bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optical genome mapping in acute myeloid leukemia: a multicenter evaluation
Authors: Levy Brynn , Baughn Linda B. , Akkari Yassmine , Chartrand Scott , LaBarge Brandon , Claxton David , Lennon P. Alan , Cujar Claudia , Kolhe Ravindra , Kroeger Kate , Pitel Beth , Sahajpal Nikhil , Sathanoori Malini , Vlad George , Zhang Lijun , Fang Min , Kanagal-Shamanna Rashmi , Broach James R. 
Published: November 2022

Abstract
Detection of hallmark genomic aberrations in acute myeloid leukemia (AML) is essential for diagnostic subtyping, prognosis, and patient management. However, cytogenetic/cytogenomic techniques used to identify those aberrations, such as karyotyping, fluorescence in situ hybridization (FISH), or chromosomal microarray analysis (CMA), are limited by the need for skilled personnel as well as significant time, cost, and labor. Optical genome mapping (OGM) provides a single, cost-effective assay with a significantly higher resolution than karyotyping and with a comprehensive genome-wide analysis comparable with CMA and the added unique ability to detect balanced structural variants (SVs). Here, we report in a real-world setting the performance of OGM in a cohort of 100 AML cases that were previously characterized by karyotype alone or karyotype and FISH or CMA. OGM identified all clinically relevant SVs and copy number variants (CNVs) reported by these standard cytogenetic methods when representative clones were present in &gt;5% allelic fraction. Importantly, OGM identified clinically relevant information in 13% of cases that had been missed by the routine methods. Three cases reported with normal karyotypes were shown to have cryptic translocations involving gene fusions. In 4% of cases, OGM findings would have altered recommended clinical management, and in an additional 8% of cases, OGM would have rendered the cases potentially eligible for clinical trials. The results from this multi-institutional study indicate that OGM effectively recovers clinically relevant SVs and CNVs found by standard-of-care methods and reveals additional SVs that are not reported. Furthermore, OGM minimizes the need for labor-intensive multiple cytogenetic tests while concomitantly maximizing diagnostic detection through a standardized workflow.
Accurate genome-wide phasing from IBD data
Authors: Noto Keith , Ruiz Luong 
Published: November 2022

AbstractAs genotype databases increase in size, so too do the number of detectable segments of identity by descent (IBD): segments of the genome where two individuals share an identical copy of one of their two parental haplotypes, due to shared ancestry. We show that given a large enough genotype database, these segments of IBD collectively overlap entire chromosomes, including instances of IBD that span multiple chromosomes, and can be used to accurately separate the alleles inherited from each parent across the entire genome. The resulting phase is not an improvement over state-of-the-art local phasing methods, but provides accurate long-range phasing that indicates which of two haplotypes in different regions of the genome, including different chromosomes, was inherited from the same parent. We are able to separate the DNA inherited from each parent completely, across the entire genome, with 98% median accuracy in a test set of 30,000 individuals. We estimate the IBD data requirements for accurate genome-wide phasing, and we propose a method for estimating confidence in the resulting phase. We show that our methods do not require the genotypes of close family, and that they are robust to genotype errors and missing data. In fact, our method can impute missing data accurately and correct genotype errors.
A novel SNP assay reveals increased genetic variability and abundance following translocations to a remnant Allegheny woodrat population
Authors: Muller-Girard Megan , Fowles Gretchen , Duchamp Joseph , Kouneski Samantha , Mollohan Cheryl , Smyser Timothy J. , Turner Gregory G. , Westrich Bradford , Doyle Jacqueline M. 
Published: November 2022

