription register) was calculated every three months with three-month evaluation periods, from five years before to five years after clinically verified diagnosis and compared to matched cohort without AD. Longitudinal association between AD and OAC use was evaluated by generalized estimating equations (GEE).

Results
OAC use was more common among people with AD until AD diagnosis, (OR 1.17; 95% CI 1.13–1.22), and less common after AD diagnosis (OR 0.87; 95% CI 0.85–0.89), compared to people without AD. At the time of AD diagnosis, prevalence was 23% and 20% among people with and without AD, respectively. OAC use among people with AD began to decline gradually two years after AD diagnosis while continuous increase was observed in the comparison cohort. Warfarin was the most common OAC, and atrial fibrillation was the most common comorbidity in OAC users.

Conclusion
Decline in OAC use among people with AD after diagnosis may be attributed to high risk of falling and problems in monitoring. However, direct oral anticoagulants (DOACs) that are nowadays more commonly used require less monitoring and may also be safer for vulnerable people with AD.
Self-monitoring of blood pressure among women with hypertensive disorders of pregnancy: a systematic review
Authors: Yeh Ping Teresa , Rhee Dong Keun , Kennedy Caitlin Elizabeth , Zera Chloe A. , Lucido Briana , Tunçalp Özge , Gomez Ponce de Leon Rodolfo , Narasimhan Manjulaa 
Published: May 2022

Abstract
Background
The World Health Organization (WHO) recommends self-monitoring of blood pressure (SMBP) for hypertension management. In addition, during the COVID-19 response, WHO guidance also recommends SMBP supported by health workers although more evidence is needed on whether SMBP of pregnant individuals with hypertension (gestational hypertension, chronic hypertension, or pre-eclampsia) may assist in early detection of pre-eclampsia, increase end-user autonomy and empowerment, and reduce health system burden. To expand the evidence base for WHO guideline on self-care interventions, we conducted a systematic review of SMBP during pregnancy on maternal and neonatal outcomes.

Methods
We searched for publications that compared SMBP with clinic-based monitoring during antenatal care. We included studies measuring any of the following outcomes: maternal mortality, pre-eclampsia, long-term risk and complications, autonomy, HELLP syndrome, C-section, antenatal hospital admission, adverse pregnancy outcomes, device-related issues, follow-up care with appropriate management, mental health and well-being, social harms, stillbirth or perinatal death, birthweight/size for gestational age, and Apgar score. After abstract screening and full-text review, we extracted data using standardized forms and summarized findings. We also reviewed studies assessing values and preferences as well as costs of SMBP.

Results
We identified 6 studies meeting inclusion criteria for the effectiveness of SMBP, 6 studies on values and preferences, and 1 study on costs. All were from high-income countries. Overall, when comparing SMBP with clinic-monitoring, there was no difference in the risks for most of the outcomes for which data were available, though there was some evidence of increased risk of C-section among pregnant women with chronic hypertension. Most end-users and providers supported SMBP, motivated by ease of use, convenience, self-empowerment and reduced anxiety. One study found SMBP would lower health sector costs.

Conclusion
Limited evidence suggests that SMBP during pregnancy is feasible and acceptable, and generally associated with maternal and neonatal health outcomes similar to clinic-based monitoring. However, more research is needed in resource-limited settings.

Systematic review registration
PROSPERO CRD42021233839.
Promoting respectful maternity care: challenges and prospects from the perspectives of midwives at a tertiary health facility in Ghana
Authors: Dzomeku Veronica Millicent , Mensah Adwoa Bemah Boamah , Nakua Emmanuel Kweku , Agbadi Pascal , Okyere Joshua , Donkor Peter , Lori Jody R. 
Published: May 2022

Abstract
Background
Evidence shows that women in Ghana experience disrespectful care (slapping, pinching, being shouted at, etc.) from midwives during childbirth. Hence, evidence-based research is needed to advance the adoption of respectful maternity care (RMC) by midwives. We therefore sought to explore and document midwives’ perspectives concerning challenges faced and prospects available for promoting RMC in a tertiary health facility.

