bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term outcomes of peripheral blood stem cell unrelated donors mobilized with filgrastim
Authors: Stefanski Heather E. , Kuxhausen Michelle , Bo-Subait Stephanie , Kobusingye Hati , Mattila Deborah , Schenfeld Jennifer , Sandschafer Darcie , De Oliveira Brandao Cisio , Burns Linda J. , Shaw Bronwen E. , Pulsipher Michael A. , Miller John P. , Devine Steven M. 
Published: April 2024

Abstract
Allogeneic hematopoietic cell transplantation is a life-saving procedure used to treat a variety of devastating diseases. It requires hematopoietic stem cells collected via filgrastim-mobilized peripheral blood stem cells (PBSCs) or bone marrow (BM) harvest from volunteer unrelated donors (URDs). There is a paucity of safety data regarding donors’ long-term adverse events. This prospective, observational study combined PBSC donors enrolled in the NMDP Investigational New Drug trial and BM donors between 1 July 1999 and 30 September 2015. The primary objective was to describe the long-term incidence of myeloid malignancies. The secondary objectives included describing the long-term incidence of lymphoid malignancies, nonhematologic malignancies, autoimmune disorders, and thrombotic events. A total of 21 643 donors (14 530 PBSCs and 7123 BM) were included. The incidence rate of myeloid disorders per 100 000 person-years in donors of PBSCs was 2.53 (95% confidence interval [CI], 0.82-7.84) and in donors of BM, it was 4.13 (95% CI, 1.33-12.8). The incidence rate ratio of PBSCs/BM donors was 0.61 (95% CI, 0.12-3.03; P = .55). The incidence of other malignancies, autoimmunity, and thrombosis did not differ between the donor types. This comprehensive study of the long-term effects of filgrastim in URDs of PBSCs provides strong evidence that donors who receive filgrastim are not at an increased risk of these events compared with BM donors. It also provides reassurance to current donors undergoing stem cell mobilization as well as individuals considering joining stem cell registries, such as NMDP.
The effect of data transformation on low-dimensional integration of single-cell RNA-seq
Authors: Park Youngjun , Hauschild Anne-Christin 
Published: April 2024

Abstract
Background
Recent developments in single-cell RNA sequencing have opened up a multitude of possibilities to study tissues at the level of cellular populations. However, the heterogeneity in single-cell sequencing data necessitates appropriate procedures to adjust for technological limitations and various sources of noise when integrating datasets from different studies. While many analysis procedures employ various preprocessing steps, they often overlook the importance of selecting and optimizing the employed data transformation methods.

Results
This work investigates data transformation approaches used in single-cell clustering analysis tools and their effects on batch integration analysis. In particular, we compare 16 transformations and their impact on the low-dimensional representations, aiming to reduce the batch effect and integrate multiple single-cell sequencing data. Our results show that data transformations strongly influence the results of single-cell clustering on low-dimensional data space, such as those generated by UMAP or PCA. Moreover, these changes in low-dimensional space significantly affect trajectory analysis using multiple datasets, as well. However, the performance of the data transformations greatly varies across datasets, and the optimal method was different for each dataset. Additionally, we explored how data transformation impacts the analysis of deep feature encodings using deep neural network-based models, including autoencoder-based models and proto-typical networks. Data transformation also strongly affects the outcome of deep neural network models.

Conclusions
Our findings suggest that the batch effect and noise in integrative analysis are highly influenced by data transformation. Low-dimensional features can integrate different batches well when proper data transformation is applied. Furthermore, we found that the batch mixing score on low-dimensional space can guide the selection of the optimal data transformation. In conclusion, data preprocessing is one of the most crucial analysis steps and needs to be cautiously considered in the integrative analysis of multiple scRNA-seq datasets.
Identification and characterization of PAL genes involved in the regulation of stem development in Saccharum spontaneum L.
Authors: Wu Xiaoqing , Cui Zetian , Li Xinyi , Yu Zehuai , Lin Pingping , Xue Li , Khan Abdullah , Ou Cailan , Deng Zuhu , Zhang Muqing , Yao Wei , Yu Fan 
Published: April 2024

