bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genomics reveals insights into anuran genome size evolution
Authors: Zuo Bin , Nneji Lotanna Micah , Sun Yan-Bo 
Published: July 2023

Abstract
Background
Amphibians, particularly anurans, display an enormous variation in genome size. Due to the unavailability of whole genome datasets in the past, the genomic elements and evolutionary causes of anuran genome size variation are poorly understood. To address this, we analyzed whole-genome sequences of 14 anuran species ranging in size from 1.1 to 6.8 Gb. By annotating multiple genomic elements, we investigated the genomic correlates of anuran genome size variation and further examined whether the genome size relates to habitat types.

Results
Our results showed that intron expansions or contraction and Transposable Elements (TEs) diversity do not contribute significantly to genome size variation. However, the recent accumulation of transposable elements (TEs) and the lack of deletion of ancient TEs primarily accounted for the evolution of anuran genome sizes. Our study showed that the abundance and density of simple repeat sequences positively correlate with genome size. Ancestral state reconstruction revealed that genome size exhibits a taxon-specific pattern of evolution, with families Bufonidae and Pipidae experiencing extreme genome expansion and contraction events, respectively. Our result showed no relationship between genome size and habitat types, although large genome-sized species are predominantly found in humid habitats.

Conclusions
Overall, our study identified the genomic element and their evolutionary dynamics accounting for anuran genome size variation, thus paving a path to a greater understanding of the size evolution of the genome in amphibians.
Genome-wide identification of SrbHLH transcription factors highlights its potential role in rebaudioside A (RA) biosynthesis in Stevia rebaudiana
Authors: Li Yuping , Qiu Yuan , Xu Xin , Luo Ming 
Published: July 2023

AbstractStevia rebaudiana Bertoni is a valuable medicinal plant and an essential source of natural sweetener, steviol glycosides (SGs), with rebaudioside A (RA) being one of the main components of SGs. bHLH transcription factors play a crucial role in plant development and secondary metabolism. In this study, 159 SrbHLH genes were identified from the S. rebaudiana genome, and each gene was named based on its chromosome location. The SrbHLH proteins were then clustered into 18 subfamilies through phylogenetic analysis. The analysis of conserved motifs and gene structure further supported the classification of the SrbHLH family. Chromosomal location and gene duplication events of SrbHLH genes were also studied. Moreover, based on the RNA-Seq data of different tissues of S. rebaudiana, 28 SrbHLHs were co-expressed with structural genes involved in RA biosynthesis. The expression pattern of candidate SrbHLH genes were confirmed by qPCR. Finally, dual luciferase reporter assays (DLAs) and subcellular localization analysis verified SrbHLH22, SrbHLH111, SrbHLH126, SrbHLH142, and SrbHLH152 are critical regulators of RA biosynthesis. This study provides new insights into the function of SrbHLHs in regulating SGs biosynthesis and lays the foundation for future applications of SrbHLH genes in molecular breeding of S. rebaudiana.
A wide range of missing imputation approaches in longitudinal data: a simulation study and real data analysis
Authors: Jahangiri Mina , Kazemnejad Anoshirvan , Goldfeld Keith S. , Daneshpour Maryam S. , Mostafaei Shayan , Khalili Davood , Moghadas Mohammad Reza , Akbarzadeh Mahdi 
Published: July 2023