Methods
We employed an exploratory descriptive qualitative study design. In total, we conducted 12 interviews with midwives educated on RMC. All audio data were transcribed verbatim and exported to NVivo-12 for data management and analyses. We relied on the Consolidated Criteria for Reporting Qualitative Research guideline in reporting this study.

Results
The findings were broadly categorised into three themes: emotional support, dignified care and respectful communication which is consistent with the WHO’s quality of care framework. For each theme, the current actions that were undertaken to promote RMC, the challenges and recommendations to improve RMC promotion were captured. Overall, the current actions that promoted RMC included provision of sacral massages and reassurance, ensuring confidentiality and consented care, and referring clients who cannot pay to the social welfare unit. The challenges to providing RMC were logistical constraints for ensuring privacy, free movement of clients, and alternative birthing positions. Poor attitudes from some midwives, workload and language barrier were other challenges that emerged. The midwives recommended the appointment of more midwives, as well as the provision of logistics to support alternative birthing positions and privacy. Also, they recommended the implementation of continuous training and capacity building.

Conclusion
We conclude that in order for midwives to deliver RMC services that include emotional support, dignified care, and respectful communication, the government and hospital administration must make the required adjustments to resolve existing challenges while improving the current supporting activities.
Optimal surveillance of intraductal papillary mucinous neoplasms of the pancreas focusing on remnant pancreas recurrence after surgical resection
Authors: Fuji Tomokazu , Umeda Yuzo , Takagi Kosei , Yoshida Ryuichi , Yoshida Kazuhiro , Yasui Kazuya , Matsumoto Kazuyuki , Kato Hironari , Yagi Takahito , Fujiwara Toshiyoshi 
Published: May 2022

Abstract
Background
The international consensus guidelines for intraductal papillary mucinous neoplasm of the pancreas (IPMN) presented clinical features as indications for surgery. Whereas surveillance for recurrence, including de novo lesions, is essential, optimal surveillance protocols have not been established.

Aim and methods
This study aimed to assess the clinical features of recurrence at the remnant pancreas (Rem-Panc) and extra-pancreas (Ex-Panc) after surgery for IPMN. Ninety-one patients of IPMN that underwent detailed preoperative assessment and pancreatectomy were retrospectively analyzed, focusing especially on the type of recurrence.

Results
The IPMNs were finally diagnosed as low-grade dysplasia (LDA, n = 42), high-grade dysplasia (HAD, n = 19), and invasive carcinoma (IPMC, n = 30). Recurrence was observed in 26 patients (29%), of which recurrence was seen at Rem-Panc in 19 patients (21%) and Ex-Panc in 7 patients (8%). The frequency of Rem-Panc recurrence was 10% in LDA, 21% in HDA, and 37% in IPMC. On the other hand, Ex-Panc recurrence was observed only in IPMC (23%). Ex-Panc recurrence showed shorter median recurrence-free survival (RFS) and overall survival (OS) than Rem-Panc recurrence (median RFS 8 months vs. 35 months, p < 0.001; median OS 25 months vs. 72 months, p < 0.001). Regarding treatment for Rem-Panc recurrence, repeat pancreatectomy resulted in better OS than no repeat pancreatectomy (MST 36 months vs. 15.5 months, p = 0.033). On multivariate analysis, main duct stenosis or disruption as a preoperative feature (hazard ratio [HR] 10.6, p = 0.002) and positive surgical margin (HR 4.4, p = 0.018) were identified as risk factors for Rem-Panc recurrence.