Abstract
Background
Saccharum spontaneumL. is a closely related species of sugarcane and has become an important genetic component of modern sugarcane cultivars. Stem development is one of the important factors for affecting the yield, while the molecular mechanism of stem development remains poorly understanding in S. spontaneum. Phenylalanine ammonia-lyase (PAL) is a vital component of both primary and secondary metabolism, contributing significantly to plant growth, development and stress defense. However, the current knowledge about PAL genes in S. spontaneum is still limited. Thus, identification and characterization of the PAL genes by transcriptome analysis will provide a theoretical basis for further investigation of the function of PAL gene in sugarcane.

Results
In this study, 42 of PAL genes were identified, including 26 SsPAL genes from S. spontaneum, 8 ShPAL genes from sugarcane cultivar R570, and 8 SbPAL genes from sorghum. Phylogenetic analysis showed that SsPAL genes were divided into three groups, potentially influenced by long-term natural selection. Notably, 20 SsPAL genes were existed on chromosomes 4 and 5, indicating that they are highly conserved in S. spontaneum. This conservation is likely a result of the prevalence of whole-genome replications within this gene family. The upstream sequence of PAL genes were found to contain conserved cis-acting elements such as G-box and SP1, GT1-motif and CAT-box, which collectively regulate the growth and development of S. spontaneum. Furthermore, quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis showed that SsPAL genes of stem had a significantly upregulated than that of leaves, suggesting that they may promote the stem growth and development, particularly in the + 6 stem (The sixth cane stalk from the top to down) during the growth stage.

Conclusions
The results of this study revealed the molecular characteristics of SsPAL genes and indicated that they may play a vital role in stem growth and development of S. spontaneum. Altogether, our findings will promote the understanding of the molecular mechanism of S. spontaneum stem development, and also contribute to the sugarcane genetic improving.
Artificial selection footprints in indigenous and commercial chicken genomes
Authors: Wu Siwen , Dou Tengfei , Wang Kun , Yuan Sisi , Yan Shixiong , Xu Zhiqiang , Liu Yong , Jian Zonghui , Zhao Jingying , Zhao Rouhan , Wu Hao , Gu Dahai , Liu Lixian , Li Qihua , Wu Dong-Dong , Ge Changrong , Su Zhengchang , Jia Junjing 
Published: April 2024

Abstract
Background
Although many studies have been done to reveal artificial selection signatures in commercial and indigenous chickens, a limited number of genes have been linked to specific traits. To identify more trait-related artificial selection signatures and genes, we re-sequenced a total of 85 individuals of five indigenous chicken breeds with distinct traits from Yunnan Province, China.

Results
We found 30 million non-redundant single nucleotide variants and small indels (< 50 bp) in the indigenous chickens, of which 10 million were not seen in 60 broilers, 56 layers and 35 red jungle fowls (RJFs) that we compared with. The variants in each breed are enriched in non-coding regions, while those in coding regions are largely tolerant, suggesting that most variants might affect cis-regulatory sequences. Based on 27 million bi-allelic single nucleotide polymorphisms identified in the chickens, we found numerous selective sweeps and affected genes in each indigenous chicken breed and substantially larger numbers of selective sweeps and affected genes in the broilers and layers than previously reported using a rigorous statistical model. Consistent with the locations of the variants, the vast majority (~ 98.3%) of the identified selective sweeps overlap known quantitative trait loci (QTLs). Meanwhile, 74.2% known QTLs overlap our identified selective sweeps. We confirmed most of previously identified trait-related genes and identified many novel ones, some of which might be related to body size and high egg production traits. Using RT-qPCR, we validated differential expression of eight genes (GHR, GHRHR, IGF2BP1, OVALX, ELF2, MGARP, NOCT, SLC25A15) that might be related to body size and high egg production traits in relevant tissues of relevant breeds.