AbstractBackgroundMissing data is a pervasive problem in longitudinal data analysis. Several single-imputation (SI) and multiple-imputation (MI) approaches have been proposed to address this issue. In this study, for the first time, the function of the longitudinal regression tree algorithm as a non-parametric method after imputing missing data using SI and MI was investigated using simulated and real data.MethodUsing different simulation scenarios derived from a real data set, we compared the performance of cross, trajectory mean, interpolation, copy-mean, and MI methods (27 approaches) to impute missing longitudinal data using parametric and non-parametric longitudinal models and the performance of the methods was assessed in real data. The real data included 3,645 participants older than 18 years within six waves obtained from the longitudinal Tehran cardiometabolic genetic study (TCGS). The data modeling was conducted using systolic and diastolic blood pressure (SBP/DBP) as the outcome variables and included predictor variables such as age, gender, and BMI. The efficiency of imputation approaches was compared using mean squared error (MSE), root-mean-squared error (RMSE), median absolute deviation (MAD), deviance, and Akaike information criteria (AIC).ResultsThe longitudinal regression tree algorithm outperformed based on the criteria such as MSE, RMSE, and MAD than the linear mixed-effects model (LMM) for analyzing the TCGS and simulated data using the missing at random (MAR) mechanism. Overall, based on fitting the non-parametric model, the performance of the 27 imputation approaches was nearly similar. However, the SI traj-mean method improved performance compared with other imputation approaches.ConclusionBoth SI and MI approaches performed better using the longitudinal regression tree algorithm compared with the parametric longitudinal models. Based on the results from both the real and simulated data, we recommend that researchers use the traj-mean method for imputing missing values of longitudinal data. Choosing the imputation method with the best performance is widely dependent on the models of interest and the data structure.
Acute myeloma kidney and SARS-COV2 infection with dialysis need: never say never - a case report
Authors: Donati Gabriele , Przygocka Agnieszka , Zappulo Fulvia , Vischini Gisella , Valente Sabrina , La Manna Gaetano 
Published: July 2023

Abstract
Background
Older individuals with multiple comorbidities and especially patients with multiple myeloma are at higher risk of contracting SARS-CoV-2. When patients with multiple myeloma (MM) are also affected by SARS-CoV-2 the time to start immunosuppressants is still a clinical dilemma especially when urgent hemodialysis is required for acute kidney injury (AKI).

Case presentation
We present a case of an 80-year-old woman who was diagnosed with AKI in MM. The patient began hemodiafiltration (HDF) with free light chain removal combined with bortezomib and dexamethasone. The reduction of free light chains concurrently was obtained by means of HDF using poly ester polymer alloy (PEPA) high-flux filter: 2 PEPA filters were used in series during each 4-h length HDF session. A total of 11 sessions was carried out. The hospitalization was complicated with acute respiratory failure caused by SARS-CoV-2 pneumonia successfully treated with both pharmacotherapy and respiratory support. Once the respiratory status stabilized MM treatment was resumed.
The patient was discharged in stable condition after 3 months of hospitalization. The follow up showed significant improvement of the residual renal function which allowed interruption of hemodialysis (HD).

Conclusions
The complexity of patients affected by MM, AKI, and SARS-CoV-2 should not discourage the attending physicians to offer the adequate treatment. The cooperation of different specialists can lead to a positive outcome in those complicated cases.
Assessing awareness of blood cancer symptoms and barriers to symptomatic presentation: measure development and results from a population survey in the UK
Authors: Boswell Laura , Harris Jenny , Ip Athena , Russell Jessica , Black Georgia B , Whitaker Katriina L 
Published: July 2023

Abstract
Background
Low levels of cancer awareness may contribute to delays in seeking medical help and subsequent delays in diagnosis. For blood cancer this may be a particularly prominent problem due to the high prevalence of undifferentiated symptoms such as bodily pain, weakness, nausea and weight loss, resulting in low symptom awareness. The delay is exacerbated by the dismissal of similar symptoms which are often interpreted as mild disease, resulting in multiple consultations prior to diagnosis. This study describes the development of a Cancer Awareness Measure for Blood Cancer (Blood CAM) and presents results from a population-representative survey using the measure.

Methods
A rapid systematic review identified constructs relevant to blood cancer. Items were taken from previous awareness measures and other literature and reviewed by expert groups including health care professionals and patients. Cognitive interviews were conducted with ten members of the public to check comprehension and clarity. A total sample of 434 participants completed the survey at Time 1 and n = 302 at Time 2 (two weeks later).

Results
Internal reliability was high across the different constructs included in the questionnaire (> 0.70) and test-retest reliability was moderate to good (0.49–0.79). The most commonly recognised blood cancer symptoms were unexplained weight loss (68.9%) and unexplained bleeding (64.9%) and the least commonly recognised symptoms were night sweats (31.3%) breathlessness and rash/itchy skin (both 44%). In terms of symptom experience, fatigue was the most commonly reported symptom (26.7%) followed by night sweats (25.4%). Exploratory factor analysis of barriers to presenting at primary care revealed three distinct categories of barriers; emotional, external/practical and service/healthcare professional related. Service and emotional barriers were most common.