Conclusions
The risk factors for Rem-Panc and Ex-Panc recurrence differ. Therefore, optimal surveillance on these features is desirable to ensure that repeat pancreatectomy for Rem-Panc recurrence can be an appropriate surgical intervention.
Validation of genomic and transcriptomic models of homologous recombination deficiency in a real-world pan-cancer cohort
Authors: Leibowitz Benjamin D. , Dougherty Bonnie V. , Bell Joshua S. K. , Kapilivsky Joshuah , Michuda Jackson , Sedgewick Andrew J. , Munson Wesley A. , Chandra Tushar A. , Dry Jonathan R. , Beaubier Nike , Igartua Catherine , Taxter Timothy 
Published: May 2022

AbstractBackgroundWith the introduction of DNA-damaging therapies into standard of care cancer treatment, there is a growing need for predictive diagnostics assessing homologous recombination deficiency (HRD) status across tumor types. Following the strong clinical evidence for the utility of DNA-sequencing-based HRD testing in ovarian cancer, and growing evidence in breast cancer, we present analytical validation of the Tempus HRD-DNA test. We further developed, validated, and explored the Tempus HRD-RNA model, which uses gene expression data from 16,750 RNA-seq samples to predict HRD status from formalin-fixed paraffin-embedded tumor samples across numerous cancer types.MethodsGenomic and transcriptomic profiling was performed using next-generation sequencing from Tempus xT, Tempus xO, Tempus xE, Tempus RS, and Tempus RS.v2 assays on 48,843 samples. Samples were labeled based on theirBRCA1, BRCA2and selected Homologous Recombination Repair pathway gene (CDK12, PALB2, RAD51B, RAD51C, RAD51D) mutational status to train and validate HRD-DNA, a genome-wide loss-of-heterozygosity biomarker, and HRD-RNA, a logistic regression model trained on gene expression.ResultsIn a sample of 2058 breast and 1216 ovarian tumors, BRCA status was predicted by HRD-DNA with F1-scores of 0.98 and 0.96, respectively. Across an independent set of 1363 samples across solid tumor types, the HRD-RNA model was predictive of BRCA status in prostate, pancreatic, and non-small cell lung cancer, with F1-scores of 0.88, 0.69, and 0.62, respectively.ConclusionsWe predict HRD-positive patients across many cancer types and believe both HRD models may generalize to other mechanisms of HRD outside of BRCA loss. HRD-RNA complements DNA-based HRD detection methods, especially for indications with low prevalence of BRCA alterations.
Risk assessment and prediction for lung cancer among Hong Kong Chinese men
Authors: Tse Lap Ah , Wang Feng , Wong Martin Chi-sang , Au Joseph Siu-kei , Yu Ignatius Tak-sun 
Published: May 2022

Abstract
Objective
Most of the previous risk prediction models for lung cancer were developed from smokers, with discriminatory power ranging from 0.57 to 0.72. We constructed an individual risk prediction model for lung cancer among the male general population of Hong Kong.

Methods
Epidemiological data of 1,069 histology confirmed male lung cancer cases and 1,208 community controls were included in this analysis. Residential radon exposure was retrospectively reconstructed based on individual lifetime residential information. Multivariable logistic regression with repeated cross-validation method was used to select optimal risk predictors for each prediction model for different smoking strata. Individual absolute risk for lung cancer was estimated by Gail model. Receiver-operator characteristic curves, area under the curve (AUC) and confusion matrix were evaluated to demonstrate the model performance and ability to differentiate cases from non-cases.

Results
Smoking and smoking cessation, education, lung disease history, family history of cancer, residential radon exposure, dietary habits, carcinogens exposure, mask use and dust control in workplace were selected as the risk predictors for lung cancer. The AUC of estimated absolute risk for all lung cancers was 0.735 (95% CI: 0.714–0.756). Using 2.83% as the cutoff point of absolute risk, the predictive accuracy, positive predictive value and negative predictive value were 0.715, 0.818 and 0.674, respectively.