AbstractBackgroundAllegheny woodrats (Neotoma magister) are found in metapopulations distributed throughout the Interior Highlands and Appalachia. Historically these metapopulations persisted as relatively fluid networks, enabling gene flow between subpopulations and recolonization of formerly extirpated regions. However, over the past 45 years, the abundance of Allegheny woodrats has declined throughout the species’ range due to a combination of habitat destruction, declining hard mast availability, and roundworm parasitism. In an effort to initiate genetic rescue of a small, genetically depauperate subpopulation in New Jersey, woodrats were translocated from a genetically robust population in Pennsylvania (PA) in 2015, 2016 and 2017. Herein, we assess the efficacy of these translocations to restore genetic diversity within the recipient population.ResultsWe designed a novel 134 single nucleotide polymorphism panel, which was used to genotype the six woodrats translocated from PA and 82 individuals from the NJ population captured before and after the translocation events. These data indicated that a minimum of two translocated individuals successfully produced at least 13 offspring, who reproduced as well. Further, population-wide observed heterozygosity rose substantially following the first set of translocations, reached levels comparable to that of populations in Indiana and Ohio, and remained elevated over the subsequent years. Abundance also increased during the monitoring period, suggesting Pennsylvania translocations initiated genetic rescue of the New Jersey population.ConclusionsOur results indicate, encouragingly, that very small numbers of translocated individuals can successfully restore the genetic diversity of a threatened population. Our work also highlights the challenges of managing very small populations, such as when translocated individuals have greater reproductive success relative to residents. Finally, we note that ongoing work with Allegheny woodrats may broadly shape our understanding of genetic rescue within metapopulations and across heterogeneous landscapes.
Bacteriomes in lesions of pulmonary tuberculosis and its association with status of Mycobacterium tuberculosis excretion
Authors: Du Weili , Zhao Yingli , Zhang Li , Che Jialu , Liu Zichen , Li Kun , Che Nanying 
Published: November 2022

Abstract
Background
Bacteria in lung play an important role in sustaining lung health. Understanding the characteristics of bacteriomes in lesions of pulmonary tuberculosis (TB) patients, who excrete Mycobacterium tuberculosis (MTB), is important for TB prevention and effective treatment.

Methods
In this study, bacteriomes in lesions from TB patients excreting bacteria (TB-E) and those from TB patients not excreting bacteria (TB-NE) with matched normal lung tissues (NT) were compared by 16S rRNA sequencing. Bacterial MetaCyc functions in TB lesions were also predicted by PICRUSt2 tool.

Results
Alpha diversity of bacteria, including Chao 1 and Shannon indexes, for TB-E was significantly higher than those in TB-NE and NT; while for TB-NE group, Chao 1 index was higher than that in NT group. Predominant phyla in TB lesions and NT were Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes, but analysis of similarity (ANOSIM, p < 0.001) revealed significantly different bacterial compositions among TB-E, TB-NE and NT samples. As for bacteriomes in TB lesions, a strong association (ANOSIM, p < 0.001) was observed with the status of MTB excretion. Indicator genera identified in TB-E and TB-NE demonstrated distinctive micro-ecological environments of TB lesions from patients with different clinical manifestations. Co-occurrence analysis revealed a densely-linked bacterial community in TB-NE compared to that in TB-E. MetaCyc functions responsible for menaquinone synthesis and chorismate metabolism that could potentially impact the persistent-state and nutrient metabolism of MTB were enriched in TB-E samples. While in TB-NE samples, enrichment of bacterial MetaCyc function responsible for heme b synthesis might contribute to TB pathology through ferroptosis.

Conclusion
Bacteriomes and their MetaCyc functions in TB lesions are elucidated, and they are associated with status of MTB excretion among pulmonary TB patients. These results serve as a basis for designing novel strategies for preventing and treating pulmonary TB disease.
High-risk diagnosis combinations in patients undergoing interhospital transfer: a retrospective observational study
Authors: Reimer Andrew P. , Schiltz Nicholas K. , Koroukian Siran M. 
Published: November 2022

Abstract
Background
There is limited research on individual patient characteristics, alone or in combination, that contribute to the higher levels of mortality in post-transfer patients. The purpose of this work is to identify significant combinations of diagnoses that identify subgroups of post-interhospital transfer patients experiencing the highest levels of mortality.

Methods
This was a retrospective cross-sectional study using structured electronic health record data from a regional health system between 2010–2017. We employed a machine learning approach, association rules mining using the Apriori algorithm to identify diagnosis combinations.
The study population includes all patients aged 21 and older that were transferred within our health system from a community hospital to one of three main receiving hospitals.