Conclusions
We developed a valid and reliable tool to assess blood cancer awareness and showed variable awareness of blood cancer symptoms which can help target public health campaigns. We also incorporated additional measures (e.g. confidence to re-consult, ability to understand symptoms) that could be used to tailor public messaging for blood cancer and for other harder to suspect and diagnose cancers.
The impact of dyslipidemia on lumbar intervertebral disc degeneration and vertebral endplate modic changes: a cross-sectional study of 1035 citizens in China
Authors: Yuan Liang , Huang Zhengqi , Han Weitao , Chang Ruiming , Sun Bo , Zhu Mingxi , Li Chenjing , Yan Jiansen , Liu Bin , Yin Haidong , Ye Wei 
Published: July 2023

Abstract
Background
Intervertebral disc degeneration (IDD) and vertebral endplate Modic changes (MCs) are common lumbar degenerative phenotypes related to low back pain (LBP). Dyslipidemia has been linked to LBP but its associations with IDD and MCs have not been fully elucidated. The present study aimed to address the possible link between dyslipidemia, IDD and MCs in the Chinese population.

Methods
1035 citizens were enrolled in the study. The levels of serum total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C) and triglycerides (TG) were collected. IDD was evaluated based on the Pfirrmann grading system and subjects with an average grade ≥ 3 were defined as having degeneration. MCs were classified into typical types 1, 2 and 3. Covariables, including age, sex, BMI and fasting plasma glucose, were included for the adjustment of the logistic analyses.

Results
The degeneration group included 446 subjects while the nondegeneration group included 589 subjects. The degeneration group had significant higher levels of TC and LDL-C (p < 0.001) whereas TG and HDL-C were not significantly different between the two groups. TC and LDL-C concentrations were significantly positively correlated with average IDD grades (p < 0.001). Multivariate logistic regression revealed that high TC (≥ 6.2 mmol/L, adjusted OR = 1.775, 95% CI = 1.209–2.606) and high LDL-C (≥ 4.1 mmol/L, adjusted OR = 1.818, 95% CI = 1.123–2.943) were independent risk factors for IDD. Type 1 MC presented in 84 (8.12%) subjects, type 2 MC presented in 244 (23.57%) subjects, type 3 MC presented in 27 (2.61%) subjects and no MC was observed in the remaining 680 (65.70%) subjects. The type 2 MC group demonstrated a higher level of TC, but the association between serum lipids and MCs could not be confirmed in further multivariate logistic regression.

Conclusions
High TC (≥ 6.2 mmol/L) and LDL-C (≥ 4.1 mmol/L) concentrations were independent risk factors for IDD for citizens in China. However, the association between dyslipidemia and MCs could not be determined. The effect of excess serum cholesterol may be critical for IDD and cholesterol lowering treatment may provide new opportunities in the management of lumbar disc degeneration.
Surgical Apgar Score can accurately predict the severity of post-operative complications following emergency laparotomy
Authors: Kyaruzi Victor Meza , Chamshama Douglas E. , Khamisi Ramadhani H. , Akoko Larry O. 
Published: July 2023

Abstract
Background
The Surgical Apgar Score (SAS) describes a feasible and objective tool for predicting surgical outcomes. However, the accuracy of the score and its correlation with the complication severity has not been well established in many grounds of low resource settings.

Objective
To determine the accuracy of Surgical Apgar Score in predicting the severity of post-operative complications among patients undergoing emergency laparotomy at Muhimbili National Hospital.