Conclusion
We identify 30 million single nucleotide variants and small indels in the five indigenous chicken breeds, 10 million of which are novel. We predict substantially more selective sweeps and affected genes than previously reported in both indigenous and commercial breeds. These variants and affected genes are good candidates for further experimental investigations of genotype-phenotype relationships and practical applications in chicken breeding programs.
Prediction of neoplastic gallbladder polyps in patients with different age level based on preoperative ultrasound: a multi-center retrospective real-world study
Authors: Li Qi , Dou Minghui , Liu Hengchao , Jia Pengbo , Wang Xintuan , Geng Xilin , Zhang Yu , Yang Rui , Li Junhui , Yang Wenbin , Yao Chunhe , Zhang Xiaodi , Lei Da , Yang Chenglin , Hao Qiwei , Liu Yimin , Guo Zhihua , Geng Zhimin , Zhang Dong 
Published: April 2024

Abstract
Background
The prevalence of neoplastic polyps in gallbladder polyps (GPs) increases sharply with age and is associated with gallbladder carcinoma (GBC). This study aims to predict neoplastic polyps and provide appropriate treatment strategies based on preoperative ultrasound features in patients with different age level.

Methods
According to the age classification of WHO, 1523 patients with GPs who underwent cholecystectomy from January 2015 to December 2019 at 11 tertiary hospitals in China were divided into young adults group (n=622), middle-aged group (n=665) and elderly group (n=236). Linear scoring models were established based on independent risk variables screened by the Logistic regression model in different age groups. The area under ROC (AUC) to evaluate the predictive ability of linear scoring models, long- and short- diameter of GPs.

Results
Independent risk factors for neoplastic polyps included the number of polyps, polyp size (long diameter), and fundus in the young adults and elderly groups, while the number of polyps, polyp size (long diameter), and polyp size (short diameter) in the middle-aged groups. In different age groups, the AUCs of its linear scoring model were higher than the AUCs of the long- and short- diameter of GPs for differentiating neoplastic and non-neoplastic polyps (all P<0.05), and Hosmer-Lemeshow goodness of fit test showed that the prediction accuracy of the linear scoring models was higher than the long- and short- diameter of GPs (all P>0.05).

Conclusion
The linear scoring models of the young adults, middle-aged and elderly groups can effectively distinguish neoplastic polyps from non-neoplastic polyps based on preoperative ultrasound features.
Primary and specialist care interaction and referral patterns for individuals with chronic kidney disease: a narrative review
Authors: Mutatiri Clyson , Ratsch Angela , McGrail Matthew , Venuthurupalli Sree Krishna , Chennakesavan Srinivas Kondalsamy 
Published: April 2024

Abstract
Background
Timely referral of individuals with chronic kidney disease from primary care to secondary care is evidenced to improve patient outcomes, especially for those whose disease progresses to kidney failure requiring kidney replacement therapy. A shortage of specialist nephrology services plus no consistent criteria for referral and reporting leads to referral pattern variability in the management of individuals with chronic kidney disease.

Objective
The objective of this review was to explore the referral patterns of individuals with chronic kidney disease from primary care to specialist nephrology services. It focused on the primary-specialist care interface, optimal timing of referral to nephrology services, adequacy of preparation for kidney replacement therapy, and the role of clinical criteria vs. risk-based prediction tools in guiding the referral process.

Methods
A narrative review was utilised to summarise the literature, with the intent of providing a broad-based understanding of the referral patterns for patients with chronic kidney disease in order to guide clinical practice decisions. The review identified original English language qualitative, quantitative, or mixed methods publications as well as systematic reviews and meta-analyses available in PubMed and Google Scholar from their inception to 24 March 2023.

Results
Thirteen papers met the criteria for detailed review. We grouped the findings into three main themes: (1) Outcomes of the timing of referral to nephrology services, (2) Adequacy of preparation for kidney replacement therapy, and (3) Comparison of clinical criteria vs. risk-based prediction tools. The review demonstrated that regardless of the time frame used to define early vs. late referral in relation to the start of kidney replacement therapy, better outcomes are evidenced in patients referred early.