Conclusion
We developed a risk prediction model with moderate discrimination for lung cancer among Hong Kong males. External validation in other populations is warranted for this model in future studies.
Place of the partial dopamine receptor agonist aripiprazole in the management of schizophrenia in adults: a Delphi consensus study
Authors: Llorca Pierre-Michel , Nuss Philippe , Fakra Éric , Alamome Isabelle , Drapier Dominique , El Hage Wissam , Jardri Renaud , Mouchabac Stéphane , Rabbani Marc , Simon Nicolas , Vacheron Marie-Noëlle , Azorin Jean-Michel 
Published: May 2022

AbstractBackgroundAripiprazole is a second-generation antipsychotic, efficacious in patients with schizophrenia during acute episodes. Due to its pharmacological profile, aripiprazole may be of interest in patients with specific clinical profiles who have not been studied extensively in randomised clinical trials.ObjectivesTo capture experience with aripiprazole in everyday psychiatric practice using the Delphi method in order to inform decision-making on the use of aripiprazole for the treatment of patients with schizophrenia in clinical situations where robust evidence from clinical trials is lacking.MethodsThe scope of the survey was defined as the management of schizophrenia in adults. A systematic literature review was performed to identify the different clinical situations in which aripiprazole has been studied, and to describe the level of clinical evidence. Clinical profiles to include in the Delphi survey were selected if there was a clear interest in terms of medical need but uncertainty over the efficacy of aripiprazole. For each clinical profile retained, five to seven specific statements were generated and included in a questionnaire. The final 41-item questionnaire was proposed to a panel of 406 French psychiatrists with experience in the treatment of schizophrenia. Panellists rated their level of agreement using a Likert scale. A second round of voting on eleven items was organised to clarify points for which a consensus was not obtained in the first round.ResultsFive clinical profiles were identified in the literature review (persistent negative symptoms, pregnancy, cognitive dysfunction, addictive comorbidity and clozapine resistance). Sixty-two psychiatrists participated in the first round of the Delphi survey and 33 in the second round. A consensus was obtained for 11 out of 41 items in the first round and for 9/11 items in the second round. According to the panellists’ clinical experience, aripiprazole can be used as maintenance treatment for pregnant women, is relevant to preserve cognitive function and can be considered an option in patients with a comorbid addictive disorder or with persistent negative symptoms.ConclusionThese findings may help physicians in choosing relevant ways to use aripiprazole and highlight areas where more research is needed to widen the evidence base.
Associations between neighborhood built, social, or toxicant conditions and child externalizing behaviors in the Detroit metro area: a cross-sectional study of the neighborhood ‘exposome’
Authors: Pearson Amber L. , Shewark Elizabeth A. , Burt S. Alexandra 
Published: May 2022

Abstract
Background
The specific ‘active ingredients’ through which neighborhood disadvantage increases risk for child psychopathology remains unclear, in large part because research to date has nearly always focused on poverty to the exclusion of other neighborhood domains. The objective of this study was to evaluate whether currently assessed neighborhood built, social, or toxicant conditions were associated with child externalizing psychopathology outcomes separately, and in a combined model, using data from the Detroit-metro county area.

Methods
We conducted principal components analyses for built, social, or toxicant conditions. Next, we fitted separate multiple regression models for each of the child externalizing psychopathology measures (oppositional defiant and conduct problems) as a function of built, social, or toxicant components.

Results
We found that built features (more non-profits, churches, and alcohol outlets, and less agriculture and vacant properties) were associated with conduct problems, while toxicant conditions (high percent industrial, toxins released and number of pre-1978 structures) were associated with oppositional defiance problems. There was no significant association between greenspace or social conditions and child externalizing outcomes. When examined simultaneously, only the significant independent association between built conditions and conduct problems remained.

Conclusions
Built, social, and toxicant neighborhood conditions are not interchangeable aspects of a given neighborhood. What’s more, built features are uniquely associated with child externalizing outcomes independently of other neighborhood characteristics. Future research should consider how changes in the built conditions of the neighborhood (e.g., development, decay) serve to shape child externalizing behaviors, with a focus on identifying potentially actionable elements.