Methods
A prospective cohort study was conducted for a period of 12 months; patients were followed for 30 days, the risk of complication was classified using the Surgical Apgar Score (SAS), severity of complication was estimated using the Clavien Dindo Classification (CDC) grading scheme and Comprehensive Complication Index (CCI). Spearman correlation and simple linear regression statistic models were applied to establish the relationship between Surgical Apgar Score (SAS) and Comprehensive Complication Index (CCI). The Accuracy of SAS was evaluated by determining its discriminatory capacity on Receiver Operating Characteristics (ROC) curve, data normality was tested by Shapiro–Wilk statistic 0.929 (p < 0.001).Analysis was done using International Business Machine Statistical Product and Service Solution (IBM SPSS) version 27.

Results
Out of the 111 patients who underwent emergency laparotomy, 71 (64%) were Male and the median age (IQR) was 49 (36, 59).The mean SAS was 4.86 (± 1.29) and the median CCI (IQR) was 36.20 (26.2, 42.40). Patients in the high-risk SAS group (0–4) were more likely to experience severe and life-threatening complications, with a mean CCI of 53.3 (95% CI: 47.2–63.4), compared to the low-risk SAS group (7–10) with a mean CCI of 21.0 (95% CI: 5.3–36.2). A negative correlation was observed between SAS and CCI, with a Spearman r of -0.575 (p < 0.001) and a regression coefficient b of -11.5 (p < 0.001). The SAS demonstrated good accuracy in predicting post-operative complications, with an area under the curve of 0.712 (95% CI: 0.523–0.902, p < 0.001) on the ROC.

Conclusion
This study has demonstrated that SAS can accurately predict the occurrence of complications following emergency laparotomy at Muhimbili National Hospital.
Continuing professional development (CPD) system development, implementation, evaluation and sustainability for healthcare professionals in low- and lower-middle-income countries: a rapid scoping review
Authors: Merry Lisa , Castiglione Sonia Angela , Rouleau Geneviève , Létourneau Dimitri , Larue Caroline , Deschênes Marie-France , Gonsalves Dolly Maria , Ahmed Lubana 
Published: July 2023

Abstract
Background
Policymakers and program developers in low-and lower-middle-income countries (LLMICs) are increasingly seeking evidence-based information and guidance on how to successfully develop and implement continuing professional development (CPD) systems. We conducted a rapid scoping review to map and synthesize what is known regarding the development, implementation, evaluation and sustainability of CPD systems for healthcare professionals in LLMICs.

Methods
We searched MEDLINE, CINAHL and Web of Science. Reference lists were screened and a cited reference search of included articles was conducted. Supplementary information on the CPD systems identified in the articles was also identified via an online targeted grey literature search. English, French and Spanish literature published from 2011 to 2021 were considered. Data were extracted and combined and summarized according to country/region and healthcare profession via tables and narrative text.

Results
We included 15 articles and 23 grey literature sources. Africa was the region most represented followed by South and Southeast Asia and the Middle East. The literature most often referred to CPD systems for nurses and midwives; CPD systems for physicians were frequently referred to as well. Findings show that leadership and buy-in from key stakeholders, including government bodies and healthcare professional organizations, and a framework are essential for the development, implementation and sustainability of a CPD system in a LLMIC. The guiding framework should incorporate a regulatory perspective, as well as a conceptual lens (that informs CPD objectives and methods), and should consider contextual factors (support for CPD, healthcare context and population health needs). In terms of important steps to undertake, these include: a needs assessment; drafting of a policy, which details the regulations (laws/norms), the CPD requirements and an approach for monitoring, including an accreditation mechanism; a financing plan; identification and production of appropriate CPD materials and activities; a communication strategy; and an evaluation process.

Conclusion
Leadership, a framework and a clearly delineated plan that is responsive to the needs and context of the setting, are essential for the development, implementation and sustainability of a CPD system for healthcare professionals in a LLMIC.
FHIR-PYrate: a data science friendly Python package to query FHIR servers
Authors: Hosch René , Baldini Giulia , Parmar Vicky , Borys Katarzyna , Koitka Sven , Engelke Merlin , Arzideh Kamyar , Ulrich Moritz , Nensa Felix 
Published: July 2023

Abstract
Background
We present FHIR-PYrate, a Python package to handle the full clinical data collection and extraction process. The software is to be plugged into a modern hospital domain, where electronic patient records are used to handle the entire patient’s history. Most research institutes follow the same procedures to build study cohorts, but mainly in a non-standardized and repetitive way. As a result, researchers spend time writing boilerplate code, which could be used for more challenging tasks.