Conclusions
This review informs the patterns and timing of referral for pre-dialysis specialist care to mitigate adverse outcomes for individuals with chronic kidney disease requiring dialysis. Enhancing current risk prediction equations will enable primary care clinicians to accurately predict the risk of clinically important outcomes and provide much-needed guidance on the timing of referral between primary care and specialist nephrology services.
Victimisation in the life of persons with severe mental illness in Uganda: a pluralistic qualitative study
Authors: Rutakumwa Rwamahe , Knizek Birthe Loa , Tusiime Christine , Mpango Richard Stephen , Birungi Carol , Kinyanda Eugene 
Published: April 2024

Abstract
Introduction
Victimisation of persons with severe mental illness is recognised as an urgent global concern, with literature pointing to higher rates of violent victimisation of persons with severe mental illness than those of the general population. Yet, for low income countries, there is a huge gap in the literature on the risk, character and victims’ in-depth experiences of victimisation of persons with severe mental illness. We explore the lived experiences and meanings of victimisation of persons with severe mental illness in Uganda, and discuss their implications for care of the mentally ill.

Methods
A pluralistic qualitative study was undertaken to explore victimisation among patients with severe mental illness. Patients who had suffered victimisation were purposively sampled from Butabika National Referral Mental Clinic and Masaka Regional Referral Hospital, following confirmation of symptom remission. In-depth interviews were held with 18 participants, comprising 13 females and 5 males from low to moderate socioeconomic status. Interpretative phenomenological analysis and thematic content analysis were conducted.

Results
Victimisation was exhibited in three main forms: (a) psychological, expressed in attitudes towards mentally ill family members as valueless and dispensable, and stigmatisation, (b) physical, as manifested in beatings, indoor confinement and tethering mostly by family members and (c) sexual victimisation, particularly rape. Also observed were victim’s various responses that pointed to the negative impact of victimisation, including a heightened risk of suicide, social withdrawal, a sense of hatefulness and a predisposition to more victimisation.

Conclusion
The family environment plays a predominant role in perpetrating victimisation of the mentally ill in some sub-Saharan African contexts such as Uganda. We propose a holistic framework for mental health interventions, incorporating biomedical but notably also social determinants of mental health, and targeted at improving familial relationships, social support and a sense of belongingness both within the family and the broader community.
Strengthening event-based surveillance (EBS): a case study from Afghanistan
Authors: Tahoun Mohamed Mostafa , Sahak Mohammad Nadir , Habibi Muzhgan , Ahadi Mohamad Jamaluddin , Rasoly Bahara , Shivji Sabrina , Aboushady Ahmed Taha , Nabeth Pierre , Sadek Mahmoud , Abouzeid Alaa 
Published: April 2024

SummaryThe sustained instability in Afghanistan, along with ongoing disease outbreaks and the impact of the COVID-19 pandemic, has significantly affected the country.During the COVID-19 pandemic, the country’s detection and response capacities faced challenges. Case identification was done in all health facilities from primary to tertiary levels but neglected cases at the community level, resulting in undetected and uncontrolled transmission from communities. This emphasizes a missed opportunity for early detection that Event-Based Surveillance (EBS) could have facilitated.Therefore, Afghanistan planned to strengthen the EBS component of the national public health surveillance system to enhance the capacity for the rapid detection and response to infectious disease outbreaks, including COVID-19 and other emerging diseases. This effort was undertaken to promptly mitigate the impact of such outbreaks.We conducted a landscape assessment of Afghanistan’s public health surveillance system to identify the best way to enhance EBS, and then we crafted an implementation work plan. The work plan included the following steps: establishing an EBS multisectoral coordination and working group, identifying EBS information sources, prioritizing public health events of importance, defining signals, establishing reporting mechanisms, and developing standard operating procedures and training guides.EBS is currently being piloted in seven provinces in Afghanistan. The lessons learned from the pilot phase will support its overall expansion throughout the country.
Assessing the safety of physical rehabilitation in critically ill patients: a Delphi study
Authors: Woodbridge Huw R. , McCarthy Christopher J. , Jones Mandy , Willis Matthew , Antcliffe David B. , Alexander Caroline M. , Gordon Anthony C. 
Published: April 2024

Abstract
Background
Physical rehabilitation of critically ill patients is implemented to improve physical outcomes from an intensive care stay. However, before rehabilitation is implemented, a risk assessment is essential, based on robust safety data. To develop this information, a uniform definition of relevant adverse events is required. The assessment of cardiovascular stability is particularly relevant before physical activity as there is uncertainty over when it is safe to start rehabilitation with patients receiving vasoactive drugs.