Results
Overall, 8893 patients were included in the analysis. Patients experiencing mortality post-transfer were on average older (70.5 vs 62.6 years) and on average had more diagnoses in 5 of the 6 diagnostic subcategories. Within the diagnostic subcategories, most diagnoses were comorbidities and active medical problems, with hypertension, atrial fibrillation, and acute respiratory failure being the most common. Several combinations of diagnoses identified patients that exceeded 50% post-interhospital transfer mortality.

Conclusions
Comorbid burden, in combination with active medical problems, were most predictive for those experiencing the highest rates of mortality. Further improving patient level prognostication can facilitate informed decision making between providers and patients to shift the paradigm from transferring all patients to higher level care to only transferring those who will benefit or desire continued care, and reduce futile transfers.
Association between variables measured in the ambulance and in-hospital mortality among adult patients with and without infection: a prospective cohort study
Authors: Wallgren Ulrika Margareta , Järnbert-Pettersson Hans , Sjölin Jan , Kurland Lisa 
Published: November 2022

Abstract
Background
Patients presenting with infection to the ambulance are common, but risk factors for poor outcome are not known. The primary aim of the current study was to study the association between variables measured in the ambulance and mortality among adult patients with and without infection. The secondary aim was to study the association between these variables and mortality in a subgroup of patients who developed sepsis within 36 h.

Methods
Prospective cohort study of 553 ambulance patients with, and 318 patients without infection, performed in Stockholm during 2017–2018. The association between 21 variables (8 keywords related to medical history, 6 vital signs, 4 blood tests, and age, gender, comorbidity) and in-hospital mortality was analysed using logistic regression.

Results
Among patients with infection, inability of the patient to answer questions relating to certain symptoms such as pain and gastrointestinal symptoms was significantly associated with mortality in univariable analysis, in addition to oxygen saturation < 94%, heart rate > 110 /min, Glasgow Coma Scale (GCS) < 15, soluble urokinase Plasminogen Activator Receptor (suPAR) 4.0–7.9 ng/mL, suPAR ≥ 8.0 ng/mL and a Charlson comorbidity score ≥ 5. suPAR ≥ 8.0 ng/mL remained significant in multivariable analysis (OR 25.4; 95% CI, 3.2–199.8). Among patients without infection, suPAR ≥ 8.0 ng/mL and a Charlson comorbidity score ≥ 5 were significantly associated with mortality in univariable analysis, while suPAR ≥ 8.0 ng/mL remained significant in multivariable analysis (OR 56.1; 95% CI, 4.5–700.0). Among patients who developed sepsis, inability to answer questions relating to pain remained significant in multivariable analysis (OR 13.2; 95% CI, 2.2–78.9), in addition to suPAR ≥ 8.0 ng/mL (OR 16.1; 95% CI, 2.0–128.6).

Conclusions
suPAR ≥ 8.0 ng/mL was associated with mortality in patients presenting to the ambulance both with and without infection and in those who developed sepsis. Furthermore, the inability of the ambulance patient with an infection to answer questions relating to specific symptoms was associated with a surprisingly high mortality. These results suggest that suPAR and medical history are valuable tools with which to identify patients at risk of poor outcome in the ambulance and could potentially signal the need of enhanced attention.

Trial registration
ClinicalTrials.gov, NCT03249597. Registered 15 August 2017—Retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT03249597.
Comprehensive analysis of the differences between left- and right-side colorectal cancer and respective prognostic prediction
Authors: Niu Mengye , Chen Chengyang , Gao Xian , Guo Yi , Zhang Bingzhou , Wang Xin , Chen Shihao , Niu Xupeng , Zhang Chao , Li Like , Li Zhongxin , Zhao Zengren , Jiang Xia 
Published: November 2022

Abstract
Background
Previous studies have reported that the tumor heterogeneity and complex oncogenic mechanisms of proximal and distal colon cancer (CRC) are divergent. Therefore, we aim to analyze the differences between left-sided CRC (L_cancer) and right-sided CRC (R_cancer), as well as constructing respective nomograms.