Methods
The package can improve and simplify existing processes in the clinical research environment. It collects all needed functionalities into a straightforward interface that can be used to query a FHIR server, download imaging studies and filter clinical documents. The full capacity of the search mechanism of the FHIR REST API is available to the user, leading to a uniform querying process for all resources, thus simplifying the customization of each use case. Additionally, valuable features like parallelization and filtering are included to make it more performant.

Results
As an exemplary practical application, the package can be used to analyze the prognostic significance of routine CT imaging and clinical data in breast cancer with tumor metastases in the lungs. In this example, the initial patient cohort is first collected using ICD-10 codes. For these patients, the survival information is also gathered. Some additional clinical data is retrieved, and CT scans of the thorax are downloaded. Finally, the survival analysis can be computed using a deep learning model with the CT scans, the TNM staging and positivity of relevant markers as input. This process may vary depending on the FHIR server and available clinical data, and can be customized to cover even more use cases.

Conclusions
FHIR-PYrate opens up the possibility to quickly and easily retrieve FHIR data, download image data, and search medical documents for keywords within a Python package. With the demonstrated functionality, FHIR-PYrate opens an easy way to assemble research collectives automatically.
Xanthine oxidoreductase gene polymorphisms are associated with high risk of sepsis and organ failure
Authors: Gao Li , Rafaels Nicholas , Dudenkov Tanda M. , Damarla Mahendra , Damico Rachel , Maloney James P. , Moss Marc , Martin Greg S. , Sevransky Jonathan , Shanholtz Carl , Herr Dan L. , Garcia Joe G.N. , Hernandez-Beeftink Tamara , Villar Jesús , Flores Carlos , Beaty Terri H. , Brower Roy , Hassoun Paul M. , Barnes Kathleen C. 
Published: July 2023

Abstract
Background
Sepsis and associated organ failures confer substantial morbidity and mortality. Xanthine oxidoreductase (XOR) is implicated in the development of tissue oxidative damage in a wide variety of respiratory and cardiovascular disorders including sepsis and sepsis-associated acute respiratory distress syndrome (ARDS). We examined whether single nucleotide polymorphisms (SNPs) in the XDH gene (encoding XOR) might influence susceptibility to and outcome in patients with sepsis.

Methods
We genotyped 28 tag SNPs in XDH gene in the CELEG cohort, including 621 European American (EA) and 353 African American (AA) sepsis patients. Serum XOR activity was measured in a subset of CELEG subjects. Additionally, we assessed the functional effects of XDH variants utilizing empirical data from different integrated software tools and datasets.

Results
Among AA patients, six intronic variants (rs206805, rs513311, rs185925, rs561525, rs2163059, rs13387204), in a region enriched with regulatory elements, were associated with risk of sepsis (P < 0.008–0.049). Two out of six SNPs (rs561525 and rs2163059) were associated with risk of sepsis-associated ARDS in an independent validation cohort (GEN-SEP) of 590 sepsis patients of European descent. Two common SNPs (rs1884725 and rs4952085) in tight linkage disequilibrium (LD) provided strong evidence for association with increased levels of serum creatinine (Padjusted<0.0005 and 0.0006, respectively), suggesting a role in increased risk of renal dysfunction. In contrast, among EA ARDS patients, the missense variant rs17011368 (I703V) was associated with enhanced mortality at 60-days (P < 0.038). We found higher serum XOR activity in 143 sepsis patients (54.5 ± 57.1 mU/mL) compared to 31 controls (20.9 ± 12.4 mU/mL, P = 1.96 × 10− 13). XOR activity was associated with the lead variant rs185925 among AA sepsis patients with ARDS (P < 0.005 and Padjusted<0.01). Multifaceted functions of prioritized XDH variants, as suggested by various functional annotation tools, support their potential causality in sepsis.

Conclusions
Our findings suggest that XOR is a novel combined genetic and biochemical marker for risk and outcome in patients with sepsis and ARDS.