Methods
A three-stage Delphi study was carried out to (a) define adverse events for a general ICU cohort, and (b) to define which risks should be assessed before physical rehabilitation of patients receiving vasoactive drugs. An international group of intensive care clinicians and clinician researchers took part. Former ICU patients and their family members/carers were involved in generating consensus for the definition of adverse events. Round one was an open round where participants gave their suggestions of what to include. In round two, participants rated their agreements with these suggestions using a five-point Likert scale; a 70% consensus agreement threshold was used. Round three was used to re-rate suggestions that had not reached consensus, whilst viewing anonymous feedback of participant ratings from round two.

Results
Twenty-four multi-professional ICU clinicians and clinician researchers from 10 countries across five continents were recruited. Average duration of ICU experience was 18 years (standard deviation 8) and 61% had publications related to ICU rehabilitation. For the adverse event definition, five former ICU patients and one patient relative were recruited. The Delphi process had a 97% response rate. Firstly, 54 adverse events reached consensus; an adverse event tool was created and informed by these events. Secondly, 50 risk factors requiring assessment before physical rehabilitation of patients receiving vasoactive drugs reached consensus. A second tool was created, informed by these suggestions.

Conclusions
The adverse event tool can be used in studies of physical rehabilitation to ensure uniform measurement of safety. The risk assessment tool can be used to inform clinical practise when risk assessing when to start rehabilitation with patients receiving vasoactive drugs.
Trial registration This study protocol was retrospectively registered on https://www.researchregistry.com/ (researchregistry2991).
Safety and efficacy of intravenous thrombolysis before mechanical thrombectomy in patients with atrial fibrillation
Authors: Bao Qiangji , Huang Xiaodong , Wu Xinting , Huang Hao , Zhang Xiaoqiang , Yang Mingfei 
Published: April 2024

Abstract
Background
Intravenous thrombolysis (IVT) before endovascular thrombectomy (EVT) is the standard treatment for patients with acute ischemic stroke caused by large vessel occlusion (AIS-LVO). However, the efficacy and safety of IVT before EVT in AIS-LVO patients with atrial fibrillation (AF) remains controversial. Thus, this study aims to assess the benefit of IVT plus EVT and direct EVT alone in AIS-LVO patients with AF.

Method
Relevant studies that evaluated the outcomes of IVT plus EVT versus direct EVT alone in AIS-LVO patients with AF were systematically searched in PubMed, Embase, and Cochrane Library from inception to August 10, 2023. The outcomes included successful reperfusion (score of 2b to 3 for thrombolysis in cerebral infarction), symptomatic intracerebral hemorrhage (sICH), good clinical outcome (modified Rankin scale score ≤ 2) at 3 months, and 3-month mortality.

Result
Eight eligible observational studies involving 6998 (3827 in the IVT plus EVT group and 3171 in the direct EVT group) patients with AIS-LVO complicated by AF were included. Compared with direct EVT, IVT plus EVT resulted in better 3-month clinical outcomes (odds ratio [OR] 1.27, 95% confidence interval [CI] 1.05–1.54) and lower 3-month mortality (OR 0.78, 95% CI 0.68–0.88). However, the incidence of sICH (OR 1.26, 95% CI 0.91–1.75) and the rate of successful reperfusion (OR 0.98, 95% CI 0.83–1.17) were not significantly different between treatment modalities.

Conclusion
IVT plus EVT leads to better functional outcomes and lower mortality in AIS-LVO patients with AF. Withholding IVT plus EVT from patients with AF alone may not be justified.