Methods
We enrolled 335 colon cancer patients (146 L_cancer patients and 189 R_cancer patients) from The Cancer Genome Atlas (TCGA) data sets, and 102 pairs of color cancer tissue and adjacent normal tissue (51 L_cancer patients and 51 R_cancer patients) from our hospital. Firstly, we analyzed the differences between the L_cancer patients and R_cancer patients, and then established the L_cancer and R_cancer prognostic models using LASSO Cox.

Results
R_cancer patients had lower survival than L_cancer patients. R_cancer patients had higher ESTIMATE and immune scores and lower tumor purity. These patterns of expression of immune checkpoint-related genes and TMB level were higher in R_cancer than in L_cancer patients. Finally, we using Lasso Cox regression analyses established a prognostic model for L_cancer patients and a prognostic model for R_cancer patients. The AUC values of the risk score for OS in L_cancer were 0.862 in the training set and 0.914 in the testing set, while those in R_cancer were 0.835 in the training set and 0.857 in the testing set. The AUC values in fivefold cross-validation were between 0.727 and 0.978, proving that the two prognostic models have great stability. The nomogram of L_cancer included prognostic genes, age, pathological M, pathological stage, and gender, the AUC values of which were 0.800 in the training set and 0.905 in the testing set. Meanwhile, the nomogram of R_cancer comprised prognostic genes, pathological N, pathological T, and age, the AUC values of which were 0.836 in the training set and 0.850 in the testing set. In the R_cancer patients, high-risk patients had a lower proportion of ‘B cells memory’, ‘Dendritic cells resting’, immune score, ESTIMATE score, immune checkpoint-related genes, and HLA-family genes, and a higher proportion of ‘T cells follicular helper’, ‘Dendritic cells activated’, and ‘Mast cells activated’.

Conclusions
We found significant differences between L_cancer and R_cancer patients and established a clinical predictive nomogram for L_cancer patients and a nomogram for R_cancer patients. Additionally, R_cancer patients in low-risk groups may be more beneficial from immunotherapy.
Association of serum klotho levels with different-staged vascular calcification status in patients with maintenance hemodialysis
Authors: Lin Yan , Huang Jiayuan , Zhou Meiyang , Pan Cuiping , Shan Aiqin , Zhou Canxin 
Published: November 2022

Abstract
Background
Vascular calcification (VC) is suggested to be associated with serum klotho levels in patients with maintenance hemodialysis (MHD), whereas there is a lack of reports on the associations of VC status in whole arteries with serum klotho contents.

Methods
One hundred forty eligible patients with MHD and a total of age-and gender-matched normal controls (NCs) were recruited. We analyzed the VC statuses of large arteries and peripheral muscular arteries by calculating the sum of scores from each artery. The levels of serum klotho were determined by ELISA. In addition, the relationship between serum klotho and VC status was evaluated using correlation analysis and regression analysis.

Results
The VC severity in MHD patients tended to be worse in comparison with NCs. Serum klotho level in patients with MHD was lower than that in the NC subjects (​P < 0.0001), which was correlated with VC scores as reflected by correlation analysis and regression analysis. Serum klotho concentrations exhibited a dynamic decline along with increased VC status stages. Subjects with higher levels of serum klotho had a higher prevalence of cardiovascular events.

Conclusion
Our study indicates serum klotho is strongly associated with VC status in a stage-dependent manner.
In the need of a digital cicerone in healthcare? – Guidance for parents
Authors: Bäckström C , Knez R , Fahlgren M , Synnergren M , Larsson V 
Published: November 2022

Abstract
Objective
To explore parents’ experiences using digital tools in relation to pregnancy, labor and birth, and the child’s first 18 months.

Background
Parents find relevant information using digital healthcare tools, material obtained from professionals, as well as personal opinions and experiences that vary in quality.

Method
Fifteen parents were interviewed and data were analyzed beginning with content analysis and followed by thematic analysis.

Results
The main theme was insecurity and responsibility for own choices and knowledge. Parents use digital tools to take responsibility for their insecurity and need for knowledge when entering parenthood.

Conclusion
The parents’ experiences highlighted that (1) insecurity can be both eased and enhanced using digital tools, (2) they took responsibility for feelings of insecurity and the search for knowledge, and (3) they needed knowledge to make the right choices and feel secure that these choices are made in the best interest of their new family.
Learning from a crisis: a qualitative study of the impact on mothers’ emotional wellbeing of changes to maternity care during the COVID-19 pandemic in England, using the National Maternity Survey 2020
Authors: McLeish Jenny , Harrison Sian , Quigley Maria , Alderdice Fiona 
Published: November 2022

Abstract
Background
Pregnancy and the postnatal period can be times of psychosocial stress and insecurity, but high quality maternity care and social support can help mothers cope with stress and feel more secure. The COVID-19 pandemic and associated social and economic disruption increased rates of antenatal and postnatal stress, anxiety and depression, and also had profound impacts on the organisation of maternity services in England.

Methods
This was a qualitative descriptive study of the impact of pandemic-related changes to maternity care on mothers’ emotional wellbeing, using inductive thematic analysis of open text responses to the National Maternity Survey (NMS) 2020 in England. A random sample of 16,050 mothers who gave birth 11-24th May 2020 were invited to take part in the survey, and 4,611 responded, with 4,384 answering at least one open text question.

Results
There were three themes: ‘Chaos: impact of uncertainty’, ‘Abandoned: impact of reduction in care’, and ‘Alone: impact of loss of social support’. Mothers valued maternity care and many experienced additional stress from chaotic changes and reduction in care during the pandemic; from health professionals’ own uncertainty and anxiety; and from restrictions on essential social support during pregnancy, labour and birth. Others felt that health professionals had communicated and cared for them well despite the changes and restrictions, and these mothers felt psychologically safe.

Conclusions
Planning for future crises should include considering how necessary adaptations to care can be implemented and communicated to minimise distress; ensuring that mothers are not deprived of social support at the time when they are at their most vulnerable; and supporting the psychological welfare of staff at a time of enormous pressure. There are also lessons for maternity care in ‘normal’ times: that care is highly valued, but trust is easily lost; that some mothers come into the maternity system with vulnerabilities that can be ameliorated or intensified by the attitudes of staff; that every effort should be made to welcome a mother’s partner or chosen companion into maternity care; and that high quality postnatal care can make a real difference to mothers’ wellbeing.
The human right to safely give birth: data from 193 countries show that gender equality does affect maternal mortality
Authors: Bagade Tanmay , Chojenta Catherine , Harris Melissa , Oldmeadow Christopher , Loxton Deborah 
Published: November 2022

Abstract
Background
While a reduction in the global maternal mortality ratio (MMR) has slowed, newer strategies are needed to achieve an ongoing and sustainable reduction of the MMR. Previous studies have investigated the association between health system-related factors such as wealth inequalities, healthcare access and use on maternal mortality. However, a women’s rights-based approach to address MMR has not been studied, excluding the health system-related factors. This study aimed to analyse the association between gender equality and MMR globally.

Methods
Using structural equation modelling (SEM), secondary and open access data from the United Nations and other international agencies from 193 countries were analysed using structural equation modelling (SEM). Gender-sensitive variables that represented the theoretical, conceptual framework of the study were selected. The association between latent variable gender equality and the outcome, MMR, was examined in the SEM. A second SEM model (n = 158) was designed to include two variables related to gender-based violence.

Findings
The latent variable, gender equality, was negatively associated with MMR (p < 0‧001, Z = –6‧96, 95% CI: − 6508.98 to − 3141.89 for Model 1 and p < 0‧001, Z = –7‧23, 95% CI: − 6045.356 to − 3467.515 for Model 2).

Interpretation
Gender equality was significantly associated with maternal mortality. Investing in higher education for women, improving their paid employment opportunities, increasing participation in leadership roles and politics, reducing intimate partner violence (IPV) and ending child marriage can significantly reduce maternal mortality.